AMBER Archive (2008) - By Author

Starting: Tue Jan 01 2008 - 19:53:35 CST
Ending: Wed Dec 31 2008 - 22:47:27 CST

• #NGUYEN CONG TRI#
  • AMBER: Conversion between truncated octahedron and orthorohombic box (Sat Oct 25 2008 - 21:36:30 CDT)
• Abdul Hameed, MohamedDiwanMo
  • AMBER: Silicon parameters (Wed Aug 20 2008 - 11:15:56 CDT)
• ABEL Stephane 175950
  • AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III (Tue Dec 16 2008 - 05:28:56 CST)
  • AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 11:33:44 CST)
  • AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 10:41:19 CST)
  • AMBER: tutorial A1, file missing readit.f (Thu Dec 11 2008 - 06:22:41 CST)
• Abhishek Singh
  • AMBER: PMEMD and polarized force field ff 02 (Thu Jul 03 2008 - 09:53:36 CDT)
  • AMBER: PMEMD and polarized force field ff 02 (Thu Jul 03 2008 - 09:50:00 CDT)
  • Re: AMBER: Regarding force field ff02 and ion library (Tue Jul 01 2008 - 14:02:28 CDT)
  • AMBER: Regarding force field ff02 and ion library (Mon Jun 30 2008 - 15:54:52 CDT)
• abiram abiram
  • AMBER: Dimension of the solvated box? (Wed Feb 20 2008 - 07:54:08 CST)
  • AMBER: Unable to create the top & crd files for a protein+ligand pdb structure (Sat Jan 12 2008 - 01:54:01 CST)
• Adelene Sim
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
  • AMBER: Simulating DNA Backbone in NAB (Tue Apr 01 2008 - 14:23:16 CDT)
• Adrian Roitberg
  • Re: AMBER: Switching function in NAMD (Tue Dec 23 2008 - 13:56:58 CST)
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 10:40:23 CST)
  • Re: AMBER: Calculating the dielectrostatic constant from simulation? (Mon Dec 15 2008 - 07:44:09 CST)
  • Re: AMBER: Constant pH dynamics (Tue Dec 09 2008 - 10:24:17 CST)
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 08:00:33 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 19:06:38 CST)
  • Re: AMBER: Buckingham potential (Tue Sep 30 2008 - 10:14:53 CDT)
  • Re: AMBER: Harmonic restraint between two atoms (Fri Sep 26 2008 - 13:42:55 CDT)
  • Re: AMBER: MD goes wrong (Tue Sep 23 2008 - 22:19:19 CDT)
  • Re: AMBER: The forming of micelle (Mon Sep 22 2008 - 13:20:50 CDT)
  • Re: AMBER: D2O (Thu Sep 11 2008 - 10:20:07 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 06:31:19 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:56:08 CDT)
  • Re: AMBER: Hydroxyproline in AMBER (Wed Jul 23 2008 - 11:14:06 CDT)
  • Re: AMBER: Trans proline (Sun Jul 20 2008 - 07:27:45 CDT)
  • Re: AMBER: a link for Amber ff ported to Charmm (Sat Jul 19 2008 - 17:10:58 CDT)
  • Re: AMBER: free energy (Wed Jul 16 2008 - 09:10:41 CDT)
  • Re: AMBER: Constant pH with new parameters (amber10) (Sat Jul 12 2008 - 18:47:41 CDT)
  • Re: AMBER: SMD RESTRAINTS (Thu Jun 12 2008 - 14:23:26 CDT)
  • Re: AMBER: SMD RESTRAINTS (Thu Jun 12 2008 - 11:51:56 CDT)
  • Re: AMBER: Problem of Ptraj analyze matrix (Mon Jun 09 2008 - 08:51:42 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Sat Jun 07 2008 - 07:36:21 CDT)
  • Re: AMBER: how to overcome theunusual bonds formation (Thu May 29 2008 - 07:07:14 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Wed May 28 2008 - 13:58:53 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Wed May 28 2008 - 12:54:09 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 12:43:09 CDT)
  • Re: AMBER: restarting molecular dynamics (Wed May 28 2008 - 10:48:45 CDT)
  • Re: AMBER: restarting molecular dynamics (Wed May 28 2008 - 08:34:17 CDT)
  • Re: AMBER: mass weighted rms fit (Sun May 25 2008 - 11:26:11 CDT)
  • Re: AMBER: analysis REMD (Tue May 20 2008 - 14:17:39 CDT)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 09:11:46 CDT)
  • Re: AMBER: steered MD initial state (Tue May 06 2008 - 12:16:52 CDT)
  • Re: AMBER: Jarzinsky relationship (Mon May 05 2008 - 10:13:51 CDT)
  • Re: AMBER: Jarzinsky relationship (Mon May 05 2008 - 09:46:53 CDT)
  • Re: AMBER: calibration of constant pH simulations (Wed Apr 30 2008 - 13:05:33 CDT)
  • Re: AMBER: Azobenzene: dihedral angle CCNN force field parameter (Sat Apr 26 2008 - 16:10:25 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 11:03:06 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 09:56:33 CDT)
  • Re: AMBER: QM/MM Heating (Mon Jan 21 2008 - 10:13:18 CST)
  • Re: AMBER: input options for replica exchange simulations (Thu Jan 10 2008 - 11:28:50 CST)
  • Re: AMBER: temperature spikes (Sun Jan 06 2008 - 10:41:50 CST)
  • Re: AMBER: About RAMD (Sat Jan 05 2008 - 11:47:33 CST)
• Adrien Delmont
  • Re: AMBER: question about simulation box (Tue Oct 21 2008 - 08:43:24 CDT)
  • AMBER: question about simulation box (Sun Oct 19 2008 - 16:04:24 CDT)
  • AMBER: using ptraj (Fri Oct 17 2008 - 16:44:16 CDT)
  • Re: AMBER: a question (Mon Sep 29 2008 - 07:53:51 CDT)
  • AMBER: a question (Sun Sep 28 2008 - 17:08:00 CDT)
  • Re: AMBER: a question (Mon Sep 29 2008 - 07:53:51 CDT)
  • Re: AMBER: united atom force field (Fri Aug 22 2008 - 14:17:10 CDT)
  • AMBER: united atom force field (Fri Aug 22 2008 - 07:35:06 CDT)
  • Re: AMBER: big molecule numbers ( simulation with many formamide molecules ) (Sat Jul 26 2008 - 10:55:11 CDT)
  • AMBER: big molecule numbers ( simulation with many formamide molecules ) (Sat Jul 26 2008 - 04:04:08 CDT)
  • AMBER: simulation with many formamide molecules (Fri Jul 25 2008 - 05:44:23 CDT)
  • AMBER: big molecule numbers (Thu Jul 24 2008 - 17:27:22 CDT)
  • AMBER: concerning force fields ( to Karl Kirschner ) (Tue Jul 01 2008 - 03:04:45 CDT)
  • Re: AMBER: concerning force fields (Sat Jun 28 2008 - 11:10:05 CDT)
  • Re: AMBER: concerning force fields (Fri Jun 27 2008 - 07:22:08 CDT)
  • Re: AMBER: concerning force fields (Thu Jun 26 2008 - 13:29:39 CDT)
  • AMBER: concerning force fields (Thu Jun 26 2008 - 10:14:15 CDT)
• Age.Skjevik_at_student.uib.no
  • AMBER: Distance in z dimension (Wed Apr 16 2008 - 09:50:55 CDT)
  • AMBER: NPT to NVT (Tue Jan 15 2008 - 07:58:22 CST)
  • Re: AMBER: problems with restart of MD (Fri Jan 11 2008 - 12:16:00 CST)
• Alan
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 06:27:31 CST)
  • Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 04:46:52 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 06:13:09 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 06:10:58 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 05:48:56 CST)
  • AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 04:27:26 CST)
  • Re: AMBER: to understand how frcmod.ff99SB works (Fri Aug 29 2008 - 04:00:01 CDT)
  • Re: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 13:36:55 CDT)
  • AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 05:29:18 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 04:34:03 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 02:42:35 CDT)
  • AMBER: value of Pi in Amber (Fri Aug 08 2008 - 05:36:06 CDT)
  • AMBER: ACPYPI announcement (Thu Jul 31 2008 - 06:17:02 CDT)
  • AMBER: opls/aa in Amber status (Thu Jul 31 2008 - 03:41:58 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Tue Jul 29 2008 - 05:10:48 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Tue Jul 29 2008 - 03:19:16 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 09:50:00 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 09:50:00 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 08:21:35 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 05:54:31 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Sun Jul 27 2008 - 01:26:32 CDT)
  • AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Sat Jul 26 2008 - 03:33:46 CDT)
  • Re: AMBER: Query about the charge of atoms in the parmtop file (Fri Jul 25 2008 - 14:13:43 CDT)
  • Re: AMBER: amber ff and how it deals with out-plane chiral C (Tue Jul 22 2008 - 09:41:27 CDT)
  • AMBER: amber ff and how it deals with out-plane chiral C (Tue Jul 22 2008 - 02:59:05 CDT)
  • Re: AMBER: a link for Amber ff ported to Charmm (Sun Jul 20 2008 - 00:50:22 CDT)
  • Re: AMBER: a link for Amber ff ported to Charmm (Sat Jul 19 2008 - 16:50:25 CDT)
  • AMBER: a link for Amber ff ported to Charmm (Sat Jul 19 2008 - 04:07:27 CDT)
  • Re: AMBER: antechamber and charmm (Thu Jul 17 2008 - 11:05:40 CDT)
  • Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. (Wed Jul 16 2008 - 07:46:15 CDT)
  • AMBER: antechamber and charmm (Thu Jul 10 2008 - 04:43:58 CDT)
  • AMBER: rdparm Segmentation fault (Wed Jun 25 2008 - 16:24:34 CDT)
  • AMBER: rdparm Segmentation fault on Ubuntu (Tue Jun 24 2008 - 10:50:12 CDT)
  • Re: AMBER: rdparm help (Mon Jun 23 2008 - 10:23:50 CDT)
  • AMBER: amber10/dat/leap/cmd/README need update (Mon Jun 23 2008 - 09:59:21 CDT)
  • AMBER: rdparm help (Fri Jun 20 2008 - 06:12:17 CDT)
  • AMBER: about gaff.dat in ambeTools 1.0 (Wed Jun 18 2008 - 09:44:02 CDT)
  • AMBER: to understand GAFF: about A and B coefficients (Tue Jun 17 2008 - 11:42:34 CDT)
  • AMBER: suggestion for next amberTools 1.1 (Tue Jun 17 2008 - 06:01:06 CDT)
  • Re: AMBER: problems with sleap (Mon Jun 16 2008 - 11:07:24 CDT)
  • Re: AMBER: updating documentation (Thu Jun 12 2008 - 18:09:24 CDT)
  • AMBER: updating documentation (Thu Jun 12 2008 - 04:52:40 CDT)
  • Re: AMBER: problems with sleap (Thu Jun 05 2008 - 01:48:03 CDT)
  • AMBER: problems with sleap (Wed Jun 04 2008 - 10:40:04 CDT)
  • Re: AMBER: gasteiger is not working with ambertools 1.0 (Tue Jun 03 2008 - 09:44:07 CDT)
  • AMBER: gasteiger is not working with ambertools 1.0 (Mon May 19 2008 - 09:51:05 CDT)
  • AMBER: ambertools: static linking of user binaries is not supported on Mac OS X (Mon May 19 2008 - 04:39:32 CDT)
• Alberto Perez
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 09:00:09 CDT)
• Alberto Sergio Garay
  • AMBER: Question about resp charges for a charged molecule... (Fri Oct 10 2008 - 05:54:22 CDT)
• Alejandro Valbuena
  • AMBER: install amber tools (Wed May 28 2008 - 05:14:35 CDT)
• Alessandro Nascimento
  • AMBER: SMD-related questions (Mon Dec 29 2008 - 07:07:05 CST)
  • Re: AMBER: Pulling using restraintmask (Thu Dec 11 2008 - 14:58:51 CST)
  • Re: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 13:28:46 CST)
  • AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 10:51:43 CST)
  • Re: AMBER: drug/protein interaction modeling setup (Mon Oct 20 2008 - 15:21:05 CDT)
  • Re: AMBER: pairwise interaction energies (Mon Oct 13 2008 - 05:35:39 CDT)
  • Re: AMBER: MM_PBSA problems in AMBER9 (Mon Oct 06 2008 - 08:04:37 CDT)
  • Re: AMBER: interaction energies (Fri Aug 15 2008 - 11:18:05 CDT)
  • Re: AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 17:02:01 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED) (Wed Jul 30 2008 - 10:29:47 CDT)
  • Re: AMBER: interaction energies in Amber (Mon Jul 28 2008 - 19:51:01 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Sun Jul 27 2008 - 19:38:56 CDT)
  • AMBER: interaction energies in Amber and VMD/NAMD (Sat Jul 26 2008 - 11:09:38 CDT)
  • Re: AMBER: nab (Mon May 12 2008 - 19:59:27 CDT)
  • Re: AMBER: MM_PBSA output file (Fri May 09 2008 - 11:22:35 CDT)
  • Re: AMBER: Tutorial B5 (Wed Apr 23 2008 - 19:25:12 CDT)
  • Re: AMBER: compiling PMEMD with MKL10.0 (Tue Feb 26 2008 - 05:36:40 CST)
  • AMBER: compiling PMEMD with MKL10.0 (Tue Feb 26 2008 - 04:20:47 CST)
• Alex Spasic
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 14:35:20 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 11:58:17 CDT)
  • AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 09:15:25 CDT)
• Alexander Klenner
  • AMBER: parameters of nonbonded potentials (Tue Feb 19 2008 - 04:43:27 CST)
• Alexander Metz
  • AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions (Thu Dec 04 2008 - 11:04:03 CST)
  • AW: AMBER: MM-PBSA (Wed Jun 18 2008 - 05:43:18 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Thu Jun 12 2008 - 03:04:08 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Thu Jun 12 2008 - 00:59:18 CDT)
  • AMBER: Torsion potential in GAFF / "statistic value of parm94" (Fri Mar 14 2008 - 07:53:10 CDT)
• Alfredo Quevedo
  • Re: AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 10:29:24 CDT)
  • Re: AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 09:08:56 CDT)
  • AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 08:35:20 CDT)
• alfredoq_at_mail.fcq.unc.edu.ar
  • AMBER: Problem with energy decomposition in MMPBSA (Tue Feb 05 2008 - 15:32:05 CST)
• alsarraj
  • Re: AMBER: xleap fails to savemol2 (Fri Sep 19 2008 - 15:59:44 CDT)
  • Re: AMBER: xleap fails to savemol2 (Thu Sep 18 2008 - 15:15:20 CDT)
  • AMBER: xleap and Sirius on ubuntu 8.04 (Thu Sep 11 2008 - 21:45:54 CDT)
• Amie Demmel
  • Re: AMBER: problems with 10-12 potential in amber8 sander (Fri Feb 29 2008 - 10:23:15 CST)
  • Re: AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 16:53:15 CST)
  • AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 14:59:27 CST)
  • AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 14:59:27 CST)
• amit
  • RE: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 12:15:34 CST)
  • Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 11:12:41 CST)
• Amit Bajaj
  • Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Sun Dec 21 2008 - 23:41:35 CST)
  • AMBER: amber 9 compilation error with mvapich and intel compilers (Sat Dec 20 2008 - 08:17:03 CST)
• amit jain
  • AMBER: shake the molecule (Fri Oct 03 2008 - 00:26:33 CDT)
• amor san juan
  • Re: AMBER: ligand unit charge is not zero (Thu May 29 2008 - 07:32:57 CDT)
  • AMBER: ligand unit charge is not zero (Thu May 29 2008 - 03:44:58 CDT)
• Anamika Awasthi
  • AMBER: is in vacuo simulation neccessary? (Mon May 26 2008 - 00:18:58 CDT)
  • Re: AMBER: regarding segfault during energy minimization (Thu May 01 2008 - 00:57:35 CDT)
  • AMBER: regarding segfault during energy minimization (Wed Apr 30 2008 - 00:13:21 CDT)
  • AMBER: segmentation fault in SANDER (Tue Apr 29 2008 - 06:44:29 CDT)
  • AMBER: query regarding energy minimization (Mon Apr 28 2008 - 08:22:24 CDT)
  • AMBER: query regarding loadpadb (Fri Apr 25 2008 - 03:33:19 CDT)
  • AMBER: initial command? (Wed Feb 27 2008 - 06:01:51 CST)
  • AMBER: XLEaP (Thu Feb 21 2008 - 03:36:20 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: High ESURF (Mon Nov 17 2008 - 02:24:02 CST)
  • Re: AMBER: nscm code (Fri Oct 10 2008 - 06:37:09 CDT)
  • Re: AMBER: F modified RNA is split in two parts when running sander simulated annealing (Wed Oct 01 2008 - 04:56:38 CDT)
  • Re: AMBER: Buckingham potential (Tue Sep 30 2008 - 09:47:27 CDT)
  • Re: AMBER: Amber GB problems on PMEMD !! (Thu Sep 25 2008 - 10:12:59 CDT)
  • Re: AMBER: nmode/nab entropy calculations memory issues (Tue Sep 16 2008 - 10:50:11 CDT)
  • Re: AMBER: Error when compiling and testing AmberTools (Fri Aug 22 2008 - 04:11:14 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 10:48:28 CDT)
  • Re: AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 10:33:28 CDT)
  • Re: AMBER: self-diffusion coefficient and Berendsen (Fri May 23 2008 - 04:22:57 CDT)
  • Re: AMBER: nab (Tue May 13 2008 - 04:39:19 CDT)
  • Re: AMBER: NAB examples (Mon Apr 07 2008 - 11:46:34 CDT)
  • Re: AMBER: using NAB to calculate normal modes (Fri Feb 15 2008 - 16:23:30 CST)
• Andrei Neamtu
  • AMBER: compiling amber 10 (Sat Nov 22 2008 - 01:26:58 CST)
• Andrew Borgert
  • AMBER: Amber 9 run error (Tue Apr 08 2008 - 16:28:07 CDT)
  • Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Tue Mar 25 2008 - 10:11:20 CDT)
  • AMBER: varying restraint_wt with nmropt=1 (Wed Feb 27 2008 - 14:18:28 CST)
• Andrew Emerson
  • AMBER: Re: amber 9 compilation problem on IBM SP5 (Mon May 05 2008 - 02:57:53 CDT)
  • AMBER: amber 9 compilation problem on IBM SP5 (Wed Apr 30 2008 - 07:44:38 CDT)
• Andrew Ring
  • AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 18:40:44 CST)
  • Re: AMBER: benchmark walltime to ps/day calculation (Thu Jan 31 2008 - 15:16:22 CST)
  • AMBER: benchmark walltime to ps/day calculation (Thu Jan 31 2008 - 14:11:05 CST)
• Andrey Semichaevsky
  • Re: AMBER: Re: Force field parameter file for CNT (Fri Feb 29 2008 - 10:38:39 CST)
  • AMBER: Re: Amber Force field for CNT: leaprc.ff23 (Fri Feb 29 2008 - 09:35:16 CST)
  • AMBER: Re: Force field parameter file for CNT (Thu Feb 28 2008 - 15:34:01 CST)
  • AMBER: Amber compilation with ifort (Wed Feb 06 2008 - 15:23:26 CST)
  • AMBER: Re: timestep problem (Thu Jan 17 2008 - 12:24:00 CST)
• aneesh cna
  • AMBER: mdout file details (Tue Dec 30 2008 - 00:20:40 CST)
  • Re: AMBER: problem with Dihedral angle potentials (Thu Oct 30 2008 - 11:35:00 CDT)
  • Re: AMBER: problem with Dihedral angle potentials (Thu Oct 30 2008 - 04:11:48 CDT)
  • AMBER: problem with Dihedral angle potentials (Wed Oct 29 2008 - 04:23:57 CDT)
  • AMBER: regarding rigid molecules (Thu Oct 16 2008 - 04:34:36 CDT)
  • AMBER: problem with parmchck (Tue Sep 30 2008 - 12:10:28 CDT)
  • AMBER: RDF output file format (Mon Aug 18 2008 - 04:48:45 CDT)
  • AMBER: problem with prep file generation (Wed Aug 13 2008 - 07:05:58 CDT)
  • AMBER: Energy analysis (Fri Jul 25 2008 - 10:12:10 CDT)
  • Re: AMBER: restraint box dimension (Fri Apr 11 2008 - 04:56:17 CDT)
  • AMBER: restraint box dimension (Tue Apr 08 2008 - 05:45:20 CDT)
  • Re: AMBER: LJ parameters (Thu Apr 03 2008 - 06:30:39 CDT)
  • AMBER: LJ parameters (Wed Apr 02 2008 - 06:46:22 CDT)
  • AMBER: PF6 parameters (Wed Mar 26 2008 - 23:43:58 CDT)
  • AMBER: OPLS force field (Wed Mar 26 2008 - 10:48:19 CDT)
  • AMBER: problem with distance restraints (Thu Mar 20 2008 - 05:13:31 CDT)
  • AMBER: problem with distance restrain (Tue Mar 18 2008 - 05:16:09 CDT)
  • AMBER: problem with antechamber (Wed Feb 27 2008 - 23:55:53 CST)
  • AMBER: dihedral energy in amber (Sat Feb 23 2008 - 04:32:08 CST)
• Anna Karawajczyk
  • AMBER: mol2, xleap, Segmentation fault (Mon Aug 25 2008 - 08:01:31 CDT)
  • AMBER: bacteriochlorophyll ff (Fri Aug 01 2008 - 05:04:44 CDT)
• Anna Reymer
  • Re: AMBER: (Tue Jul 01 2008 - 07:46:24 CDT)
  • AMBER: AMBER10: ambpdb problems (Tue Jul 01 2008 - 03:37:38 CDT)
  • AMBER: (Tue Jul 01 2008 - 03:36:12 CDT)
• anna.schrey_at_gmx.de
  • Re: AMBER: Problems with neglected restaints (Thu Mar 20 2008 - 14:43:20 CDT)
  • AMBER: Problems with neglected restaints (Tue Mar 18 2008 - 11:40:20 CDT)
  • Re: AMBER: Atom types/parameters for chromene (Thu Mar 06 2008 - 07:35:06 CST)
  • AMBER: Atom types/parameters for chromene (Wed Mar 05 2008 - 03:34:24 CST)
  • Re: AMBER: problem with group input (Mon Jan 21 2008 - 08:22:48 CST)
• Anselm Horn
  • Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 04:06:17 CST)
  • AMBER: Indentifying cluster center structures in trajectory (Wed Jul 23 2008 - 02:14:41 CDT)
  • AMBER: Weighting factors in RESP charge fitting (Fri May 16 2008 - 07:32:22 CDT)
  • AMBER: vlimit-problems after image and restart (Tue Apr 22 2008 - 04:04:46 CDT)
• Anthony Cruz
  • Re: AMBER: AMBER10 Compilation (SGI Altix) (Tue Sep 16 2008 - 11:56:45 CDT)
  • AMBER: AMBER10 Compilation (SGI Altix) (Mon Sep 15 2008 - 13:21:49 CDT)
  • AMBER: Amber10 Compilation (Tue Sep 09 2008 - 09:26:04 CDT)
  • AMBER: Conformation search... (Thu Apr 17 2008 - 14:32:52 CDT)
  • Re: AMBER: chromophore parameters for Molecular Dynamics (Wed Jan 16 2008 - 07:47:42 CST)
  • AMBER: chromophore parameters for Molecular Dynamics (Fri Jan 11 2008 - 09:32:31 CST)
• Antonios Samiotakis
  • AMBER: Question on Urea box (Tue Oct 07 2008 - 14:31:44 CDT)
• Anuradha Mittal
  • AMBER: solvate without translating (Wed Sep 24 2008 - 14:38:31 CDT)
• Arturas Ziemys
  • AMBER: molsurf fails (Tue Nov 25 2008 - 09:27:27 CST)
  • Re: AMBER: problem (Tue Nov 18 2008 - 09:07:19 CST)
  • RE: AMBER: problem (Mon Nov 17 2008 - 22:36:25 CST)
  • AMBER: problem (Sun Nov 16 2008 - 23:07:38 CST)
  • AMBER: MM-PBSA and trajectory input (Thu Nov 13 2008 - 11:22:36 CST)
  • AMBER: aromatic bent ligand (Mon Oct 27 2008 - 21:34:49 CDT)
  • AMBER: mm_pbsa_statistics / 3 traj (Mon Oct 20 2008 - 11:18:26 CDT)
  • Re: AMBER: nmode units (Thu Sep 04 2008 - 10:22:41 CDT)
  • Re: AMBER: nmode units (Thu Sep 04 2008 - 09:26:57 CDT)
  • AMBER: nmode units (Wed Sep 03 2008 - 17:28:44 CDT)
  • AMBER: wrapping w/ ptraj (Fri Aug 29 2008 - 16:57:52 CDT)
  • AMBER: interaction energies (Thu Aug 14 2008 - 10:21:34 CDT)
  • Re: AMBER: mm-pbsa / sander.MPI ? (Thu Aug 14 2008 - 09:42:02 CDT)
  • AMBER: mm-pbsa / sander.MPI ? (Wed Aug 13 2008 - 17:26:56 CDT)
  • AMBER: glycoprotein setup (Tue Aug 12 2008 - 22:35:35 CDT)
  • Re: AMBER: amber9 / difference of igb=0 and igb=6 (Wed Jul 09 2008 - 16:03:32 CDT)
  • AMBER: amber9 / difference of igb=0 and igb=6 (Wed Jul 09 2008 - 14:45:32 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:48:47 CDT)
  • AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:10:47 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 15:19:32 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 12:17:54 CDT)
  • AMBER: "radius = 0.000" (Tue Jul 01 2008 - 11:08:45 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 13:19:36 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 12:56:57 CDT)
  • AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 12:00:34 CDT)
  • AMBER: sander.MPI / openmpi on PBS (Wed Jun 11 2008 - 13:59:52 CDT)
  • Re: AMBER: parallel test / libmpi_f90.so.0 (Wed May 28 2008 - 10:24:14 CDT)
  • AMBER: parallel test / libmpi_f90.so.0 (Wed May 28 2008 - 10:10:36 CDT)
  • AMBER: parallel error : undefined reference to `MAIN_' (Fri Apr 25 2008 - 16:14:59 CDT)
  • Re: AMBER: silica slab (Tue Feb 05 2008 - 12:35:03 CST)
  • AMBER: silica slab (Tue Feb 05 2008 - 11:28:55 CST)
  • AMBER: silica slab / FF (Fri Feb 01 2008 - 15:42:13 CST)
• Ashish Sangwai
  • Re: AMBER: Restraints (Thu Nov 13 2008 - 13:11:45 CST)
  • AMBER: using "EP" for dummy atom (Thu Nov 06 2008 - 19:24:23 CST)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 19:37:51 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Sun Apr 20 2008 - 18:09:03 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Fri Apr 18 2008 - 19:18:32 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Fri Apr 18 2008 - 19:28:02 CDT)
  • AMBER: hydrogens are flying in replica exchange simulations (Fri Apr 18 2008 - 18:43:01 CDT)
• Atro Tossavainen
  • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Tue Dec 16 2008 - 06:17:48 CST)
  • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 08:40:41 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 08:27:05 CST)
  • AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 06:51:16 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 05:12:53 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 04:06:51 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 03:36:09 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sun Dec 14 2008 - 14:11:53 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sat Dec 13 2008 - 16:12:30 CST)
  • AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sat Dec 13 2008 - 15:18:45 CST)
  • Re: AMBER: amber10 installation on sgi_mips (Thu Oct 02 2008 - 14:39:33 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Thu Oct 02 2008 - 04:59:34 CDT)
  • Re: AMBER: compilation problem (Sat Sep 27 2008 - 14:18:13 CDT)
  • Re: AMBER: compilation problem (Thu Sep 25 2008 - 14:32:06 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Thu Sep 18 2008 - 03:06:57 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Tue Jun 24 2008 - 09:37:57 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Sat May 31 2008 - 06:23:31 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Fri May 30 2008 - 01:42:02 CDT)
  • Re: AMBER: compilation problem with AMBER10 (Wed May 28 2008 - 03:04:09 CDT)
  • Re: AMBER: massively parallel computation (Wed May 21 2008 - 12:49:03 CDT)
  • Re: AMBER: massively parallel computation (Wed May 21 2008 - 02:17:10 CDT)
  • AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) (Tue Mar 11 2008 - 09:33:33 CDT)
  • Re: AMBER: AMBER install problem (Tue Mar 11 2008 - 01:51:18 CDT)
  • Re: AMBER: Compiler issues with Altix450 (Mon Mar 10 2008 - 18:13:45 CDT)
  • Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? (Mon Mar 10 2008 - 08:24:33 CDT)
  • Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? (Mon Mar 10 2008 - 03:04:20 CDT)
  • Re: AMBER: Compiler issues with Altix450 (Sat Mar 08 2008 - 16:19:36 CST)
  • Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 (Thu Feb 14 2008 - 01:02:22 CST)
  • Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 (Wed Feb 13 2008 - 14:49:57 CST)
  • Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 (Wed Feb 13 2008 - 14:27:29 CST)
  • AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 (Wed Feb 13 2008 - 07:31:54 CST)
  • Re: AMBER: Amber compilation with ifort (Thu Feb 07 2008 - 01:45:09 CST)
• Aust, Susanne
  • AMBER: MD simulation crashed (Wed Sep 17 2008 - 08:10:17 CDT)
  • AW: AMBER: tleap and Zn parameter (Wed Sep 03 2008 - 02:18:28 CDT)
  • AW: AMBER: tleap and Zn parameter (Tue Sep 02 2008 - 01:46:23 CDT)
  • AMBER: tleap and Zn parameter (Mon Sep 01 2008 - 03:14:53 CDT)
• Austin B. Yongye
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 20:59:47 CDT)
  • Re: AMBER: about glycam06 (Wed Apr 30 2008 - 16:47:32 CDT)
  • Re: AMBER: about glycam06 (Wed Apr 30 2008 - 12:26:44 CDT)
• babak minoofar
  • Re: AMBER: N(CN2)- ion (Fri Dec 12 2008 - 03:29:54 CST)
  • Re: AMBER: N(CN2)- ion (Thu Dec 04 2008 - 10:00:58 CST)
  • AMBER: N(CN2)- ion (Fri Nov 28 2008 - 07:12:26 CST)
  • AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) (Sun Sep 21 2008 - 09:34:39 CDT)
• backy
  • AMBER: The energy minimization of SIngle RNA chain (Thu Jan 10 2008 - 02:33:20 CST)
• Badry Bursulaya
  • AMBER: mm_pbsa problem (Mon Feb 11 2008 - 16:45:29 CST)
• balaji nagarajan
  • AMBER: (Mon Dec 22 2008 - 07:36:38 CST)
  • RE: AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 22:06:55 CST)
  • AMBER: reg.concentration of ions (Fri Dec 12 2008 - 10:34:49 CST)
  • RE: AMBER: reg.building ions (Fri Dec 12 2008 - 06:14:57 CST)
  • AMBER: reg.building ions (Fri Dec 12 2008 - 04:40:07 CST)
  • AMBER: reg-antichamber run (Wed Dec 10 2008 - 11:08:17 CST)
  • AMBER: parallel installation (Tue Dec 09 2008 - 21:56:20 CST)
  • RE: AMBER: reg-adding ions (Mon Dec 08 2008 - 22:32:14 CST)
  • AMBER: reg-adding ions (Mon Dec 08 2008 - 02:20:05 CST)
  • RE: AMBER: regad-tutorial-dna-polyAT (Mon Dec 08 2008 - 00:40:39 CST)
  • AMBER: regad-tutorial-dna-polyAT (Sun Dec 07 2008 - 22:45:10 CST)
  • RE: AMBER: reg unstability of structure in md (Thu Dec 04 2008 - 22:32:21 CST)
  • AMBER: reg unstability of structure in md (Wed Dec 03 2008 - 22:17:51 CST)
  • RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 10:56:44 CST)
  • RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 10:51:00 CST)
  • AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 08:05:52 CST)
• Balazs JOJART
  • Re: AMBER: Electrostatic Energy Components (Mon Nov 24 2008 - 06:19:42 CST)
  • Re: AMBER: how to generate psf file using the AMBER topology file (Fri Jul 18 2008 - 06:09:21 CDT)
  • Re: AMBER: how to derive torsional angle parameters in gaff (Thu Jun 26 2008 - 03:53:40 CDT)
• baohua zhang
  • AMBER: MD goes wrong (Tue Sep 23 2008 - 21:17:57 CDT)
  • AMBER: Volume of ucell too big (Tue Jul 29 2008 - 22:30:43 CDT)
• Barbault Florent
  • Re: AMBER: MM/GBSA Error during deccomposition (Wed Dec 03 2008 - 14:32:14 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 08:45:20 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 10:21:17 CST)
  • AMBER: problem with cartesian restraints with NTP simulations (Wed Nov 19 2008 - 08:50:13 CST)
  • Re: AMBER: Folate parameters (Thu Oct 30 2008 - 09:03:09 CDT)
  • Re: AMBER: drug/protein interaction modeling setup (Mon Oct 20 2008 - 15:37:24 CDT)
  • Re: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? (Sat Sep 20 2008 - 15:40:34 CDT)
  • AMBER: mulliken charges in QM/MM calculation (Sun Sep 14 2008 - 03:26:25 CDT)
  • Re: AMBER: Trans proline (Sun Jul 20 2008 - 01:27:37 CDT)
  • AMBER: problem with restraints (Thu Jul 10 2008 - 13:59:15 CDT)
  • Re: AMBER: trajout input (Fri Jun 20 2008 - 04:43:28 CDT)
  • Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Tue Apr 29 2008 - 15:56:09 CDT)
  • Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Sat Apr 26 2008 - 08:13:47 CDT)
  • Re: AMBER: artifacts in ptraj avg output (Sat Apr 05 2008 - 04:11:37 CDT)
• Beale, John
  • AMBER: RMS plot (Wed Dec 31 2008 - 13:11:39 CST)
  • AMBER: (Wed Dec 24 2008 - 07:19:48 CST)
  • AMBER: Constant pH dynamics (Tue Dec 09 2008 - 06:51:39 CST)
  • RE: AMBER: peptide MD (Mon Oct 27 2008 - 12:47:42 CDT)
  • RE: AMBER: peptide MD (Mon Oct 27 2008 - 12:13:47 CDT)
  • AMBER: peptide MD (Mon Oct 27 2008 - 10:38:48 CDT)
  • AMBER: Contacts (Mon Oct 20 2008 - 09:29:06 CDT)
  • AMBER: Ring flips (Fri Oct 10 2008 - 12:09:52 CDT)
  • AMBER: Radius of Gyration (Fri Oct 10 2008 - 06:27:22 CDT)
  • AMBER: MD at a given pH (Fri Sep 26 2008 - 11:44:32 CDT)
  • AMBER: Question (Wed Sep 17 2008 - 06:14:15 CDT)
  • AMBER: Tutorial 6 (Mon Jul 14 2008 - 11:48:21 CDT)
• Ben Eisenbraun
  • AMBER: Building Amber 10 with Intel MKL and compiler mini howto (Wed Dec 10 2008 - 11:45:04 CST)
• Ben Roberts
  • Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors (Tue Sep 09 2008 - 12:38:56 CDT)
  • Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors (Mon Sep 08 2008 - 16:24:30 CDT)
  • AMBER: Another problem when trying to compile Sander in debug mode (Mon Sep 08 2008 - 10:49:52 CDT)
  • AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors (Mon Sep 08 2008 - 10:43:47 CDT)
  • AMBER: Error when compiling and testing AmberTools (Thu Aug 21 2008 - 16:46:43 CDT)
• ben rodriguez
  • RE: AMBER: RED III execution problem (Mon Jul 07 2008 - 14:21:11 CDT)
  • AMBER: RED III execution problem (Wed Jul 02 2008 - 20:24:19 CDT)
• Benjamin Juhl
  • AMBER: protonate in Amber10 (Wed May 28 2008 - 09:55:06 CDT)
  • Re: AMBER: reset time and comments (Thu May 08 2008 - 04:12:11 CDT)
• Benjamin Roberts
  • AMBER: Clarification re qmmask (Thu Oct 16 2008 - 12:24:45 CDT)
• Bert
  • AMBER: DNA structure analysis (Wed Oct 22 2008 - 06:27:38 CDT)
• Bertrand P. S. Russell
  • Re: AMBER: RDF output file format (Mon Aug 18 2008 - 05:26:08 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 07:40:56 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 02:09:20 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 02:03:39 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Sun May 04 2008 - 20:50:13 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 05:11:15 CDT)
  • AMBER: Happy holi (Thu Mar 20 2008 - 04:03:22 CDT)
  • Re: AMBER: AMBER installation problem (Sat Jan 26 2008 - 09:53:43 CST)
• bhargav patel
  • Re: AMBER: Installation Problem of AMBER10 (Tue Jun 24 2008 - 05:06:45 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Fri Jun 20 2008 - 04:07:12 CDT)
  • AMBER: Installation Problem of AMBER10 (Thu Jun 19 2008 - 05:57:26 CDT)
  • AMBER: compilation problem with AMBER10 (Wed May 28 2008 - 00:56:15 CDT)
• Bill K
  • Re: AMBER: How do you evaluate forces on a fixed atom? (Tue Dec 02 2008 - 19:54:35 CST)
  • AMBER: How do you evaluate forces on a fixed atom? (Mon Dec 01 2008 - 12:45:42 CST)
• Bill Ross
  • Re: AMBER: load opls force field (Thu Nov 13 2008 - 14:32:19 CST)
  • Re: AMBER: Extracting periodic box size deviation (Thu Nov 06 2008 - 19:42:35 CST)
  • RE: AMBER: stripping water from a restart file (Fri Oct 24 2008 - 10:21:59 CDT)
  • RE: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 18:48:59 CDT)
  • Re: AMBER: Metal parameter values (Thu Oct 23 2008 - 13:23:08 CDT)
  • RE: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 13:13:43 CDT)
  • RE: AMBER: stripping water from a restart file (Wed Oct 22 2008 - 15:38:11 CDT)
  • Re: AMBER: stripping water from a restart file (Wed Oct 22 2008 - 12:12:29 CDT)
  • Re: AMBER: Heme cysteine (Tue Oct 21 2008 - 11:20:38 CDT)
  • Re: AMBER: drug/protein interaction modeling setup (Mon Oct 20 2008 - 17:39:04 CDT)
  • Re: AMBER: Sources of disruption during NVE (Fri Oct 03 2008 - 10:27:37 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Thu Oct 02 2008 - 15:09:53 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Thu Oct 02 2008 - 12:36:58 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Thu Oct 02 2008 - 12:05:17 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Wed Oct 01 2008 - 17:11:08 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Tue Sep 30 2008 - 13:11:12 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Mon Sep 29 2008 - 17:03:28 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Mon Sep 29 2008 - 13:38:46 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Wed Sep 17 2008 - 13:04:32 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Wed Sep 17 2008 - 12:41:28 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 14:36:24 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 14:15:52 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 12:47:00 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 13:51:29 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 11:22:18 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:28:34 CDT)
  • Re: AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 18:51:18 CDT)
  • Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP (Mon Jul 28 2008 - 19:26:35 CDT)
  • Re: AMBER: solvate dna in TIP3PBOX 10.0 (Sat Jul 26 2008 - 13:11:44 CDT)
  • Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP (Fri Jul 25 2008 - 15:40:27 CDT)
  • RE: AMBER: Regarding ff03 forcefield (Fri Jul 25 2008 - 15:32:02 CDT)
  • Re: AMBER: solvate dna in TIP3PBOX 10.0 (Fri Jul 25 2008 - 15:28:46 CDT)
  • Re: Re: AMBER: improper dihedral in ff03 united atom forcefield (Wed Jul 23 2008 - 13:19:31 CDT)
  • Re: AMBER: improper dihedral in ff03 united atom forcefield (Tue Jul 22 2008 - 23:28:07 CDT)
  • Re: AMBER: amber ff and how it deals with out-plane chiral C (Tue Jul 22 2008 - 16:44:36 CDT)
  • Re: AMBER: question about the improper torsion (Tue Jul 15 2008 - 11:48:24 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Fri Jun 20 2008 - 15:46:35 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Thu Jun 19 2008 - 12:31:42 CDT)
  • Re: AMBER: potassium ion (Sat Jun 14 2008 - 15:04:31 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Wed May 28 2008 - 13:18:06 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Wed May 28 2008 - 13:11:30 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Wed May 28 2008 - 12:47:28 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Tue May 27 2008 - 11:44:23 CDT)
  • Re: AMBER: potassium ion (Thu May 22 2008 - 13:27:21 CDT)
  • Re: AMBER: to unsubscribe email (Mon May 12 2008 - 12:46:24 CDT)
  • Re: AMBER: Improper dihedral parameters (Tue May 06 2008 - 14:23:55 CDT)
  • Re: AMBER: about glycam06 (Sun May 04 2008 - 17:46:05 CDT)
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 15:16:27 CDT)
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 15:12:12 CDT)
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 12:28:51 CDT)
  • Re: AMBER: addions and addions2 (Tue Mar 25 2008 - 12:34:52 CDT)
  • Re: AMBER: XMGRACE on Linux 64 Bit (Thu Mar 06 2008 - 18:12:51 CST)
  • Re: Fwd: Re: AMBER: xleap screen output (Tue Mar 04 2008 - 11:59:58 CST)
  • Re: AMBER: xleap screen output (Mon Mar 03 2008 - 16:08:17 CST)
  • Re: AMBER: Lennard-Jones parameters (Thu Feb 28 2008 - 14:07:31 CST)
  • Re: AMBER: Lennard-Jones parameters (Wed Feb 27 2008 - 18:09:10 CST)
  • RE: AMBER: initial command? (Wed Feb 27 2008 - 12:56:20 CST)
  • Re: AMBER: Deleting solute from box (Thu Feb 07 2008 - 15:37:27 CST)
  • Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program (Wed Feb 06 2008 - 18:18:38 CST)
• Biman Jana
  • AMBER: How to adjust the problem of "Vlimit exceeded" (Mon Jun 23 2008 - 02:28:27 CDT)
  • AMBER: TIP5P water simulation with AMBER7 (Tue Apr 01 2008 - 02:14:54 CDT)
  • AMBER: RMSD calculation using AMBER7 (Sat Jan 19 2008 - 07:16:46 CST)
• Binbin Liu
  • AMBER: NMROPT=1 in minimisation (Sat Jan 05 2008 - 17:38:51 CST)
• Boutheina Kerkeni
  • Re: AMBER: free energy (Wed Jul 16 2008 - 11:30:44 CDT)
  • AMBER: free energy (Wed Jul 16 2008 - 10:54:39 CDT)
  • RE: AMBER: empty output (Tue Jul 15 2008 - 12:31:50 CDT)
  • AMBER: empty output (Sat Jul 12 2008 - 10:29:47 CDT)
  • AMBER: size of pdb (Fri Jul 11 2008 - 10:13:57 CDT)
  • Re: AMBER: bond command (Fri Jul 11 2008 - 07:00:48 CDT)
  • AMBER: bond command (Thu Jul 10 2008 - 12:30:46 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 07:27:59 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 06:44:20 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 06:02:10 CDT)
  • AMBER: (Fri Jul 04 2008 - 05:34:55 CDT)
  • Re: AMBER: hold atoms fixed (Mon Jun 30 2008 - 08:12:33 CDT)
  • Re: AMBER: hold atoms fixed (Mon Jun 30 2008 - 08:12:33 CDT)
  • AMBER: hold atoms fixed (Mon Jun 30 2008 - 07:51:17 CDT)
  • AMBER: graphite (Fri Jan 11 2008 - 05:26:58 CST)
• Brad Lambeth
  • AMBER: Where is ICO read from the ix array? (Mon Jul 21 2008 - 14:49:44 CDT)
  • AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 (Sat Jul 12 2008 - 19:20:09 CDT)
• Brendan Duggan
  • AMBER: xleap segmentation fault on SaveAmberParm (Tue Apr 15 2008 - 14:15:46 CDT)
  • AMBER: offset residue numbering (Mon Jan 07 2008 - 14:14:30 CST)
• Brent Krueger
  • Re: AMBER: RESP GAUSSIAN AMBER (Sun Dec 14 2008 - 20:52:14 CST)
  • Re: AMBER: Trans proline (Sat Aug 02 2008 - 22:47:16 CDT)
• brmeher_at_iitg.ernet.in
  • AMBER: AMBER-8 parallel installation - test run failure (Thu Jan 03 2008 - 04:10:58 CST)
• Campbell, Patrick
  • AMBER: Question on AMBER MD Implications (Sat Nov 01 2008 - 05:01:17 CDT)
  • AMBER: Question on AMBER MD Implications (Fri Oct 31 2008 - 11:27:41 CDT)
  • Re:AMBER:VMD Movie.mdcrd (Fri Jun 06 2008 - 13:56:52 CDT)
  • AMBER: VMD Movie .mdcrd file ptraj (Fri Jun 06 2008 - 08:22:50 CDT)
  • AMBER: VMD file generation 4 - mdcrd analysis (Mon Jun 02 2008 - 15:21:00 CDT)
  • RE:AMBER: VMD file generation 4 - mdcrd ptraj analysis (Mon Jun 02 2008 - 14:54:06 CDT)
  • AMBER: VMD file generation 4 - mdcrd ptraj analysis (Mon Jun 02 2008 - 13:26:15 CDT)
  • AMBER: VMD Movie 3 (Fri May 30 2008 - 09:56:41 CDT)
  • AMBER: VMD Movie 4 (Thu May 29 2008 - 14:37:43 CDT)
  • AMBER: VMD Movie 3 (Thu May 29 2008 - 13:12:20 CDT)
  • AMBER: VMD Movie 2 (Thu May 29 2008 - 12:39:20 CDT)
  • AMBER: VMD Movie (Wed May 28 2008 - 18:33:39 CDT)
  • FW: FW: AMBER: FW: MD run time inquiry (Thu Mar 27 2008 - 08:55:28 CDT)
  • FW: AMBER: FW: MD run time inquiry (Thu Mar 27 2008 - 07:14:16 CDT)
  • AMBER: FW: MD run time inquiry (Thu Mar 27 2008 - 05:13:00 CDT)
  • RE: AMBER: cntrl namelist error (Sat Mar 22 2008 - 11:22:18 CDT)
  • RE: AMBER: cntrl namelist error (Sat Mar 22 2008 - 11:11:39 CDT)
  • AMBER: cntrl namelist error (Sat Mar 22 2008 - 10:40:16 CDT)
  • RE: AMBER: INPCRD error on open (Thu Mar 20 2008 - 13:35:37 CDT)
  • RE: AMBER: INPCRD error on open (Thu Mar 20 2008 - 13:37:45 CDT)
  • RE: AMBER: INPCRD error on open (Thu Mar 20 2008 - 12:02:12 CDT)
  • AMBER: INPCRD error on open (Thu Mar 20 2008 - 10:17:32 CDT)
  • RE: AMBER: Clarification on error message (Sat Mar 08 2008 - 15:15:36 CST)
  • AMBER: Clarification on error message (Sat Mar 08 2008 - 14:09:23 CST)
  • RE: AMBER: Input file for Minimization (Tue Feb 12 2008 - 11:43:34 CST)
  • AMBER: Input file for Minimization (Sat Feb 09 2008 - 15:18:51 CST)
• caoch
  • AMBER: local coordinate system question (Wed Jun 25 2008 - 04:33:15 CDT)
  • RE: AMBER: PF6 parameters (Thu Mar 27 2008 - 23:28:03 CDT)
• Carlos Simmerling
  • Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 09:24:09 CST)
  • Re: AMBER: restraintmask - reference file is not working (Thu Dec 18 2008 - 06:14:27 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 05:45:13 CST)
  • Re: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 13:51:35 CST)
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:12:32 CST)
  • Re: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 07:19:25 CST)
  • Re: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 19:05:03 CST)
  • Re: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 18:38:14 CST)
  • Re: AMBER: problem with toturial A3 (MM-PBSA) (Tue Dec 16 2008 - 07:57:42 CST)
  • Re: AMBER: ff99 (PK/IDIVF) (Tue Dec 16 2008 - 06:01:32 CST)
  • Re: AMBER: ff99 (PK/IDIVF) (Sun Dec 14 2008 - 12:38:23 CST)
  • Re: AMBER: problem with toturial A3 (MM-PBSA) (Sat Dec 13 2008 - 09:35:13 CST)
  • Re: AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 08:05:11 CST)
  • Re: AMBER: DNA: GB solvent with salt (Fri Dec 12 2008 - 05:33:14 CST)
  • Re: AMBER: Distorted ring... (Thu Dec 11 2008 - 06:15:57 CST)
  • Re: AMBER: reg unstability of structure in md (Fri Dec 05 2008 - 05:41:40 CST)
  • Re: AMBER: reg unstability of structure in md (Thu Dec 04 2008 - 05:28:12 CST)
  • Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Mon Dec 01 2008 - 05:16:02 CST)
  • Re: AMBER: Questions on TIP4P model? (Fri Nov 28 2008 - 14:03:14 CST)
  • Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Fri Nov 28 2008 - 06:33:16 CST)
  • Re: AMBER: Heating up (Fri Nov 28 2008 - 06:30:29 CST)
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 05:08:40 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:42:53 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:41:48 CST)
  • Re: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 17:46:10 CST)
  • Re: AMBER: ptraj center problem (Fri Nov 21 2008 - 12:42:17 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 10:21:51 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:51:18 CST)
  • Re: AMBER: PB Radii (Mon Nov 17 2008 - 05:30:41 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 06:42:22 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sat Nov 15 2008 - 09:44:32 CST)
  • Re: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 15:00:30 CST)
  • Re: AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 14:47:56 CST)
  • Re: AMBER: changing pdb structure (Tue Nov 11 2008 - 05:35:42 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 14:37:32 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 14:39:29 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 12:13:29 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 10:53:09 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 11:53:48 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 10:41:22 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:35:46 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 12:52:23 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:45:22 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 05:29:25 CST)
  • Re: AMBER: Question on AMBER MD Implications (Fri Oct 31 2008 - 11:51:21 CDT)
  • Re: AMBER: Query on restart file (Thu Oct 30 2008 - 21:03:53 CDT)
  • Re: AMBER: problem with Dihedral angle potentials (Thu Oct 30 2008 - 17:07:27 CDT)
  • Re: AMBER: Optimal compiling of amber on XT3 (Thu Oct 30 2008 - 05:22:35 CDT)
  • Re: AMBER: problem with Dihedral angle potentials (Thu Oct 30 2008 - 05:20:59 CDT)
  • Re: AMBER: problem with Dihedral angle potentials (Wed Oct 29 2008 - 05:09:15 CDT)
  • Re: AMBER: peptide MD (Mon Oct 27 2008 - 13:07:11 CDT)
  • Re: AMBER: peptide MD (Mon Oct 27 2008 - 12:35:57 CDT)
  • Re: AMBER: peptide MD (Mon Oct 27 2008 - 12:05:00 CDT)
  • Re: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 17:05:07 CDT)
  • Re: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 07:22:00 CDT)
  • Re: AMBER: stripping water from a restart file (Wed Oct 22 2008 - 11:29:32 CDT)
  • Re: AMBER: Does LEaP understant capping with ACE/NME? (Tue Oct 21 2008 - 11:02:41 CDT)
  • Re: AMBER: equilibration (Tue Oct 21 2008 - 06:30:12 CDT)
  • Re: AMBER: equilibration (Tue Oct 21 2008 - 06:20:13 CDT)
  • Re: AMBER: equilibration (Tue Oct 21 2008 - 06:01:54 CDT)
  • Re: AMBER: about SASA and AMBER (Mon Oct 20 2008 - 12:17:42 CDT)
  • Re: AMBER: Addions in GB Mode? (Mon Oct 20 2008 - 05:12:52 CDT)
  • Re: AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 05:41:01 CDT)
  • Re: AMBER: High Bfactor values for the terminal residues/atoms (Tue Oct 14 2008 - 05:25:25 CDT)
  • Re: AMBER: large number of solvent molecules were added for protein with 221 AA residues (Tue Oct 14 2008 - 05:21:46 CDT)
  • Re: AMBER: Radius of Gyration (Fri Oct 10 2008 - 06:48:21 CDT)
  • Re: AMBER: AddIons approach (Fri Oct 10 2008 - 06:17:08 CDT)
  • Re: AMBER: nscm code (Fri Oct 10 2008 - 05:32:25 CDT)
  • Re: AMBER: ptraj average structure (Sat Oct 04 2008 - 08:55:31 CDT)
  • AMBER: Oct 6 deadline for ACS computational chemistry awards (Thu Oct 02 2008 - 12:45:35 CDT)
  • Re: AMBER: Temperature regulation (Wed Oct 01 2008 - 21:04:36 CDT)
  • Re: AMBER: Temperature regulation (Wed Oct 01 2008 - 12:49:26 CDT)
  • Re: AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 16:33:12 CDT)
  • Re: AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 16:09:59 CDT)
  • Re: AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 15:45:58 CDT)
  • Re: AMBER: Location of vdw radii and partial charges for ff99SB (Mon Sep 29 2008 - 09:58:45 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 13:21:19 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 12:07:03 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 08:56:22 CDT)
  • Re: AMBER: Problem In Paralklel Amber (Fri Sep 26 2008 - 06:52:00 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 13:28:17 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 12:51:58 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 11:55:35 CDT)
  • Re: AMBER: how to enlarge the TIP3PBOX size (Wed Sep 24 2008 - 18:01:44 CDT)
  • Re: AMBER: error while running REMD in amber9 (Wed Sep 24 2008 - 13:27:22 CDT)
  • Re: AMBER: replica exchange with amber9 (Tue Sep 23 2008 - 17:52:04 CDT)
  • Re: AMBER: problems with ptraj and strip waters (Thu Sep 18 2008 - 16:29:56 CDT)
  • Re: AMBER: RMSD restraint in umbrella sampling (Thu Sep 18 2008 - 16:23:01 CDT)
  • Re: AMBER: problem with traj and strip waters (Thu Sep 18 2008 - 09:22:30 CDT)
  • Re: AMBER: problem with traj and strip waters (Thu Sep 18 2008 - 08:19:17 CDT)
  • Re: AMBER: Single point energy calculations with explicit solvent. (Thu Sep 18 2008 - 07:55:00 CDT)
  • Re: AMBER: Dihedral: ptraj (Thu Sep 18 2008 - 04:32:38 CDT)
  • Re: AMBER: Dihedral: ptraj (Thu Sep 18 2008 - 04:04:24 CDT)
  • Re: AMBER: MD simulation crashed (Wed Sep 17 2008 - 08:27:59 CDT)
  • Re: AMBER: Question (Wed Sep 17 2008 - 06:18:19 CDT)
  • Re: AMBER: Temperature regulation (Tue Sep 16 2008 - 13:22:55 CDT)
  • Re: AMBER: top and crd files without hydrogen (Tue Sep 16 2008 - 05:04:36 CDT)
  • Re: AMBER: Temperature regulation (Mon Sep 15 2008 - 20:07:57 CDT)
  • Re: AMBER: Minimizaton stops after Ncyc steps only (Mon Sep 15 2008 - 12:23:00 CDT)
  • AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting (Mon Sep 15 2008 - 11:39:58 CDT)
  • Re: AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 11:24:07 CDT)
  • Re: AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 10:54:25 CDT)
  • Re: AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 10:01:41 CDT)
  • Re: AMBER: D2O (Thu Sep 11 2008 - 09:44:06 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 06:23:51 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 05:32:02 CDT)
  • Re: AMBER: Preparing peptides with D-amino acids (Tue Sep 09 2008 - 20:14:34 CDT)
  • Re: AMBER: Preparing peptides with D-amino acids (Tue Sep 09 2008 - 19:28:08 CDT)
  • Re: AMBER: Preparing peptides with D-amino acids (Tue Sep 09 2008 - 19:26:20 CDT)
  • Re: AMBER: D2O (Tue Sep 09 2008 - 18:09:41 CDT)
  • Re: AMBER: D2O (Tue Sep 09 2008 - 13:08:37 CDT)
  • Re: AMBER: Need help... High energies for complex... (Tue Sep 09 2008 - 08:56:00 CDT)
  • Re: AMBER: Need help... High energies for complex... (Tue Sep 09 2008 - 08:46:19 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Mon Sep 08 2008 - 15:46:45 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 15:16:16 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 13:51:49 CDT)
  • Re: AMBER: Need help... High energies for complex... (Mon Sep 08 2008 - 11:45:51 CDT)
  • Re: AMBER: Changes in the Amber web site (Mon Sep 08 2008 - 10:14:33 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 09:56:48 CDT)
  • Re: AMBER: amber minimisation (Mon Sep 08 2008 - 07:40:44 CDT)
  • Re: AMBER: Need help... High energies for complex... (Fri Sep 05 2008 - 05:07:01 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 11:21:42 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 10:41:38 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 09:35:02 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 09:33:32 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 05:39:48 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 12:53:33 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 11:23:28 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 10:41:48 CDT)
  • Re: AMBER: Need help... High energies for complex... (Wed Sep 03 2008 - 07:04:07 CDT)
  • Re: AMBER: Need help... High energies for complex... (Wed Sep 03 2008 - 06:27:06 CDT)
  • Re: AMBER: solvent interaction in active site (Mon Sep 01 2008 - 08:49:20 CDT)
  • Re: AMBER: Critical patch for pmemd 10 extra points code (Sun Aug 31 2008 - 08:54:33 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:58:27 CDT)
  • Re: AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 17:15:42 CDT)
  • Re: AMBER: pmemd iwrap trouble (Wed Aug 27 2008 - 08:26:54 CDT)
  • Re: AMBER: Querry (Wed Aug 27 2008 - 08:20:55 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:21:31 CDT)
  • Re: AMBER: molecular structure (Tue Aug 26 2008 - 17:32:51 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:20:40 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:57:28 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 09:26:53 CDT)
  • Re: AMBER: Querry (Tue Aug 26 2008 - 09:09:25 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 11:35:53 CDT)
  • Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Sat Aug 23 2008 - 07:39:16 CDT)
  • Re: AMBER: vdw 6-9 potential (Sat Aug 23 2008 - 05:51:24 CDT)
  • Re: AMBER: vdw 6-9 potential (Fri Aug 22 2008 - 16:02:48 CDT)
  • Re: AMBER: Error runing Addles (Fri Aug 22 2008 - 07:48:07 CDT)
  • Re: AMBER: Force field equation (Thu Aug 21 2008 - 07:21:55 CDT)
  • Re: AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:46:12 CDT)
  • Re: AMBER: Force field equation (Wed Aug 20 2008 - 12:53:03 CDT)
  • Re: AMBER: NMR average structure (Wed Aug 20 2008 - 12:50:28 CDT)
  • Re: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange (Wed Aug 20 2008 - 12:47:12 CDT)
  • Re: AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 05:45:14 CDT)
  • Re: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:38:52 CDT)
  • Re: AMBER: problem with minimization (Thu Aug 07 2008 - 10:29:10 CDT)
  • Re: AMBER: addles (Tue Aug 05 2008 - 06:02:47 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 13:28:36 CDT)
  • Re: AMBER: Bonds getting shorter in sander (Fri Aug 01 2008 - 08:18:36 CDT)
  • Re: AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? (Thu Jul 31 2008 - 07:07:21 CDT)
  • Re: AMBER: Amber 10 on the BlueGene (Mon Jul 28 2008 - 13:37:59 CDT)
  • Re: AMBER: Amber 10 on the BlueGene (Mon Jul 28 2008 - 13:37:59 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 08:52:08 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 07:54:51 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Sat Jul 26 2008 - 19:46:58 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Sat Jul 26 2008 - 12:20:11 CDT)
  • Re: AMBER: Query about the charge of atoms in the parmtop file (Thu Jul 24 2008 - 08:09:45 CDT)
  • Re: AMBER: Query about the charge of atoms in the parmtop file (Wed Jul 23 2008 - 12:16:09 CDT)
  • Re: AMBER: Hydroxyproline in AMBER (Wed Jul 23 2008 - 11:03:01 CDT)
  • Re: AMBER: High force constant for MD ??? (Wed Jul 23 2008 - 06:02:13 CDT)
  • Re: AMBER: amber ff and how it deals with out-plane chiral C (Tue Jul 22 2008 - 10:15:56 CDT)
  • Re: AMBER: amber ff and how it deals with out-plane chiral C (Tue Jul 22 2008 - 06:57:04 CDT)
  • Re: AMBER: targeted MD (Tue Jul 22 2008 - 06:48:15 CDT)
  • Re: AMBER: Trans proline (Sun Jul 20 2008 - 06:50:39 CDT)
  • Re: AMBER: The list-directed or NAMELIST READ statement cannot be completed (Thu Jul 17 2008 - 11:47:24 CDT)
  • Re: AMBER:Some questions about replica exchan ge (Wed Jul 16 2008 - 10:04:25 CDT)
  • Re: Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 08:11:33 CDT)
  • Re: Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:12:51 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:00:58 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:00:58 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:00:58 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 06:23:39 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 06:23:39 CDT)
  • Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 05:59:03 CDT)
  • Re: AMBER: REMD temperature profile (Wed Jul 09 2008 - 10:28:59 CDT)
  • Re: AMBER: Force fields for REMD with GB solvent (Wed Jul 09 2008 - 08:37:36 CDT)
  • Re: AMBER: Force fields for REMD with GB solvent (Tue Jul 08 2008 - 17:03:31 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 07:37:29 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 06:50:44 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 06:09:07 CDT)
  • Re: AMBER: (Fri Jul 04 2008 - 05:42:27 CDT)
  • Re: AMBER: How to obtain the oriented trajectories? (Thu Jul 03 2008 - 09:22:03 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 11:16:38 CDT)
  • Re: AMBER: (Tue Jul 01 2008 - 07:15:15 CDT)
  • Re: AMBER: hold atoms fixed (Mon Jun 30 2008 - 08:02:19 CDT)
  • Re: AMBER: question about the charge (Fri Jun 27 2008 - 15:52:22 CDT)
  • Re: AMBER: ptraj - read in part of trajectory (Fri Jun 27 2008 - 12:00:32 CDT)
  • Re: AMBER: REMD Amber10 : error in reading namelist cntrl (Fri Jun 27 2008 - 09:47:42 CDT)
  • Re: AMBER: concerning force fields (Fri Jun 27 2008 - 07:34:21 CDT)
  • Re: AMBER: Dihedral Angle Parameters (Thu Jun 26 2008 - 16:30:53 CDT)
  • Re: AMBER: Dihedral Angle Parameters (Thu Jun 26 2008 - 17:20:41 CDT)
  • Re: AMBER: concerning force fields (Thu Jun 26 2008 - 14:25:04 CDT)
  • Re: AMBER: concerning force fields (Thu Jun 26 2008 - 11:16:48 CDT)
  • Re: AMBER: A problem of dihedral angle (Wed Jun 25 2008 - 10:53:16 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Thu Jun 19 2008 - 06:05:21 CDT)
  • Re: AMBER: How to create average structure? (Wed Jun 18 2008 - 23:52:35 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 13:28:04 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 12:43:39 CDT)
  • Re: AMBER: MM-GBSA with very positive GB value (Fri Jun 13 2008 - 02:46:55 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Thu Jun 12 2008 - 03:05:15 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Tue Jun 10 2008 - 03:03:02 CDT)
  • Re: AMBER: problem in starting sander (Sun Jun 08 2008 - 23:36:32 CDT)
  • Re: AMBER: problem in starting sander (Sun Jun 08 2008 - 14:53:33 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Sun Jun 08 2008 - 14:33:47 CDT)
  • Re: AMBER: NAN errors still exist (Fri Jun 06 2008 - 05:57:49 CDT)
  • Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC (Thu Jun 05 2008 - 07:16:22 CDT)
  • Re: AMBER: syn and anti conformation (Wed Jun 04 2008 - 14:34:31 CDT)
  • Re: AMBER: corrupted restart file (Tue Jun 03 2008 - 05:15:21 CDT)
  • Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis (Mon Jun 02 2008 - 15:06:39 CDT)
  • Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis (Mon Jun 02 2008 - 14:11:24 CDT)
  • Re: AMBER: VMD Movie 2 (Thu May 29 2008 - 12:48:10 CDT)
  • Re: AMBER: VMD Movie (Wed May 28 2008 - 19:10:03 CDT)
  • Re: AMBER: using amber ports in Gromacs (Sun May 25 2008 - 14:32:05 CDT)
  • Re: AMBER: about hydrogen bond in amber force field (Thu May 22 2008 - 02:08:08 CDT)
  • Re: AMBER: analysis REMD (Wed May 21 2008 - 12:18:06 CDT)
  • Re: AMBER: analysis REMD (Tue May 20 2008 - 07:11:29 CDT)
  • Re: AMBER: Hybrid REMD amber10 (Tue May 20 2008 - 01:55:06 CDT)
  • Re: AMBER: analysis REMD (Tue May 20 2008 - 01:51:22 CDT)
  • Re: AMBER: GBSA SA calculation (Tue May 13 2008 - 12:46:30 CDT)
  • Re: AMBER: initial velocities of MD (Tue May 13 2008 - 11:59:26 CDT)
  • Re: AMBER: GBSA SA calculation (Wed May 07 2008 - 17:05:26 CDT)
  • Re: AMBER: GBSA SA calculation (Wed May 07 2008 - 14:05:44 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Tue Apr 22 2008 - 13:57:11 CDT)
  • Re: AMBER: aromatic residues lost planarity during MD simulation (Mon Apr 21 2008 - 15:25:19 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 11:30:12 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 10:10:46 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Sat Apr 19 2008 - 08:49:56 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Fri Apr 18 2008 - 19:02:39 CDT)
  • Re: AMBER: imaging problem (Tue Apr 15 2008 - 07:22:18 CDT)
  • Re: AMBER: query about Generalized Born simulation (Fri Apr 11 2008 - 09:15:53 CDT)
  • Re: AMBER: Tutorial B3- Section6 (Fri Apr 11 2008 - 05:26:28 CDT)
  • Re: AMBER: restraint box dimension (Fri Apr 11 2008 - 05:22:38 CDT)
  • Re: AMBER: tempi in Replica Exchange (Thu Apr 10 2008 - 10:37:46 CDT)
  • Re: FW: AMBER: FW: MD run time inquiry (Thu Mar 27 2008 - 08:15:09 CDT)
  • Re: AMBER: FW: MD run time inquiry (Thu Mar 27 2008 - 05:41:02 CDT)
  • Re: AMBER: hybrid remd imaging (Mon Mar 24 2008 - 10:59:24 CDT)
  • Re: AMBER: INPCRD error on open (Thu Mar 20 2008 - 12:10:23 CDT)
  • Re: AMBER: INPCRD error on open (Thu Mar 20 2008 - 10:22:56 CDT)
  • Re: AMBER: replica exchange : problem with sander (Thu Mar 20 2008 - 09:47:32 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 08:49:23 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 08:25:11 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 07:47:04 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 12:12:03 CDT)
  • Re: AMBER: Problems with neglected restaints (Tue Mar 18 2008 - 12:05:11 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 11:39:01 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 09:29:38 CDT)
  • Re: AMBER: Temperature Range For REMD (Thu Mar 13 2008 - 10:26:44 CDT)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 17:39:23 CST)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 05:04:38 CST)
  • AMBER: ACS COMP Division awards- deadline this week (Mon Mar 03 2008 - 18:14:03 CST)
  • Re: AMBER: problems with Replica Exchange (Fri Feb 29 2008 - 12:33:59 CST)
  • Re: AMBER: Plea for REMD tutorial (Fri Feb 29 2008 - 11:47:47 CST)
  • Re: AMBER: problems with Replica Exchange (Thu Feb 28 2008 - 10:14:14 CST)
  • Re: AMBER: Plea for REMD tutorial (Thu Feb 28 2008 - 08:08:26 CST)
  • Re: AMBER: problems with Replica Exchange (Thu Feb 28 2008 - 06:46:57 CST)
  • Re: AMBER: change in secondary structure during MD (Thu Feb 28 2008 - 06:15:58 CST)
  • Re: AMBER: initial command? (Wed Feb 27 2008 - 06:10:01 CST)
  • Re: AMBER: More on tweaking a topology file (Sat Feb 23 2008 - 06:08:30 CST)
  • Re: AMBER: Input file for Minimization (Tue Feb 12 2008 - 11:55:18 CST)
  • Re: AMBER: leaprc help (Mon Feb 11 2008 - 11:56:38 CST)
  • Re: AMBER: Input file for Minimization (Mon Feb 11 2008 - 11:06:42 CST)
  • Re: AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? (Tue Jan 29 2008 - 06:21:37 CST)
  • Re: AMBER: RMSD calculation using AMBER7 (Sat Jan 19 2008 - 08:19:45 CST)
  • Re: AMBER: Regarding neutral Arginine unit (Tue Jan 15 2008 - 10:28:21 CST)
  • Re: AMBER: input options for replica exchange simulations (Thu Jan 10 2008 - 14:50:18 CST)
  • Re: AMBER: input options for replica exchange simulations (Thu Jan 10 2008 - 10:57:12 CST)
  • Re: AMBER: Cluster analysis (Mon Jan 07 2008 - 10:18:22 CST)
  • Re: AMBER: Structure comparison-NMR and X-ray structure using AMBER9 (Mon Jan 07 2008 - 10:16:16 CST)
  • Re: AMBER: About RAMD (Sat Jan 05 2008 - 10:46:32 CST)
  • Re: AMBER: About RAMD (Sat Jan 05 2008 - 10:12:40 CST)
  • Re: Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 11:56:04 CST)
  • Re: Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 11:30:31 CST)
  • Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 10:44:55 CST)
  • Re: AMBER: Combine mdcrd files (Thu Jan 03 2008 - 17:09:23 CST)
• Carra, Claudio (JSC-SK)[USRA]
  • AMBER: mwcovar limit? (Mon Dec 29 2008 - 16:31:27 CST)
  • AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10 (Wed Oct 01 2008 - 12:05:55 CDT)
  • AMBER: MM-PBSA problem : Missing PBCAV for PB (Tue Sep 30 2008 - 11:49:26 CDT)
  • AMBER: MM-PBSA multiple trajectory problem (Wed Aug 27 2008 - 09:16:38 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 17:44:09 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 16:14:12 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 11:19:52 CDT)
  • AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 10:04:38 CDT)
  • AMBER: DFTB parameters for O-P (Tue May 06 2008 - 15:01:55 CDT)
  • AMBER: test.parallel.QMMM problem (Fri May 02 2008 - 08:37:28 CDT)
• Catein Catherine
  • RE: AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 23:12:32 CST)
  • AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 21:33:41 CST)
  • AMBER: DNA: GB solvent with salt (Fri Dec 12 2008 - 03:31:13 CST)
  • AMBER: temperature error in md calculation (Wed Nov 05 2008 - 02:11:41 CST)
  • RE: AMBER: error message of xleap (Mon Nov 03 2008 - 03:52:24 CST)
  • AMBER: error message of xleap (Thu Oct 30 2008 - 22:40:49 CDT)
  • AMBER: atom type for carbon and nitrogen atoms (Mon Oct 27 2008 - 03:58:51 CDT)
  • AMBER: atom type for carbon and nitrogen atoms (Mon Oct 27 2008 - 03:56:06 CDT)
  • RE: AMBER: MM-GBSA with very positive GB value (Fri Jun 13 2008 - 20:49:53 CDT)
  • AMBER: MM-GBSA with very positive GB value (Fri Jun 13 2008 - 02:05:02 CDT)
  • AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- (Tue May 13 2008 - 05:17:29 CDT)
  • AMBER: Charge derivation: RESP vs. antechamber (Tue Apr 29 2008 - 05:21:55 CDT)
  • AMBER: Charge derivation: RESP vs. antechamber (Tue Apr 29 2008 - 05:21:54 CDT)
  • AMBER: PMF calculation for binding constant or rate constant? (Tue Apr 15 2008 - 21:26:46 CDT)
  • AMBER: PMF calculation for rate constant or binding constant? (Tue Apr 15 2008 - 21:28:43 CDT)
  • AMBER: potential of mean force: Unit of PMF energies and min path (Thu Mar 20 2008 - 00:26:43 CDT)
• Cen Gao
  • AMBER: Thermodynamic integration with positional restraint? (Thu Jan 03 2008 - 10:43:32 CST)
• Cenk \(Jenk\) Andac
  • Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 10:03:17 CST)
  • Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 06:28:41 CST)
  • AMBER: FAD RESP charges and parameters (Mon Dec 29 2008 - 16:51:49 CST)
  • Re: AMBER: PMEMD installation problem. (Mon Sep 08 2008 - 07:46:19 CDT)
  • RE: AMBER: PMEMD installation problem. (Mon Sep 08 2008 - 04:16:38 CDT)
  • AMBER: PMEMD installation problem. (Mon Sep 08 2008 - 01:58:42 CDT)
  • Re: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:40:30 CDT)
  • Re: AMBER: mol2, xleap, Segmentation fault (Mon Aug 25 2008 - 09:38:28 CDT)
  • Re: AMBER: corrupted restart file (Tue Jun 03 2008 - 05:13:29 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 29 2008 - 19:24:38 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 24 2008 - 07:26:37 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 24 2008 - 07:02:34 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Fri May 23 2008 - 11:35:36 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Fri May 23 2008 - 09:57:48 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 22 2008 - 17:29:55 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 22 2008 - 17:28:34 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 22 2008 - 17:24:33 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Wed May 21 2008 - 08:33:35 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 16:18:11 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 15:40:37 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 11:48:21 CDT)
  • RE: AMBER: Amber10 testing problem (Wed May 14 2008 - 04:13:13 CDT)
  • AMBER: Amber10 testing problem (Tue May 13 2008 - 14:46:02 CDT)
  • Re: AMBER: rms (Mon May 12 2008 - 08:51:56 CDT)
  • AMBER: parmbsc0 parameters for RNA.DNA systems (Sat May 10 2008 - 08:47:50 CDT)
• Cenk Andac
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 13:08:58 CDT)
  • Re: AMBER: LEap error message for parmBSC0 force field (Thu Apr 03 2008 - 07:52:37 CDT)
  • AMBER: LEap error message for parmBSC0 force field (Tue Apr 01 2008 - 18:31:17 CDT)
  • Re: AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 15:55:23 CDT)
  • Re: AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 15:43:50 CDT)
  • Re: AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 15:25:25 CDT)
• cgji
  • Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? (Sat Sep 20 2008 - 11:22:07 CDT)
  • Re: AMBER: all & united atoms force field (Thu Aug 21 2008 - 17:28:49 CDT)
  • AMBER: Is G_disp calculated in MM_PBSA now? (Sat Aug 09 2008 - 07:51:55 CDT)
  • AMBER: About Hydrophobic Interactions. (Mon May 12 2008 - 11:14:00 CDT)
  • AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? (Tue Apr 15 2008 - 10:27:08 CDT)
• chaitanya koppisetty
  • AMBER: nmode/nab entropy calculations without hydrogens (Wed Sep 17 2008 - 02:47:58 CDT)
  • AMBER: nmode/nab entropy calculations memory issues (Tue Sep 16 2008 - 09:58:01 CDT)
• CHAMI F.
  • AMBER: building new ions (Mon Dec 15 2008 - 07:50:50 CST)
  • AMBER: building new ions (Fri Dec 12 2008 - 06:23:20 CST)
  • AMBER: Choline chloride salt (Wed Nov 26 2008 - 08:49:45 CST)
  • AMBER: subroutine Work : Jarynski work theorem (Wed Nov 26 2008 - 06:21:07 CST)
  • AMBER: subroutine for torsional potential (Fri Nov 14 2008 - 08:16:37 CST)
  • RE: AMBER: stripping water from a restart file (Fri Oct 24 2008 - 04:58:58 CDT)
  • RE: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 16:59:03 CDT)
  • RE: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 07:45:19 CDT)
  • RE: AMBER: stripping water from a restart file (Thu Oct 23 2008 - 06:33:29 CDT)
  • RE: AMBER: stripping water from a restart file (Wed Oct 22 2008 - 15:29:45 CDT)
  • AMBER: stripping water from a restart file (Wed Oct 22 2008 - 11:11:46 CDT)
  • AMBER: stripping water from a restart file (Wed Oct 22 2008 - 11:11:46 CDT)
  • RE: AMBER: binding energy: high ELE (Thu Sep 11 2008 - 12:24:23 CDT)
  • AMBER: binding energy: high ELE (Wed Sep 10 2008 - 10:15:40 CDT)
  • AMBER: mm_pbsa error : Scale paremeter for PBSA (Fri Sep 05 2008 - 12:26:46 CDT)
• Charles Letner, Ph.D.
  • AMBER: Location of vdw radii and partial charges for ff99SB (Mon Sep 29 2008 - 08:08:27 CDT)
  • AMBER: AMBER under cygwin on 64 bit Vista (Sun Aug 31 2008 - 16:30:08 CDT)
• chen
  • Re: AMBER: Error while compiling Amber (Sat Feb 09 2008 - 18:00:09 CST)
• chen bents
  • Re: AMBER: amber 9 install (Wed Sep 17 2008 - 02:44:46 CDT)
  • AMBER: amber 9 install (Tue Sep 16 2008 - 22:14:47 CDT)
  • AMBER: AMBER9 Compilation (Tue Sep 16 2008 - 20:25:59 CDT)
  • AMBER: Calculate the RESP charge Fe3+ of heme (p450) (Thu May 22 2008 - 21:16:12 CDT)
• chengtao_at_sjtu.edu.cn
  • Re: AMBER: pressure component (Tue Dec 16 2008 - 02:42:00 CST)
  • AMBER: pressure component (Mon Dec 15 2008 - 02:17:21 CST)
• ChengZhong Zhang
  • AMBER: SMD using amber (Mon Mar 10 2008 - 20:54:23 CDT)
• Chih-Ying Lin
  • AMBER: Br - ion defined ? (Wed Nov 05 2008 - 11:20:36 CST)
  • AMBER: How to assign /make the ionion bond? (Fri Oct 17 2008 - 17:30:07 CDT)
  • Re: AMBER: The forming of micelle (CMC) (Wed Sep 24 2008 - 13:02:22 CDT)
  • Re: AMBER: The forming of micelle (Tue Sep 23 2008 - 19:07:47 CDT)
  • AMBER: The size of the simulation box and the # of solute / water molecules? (Mon Sep 22 2008 - 14:19:06 CDT)
  • Re: AMBER: The forming of micelle (Mon Sep 22 2008 - 14:02:30 CDT)
  • AMBER: The forming of micelle (Mon Sep 22 2008 - 13:06:24 CDT)
  • Re: AMBER: D2O (Thu Sep 11 2008 - 19:51:03 CDT)
  • Re: AMBER: D2O (Thu Sep 11 2008 - 09:32:03 CDT)
  • Re: AMBER: D2O (Tue Sep 09 2008 - 14:59:13 CDT)
  • AMBER: D2O (Tue Sep 09 2008 - 12:00:59 CDT)
  • AMBER: QM/MM (Fri Sep 05 2008 - 17:33:23 CDT)
  • AMBER: Question: GAFF (Fri Sep 05 2008 - 16:33:14 CDT)
  • AMBER: molecular structure (Tue Aug 26 2008 - 17:24:29 CDT)
  • AMBER: pdb file ?? (Thu Aug 21 2008 - 01:21:47 CDT)
  • Re: AMBER: Force field equation (Thu Aug 21 2008 - 00:16:42 CDT)
  • AMBER: Force field equation (Wed Aug 20 2008 - 11:05:39 CDT)
  • AMBER: Force Field parameters : A new chemical compound (Thu Jul 03 2008 - 12:52:17 CDT)
  • AMBER: is amber workshop available this summer?? (Wed Jul 02 2008 - 18:29:03 CDT)
  • Re: AMBER: Error message: Install Amber9 on fedora 9 (Wed Jun 04 2008 - 22:54:29 CDT)
  • AMBER: Error message: Install Amber9 on fedora 9 (Mon Jun 02 2008 - 17:33:42 CDT)
  • AMBER: Force field in water and in vacuum ?? (Thu May 22 2008 - 10:46:15 CDT)
  • AMBER: Adjust Force Field parameters (Thu May 08 2008 - 18:46:21 CDT)
  • AMBER: Azobenzene: AMBER+Gromos Force Field parameters (Wed May 07 2008 - 16:43:17 CDT)
  • AMBER: Improper dihedral parameters (Tue May 06 2008 - 14:00:36 CDT)
  • Re: AMBER: NON-BONDED parameters (Mon May 05 2008 - 17:10:05 CDT)
  • AMBER: NON-BONDED parameters (Mon May 05 2008 - 12:32:23 CDT)
  • Re: RE: RE: AMBER: point charges (Sat May 03 2008 - 16:47:23 CDT)
  • Re: RE: AMBER: point charges (Fri May 02 2008 - 17:42:18 CDT)
  • AMBER: point charges (Fri May 02 2008 - 15:53:50 CDT)
  • AMBER: Parrallel computing (Mon Apr 28 2008 - 19:14:10 CDT)
  • AMBER: Azobenzene: dihedral angle CCNN force field parameter (Sat Apr 26 2008 - 14:09:03 CDT)
  • AMBER: How to print out the improper dihedral angles/wilson angles? (Thu Apr 24 2008 - 19:23:51 CDT)
  • Re: RE: AMBER: Tutorial B5 (Wed Apr 23 2008 - 22:08:19 CDT)
  • Re: AMBER: Tutorial B5 (Wed Apr 23 2008 - 20:09:23 CDT)
  • AMBER: Tutorial B5 (Wed Apr 23 2008 - 17:13:56 CDT)
  • AMBER: trans-azobenzene under minimisation (Thu Apr 10 2008 - 19:29:37 CDT)
  • Re: AMBER: Tutorial B3- Section6 (Thu Apr 10 2008 - 18:50:14 CDT)
  • AMBER: Force field Parameters (Wed Apr 09 2008 - 21:17:51 CDT)
  • Re: AMBER: Tutorial B3- Section6 (Wed Apr 09 2008 - 21:13:32 CDT)
  • AMBER: Tutorial B3- Section6 (Wed Apr 09 2008 - 20:30:27 CDT)
  • AMBER: Collect dihedral angles (Wed Apr 09 2008 - 16:35:09 CDT)
  • AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? (Tue Apr 08 2008 - 20:09:24 CDT)
  • AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? (Tue Apr 08 2008 - 20:03:53 CDT)
  • AMBER: anything wrong with this script (Tue Apr 08 2008 - 19:27:50 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Tue Apr 08 2008 - 17:39:39 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Tue Apr 08 2008 - 17:31:27 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 17:27:52 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 17:00:20 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 16:51:51 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene----an electron-withdrew atom (Tue Apr 08 2008 - 16:45:51 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Tue Apr 08 2008 - 16:41:38 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 23:40:20 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Mon Apr 07 2008 - 23:13:39 CDT)
  • AMBER: how to change the force field parameters inside the prmtop file? (Mon Apr 07 2008 - 16:24:17 CDT)
  • AMBER: Trans-azobenzene and cis-azobenzene (Mon Apr 07 2008 - 13:13:01 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 13:03:18 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 12:31:51 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 12:10:43 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Sun Apr 06 2008 - 19:33:11 CDT)
  • AMBER: Minimisation: cis-azobenzene parameters (Sat Apr 05 2008 - 08:45:34 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Sat Apr 05 2008 - 08:33:46 CDT)
  • AMBER: Amber Workshop (Mon Mar 31 2008 - 15:40:52 CDT)
  • AMBER: running minimisation on cis-azobenzene (Mon Mar 31 2008 - 14:45:20 CDT)
  • AMBER: Amber Workshop (Sat Mar 29 2008 - 00:58:14 CDT)
• Chin, Keith B
  • RE: AMBER: Questions on TIP4P model? (Sat Nov 29 2008 - 17:43:21 CST)
  • AMBER: Questions on TIP4P model? (Fri Nov 28 2008 - 13:20:38 CST)
  • RE: AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 19:15:17 CST)
  • AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 13:58:41 CST)
  • AMBER: (Tue Nov 18 2008 - 17:39:26 CST)
  • AMBER: How to create *.top & *.crd file with hexagonal lattice (Sun Nov 16 2008 - 19:02:05 CST)
  • RE: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 14:55:57 CST)
  • AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 13:43:41 CST)
• Chris C.
  • Re: AMBER: Problem running NEB in AMBER10 (Wed Dec 03 2008 - 12:29:48 CST)
  • AMBER: Problem running NEB in AMBER10 (Wed Nov 26 2008 - 12:38:17 CST)
• Chris Moth
  • Re: AMBER: nmode units (Wed Sep 03 2008 - 18:10:19 CDT)
  • AMBER: analysing normal modes (Wed Jul 09 2008 - 14:45:57 CDT)
  • Re: AMBER: how to calculate delta G from IC50 (Tue May 20 2008 - 07:30:29 CDT)
  • Re: AMBER: mm-pbsa multiple trajectory approach? (Wed Apr 02 2008 - 16:18:06 CDT)
  • Re: AMBER: ptraj / covariance / quasiharmonic approximation / entropy (Wed Apr 02 2008 - 16:09:14 CDT)
  • RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Wed Mar 26 2008 - 17:27:35 CDT)
  • Re: AMBER: mm-pbsa multiple trajectory approach? (Wed Mar 26 2008 - 17:21:25 CDT)
  • AMBER: (Wed Jan 16 2008 - 09:11:07 CST)
  • Re: AMBER: Torsional Forcing to generate PES? (Tue Jan 08 2008 - 11:08:12 CST)
  • Re: AMBER: MD of protein-ligand comlex (Mon Jan 07 2008 - 06:10:23 CST)
• Christopher Gaughan
  • AMBER: # of ligands and receptors in mmpbsa (Fri Jul 25 2008 - 09:57:03 CDT)
  • Re: AMBER: free energy (Wed Jul 16 2008 - 11:03:26 CDT)
  • AMBER: mm/pbsa and saltcon effect (Fri Jan 04 2008 - 15:40:17 CST)
• Christopher Illingworth
  • Re: AMBER: Generating RESP charges (Tue Feb 19 2008 - 10:11:21 CST)
  • AMBER: Generating RESP charges (Tue Feb 19 2008 - 05:39:22 CST)
• CJ Dickson
  • AMBER: Extracting periodic box size deviation (Thu Nov 06 2008 - 17:29:20 CST)
• cniu_at_ualberta.ca
  • AMBER: aromatic residues lost planarity during MD simulation (Mon Apr 21 2008 - 15:18:26 CDT)
  • AMBER: umbrella sampling for proton transfer (Tue Mar 25 2008 - 19:30:33 CDT)
• Collins Nganou
  • AMBER: solvate dna in TIP3PBOX 10.0 (Sat Jul 26 2008 - 04:08:26 CDT)
  • AMBER: solvate dna in TIP3PBOX 10.0 (Fri Jul 25 2008 - 01:51:54 CDT)
  • AMBER: solvate dna in TIP3PBOX 10.0 (Thu Jul 24 2008 - 04:28:44 CDT)
• Cooper, Matthew
  • AMBER: Using mdcrd files to look at minor charge changes (Thu Apr 03 2008 - 13:45:12 CDT)
• Craig Gough
  • AMBER: Benchmarks on Fujitsu PrimePower 2500? (Mon Mar 10 2008 - 00:36:28 CDT)
• Cristina Sisu
  • Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 05:27:48 CST)
  • AMBER: MM-PBSA -energy decomposition error (Wed Oct 22 2008 - 17:07:43 CDT)
  • AMBER: Ca ions not recognized (Tue Sep 30 2008 - 09:00:24 CDT)
  • AMBER: MMPBSA error (Tue Sep 23 2008 - 05:30:38 CDT)
  • Re: AMBER: MMPBSA error (Sat May 31 2008 - 09:53:32 CDT)
  • AMBER: MMPBSA error (Sat May 31 2008 - 09:00:08 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 10:22:10 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 09:32:27 CDT)
  • AMBER: Sander instead of PMEMD (Fri May 30 2008 - 08:47:13 CDT)
  • AMBER: using amber ports in Gromacs (Sun May 25 2008 - 13:28:26 CDT)
  • AMBER: using amber ports in gromacs (Sun May 25 2008 - 13:22:58 CDT)
  • Re: AMBER: from Gromax to AMBER (Tue May 13 2008 - 08:49:12 CDT)
  • AMBER: from Gromax to AMBER (Tue May 13 2008 - 05:00:24 CDT)
  • Re: AMBER: loading pdb in leap to create parameter files (Tue Apr 15 2008 - 09:50:12 CDT)
  • AMBER: loading pdb in leap to create parameter files (Tue Apr 15 2008 - 08:43:57 CDT)
• Cyril Bauvais
  • AMBER: Re: £º Re: AMBER: problems form the pdb to the mol2 (Wed Jun 25 2008 - 08:00:54 CDT)
  • Re: AMBER: problems form the pdb to the mol2 (Tue Jun 24 2008 - 09:05:36 CDT)
  • Re: AMBER: INPCRD error on open (Thu Mar 20 2008 - 11:04:31 CDT)
• D.J. Cole
  • AMBER: Hydroxide ion in POL3 water (Thu Dec 18 2008 - 06:13:58 CST)
• D.Usharani
  • Re: AMBER: query regarding energy minimization (Tue Apr 29 2008 - 00:20:29 CDT)
  • AMBER: Reg cysteine protonation states (Tue Jan 29 2008 - 21:58:22 CST)
  • AMBER: Reg cysteine protonaitons states in pH constant MD (Sun Jan 27 2008 - 23:15:58 CST)
• d90223013_at_ntu.edu.tw
  • AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? (Tue Jan 29 2008 - 01:35:08 CST)
  • AMBER: Number of Hydrogen Bonds? (Thu Jan 24 2008 - 19:07:39 CST)
• Da-Wei Li
  • Re: AMBER: Improper dihedral parameters (Tue May 06 2008 - 14:30:29 CDT)
  • Re: AMBER: (Thu Apr 17 2008 - 10:18:04 CDT)
  • Re: AMBER: loading pdb in leap to create parameter files (Tue Apr 15 2008 - 08:53:06 CDT)
  • Re: AMBER: RMSD of two different molecules (Wed Mar 26 2008 - 15:39:19 CDT)
  • Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Tue Mar 25 2008 - 12:08:29 CDT)
  • Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Mon Mar 24 2008 - 15:12:42 CDT)
• Daniel B. Kaplan
  • AMBER: (no subject) (Wed Jun 25 2008 - 21:23:43 CDT)
  • AMBER: Antechamber Question (Mon Jun 23 2008 - 11:51:28 CDT)
  • AMBER: (no subject) (Sun Jun 22 2008 - 18:46:17 CDT)
• Daniel Cappel
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 08:37:19 CDT)
  • AMBER: energy problems in simulation with restraints (Mon Mar 31 2008 - 04:39:13 CDT)
  • Re: AMBER: varying restraint_wt with nmropt=1 (Thu Feb 28 2008 - 01:50:02 CST)
• Daniel Emery
  • AMBER: Problem with MMPBSA (Mon Dec 08 2008 - 10:28:22 CST)
• Daniel Oehme
  • Re: AMBER: Variable PBCAL values in MM-PBSA calculations (Sun Dec 07 2008 - 23:56:58 CST)
  • Re: AMBER: Variable PBCAL values in MM-PBSA calculations (Thu Dec 04 2008 - 00:34:42 CST)
  • AMBER: Variable PBCAL values in MM-PBSA calculations (Mon Dec 01 2008 - 17:45:23 CST)
  • Re: AMBER: MM-PBSA/NMODE in Amber 10 (Mon Sep 22 2008 - 02:13:55 CDT)
  • Re: AMBER: MM-PBSA/NMODE in Amber 10 (Mon Sep 15 2008 - 20:23:26 CDT)
  • AMBER: MM-PBSA in AMBER 10 (Mon Jun 23 2008 - 20:32:24 CDT)
  • AMBER: MM-PBSA in AMBER 10 (Mon Jun 23 2008 - 00:07:34 CDT)
  • AMBER: MM-PBSA in AMBER 10 (Thu Jun 05 2008 - 22:52:12 CDT)
  • AMBER: MM-PBSA in AMBER 10 (Thu Jun 05 2008 - 00:27:39 CDT)
• Daniel Smith
  • Re: AMBER: [Fwd: failure to load box parameters] (Wed Jun 25 2008 - 13:30:18 CDT)
  • Re: AMBER: [Fwd: failure to load box parameters] (Mon Jun 23 2008 - 16:26:22 CDT)
  • AMBER: [Fwd: failure to load box parameters] (Wed Jun 18 2008 - 22:58:10 CDT)
  • AMBER: Calcium and Magnesium LJ parameters (Mon Jun 09 2008 - 18:02:28 CDT)
  • Re: AMBER: Simple Minimization - Error (Thu Apr 03 2008 - 15:10:28 CDT)
  • AMBER: NTR Restraints (Tue Mar 25 2008 - 20:17:27 CDT)
• Darek Czapiewski
  • AMBER: peptide at the box center during NVT-MD (Mon May 26 2008 - 05:01:45 CDT)
• darkcz_at_tlen.pl
  • AMBER: solvateBox/solvateDontClip (Tue Jan 08 2008 - 10:02:19 CST)
• Dave Rogers
  • Re: AMBER: ptraj and netcdf with AmberTools1.2 ? (Wed Nov 05 2008 - 15:34:21 CST)
  • Re: AMBER: Amber dipole printout. (Tue Oct 14 2008 - 13:14:21 CDT)
• David A. Case
  • Re: AMBER: mdout file details (Wed Dec 31 2008 - 10:50:05 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 15:31:56 CST)
  • Re: AMBER: a question about ff03ua (Thu Dec 25 2008 - 15:01:56 CST)
  • Re: AMBER: GB offset for proteins (Wed Dec 24 2008 - 13:11:21 CST)
  • Re: AMBER: installation amber9 in fedora9 using bash shell (Wed Dec 24 2008 - 13:07:35 CST)
  • Re: AMBER: xleap error (Wed Dec 24 2008 - 13:02:11 CST)
  • Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 13:45:06 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 23 2008 - 07:26:15 CST)
  • Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 07:35:28 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Sat Dec 20 2008 - 17:48:23 CST)
  • Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Sat Dec 20 2008 - 16:42:28 CST)
  • Re: AMBER: Solvatebox problem (Fri Dec 19 2008 - 07:19:18 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:49:56 CST)
  • Re: AMBER: solvent box again (Tue Dec 16 2008 - 14:02:05 CST)
  • Re: AMBER: distance restraint in minimization (Tue Dec 16 2008 - 13:57:44 CST)
  • Re: AMBER: relative weight of RDC constraints (Mon Dec 15 2008 - 10:44:19 CST)
  • Re: AMBER: Initial velocities based on date and time are NOT changing ? (Mon Dec 15 2008 - 07:38:03 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 06:54:33 CST)
  • Re: AMBER: pressure component (Mon Dec 15 2008 - 06:43:44 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sun Dec 14 2008 - 08:20:36 CST)
  • Re: AMBER: ld: cannot find -lgcc_s (Fri Dec 12 2008 - 08:26:00 CST)
  • Re: AMBER: reg.building ions (Fri Dec 12 2008 - 06:42:28 CST)
  • Re: AMBER: reg.building ions (Fri Dec 12 2008 - 06:04:58 CST)
  • Re: AMBER: tutorial A1, file missing readit.f (Thu Dec 11 2008 - 07:19:38 CST)
  • Re: AMBER: how to add new solvent type in Amber (Wed Dec 10 2008 - 17:18:56 CST)
  • Re: AMBER: reg-antichamber run (Wed Dec 10 2008 - 17:14:31 CST)
  • Re: AMBER: parallel installation (Wed Dec 10 2008 - 07:09:00 CST)
  • Re: AMBER: Constant pH dynamics (Tue Dec 09 2008 - 09:27:51 CST)
  • Re: AMBER: interaction energies (Mon Dec 08 2008 - 10:59:28 CST)
  • Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0 (Fri Dec 05 2008 - 10:45:20 CST)
  • Re: AMBER: using packmol file in Amber (Fri Dec 05 2008 - 09:58:51 CST)
  • Re: AMBER: N(CN2)- ion (Fri Dec 05 2008 - 06:23:05 CST)
  • Re: AMBER: using packmol file in Amber (Thu Dec 04 2008 - 10:32:49 CST)
  • Re: AMBER: unable to open pdb file (Thu Dec 04 2008 - 05:41:32 CST)
  • Re: AMBER: How do you evaluate forces on a fixed atom? (Tue Dec 02 2008 - 08:39:37 CST)
  • Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 08:19:20 CST)
  • Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 06:14:47 CST)
  • Re: AMBER: makeDIST_RST error -- no map function for HH TYR (Mon Dec 01 2008 - 15:22:46 CST)
  • Re: AMBER: Running Amber8 - Sander (Mon Dec 01 2008 - 09:37:32 CST)
  • Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms (Mon Dec 01 2008 - 09:34:47 CST)
  • Re: AMBER: N(CN2)- ion (Mon Dec 01 2008 - 08:47:14 CST)
  • Re: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 08:29:41 CST)
  • Re: AMBER: Questions on TIP4P model? (Sat Nov 29 2008 - 13:21:01 CST)
  • Re: AMBER: Gradual releasing of position restraints (Wed Nov 26 2008 - 11:00:41 CST)
  • Re: AMBER: Referencing AMBER (Wed Nov 26 2008 - 10:25:20 CST)
  • Re: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 06:46:41 CST)
  • Re: AMBER: using packmol file in Amber (Tue Nov 25 2008 - 13:45:29 CST)
  • Re: AMBER: molsurf fails (Tue Nov 25 2008 - 13:26:14 CST)
  • Re: AMBER: Fully QM periodic runs (Tue Nov 25 2008 - 05:56:51 CST)
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 11:19:54 CST)
  • Re: AMBER: Electrostatic Energy Components (Mon Nov 24 2008 - 06:14:13 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Sun Nov 23 2008 - 15:49:37 CST)
  • Re: AMBER: AdoMet parameterization with antechamber (Sun Nov 23 2008 - 15:13:23 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 14:37:51 CST)
  • Re: AMBER: compiling amber 10 (Sat Nov 22 2008 - 14:33:54 CST)
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 08:53:50 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Fri Nov 21 2008 - 11:44:58 CST)
  • Re: AMBER: Problems for use manganese molecules (Fri Nov 21 2008 - 06:46:22 CST)
  • Re: AMBER: How to manually adjust periodic boundary conditions (PBC) (Thu Nov 20 2008 - 14:52:57 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 14:50:27 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 09:56:15 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 07:38:37 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 07:36:48 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 06:04:22 CST)
  • Re: AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 17:35:33 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Wed Nov 19 2008 - 09:08:02 CST)
  • Re: AMBER: problem with cartesian restraints with NTP simulations (Wed Nov 19 2008 - 09:02:56 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Wed Nov 19 2008 - 08:35:45 CST)
  • Re: AMBER: AMBER10 compiling SANDER parallel problem (Tue Nov 18 2008 - 15:25:23 CST)
  • Re: AMBER: segmentation fault when restarting periodic structure (Tue Nov 18 2008 - 08:20:41 CST)
  • Re: AMBER: How to create *.top & *.crd file with hexagonal lattice (Tue Nov 18 2008 - 08:05:12 CST)
  • Re: AMBER: problem (Tue Nov 18 2008 - 06:15:57 CST)
  • Re: AMBER: SPCFW temperature oscillations (Tue Nov 18 2008 - 06:13:16 CST)
  • Re: AMBER: AMBER10 installation question (Tue Nov 18 2008 - 06:05:07 CST)
  • Re: AMBER: velocity units? (Mon Nov 17 2008 - 10:53:19 CST)
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Thu Nov 13 2008 - 14:39:41 CST)
  • Re: AMBER: load opls force field (Thu Nov 13 2008 - 06:06:40 CST)
  • Re: AMBER: PB Radii (Thu Nov 13 2008 - 06:01:57 CST)
  • Re: AMBER: ff02 in nmode gives error "too many dihedrals" ? (Wed Nov 12 2008 - 09:13:45 CST)
  • Re: AMBER: Amber 9 installation problems (Tue Nov 11 2008 - 17:22:54 CST)
  • Re: AMBER: test sander error in amber7 (Tue Nov 11 2008 - 06:15:51 CST)
  • Re: AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 11:32:39 CST)
  • Re: AMBER: looks like I have problem with "make clean" command (Mon Nov 10 2008 - 06:39:26 CST)
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Sun Nov 09 2008 - 11:16:52 CST)
  • Re: AMBER: problem with zMatrix in tleap (Sun Nov 09 2008 - 11:17:02 CST)
  • Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj (Fri Nov 07 2008 - 23:33:48 CST)
  • Re: AMBER: ptraj and netcdf with AmberTools1.2 ? (Thu Nov 06 2008 - 06:08:00 CST)
  • Re: AMBER: temperature error in md calculation (Wed Nov 05 2008 - 08:10:41 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:01:59 CST)
  • Re: AMBER: problem with zMatrix in tleap (Fri Oct 31 2008 - 09:37:11 CDT)
  • Re: AMBER: problem with zMatrix in tleap (Fri Oct 31 2008 - 07:33:44 CDT)
  • Re: AMBER: Lone pairs in antechamber (Thu Oct 30 2008 - 09:27:31 CDT)
  • Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Thu Oct 30 2008 - 08:17:12 CDT)
  • Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Thu Oct 30 2008 - 06:24:12 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Wed Oct 29 2008 - 05:49:06 CDT)
  • Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber (Tue Oct 28 2008 - 17:15:11 CDT)
  • Re: AMBER: SPCFW problems (Tue Oct 28 2008 - 17:12:02 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 17:09:38 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 12:57:49 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 12:41:45 CDT)
  • Re: AMBER: SPCFW problems (Tue Oct 28 2008 - 12:25:23 CDT)
  • Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber (Tue Oct 28 2008 - 07:57:22 CDT)
  • Re: AMBER: SPCFW problems (Tue Oct 28 2008 - 05:49:37 CDT)
  • Re: AMBER: problem with amber8 installation (Sat Oct 25 2008 - 08:30:30 CDT)
  • Re: AMBER: Atom names CL and four characters (Fri Oct 24 2008 - 14:21:51 CDT)
  • Re: AMBER: energy leakage? (Thu Oct 23 2008 - 06:00:29 CDT)
  • Re: AMBER: LEaP problem with LEU first residue? (Mon Oct 20 2008 - 06:00:09 CDT)
  • Re: AMBER: antechamber errors (Fri Oct 17 2008 - 09:20:51 CDT)
  • Re: AMBER: Using charmm force field in amber (Thu Oct 16 2008 - 16:51:45 CDT)
  • Re: AMBER: antechamber (Thu Oct 16 2008 - 16:25:17 CDT)
  • Re: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 06:06:42 CDT)
  • Re: AMBER: antechamber test failure (Thu Oct 16 2008 - 06:04:13 CDT)
  • Re: AMBER: Installation Error (Wed Oct 15 2008 - 08:35:19 CDT)
  • Re: AMBER: LEaP problem with LEU first residue? (Wed Oct 15 2008 - 08:18:58 CDT)
  • Re: AMBER: antechamber test failure (Wed Oct 15 2008 - 08:16:06 CDT)
  • Re: AMBER: antechamber (Mon Oct 13 2008 - 17:43:00 CDT)
  • Re: AMBER: question about pression (Mon Oct 13 2008 - 09:55:57 CDT)
  • Re: AMBER: removing COM and rotation in explicit solvation (Sun Oct 12 2008 - 16:32:54 CDT)
  • Re: AMBER: AddIons approach (Fri Oct 10 2008 - 06:52:52 CDT)
  • Re: AMBER: velocity-verlet algorithm and ensembles (Thu Oct 09 2008 - 07:46:08 CDT)
  • Re: AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL (Tue Oct 07 2008 - 16:05:07 CDT)
  • Re: AMBER: shake the molecule (Fri Oct 03 2008 - 11:28:32 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Wed Oct 01 2008 - 14:24:56 CDT)
  • Re: AMBER: How to set up a water slab in Amber? (Wed Oct 01 2008 - 06:51:17 CDT)
  • Re: AMBER: MD at a given pH (Sat Sep 27 2008 - 06:53:56 CDT)
  • Re: AMBER: Constant pH simulation force field (Sat Sep 27 2008 - 07:10:39 CDT)
  • Re: AMBER: compilation problem (Sat Sep 27 2008 - 07:29:53 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 09:12:40 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 11:29:23 CDT)
  • Re: AMBER: compilation problem (Fri Sep 26 2008 - 11:06:46 CDT)
  • Re: AMBER: how to enlarge the TIP3PBOX size (Fri Sep 26 2008 - 11:06:37 CDT)
  • Re: AMBER: compilation problem (Mon Sep 22 2008 - 07:19:47 CDT)
  • Re: AMBER: increasing temperature smoothly (Mon Sep 22 2008 - 06:44:02 CDT)
  • Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? (Mon Sep 22 2008 - 06:25:38 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Sat Sep 20 2008 - 07:38:55 CDT)
  • Re: AMBER: increasing temperature smoothly (Fri Sep 19 2008 - 11:49:46 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Thu Sep 18 2008 - 13:35:27 CDT)
  • Re: AMBER: problem with traj and strip waters (Thu Sep 18 2008 - 08:34:18 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Thu Sep 18 2008 - 06:10:12 CDT)
  • Re: AMBER: mmpbsa molsurf.c error (Wed Sep 17 2008 - 07:10:40 CDT)
  • Re: AMBER: problem with editing with xleap (Wed Sep 17 2008 - 06:30:55 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Wed Sep 17 2008 - 06:26:07 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 09:15:12 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 07:06:08 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 06:15:52 CDT)
  • Re: AMBER: compilation problem (Fri Sep 12 2008 - 07:04:59 CDT)
  • Re: AMBER: about NMR refinement in explicit solvent (Thu Sep 11 2008 - 12:24:37 CDT)
  • Re: AMBER: Nonbonded FE parameter missing in frcmod. (Thu Sep 11 2008 - 12:19:53 CDT)
  • Re: AMBER: binding energy: high ELE (Thu Sep 11 2008 - 10:42:56 CDT)
  • Re: AMBER: NAB parameter: wcons (Wed Sep 10 2008 - 07:19:32 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 06:30:27 CDT)
  • Re: AMBER: Install problems (Tue Sep 09 2008 - 14:53:18 CDT)
  • Re: AMBER: problem when running energy minimization with polarizable potential (Tue Sep 09 2008 - 13:32:27 CDT)
  • Re: AMBER: D2O (Tue Sep 09 2008 - 13:21:37 CDT)
  • Re: AMBER: Install problems (Tue Sep 09 2008 - 06:37:16 CDT)
  • Re: AMBER: who can give a sample input file regarding the energy decomposition with sander? (Mon Sep 08 2008 - 16:31:50 CDT)
  • Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors (Mon Sep 08 2008 - 16:09:53 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 15:51:50 CDT)
  • AMBER: Changes in the Amber web site (Mon Sep 08 2008 - 08:25:41 CDT)
  • Re: AMBER: amber minimisation (Mon Sep 08 2008 - 07:59:26 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Sun Sep 07 2008 - 17:12:22 CDT)
  • Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine (Sun Sep 07 2008 - 17:07:14 CDT)
  • Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine (Sun Sep 07 2008 - 07:50:57 CDT)
  • Re: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 10:20:40 CDT)
  • Re: AMBER: nmode units (Thu Sep 04 2008 - 09:58:22 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 09:36:37 CDT)
  • Re: AMBER: tleap and Zn parameter (Tue Sep 02 2008 - 15:41:21 CDT)
  • Re: AMBER: compilation problem (Tue Sep 02 2008 - 09:32:45 CDT)
  • Re: AMBER: tleap and Zn parameter (Mon Sep 01 2008 - 08:53:26 CDT)
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Fri Aug 22 2008 - 22:11:14 CDT)
  • Re: AMBER: trying ff99SP (Wed Aug 20 2008 - 13:31:22 CDT)
  • Re: AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. (Wed Aug 20 2008 - 12:24:17 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Wed Aug 20 2008 - 12:14:03 CDT)
  • Re: AMBER: Proton Parameters (Wed Aug 20 2008 - 12:12:02 CDT)
  • Re: AMBER: MD with NMR restraints (Wed Aug 20 2008 - 12:07:15 CDT)
  • Re: AMBER: questions about previous posts (Sat Aug 16 2008 - 10:00:38 CDT)
  • Re: AMBER: Using RDCs for structure refinement (Tue Aug 12 2008 - 11:36:24 CDT)
  • Re: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 16:40:49 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Fri Aug 08 2008 - 17:50:55 CDT)
  • Re: AMBER: NMR structure as initial structure (Tue Aug 05 2008 - 19:09:25 CDT)
  • Re: AMBER: Set 251 is corrupted, ptraj error... (Mon Aug 04 2008 - 10:31:28 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 10:26:51 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sun Aug 03 2008 - 23:28:45 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sat Aug 02 2008 - 20:37:10 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Fri Aug 01 2008 - 14:48:55 CDT)
  • Re: AMBER: how to get the potential energy of a protein from the system (Thu Jul 31 2008 - 09:45:47 CDT)
  • Re: AMBER: Volume of ucell too big (Wed Jul 30 2008 - 00:19:31 CDT)
  • Re: AMBER: interaction energies in Amber and VMD/NAMD (Sat Jul 26 2008 - 19:36:46 CDT)
  • Re: AMBER: fortran runtime error in "make test.serial" with gfortran (Fri Jul 25 2008 - 18:03:57 CDT)
  • Re: AMBER: Regarding ff03 forcefield (Fri Jul 25 2008 - 15:46:26 CDT)
  • Re: AMBER: amber10: pmemd gfortran (Fri Jul 25 2008 - 14:05:23 CDT)
  • Re: AMBER: big molecule numbers (Thu Jul 24 2008 - 20:43:26 CDT)
  • Re: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 (Thu Jul 24 2008 - 18:37:32 CDT)
  • Re: AMBER: calculating the enthalpy of evaporation (Thu Jul 24 2008 - 15:31:01 CDT)
  • Re: AMBER: adding missing residues (Thu Jul 24 2008 - 10:37:36 CDT)
  • Re: AMBER: amber9 install problem (Thu Jul 24 2008 - 10:08:21 CDT)
  • Re: AMBER: SHIFTS compile error (Wed Jul 23 2008 - 12:22:32 CDT)
  • Re: AMBER: Where is ICO read from the ix array? (Mon Jul 21 2008 - 18:54:18 CDT)
  • Re: AMBER: Amber tools 1.2 test failure (installation) (Mon Jul 21 2008 - 18:36:16 CDT)
  • AMBER: Release of version 1.2 of AmberTools (Mon Jul 21 2008 - 12:01:29 CDT)
  • Re: AMBER: a link for Amber ff ported to Charmm (Sat Jul 19 2008 - 13:29:18 CDT)
  • Re: AMBER: antechamber and charmm (Thu Jul 17 2008 - 11:16:02 CDT)
  • Re: AMBER: sleap test failures (Tue Jul 15 2008 - 17:46:00 CDT)
  • Re: AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) (Tue Jul 15 2008 - 13:57:52 CDT)
  • Re: AMBER: files in Amber directory ( to Junmei Wang ) (Tue Jul 15 2008 - 13:55:41 CDT)
  • Re: AMBER: Nmode entropy calcs (Sun Jul 13 2008 - 10:45:56 CDT)
  • Re: AMBER: question about the improper torsion (Sat Jul 12 2008 - 09:43:46 CDT)
  • Re: AMBER: size of pdb (Sat Jul 12 2008 - 09:45:51 CDT)
  • Re: AMBER: Constant pH with new parameters (amber10) (Fri Jul 11 2008 - 13:41:09 CDT)
  • Re: AMBER: NMA (Fri Jul 11 2008 - 13:19:06 CDT)
  • Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap (Thu Jul 10 2008 - 23:42:28 CDT)
  • Re: AMBER: difference between sander and NAB (Thu Jul 10 2008 - 17:22:49 CDT)
  • Re: AMBER: trouble interpreting <P2> time correlation function data (Sun Jul 06 2008 - 10:04:30 CDT)
  • Re: AMBER: PMEMD and polarized force field ff 02 (Thu Jul 03 2008 - 10:10:06 CDT)
  • Re: AMBER: NMR refinement (Wed Jul 02 2008 - 19:21:54 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:58:36 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:25:18 CDT)
  • Re: AMBER: NONBONDED_PARM_INDEX (Wed Jul 02 2008 - 10:04:26 CDT)
  • Re: AMBER: Regarding force field ff02 and ion library (Mon Jun 30 2008 - 16:14:37 CDT)
  • Re: AMBER: error in reading namelist cntrl (Mon Jun 30 2008 - 15:28:36 CDT)
  • Re: AMBER: NMR refinement (Mon Jun 30 2008 - 09:44:51 CDT)
  • Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? (Sat Jun 28 2008 - 11:37:45 CDT)
  • Re: AMBER: (Fri Jun 27 2008 - 13:55:04 CDT)
  • Re: AMBER: Test scripts (Fri Jun 27 2008 - 11:44:25 CDT)
  • Re: AMBER: sleap - TER-card (Thu Jun 26 2008 - 20:19:01 CDT)
  • Re: AMBER: rdparm Segmentation fault (Wed Jun 25 2008 - 19:07:20 CDT)
  • Re: AMBER: sleap - TER-card (Wed Jun 25 2008 - 17:05:59 CDT)
  • Re: AMBER: [Fwd: failure to load box parameters] (Wed Jun 25 2008 - 14:09:28 CDT)
  • Re: AMBER: amber10 compile gfortran question (Wed Jun 25 2008 - 14:03:54 CDT)
  • Re: AMBER: local coordinate system question (Wed Jun 25 2008 - 09:32:16 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 17:06:15 CDT)
  • Re: AMBER: [Fwd: failure to load box parameters] (Tue Jun 24 2008 - 10:14:51 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 09:55:10 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Tue Jun 24 2008 - 09:49:26 CDT)
  • Re: AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:51:46 CDT)
  • Re: AMBER: MM-PBSA in AMBER 10 (Mon Jun 23 2008 - 20:47:44 CDT)
  • Re: AMBER: How to adjust the problem of "Vlimit exceeded" (Mon Jun 23 2008 - 10:16:05 CDT)
  • Re: AMBER: How to confirm atom types of small molecule perceived by antechamber (Mon Jun 23 2008 - 09:56:17 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Fri Jun 20 2008 - 14:34:09 CDT)
  • Re: AMBER: AmberTools 1.0 installation error: x86_64 (Fri Jun 20 2008 - 11:17:35 CDT)
  • Re: AMBER: simple sander (Thu Jun 19 2008 - 20:40:46 CDT)
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Thu Jun 19 2008 - 19:22:34 CDT)
  • Re: AMBER: Installation Problem of AMBER10 (Thu Jun 19 2008 - 09:53:03 CDT)
  • Re: AMBER: [Fwd: failure to load box parameters] (Thu Jun 19 2008 - 00:35:53 CDT)
  • Re: AMBER: tip3p water and shake (Thu Jun 19 2008 - 00:15:48 CDT)
  • Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 (Wed Jun 18 2008 - 19:32:36 CDT)
  • Re: AMBER: sp carbon notation? (Wed Jun 18 2008 - 19:22:14 CDT)
  • Re: AMBER: to understand GAFF: about A and B coefficients (Tue Jun 17 2008 - 11:52:41 CDT)
  • Re: AMBER: suggestion for next amberTools 1.1 (Tue Jun 17 2008 - 10:42:14 CDT)
  • Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? (Tue Jun 17 2008 - 10:18:08 CDT)
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Mon Jun 16 2008 - 18:42:47 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 13:33:35 CDT)
  • Re: AMBER: problems with sleap (Mon Jun 16 2008 - 10:48:42 CDT)
  • Re: AMBER: Problem with running refinement of NMR structures with RDCs (Sun Jun 15 2008 - 20:50:53 CDT)
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Sat Jun 14 2008 - 14:09:02 CDT)
  • Re: AMBER: Sander crashes >99999 atoms (Fri Jun 13 2008 - 11:59:32 CDT)
  • Re: AMBER: updating documentation (Fri Jun 13 2008 - 11:52:14 CDT)
  • Re: AMBER: Sander crashes >99999 atoms (Thu Jun 12 2008 - 20:25:31 CDT)
  • Re: AMBER: using Velocity-Verlet algorithm (Thu Jun 12 2008 - 11:09:49 CDT)
  • Re: AMBER: Antechamber and topology file (Thu Jun 12 2008 - 11:03:50 CDT)
  • Re: AMBER: Coordinated Zinc (Thu Jun 12 2008 - 10:59:42 CDT)
  • Re: AMBER: updating documentation (Thu Jun 12 2008 - 10:10:36 CDT)
  • Re: AMBER: anisotropic pressure scaling ntp=2 (Thu Jun 12 2008 - 10:13:52 CDT)
  • Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating (Wed Jun 11 2008 - 12:53:20 CDT)
  • Re: AMBER: box shape changed at NVT (Wed Jun 11 2008 - 10:18:46 CDT)
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Wed Jun 11 2008 - 10:15:00 CDT)
  • Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating (Tue Jun 10 2008 - 07:50:27 CDT)
  • Re: AMBER: Problem of Ptraj analyze matrix (Sun Jun 08 2008 - 20:38:13 CDT)
  • Re: AMBER: NAB documentation (Sun Jun 08 2008 - 20:38:05 CDT)
  • Re: AMBER: A problem of installing Amber10 (Fri Jun 06 2008 - 15:21:52 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 13:59:52 CDT)
  • Re: AMBER: Error message: Install Amber9 on fedora 9 (Thu Jun 05 2008 - 14:17:50 CDT)
  • Re: AMBER: A problem of installing Amber10 (Thu Jun 05 2008 - 14:13:16 CDT)
  • Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint? (Thu Jun 05 2008 - 13:50:16 CDT)
  • Re: AMBER: NMODE units and hrmax value for Langevine modes (Thu Jun 05 2008 - 13:12:24 CDT)
  • Re: AMBER: A problem of installing Amber10 (Thu Jun 05 2008 - 12:49:58 CDT)
  • Re: AMBER: problems with sleap (Wed Jun 04 2008 - 18:52:00 CDT)
  • Re: AMBER: amber installation on cluster (Wed Jun 04 2008 - 12:55:39 CDT)
  • Re: AMBER: NMODE units and hrmax value for Langevine modes (Wed Jun 04 2008 - 12:30:36 CDT)
  • Re: AMBER: solvate box : buffer list (Tue Jun 03 2008 - 13:22:16 CDT)
  • Re: AMBER: Temperature controlling method in AMBER (Tue Jun 03 2008 - 09:56:51 CDT)
  • Re: AMBER: gasteiger is not working with ambertools 1.0 (Mon Jun 02 2008 - 19:12:55 CDT)
  • Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error (Mon Jun 02 2008 - 18:23:46 CDT)
  • Re: AMBER: MAXAT can not be changed for AMBERTool 1.0 (Mon Jun 02 2008 - 18:15:38 CDT)
  • Re: AMBER: Error message: Install Amber9 on fedora 9 (Mon Jun 02 2008 - 18:04:48 CDT)
  • Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 (Mon Jun 02 2008 - 12:56:16 CDT)
  • Re: AMBER: igb and ibelly (Fri May 30 2008 - 15:20:52 CDT)
  • Re: AMBER: nab (Fri May 30 2008 - 09:55:10 CDT)
  • Re: AMBER: protonate in Amber10 (Thu May 29 2008 - 16:10:34 CDT)
  • Re: AMBER: Segmentation faults trying to run sander mpi (Thu May 29 2008 - 10:20:08 CDT)
  • Re: AMBER: Which is best temperature controlling method (Thu May 29 2008 - 09:35:36 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 12:32:33 CDT)
  • Re: AMBER: mbondi radii for gaff atom types (Wed May 28 2008 - 12:31:30 CDT)
  • Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error (Wed May 28 2008 - 12:27:31 CDT)
  • Re: AMBER: Hydration free energies of charged ions using PME (Wed May 28 2008 - 11:51:26 CDT)
  • Re: AMBER: Segmentation faults trying to run sander mpi (Wed May 28 2008 - 12:00:34 CDT)
  • Re: AMBER: install amber tools (Wed May 28 2008 - 11:56:30 CDT)
  • Re: AMBER: Parallel Self-guided Langevin simulation (Wed May 28 2008 - 11:46:55 CDT)
  • Re: AMBER: bugfix (imin=5) in amber9 (Wed May 28 2008 - 00:16:40 CDT)
  • Re: AMBER: Which is best temperature controlling method (Tue May 27 2008 - 23:59:23 CDT)
  • Re: AMBER: peptide at the box center during NVT-MD (Mon May 26 2008 - 11:09:51 CDT)
  • Re: AMBER: Parallel Self-guided Langevin simulation (Mon May 26 2008 - 01:06:03 CDT)
  • Re: AMBER: self-diffusion coefficient and Berendsen (Sun May 25 2008 - 23:09:32 CDT)
  • Re: AMBER: self-diffusion coefficient and Berendsen (Sat May 24 2008 - 15:20:27 CDT)
  • Re: AMBER: how to extract energy (Sat May 24 2008 - 15:21:22 CDT)
  • Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450) (Fri May 23 2008 - 00:35:29 CDT)
  • Re: AMBER: COM RESTRAINT (Fri May 23 2008 - 00:19:24 CDT)
  • Re: AMBER: Parallel Self-guided Langevin simulation (Thu May 22 2008 - 05:16:23 CDT)
  • Re: AMBER: amber tools installation (Wed May 21 2008 - 10:30:32 CDT)
  • Re: AMBER: xLeap compilation issues (Wed May 21 2008 - 00:27:53 CDT)
  • Re: AMBER: building quadruplex with nab (Wed May 21 2008 - 00:08:10 CDT)
  • Re: AMBER: anal (Tue May 20 2008 - 03:25:13 CDT)
  • Re: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- (Sun May 18 2008 - 15:09:00 CDT)
  • Re: AMBER: Amber 10 ambpdb bug? (Sat May 17 2008 - 23:37:09 CDT)
  • AMBER: Versions of mopac (Fri May 16 2008 - 21:04:10 CDT)
  • Re: AMBER: MKL libraries/Amber10 (Fri May 16 2008 - 15:27:40 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Fri May 16 2008 - 15:24:08 CDT)
  • Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 (Fri May 16 2008 - 15:16:56 CDT)
  • Re: AMBER: PGI amber9 problems (Fri May 16 2008 - 06:29:06 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Thu May 15 2008 - 23:47:19 CDT)
  • Re: AMBER: Amber10:Compiling with gcc 2.4.1 (Thu May 15 2008 - 22:42:31 CDT)
  • Re: AMBER: periodic boundary condition (Wed May 14 2008 - 08:50:40 CDT)
  • Re: AMBER: Ewald PARAMETER RANGE WRONG (Mon May 12 2008 - 11:00:44 CDT)
  • Re: AMBER: cannot read big .pdb files (Sat May 10 2008 - 10:24:41 CDT)
  • Re: AMBER: parmbsc0 parameters for RNA.DNA systems (Sat May 10 2008 - 10:27:36 CDT)
  • Re: AMBER: velocity autocorrelation function for SPC felxible water model (Thu May 08 2008 - 17:54:57 CDT)
  • Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands (Thu May 08 2008 - 15:49:31 CDT)
  • Re: AMBER: AmberTools on OS X fails tests (Thu May 08 2008 - 14:30:53 CDT)
  • Re: AMBER: velocity autocorrelation function for SPC felxible water model (Thu May 08 2008 - 13:00:28 CDT)
  • Re: AMBER: xleap (draw using edit) (Thu May 08 2008 - 13:02:58 CDT)
  • Re: AMBER: Discontinuous Constant pH Restarts (Thu May 08 2008 - 12:21:57 CDT)
  • Re: AMBER: mm_pbsa problem: bad atom type: IP (Thu May 08 2008 - 12:27:22 CDT)
  • Re: AMBER: Ewald error estimate (Thu May 08 2008 - 12:16:43 CDT)
  • Re: AMBER: How to transfer unformatted coordinates into formatted ones (Thu May 08 2008 - 12:13:59 CDT)
  • Re: AMBER: Hydroxyprolines!!! (Wed May 07 2008 - 20:26:16 CDT)
  • Re: AMBER: How to transfer unformatted coordinates into formatted ones (Wed May 07 2008 - 20:14:04 CDT)
  • Re: AMBER: Discontinuous Constant pH Restarts (Wed May 07 2008 - 16:34:23 CDT)
  • Re: AMBER: GBSA SA calculation (Wed May 07 2008 - 16:17:07 CDT)
  • Re: AMBER: uninstall of AMBER (Wed May 07 2008 - 11:07:25 CDT)
  • Re: AMBER: Ewald error estimate (Wed May 07 2008 - 10:57:03 CDT)
  • Re: AMBER: single stranded DNA (Tue May 06 2008 - 17:41:29 CDT)
  • Re: AMBER: mm_pbsa.pl not reading parameters for nmode (Tue May 06 2008 - 13:13:54 CDT)
  • Re: AMBER: Minimization in Octahedric Box (Tue May 06 2008 - 12:28:20 CDT)
  • Re: AMBER: NON-BONDED parameters (Mon May 05 2008 - 18:54:32 CDT)
  • Re: AMBER: About reading in heme and CO molecule together with myoglobin (Mon May 05 2008 - 18:51:44 CDT)
  • Re: AMBER: Units, units units (Mon May 05 2008 - 18:02:57 CDT)
  • Re: AMBER: misplacement of TER by leap (Mon May 05 2008 - 13:55:29 CDT)
  • Re: AMBER: unable to compile AmberTools 1.0 (Mon May 05 2008 - 13:14:44 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Sun May 04 2008 - 20:32:02 CDT)
  • Re: AMBER: Help with NMODE (Sun May 04 2008 - 20:26:07 CDT)
  • Re: AMBER: Amber10 Installation error - incorrect file suffix (Sun May 04 2008 - 20:20:55 CDT)
  • Re: AMBER: GAFF Schema (Sun May 04 2008 - 20:21:59 CDT)
  • Re: RE: RE: AMBER: point charges (Sat May 03 2008 - 19:36:08 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 19:32:10 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Sat May 03 2008 - 18:56:32 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 18:49:27 CDT)
  • Re: AMBER: Example .prepi file for nonstandard amino acids (Fri May 02 2008 - 17:54:03 CDT)
  • Re: AMBER: Discontinuous Constant pH Restarts (Fri May 02 2008 - 14:44:31 CDT)
  • Re: AMBER: Help with NMODE (Fri May 02 2008 - 14:28:51 CDT)
  • Re: AMBER: cfortran.h error with xlf90 compiler (Fri May 02 2008 - 12:10:54 CDT)
  • Re: AMBER: Help with NMODE (Fri May 02 2008 - 12:06:33 CDT)
  • Re: AMBER: Help with NMODE (Fri May 02 2008 - 11:23:34 CDT)
  • Re: AMBER: Amber10 installation error (Fri May 02 2008 - 11:07:50 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Thu May 01 2008 - 13:55:17 CDT)
  • Re: AMBER: Cysteine sulphonic acid parameters (Wed Apr 30 2008 - 19:06:02 CDT)
  • Re: AMBER: amber 9 compilation problem on IBM SP5 (Wed Apr 30 2008 - 13:37:11 CDT)
  • Re: AMBER: Dose AMBER 10 pmemd support openmpi? (Wed Apr 30 2008 - 10:22:48 CDT)
  • Re: AMBER: Charge derivation: RESP vs. antechamber (Tue Apr 29 2008 - 18:40:40 CDT)
  • Re: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 13:58:30 CDT)
  • Re: RE: RE: AMBER: memory usage (Mon Apr 28 2008 - 12:26:22 CDT)
  • Re: AMBER: Read trajectories generated by CHARMM (Mon Apr 28 2008 - 10:25:13 CDT)
  • Re: AMBER: NMR restraints (Mon Apr 28 2008 - 10:20:53 CDT)
  • Re: AMBER: sander & imin=5 (Fri Apr 25 2008 - 13:38:25 CDT)
  • Re: AMBER: saveamberparm (Thu Apr 24 2008 - 09:58:20 CDT)
  • Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error (Wed Apr 23 2008 - 13:34:30 CDT)
  • Re: AMBER: cross time correlation function (Wed Apr 23 2008 - 12:10:46 CDT)
  • Re: AMBER: Topology file format for Amber9 (Wed Apr 23 2008 - 11:01:13 CDT)
  • Re: AMBER: cross time correlation function (Wed Apr 23 2008 - 10:55:07 CDT)
  • Re: AMBER: pressure varies in constant pressure membrane simulation (Tue Apr 22 2008 - 13:31:53 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Tue Apr 22 2008 - 10:13:38 CDT)
  • Re: AMBER: How to change default radius assigned to an atom (Tue Apr 22 2008 - 00:36:16 CDT)
  • Re: AMBER: nmode (Mon Apr 21 2008 - 16:05:20 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 15:55:26 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 14:05:38 CDT)
  • Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits (Fri Apr 18 2008 - 17:00:23 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Fri Apr 18 2008 - 16:17:32 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Fri Apr 18 2008 - 15:44:36 CDT)
  • Re: AMBER: compile Amber9 on 64bit AMD Opteron (Fri Apr 18 2008 - 10:23:48 CDT)
  • Re: AMBER: xLeap unit editor "seg fault" (Thu Apr 17 2008 - 19:53:29 CDT)
  • Re: AMBER: Scale LJ parameters (Thu Apr 17 2008 - 19:54:43 CDT)
  • Re: AMBER: Performance issues on Ethernet clusters (Thu Apr 17 2008 - 14:02:45 CDT)
  • AMBER: H atom names in Amber (Thu Apr 17 2008 - 10:16:19 CDT)
  • Re: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 19:26:05 CDT)
  • Re: AMBER: PMF calculation for binding constant or rate constant? (Wed Apr 16 2008 - 16:26:13 CDT)
  • Re: AMBER: topology file (Wed Apr 16 2008 - 12:45:52 CDT)
  • Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? (Tue Apr 15 2008 - 16:01:15 CDT)
  • Re: AMBER: xleap segmentation fault on SaveAmberParm (Tue Apr 15 2008 - 16:00:47 CDT)
  • Re: AMBER: questions about run MD at different pH (Tue Apr 15 2008 - 15:59:27 CDT)
  • Re: AMBER: questions about run MD at different pH (Tue Apr 15 2008 - 12:19:11 CDT)
  • Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits (Tue Apr 15 2008 - 00:26:45 CDT)
  • AMBER: ANNOUNCEMENT: release of Amber 10 (Mon Apr 14 2008 - 12:18:40 CDT)
  • Re: AMBER: error in compilation elsize.cc (Mon Apr 14 2008 - 12:11:33 CDT)
  • Re: AMBER: protein-ligand complex problem (Thu Apr 10 2008 - 18:51:55 CDT)
  • Re: AMBER: solvateOct produces strange residues compared to solvateCap (Thu Apr 10 2008 - 14:29:52 CDT)
  • Re: AMBER: Gbsa in NAB (Thu Apr 10 2008 - 12:24:17 CDT)
  • Re: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f (Thu Apr 10 2008 - 00:03:14 CDT)
  • Re: AMBER: Tutorial B3- Section6 (Wed Apr 09 2008 - 20:46:16 CDT)
  • Re: AMBER: Build a MPI NAB (Wed Apr 09 2008 - 11:27:28 CDT)
  • Re: AMBER: Protein rotating out of box (Tue Apr 08 2008 - 20:54:29 CDT)
  • Re: AMBER: restraint box dimension (Tue Apr 08 2008 - 19:34:05 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Tue Apr 08 2008 - 17:08:00 CDT)
  • Re: AMBER: Build a MPI NAB (Tue Apr 08 2008 - 16:35:41 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Mon Apr 07 2008 - 23:58:53 CDT)
  • Re: AMBER: how to change the force field parameters inside the prmtop file? (Mon Apr 07 2008 - 19:05:21 CDT)
  • Re: AMBER: Build a MPI NAB (Mon Apr 07 2008 - 16:28:54 CDT)
  • Re: AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water (Mon Apr 07 2008 - 15:40:27 CDT)
  • Re: AMBER: NAB examples (Mon Apr 07 2008 - 12:42:34 CDT)
  • Re: AMBER: NAB examples (Mon Apr 07 2008 - 11:26:58 CDT)
  • Re: AMBER: NAB examples (Mon Apr 07 2008 - 10:33:26 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 10:39:24 CDT)
  • Re: AMBER: Minimisation: cis-azobenzene parameters (Sat Apr 05 2008 - 16:11:17 CDT)
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 10:59:08 CDT)
  • Re: AMBER: imem keyword using mmpbsa (Thu Apr 03 2008 - 23:04:11 CDT)
  • Re: AMBER: MPI run problem (Thu Apr 03 2008 - 15:38:38 CDT)
  • Re: AMBER: Simple Minimization - Error (Thu Apr 03 2008 - 15:11:13 CDT)
  • Re: AMBER: Using mdcrd files to look at minor charge changes (Thu Apr 03 2008 - 14:46:46 CDT)
  • Re: AMBER: NAD parameters (Thu Apr 03 2008 - 10:01:46 CDT)
  • Re: AMBER: multiple dihedral restraints using group (Wed Apr 02 2008 - 15:44:20 CDT)
  • Re: AMBER: Simulating DNA Backbone in NAB (Wed Apr 02 2008 - 15:24:25 CDT)
  • Re: AMBER: residual dipolar couplings - alignment tensor energy (Wed Apr 02 2008 - 12:53:38 CDT)
  • Re: AMBER: Regarding SHAKE (Wed Apr 02 2008 - 12:54:59 CDT)
  • Re: AMBER: Nmode segmentation fault (Wed Apr 02 2008 - 12:50:09 CDT)
  • AMBER: ANNOUNCE: Release of AmberTools, version 1.0 (Wed Apr 02 2008 - 11:49:20 CDT)
  • Re: AMBER: meet problems in adding ions and waterbox (Wed Apr 02 2008 - 11:37:05 CDT)
  • Re: AMBER: meet problems in adding ions and waterbox (Wed Apr 02 2008 - 00:22:52 CDT)
  • Re: AMBER: memory limitation of Amber 9 (Tue Apr 01 2008 - 00:50:41 CDT)
  • Re: AMBER: nmode (Mon Mar 31 2008 - 14:25:52 CDT)
  • Re: AMBER: installation amber9 (Mon Mar 31 2008 - 12:51:45 CDT)
  • Re: AMBER: energy problems in simulation with restraints (Mon Mar 31 2008 - 10:35:58 CDT)
  • Re: AMBER: AMBER 9 testing (Sun Mar 30 2008 - 11:23:15 CDT)
  • Re: AMBER: problem with nmod (Fri Mar 28 2008 - 19:19:40 CDT)
  • Re: AMBER: AMBER 9 testing (Fri Mar 28 2008 - 19:10:02 CDT)
  • Re: AMBER: NTR Restraints (Thu Mar 27 2008 - 15:17:31 CDT)
  • Re: AMBER: how to link two different atoms in xLeap (Wed Mar 26 2008 - 23:52:18 CDT)
  • Re: AMBER: Error with a binary restart file (Wed Mar 26 2008 - 20:11:58 CDT)
  • Re: AMBER: OPLS force field (Wed Mar 26 2008 - 11:08:57 CDT)
  • Re: AMBER: help regarding warning message (Tue Mar 25 2008 - 13:51:07 CDT)
  • Re: AMBER: Nmode segmentation fault (Tue Mar 25 2008 - 13:44:51 CDT)
  • Re: AMBER: Nmode segmentation fault (Tue Mar 25 2008 - 11:34:37 CDT)
  • Re: AMBER: RE: Force Field Parameterizing (Tue Mar 25 2008 - 10:23:34 CDT)
  • Re: AMBER: equilibration of peptide (Sat Mar 22 2008 - 12:51:47 CDT)
  • Re: AMBER: standard residues (Sat Mar 22 2008 - 11:30:03 CDT)
  • Re: AMBER: cntrl namelist error (Sat Mar 22 2008 - 11:11:52 CDT)
  • Re: AMBER: problem with distance restraints (Fri Mar 21 2008 - 12:56:28 CDT)
  • Re: AMBER: Amber9 Installation Problem (Thu Mar 20 2008 - 18:23:53 CDT)
  • Re: AMBER: What's making my system lose total energy? (Wed Mar 19 2008 - 20:46:31 CDT)
  • Re: AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 20:37:57 CDT)
  • Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Wed Mar 19 2008 - 17:54:24 CDT)
  • Re: AMBER: Inquiry on analyzing the amplitude from nmdout results (Wed Mar 19 2008 - 17:49:21 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Wed Mar 19 2008 - 16:57:54 CDT)
  • Re: AMBER: Inquiry on analyzing the amplitude from nmdout results (Wed Mar 19 2008 - 16:46:10 CDT)
  • Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Wed Mar 19 2008 - 10:42:13 CDT)
  • Re: AMBER: problem with distance restrain (Tue Mar 18 2008 - 14:00:11 CDT)
  • Re: AMBER: Problems with neglected restaints (Tue Mar 18 2008 - 12:15:56 CDT)
  • Re: Fwd: AMBER: lastrst problem (Tue Mar 18 2008 - 10:37:48 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Tue Mar 18 2008 - 00:30:48 CDT)
  • Re: AMBER: compiling AMBER9 with bintraj option on AMD64 (Mon Mar 17 2008 - 18:48:00 CDT)
  • Re: AMBER: study of protein stability in different ion using AMBER (Sat Mar 15 2008 - 00:48:13 CDT)
  • Re: AMBER: problem with antech amber (Sat Mar 15 2008 - 00:09:00 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 23:41:09 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 22:40:35 CDT)
  • Re: AMBER: distance restraint (Thu Mar 13 2008 - 15:40:07 CDT)
  • Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 (Wed Mar 12 2008 - 00:43:26 CDT)
  • Re: AMBER: AMBER install problem (Tue Mar 11 2008 - 19:47:58 CDT)
  • Re: AMBER: AMBER install problem (Mon Mar 10 2008 - 19:50:30 CDT)
  • Re: AMBER: Fwd: positive potential energy and large 1-4 EEL (Mon Mar 10 2008 - 19:19:51 CDT)
  • Re: AMBER: output effective Born radii (Mon Mar 10 2008 - 19:07:39 CDT)
  • Re: AMBER: Compiler issues with Altix450 (Mon Mar 10 2008 - 18:29:50 CDT)
  • Re: AMBER: Microcannonical MD Reference (Fri Mar 07 2008 - 16:47:02 CST)
  • Re: AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis (Fri Mar 07 2008 - 15:36:33 CST)
  • Re: AMBER: NVE energy and temperature drift (Fri Mar 07 2008 - 10:32:51 CST)
  • Re: AMBER: Atom types/parameters for chromene (Wed Mar 05 2008 - 13:15:25 CST)
  • Re: AMBER: questions about run MD at different pH (Tue Mar 04 2008 - 19:59:49 CST)
  • Re: AMBER: Problem running implicit minimization (Mon Mar 03 2008 - 23:59:00 CST)
  • Re: AMBER: questions about run MD at different pH (Mon Mar 03 2008 - 23:07:00 CST)
  • Re: AMBER: xleap screen output (Mon Mar 03 2008 - 15:31:17 CST)
  • Re: AMBER: Writing pressure in md.out file in NVT simulation (Mon Mar 03 2008 - 13:24:20 CST)
  • Re: AMBER: for NMR refinement (Fri Feb 29 2008 - 12:53:59 CST)
  • Re: AMBER: Re: Force field parameter file for CNT (Fri Feb 29 2008 - 10:19:47 CST)
  • Re: AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 17:47:10 CST)
  • Re: AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 16:27:47 CST)
  • Re: AMBER: DFTB/SCC-DFTB (Thu Feb 28 2008 - 00:15:48 CST)
  • Re: AMBER: Lennard-Jones parameters (Wed Feb 27 2008 - 16:16:34 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 12:25:02 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 18:41:26 CST)
  • Re: AMBER: Using restart files (Tue Feb 26 2008 - 18:45:34 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Tue Feb 26 2008 - 15:34:07 CST)
  • Re: AMBER: mol2 save (Tue Feb 26 2008 - 11:51:19 CST)
  • Re: AMBER: Force fields (Tue Feb 26 2008 - 11:31:19 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 11:16:46 CST)
  • Re: AMBER: dihedral energy in amber (Sat Feb 23 2008 - 10:37:09 CST)
  • Re: AMBER: Question: tweaking topology files to add SHAKE-constrained bonds (Fri Feb 22 2008 - 11:14:59 CST)
  • Re: AMBER: NAB to calcuate entropy. . (Thu Feb 21 2008 - 14:26:06 CST)
  • Re: AMBER: simulated annealing (Thu Feb 21 2008 - 14:04:26 CST)
  • Re: AMBER: NAB to calcuate entropy. . (Thu Feb 21 2008 - 11:10:16 CST)
  • Re: AMBER: NAB to calcuate entropy. . (Thu Feb 21 2008 - 11:10:36 CST)
  • Re: AMBER: XLEaP (Thu Feb 21 2008 - 10:45:08 CST)
  • Re: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 17:18:32 CST)
  • Re: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 17:16:14 CST)
  • Re: AMBER: NAB to calcuate entropy (Wed Feb 20 2008 - 15:36:15 CST)
  • Re: AMBER: Dimension of the solvated box? (Wed Feb 20 2008 - 10:31:36 CST)
  • Re: AMBER: NAB to calcuate entropy (Tue Feb 19 2008 - 19:33:59 CST)
  • Re: AMBER: united atom force field: antechamber (Tue Feb 19 2008 - 17:33:32 CST)
  • Re: AMBER: parameters of nonbonded potentials (Tue Feb 19 2008 - 10:05:07 CST)
  • Re: AMBER: TERs (Mon Feb 18 2008 - 10:49:55 CST)
  • Re: AMBER: setting perioding box in AMBER (Sun Feb 17 2008 - 20:14:31 CST)
  • Re: AMBER: setbox for solvateoct model (Fri Feb 15 2008 - 20:52:14 CST)
  • Re: AMBER: Is boiling point a good way to validate solvent paramters? (Fri Feb 15 2008 - 20:49:12 CST)
  • Re: AMBER: using NAB to calculate normal modes. . (Fri Feb 15 2008 - 17:54:46 CST)
  • Re: AMBER: using NAB to calculate normal modes (Fri Feb 15 2008 - 16:17:23 CST)
  • AMBER: problem with ambmask (Fri Feb 15 2008 - 12:07:54 CST)
  • Re: AMBER: ambmask problem (Fri Feb 15 2008 - 11:32:46 CST)
  • Re: AMBER: sander error on Make test.serial (Wed Feb 13 2008 - 23:57:32 CST)
  • Re: AMBER: xmgr graphics display program (Wed Feb 13 2008 - 23:46:40 CST)
  • Re: AMBER: Is boiling point a good way to validate solvent paramters? (Wed Feb 13 2008 - 14:34:01 CST)
  • Re: AMBER: RDCs in AMBER 10 (Tue Feb 12 2008 - 17:56:52 CST)
  • Re: AMBER: PKa calculation (Tue Feb 12 2008 - 11:15:55 CST)
  • Re: AMBER: Which install compiler and flags? (Fri Feb 08 2008 - 11:04:55 CST)
  • Re: AMBER: Error while compiling Amber (Thu Feb 07 2008 - 19:42:31 CST)
  • Re: AMBER: Amber compilation with ifort (Wed Feb 06 2008 - 15:47:20 CST)
  • Re: AMBER: using NAB to calculate entropy. . (Wed Feb 06 2008 - 15:37:40 CST)
  • Re: AMBER: using NAB to calculate entropy (Wed Feb 06 2008 - 14:21:28 CST)
  • Re: AMBER: Binary restart file !! (Wed Feb 06 2008 - 10:35:42 CST)
  • Re: AMBER: Query related to implicit solvent EXTDIEL (Wed Feb 06 2008 - 10:31:08 CST)
  • Re: AMBER: silica slab (Tue Feb 05 2008 - 12:00:33 CST)
  • AMBER: infinite polymers in CHARMM (Tue Feb 05 2008 - 10:39:45 CST)
  • Re: AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 19:55:47 CST)
  • Re: AMBER: VLIMIT units; TGTFITMASK (Mon Feb 04 2008 - 17:18:39 CST)
  • Re: AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 15:46:00 CST)
  • Re: AMBER: twin cut-off radii (Mon Feb 04 2008 - 10:09:51 CST)
  • Re: AMBER: Back on track (Wed Jan 30 2008 - 19:33:46 CST)
  • Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? (Mon Jan 28 2008 - 10:11:02 CST)
  • Re: AMBER: AMBER installation problem (Mon Jan 28 2008 - 10:06:54 CST)
  • Re: AMBER: QM/MM: input conversion error (Fri Jan 25 2008 - 16:59:35 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 20:25:33 CST)
  • Re: AMBER: NMR refinement (Thu Jan 24 2008 - 20:18:48 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 12:42:56 CST)
  • Re: AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 (Thu Jan 24 2008 - 11:25:09 CST)
  • Re: AMBER: antechamber run on charged system (Wed Jan 23 2008 - 12:37:06 CST)
  • Re: AMBER: Installing OpenMPI (Wed Jan 23 2008 - 11:07:46 CST)
  • Re: AMBER: regarding :scee (Wed Jan 23 2008 - 10:45:07 CST)
  • Re: AMBER: vlimit exceeded error (Wed Jan 23 2008 - 10:29:18 CST)
  • Re: AMBER: distorted aromatic rings (Wed Jan 23 2008 - 10:24:15 CST)
  • Re: AMBER: Amber 9: Question regarding Test Failures and Compilers (Wed Jan 23 2008 - 10:22:04 CST)
  • Re: AMBER: NMR refinement (Sat Jan 19 2008 - 12:39:08 CST)
  • Re: ?????? RE: AMBER: A problem to loadup the molecular in the xleap (Sat Jan 19 2008 - 12:17:16 CST)
  • Re: AMBER: NMR refinement (Fri Jan 18 2008 - 11:35:37 CST)
  • Re: AMBER: NMR refinement (Fri Jan 18 2008 - 11:11:54 CST)
  • Re: AMBER: Tinker 4.3 (Fri Jan 18 2008 - 11:07:50 CST)
  • Re: AMBER: Re: timestep problem (Thu Jan 17 2008 - 14:27:56 CST)
  • Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist (Wed Jan 16 2008 - 10:46:35 CST)
  • Re: AMBER: How to build a dimer using amber (Tue Jan 15 2008 - 11:18:14 CST)
  • Re: AMBER: How to build a dimer using amber (Tue Jan 15 2008 - 01:51:50 CST)
  • Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) (Mon Jan 14 2008 - 00:16:31 CST)
  • Re: AMBER: build RNA by nucgen (Sun Jan 13 2008 - 11:56:32 CST)
  • Re: AMBER: problem:capping (Sun Jan 13 2008 - 11:10:55 CST)
  • Re: AMBER: connectivity lose during the minimizations (Sat Jan 12 2008 - 14:28:37 CST)
  • Re: AMBER: offset residue numbering (Sat Jan 12 2008 - 01:10:08 CST)
  • Re: AMBER: ANTECHAMBER NAMING (Thu Jan 10 2008 - 21:32:30 CST)
  • Re: AMBER: NMROPT=1 in minimisation (Sun Jan 06 2008 - 14:59:03 CST)
  • Re: AMBER: MM-PBSA problem (Fri Jan 04 2008 - 20:07:07 CST)
  • Re: AMBER: check COM velocity (Fri Jan 04 2008 - 10:29:09 CST)
  • Re: AMBER: Thermodynamic integration with positional restraint? (Thu Jan 03 2008 - 11:31:19 CST)
• David Beveridge
  • AMBER: matrix correl (Sat Feb 16 2008 - 03:09:29 CST)
• David Case
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Fri Jun 06 2008 - 11:25:45 CDT)
  • AMBER: NAB documentation (Fri Jun 06 2008 - 11:24:44 CDT)
  • Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Fri Jun 06 2008 - 11:27:06 CDT)
• David Cerutti
  • Re: AMBER: Average structure (Mon Apr 21 2008 - 11:12:30 CDT)
  • AMBER: Short trajectory segments / frequent restarts causes explosion (Thu Apr 17 2008 - 16:04:14 CDT)
  • AMBER: WHAM: how frequently do I need data on the system coordinates? (Thu Apr 10 2008 - 11:14:23 CDT)
  • Re: AMBER: What's making my system lose total energy? (Tue Mar 18 2008 - 13:43:42 CDT)
  • Re: AMBER: What's making my system lose total energy? (Mon Mar 17 2008 - 22:52:10 CDT)
  • AMBER: What's making my system lose total energy? (Mon Mar 17 2008 - 19:20:30 CDT)
  • AMBER: More on tweaking a topology file (Fri Feb 22 2008 - 21:15:40 CST)
  • AMBER: Question: tweaking topology files to add SHAKE-constrained bonds (Thu Feb 21 2008 - 23:37:28 CST)
  • Re: AMBER: Problem:neturalization (Thu Feb 07 2008 - 01:42:39 CST)
  • AMBER: A new program for doing RESP (Thu Feb 07 2008 - 00:56:04 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 12:55:48 CST)
  • AMBER: Tough time with antechamber (UPDATE, still need help) (Thu Jan 24 2008 - 02:09:42 CST)
  • AMBER: Tough time with antechamber (Thu Jan 24 2008 - 01:29:38 CST)
  • Re: AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 13:13:42 CST)
  • AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 10:10:10 CST)
• David LeBard
  • Re: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 14:43:52 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 13:07:21 CDT)
  • Re: AMBER: sander.MPI / parallel (Mon Jun 16 2008 - 13:08:20 CDT)
  • AMBER: Timing analysis on Ranger (Sun Mar 09 2008 - 15:06:18 CDT)
  • Re: AMBER: XMGRACE on Linux 64 Bit (Fri Mar 07 2008 - 12:53:47 CST)
  • Re: AMBER: AMBER parameters for Chlorophyll (Sat Feb 16 2008 - 11:25:51 CST)
• David Mobley
  • Re: AMBER: improving GAFF sulfonamide parameters (Thu Jun 26 2008 - 15:50:03 CDT)
  • Re: AMBER: Free energy of dissociation (Thu Jun 05 2008 - 11:22:24 CDT)
  • Re: AMBER: Jarzynski (Mon Jun 02 2008 - 12:25:16 CDT)
  • Re: AMBER: Jarzynski (Fri May 30 2008 - 11:02:28 CDT)
  • Re: AMBER: Jarzinsky relationship (Thu May 08 2008 - 16:29:29 CDT)
  • Re: AMBER: convergence of free energy calculations (Thu Jan 24 2008 - 12:20:35 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 12:14:42 CST)
  • Re: AMBER: about AM1-BCC in antechamber (Fri Jan 18 2008 - 16:21:44 CST)
• David Rangel
  • Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 (Wed Mar 12 2008 - 12:04:18 CDT)
  • AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 (Tue Mar 11 2008 - 22:30:14 CDT)
• David Smith
  • Re: AMBER: imaging problem (Tue Apr 15 2008 - 08:30:48 CDT)
• David Watson
  • Re: AMBER: mpirun Permission denied. (Tue Dec 30 2008 - 23:04:40 CST)
  • Re: AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 19:17:57 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 16:30:32 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 15:53:15 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:32:45 CST)
  • Re: AMBER: Ring flips (Fri Oct 10 2008 - 12:36:36 CDT)
  • Re: AMBER: Ring flips (Fri Oct 10 2008 - 12:30:37 CDT)
  • Re: AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) (Sun Sep 21 2008 - 11:01:04 CDT)
  • Re: AMBER: Preparing peptides with D-amino acids (Tue Sep 09 2008 - 20:04:44 CDT)
  • AMBER: Preparing peptides with D-amino acids (Tue Sep 09 2008 - 19:06:58 CDT)
  • Re: AMBER: ptraj selection (Thu Jul 10 2008 - 01:01:01 CDT)
  • Re: AMBER: ptraj selection (Wed Jul 09 2008 - 22:59:27 CDT)
  • Re: AMBER: ptraj selection (Wed Jul 09 2008 - 21:11:16 CDT)
  • Re: AMBER: VMD Movie .mdcrd file ptraj (Fri Jun 06 2008 - 09:57:16 CDT)
  • Re: AMBER: cannot read big .pdb files (Mon May 12 2008 - 18:32:49 CDT)
• David Witte
  • AMBER: relative weight of RDC constraints (Mon Dec 15 2008 - 10:21:34 CST)
  • AMBER: Using RDCs for structure refinement (Tue Aug 12 2008 - 02:52:53 CDT)
• DawsonSean
  • AMBER: (Wed Jan 16 2008 - 02:52:07 CST)
• Deepangi Pandit
  • AMBER: ESURF - SASA - isolate residues (Fri Sep 05 2008 - 09:23:23 CDT)
  • AMBER: MM_PBSA - SASA - Question (Tue Sep 02 2008 - 21:10:13 CDT)
  • AMBER: Solvent Accesible Surface Area (SASA) - Confused (Fri Aug 29 2008 - 13:45:19 CDT)
  • Re: AMBER: query regarding energy minimization (Mon Apr 28 2008 - 09:39:39 CDT)
• Denzil Bernard
  • AMBER: charge derivation for modified amino acids (Tue Feb 26 2008 - 19:14:44 CST)
• Diddo Diddens
  • AMBER: segmentation fault when restarting periodic structure (Fri Nov 14 2008 - 06:47:23 CST)
  • AMBER: Lone pairs in antechamber (Thu Oct 30 2008 - 08:25:35 CDT)
  • Re: AMBER: Buckingham potential (Tue Sep 30 2008 - 10:01:57 CDT)
  • AMBER: Buckingham potential (Tue Sep 30 2008 - 09:16:47 CDT)
• dipti lele
  • AMBER: antechamber (Sat Oct 11 2008 - 23:43:33 CDT)
  • Re: AMBER: Querry (Wed Aug 27 2008 - 08:33:45 CDT)
  • AMBER: querry (Wed Aug 27 2008 - 04:07:52 CDT)
  • Re: AMBER: Querry (Wed Aug 27 2008 - 04:00:46 CDT)
  • AMBER: Querry (Tue Aug 26 2008 - 06:50:32 CDT)
  • AMBER: Glycoprotein once again.......... (Thu Aug 14 2008 - 07:10:10 CDT)
  • AMBER: Querry (Wed Aug 13 2008 - 07:15:11 CDT)
  • AMBER: Querry about simulating a glycopeptide (Tue Aug 12 2008 - 05:23:24 CDT)
  • AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 05:03:10 CDT)
  • AMBER: Query (Sun Jul 27 2008 - 01:40:54 CDT)
  • AMBER: Trans proline (Wed Jul 23 2008 - 06:01:28 CDT)
  • AMBER: Trans proline (Sun Jul 20 2008 - 00:53:00 CDT)
  • AMBER: querry (Mon Jul 14 2008 - 03:05:15 CDT)
• Dirar Homouz
  • RE: AMBER: restraintmask - reference file is not working (Thu Dec 18 2008 - 17:46:23 CST)
  • RE: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 13:40:48 CST)
  • RE: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 03:41:00 CST)
  • RE: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 18:51:08 CST)
  • RE: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 18:45:44 CST)
  • AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 18:05:24 CST)
  • AMBER: Pulling using restraintmask (Thu Dec 11 2008 - 14:30:00 CST)
  • RE: AMBER: Parallel Self-guided Langevin simulation (Thu May 29 2008 - 00:18:34 CDT)
  • RE: AMBER: Parallel Self-guided Langevin simulation (Wed May 28 2008 - 01:31:03 CDT)
  • RE: AMBER: Parallel Self-guided Langevin simulation (Thu May 22 2008 - 10:58:27 CDT)
  • AMBER: Parallel Self-guided Langevin simulation (Wed May 21 2008 - 17:23:27 CDT)
• Dmitri Nilov
  • AMBER: Gradual releasing of position restraints (Tue Nov 25 2008 - 08:23:02 CST)
  • AMBER: Equilibration protocol for large protein (Tue Nov 18 2008 - 10:33:26 CST)
  • Re: AMBER: Again: Installation problem of AMBER on cluster (Sat Oct 25 2008 - 07:30:43 CDT)
  • AMBER: Again: Installation problem of AMBER on cluster (Tue Oct 21 2008 - 11:31:52 CDT)
  • AMBER: NAD+ parameters problem using tleap (Fri Oct 17 2008 - 11:24:50 CDT)
  • AMBER: Amber10: Problem with tgtmd and ncsu testing (Wed Oct 15 2008 - 08:00:11 CDT)
• Dong Xu
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue Jul 29 2008 - 02:40:04 CDT)
  • AMBER: Energy minimization of protein-ligand complex (Tue Jul 29 2008 - 02:18:57 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue Jul 08 2008 - 01:37:54 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri Jul 04 2008 - 14:21:31 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri Jul 04 2008 - 01:33:03 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri Jul 04 2008 - 01:28:44 CDT)
  • AMBER: ligand partial charge and conformation question (Thu Jun 26 2008 - 13:01:31 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 01:21:03 CDT)
  • AMBER: Antechamber/mopac am1-bcc charge (Wed Jun 25 2008 - 17:09:39 CDT)
  • AMBER: ptraj has trouble with x-plor psf file from VMD (Thu May 29 2008 - 15:23:56 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Thu May 29 2008 - 14:19:53 CDT)
  • AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Thu May 29 2008 - 00:56:48 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue May 27 2008 - 13:20:09 CDT)
  • AMBER: mass weighted rms fit (Sun May 25 2008 - 11:11:43 CDT)
  • AMBER: ptraj mask not working with psf file (Fri May 23 2008 - 21:53:27 CDT)
  • Re: AMBER: AMBER entropy calculation (Wed May 14 2008 - 19:37:27 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Mon May 12 2008 - 23:09:11 CDT)
  • AMBER: Ligand energy minimization (Mon May 12 2008 - 17:07:31 CDT)
  • AMBER: Calculate number of ions (Sat May 10 2008 - 13:32:01 CDT)
• Douglas Kojetin
  • Re: AMBER: residual dipolar couplings - alignment tensor energy (Tue Apr 01 2008 - 10:53:55 CDT)
  • Re: AMBER: residual dipolar couplings - alignment tensor energy (Tue Apr 01 2008 - 10:23:59 CDT)
  • AMBER: residual dipolar couplings - alignment tensor energy (Wed Mar 26 2008 - 14:46:48 CDT)
  • Re: AMBER: RDCs in AMBER 10 (Tue Feb 12 2008 - 19:01:30 CST)
  • AMBER: RDCs in AMBER 10 (Tue Feb 12 2008 - 17:39:37 CST)
• dpandit_at_brandeis.edu
  • Re: AMBER: PTRAJ - Segmentation Fault (Wed Jun 11 2008 - 14:40:25 CDT)
  • AMBER: Trajectory - Average Structure - Equilibration (Wed Jun 11 2008 - 14:37:46 CDT)
  • RE: AMBER: Equilibration/Heating - Protein fixed -Problem (Wed Jun 11 2008 - 13:17:56 CDT)
  • Re: AMBER: PTRAJ - Segmentation Fault (Wed Jun 11 2008 - 12:48:54 CDT)
  • AMBER: Equilibration/Heating - Protein fixed -Problem (Wed Jun 11 2008 - 10:31:40 CDT)
  • AMBER: PTRAJ - Segmentation Fault (Tue Jun 10 2008 - 16:36:08 CDT)
  • RE: AMBER: NTC and NTF (Thu May 29 2008 - 14:39:33 CDT)
  • AMBER: NTC and NTF (Thu May 29 2008 - 14:18:14 CDT)
  • RE: AMBER: Restart MD Simulation (Sat May 24 2008 - 08:40:40 CDT)
  • AMBER: Restart MD Simulation (Fri May 23 2008 - 16:56:23 CDT)
  • AMBER: Accessing Equilibration Results (Thu Apr 17 2008 - 08:29:35 CDT)
  • RE: AMBER: Whole System Equilibration & Pressure (Tue Apr 15 2008 - 09:16:35 CDT)
  • AMBER: Whole System Equilibration & Pressure (Mon Apr 14 2008 - 15:57:54 CDT)
  • AMBER: Initial Equilibration (Thu Apr 10 2008 - 15:45:01 CDT)
  • AMBER: Restraintmask and Restraint_WT : Question (Fri Apr 04 2008 - 10:24:32 CDT)
  • AMBER: Simple Minimization - Error (Thu Apr 03 2008 - 14:55:08 CDT)
  • AMBER: addions and addions2 (Tue Mar 25 2008 - 09:38:22 CDT)
  • RE: AMBER: XMGRACE on Linux 64 Bit (Fri Mar 07 2008 - 12:40:19 CST)
  • Re: AMBER: XMGRACE on Linux 64 Bit (Thu Mar 06 2008 - 19:50:55 CST)
  • AMBER: XMGRACE on Linux 64 Bit (Thu Mar 06 2008 - 17:15:00 CST)
• Dr. Suzie Byun
  • AMBER: parmbsc0 (Sat Jul 19 2008 - 10:40:05 CDT)
• Dr. Xiaofeng (Frank) Duan
  • AMBER: qmmm_DFTB problem (Tue Jun 24 2008 - 08:58:46 CDT)
• drugdesign
  • AMBER: mpirun Permission denied. (Thu Dec 25 2008 - 00:49:31 CST)
  • Re: AMBER: Amber 9 installation problems (Thu Nov 13 2008 - 10:25:34 CST)
  • Re: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 13:09:47 CST)
  • Re: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 01:36:51 CST)
  • Re: AMBER: Amber 9 installation problems (Tue Nov 11 2008 - 08:13:32 CST)
  • AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 05:27:39 CST)
  • AMBER: looks like I have problem with "make clean" command (Mon Nov 10 2008 - 01:27:22 CST)
• E.M.
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Sun Nov 09 2008 - 17:08:05 CST)
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 07:22:25 CDT)
  • Re: AMBER: Eigenmode dynamics - imaging traj (Wed Jun 18 2008 - 06:16:49 CDT)
  • AMBER: divcon (Tue May 13 2008 - 11:58:49 CDT)
  • Re: AMBER: distance (Fri May 09 2008 - 09:43:12 CDT)
  • Re: AMBER: Jarzinsky relationship (Thu May 08 2008 - 05:58:10 CDT)
  • AMBER: reset time and comments (Wed May 07 2008 - 23:13:02 CDT)
  • AMBER: Units, units units (Mon May 05 2008 - 17:18:37 CDT)
  • Re: AMBER: Jarzinsky relationship (Mon May 05 2008 - 10:02:49 CDT)
  • AMBER: Torsion angle restrains and Jarzinsky (Mon May 05 2008 - 02:06:56 CDT)
  • AMBER: Jarzinsky relationship (Sun May 04 2008 - 21:39:51 CDT)
  • AMBER: MNDO parameters for Mg+2 (Wed Mar 19 2008 - 12:28:09 CDT)
• ecustipp
  • AMBER: vertex atom mismatch (Fri Dec 26 2008 - 04:09:45 CST)
  • Re:Re: AMBER: about mmpbsa out data (Wed Dec 24 2008 - 03:11:50 CST)
  • AMBER: about mmpbsa out data (Tue Dec 23 2008 - 20:21:22 CST)
• ecustipp_at_163.com
  • Re: AMBER: (no subject) (Mon Dec 29 2008 - 01:58:20 CST)
• Ed Pate
  • AMBER: Amber 10 timing (Fri Jun 20 2008 - 12:08:37 CDT)
  • AMBER: amber10 installation problem (Tue Jun 10 2008 - 15:59:47 CDT)
  • AMBER: problem with group input (Mon Jan 21 2008 - 00:53:28 CST)
• Eddie Mende
  • AMBER: DFTB/SCC-DFTB (Wed Feb 27 2008 - 13:21:42 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 16:55:20 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 15:04:02 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 14:49:04 CST)
  • AMBER: bond breaking in proteins (Tue Feb 26 2008 - 17:40:03 CST)
  • AMBER: bond breaking in proteins (Tue Feb 26 2008 - 16:41:22 CST)
  • AMBER: bond breaking in proteins (Tue Feb 26 2008 - 10:16:21 CST)
  • Re: AMBER: (no subject) (Fri Feb 22 2008 - 00:33:07 CST)
  • Re: AMBER: (no subject) (Fri Feb 22 2008 - 00:31:01 CST)
  • AMBER: PB Bomb in pb_atmlist(): maxnba too short (Fri Feb 08 2008 - 07:22:07 CST)
  • Re: AMBER: Entropy calculations using NMODE (Sat Feb 02 2008 - 07:17:06 CST)
• Edward M
  • AMBER: AMBER question: perturbed charge twice the unperturbed (Sat Nov 08 2008 - 23:36:54 CST)
• Edyta Malolepsza
  • Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Mon Mar 31 2008 - 08:05:42 CDT)
  • Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Wed Mar 19 2008 - 11:49:45 CDT)
  • AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Thu Mar 06 2008 - 06:23:06 CST)
• Emilio Xavier Esposito
  • Re: AMBER: meet problem in adding ions and waterbox (Sun Mar 30 2008 - 12:26:45 CDT)
• Enghui Yap
  • AMBER: bad nonbon in nmode (amber9) (Mon Jul 14 2008 - 11:25:29 CDT)
• Enguerran Vanquelef
  • Re: AMBER: Zn2+ Bondi radius value (Wed Oct 08 2008 - 06:55:21 CDT)
• Eric Germaneau
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 12:49:40 CDT)
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 09:10:31 CDT)
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 03:27:07 CDT)
  • AMBER: GAFF (Fri Apr 04 2008 - 03:18:03 CDT)
  • AMBER: GAFF (Fri Mar 28 2008 - 07:38:41 CDT)
• Evan Kelly
  • Re: AMBER: Imaging before HBond analysis? (Fri Apr 11 2008 - 18:09:32 CDT)
  • Re: AMBER: Imaging before HBond analysis? (Fri Apr 11 2008 - 17:41:51 CDT)
  • AMBER: Imaging before HBond analysis? (Fri Apr 11 2008 - 15:34:41 CDT)
  • AMBER: "Assuming uniform neutralizing plasma" (Tue Feb 26 2008 - 20:01:52 CST)
  • Re: AMBER: sander error on Make test.serial (Thu Feb 14 2008 - 12:36:25 CST)
  • Re: AMBER: sander error on Make test.serial (Wed Feb 13 2008 - 15:03:58 CST)
  • AMBER: sander error on Make test.serial (Wed Feb 13 2008 - 14:26:25 CST)
• Fan Yanping
  • AMBER: internal energy INT is not zero from MM_GBSA (Tue Oct 07 2008 - 01:08:14 CDT)
• fatima.chami_at_durham.ac.uk
  • Re: AMBER: RE: Personal favor (Mon Sep 01 2008 - 06:29:46 CDT)
  • Re: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 07:53:42 CDT)
  • AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 05:47:17 CDT)
  • Re: AMBER: vdw 6-9 potential (Tue Aug 26 2008 - 11:03:55 CDT)
  • Re: AMBER: vdw 6-9 potential (Sat Aug 23 2008 - 05:34:57 CDT)
  • AMBER: vdw 6-9 potential (Fri Aug 22 2008 - 15:56:57 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 15:46:11 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 08:31:34 CDT)
  • AMBER: all & united atoms force field (Thu Aug 21 2008 - 17:05:12 CDT)
  • AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 08:41:24 CDT)
  • RE: AMBER: ptraj problem with imaging (Thu Jul 03 2008 - 11:11:19 CDT)
  • AMBER: ptraj problem with imaging (Wed Jul 02 2008 - 11:52:32 CDT)
  • AMBER: RDF in ptraj (Tue Jul 01 2008 - 08:34:35 CDT)
  • AMBER: (no subject) (Mon Jun 30 2008 - 11:26:23 CDT)
  • AMBER: wrapping a restart file (Mon Jun 30 2008 - 09:40:58 CDT)
  • Re: AMBER: hold atoms fixed (Mon Jun 30 2008 - 08:16:09 CDT)
  • AMBER: Constrained group (Mon Jun 30 2008 - 04:54:02 CDT)
  • AMBER: Group specification problem (Fri Jun 27 2008 - 07:59:09 CDT)
  • Re: SV: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 11:05:36 CDT)
  • Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? (Thu Jun 19 2008 - 11:00:32 CDT)
  • Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? (Thu Jun 19 2008 - 09:47:50 CDT)
  • RE: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 08:46:22 CDT)
  • RE: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 08:43:39 CDT)
  • AMBER: how to extract x,y,z of a set of atoms from an MD trajectories (Thu Jun 19 2008 - 04:16:52 CDT)
  • AMBER: cross correlation function using iRED matrix (Wed Jun 18 2008 - 12:07:25 CDT)
  • AMBER: ptraj (Wed Jun 18 2008 - 10:21:50 CDT)
  • AMBER: Eigenmode dynamics - imaging traj (Wed Jun 18 2008 - 05:09:26 CDT)
  • Re: AMBER: multiple dihedral restraints using group (in Amber 10) (Wed Jun 18 2008 - 05:05:40 CDT)
  • AMBER: IRED to time correlation (Mon Jun 16 2008 - 15:25:22 CDT)
  • AMBER: Eigenmode dynamics in Ptraj (Mon Jun 16 2008 - 07:59:42 CDT)
  • Re: AMBER: SMD RESTRAINTS (Thu Jun 12 2008 - 12:07:49 CDT)
  • AMBER: SMD RESTRAINTS (Thu Jun 12 2008 - 11:23:00 CDT)
  • AMBER: anisotropic pressure scaling ntp=2 (Thu Jun 12 2008 - 08:18:13 CDT)
  • AMBER: box shape changed at NVT (Wed Jun 11 2008 - 09:25:09 CDT)
  • AMBER: SMD pulling velocity (Tue Jun 10 2008 - 09:06:38 CDT)
  • Re: AMBER: Free energy of dissociation (Thu Jun 05 2008 - 10:13:03 CDT)
  • AMBER: Free energy of dissociation (Thu Jun 05 2008 - 07:02:43 CDT)
  • Re: AMBER: solvate box : buffer list (Wed Jun 04 2008 - 05:07:06 CDT)
  • AMBER: solvate box : buffer list (Tue Jun 03 2008 - 12:51:55 CDT)
  • Re: AMBER: Jarzynski (Sat May 31 2008 - 06:50:24 CDT)
  • AMBER: Jarzynski (Fri May 30 2008 - 06:44:41 CDT)
  • AMBER: solvatebox (Thu May 29 2008 - 06:46:42 CDT)
  • AMBER: PBC in 2D (Fri May 23 2008 - 08:13:39 CDT)
  • AMBER: COM RESTRAINT (Thu May 22 2008 - 07:17:09 CDT)
  • Re: AMBER: STEERED MD (Sat May 17 2008 - 05:26:28 CDT)
  • AMBER: STEERED MD (Fri May 16 2008 - 11:25:55 CDT)
  • Re: AMBER: cross time correlation function (Wed Apr 23 2008 - 12:00:43 CDT)
  • AMBER: cross time correlation function (Wed Apr 23 2008 - 07:55:28 CDT)
  • AMBER: Scale LJ parameters (Thu Apr 17 2008 - 06:20:40 CDT)
  • AMBER: TI: perturbation method (Mon Mar 31 2008 - 03:40:40 CDT)
  • AMBER: united atom force field: antechamber (Tue Feb 19 2008 - 15:59:42 CST)
  • AMBER: time autocorrelation: ?? (Mon Feb 04 2008 - 12:05:47 CST)
  • AMBER: LEAP: solute concentration (Thu Jan 31 2008 - 09:12:24 CST)
  • Re: AMBER: problem to compile PMEMD? (Tue Jan 29 2008 - 18:10:48 CST)
  • AMBER: problem to compile PMEMD? (Tue Jan 29 2008 - 16:45:41 CST)
  • Re: AMBER: Amber parallel version on CPU power of 2 only (Tue Jan 29 2008 - 15:04:56 CST)
  • RE: AMBER: Amber parallel version on CPU power of 2 only (Tue Jan 29 2008 - 12:19:22 CST)
  • AMBER: Amber parallel version on CPU power of 2 only (Tue Jan 29 2008 - 07:38:34 CST)
• Fenghui Fan
  • RE: AMBER: change in secondary structure during MD (Thu Feb 28 2008 - 16:48:53 CST)
  • AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein (Thu Feb 28 2008 - 08:38:23 CST)
• finke_at_oakland.edu
  • Re: AMBER: Example .prepi file for nonstandard amino acids (Fri May 02 2008 - 20:06:30 CDT)
  • AMBER: Example .prepi file for nonstandard amino acids (Fri May 02 2008 - 17:00:45 CDT)
  • Re: AMBER: Compiler issues with Altix450 (Mon Mar 10 2008 - 15:45:37 CDT)
  • AMBER: Compiler issues with Altix450 (Sat Mar 08 2008 - 12:37:25 CST)
• Fiona McRobb
  • RE: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender (Wed Aug 13 2008 - 00:09:49 CDT)
  • AMBER: GPCR membrane simulation, setting surface tension (Mon Aug 11 2008 - 20:42:47 CDT)
• Florian Haberl
  • Re: AMBER: pdb structure is only half the molecule. (Fri Oct 24 2008 - 05:18:45 CDT)
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 07:47:21 CDT)
  • Re: AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 08:41:31 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 10:31:18 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 10:06:42 CDT)
  • Re: AMBER: how to overcome theunusual bonds formation (Thu May 29 2008 - 06:54:20 CDT)
  • Re: AMBER: trajectories into trajectory (Sun May 25 2008 - 07:10:41 CDT)
  • Re: AMBER: (Thu Apr 17 2008 - 10:17:24 CDT)
  • Re: AMBER: amber :antechamber problem (Mon Jan 07 2008 - 10:33:02 CST)
• Floris Buelens
  • AMBER: improving GAFF sulfonamide parameters (Tue Jun 17 2008 - 04:57:46 CDT)
• flyanping
  • AMBER: internal energy INT is not zero from MM_GBSA (Tue Oct 07 2008 - 01:18:49 CDT)
• Francesca Poletti
  • AMBER: Differentiating the force constant of distance restraints (Thu Oct 16 2008 - 03:40:16 CDT)
• Francesco Pietra
  • Re: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 05:13:13 CST)
  • Re: AMBER: Heating up (Fri Nov 28 2008 - 09:57:49 CST)
  • Re: AMBER: Setting GROUP for pmemd (Fri Nov 28 2008 - 04:12:07 CST)
  • Re: AMBER: Setting GROUP for pmemd (Fri Nov 28 2008 - 04:12:07 CST)
  • AMBER: Heating up (Thu Nov 27 2008 - 12:29:30 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:47:35 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 14:59:35 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 02:00:38 CST)
  • Re: AMBER: RE: About restart amber (Mon Nov 24 2008 - 15:22:44 CST)
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 09:33:43 CST)
  • AMBER: GB versus explicit medium (Mon Nov 24 2008 - 03:39:58 CST)
  • Re: AMBER: RE: About restart amber (Sat Nov 22 2008 - 10:03:02 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 12:44:21 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 10:38:29 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 15:30:54 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 13:21:01 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 12:00:25 CST)
  • Fwd: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:35:04 CST)
  • AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:15:17 CST)
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Sun Nov 16 2008 - 05:17:00 CST)
  • AMBER: Chloride anion ligands leave the protein during MD (Thu Nov 13 2008 - 09:06:06 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Tue Nov 04 2008 - 01:27:55 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 12:07:14 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:17:34 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:08:42 CST)
  • AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 02:58:58 CST)
  • Re: AMBER: how to ger resp charge for a residue? (Fri Oct 31 2008 - 02:59:31 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Fri Oct 31 2008 - 01:25:44 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 18:28:37 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 16:56:27 CDT)
  • AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 14:10:39 CDT)
  • Re: AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 13:57:40 CDT)
  • Re: AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 11:33:57 CDT)
  • AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 04:32:39 CDT)
  • Re: AMBER: Atom names CL and four characters (Fri Oct 24 2008 - 17:44:31 CDT)
  • AMBER: Atom names CL and four characters (Fri Oct 24 2008 - 13:55:05 CDT)
  • Re: AMBER: Does LEaP understant capping with ACE/NME? (Tue Oct 21 2008 - 12:31:36 CDT)
  • AMBER: Does LEaP understant capping with ACE/NME? (Tue Oct 21 2008 - 10:57:12 CDT)
  • Fwd: AMBER: Restricting the system to simulate (Sat Oct 18 2008 - 02:44:19 CDT)
  • AMBER: Restricting the system to simulate (Fri Oct 17 2008 - 11:00:50 CDT)
  • AMBER: capping with non charged residues (Thu Oct 16 2008 - 17:24:44 CDT)
  • Re: Fwd: AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 17:58:08 CDT)
  • Fwd: AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 12:58:33 CDT)
  • Re: AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 08:42:55 CDT)
  • AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 05:26:25 CDT)
  • AMBER: LEU as first residue (Mon Oct 13 2008 - 11:20:00 CDT)
  • AMBER: PDB standards (Mon Oct 13 2008 - 03:18:23 CDT)
  • AMBER: Parameters for alkali cations and halogen anions (Sun Oct 05 2008 - 02:29:45 CDT)
  • Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL (Thu Oct 02 2008 - 16:35:45 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Thu Oct 02 2008 - 14:15:54 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Thu Oct 02 2008 - 10:47:31 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Tue Sep 30 2008 - 05:05:13 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Mon Sep 29 2008 - 15:13:05 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 14:31:51 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 13:11:49 CDT)
  • AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 08:46:10 CDT)
  • Re: AMBER: Leap atoms CL and OXT do not have a type (Sat Sep 27 2008 - 10:36:47 CDT)
  • AMBER: Failure of antechamber in amber10 (Sun Sep 14 2008 - 09:18:49 CDT)
  • AMBER: Parameters for chloride ion in contact with a protein (Mon Aug 25 2008 - 09:25:13 CDT)
  • AMBER: Biased MD with Amber 10 (Mon Aug 04 2008 - 13:35:31 CDT)
  • AMBER: PDB files in Amber10 (Sat Aug 02 2008 - 02:21:58 CDT)
  • AMBER: Seed for random number generator (Sun Jun 29 2008 - 03:22:12 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Sat Jun 28 2008 - 12:22:44 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Fri Jun 27 2008 - 17:02:21 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 12:29:12 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Wed Jun 25 2008 - 03:17:59 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 16:52:09 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 11:28:18 CDT)
  • AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 09:32:54 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Thu Jun 12 2008 - 02:09:28 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Wed Jun 11 2008 - 09:57:59 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Tue Jun 10 2008 - 02:37:34 CDT)
  • AMBER: Combine mdcrd while stripping WAT problem (Sun Jun 08 2008 - 10:40:07 CDT)
  • Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' (Mon Jun 02 2008 - 05:22:38 CDT)
  • RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' (Sun Jun 01 2008 - 02:12:12 CDT)
  • Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' (Sat May 31 2008 - 13:31:04 CDT)
  • Fw: RE: Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 31 2008 - 09:22:35 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 31 2008 - 01:44:24 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 12:59:35 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 12:47:57 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 10:17:15 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Fri May 30 2008 - 04:40:41 CDT)
  • AMBER: Fw: rmsd vs frame (Wed May 28 2008 - 18:19:11 CDT)
  • AMBER: rmsd vs frame (Wed May 28 2008 - 17:56:24 CDT)
  • AMBER: Fw: Amber9 vs Amber10+MKL benchmark (Sat May 24 2008 - 09:50:45 CDT)
  • AMBER: Fw: Amber9 vs Amber10+MKL benchmark (Sat May 24 2008 - 08:51:53 CDT)
  • AMBER: Amber9 vs Amber10+MKL benchmark (Sat May 24 2008 - 08:48:12 CDT)
  • RE: AMBER: how to extract energy (Sat May 24 2008 - 02:24:13 CDT)
  • Re: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 12:48:49 CDT)
  • RE: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 10:44:10 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 22 2008 - 05:06:48 CDT)
  • Re: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 04:14:55 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Wed May 21 2008 - 14:09:10 CDT)
  • AMBER: $AMBERHOME/dat/slko (Wed May 21 2008 - 07:47:59 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 16:17:25 CDT)
  • Re: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 10:24:43 CDT)
  • Fw: RE: AMBER: MKL libraries/Amber10 (Sun May 18 2008 - 12:33:54 CDT)
  • Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 17 2008 - 16:14:18 CDT)
  • Fw: RE: AMBER: MKL libraries/Amber10 (Sat May 17 2008 - 12:33:10 CDT)
  • RE: AMBER: MKL libraries/Amber10 (Sat May 17 2008 - 12:12:06 CDT)
  • RE: AMBER: MKL libraries/Amber10 (Fri May 16 2008 - 11:31:17 CDT)
  • AMBER: MKL libraries/Amber10 (Thu May 15 2008 - 13:01:34 CDT)
  • AMBER: Solvent mixture box (Sun May 11 2008 - 12:04:52 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Sat Apr 26 2008 - 15:56:13 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Sat Apr 26 2008 - 02:01:46 CDT)
  • Fw: Re: AMBER: AMD Opteron: compiler recommendations? (Sat Apr 26 2008 - 02:05:18 CDT)
  • RE: AMBER: Average structure (Tue Apr 22 2008 - 02:02:23 CDT)
  • Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? (Wed Mar 19 2008 - 12:26:24 CDT)
  • Re: AMBER: Atom types/parameters for chromene (Wed Mar 05 2008 - 12:07:05 CST)
  • Fwd: Re: AMBER: xleap screen output SOLVED (Tue Mar 04 2008 - 14:44:15 CST)
  • Fwd: Re: AMBER: xleap screen output (Tue Mar 04 2008 - 11:33:34 CST)
  • Re: AMBER: xleap screen output (Tue Mar 04 2008 - 11:27:00 CST)
  • Re: AMBER: xleap screen output (Mon Mar 03 2008 - 15:48:59 CST)
  • AMBER: xleap screen output (Mon Mar 03 2008 - 15:02:54 CST)
  • Re: AMBER: Amber: shared memory vs cluster (Wed Feb 27 2008 - 15:00:32 CST)
  • AMBER: Amber: shared memory vs cluster (Wed Feb 27 2008 - 12:08:19 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 12:14:56 CST)
  • Re: AMBER: compiling PMEMD with MKL10.0 (Tue Feb 26 2008 - 05:00:32 CST)
  • AMBER: Reference for rmsd (Mon Jan 28 2008 - 11:51:02 CST)
  • Re: AMBER: Installing OpenMPI (Wed Jan 23 2008 - 12:18:44 CST)
  • AMBER: Re: Systematic drift (Wed Jan 23 2008 - 01:23:07 CST)
  • AMBER: Systematic drift (Tue Jan 22 2008 - 16:06:46 CST)
  • AMBER: Fwd: Distorsion in protein and ligand during MD (Sun Jan 13 2008 - 03:57:43 CST)
  • AMBER: Distorsion in protein and ligand during MD (Sun Jan 13 2008 - 03:46:23 CST)
  • AMBER: Cluster analysis (Mon Jan 07 2008 - 10:00:40 CST)
  • Re: AMBER: About RAMD (Sat Jan 05 2008 - 10:26:01 CST)
  • AMBER: About RAMD (Sat Jan 05 2008 - 04:39:44 CST)
  • Re: Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 15:26:32 CST)
  • Fwd: Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 11:36:49 CST)
  • Fwd: Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 11:23:45 CST)
  • Re: AMBER: Combine mdcrd (Fri Jan 04 2008 - 11:07:15 CST)
  • AMBER: Combine mdcrd (Fri Jan 04 2008 - 10:37:07 CST)
  • AMBER: Combine mdcrd files (Thu Jan 03 2008 - 17:01:47 CST)
• Francois Theillet
  • AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters (Fri Nov 07 2008 - 09:24:36 CST)
• frustrated modeller
  • AMBER: bye (Mon May 19 2008 - 13:29:40 CDT)
• Furia Gargano
  • AMBER: rmsd per residue (Tue May 06 2008 - 09:28:59 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: B-factor (Tue Apr 01 2008 - 14:05:36 CDT)
  • AMBER: atomic posiltional fluctuation (Tue Apr 01 2008 - 09:11:12 CDT)
• FyD
  • Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 08:19:15 CST)
  • Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 02:45:01 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Wed Dec 17 2008 - 03:12:38 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III (Tue Dec 16 2008 - 06:17:15 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 16:05:46 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 14:41:24 CST)
  • Re: AMBER: building new ions (Mon Dec 15 2008 - 08:09:04 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Sat Dec 13 2008 - 02:02:23 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Sat Dec 13 2008 - 01:23:10 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 12:24:25 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 11:14:05 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 09:16:01 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 08:25:06 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Thu Dec 11 2008 - 05:42:20 CST)
  • Re: AMBER: reg-antichamber run (Thu Dec 11 2008 - 03:57:26 CST)
  • Re: AMBER: RED vIII-lack of charges in mol2 (Sat Nov 29 2008 - 10:23:34 CST)
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Sat Nov 29 2008 - 01:30:19 CST)
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 10:02:55 CST)
  • Re: AMBER: problem (Mon Nov 17 2008 - 01:40:33 CST)
  • Re: AMBER: organic solvents (Sat Nov 15 2008 - 01:56:30 CST)
  • Re: AMBER: how to ger resp charge for a residue? (Fri Oct 31 2008 - 08:21:13 CDT)
  • Re: AMBER: how to ger resp charge for a residue? (Fri Oct 31 2008 - 01:33:42 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Wed Oct 29 2008 - 02:19:41 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Wed Oct 22 2008 - 10:15:15 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sun Oct 19 2008 - 03:12:03 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sat Oct 18 2008 - 16:30:33 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sat Oct 18 2008 - 06:54:56 CDT)
  • Re: AMBER: xleap fails to savemol2 (Tue Oct 14 2008 - 14:15:48 CDT)
  • Re: AMBER: amber: parameters for 5' nucleotide monophosphates (Mon Oct 13 2008 - 14:44:47 CDT)
  • Re: AMBER: Question about resp charges for a charged molecule... (Fri Oct 10 2008 - 08:37:48 CDT)
  • Fwd: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Thu Oct 09 2008 - 11:57:07 CDT)
  • Re: AMBER: xleap fails to savemol2 (Thu Oct 09 2008 - 01:54:05 CDT)
  • Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Wed Oct 08 2008 - 14:00:33 CDT)
  • Re: AMBER: Ac-Co Parameters for Amber (Wed Oct 01 2008 - 16:26:54 CDT)
  • Re: AMBER: Ac-Co Parameters for Amber (Wed Oct 01 2008 - 01:14:39 CDT)
  • Re: AMBER: to prepare pdb file fro unusual amino acid. (Wed Sep 24 2008 - 13:36:03 CDT)
  • Re: AMBER: xleap fails to savemol2 (Thu Sep 04 2008 - 14:45:49 CDT)
  • AMBER: ptraj & imaging of velocities (Tue Sep 02 2008 - 08:06:08 CDT)
  • Re: AMBER: xleap fails to savemol2 (Sat Aug 30 2008 - 01:58:21 CDT)
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 16:14:42 CDT)
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 10:19:23 CDT)
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 02:50:42 CDT)
  • Re: AMBER: xleap fails to savemol2 (Thu Aug 28 2008 - 23:58:08 CDT)
  • Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? (Mon Jul 28 2008 - 07:28:50 CDT)
  • RE: AMBER: RED III execution problem (Mon Jul 07 2008 - 15:54:30 CDT)
  • Re: AMBER: RESP calculation on Copper containing molecule (Fri Jul 04 2008 - 05:25:42 CDT)
  • Re: AMBER: RED III execution problem (Thu Jul 03 2008 - 04:25:24 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Sun Jun 29 2008 - 08:18:15 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Sat Jun 28 2008 - 02:47:54 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Fri Jun 27 2008 - 04:07:45 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 15:53:20 CDT)
  • Re: AMBER: about resp charges (Tue Jun 17 2008 - 07:58:03 CDT)
  • Re: AMBER: Coordinated Zinc (Fri Jun 13 2008 - 02:56:08 CDT)
  • Re: AMBER: Iron-Sulfur Cluster (Sat May 31 2008 - 07:35:31 CDT)
  • Re: AMBER: RESP charges of an unusual substrate (Mon May 19 2008 - 01:46:40 CDT)
  • Re: AMBER: neutral C-terminus and N-terminus parameters for amber (Sat May 10 2008 - 02:52:10 CDT)
  • Re: AMBER: Deriving Force Field Parameters (Mon May 05 2008 - 09:14:22 CDT)
  • Re: AMBER: Cysteine sulphonic acid parameters (Thu May 01 2008 - 07:03:19 CDT)
  • RE: AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 08:32:30 CDT)
  • RE: AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 06:19:49 CDT)
  • Re: AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 05:31:39 CDT)
  • Re: AMBER: FAD and NAD parameters (Wed Mar 26 2008 - 05:57:27 CDT)
  • Re: AMBER: anion and cation simulaton (Tue Mar 25 2008 - 14:54:56 CDT)
  • AMBER: RE: Force Field Parameterizing (Tue Mar 25 2008 - 14:42:03 CDT)
  • Re: AMBER: Charge scheme for simulating protonated adenine (Fri Mar 21 2008 - 02:43:51 CDT)
  • Re: AMBER: charge derivation for modified amino acids (Wed Feb 27 2008 - 00:35:10 CST)
  • Re: AMBER: mol2 save (Tue Feb 26 2008 - 11:38:40 CST)
  • RE: AMBER: Is boiling point a good way to validate solvent paramters? (Sat Feb 16 2008 - 01:31:14 CST)
  • Re: AMBER: RESP (Wed Jan 30 2008 - 23:47:38 CST)
  • Re: AMBER: flexible molecule parameterization (Sun Jan 27 2008 - 08:09:37 CST)
  • Re: AMBER: PEO-PLA/PCE (Fri Jan 18 2008 - 14:42:06 CST)
  • Re: AMBER: Help in radii (Wed Jan 16 2008 - 14:31:07 CST)
  • Re: AMBER: chromophore parameters for Molecular Dynamics (Wed Jan 16 2008 - 08:59:31 CST)
  • Re: AMBER: chromophore parameters for Molecular Dynamics (Fri Jan 11 2008 - 14:57:19 CST)
  • Re: AMBER: ANTECHAMBER NAMING (Fri Jan 11 2008 - 01:53:04 CST)
  • Re: AMBER: RESP (Thu Jan 10 2008 - 01:39:01 CST)
  • Re: AMBER: RESP (Tue Jan 08 2008 - 13:49:31 CST)
  • Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine (Fri Jan 04 2008 - 04:34:00 CST)
  • Re: AMBER: Help reg. input file (Wed Jan 02 2008 - 14:21:03 CST)
  • Re: AMBER: Help reg. input file (Wed Jan 02 2008 - 13:34:40 CST)
  • Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine (Wed Jan 02 2008 - 02:52:15 CST)
• Geoff Wood
  • AMBER: amber 9 on Intel Harpertown (Wed Aug 13 2008 - 04:45:36 CDT)
  • Re: AMBER: Hybrid REMD amber10 (Tue May 20 2008 - 09:24:11 CDT)
  • AMBER: Hybrid REMD amber10 (Mon May 19 2008 - 07:41:54 CDT)
  • AMBER: hybrid remd imaging (Tue Apr 01 2008 - 02:47:18 CDT)
  • AMBER: installation amber9 (Mon Mar 31 2008 - 06:02:01 CDT)
  • Re: AMBER: hybrid remd imaging (Thu Mar 27 2008 - 07:56:30 CDT)
  • Re: AMBER: hybrid remd imaging (Mon Mar 24 2008 - 11:16:25 CDT)
  • Re: AMBER: hybrid remd imaging (Mon Mar 24 2008 - 11:21:41 CDT)
  • AMBER: hybrid remd imaging (Mon Mar 24 2008 - 10:51:51 CDT)
• George Tzotzos
  • AMBER: AMBER10: Fortran Runtime Error (Fri Jul 25 2008 - 10:19:03 CDT)
  • AMBER: AMBER 10: Fortran Runtime Error (Fri Jul 25 2008 - 09:38:32 CDT)
  • AMBER: Installation of Amber 10 on Dual-Core Intel Mac (Fri Jul 11 2008 - 15:33:55 CDT)
  • AMBER: Installation on Mac OSX G5 dual processor (Fri Jul 11 2008 - 15:30:21 CDT)
• Germain Vallverdu
  • Re: AMBER: input (Tue Oct 21 2008 - 04:36:40 CDT)
  • Re: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 06:02:49 CDT)
  • Re: AMBER: Differentiating the force constant of distance restraints (Thu Oct 16 2008 - 04:07:07 CDT)
  • Re: AMBER: AddIons approach (Fri Oct 10 2008 - 06:23:00 CDT)
  • Re: AMBER: Question about resp charges for a charged molecule... (Fri Oct 10 2008 - 06:20:45 CDT)
  • Re: AMBER: increasing temperature smoothly (Mon Sep 22 2008 - 04:00:19 CDT)
  • Re: AMBER: increasing temperature smoothly (Mon Sep 22 2008 - 06:31:56 CDT)
  • AMBER: increasing temperature smoothly (Fri Sep 19 2008 - 10:17:56 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 07:10:49 CDT)
  • Re: AMBER: steered MD (Wed Sep 10 2008 - 06:17:10 CDT)
  • AMBER: steered MD (Wed Sep 10 2008 - 05:26:31 CDT)
  • AMBER: PMEMD and sander.MPI (Tue Sep 09 2008 - 08:50:40 CDT)
  • Re: AMBER: Using AMBER forces (Tue Sep 09 2008 - 08:48:32 CDT)
  • AMBER: targeted MD (Tue Jul 22 2008 - 05:08:04 CDT)
  • AMBER: dihedral potential with odd periodicity (Tue Jun 24 2008 - 09:43:26 CDT)
  • AMBER: source of AMBER9 (Mon Jun 23 2008 - 09:09:29 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 15:24:55 CDT)
  • Re: AMBER: restarting molecular dynamics (Wed May 28 2008 - 09:25:23 CDT)
  • AMBER: restarting molecular dynamics (Wed May 28 2008 - 08:18:16 CDT)
• German Erlenkamp
  • AMBER: Umbrella Sampling for proteins (Mon May 26 2008 - 04:23:56 CDT)
• Gert Kiss
  • AMBER: normal-vector of a plane with 'corrplane' (Thu Nov 27 2008 - 14:28:46 CST)
• Gigil Toton
  • AMBER: net charge (Wed Aug 27 2008 - 00:03:19 CDT)
  • AMBER: NMR average structure (Wed Aug 20 2008 - 12:42:08 CDT)
  • AMBER: general question (Wed Aug 13 2008 - 01:49:12 CDT)
• Giuseppe De Marco
  • AMBER: topology file (Mon Apr 14 2008 - 04:38:37 CDT)
• Gohlke_at_bioinformatik.uni-frankfurt.de
  • Re: AMBER: mmpbsa INSTRNG error? (Sun Mar 09 2008 - 11:13:05 CDT)
• Grange Hermitage
  • AMBER: fix for POL3 heating problem? (Mon Sep 22 2008 - 04:35:02 CDT)
  • AMBER: RESP charges fitting for polarizable force fields (Sat Aug 30 2008 - 23:48:37 CDT)
  • AMBER: new residues in AMOEBA (Thu Aug 21 2008 - 02:14:59 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 19:30:25 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 04:01:38 CDT)
  • AMBER: trying ff99SP (Mon Aug 18 2008 - 01:12:33 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 00:04:18 CDT)
  • Re: AMBER: Prepgen (Sun Aug 17 2008 - 22:22:32 CDT)
  • AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Sun Aug 17 2008 - 21:28:17 CDT)
  • Re: AMBER: Prepgen (Fri Aug 15 2008 - 01:12:50 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 22:08:49 CDT)
  • AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 20:12:05 CDT)
  • Re: AMBER: Prepgen (Mon Aug 11 2008 - 02:10:00 CDT)
  • AMBER: respgen -a charge groups function ineffective unless (Sat Aug 02 2008 - 00:00:29 CDT)
  • Re: AMBER: Prepgen (Thu Jul 31 2008 - 22:21:54 CDT)
  • Re: AMBER: Prepgen (Thu Jul 31 2008 - 21:29:45 CDT)
  • AMBER: antechamber generated input for gaussian error (Sat Jul 19 2008 - 19:53:49 CDT)
  • Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Mon Jul 14 2008 - 19:18:40 CDT)
  • Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Mon Jul 14 2008 - 02:41:40 CDT)
  • AMBER: POL3 with gaff and ff02EP (Sun Jul 13 2008 - 20:15:43 CDT)
  • AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Sun Jul 13 2008 - 20:06:33 CDT)
• greddy1_at_umd.edu
  • AMBER: Harmonic restraint between two atoms (Fri Sep 26 2008 - 13:37:34 CDT)
  • AMBER: replica exchange with amber9 (Tue Sep 23 2008 - 17:44:24 CDT)
• guardiani_at_fi.infn.it
  • AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 13:29:08 CST)
  • AMBER: REMD temperature profile (Wed Jul 09 2008 - 08:47:13 CDT)
  • Re: AMBER: Force fields for REMD with GB solvent (Wed Jul 09 2008 - 04:37:43 CDT)
  • AMBER: Force fields for REMD with GB solvent (Tue Jul 08 2008 - 11:24:27 CDT)
  • AMBER: Minimization in Octahedric Box (Tue May 06 2008 - 06:31:50 CDT)
• Guillaume Renvez
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Mon Jun 23 2008 - 03:27:27 CDT)
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Tue Jun 17 2008 - 02:48:34 CDT)
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Tue Jun 17 2008 - 02:50:33 CDT)
  • AMBER: [Fwd: segmentation fault in nmode] (Mon Jun 16 2008 - 09:31:12 CDT)
  • AMBER: REMD simulation error (Wed Apr 02 2008 - 07:47:20 CDT)
  • AMBER: REMD simulation error (Fri Mar 28 2008 - 09:01:20 CDT)
  • Re: AMBER: replica exchange : problem with sander (Thu Mar 20 2008 - 10:02:29 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 08:57:55 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 08:35:55 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 08:13:01 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 07:14:38 CDT)
  • Re: AMBER: replica exchange : problem with sander (Wed Mar 19 2008 - 07:14:38 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 12:24:10 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 12:07:54 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 11:21:21 CDT)
  • Re: AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 10:29:39 CDT)
  • AMBER: replica exchange : problem with sander (Tue Mar 18 2008 - 09:09:34 CDT)
• Guillermo Mulliert Carlín
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 01:20:30 CST)
  • AMBER: cluster for running amber10 (Tue Sep 30 2008 - 10:14:07 CDT)
  • Re: AMBER: Mn2+ parameters in AMBER (Fri May 23 2008 - 01:26:51 CDT)
• gurpreet singh
  • Re: AMBER: Res minimization (Tue Jul 15 2008 - 23:25:54 CDT)
  • Re: AMBER: RMSD per residue (Tue Jul 15 2008 - 23:13:59 CDT)
  • AMBER: Constat area simulation (Wed Apr 30 2008 - 06:23:35 CDT)
  • AMBER: Regarding SHAKE (Sun Mar 30 2008 - 05:38:48 CDT)
  • AMBER: anion and cation simulaton (Tue Mar 25 2008 - 11:22:29 CDT)
  • AMBER: distance restraint (Thu Mar 13 2008 - 06:28:28 CDT)
  • AMBER: Antechamber, net molecular charge (Sun Mar 09 2008 - 23:51:58 CDT)
  • Re: AMBER: regarding:calculation of b factor using ptraj (Sun Mar 02 2008 - 11:24:29 CST)
  • Re: AMBER: antechamber problem (Thu Jan 10 2008 - 22:05:38 CST)
  • AMBER: antechamber problem (Thu Jan 10 2008 - 11:49:15 CST)
• gurvisha_at_leadinvent.com
  • AMBER: query about Generalized Born simulation (Fri Apr 11 2008 - 08:42:23 CDT)
• Gustavo Seabra
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Thu Dec 18 2008 - 08:58:13 CST)
  • Re: AMBER: using packmol file in Amber (Mon Dec 15 2008 - 10:39:53 CST)
  • Re: AMBER: Radial Distribution Function (Mon Dec 15 2008 - 01:41:02 CST)
  • Re: AMBER: Radial Distribution Function (Wed Dec 10 2008 - 07:49:42 CST)
  • Re: AMBER: Radial Distribution Function (Tue Dec 09 2008 - 09:38:54 CST)
  • Re: AMBER: subroutine Work : Jarynski work theorem (Wed Dec 03 2008 - 07:59:06 CST)
  • Re: AMBER: QM/MM and unpaired spin (Wed Dec 03 2008 - 07:53:00 CST)
  • Re: AMBER: QM/MM and unpaired spin (Tue Dec 02 2008 - 21:11:25 CST)
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 13:19:22 CST)
  • Re: AMBER: ptraj closest command (Mon Nov 17 2008 - 10:51:42 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 10:05:42 CST)
  • Re: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 14:30:21 CST)
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 07:40:45 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:48:01 CST)
  • Re: AMBER: Steered MD and Jarzynski in pulling simulations (Sun Nov 09 2008 - 20:36:38 CST)
  • Re: AMBER: peptide MD (Mon Oct 27 2008 - 12:52:25 CDT)
  • Re: AMBER: peptide MD (Mon Oct 27 2008 - 12:36:35 CDT)
  • Re: AMBER: atom type for carbon and nitrogen atoms (Mon Oct 27 2008 - 12:28:31 CDT)
  • Re: AMBER: stripping water from a restart file (Mon Oct 27 2008 - 12:12:04 CDT)
  • Re: AMBER: Conversion between truncated octahedron and orthorohombic box (Mon Oct 27 2008 - 12:19:59 CDT)
  • Re: AMBER: pdb structure is only half the molecule. (Thu Oct 23 2008 - 15:19:05 CDT)
  • Re: AMBER: scyld beowulf --amber10--openmpi (Mon Oct 20 2008 - 21:56:35 CDT)
  • Re: AMBER: question about simulation box (Mon Oct 20 2008 - 08:09:03 CDT)
  • Re: AMBER: using ptraj (Fri Oct 17 2008 - 20:35:23 CDT)
  • Re: AMBER: Clarification re qmmask (Thu Oct 16 2008 - 13:22:41 CDT)
  • Re: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 10:16:39 CDT)
  • Re: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 08:34:56 CDT)
  • Re: AMBER: Origin of periodic box (Thu Oct 16 2008 - 08:24:50 CDT)
  • Re: AMBER: Installation Error (Wed Oct 15 2008 - 08:21:14 CDT)
  • Re: AMBER: amber10 installation problem in cygwin (Tue Oct 14 2008 - 10:56:20 CDT)
  • Re: AMBER: Sources of disruption during NVE (Fri Oct 03 2008 - 08:39:05 CDT)
  • Re: AMBER: Sources of disruption during NVE (Wed Oct 01 2008 - 14:32:06 CDT)
  • Re: AMBER: FW: Amber 9 (Tue Sep 30 2008 - 14:12:19 CDT)
  • Re: AMBER: The forming of micelle (CMC) (Wed Sep 24 2008 - 17:00:45 CDT)
  • Re: AMBER: problems with ptraj and strip waters (Thu Sep 18 2008 - 18:18:44 CDT)
  • Re: AMBER: xleap and Sirius on ubuntu 8.04 (Thu Sep 11 2008 - 22:13:58 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 14:07:28 CDT)
  • Re: AMBER: Install problems (Mon Sep 08 2008 - 13:58:02 CDT)
  • Re: AMBER: Which CO2 potential? (Thu Jul 24 2008 - 08:08:53 CDT)
  • Re: AMBER: SCC-DFTB for Zinc atom (Fri Jul 18 2008 - 18:21:45 CDT)
  • Re: AMBER: SCC-DFTB for Zinc atom (Thu Jul 17 2008 - 10:48:33 CDT)
  • Re: AMBER: about RMSD per residue (Wed Jul 16 2008 - 10:22:39 CDT)
  • Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. (Wed Jul 16 2008 - 09:08:45 CDT)
  • Re: AMBER: about QMMM output (Fri Jul 04 2008 - 10:33:06 CDT)
  • Re: AMBER: wrapping a restart file (Mon Jun 30 2008 - 10:31:53 CDT)
  • Re: AMBER: hold atoms fixed (Mon Jun 30 2008 - 09:10:53 CDT)
  • Re: AMBER: qmmm_DFTB problem (Tue Jun 24 2008 - 09:31:15 CDT)
  • Re: AMBER: Compile amber10 parallel with suppied LAM (Thu Jun 12 2008 - 13:20:24 CDT)
  • Re: AMBER: Compile amber10 parallel with suppied LAM (Thu Jun 12 2008 - 12:39:34 CDT)
  • Re: AMBER: QM/MM (Wed Jun 11 2008 - 10:22:16 CDT)
  • Re: AMBER: SMD pulling velocity (Tue Jun 10 2008 - 09:22:48 CDT)
  • Re: AMBER: Combine mdcrd while stripping WAT problem (Sun Jun 08 2008 - 13:58:34 CDT)
  • Re: AMBER: Free energy of dissociation (Thu Jun 05 2008 - 08:41:03 CDT)
  • Re: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 13:41:41 CDT)
  • Re: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 12:00:36 CDT)
  • Re: AMBER: $AMBERHOME/dat/slko (Wed May 21 2008 - 09:29:35 CDT)
  • Re: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 09:18:07 CDT)
  • Re: AMBER: MKL libraries/Amber10 (Thu May 15 2008 - 18:02:42 CDT)
  • Re: AMBER: Amber10:Compiling with gcc 2.4.1 (Thu May 15 2008 - 17:58:05 CDT)
  • Re: AMBER: divcon (Tue May 13 2008 - 12:43:35 CDT)
  • Re: AMBER: help to install AMBER9 (Mon May 12 2008 - 09:56:41 CDT)
  • Re: AMBER: help to install AMBER9 (Fri May 09 2008 - 10:01:04 CDT)
  • Re: AMBER: QM/MM (Fri May 09 2008 - 09:18:21 CDT)
  • Re: AMBER: DFTB parameters for O-P (Wed May 07 2008 - 14:19:50 CDT)
  • Re: AMBER: steered MD initial state (Tue May 06 2008 - 11:37:54 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 16:16:22 CDT)
  • Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" (Thu Apr 24 2008 - 12:51:10 CDT)
  • Re: AMBER: bond breaking in proteins (Wed Feb 27 2008 - 10:09:58 CST)
  • Re: AMBER: bond breaking in proteins (Tue Feb 26 2008 - 13:58:22 CST)
  • Re: AMBER: compiling PMEMD with MKL10.0 (Tue Feb 26 2008 - 13:46:24 CST)
  • Re: AMBER: problem bull linux compiling (Tue Feb 26 2008 - 11:18:27 CST)
  • Re: AMBER: problem bull linux compiling (Fri Feb 22 2008 - 09:56:25 CST)
  • Re: AMBER: mpd error in submitting parallel job (Thu Feb 14 2008 - 13:45:47 CST)
  • Re: AMBER: xmgr graphics display program (Wed Feb 13 2008 - 20:29:26 CST)
• gustavo.seabra_at_gmail.com
  • Re: AMBER: Which CO2 potential? (Wed Jul 23 2008 - 22:32:58 CDT)
• haixiao jin
  • Re: AMBER: MM_PBSA snapshot statistic calc problem (Sat Sep 27 2008 - 01:40:20 CDT)
  • AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA (Sat Sep 27 2008 - 02:45:06 CDT)
  • Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine (Sun Sep 07 2008 - 08:26:31 CDT)
  • AMBER: Test error in installing amber 10 using four threads on a single-cpu machine (Sun Sep 07 2008 - 04:42:10 CDT)
• Hakkim Boy
  • Re: AMBER: to prepare pdb file fro unusual amino acid. (Wed Sep 24 2008 - 09:41:33 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 07:30:04 CDT)
  • AMBER: solvent interaction in active site (Wed Aug 27 2008 - 21:41:24 CDT)
  • AMBER: trajectories into trajectory (Sun May 25 2008 - 06:30:22 CDT)
• Hannes Kopitz
  • Re: AMBER: ptraj: how to select all non-hydrogen atoms (Wed Dec 03 2008 - 14:27:33 CST)
  • Re: RE: AMBER: mmpbsa (Wed Sep 03 2008 - 04:15:19 CDT)
  • Re: AMBER: mmpbsa (Tue Sep 02 2008 - 13:15:47 CDT)
  • Re: AMBER: How to solve - Missing BELE for MM in 1 in amber. (Tue Jun 17 2008 - 03:32:31 CDT)
  • Re: AMBER: PCAL and polar contribution in the output file (Sun Jun 15 2008 - 08:30:23 CDT)
• Hannes Loeffler
  • Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? (Wed Jul 23 2008 - 06:11:57 CDT)
  • AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? (Tue Jul 22 2008 - 09:08:36 CDT)
• Hannes Wallnoefer
  • AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 07:14:34 CDT)
  • AMBER: PBCAL in MM_PBSA (Fri Aug 08 2008 - 09:19:30 CDT)
  • AMBER: MM_PBSA snapshot statistic calc problem (Tue Aug 05 2008 - 07:45:48 CDT)
  • Re: AMBER: radius of calcium ion in MM_PBSA (Mon Jul 28 2008 - 04:28:01 CDT)
  • AMBER: radius of calcium ion in MM_PBSA (Mon Jul 28 2008 - 03:18:22 CDT)
  • AMBER: ptraj problem with centering in the box (Wed Jul 02 2008 - 09:00:33 CDT)
  • Re: AMBER: nmode problem (Fri Apr 18 2008 - 04:44:38 CDT)
  • AMBER: nmode problem (Fri Apr 18 2008 - 04:01:27 CDT)
  • AMBER: ligand slips out of pocket (Fri Apr 04 2008 - 02:58:29 CDT)
• Hans Martin Senn
  • Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X (Mon May 19 2008 - 05:35:24 CDT)
  • AMBER: AmberTools on OS X fails tests (Thu May 08 2008 - 13:59:12 CDT)
  • AMBER: GAFF atom types for flavin (again) (Thu Jan 17 2008 - 14:47:54 CST)
• Harianto Tjong
  • AMBER: adding new potential function (Wed Sep 17 2008 - 14:12:34 CDT)
• Harry (Yicun) Ni
  • AMBER: Using charmm force field in amber (Thu Oct 16 2008 - 16:20:45 CDT)
  • AMBER: question about dihedral angles (Mon Sep 15 2008 - 09:41:31 CDT)
  • Re: AMBER: question about the improper torsion (Mon Jul 14 2008 - 23:12:57 CDT)
  • AMBER: question about the improper torsion (Fri Jul 11 2008 - 11:34:17 CDT)
  • AMBER: problem with rdparm (Thu Jul 10 2008 - 17:05:41 CDT)
  • Re: AMBER: question about the charge (Fri Jun 27 2008 - 18:57:37 CDT)
  • AMBER: question about the charge (Fri Jun 27 2008 - 15:37:55 CDT)
  • Re: AMBER: A problem of dihedral angle (Wed Jun 25 2008 - 14:42:09 CDT)
  • AMBER: A problem of dihedral angle (Wed Jun 25 2008 - 10:31:24 CDT)
• Harry Ni
  • Re: AMBER: A problem of installing Amber10 (Fri Jun 06 2008 - 16:36:48 CDT)
  • Re: AMBER: A problem of installing Amber10 (Fri Jun 06 2008 - 14:00:19 CDT)
  • Re: AMBER: A problem of installing Amber10 (Thu Jun 05 2008 - 13:27:23 CDT)
• Hashem Taha
  • AMBER: Dihedral Drive (Sat Sep 20 2008 - 02:31:13 CDT)
• Hazard, E. Starr
  • AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:12:54 CST)
  • AMBER: AMBER10 failing to compile PMEMD (Sat Nov 22 2008 - 16:06:03 CST)
  • AMBER: AMBER10 compiling SANDER parallel problem (Tue Nov 18 2008 - 14:48:31 CST)
• Heikki Salo
  • Re: AMBER: Prepgen (Wed Jul 30 2008 - 03:58:28 CDT)
• Henar Martínez
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 12:30:33 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 12:28:13 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 05:14:58 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 04:58:09 CST)
  • AMBER: autodock pdb to obtain parm with tleap (Tue Feb 26 2008 - 11:23:43 CST)
• Henrik Öberg
  • RE: AMBER: mmpbsa (Wed Sep 03 2008 - 02:30:43 CDT)
  • RE: AMBER: mmpbsa (Tue Sep 02 2008 - 09:18:56 CDT)
  • AMBER: mmpbsa (Tue Sep 02 2008 - 06:36:55 CDT)
  • AMBER: coordinate change of pdb structure using xleap (Wed Aug 27 2008 - 01:26:42 CDT)
• hfox1_at_nd.edu
  • RE: AMBER: Fully QM periodic runs (Mon Nov 24 2008 - 15:28:36 CST)
• hklwatergod
  • Re: Re: RE: AMBER: the install problem (Tue Oct 14 2008 - 02:19:02 CDT)
  • AMBER: Segmentation fault (Tue Oct 14 2008 - 01:52:36 CDT)
  • Re: RE: AMBER: the install problem (Mon Jul 28 2008 - 09:22:58 CDT)
  • AMBER: the install problem (Sun Jul 27 2008 - 01:34:55 CDT)
  • AMBER: the pmemd problem (Fri Jul 25 2008 - 06:51:32 CDT)
  • AMBER: amber9 install problem (Thu Jul 24 2008 - 01:11:33 CDT)
• Holger Gohlke
  • Re: AMBER: mm_pbsa.pl and Amber10 (Mon Nov 10 2008 - 11:12:16 CST)
  • Re: AMBER: matrix correl (Mon Feb 18 2008 - 06:56:07 CST)
• Holly Freedman
  • Re: AMBER: igb and ibelly (Fri May 30 2008 - 17:36:03 CDT)
  • RE: AMBER: igb and ibelly (Fri May 30 2008 - 15:21:06 CDT)
  • AMBER: igb and ibelly (Fri May 30 2008 - 14:23:21 CDT)
  • Re: AMBER: standard residues (Sat Mar 22 2008 - 17:27:07 CDT)
  • AMBER: standard residues (Wed Mar 19 2008 - 15:03:02 CDT)
  • Re: AMBER: output effective Born radii (Mon Mar 10 2008 - 21:24:32 CDT)
  • AMBER: output effective Born radii (Mon Mar 10 2008 - 17:57:06 CDT)
  • Re: AMBER: simulated annealing (Thu Feb 21 2008 - 14:52:42 CST)
  • AMBER: simulated annealing (Thu Feb 21 2008 - 13:31:48 CST)
• Hongyan Li
  • AMBER: refine cyana structures! (Tue Apr 22 2008 - 20:33:08 CDT)
• Hopkins, Robert
  • RE: AMBER: problem with ambmask (Mon Feb 18 2008 - 15:57:07 CST)
  • Re: AMBER: xmgr graphics display program (Sun Feb 17 2008 - 14:38:41 CST)
  • AMBER: xmgr graphics display program (Wed Feb 13 2008 - 20:02:23 CST)
  • AMBER: ambmask problem (Wed Feb 13 2008 - 18:42:53 CST)
  • RE: AMBER: VLIMIT units; TGTFITMASK (Tue Feb 05 2008 - 09:08:07 CST)
  • AMBER: VLIMIT units; TGTFITMASK (Mon Feb 04 2008 - 16:55:03 CST)
  • Re: AMBER: Installing OpenMPI (Wed Jan 23 2008 - 18:40:22 CST)
  • AMBER: Installing OpenMPI (Tue Jan 22 2008 - 17:57:49 CST)
  • AMBER: Amber DNA Model for X-ray Crystallography (Fri Jan 11 2008 - 17:32:00 CST)
• Hu, Shaowen (JSC-SK)[USRA]
  • RE: AMBER: difference between sander and NAB (Fri Jul 11 2008 - 08:02:51 CDT)
  • AMBER: difference between sander and NAB (Thu Jul 10 2008 - 14:44:41 CDT)
  • AMBER: MAXAT can not be changed for AMBERTool 1.0 (Mon Jun 02 2008 - 14:41:54 CDT)
  • RE: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 11:24:39 CDT)
  • RE: AMBER: Dose AMBER 10 pmemd support openmpi? (Wed Apr 30 2008 - 11:07:39 CDT)
  • AMBER: Dose AMBER 10 pmemd support openmpi? (Wed Apr 30 2008 - 08:04:28 CDT)
  • AMBER: Gbsa in NAB (Thu Apr 10 2008 - 12:04:14 CDT)
  • RE: AMBER: Build a MPI NAB (Wed Apr 09 2008 - 09:12:57 CDT)
  • RE: AMBER: Build a MPI NAB (Tue Apr 08 2008 - 15:19:22 CDT)
  • AMBER: Build a MPI NAB (Mon Apr 07 2008 - 15:45:53 CDT)
  • RE: AMBER: NAB examples (Mon Apr 07 2008 - 11:43:06 CDT)
  • RE: AMBER: NAB examples (Mon Apr 07 2008 - 11:09:44 CDT)
  • AMBER: NAB examples (Mon Apr 07 2008 - 09:32:07 CDT)
• huzehan19870731_at_126.com
  • AMBER:Some questions about replica exchan ge (Wed Jul 16 2008 - 08:07:46 CDT)
• Ian
  • Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Wed Jun 11 2008 - 05:53:42 CDT)
  • AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Fri Jun 06 2008 - 04:19:58 CDT)
  • AMBER: Ptraj | Multiple trajout commands? (Fri May 30 2008 - 03:39:23 CDT)
• Ibrahim Moustafa
  • Re: AMBER: changing pdb structure (Fri Oct 10 2008 - 09:24:30 CDT)
  • AMBER: PCA analysis (Mon Jun 02 2008 - 16:09:17 CDT)
  • AMBER: PCA - analysis (Sun Jun 01 2008 - 13:00:35 CDT)
  • Re: AMBER: VMD Movie 3 (Thu May 29 2008 - 16:03:16 CDT)
  • Re: AMBER: amber10 installation (Thu May 22 2008 - 10:03:15 CDT)
  • Re: AMBER: distance (Fri May 09 2008 - 09:49:37 CDT)
  • AMBER: DCCM correlation analysis (Mon May 05 2008 - 15:21:37 CDT)
  • RE: AMBER: change in secondary structure during MD (Thu Feb 28 2008 - 16:12:49 CST)
  • AMBER: change in secondary structure during MD (Wed Feb 27 2008 - 19:45:21 CST)
  • RE: AMBER: (no subject) (Fri Feb 22 2008 - 10:29:59 CST)
  • RE: AMBER: matrix correl (Wed Feb 20 2008 - 12:19:31 CST)
  • RE: AMBER: matrix correl (Wed Feb 20 2008 - 11:22:53 CST)
• iccy liu
  • RE: AMBER: solvent box again (Thu Dec 18 2008 - 13:41:41 CST)
  • AMBER: solvent box again (Tue Dec 16 2008 - 12:32:32 CST)
  • AMBER: how to add new solvent type in Amber (Mon Dec 08 2008 - 18:23:11 CST)
• Idan Gabdank
  • Re: AMBER: Segmentation faults trying to run sander mpi (Thu May 29 2008 - 09:57:07 CDT)
  • AMBER: Segmentation faults trying to run sander mpi (Wed May 28 2008 - 05:59:09 CDT)
• Ignacio J. General
  • AMBER: hbonds in first solvation shells (Fri Feb 01 2008 - 13:02:30 CST)
• Ilyas Yildirim
  • Re: AMBER: distance restraint between non-bonded molecules] (Sun Dec 21 2008 - 21:08:38 CST)
  • Re: AMBER: distance restraint between non-bonded molecules] (Fri Dec 19 2008 - 17:06:35 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 09:22:32 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 15:29:26 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 13:29:30 CST)
  • RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 11:10:13 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 18:12:44 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 16:11:14 CST)
  • Re: AMBER: molecule drift out of water box? (Sun Sep 21 2008 - 21:52:17 CDT)
  • Re: AMBER: molecule drift out of water box? (Sun Sep 21 2008 - 15:45:45 CDT)
  • Re: AMBER: Dihedral Drive (Sat Sep 20 2008 - 03:07:07 CDT)
  • Re: AMBER: molecule drift out of water box? (Fri Sep 19 2008 - 19:00:03 CDT)
  • Re: AMBER: question about dihedral angles (Mon Sep 15 2008 - 10:10:55 CDT)
  • Re: AMBER: mmpbsa molsurf.c error (Thu Sep 04 2008 - 19:45:58 CDT)
  • AMBER: mmpbsa molsurf.c error (Wed Sep 03 2008 - 18:56:59 CDT)
  • RE: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 16:58:03 CDT)
  • AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 16:04:14 CDT)
  • AMBER: Dell 2 Quad Core System Performance (Fri Aug 22 2008 - 20:16:49 CDT)
  • AMBER: Negative dihedral coefficients in amber99 - Possible? (Sun Aug 17 2008 - 21:33:16 CDT)
  • AMBER: Model of deoxyadenosine in Cornell 95 paper (Sun Jul 13 2008 - 18:14:48 CDT)
  • Re: AMBER: ptraj selection (Thu Jul 10 2008 - 19:58:08 CDT)
  • Re: AMBER: ptraj selection (Wed Jul 09 2008 - 23:27:35 CDT)
  • Re: AMBER: ptraj selection (Wed Jul 09 2008 - 22:13:22 CDT)
  • Re: AMBER: ptraj selection (Wed Jul 09 2008 - 22:13:22 CDT)
  • AMBER: ptraj selection (Wed Jul 09 2008 - 20:07:39 CDT)
  • Re: AMBER: NMR refinement (Wed Jul 02 2008 - 04:58:05 CDT)
  • Re: AMBER: Dihedral Angle Parameters (Thu Jun 26 2008 - 17:07:55 CDT)
  • AMBER: Dihedral Angle Parameters (Thu Jun 26 2008 - 16:07:16 CDT)
  • AMBER: NMR restraints (Mon Apr 28 2008 - 01:53:51 CDT)
• In Hee Park
  • AMBER: idecomp=2 & RRES/LRES group specification (Fri Dec 19 2008 - 19:19:43 CST)
  • AMBER: IGB=10 in Amber10 (Tue Aug 19 2008 - 13:55:05 CDT)
  • Re: AMBER: sleap - TER-card (Thu Jun 26 2008 - 19:31:40 CDT)
  • AMBER: sleap - TER-card (Wed Jun 25 2008 - 14:14:39 CDT)
• IN SUK JOUNG
  • AMBER: NAB: getseq_from_pdb() (Tue Aug 05 2008 - 19:00:21 CDT)
  • AMBER: divcon.rst ?? (Mon Aug 04 2008 - 19:06:43 CDT)
  • AMBER: SHIFTS compile error (Tue Jul 22 2008 - 15:25:43 CDT)
• inonshar_at_post.tau.ac.il
  • AMBER: xLeap unit editor "seg fault" (Thu Apr 17 2008 - 00:49:01 CDT)
• Irene Newhouse
  • RE: AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 11:28:44 CST)
• Ivelin Georgiev
  • Re: AMBER: Water Topology (Thu Mar 20 2008 - 08:44:51 CDT)
  • AMBER: Water Topology (Wed Mar 19 2008 - 23:12:28 CDT)
• j00323240_at_students.jsums.edu
  • AMBER: problem with AMOEBA (Wed Nov 26 2008 - 13:07:13 CST)
• Jaber Jahanbin Sardroodi
  • AMBER: help me for filling a nanotube with water?? (Mon Aug 04 2008 - 20:39:05 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sun Aug 03 2008 - 03:15:19 CDT)
  • AMBER: error in parallel amber 9 test (Sat Aug 02 2008 - 16:12:07 CDT)
  • AMBER: fortran runtime error in "make test.serial" with gfortran (Fri Jul 25 2008 - 17:23:25 CDT)
• Jack Lei
  • Re: AMBER: Error while compiling Amber (Thu Feb 14 2008 - 06:50:57 CST)
  • Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? (Mon Jan 28 2008 - 08:35:06 CST)
  • AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? (Mon Jan 28 2008 - 06:59:38 CST)
  • Re: AMBER: Number of Hydrogen Bonds? (Fri Jan 25 2008 - 07:20:53 CST)
  • Re: AMBER: MM-PBSA problem (Fri Jan 04 2008 - 19:31:05 CST)
• Jackie. J. Shen
  • Re: AMBER: mpirun Permission denied. (Tue Dec 30 2008 - 20:32:17 CST)
  • Re: AMBER: SMD-related questions (Tue Dec 30 2008 - 20:27:16 CST)
• Jacob Kongsted
  • AMBER: ff02 in nmode gives error "too many dihedrals" ? (Mon Nov 10 2008 - 03:16:36 CST)
• Jacopo Sgrignani
  • AMBER: minimization (Fri Oct 31 2008 - 03:52:12 CDT)
  • AMBER: minimization (Thu Oct 30 2008 - 13:03:29 CDT)
  • AMBER: tan luo radii (Tue Aug 26 2008 - 04:06:39 CDT)
  • Re: AMBER: MM_PBSA problem in binding_energy (Wed May 14 2008 - 13:43:55 CDT)
• jacopo.sgrignani_at_unifi.it
  • AMBER: DMSOBOX (Wed Jul 30 2008 - 02:05:00 CDT)
  • RE: AMBER: from Gromax to AMBER (Tue May 13 2008 - 08:19:19 CDT)
  • AMBER: molsurf (Wed May 07 2008 - 06:11:34 CDT)
  • AMBER: nmode output (Fri Apr 25 2008 - 03:36:35 CDT)
  • AMBER: water in the binding site MMPBSA (Thu Apr 24 2008 - 08:51:43 CDT)
  • AMBER: nmode (Mon Apr 21 2008 - 12:38:44 CDT)
  • AMBER: mmpbsa with gromacs trajectory (Tue Apr 15 2008 - 09:10:21 CDT)
  • AMBER: Amber installation (Fri Apr 11 2008 - 08:23:24 CDT)
• Jagan Mohan
  • Re: AMBER: Installation Error (Wed Oct 15 2008 - 09:03:04 CDT)
  • Re: AMBER: Installation Error (Wed Oct 15 2008 - 03:51:03 CDT)
  • AMBER: Installation Error (Wed Oct 15 2008 - 02:50:18 CDT)
• James Thomas
  • AMBER: Inquiry on B-factor of NMR (Fri May 02 2008 - 14:31:09 CDT)
  • AMBER: Average structure (Mon Apr 21 2008 - 05:21:26 CDT)
  • AMBER: nmode (Mon Mar 31 2008 - 13:48:43 CDT)
  • Re: AMBER: Nmode segmentation fault (Tue Mar 25 2008 - 14:00:44 CDT)
  • Re: AMBER: Nmode segmentation fault (Tue Mar 25 2008 - 12:22:43 CDT)
  • AMBER: Nmode segmentation fault (Tue Mar 25 2008 - 06:53:21 CDT)
  • Re: AMBER: Inquiry on analyzing the amplitude from nmdout results (Wed Mar 19 2008 - 17:00:35 CDT)
  • AMBER: Inquiry on analyzing the amplitude from nmdout results (Wed Mar 19 2008 - 11:09:05 CDT)
  • AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis (Fri Mar 07 2008 - 11:30:58 CST)
• JAMES W CALDWELL
  • Re: AMBER: simple sander (Thu Jun 19 2008 - 20:47:32 CDT)
  • Re: AMBER: [Fwd: segmentation fault in nmode] (Mon Jun 16 2008 - 19:53:03 CDT)
• James W. Caldwell
  • RE: AMBER: amber10: pmemd gfortran (Fri Jul 25 2008 - 17:06:01 CDT)
  • AMBER: amber10: pmemd gfortran (Fri Jul 25 2008 - 13:23:06 CDT)
  • RE: AMBER: Test scripts (Fri Jun 27 2008 - 11:54:56 CDT)
  • AMBER: Test scripts (Fri Jun 27 2008 - 11:35:26 CDT)
  • RE: AMBER: amber10 compile gfortran question (Wed Jun 25 2008 - 14:11:58 CDT)
  • AMBER: amber10 compile gfortran question (Wed Jun 25 2008 - 13:10:58 CDT)
  • AMBER: simple sander (Thu Jun 19 2008 - 18:30:39 CDT)
  • AMBER: amber10 make fails for static/parallel (Fri Jun 13 2008 - 17:50:19 CDT)
  • RE: AMBER: Compile amber10 parallel with suppied LAM (Fri Jun 13 2008 - 12:17:57 CDT)
  • RE: AMBER: Compile amber10 parallel with suppied LAM (Fri Jun 13 2008 - 12:06:19 CDT)
  • RE: AMBER: Compile amber10 parallel with suppied LAM (Thu Jun 12 2008 - 13:08:54 CDT)
  • RE: AMBER: Compile amber10 parallel with suppied LAM (Thu Jun 12 2008 - 12:32:13 CDT)
  • AMBER: Compile amber10 parallel with suppied LAM (Thu Jun 12 2008 - 11:31:03 CDT)
• Jan Goeman
  • Re: AMBER: installing amber on new linux (Sun Oct 26 2008 - 19:25:49 CDT)
  • AMBER: installing amber on new linux (Wed Oct 22 2008 - 16:06:48 CDT)
• Jan Schulze
  • AMBER: Amber 9: Question regarding Test Failures and Compilers (Wed Jan 23 2008 - 04:01:04 CST)
• jani sahil
  • Re: AMBER: regad-tutorial-dna-polyAT (Sun Dec 07 2008 - 23:13:30 CST)
  • AMBER: regarding:calculation of b factor using ptraj (Sat Mar 01 2008 - 10:10:10 CST)
  • AMBER: Regarding:PME and neturalization (Tue Feb 19 2008 - 23:12:45 CST)
  • AMBER: Problem:neturalization (Wed Feb 06 2008 - 23:03:35 CST)
  • Re: AMBER: regarding :scee (Wed Jan 23 2008 - 22:37:48 CST)
  • AMBER: regarding :scee (Wed Jan 23 2008 - 09:50:45 CST)
  • AMBER: Regarding neutral Arginine unit (Tue Jan 15 2008 - 10:19:00 CST)
  • AMBER: Amber : neutralizing without adding ions (Mon Jan 14 2008 - 05:43:01 CST)
  • AMBER: problem in neturalization (Sat Jan 12 2008 - 21:27:31 CST)
  • AMBER: problem:capping (Sat Jan 12 2008 - 20:53:24 CST)
  • AMBER: antechamber problems (Fri Jan 04 2008 - 21:49:10 CST)
  • AMBER: amber :antechamber problem (Fri Jan 04 2008 - 21:51:56 CST)
• Jarrod Smith
  • Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 (Tue Jun 03 2008 - 14:29:31 CDT)
  • AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 (Mon Jun 02 2008 - 11:43:24 CDT)
• Jed W Pitera
  • Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE (Tue Sep 30 2008 - 13:56:18 CDT)
  • Re: AMBER: diblock copolymer (Tue Jan 22 2008 - 19:01:03 CST)
• Jeff Schwinefus
  • AMBER: amber: parameters for 5' nucleotide monophosphates (Mon Oct 13 2008 - 12:52:55 CDT)
  • Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap (Fri Jul 11 2008 - 11:41:21 CDT)
  • AMBER: Question about loading frcmod.ionsjc_tip3p in xleap (Wed Jul 09 2008 - 16:27:46 CDT)
• Jeffrey
  • AMBER: definition of dihedral in amber (Thu Dec 25 2008 - 09:38:38 CST)
  • AMBER: How to build a cubic box of a newly synthesized compound? (Wed Dec 24 2008 - 00:34:13 CST)
  • Re: RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 20:18:29 CST)
  • AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 03:15:17 CST)
  • Re: Re: AMBER: Calculating the dielectrostatic constant from simulation? (Mon Dec 15 2008 - 19:34:54 CST)
  • AMBER: Calculating the dielectrostatic constant from simulation? (Mon Dec 15 2008 - 01:07:25 CST)
  • Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Thu Nov 27 2008 - 09:30:33 CST)
  • Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Wed Nov 26 2008 - 08:44:27 CST)
  • Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Tue Nov 25 2008 - 10:14:44 CST)
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 10:19:41 CST)
  • AMBER: AdoMet parameterization with antechamber (Sun Nov 23 2008 - 09:55:30 CST)
  • Re: Re: AMBER: AMBER10 installation question (Wed Nov 19 2008 - 07:27:13 CST)
  • AMBER: AMBER10 installation question (Mon Nov 17 2008 - 21:20:14 CST)
  • Re: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Thu Aug 21 2008 - 02:11:55 CDT)
  • Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 19:43:58 CDT)
  • AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 06:30:35 CDT)
  • Re: Re: AMBER: help to install AMBER9 (Mon May 12 2008 - 19:51:46 CDT)
  • Re: AMBER: help to install AMBER9 (Sun May 11 2008 - 04:12:18 CDT)
  • AMBER: help to install AMBER9 (Fri May 09 2008 - 09:47:16 CDT)
  • Re: Re: AMBER: Read trajectories generated by CHARMM (Mon Apr 28 2008 - 19:58:36 CDT)
  • AMBER: Read trajectories generated by CHARMM (Mon Apr 28 2008 - 08:06:17 CDT)
  • AMBER: compile Amber9 on 64bit AMD Opteron (Fri Apr 18 2008 - 02:02:24 CDT)
• Jena M
  • AMBER: initial velocities of MD (Tue May 13 2008 - 11:37:31 CDT)
  • AMBER: misplacement of TER by leap (Mon May 05 2008 - 06:00:55 CDT)
  • AMBER: RE: amber8 files in amber9 (Wed Apr 30 2008 - 10:55:45 CDT)
  • AMBER: RESP charges (Tue Apr 22 2008 - 07:31:54 CDT)
• Jennifer.Thomas_at_cbt.uhp-nancy.fr
  • Re: AMBER: self-diffusion coefficient and Berendsen (Sun May 25 2008 - 05:47:22 CDT)
  • AMBER: self-diffusion coefficient and Berendsen (Fri May 23 2008 - 03:03:49 CDT)
• Jens Lattig
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Wed Jun 11 2008 - 03:59:12 CDT)
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Tue Jun 10 2008 - 03:00:08 CDT)
  • AMBER: PROBLEM: AmberTools Installation using Ubuntu (Fri Jun 06 2008 - 03:13:06 CDT)
  • AMBER: netcdf configure returned 1 - PROBLEM SOLVED (Thu Jun 05 2008 - 09:42:03 CDT)
  • AMBER: netcdf configure returned 1 (Thu Jun 05 2008 - 08:46:45 CDT)
• Jeremy Harris
  • AMBER: pmemd (Thu Nov 20 2008 - 10:27:14 CST)
• Jerome.GOLEBIOWSKI_at_unice.fr
  • Re: AMBER: Re: reaction coordinate in umbrella sampling (Tue Sep 23 2008 - 02:33:43 CDT)
  • Re: AMBER: dihedral energy calculation inconsistent with gaussian's result (Tue Jun 24 2008 - 03:01:35 CDT)
• Jesse Jun
  • AMBER: Ptraj Normal Mode Analysis (Fri Nov 14 2008 - 15:19:31 CST)
• jessica stolee
  • AMBER: calculating the enthalpy of evaporation (Thu Jul 24 2008 - 14:24:40 CDT)
• jialei
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Fri Aug 15 2008 - 11:38:38 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 19:15:39 CDT)
  • AMBER: Compile AMBER 9 on TACC Ranger super computer (Wed Aug 13 2008 - 17:26:07 CDT)
• Jianyin Shao
  • Re: AMBER: question about ptraj (Thu Nov 13 2008 - 17:38:44 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Fri Nov 07 2008 - 10:24:03 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 16:48:47 CST)
  • Re: AMBER: ptraj - closest command (Wed Oct 08 2008 - 14:50:29 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Sat Aug 02 2008 - 21:23:53 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri Aug 01 2008 - 14:43:14 CDT)
  • Re: AMBER: mask for oligosaccharide (Wed Jul 30 2008 - 17:26:31 CDT)
  • Re: AMBER: Does clustering involve fitting? (Wed Jul 30 2008 - 16:29:57 CDT)
  • Re: AMBER: ptraj selection (Thu Jul 10 2008 - 10:56:55 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue Jul 08 2008 - 23:45:46 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Mon Jul 07 2008 - 17:41:03 CDT)
  • Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? (Tue Jun 17 2008 - 10:36:01 CDT)
  • Re: AMBER: 2D RMS plot (Wed Jun 11 2008 - 17:17:43 CDT)
  • Re: AMBER: PTRAJ - Segmentation Fault (Wed Jun 11 2008 - 11:01:07 CDT)
  • Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Wed Jun 11 2008 - 10:55:12 CDT)
  • Re: AMBER: ptraj imaging issue (Thu Jun 05 2008 - 11:23:52 CDT)
  • Re: AMBER: ptraj imaging issue (Wed Jun 04 2008 - 16:25:27 CDT)
  • Re: AMBER: Ptraj | Multiple trajout commands? (Sat May 31 2008 - 19:02:17 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri May 30 2008 - 12:11:24 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Thu May 29 2008 - 16:47:43 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Thu May 29 2008 - 13:15:15 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Wed May 28 2008 - 23:07:18 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Wed May 28 2008 - 10:51:12 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue May 27 2008 - 14:29:43 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue May 27 2008 - 11:03:54 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue May 27 2008 - 10:37:57 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri May 09 2008 - 15:05:39 CDT)
  • Re: AMBER: (Thu Mar 06 2008 - 15:24:03 CST)
  • Re: AMBER: ptraj: new mask parser (Thu Jan 24 2008 - 11:23:53 CST)
• Jiapu.Zhang_at_csiro.au
  • RE: AMBER: Number of Hydrogen Bonds? (Thu Jan 24 2008 - 19:35:04 CST)
• Jiayun Pang
  • AMBER: RESP charges of an unusual substrate (Fri May 16 2008 - 05:45:54 CDT)
• Jifeng Wang
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:16:08 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 10:50:56 CST)
  • Re: AMBER: SCC-DFTB for Zinc atom (Fri Jul 18 2008 - 12:10:17 CDT)
  • AMBER: SCC-DFTB for Zinc atom (Thu Jul 17 2008 - 10:33:15 CDT)
• Jiri Sponer
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 08:19:33 CST)
• Jiten
  • Re: AMBER: Unable to create the top & crd files for a protein+ligand pdb structure (Sat Jan 12 2008 - 02:21:01 CST)
• jitrayut jitonnom
  • AMBER: MM-PBSA : bad atom type: ZN (Mon Dec 08 2008 - 10:51:12 CST)
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 17:34:43 CST)
  • AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Thu Nov 27 2008 - 19:26:54 CST)
  • Re: AMBER: Mn2+ parameters in AMBER (Fri May 23 2008 - 03:58:10 CDT)
  • Re: AMBER: AMBER Parallel test error (Thu May 08 2008 - 04:10:49 CDT)
  • Re: AMBER: AMBER Parallel test error (Tue May 06 2008 - 08:38:53 CDT)
  • Re: AMBER: AMBER Parallel test error (Tue May 06 2008 - 08:09:10 CDT)
  • AMBER: AMBER Parallel test error (Mon May 05 2008 - 13:37:39 CDT)
  • AMBER: Mn2+ parameters in AMBER (Fri May 02 2008 - 13:46:25 CDT)
• Joachim Reichelt
  • AMBER: MOLYBDENUM (Wed Nov 19 2008 - 08:14:31 CST)
  • Re: AMBER: nmode analysis (Mon Jun 30 2008 - 07:36:32 CDT)
  • AMBER: nmode analysis (Mon Jun 30 2008 - 06:53:21 CDT)
  • AMBER: nab (Fri May 30 2008 - 04:48:56 CDT)
  • AMBER: Iron-Sulfur Cluster (Fri May 30 2008 - 04:46:30 CDT)
• Jochen Heil
  • AMBER: Your "bellymask-patch" (Thu Nov 13 2008 - 07:45:30 CST)
  • AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 11:48:38 CST)
• Joel Tyndall
  • RE: AMBER: pdb structure is only half the molecule. (Thu Oct 23 2008 - 15:18:36 CDT)
• John Bennett
  • AMBER: ptraj (Tue Oct 21 2008 - 09:32:07 CDT)
  • Re: AMBER: files in Amber directory ( to Junmei Wang ) (Fri Jul 18 2008 - 06:25:38 CDT)
  • AMBER: files in Amber directory ( to Junmei Wang ) (Tue Jul 15 2008 - 06:10:40 CDT)
  • AMBER: missing torsion parameters (Mon Jun 30 2008 - 16:06:07 CDT)
• John Chodera
  • AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Tue Nov 18 2008 - 13:58:22 CST)
  • Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber (Tue Oct 28 2008 - 10:57:42 CDT)
  • AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber (Mon Oct 27 2008 - 17:12:31 CDT)
  • AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (Sun Oct 26 2008 - 20:16:48 CDT)
  • Re: AMBER: Can sander provide ESP with PBC? (Mon Apr 21 2008 - 21:24:25 CDT)
  • Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms (Wed Apr 16 2008 - 17:15:19 CDT)
  • AMBER: Extracting the electric field (and its gradient) on particular solute atoms (Tue Apr 15 2008 - 19:36:01 CDT)
  • Re: AMBER: WHAM: how frequently do I need data on the system coordinates? (Thu Apr 10 2008 - 12:47:57 CDT)
  • AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine (Tue Jan 01 2008 - 19:44:34 CST)
• John Finke
  • Re: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 17:43:09 CST)
  • AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 14:51:54 CST)
  • AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system (Fri Oct 31 2008 - 13:05:57 CDT)
• John Palmeri
  • AMBER: Debugf AMBER9 (Wed Jun 25 2008 - 02:38:53 CDT)
• john smith
  • Re: AMBER: forrtl severe(174) error with minimization and md (Mon Dec 15 2008 - 02:46:56 CST)
  • AMBER: forrtl severe(174) error with minimization and md (Wed Dec 10 2008 - 00:20:57 CST)
  • Re: AMBER: antechamber test failure (Thu Oct 16 2008 - 00:53:50 CDT)
  • AMBER: antechamber test failure (Tue Oct 14 2008 - 00:47:28 CDT)
  • Re: AMBER: compilation problem (Mon Sep 22 2008 - 06:59:17 CDT)
  • Re: AMBER: compilation problem (Fri Sep 12 2008 - 00:51:22 CDT)
  • Re: AMBER: compilation problem (Tue Sep 02 2008 - 05:03:14 CDT)
  • AMBER: compilation problem (Sat Aug 30 2008 - 06:51:07 CDT)
• Jojart Balazs
  • Re: AMBER: Electrostatic Energy Components (Sun Nov 23 2008 - 02:34:01 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 01:53:46 CST)
  • Re: AMBER: ptraj, hbond and non-bonded contacts (Fri Mar 14 2008 - 03:19:37 CDT)
  • Re: AMBER: running AMBER in NAMD Trucated Octahedron (Mon Jan 14 2008 - 16:31:05 CST)
• Jones de Andrade
  • Re: AMBER: Which CO2 potential? (Wed Jul 23 2008 - 22:45:00 CDT)
  • AMBER: Which CO2 potential? (Wed Jul 23 2008 - 19:27:58 CDT)
• Jose Borreguero
  • AMBER: velocity units? (Mon Nov 17 2008 - 10:14:35 CST)
  • AMBER: multiple heat baths in a single simulation? (Sun Sep 21 2008 - 18:09:41 CDT)
  • AMBER: help can amber couple part of the system to different heat bath? (Thu Sep 18 2008 - 16:09:23 CDT)
  • AMBER: help can amber couple part of the system to different heat bath? (Thu Sep 18 2008 - 16:09:27 CDT)
  • Re: AMBER: Help...which commands in ptraj does clustering by RMSD? (Thu Sep 11 2008 - 17:01:02 CDT)
  • Re: AMBER: Help...which commands in ptraj does clustering by RMSD? (Thu Sep 11 2008 - 16:12:00 CDT)
  • AMBER: Help...which commands in ptraj does clustering by RMSD? (Thu Sep 11 2008 - 15:28:49 CDT)
  • Re: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 11:26:23 CDT)
  • Re: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 10:43:39 CDT)
  • AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 10:06:42 CDT)
  • AMBER: help... structure factors from amber trajectories? (Thu Sep 04 2008 - 12:35:57 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 13:28:02 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 12:26:57 CDT)
  • Re: AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 11:12:30 CDT)
  • AMBER: help...ptraj does not output bounding box info (Wed Sep 03 2008 - 10:39:41 CDT)
  • AMBER: conversion from crd to netcdf returns almost identical file! (Thu Aug 28 2008 - 15:38:50 CDT)
  • AMBER: parameters for Fe coordinated to four CYS ? (Tue Jul 01 2008 - 19:12:37 CDT)
• Joseph Nachman
  • AMBER: Referencing AMBER (Wed Nov 26 2008 - 10:01:57 CST)
  • AMBER: Restraints (Thu Nov 13 2008 - 12:59:23 CST)
• Jufang Shan
  • Re: AMBER: ptraj has trouble with x-plor psf file from VMD (Mon Jun 02 2008 - 10:52:28 CDT)
• julliane Yoneda
  • Re: AMBER: Temperature regulation (Wed Oct 08 2008 - 12:52:52 CDT)
  • Re: AMBER: Temperature regulation (Wed Oct 01 2008 - 20:10:27 CDT)
  • Re: AMBER: Temperature regulation (Wed Oct 01 2008 - 12:22:06 CDT)
  • Re: AMBER: Temperature regulation (Tue Sep 16 2008 - 18:36:01 CDT)
  • Re: AMBER: Temperature regulation (Tue Sep 16 2008 - 18:34:52 CDT)
  • Re: AMBER: Temperature regulation (Tue Sep 16 2008 - 13:05:27 CDT)
  • AMBER: Temperature regulation (Mon Sep 15 2008 - 19:48:50 CDT)
  • AMBER: Problems in restrained minimization (Wed Jul 23 2008 - 08:08:32 CDT)
  • AMBER: Problems with Frozen atoms (Fri Jul 18 2008 - 15:06:54 CDT)
• Jun Liu
  • AMBER: AMBER installation problem (Fri Jan 25 2008 - 12:59:29 CST)
• JunJun Liu
  • Re: AMBER: RMSD of two different molecules (Wed Mar 26 2008 - 16:54:11 CDT)
  • AMBER: RMSD of two different molecules (Wed Mar 26 2008 - 15:35:32 CDT)
  • Re: AMBER: problems of antechamber (Tue Jan 22 2008 - 08:45:26 CST)
• Junmei Wang
  • Re: AMBER: Electrostatic Energy Components (Sun Nov 23 2008 - 21:36:38 CST)
  • Re: AMBER: respgen -a charge groups function ineffective unless (Wed Aug 27 2008 - 15:55:47 CDT)
  • AMBER: latest update on residuegen (Tue Aug 26 2008 - 08:55:09 CDT)
  • Re: AMBER: Silicon parameters (Fri Aug 22 2008 - 15:29:05 CDT)
  • Re: AMBER: Prepgen (Fri Aug 15 2008 - 08:52:27 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 14:34:50 CDT)
  • Re: AMBER: problem with prep file generation (Wed Aug 13 2008 - 11:59:49 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 11:45:11 CDT)
  • Re: AMBER: Prepgen (Tue Aug 12 2008 - 17:30:45 CDT)
  • Re: AMBER: Prepgen (Tue Aug 05 2008 - 10:50:00 CDT)
  • Re: AMBER: antechamber generated input for gaussian error (Wed Jul 23 2008 - 10:29:21 CDT)
  • Re: AMBER: antechamber and charmm (Thu Jul 17 2008 - 09:33:23 CDT)
  • Re: AMBER: files in Amber directory ( to Junmei Wang ) (Thu Jul 17 2008 - 09:56:06 CDT)
  • AMBER: compile amber10 on Mac (Tue Jul 01 2008 - 16:45:31 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Fri Jun 27 2008 - 10:35:23 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 17:25:32 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 13:27:10 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Thu Jun 26 2008 - 09:33:44 CDT)
  • Re: AMBER: Antechamber/mopac am1-bcc charge (Wed Jun 25 2008 - 17:44:07 CDT)
  • AMBER: Re: AMBER: Re: £º Re: AMBER: problems form the pdb to the mol2 (Wed Jun 25 2008 - 11:29:44 CDT)
  • AMBER: how to derive torsional angle parameters in gaff (Tue Jun 24 2008 - 20:45:42 CDT)
  • Re: AMBER: Further request answers from Dr. Junmei Wang (Tue Jun 24 2008 - 11:58:49 CDT)
  • Re: AMBER: improving GAFF sulfonamide parameters (Tue Jun 24 2008 - 09:34:28 CDT)
  • Re: AMBER: problems form the pdb to the mol2 (Tue Jun 24 2008 - 08:47:24 CDT)
  • Re: AMBER: about gaff.dat in ambeTools 1.0 (Tue Jun 24 2008 - 08:37:09 CDT)
  • Re: AMBER: Antechamber Question (Tue Jun 24 2008 - 08:33:58 CDT)
  • Re: AMBER: GAFF for organic crystals (Mon Jun 23 2008 - 10:16:50 CDT)
  • Re: AMBER: (no subject) (Mon Jun 23 2008 - 10:01:39 CDT)
  • Re: AMBER: How to confirm atom types of small molecule perceived by antechamber (Mon Jun 23 2008 - 09:57:18 CDT)
  • Re: AMBER: Missing gaff angle parameters for dimethyl esters (Tue Jun 03 2008 - 08:19:25 CDT)
  • Re: AMBER: Prepgen (Thu May 15 2008 - 10:46:34 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 17:11:35 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 16:37:54 CDT)
  • Re: AMBER: can't make antechamber work for regular nucleotides (Tue Mar 18 2008 - 16:08:46 CDT)
  • Re: AMBER: Torsion potential in GAFF / "statistic value of parm94" (Fri Mar 14 2008 - 22:01:20 CDT)
  • Re: AMBER: can't make antechamber work for regular nucleotides (Fri Mar 14 2008 - 21:10:41 CDT)
  • Re: AMBER: question on antechamber: jaguar ouput (Tue Mar 11 2008 - 13:22:52 CDT)
  • Re: AMBER: Antechamber, net molecular charge (Mon Mar 10 2008 - 09:39:08 CDT)
  • Re: AMBER: Atom types/parameters for chromene (Wed Mar 05 2008 - 10:23:19 CST)
  • Re: AMBER: missing gaff parameters (Tue Mar 04 2008 - 08:53:39 CST)
  • Re: AMBER: problem with antechamber (Thu Feb 28 2008 - 09:06:31 CST)
  • Re: AMBER: autodock pdb to obtain parm with tleap (Wed Feb 27 2008 - 11:42:52 CST)
  • Re: AMBER: saveAmberPrep in internal coordinates (Wed Feb 20 2008 - 11:43:31 CST)
  • Re: AMBER: Generating RESP charges (Tue Feb 19 2008 - 13:22:59 CST)
  • Re: AMBER: Generating RESP charges (Tue Feb 19 2008 - 12:04:44 CST)
  • Re: AMBER: Generating RESP charges (Tue Feb 19 2008 - 09:05:39 CST)
  • Re: AMBER: Error while compiling Amber (Fri Feb 15 2008 - 11:16:47 CST)
  • Re: AMBER: Error while compiling Amber (Thu Feb 14 2008 - 15:13:30 CST)
  • Re: AMBER: xmgr graphics display program (Thu Feb 14 2008 - 14:04:16 CST)
  • Re: AMBER: Using antechamber without AMBER program (Fri Feb 08 2008 - 09:10:27 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 17:49:51 CST)
  • Re: AMBER: Tough time with antechamber (Thu Jan 24 2008 - 09:23:08 CST)
  • Re: AMBER: about AM1-BCC in antechamber (Tue Jan 22 2008 - 11:56:55 CST)
  • Re: AMBER: about AM1-BCC in antechamber (Fri Jan 18 2008 - 23:31:06 CST)
  • Re: AMBER: GAFF atom types for flavin (again) (Thu Jan 17 2008 - 23:21:21 CST)
  • Re: AMBER: problems of antechamber (Thu Jan 17 2008 - 23:24:52 CST)
  • Re: AMBER: antechamber problem (Thu Jan 10 2008 - 12:29:23 CST)
  • Re: AMBER: connectivity problem (Thu Jan 10 2008 - 09:27:07 CST)
  • Re: AMBER: connectivity problem (Wed Jan 09 2008 - 09:51:05 CST)
  • Re: AMBER: A problem about antechamber (Tue Jan 08 2008 - 16:19:15 CST)
  • Re: AMBER: antechamber problems (Sat Jan 05 2008 - 23:35:04 CST)
  • Re: AMBER: question about antechamber (Thu Jan 03 2008 - 09:18:34 CST)
• Justin A. Lemkul
  • Re: AMBER: Installing PMEMD with Amber10 (Sat May 31 2008 - 07:24:30 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Fri May 30 2008 - 05:42:53 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Thu May 29 2008 - 15:41:30 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Thu May 29 2008 - 14:12:26 CDT)
  • AMBER: Installing PMEMD with Amber10 (Thu May 29 2008 - 08:23:05 CDT)
• Justine Condo
  • Re: AMBER: Iron-Sulfur Cluster (Fri May 30 2008 - 12:52:24 CDT)
  • AMBER: Points on a Sphere (Thu May 15 2008 - 11:27:06 CDT)
• juyong Lee
  • AMBER: Installation error on IBM cluster (Mon May 05 2008 - 03:40:59 CDT)
  • Re: AMBER: Amber10 Installation error - incorrect file suffix (Sun May 04 2008 - 21:01:02 CDT)
  • AMBER: Amber10 Installation error - incorrect file suffix (Sun May 04 2008 - 07:46:10 CDT)
  • AMBER: Compiling amber10 with xlf90 fortran compiler (Fri May 02 2008 - 13:27:10 CDT)
  • AMBER: cfortran.h error with xlf90 compiler (Fri May 02 2008 - 11:35:32 CDT)
  • Re: AMBER: Amber10 installation error (Thu May 01 2008 - 23:52:10 CDT)
  • AMBER: Amber10 installation error (Thu May 01 2008 - 21:28:07 CDT)
• Kailee
  • Re: AMBER: questions about run MD at different pH (Tue Mar 04 2008 - 05:40:30 CST)
  • AMBER: questions about run MD at different pH (Mon Mar 03 2008 - 08:51:40 CST)
• kanazta1_at_yahoo.co.jp
  • AMBER: Re: bad atom type f(fluorine) in MM-PBSA (Mon Feb 04 2008 - 11:32:51 CST)
• Karl Kirschner
  • Re: AMBER: AMBER file preparation for protein-carbohydrate complex (Sun May 25 2008 - 04:25:35 CDT)
• Karl Kirschner (kkirschn)
  • Re: AMBER: concerning force fields ( to Karl Kirschner ) (Tue Jul 01 2008 - 10:06:29 CDT)
  • Re: AMBER: concerning force fields (Fri Jun 27 2008 - 08:02:03 CDT)
  • Re: AMBER: hydrogens are flying in replica exchange simulations (Mon Apr 21 2008 - 10:47:37 CDT)
• Karol Kaszuba
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sun Oct 19 2008 - 08:00:35 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sun Oct 19 2008 - 01:57:23 CDT)
  • Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sat Oct 18 2008 - 11:32:58 CDT)
  • AMBER: REDvIII_I_lack_of_charges_in_mol2 (Sat Oct 18 2008 - 06:08:53 CDT)
• Kateryna Miroshnychenko
  • Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error (Tue Jun 03 2008 - 02:05:51 CDT)
  • Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error (Thu May 29 2008 - 02:22:17 CDT)
  • AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error (Wed May 28 2008 - 10:08:19 CDT)
• KazuoOhta
  • Re: AMBER: LEaP problem with LEU first residue? (Sun Oct 19 2008 - 22:04:38 CDT)
• ke dong
  • AMBER: caculating nonpolar solvation energies (Sat May 24 2008 - 09:53:17 CDT)
  • Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params (Sat May 24 2008 - 09:46:19 CDT)
• Kefa Lu
  • AMBER: convert AMBER format input files into DL_POLY format input files? (Tue Mar 11 2008 - 03:27:23 CDT)
• Keith Van Nostrand
  • AMBER: Regarding sleap - documentation and output behavior (Fri Oct 24 2008 - 10:26:58 CDT)
  • Re: AMBER: Using VMD to calculate end-to-end distance? (Mon Jan 14 2008 - 21:35:42 CST)
  • Re: AMBER: Nudged Elastic Band initial heating problem (Tue Jan 08 2008 - 07:32:31 CST)
• Kevin Abbey
  • AMBER: SiCortex as an alternative to Ethernet and infiniband clusters (Thu Apr 17 2008 - 16:37:23 CDT)
• Kevin Davies
  • Re: AMBER: Deleting solute from box (Thu Feb 07 2008 - 16:21:22 CST)
  • AMBER: Deleting solute from box (Thu Feb 07 2008 - 14:45:48 CST)
• Kevin Parkes
  • RE: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 08:36:36 CST)
  • AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 04:33:35 CST)
• Khaled Barakat
  • AMBER: MM_PBSA doesn't terminate (Wed Oct 22 2008 - 10:27:55 CDT)
  • AMBER: MM_PBSA doesn't terminate (Tue Oct 21 2008 - 11:58:12 CDT)
  • AMBER: Error when performing Alanine scanning (Mon Jul 14 2008 - 20:41:26 CDT)
  • AMBER: Alanine scanning (Sun Jul 13 2008 - 20:50:47 CDT)
  • AMBER: Coordinated Zinc (Wed Jun 11 2008 - 14:29:18 CDT)
• Khatcharin Siriwong
  • Re: AMBER: Can sander provide ESP with PBC? (Wed Apr 23 2008 - 20:43:12 CDT)
  • AMBER: ESP on atoms (2) (Wed Apr 23 2008 - 09:29:04 CDT)
  • AMBER: Can sander provide ESP with PBC? (Mon Apr 21 2008 - 20:36:17 CDT)
• khuram sb
  • AMBER: unsubscribe (Mon Aug 18 2008 - 03:56:36 CDT)
  • AMBER: 1.5ns rst file to PDB file Conversion Error (Wed Jul 23 2008 - 00:07:24 CDT)
  • AMBER: Restarting Problem in MD Simulation (Fri Jul 18 2008 - 05:37:07 CDT)
• Kijeong Kwac
  • AMBER: Error with a binary restart file (Wed Mar 26 2008 - 18:07:51 CDT)
  • AMBER: RE: Re: AMBER: AMBER install problem (Thu Mar 13 2008 - 12:35:10 CDT)
  • AMBER: AMBER install problem (Fri Mar 07 2008 - 12:12:08 CST)
• Klenner_at_bioinformatik.uni-frankfurt.de
  • Re: AMBER: Lennard-Jones parameters (Wed Feb 27 2008 - 16:11:50 CST)
• Kliman, Michal
  • AMBER: protonated guanine, cytosine parameters (Tue Jul 22 2008 - 17:22:19 CDT)
  • AMBER: Protonated Phosphate Problem (Tue Jul 01 2008 - 12:20:14 CDT)
• Lachele Foley (Lists)
  • Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters (Fri Nov 07 2008 - 15:25:18 CST)
  • Re: AMBER: Glycam (Thu Nov 06 2008 - 09:01:48 CST)
  • Re: AMBER: about SASA and AMBER (Mon Oct 20 2008 - 12:07:06 CDT)
  • Re: AMBER: Need help... High energies for complex... (Tue Sep 09 2008 - 09:09:06 CDT)
  • Re: AMBER: No bond and angle parameters for - -????? (Thu Sep 04 2008 - 09:03:08 CDT)
  • Re: AMBER: Glycoprotein once again.......... (Thu Aug 14 2008 - 08:28:30 CDT)
  • Re: AMBER: Querry (Wed Aug 13 2008 - 10:03:49 CDT)
  • Re: AMBER: Querry about simulating a glycopeptide (Tue Aug 12 2008 - 09:03:14 CDT)
  • Re: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:44:07 CDT)
  • Fwd: AMBER: prepare an initial structure in Amber (Fri Aug 01 2008 - 09:52:50 CDT)
  • Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP (Fri Jul 25 2008 - 09:47:54 CDT)
  • Re: AMBER: querry (Tue Jul 22 2008 - 08:55:08 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Tue Jul 15 2008 - 09:45:19 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Fri Jul 11 2008 - 09:19:17 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Thu Jul 10 2008 - 12:24:41 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Tue Jul 08 2008 - 11:08:52 CDT)
  • Re: AMBER: AMBER file preparation for protein-carbohydrate complex (Thu May 22 2008 - 16:39:44 CDT)
  • Re: AMBER: atom type in glycam06 (Wed May 21 2008 - 08:37:51 CDT)
  • Re: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 14:21:43 CDT)
  • Re: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 13:25:53 CDT)
  • Re: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 11:13:41 CDT)
  • AMBER: prmtop spec trivia (Tue Apr 29 2008 - 10:07:29 CDT)
  • Re: AMBER: nmode output (Fri Apr 25 2008 - 09:09:37 CDT)
  • Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" (Thu Apr 24 2008 - 14:16:50 CDT)
  • AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" (Thu Apr 24 2008 - 09:22:42 CDT)
• Larry Layne
  • AMBER: alascan error (Wed Dec 17 2008 - 14:19:22 CST)
  • AMBER: alascan MUTANT_KEEP error (Tue Dec 16 2008 - 13:07:51 CST)
  • Re: AMBER: MM_PBSA binding error (Tue Nov 04 2008 - 07:51:22 CST)
  • RE: AMBER: MM_PBSA binding error (Fri Oct 31 2008 - 07:56:42 CDT)
  • AMBER: MM_PBSA binding error (Thu Oct 30 2008 - 13:54:24 CDT)
• Lars Skjærven
  • Re: AMBER: ptraj & imaging of velocities (Tue Sep 02 2008 - 08:15:49 CDT)
  • AMBER: ptraj and netcdf with AmberTools1.2 ? (Mon Sep 01 2008 - 04:11:23 CDT)
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 05:38:02 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 13:36:06 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:23:31 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 17:03:14 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 09:58:01 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 08:32:26 CDT)
  • AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 05:25:09 CDT)
  • Re: AMBER: potassium ion (Thu Jun 12 2008 - 12:46:36 CDT)
  • AMBER: potassium ion (Thu May 22 2008 - 08:09:59 CDT)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 09:28:24 CDT)
  • Re: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 16:01:54 CDT)
  • Re: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 14:17:23 CDT)
  • Re: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 07:36:20 CDT)
  • AMBER: Protein rotating out of box (Thu Mar 27 2008 - 16:34:48 CDT)
  • Re: AMBER: NVE energy and temperature drift (Fri Mar 07 2008 - 11:34:33 CST)
  • AMBER: NVE energy and temperature drift (Fri Mar 07 2008 - 09:36:48 CST)
  • Re: AMBER: matrix correl (Wed Feb 20 2008 - 11:35:30 CST)
  • Re: AMBER: Regarding:PME and neturalization (Wed Feb 20 2008 - 02:39:59 CST)
  • Re: AMBER: Amber : neutralizing without adding ions (Mon Jan 14 2008 - 09:41:55 CST)
  • Re: AMBER: check COM velocity (Fri Jan 04 2008 - 10:36:53 CST)
• Laura Benton
  • AMBER: sp carbon notation? (Wed Jun 18 2008 - 18:16:35 CDT)
• Li Dawei
  • AMBER: Energy calculation and replica exchange in Amber9 (Thu Mar 13 2008 - 08:50:49 CDT)
• Lili Peng
  • Re: AMBER: AMBER minimization problems (Sat Dec 20 2008 - 17:53:54 CST)
  • Re: AMBER: AMBER minimization problems (Wed Dec 17 2008 - 10:35:58 CST)
  • AMBER: AMBER minimization problems (Wed Dec 17 2008 - 01:14:00 CST)
  • Re: AMBER: Force field for Gd3+ (metal ion)? (Thu Nov 20 2008 - 18:00:29 CST)
  • Re: AMBER: xLeap error (Mon Nov 10 2008 - 15:49:53 CST)
  • AMBER: xLeap error (Mon Nov 10 2008 - 14:45:58 CST)
  • AMBER: Force field for Gd (gadolinium)? (Thu Nov 06 2008 - 03:05:26 CST)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 19:29:36 CST)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 17:25:32 CST)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 00:17:27 CST)
  • AMBER: Problem running implicit minimization (Mon Mar 03 2008 - 23:10:52 CST)
  • AMBER: Using restart files (Tue Feb 26 2008 - 17:36:50 CST)
  • Re: AMBER: Error while compiling Amber (Thu Feb 14 2008 - 16:24:02 CST)
  • Re: AMBER: Error while compiling Amber (Thu Feb 14 2008 - 11:41:18 CST)
  • Re: AMBER: Error while compiling Amber (Thu Feb 14 2008 - 03:09:22 CST)
  • AMBER: mpd error in submitting parallel job (Thu Feb 14 2008 - 03:11:25 CST)
  • Re: AMBER: Error while compiling Amber (Sat Feb 09 2008 - 13:11:39 CST)
  • Re: AMBER: Error while compiling Amber (Fri Feb 08 2008 - 19:51:55 CST)
  • AMBER: Error while compiling Amber (Thu Feb 07 2008 - 19:14:42 CST)
  • AMBER: radial distribution function in ptraj (Tue Jan 29 2008 - 03:36:37 CST)
  • AMBER: Units of atomicfluct (Wed Jan 23 2008 - 18:27:16 CST)
  • AMBER: Using VMD to calculate end-to-end distance? (Mon Jan 14 2008 - 16:41:55 CST)
• Lillian Chong
  • AMBER: calibration of constant pH simulations (Wed Apr 30 2008 - 12:17:47 CDT)
• Lin, Pohan
  • RE: AMBER: Missing gaff angle parameters for dimethyl esters (Tue Jun 03 2008 - 14:56:32 CDT)
  • AMBER: Missing gaff angle parameters for dimethyl esters (Mon Jun 02 2008 - 16:20:24 CDT)
• linfu
  • RE: RE: AMBER: about QMMM output (Sat Jul 05 2008 - 21:25:47 CDT)
  • Re: RE: AMBER: about QMMM output (Fri Jul 04 2008 - 12:09:23 CDT)
  • AMBER: about QMMM output (Thu Jul 03 2008 - 21:40:33 CDT)
• Lisa Perez
  • AMBER: neutral C-terminus and N-terminus parameters for amber (Fri May 09 2008 - 12:32:13 CDT)
• Lishan Yao
  • Re: AMBER: Electric field on atoms in equallibrium (Tue Apr 01 2008 - 13:21:20 CDT)
  • AMBER: Electric field on atoms in equallibrium (Tue Apr 01 2008 - 11:55:39 CDT)
• liu junjun
  • Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE (Tue Sep 30 2008 - 13:48:11 CDT)
  • Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE (Tue Sep 30 2008 - 14:17:26 CDT)
  • AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE (Tue Sep 30 2008 - 13:07:09 CDT)
  • Re: AMBER: problems of antechamber (Sun Jan 20 2008 - 09:21:49 CST)
  • AMBER: problems of antechamber (Thu Jan 17 2008 - 20:15:54 CST)
• llduan_at_itcc.nju.edu.cn
  • AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu (Sat Dec 13 2008 - 08:36:45 CST)
• Lorenzo Gontrani
  • Re: AMBER: PGI amber9 problems (Fri May 16 2008 - 07:02:53 CDT)
  • AMBER: PGI amber9 problems (Fri May 16 2008 - 04:52:21 CDT)
• luzhenw1_at_msu.edu
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:17:28 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 09:10:49 CST)
  • AMBER: generate topology file for alanine scanning (mmpbsa) (Thu Aug 14 2008 - 14:32:56 CDT)
  • AMBER: problem with minimization (Thu Aug 07 2008 - 10:13:17 CDT)
  • AMBER: about RMSD per residue (Wed Jul 16 2008 - 08:48:05 CDT)
  • AMBER: RMSD per residue (Tue Jul 15 2008 - 15:28:08 CDT)
  • AMBER: how generate the final output file using mmpbsa (Fri May 23 2008 - 15:49:33 CDT)
• Lwin, ThuZar
  • RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . . (Tue Mar 18 2008 - 11:45:49 CDT)
  • AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). (Fri Mar 14 2008 - 10:32:25 CDT)
  • AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) (Thu Mar 13 2008 - 19:13:57 CDT)
• Lynn
  • AMBER: protein-ligand complex problem (Thu Apr 10 2008 - 17:51:32 CDT)
  • AMBER: question about antechamber (Thu Jan 03 2008 - 08:32:56 CST)
• Lynn F. Ten Eyck
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Fri May 16 2008 - 10:12:49 CDT)
  • Re: AMBER: cannot read big .pdb files (Sat May 10 2008 - 11:37:02 CDT)
  • Re: AMBER: problems with 10-12 potential in amber8 sander (Thu Feb 28 2008 - 16:54:47 CST)
  • AMBER: Antechamber/mopac query (Fri Feb 08 2008 - 19:15:12 CST)
• M. L. Dodson
  • Re: AMBER: SMD-related questions (Mon Dec 29 2008 - 12:25:19 CST)
  • Re: AMBER: How to build a cubic box of a newly synthesized compound? (Wed Dec 24 2008 - 11:45:23 CST)
  • Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 14:00:13 CST)
  • Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 10:45:46 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 15:36:08 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 11:52:48 CST)
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 09:43:52 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Mon Nov 10 2008 - 12:23:17 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Fri Nov 07 2008 - 17:15:06 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 17:49:49 CST)
  • AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 12:31:07 CST)
  • Re: AMBER: Steered MD and Jarzynski in pulling simulations (Wed Nov 05 2008 - 09:04:23 CST)
  • Re: AMBER: Install problems (Tue Sep 09 2008 - 13:41:07 CDT)
  • AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs (Thu Aug 21 2008 - 12:56:38 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 21:29:54 CDT)
  • Re: AMBER: Help compiling Nab programs for AMBER tools (Thu Aug 14 2008 - 14:50:51 CDT)
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 10:34:05 CDT)
  • AMBER: Re: FreeBSD "port" for AmberTools-1.2 (Wed Jul 23 2008 - 09:17:56 CDT)
  • Re: AMBER: FreeBSD "port" for AmberTools-1.2 (Tue Jul 22 2008 - 14:30:27 CDT)
  • AMBER: FreeBSD "port" for AmberTools-1.2 (Tue Jul 22 2008 - 14:15:48 CDT)
  • AMBER: AmberTools-1.1 port for FreeBSD (Thu Jul 17 2008 - 12:59:05 CDT)
  • Re: AMBER: bond command (Thu Jul 10 2008 - 13:34:33 CDT)
  • libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 (Wed Jun 18 2008 - 10:43:44 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Sat Jun 07 2008 - 09:53:57 CDT)
  • Re: AMBER: steered MD initial state (Tue May 06 2008 - 12:39:04 CDT)
  • Re: AMBER: steered MD initial state (Tue May 06 2008 - 12:27:03 CDT)
  • AMBER: steered MD initial state (Tue May 06 2008 - 11:04:09 CDT)
  • AMBER: dockmolecules in examples directory of AmberTools-1.0 (Thu Apr 03 2008 - 10:54:50 CDT)
  • Re: AMBER: Generating RESP charges (Tue Feb 19 2008 - 12:38:22 CST)
  • Re: AMBER: QM/MM: input conversion error (Fri Jan 25 2008 - 14:56:38 CST)
  • Re: AMBER: QM/MM: input conversion error (Thu Jan 24 2008 - 13:25:03 CST)
  • Re: AMBER: QM/MM: input conversion error (Thu Jan 24 2008 - 12:31:44 CST)
• Madhumalar Arumugam
  • AMBER: ANAL (Wed Oct 29 2008 - 03:44:57 CDT)
• Madjid Taghdir
  • AMBER: problem with antech amber (Mon Mar 10 2008 - 10:07:16 CDT)
• Maicon Sartin
  • Re: AMBER: Source FIles of SANDER (Wed Aug 27 2008 - 07:47:47 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:18:49 CDT)
  • AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:17:39 CDT)
  • AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:17:39 CDT)
  • Re: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:52:01 CDT)
  • AMBER: SANDER Parallel (Thu Aug 21 2008 - 07:36:56 CDT)
  • AMBER: Fwd: Welcome to amber (Thu Aug 21 2008 - 07:33:08 CDT)
• Majeed Shaik
  • RE: AMBER: Cutoff list exceeds largest sphere in unit cell (Thu Sep 11 2008 - 06:49:09 CDT)
  • RE: AMBER: Cutoff list exceeds largest sphere in unit cell (Wed Sep 10 2008 - 12:44:52 CDT)
  • RE: AMBER: Cutoff list exceeds largest sphere in unit cell (Wed Sep 10 2008 - 12:42:58 CDT)
  • AMBER: Cutoff list exceeds largest sphere in unit cell (Wed Sep 10 2008 - 09:54:58 CDT)
  • RE: AMBER: Changes in the Amber web site (Mon Sep 08 2008 - 10:07:21 CDT)
  • AMBER: amber minimisation (Mon Sep 08 2008 - 07:32:17 CDT)
• Manikandan Chandrasekaran
  • Re: AMBER: compilation problem (Fri Sep 26 2008 - 22:51:50 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Fri Sep 19 2008 - 14:49:41 CDT)
  • Re: AMBER: Some Problems With the Installation of Ambertools (Thu Sep 18 2008 - 11:43:39 CDT)
  • AMBER: Some Problems With the Installation of Ambertools (Wed Sep 17 2008 - 18:21:06 CDT)
• Marc Cozzi
  • AMBER: Amber9 fails test.parallel (Wed Jan 30 2008 - 12:58:41 CST)
• Marc Lindner
  • AMBER: mm_pbsa: vertex atom mismatch (Tue Feb 05 2008 - 04:47:23 CST)
  • Re: AMBER: mmpbsa binding energy (Thu Jan 24 2008 - 04:16:23 CST)
  • AMBER: distorted aromatic rings (Wed Jan 23 2008 - 04:40:20 CST)
• Marcela Madrid
  • Re: AMBER: antechamber (Tue Oct 21 2008 - 12:02:54 CDT)
  • AMBER: antechamber (Thu Oct 16 2008 - 15:37:07 CDT)
• Marcelo Puiatti
  • AMBER: organic solvents (Fri Nov 14 2008 - 17:20:30 CST)
  • AMBER: Estimating dielectric constant (Wed Apr 09 2008 - 09:42:40 CDT)
  • Re: AMBER: question on antechamber: jaguar ouput (Tue Mar 11 2008 - 13:35:10 CDT)
• Marcin Krol
  • AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params (Tue May 13 2008 - 08:44:48 CDT)
  • Re: AMBER: imaging problem (Tue Apr 15 2008 - 08:38:07 CDT)
  • Re: AMBER: imaging problem (Tue Apr 15 2008 - 08:16:01 CDT)
  • AMBER: imaging problem (Tue Apr 15 2008 - 06:54:30 CDT)
  • Re: AMBER: disulfide bridge with ff03ua FF (Wed Feb 13 2008 - 09:32:18 CST)
  • Re: AMBER: disulfide bridge with ff03ua FF (Mon Feb 11 2008 - 09:01:30 CST)
  • Re: AMBER: disulfide bridge with ff03ua FF (Fri Feb 08 2008 - 11:00:25 CST)
  • AMBER: disulfide bridge with ff03ua FF (Thu Feb 07 2008 - 08:50:16 CST)
  • AMBER: disulfide bridge with ff03ua FF (Thu Jan 31 2008 - 12:30:56 CST)
• Marco A. Lopez
  • RE: AMBER: principal component analysis (Mon Feb 04 2008 - 13:22:36 CST)
• Marek Malý
  • Re: AMBER: Explanation of the energy unit ? (Wed Sep 10 2008 - 05:24:17 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 15:19:47 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 15:15:43 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 14:02:37 CDT)
  • Re: AMBER: Explanation of the energy unit ? (Mon Sep 08 2008 - 10:01:10 CDT)
  • AMBER: Explanation of the energy unit ? (Sat Sep 06 2008 - 09:29:06 CDT)
• Margaret Johnson
  • AMBER: PMEMD with AMOEBA parms including a lone pair site (Tue Nov 18 2008 - 20:29:04 CST)
• Maria Frushicheva
  • AMBER: error in reading namelist cntrl (Mon Jun 30 2008 - 15:02:50 CDT)
• Marie Brut
  • AMBER: Atomic restraints (Mon Jan 21 2008 - 07:34:42 CST)
• Marina Grabar
  • AMBER: interaction energies (Mon Dec 08 2008 - 05:29:36 CST)
  • Re: AMBER: anal (Tue May 20 2008 - 04:20:04 CDT)
  • AMBER: anal (Mon May 19 2008 - 08:30:13 CDT)
• Marisa Frechero
  • RE: AMBER: Install problems (Mon Sep 08 2008 - 13:35:08 CDT)
  • AMBER: (Wed Sep 03 2008 - 13:38:06 CDT)
• Mark Abraham
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 02:02:14 CDT)
  • Re: AMBER: is in vacuo simulation neccessary? (Mon May 26 2008 - 00:44:20 CDT)
  • AMBER: reading PDB trajectory (Thu May 15 2008 - 22:49:55 CDT)
• Mark M Huntress
  • AMBER: resp charges in parameterization (Wed Nov 12 2008 - 10:24:55 CST)
• Mark Williamson
  • Re: AMBER: organic solvents (Fri Nov 14 2008 - 17:28:10 CST)
  • Re: AMBER: xLeap error (Mon Nov 10 2008 - 15:58:27 CST)
  • Re: AMBER: xleap fails to savemol2 (Mon Sep 22 2008 - 13:43:35 CDT)
  • Re: AMBER: Install problems (Tue Sep 09 2008 - 13:16:38 CDT)
  • Re: AMBER: Install problems (Mon Sep 08 2008 - 18:56:35 CDT)
  • Re: AMBER: XLeap Problems (Wed Jul 09 2008 - 11:41:51 CDT)
  • Re: AMBER: nmode analysis (Mon Jun 30 2008 - 07:12:09 CDT)
  • Re: AMBER: SIZE.h problems (Sat Jun 21 2008 - 16:22:37 CDT)
  • Re: AMBER: questions about gaff (Wed Jun 18 2008 - 21:35:42 CDT)
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Sat Jun 14 2008 - 10:13:18 CDT)
  • Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu (Tue Jun 10 2008 - 06:31:48 CDT)
  • Re: AMBER: Amber compilation with ifort (Wed Feb 06 2008 - 16:24:16 CST)
  • Re: AMBER: principal component analysis (Mon Feb 04 2008 - 06:55:47 CST)
  • Re: AMBER: Amber9 fails test.parallel (Wed Jan 30 2008 - 14:04:31 CST)
• Markus Kaukonen
  • Re: AMBER: Initial velocities based on date and time are NOT changing ? (Tue Dec 16 2008 - 03:41:40 CST)
  • AMBER: Initial velocities based on date and time are NOT changing ? (Mon Dec 15 2008 - 07:14:38 CST)
  • AMBER: QM/MM and unpaired spin (Mon Dec 01 2008 - 01:30:02 CST)
  • AMBER: Comment: constant pH, non-integer charge -> weird error (Sun Sep 14 2008 - 02:51:58 CDT)
  • AMBER: resp and 99999 (Fri Sep 05 2008 - 01:13:10 CDT)
  • Re: AMBER: help me for filling a nanotube with water?? (Wed Aug 13 2008 - 01:29:48 CDT)
  • Re: AMBER: Constant pH with new parameters (amber10) (Sun Jul 20 2008 - 03:08:35 CDT)
  • Re: AMBER: Constant pH with new parameters (amber10) (Sat Jul 12 2008 - 14:24:05 CDT)
  • AMBER: Constant pH with new parameters (amber10) (Tue Jul 08 2008 - 02:39:57 CDT)
  • AMBER: Hydration free energies of charged ions using PME (Wed May 28 2008 - 01:51:26 CDT)
  • AMBER: solvateOct produces strange residues compared to solvateCap (Fri Apr 04 2008 - 03:08:53 CDT)
  • AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water (Mon Mar 31 2008 - 01:34:48 CDT)
• Marta Rossini
  • RE: AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 07:57:04 CDT)
  • RE: AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 06:00:52 CDT)
  • AMBER: Select specific residues (leap) (Mon Mar 31 2008 - 04:28:31 CDT)
• Marudachalam S
  • AMBER: Amber on linux (Wed Nov 19 2008 - 11:58:10 CST)
• Maryam Hamzehee
  • Re: AMBER: problem with toturial A3 (MM-PBSA) (Sun Dec 14 2008 - 05:25:00 CST)
  • AMBER: problem with toturial A3 (MM-PBSA) (Sat Dec 13 2008 - 09:22:58 CST)
• mathew k varghese
  • Re: AMBER: AMBER parameters for Chlorophyll (Sat Feb 16 2008 - 08:09:30 CST)
• Mathy Froeyen
  • Re: AMBER: Calculate number of ions (Tue May 13 2008 - 02:50:29 CDT)
• Matthew Danielson
  • AMBER: AmberTools 1.0 installation error: x86_64 (Fri Jun 20 2008 - 10:44:21 CDT)
• Matthew Peterson
  • Re: AMBER: mmpbsa (Tue Sep 02 2008 - 08:57:24 CDT)
• Matthew Tessier
  • RE: AMBER: Running md using glycam in AMBER (Thu Dec 11 2008 - 14:52:28 CST)
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 11:09:16 CST)
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:40:43 CST)
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:15:56 CST)
  • RE: AMBER: AMBER force field for glycolipid (Thu Oct 09 2008 - 08:57:59 CDT)
  • RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 10:07:22 CDT)
• Max
  • AMBER: NONBONDED_PARM_INDEX (Wed Jul 02 2008 - 03:54:35 CDT)
• meandme meandme
  • AMBER: amber 10 parallel cpu utlization (Mon Sep 15 2008 - 12:30:49 CDT)
  • AMBER: parallel amber 10 sander.MPI (low cpu utilization) (Mon Sep 15 2008 - 12:27:06 CDT)
• Melinda Layten
  • Re: AMBER: cnstph test case failure or expected divergence? (Tue Oct 21 2008 - 10:38:31 CDT)
  • AMBER: cnstph test case failure or expected divergence? (Mon Oct 20 2008 - 15:23:08 CDT)
  • Re: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 09:55:40 CDT)
  • Re: AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 12:43:23 CST)
• Mengjuei Hsieh
  • Re: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 20:39:23 CST)
  • Re: AMBER: Amber installation (Fri Apr 11 2008 - 16:39:48 CDT)
• Mey Khalili
  • Re: AMBER: can't make antechamber work for regular nucleotides (Mon Mar 17 2008 - 08:59:01 CDT)
  • AMBER: can't make antechamber work for regular nucleotides (Thu Mar 13 2008 - 09:03:45 CDT)
  • AMBER: Fwd: positive potential energy and large 1-4 EEL (Fri Mar 07 2008 - 10:54:28 CST)
• mhamed_at_birzeit.edu
  • AMBER: FW: Amber 9 (Tue Sep 30 2008 - 12:22:07 CDT)
• Michael Entz
  • AMBER: Hydroxyproline in AMBER (Wed Jul 23 2008 - 10:40:05 CDT)
• Michael Lerner
  • AMBER: Folate parameters (Wed Oct 29 2008 - 12:03:06 CDT)
• Miguel Ortiz-Lombardía
  • Re: AMBER: mm-pbsa / sander.MPI ? (Thu Aug 14 2008 - 02:58:54 CDT)
  • Re: AMBER: MM-PBSA (Wed Jun 18 2008 - 09:41:12 CDT)
  • AMBER: ptraj analyze modes from nmode (Sat May 31 2008 - 10:40:50 CDT)
  • Re: AMBER: how generate the final output file using mmpbsa (Sat May 24 2008 - 01:40:40 CDT)
• Mike Hanby
  • AMBER: Amber 10 on the BlueGene (Mon Jul 28 2008 - 11:15:58 CDT)
  • RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 (Fri Jul 25 2008 - 11:16:37 CDT)
  • AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 (Thu Jul 24 2008 - 16:47:34 CDT)
• Mike Summers
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Tue Apr 22 2008 - 07:22:18 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Tue Apr 22 2008 - 07:03:53 CDT)
  • AMBER: Back on track (Mon Jan 28 2008 - 19:39:32 CST)
• Mike Wykes
  • AMBER: Non aqueous implicit solvation (Fri Feb 29 2008 - 12:56:01 CST)
  • RE: AMBER: Is boiling point a good way to validate solvent paramters? (Fri Feb 15 2008 - 09:27:35 CST)
  • AMBER: Is boiling point a good way to validate solvent paramters? (Wed Feb 13 2008 - 08:08:25 CST)
  • AMBER: Nudged Elastic Band initial heating problem (Tue Jan 08 2008 - 04:42:09 CST)
• Ming Lei
  • Re: AMBER: AMBER-8 parallel installation - test run failure (Thu Jan 03 2008 - 08:08:46 CST)
• Mingfeng Yang
  • AMBER: ptraj: how to select all non-hydrogen atoms (Wed Dec 03 2008 - 13:37:00 CST)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 11:58:56 CDT)
  • AMBER: massively parallel computation (Tue May 20 2008 - 02:03:51 CDT)
• mirzo_at_jinr.ru
  • Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 04:23:08 CST)
  • AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 02:01:42 CST)
• mkseo
  • AMBER: multiple dihedral restraints using group (in Amber 10) (Tue Jun 17 2008 - 16:00:50 CDT)
  • AMBER: multiple dihedral restraints using group (Mon Mar 31 2008 - 12:11:30 CDT)
• Mohd Farid Ismail
  • RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program (Tue Mar 04 2008 - 19:09:52 CST)
  • AMBER: Amber 8 Equivalent of the Amber 5 - Edit program (Wed Feb 06 2008 - 16:07:55 CST)
• moitrayee_at_mbu.iisc.ernet.in
  • AMBER: ld: cannot find -lgcc_s (Fri Dec 12 2008 - 07:52:08 CST)
  • Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Thu Oct 30 2008 - 07:49:44 CDT)
  • RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Thu Oct 30 2008 - 00:56:51 CDT)
  • AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Wed Oct 29 2008 - 08:07:23 CDT)
  • RE: AMBER: problem with amber8 installation (Sat Oct 25 2008 - 01:36:27 CDT)
  • Re: AMBER: problem with running mm-pbsa (Sat Oct 25 2008 - 01:30:11 CDT)
  • AMBER: problem with amber8 installation (Fri Oct 24 2008 - 07:20:17 CDT)
  • AMBER: problem with amber8 installation (Fri Oct 24 2008 - 07:22:40 CDT)
  • AMBER: problem with running mm-pbsa (Fri Oct 24 2008 - 02:14:49 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Wed Sep 17 2008 - 01:43:49 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 13:12:24 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 13:01:59 CDT)
  • AMBER: problem with editing with xleap (Tue Sep 16 2008 - 10:50:38 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Tue Sep 16 2008 - 06:39:25 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 10:36:31 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 06:46:56 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 06:20:19 CDT)
  • AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 01:35:39 CDT)
  • Re: AMBER: Nonbonded FE parameter missing in frcmod. (Thu Sep 11 2008 - 12:16:34 CDT)
  • AMBER: Nonbonded FE parameter missing in frcmod. (Thu Sep 11 2008 - 07:22:58 CDT)
  • AMBER: antechamber cannot generate prep files (Thu Sep 04 2008 - 06:47:17 CDT)
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 06:41:21 CDT)
  • AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 01:56:24 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 23:51:50 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 11:55:40 CDT)
  • Re: AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 17:10:03 CDT)
  • AMBER: frcmod:attn needs revision (Tue Aug 12 2008 - 17:18:02 CDT)
  • AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 16:20:19 CDT)
• mon_sharma_at_research.iiit.ac.in
  • AMBER: Minimizaton stops after Ncyc steps only (Mon Sep 15 2008 - 11:34:22 CDT)
• mori_at_cerm.unifi.it
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:09:28 CST)
  • Re: AMBER: ligand complexed simulation (Tue Jun 17 2008 - 06:15:11 CDT)
  • Re: AMBER: ligand unit charge is not zero (Thu May 29 2008 - 04:17:55 CDT)
  • AMBER: MM_PBSA problem in binding_energy (Wed May 14 2008 - 09:17:40 CDT)
  • AMBER: mm_pbsa problem: bad atom type: IP (Thu May 08 2008 - 06:59:12 CDT)
• musa özboyacý
  • AMBER: Switching function in NAMD (Tue Dec 23 2008 - 13:52:37 CST)
  • AMBER: Solvatebox problem (Fri Dec 19 2008 - 04:24:56 CST)
  • Re: AMBER: Metal parameter values (Thu Oct 23 2008 - 14:09:35 CDT)
  • AMBER: Metal parameter values (Thu Oct 23 2008 - 06:59:13 CDT)
  • AMBER: Error in creating topology file (Mon Oct 20 2008 - 06:00:48 CDT)
• Myunggi Yi
  • Re: AMBER: Temperature regulation (Tue Sep 16 2008 - 16:28:21 CDT)
  • Re: AMBER: Amber tools 1.2 test failure (installation) (Thu Jul 24 2008 - 12:09:11 CDT)
  • AMBER: Amber tools 1.2 test failure (installation) (Mon Jul 21 2008 - 17:17:05 CDT)
  • Re: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 11:06:36 CDT)
  • Re: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 08:14:51 CDT)
  • Re: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 07:52:55 CDT)
  • Re: AMBER: cross correlation function using iRED matrix (Wed Jun 18 2008 - 13:07:03 CDT)
  • Re: AMBER: Eigenmode dynamics - imaging traj (Wed Jun 18 2008 - 08:33:07 CDT)
• n.gandhiau_at_gmail.com
  • Re: AMBER: AMBER file preparation for protein-carbohydrate complex (Sun May 25 2008 - 02:17:55 CDT)
• N.R. Jena
  • Re: AMBER: reg unstability of structure in md (Fri Dec 05 2008 - 00:48:50 CST)
  • Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 22:13:44 CST)
  • Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 07:08:45 CST)
  • Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 05:01:36 CST)
  • AMBER: MM/GBSA Error during deccomposition (Wed Dec 03 2008 - 06:01:04 CST)
• nag raj
  • RE: AMBER: Regarding binding free energy calculation using MM_PBSA method (Thu May 22 2008 - 07:18:59 CDT)
  • AMBER: Regarding binding free energy calculation using MM_PBSA method (Wed May 21 2008 - 02:01:14 CDT)
  • AMBER: Entropy calculation (Thu Jan 31 2008 - 06:47:51 CST)
  • AMBER: Entropy calculation (Wed Jan 30 2008 - 03:51:26 CST)
• Naser Alijabbari
  • AMBER: SPCFW temperature oscillations (Mon Nov 17 2008 - 22:19:12 CST)
  • AMBER: process_mdout modify (Tue Nov 04 2008 - 00:20:07 CST)
  • Re: AMBER: SPCFW problems (Tue Oct 28 2008 - 12:57:59 CDT)
  • Re: AMBER: SPCFW problems (Tue Oct 28 2008 - 10:50:49 CDT)
  • AMBER: SPCFW problems (Mon Oct 27 2008 - 21:37:12 CDT)
  • AMBER: Origin of periodic box (Wed Oct 15 2008 - 20:34:00 CDT)
  • AMBER: removing COM and rotation in explicit solvation (Sun Oct 12 2008 - 15:02:22 CDT)
  • AMBER: nscm code (Fri Oct 10 2008 - 00:05:59 CDT)
  • Re: AMBER: Sources of disruption during NVE (Wed Oct 01 2008 - 20:10:43 CDT)
  • AMBER: Sources of disruption during NVE (Wed Oct 01 2008 - 10:59:29 CDT)
  • AMBER: questions about previous posts (Mon Aug 11 2008 - 23:17:40 CDT)
• Navnit Kumar Mishra
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 07:04:20 CST)
  • Re: AMBER: radius of calcium ion in MM_PBSA (Mon Jul 28 2008 - 04:55:33 CDT)
  • Re: AMBER: MM-PBSA and delphi (Mon Jun 09 2008 - 04:05:38 CDT)
  • Re: AMBER: MM-PBSA for carbohydrates (Tue May 20 2008 - 06:25:20 CDT)
  • Re: AMBER: MM_PBSA output file (Fri May 09 2008 - 11:21:17 CDT)
• Neelanjana Sengupta
  • Re: AMBER: simulate dipole moment (Wed May 14 2008 - 16:14:54 CDT)
• Neha Gandhi
  • AMBER: Running md using glycam in AMBER (Thu Dec 11 2008 - 01:15:54 CST)
  • AMBER: RED vIII-lack of charges in mol2 (Sat Nov 29 2008 - 08:24:30 CST)
  • AMBER: Glycam (Wed Nov 05 2008 - 22:02:01 CST)
  • Re: AMBER: Query on restart file (Thu Oct 30 2008 - 21:22:49 CDT)
  • AMBER: Query on restart file (Thu Oct 30 2008 - 20:49:30 CDT)
  • AMBER: Ptraj pucker for pyranose (Mon Oct 13 2008 - 04:43:33 CDT)
  • Re: AMBER: Need help... High energies for complex... (Wed Sep 03 2008 - 07:41:16 CDT)
  • Re: AMBER: mmpbsa (Tue Sep 02 2008 - 07:49:33 CDT)
  • Re: AMBER: radius of calcium ion in MM_PBSA (Mon Jul 28 2008 - 03:46:50 CDT)
  • Re: AMBER: mm_pbsa incorrect complex prmtop file (Thu Jul 10 2008 - 03:02:27 CDT)
  • Re: AMBER: mm_pbsa incorrect complex prmtop file (Thu Jul 10 2008 - 03:02:27 CDT)
  • AMBER: MM-PBSA (Wed Jun 18 2008 - 02:37:33 CDT)
  • Re: AMBER: PCAL and polar contribution in the output file (Sun Jun 15 2008 - 08:56:20 CDT)
  • AMBER: PCAL and polar contribution in the output file (Fri Jun 13 2008 - 00:42:54 CDT)
  • Re: AMBER: MM-PBSA and delphi (Mon Jun 09 2008 - 04:57:21 CDT)
  • Re: AMBER: MM-PBSA and delphi (Mon Jun 09 2008 - 00:56:00 CDT)
  • AMBER: MM-PBSA and delphi (Mon Jun 09 2008 - 00:49:54 CDT)
  • AMBER: Query on MM-PBSA (Fri Jun 06 2008 - 00:46:32 CDT)
  • AMBER: AMBER file preparation for protein-carbohydrate complex (Thu May 22 2008 - 09:31:50 CDT)
  • AMBER: MM-PBSA for carbohydrates (Mon May 19 2008 - 21:07:24 CDT)
• Neil Bruce
  • Re: AMBER: Discontinuous Constant pH Restarts (Wed May 07 2008 - 15:21:28 CDT)
  • AMBER: Discontinuous Constant pH Restarts (Thu May 01 2008 - 08:41:21 CDT)
  • AMBER: Protonation states in Constant pH Simulations (Wed Apr 16 2008 - 07:54:44 CDT)
  • AMBER: Non-polar Parameters For MM_PBSA Calculation (Tue Feb 12 2008 - 05:54:02 CST)
• Neil J. Henson
  • Re: AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 19:03:52 CDT)
  • AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 18:16:17 CDT)
• Neko Maryam.
  • Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) (Mon Jan 14 2008 - 00:54:28 CST)
  • Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) (Mon Jan 14 2008 - 00:23:58 CST)
  • AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) (Sun Jan 13 2008 - 23:44:10 CST)
• neva_at_mmb.pcb.ub.es
  • AMBER: el w-end en galicia! (Wed Mar 05 2008 - 03:05:09 CST)
• neville forlemu
  • Re: AMBER: Non bond list error (Fri Oct 24 2008 - 14:40:08 CDT)
  • Re: AMBER: Non bond list error (Fri Oct 24 2008 - 13:12:58 CDT)
  • RE: AMBER: Non bond list error (Fri Oct 24 2008 - 11:34:44 CDT)
  • RE: AMBER: Non bond list error (Fri Oct 24 2008 - 00:13:13 CDT)
  • Re: AMBER: Non bond list error (Thu Oct 23 2008 - 23:48:01 CDT)
• Nick Holway
  • Re: AMBER: PMEND 9 compilation problems (Wed Jul 30 2008 - 08:50:42 CDT)
  • AMBER: PMEND 9 compilation problems (Tue Jul 29 2008 - 11:04:36 CDT)
• Nicolas Lux Fawzi
  • Re: AMBER: D2O (Mon Sep 15 2008 - 11:54:17 CDT)
• NIEL MICHAEL HENRIKSEN
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 18:07:27 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 14:31:13 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 08:50:05 CDT)
• Nina Fischer
  • AMBER: cis - trans isomerization (Thu Nov 27 2008 - 08:39:21 CST)
  • AMBER: leap - using default radius 1.500000 for HO3 (Wed Apr 16 2008 - 04:08:59 CDT)
• nurith_at_rice.edu
  • AMBER: RMSD restraint in umbrella sampling (Thu Sep 18 2008 - 15:36:24 CDT)
• oguz gurbulak
  • AMBER: a question about ff03ua (Thu Dec 25 2008 - 08:06:33 CST)
  • Re: AMBER: using packmol file in Amber (Mon Dec 15 2008 - 09:57:08 CST)
  • Re: AMBER: using packmol file in Amber (Fri Dec 05 2008 - 09:49:39 CST)
  • Re: AMBER: using packmol file in Amber (Thu Dec 04 2008 - 09:36:03 CST)
  • Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 08:02:59 CST)
  • Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 05:06:10 CST)
  • AMBER: using packmol file in Amber (Tue Nov 25 2008 - 09:49:19 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Sun Nov 23 2008 - 10:43:48 CST)
  • AMBER: question - gaff and leaprc.ff03ua (Wed Nov 19 2008 - 07:56:17 CST)
  • AMBER: load opls force field (Thu Nov 13 2008 - 04:38:11 CST)
  • AMBER: antechamber errors (Fri Oct 17 2008 - 08:07:37 CDT)
  • AMBER: velocity-verlet algorithm and ensembles (Wed Oct 08 2008 - 13:59:46 CDT)
  • RE: AMBER: a question (Mon Sep 29 2008 - 05:23:09 CDT)
  • RE: AMBER: a question (Mon Sep 29 2008 - 04:55:29 CDT)
  • AMBER: prepare an initial structure in Amber (Thu Jul 31 2008 - 11:58:24 CDT)
  • AMBER: using Velocity-Verlet algorithm (Thu Jun 12 2008 - 07:07:20 CDT)
  • AMBER: force field (Thu Mar 13 2008 - 17:00:58 CDT)
  • AMBER: Force fields (Tue Feb 26 2008 - 10:12:48 CST)
• Pablo Englebienne
  • AMBER: MM-PBSA error in Amber10: possible bug? (Fri Oct 31 2008 - 22:38:15 CDT)
  • Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support (Thu Sep 25 2008 - 14:07:48 CDT)
  • AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support (Wed Sep 24 2008 - 14:04:46 CDT)
  • Re: AMBER: Using Na+ ions as input to leap? - solved (Wed Aug 20 2008 - 14:25:25 CDT)
  • AMBER: Using Na+ ions as input to leap? (Wed Aug 20 2008 - 12:40:11 CDT)
• Pankaj R. Daga
  • AMBER: amber installation on cluster (Wed Jun 04 2008 - 12:27:57 CDT)
  • AMBER: SANDER BOMB in subroutine nonbond_list (Wed Jan 30 2008 - 09:13:45 CST)
  • RE: AMBER: QM/MM: input conversion error (Fri Jan 25 2008 - 16:02:47 CST)
  • RE: AMBER: QM/MM: input conversion error (Fri Jan 25 2008 - 14:11:24 CST)
  • RE: AMBER: QM/MM: input conversion error (Thu Jan 24 2008 - 13:05:31 CST)
  • AMBER: QM/MM: input conversion error (Thu Jan 24 2008 - 12:11:36 CST)
  • RE: AMBER: problems with restart of MD (Fri Jan 11 2008 - 12:34:13 CST)
  • AMBER: check COM velocity (Fri Jan 04 2008 - 10:06:26 CST)
• Panwang Zhou
  • Re: AMBER: DMSOBOX (Wed Jul 30 2008 - 02:31:53 CDT)
  • AMBER: How to obtain the oriented trajectories? (Thu Jul 03 2008 - 09:06:58 CDT)
  • Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? (Thu Jun 19 2008 - 10:34:02 CDT)
  • AMBER: How to extract solvent box information from .rst or .mdcrd files? (Thu Jun 19 2008 - 09:13:18 CDT)
• parul sharma
  • AMBER: AMBER : Inconsistent MD length and no of angles after ptraj (Fri Nov 07 2008 - 03:52:07 CST)
  • Re: AMBER: Addions in GB Mode? (Mon Oct 20 2008 - 04:25:22 CDT)
  • Re: AMBER: AddIons approach (Fri Oct 10 2008 - 06:44:41 CDT)
  • AMBER: AddIons approach (Fri Oct 10 2008 - 06:13:51 CDT)
• parvesh singh
  • Re: AMBER: mmpbsa molsurf.c error (Mon Sep 22 2008 - 04:26:29 CDT)
  • AMBER: acetone box (Wed Sep 17 2008 - 06:09:01 CDT)
• Patrick McCarren
  • Re: AMBER: Optimal compiling of amber on XT3 (Sat Nov 01 2008 - 02:13:08 CDT)
  • AMBER: Optimal compiling of amber on XT3 (Wed Oct 29 2008 - 23:30:56 CDT)
• Paul Johns
  • Re: AMBER: Heating POL3 Box Troubles (Wed Mar 19 2008 - 14:22:50 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Mon Mar 17 2008 - 15:07:02 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 16:01:22 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 14:13:02 CDT)
  • AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 13:44:44 CDT)
• Paulo Couto
  • AMBER: Tinker 4.3 (Fri Jan 18 2008 - 09:22:25 CST)
• Pavan G
  • AMBER: Ewald error estimate (Sun Jun 15 2008 - 09:22:48 CDT)
  • AMBER: ptraj rmsd calculation (Thu May 29 2008 - 13:08:36 CDT)
  • AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system (Thu May 22 2008 - 10:37:56 CDT)
• Peseckis, Steven M.
  • AMBER: RE: AMBER 10 failure to run in UBUNTU (Sun Jun 29 2008 - 19:13:38 CDT)
  • AMBER: (Thu Jun 26 2008 - 10:54:05 CDT)
• Peter Gannett
  • AMBER: Bonds getting shorter in sander (Fri Aug 01 2008 - 07:47:02 CDT)
  • Re: AMBER: MMPBSA error (Sat May 31 2008 - 09:15:40 CDT)
• Peter Kiss
  • Re: AMBER: ff99 and ff03 forcefield parameters (Fri May 23 2008 - 13:42:48 CDT)
  • Re: AMBER: ff99 and ff03 forcefield parameters (Fri May 23 2008 - 09:27:15 CDT)
  • AMBER: ff99 and ff03 forcefield parameters (Wed May 21 2008 - 16:01:47 CDT)
  • AMBER: parameters in ff03 and ff99 (Mon May 19 2008 - 06:21:21 CDT)
• Peter Podbev¹ek
  • RE: AMBER: F modified RNA is split in two parts when running sander simulated annealing (Thu Oct 02 2008 - 08:08:51 CDT)
  • AMBER: F modified RNA is split in two parts when running sander simulated annealing (Wed Oct 01 2008 - 04:01:52 CDT)
• Peter Varnai
  • AMBER: amber10 on SiCortex hardware (Fri Oct 03 2008 - 11:27:21 CDT)
• Peterson, Matthew W.
  • RE: AMBER: Ca ions not recognized (Tue Sep 30 2008 - 09:08:16 CDT)
  • RE: AMBER: MM_PBSA snapshot statistic calc problem (Mon Sep 29 2008 - 16:25:57 CDT)
  • AMBER: MM-PBSA Issue in Amber 10 (Tue Aug 12 2008 - 12:44:29 CDT)
• Peterson, Matthew W. (MPETERSON)
  • AMBER: MM-PBSA/NMODE in Amber 10 (Mon Sep 15 2008 - 15:37:41 CDT)
• Piotr Cieplak
  • RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 14:12:20 CST)
  • Re: AMBER: Model of deoxyadenosine in Cornell 95 paper (Wed Jul 16 2008 - 01:32:08 CDT)
  • Re: AMBER: Weighting factors in RESP charge fitting (Fri May 16 2008 - 13:46:51 CDT)
  • AMBER: printing dipoles in Amber10 (and earlier) (Fri May 02 2008 - 15:29:49 CDT)
• Piyush Wanjari
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Mon Aug 25 2008 - 17:00:33 CDT)
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Mon Aug 25 2008 - 14:52:37 CDT)
  • AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Wed Aug 20 2008 - 23:36:20 CDT)
• plmallip_at_mail.uh.edu
  • Re: AMBER: Sander crashes >99999 atoms (Thu Jun 12 2008 - 23:47:47 CDT)
  • AMBER: Sander crashes >99999 atoms (Thu Jun 12 2008 - 18:26:57 CDT)
• prabhakar g
  • Re: AMBER: Radial Distribution Function (Fri Dec 12 2008 - 20:31:48 CST)
  • Re: AMBER: Radial Distribution Function (Tue Dec 09 2008 - 21:33:27 CST)
  • AMBER: Radial Distribution Function (Mon Dec 08 2008 - 20:37:52 CST)
• Pradipta Bandyopadhyay
  • Re: AMBER: calibration of constant pH simulations (Wed Apr 30 2008 - 23:02:55 CDT)
• prateeksha s
  • Re: AMBER: Charge scheme for simulating protonated adenine (Thu Apr 10 2008 - 01:19:40 CDT)
  • Re: AMBER: Charge scheme for simulating protonated adenine (Thu Apr 10 2008 - 01:11:35 CDT)
  • Re: AMBER: Charge scheme for simulating protonated adenine (Fri Mar 21 2008 - 11:32:14 CDT)
  • Re: AMBER: Charge scheme for simulating protonated adenine (Fri Mar 21 2008 - 11:32:06 CDT)
  • AMBER: Charge scheme for simulating protonated adenine (Fri Mar 21 2008 - 01:58:19 CDT)
• Praveena Gopal
  • AMBER: NAN errors still exist (Fri Jun 06 2008 - 04:56:58 CDT)
  • Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC (Fri Jun 06 2008 - 01:16:40 CDT)
  • AMBER: NAN errors in Etot, EPtot, EKtot and EELEC (Thu Jun 05 2008 - 07:04:00 CDT)
  • AMBER: Torsional Forcing to generate PES? (Mon Jan 07 2008 - 22:42:04 CST)
• Prem Prakash Pathak
  • AMBER: unsubscribe amber (Tue Dec 16 2008 - 21:09:54 CST)
  • AMBER: (Mon Nov 03 2008 - 21:20:09 CST)
  • AMBER: study of protein stability in different ion using AMBER (Thu Mar 13 2008 - 01:20:31 CDT)
  • AMBER: Structure comparison-NMR and X-ray structure using AMBER9 (Mon Jan 07 2008 - 10:11:22 CST)
• priya priya
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 14:00:48 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 11:22:33 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 10:05:05 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 11:38:37 CST)
  • RE: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 10:16:34 CST)
  • AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:20:09 CST)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 13:04:26 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 12:44:13 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 12:44:13 CDT)
  • Re: AMBER: error while running REMD in amber9 (Thu Sep 25 2008 - 11:49:28 CDT)
  • Re: AMBER: to prepare pdb file fro unusual amino acid. (Thu Sep 25 2008 - 11:40:07 CDT)
  • AMBER: error while running REMD in amber9 (Wed Sep 24 2008 - 12:53:09 CDT)
  • AMBER: to prepare pdb file fro unusual amino acid. (Wed Sep 24 2008 - 03:03:06 CDT)
  • AMBER: Membrane simulations (Thu Aug 28 2008 - 03:31:57 CDT)
  • AMBER: calculating the energy from the restart file (Sat May 24 2008 - 09:03:46 CDT)
  • AMBER: distance matrix command (Wed Apr 30 2008 - 04:01:24 CDT)
  • AMBER: matrxi dist command (Tue Apr 22 2008 - 06:37:50 CDT)
  • AMBER: Microcannonical MD Reference (Fri Mar 07 2008 - 07:40:34 CST)
  • AMBER: vlimit exceeded error (Wed Jan 23 2008 - 05:27:37 CST)
• Purisima, Enrico
  • RE: AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 09:39:49 CDT)
  • RE: AMBER: Trajectory in "Sietraj" (Tue Jun 03 2008 - 08:55:20 CDT)
• Q733
  • AMBER: improper dihedrals in 03 united atom force field (Tue Jul 22 2008 - 21:00:03 CDT)
  • AMBER: dihedral energy calculation inconsistent with gaussian's result (Mon Jun 23 2008 - 21:43:36 CDT)
• Qi Yan
  • AMBER: How to get all eigenvalues by "analyze matrix" (Thu Jun 12 2008 - 12:39:52 CDT)
  • AMBER: Question for how to get all eigenvalues by "analyze matrix" (Wed Jun 11 2008 - 16:34:40 CDT)
  • RE: AMBER: MM-PBSA and delphi (Mon Jun 09 2008 - 14:58:28 CDT)
  • RE: AMBER: Problem of Ptraj analyze matrix (Mon Jun 09 2008 - 09:47:16 CDT)
  • AMBER: Problem of Ptraj analyze matrix (Mon Jun 09 2008 - 08:37:01 CDT)
  • AMBER: Problem of Ptraj analyze matrix (Sat Jun 07 2008 - 13:24:55 CDT)
  • AMBER: MM_PBSA output file (Fri May 09 2008 - 11:03:38 CDT)
  • RE: AMBER: How to transfer unformatted coordinates into formatted ones (Wed May 07 2008 - 21:55:18 CDT)
  • AMBER: nmode: number of atoms limitation (Wed May 07 2008 - 13:10:48 CDT)
  • AMBER: How to transfer unformatted coordinates into formatted ones (Wed May 07 2008 - 14:44:10 CDT)
  • AMBER: nmode: number of atoms limitation (Wed May 07 2008 - 13:25:58 CDT)
  • RE: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f (Mon Apr 14 2008 - 16:50:27 CDT)
  • AMBER: ASSERTion ' ier == 0 ' failed in nmode.f (Wed Apr 09 2008 - 18:24:08 CDT)
  • RE: AMBER: MPI run problem (Thu Apr 03 2008 - 16:59:27 CDT)
  • AMBER: MPI run problem (Thu Apr 03 2008 - 11:33:19 CDT)
  • RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Wed Mar 26 2008 - 09:42:54 CDT)
  • RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Tue Mar 25 2008 - 12:00:35 CDT)
  • RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Mon Mar 24 2008 - 15:50:40 CDT)
  • AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Mon Mar 24 2008 - 15:01:35 CDT)
  • RE: AMBER: mm_pbsa positive ELE (Mon Mar 17 2008 - 14:23:52 CDT)
  • AMBER: mm_pbsa positive ELE (Mon Mar 17 2008 - 13:20:21 CDT)
• Qi Zhang
  • Re: AMBER: problems with sleap (Mon Jun 16 2008 - 06:46:26 CDT)
  • AMBER: Problem with running refinement of NMR structures with RDCs (Sun Jun 15 2008 - 15:20:21 CDT)
• Qiang Li
  • Re: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 12:35:04 CDT)
  • Re: AMBER: meet problems in adding ions and waterbox (Wed Apr 02 2008 - 01:12:13 CDT)
  • AMBER: meet problems in adding ions and waterbox (Wed Apr 02 2008 - 00:12:31 CDT)
  • AMBER: meet problem in adding ions and waterbox (Sun Mar 30 2008 - 00:43:54 CDT)
• Qicun Shi
  • AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? (Wed Jul 30 2008 - 22:51:17 CDT)
• Qiuting Hong
  • Re: AMBER: how to enlarge the TIP3PBOX size (Fri Sep 26 2008 - 02:28:53 CDT)
  • AMBER: how to enlarge the TIP3PBOX size (Wed Sep 24 2008 - 17:56:10 CDT)
  • Re: AMBER: molecule drift out of water box? (Sun Sep 21 2008 - 20:43:38 CDT)
  • Re: AMBER: molecule drift out of water box? (Sun Sep 21 2008 - 15:22:19 CDT)
  • AMBER: molecule drift out of water box? (Fri Sep 19 2008 - 18:39:42 CDT)
  • Re: AMBER: problem in starting sander (Sun Jun 08 2008 - 21:40:52 CDT)
  • Re: AMBER: problem in starting sander (Sun Jun 08 2008 - 16:52:34 CDT)
  • AMBER: problem in starting sander (Sun Jun 08 2008 - 13:25:43 CDT)
  • AMBER: help MD running error (Fri May 23 2008 - 03:40:12 CDT)
  • AMBER: build proline (Fri May 16 2008 - 16:32:47 CDT)
  • AMBER: simulate dipole moment (Wed May 14 2008 - 15:52:33 CDT)
• Rabin
  • AMBER: unsubscribe amber (Wed Jun 25 2008 - 19:48:51 CDT)
  • AMBER: syn and anti conformation (Wed Jun 04 2008 - 14:29:58 CDT)
  • Re: AMBER: building quadruplex with nab (Tue May 20 2008 - 17:30:17 CDT)
  • AMBER: building quadruplex with nab (Tue May 13 2008 - 08:38:15 CDT)
  • Re: AMBER: nab (Tue May 13 2008 - 08:17:51 CDT)
  • AMBER: nab (Mon May 12 2008 - 19:40:54 CDT)
  • Re: AMBER: to unsubscribe email (Mon May 12 2008 - 16:29:56 CDT)
  • AMBER: to unsubscribe email (Mon May 12 2008 - 10:47:43 CDT)
  • AMBER: unable to compile AmberTools 1.0 (Mon May 05 2008 - 12:07:00 CDT)
• Rabone, Jeremy
  • AMBER: GAFF for organic crystals (Fri Jun 20 2008 - 03:05:18 CDT)
• Ragnarok sdf
  • AMBER: Help compiling Nab programs for AMBER tools (Thu Aug 14 2008 - 14:36:04 CDT)
• Rahaman, Asif
  • RE: AMBER: velocity autocorrelation function for SPC felxible water model (Thu May 08 2008 - 15:42:22 CDT)
  • AMBER: velocity autocorrelation function for SPC felxible water model (Thu May 08 2008 - 12:07:41 CDT)
• rai001_at_student.ucr.edu
  • Re: AMBER: question about ptraj (Thu Nov 13 2008 - 17:56:49 CST)
  • AMBER: question about ptraj (Thu Nov 13 2008 - 00:30:48 CST)
• raja pandian
  • Re: AMBER: disulfide bridge with ff03ua FF (Fri Feb 08 2008 - 22:17:48 CST)
  • Re: AMBER: disulfide bridge with ff03ua FF (Fri Feb 08 2008 - 10:17:50 CST)
• Rajendra P. OJHA
  • AMBER: (no subject) (Fri Dec 26 2008 - 06:35:12 CST)
  • AMBER: Error: PB bomb in pb_reslist(): maxnbr too small (Thu Sep 18 2008 - 09:34:15 CDT)
  • AMBER: Prepgen (Wed May 14 2008 - 04:45:47 CDT)
  • AMBER: Prepgen does not give correct result? (Fri May 09 2008 - 11:13:58 CDT)
• rams rams
  • AMBER: program to calculate rmsd (Mon Jun 16 2008 - 21:28:24 CDT)
  • AMBER: mm_pbsa error (Thu Apr 03 2008 - 11:28:56 CDT)
  • Re: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! (Sun Feb 10 2008 - 23:32:01 CST)
  • AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! (Thu Feb 07 2008 - 23:36:15 CST)
  • AMBER: segmentation fault while generating the covariance matrix (Tue Feb 05 2008 - 23:12:29 CST)
  • Re: AMBER: principal component analysis (Mon Feb 04 2008 - 09:45:17 CST)
  • AMBER: principal component analysis (Mon Feb 04 2008 - 06:26:31 CST)
  • AMBER: connectivity lose during the minimizations (Sat Jan 12 2008 - 05:40:21 CST)
  • Re: AMBER: connectivity problem (Wed Jan 09 2008 - 23:04:41 CST)
  • AMBER: connectivity problem (Wed Jan 09 2008 - 08:53:55 CST)
• Ramu Anandakrishnan
  • Re: AMBER: NAB documentation (Fri Jun 06 2008 - 23:08:51 CDT)
• ramu_at_vt.edu
  • AMBER: NAB parameter: wcons (Mon Sep 08 2008 - 16:06:54 CDT)
  • AMBER: NAB documentation for programmers (Wed Jun 04 2008 - 13:59:27 CDT)
• Ranga Swamy
  • Re: AMBER: Problem In Paralklel Amber (Mon Sep 29 2008 - 00:23:57 CDT)
  • AMBER: Problem In Paralklel Amber (Fri Sep 26 2008 - 06:10:13 CDT)
  • RE: AMBER: Compailation problum in Amber 10 (Fri Aug 08 2008 - 03:12:56 CDT)
  • AMBER: Problem While Installing Amber (Fri Jun 06 2008 - 04:34:17 CDT)
• Raphael Chaleil
  • AMBER: pmemd 9.0 compilation error (Mon Jan 14 2008 - 08:38:12 CST)
• Ray Luo
  • RE: AMBER: Problem with MMPBSA (Mon Dec 08 2008 - 13:47:15 CST)
  • RE: AMBER: Variable PBCAL values in MM-PBSA calculations (Thu Dec 04 2008 - 13:06:45 CST)
  • RE: AMBER: Variable PBCAL values in MM-PBSA calculations (Mon Dec 01 2008 - 19:55:37 CST)
  • RE: AMBER: MM_PBSA binding error (Tue Nov 04 2008 - 13:18:54 CST)
  • Re: AMBER: MM_PBSA binding error (Fri Oct 31 2008 - 17:16:41 CDT)
  • RE: AMBER: MM_PBSA binding error (Thu Oct 30 2008 - 14:35:36 CDT)
  • RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations (Wed Oct 29 2008 - 11:41:38 CDT)
  • RE: AMBER: something puzzled with mm_pbsa (Mon Oct 27 2008 - 11:56:54 CDT)
  • Re: AMBER: problem with running mm-pbsa (Fri Oct 24 2008 - 11:24:59 CDT)
  • Re: AMBER: something puzzled with mm_pbsa (Fri Oct 24 2008 - 11:21:59 CDT)
  • Re: AMBER: MM_PBSA problems in AMBER9 (Sun Oct 05 2008 - 22:20:01 CDT)
  • RE: AMBER: mm_pbsa error : Scale paremeter for PBSA (Fri Sep 05 2008 - 12:45:12 CDT)
  • RE: AMBER: united atom force field (Tue Aug 26 2008 - 18:11:47 CDT)
  • RE: AMBER: tan luo radii (Tue Aug 26 2008 - 14:12:57 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 12:44:16 CDT)
  • Re: AMBER: united atom force field (Fri Aug 22 2008 - 12:37:38 CDT)
  • RE: AMBER: Is G_disp calculated in MM_PBSA now? (Mon Aug 11 2008 - 14:33:14 CDT)
  • RE: AMBER: PBCAL in MM_PBSA (Fri Aug 08 2008 - 13:27:17 CDT)
  • RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params (Thu May 22 2008 - 15:37:04 CDT)
  • RE: AMBER: How to set a ZN atom radius for PB calculations (Thu May 22 2008 - 15:41:36 CDT)
  • Re: AMBER: mm_pbsa positive ELE (Mon Mar 17 2008 - 15:14:57 CDT)
  • Re: AMBER: mm_pbsa positive ELE (Mon Mar 17 2008 - 13:33:11 CDT)
  • Re: AMBER: disulfide bridge with ff03ua FF (Tue Feb 12 2008 - 16:52:37 CST)
• rdauria_at_uci.edu
  • Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist (Wed Jan 16 2008 - 12:19:27 CST)
  • AMBER: Problem with: Increase lastrst in the &cntrl namelist (Tue Jan 15 2008 - 22:46:04 CST)
• rebeca
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 07:33:19 CST)
  • AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 05:12:23 CST)
  • AMBER: The list-directed or NAMELIST READ statement cannot be completed (Thu Jul 17 2008 - 11:42:25 CDT)
  • AMBER: watershell cero? (Mon Jun 30 2008 - 11:22:11 CDT)
  • AMBER: REMD Amber10 : error in reading namelist cntrl (Fri Jun 27 2008 - 04:01:26 CDT)
  • AMBER: analysis REMD (Mon May 19 2008 - 13:41:15 CDT)
• rebeca_at_mmb.pcb.ub.es
  • AMBER: minimization stops or does not write anything (Thu Aug 14 2008 - 04:01:17 CDT)
  • AMBER: Not integral charge increasing with number of lipids (Thu Aug 07 2008 - 05:18:01 CDT)
  • AMBER: Problems with the charge (membrane simulation) (Wed Aug 06 2008 - 13:20:30 CDT)
  • AMBER: amb2gmx for big systems (Thu Jul 31 2008 - 05:40:39 CDT)
  • Re: AMBER: analysis REMD (Wed May 21 2008 - 12:03:59 CDT)
  • Re: AMBER: analysis REMD (Tue May 20 2008 - 13:31:30 CDT)
  • Re: AMBER: analysis REMD (Tue May 20 2008 - 05:49:00 CDT)
  • AMBER: tempi in Replica Exchange (Thu Apr 10 2008 - 04:23:00 CDT)
  • AMBER: measuring contacts: error "glibc detected" (Fri Mar 28 2008 - 07:26:42 CDT)
  • AMBER: implicit energy calculations (Thu Mar 13 2008 - 11:26:43 CDT)
  • Re: AMBER: problems with Replica Exchange (Thu Feb 28 2008 - 09:16:27 CST)
  • AMBER: problems with Replica Exchange (Thu Feb 28 2008 - 06:29:23 CST)
  • AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 (Thu Jan 24 2008 - 10:50:22 CST)
  • Re: AMBER: input options for replica exchange simulations (Thu Jan 10 2008 - 12:00:10 CST)
  • AMBER: input options for replica exchange simulations (Thu Jan 10 2008 - 10:46:42 CST)
• Reena .....
  • AMBER: Regarding ff03 forcefield (Fri Jul 25 2008 - 02:24:41 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 00:34:39 CDT)
  • Re: AMBER: query regarding loadpadb (Fri Apr 25 2008 - 06:07:21 CDT)
  • Re: AMBER: leaprc help (Mon Feb 11 2008 - 22:19:22 CST)
  • Re: AMBER: (Wed Jan 16 2008 - 03:07:30 CST)
  • Re: AMBER: How to build a dimer using amber (Tue Jan 15 2008 - 03:29:03 CST)
  • Re: AMBER: How to build a dimer using amber (Tue Jan 15 2008 - 03:31:24 CST)
  • AMBER: How to build a dimer using amber (Tue Jan 15 2008 - 01:19:45 CST)
• Rilei Yu
  • £º Re: AMBER: problems form the pdb to the mol2 (Tue Jun 24 2008 - 11:14:15 CDT)
  • AMBER: Further request answers from Dr. Junmei Wang (Tue Jun 24 2008 - 10:59:05 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
  • AMBER: problems form the pdb to the mol2 (Mon Jun 23 2008 - 20:01:33 CDT)
• Rima Chaudhuri
  • Re: AMBER: scyld beowulf --amber10--openmpi (Mon Oct 20 2008 - 20:46:13 CDT)
  • AMBER: scyld beowulf --amber10--openmpi (Mon Oct 20 2008 - 19:00:27 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Thu Oct 02 2008 - 11:42:25 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Wed Oct 01 2008 - 21:31:06 CDT)
  • Re: AMBER: amber10 installation on sgi_mips (Wed Oct 01 2008 - 15:47:14 CDT)
  • AMBER: amber10 installation on sgi_mips (Wed Oct 01 2008 - 14:05:06 CDT)
  • Re: AMBER: Cysteine sulphonic acid parameters (Thu May 01 2008 - 10:43:48 CDT)
  • AMBER: Cysteine sulphonic acid parameters (Wed Apr 30 2008 - 17:48:42 CDT)
• Rita Cassia
  • Re: AMBER: solvate with methanol (Tue Mar 11 2008 - 07:33:46 CDT)
  • AMBER: Liquid/Gas Phase (Thu Feb 28 2008 - 10:34:00 CST)
• rluo_at_uci.edu
  • RE: AMBER: Non-polar Parameters For MM_PBSA Calculation (Tue Feb 12 2008 - 17:23:40 CST)
• robaldo_at_dna.uba.ar
  • Re: AMBER: ptraj center problem (Fri Nov 21 2008 - 14:04:56 CST)
  • AMBER: ptraj center problem (Fri Nov 21 2008 - 11:31:27 CST)
• Robert Duke
  • Re: AMBER: amber 9 compilation error with mvapich and intelcompilers (Mon Dec 22 2008 - 08:36:33 CST)
  • Re: AMBER: AMBER minimization problems (Sat Dec 20 2008 - 18:10:03 CST)
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 11:02:25 CST)
  • Fw: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 11:20:40 CST)
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 11:18:46 CST)
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 10:42:07 CST)
  • Re: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 07:55:47 CST)
  • Fw: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 08:56:13 CST)
  • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 09:26:12 CST)
  • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 07:45:34 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 16:46:57 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 15:15:55 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:32:04 CST)
  • Re: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 08:37:20 CST)
  • Re: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 11:28:14 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:55:15 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:23:09 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 08:27:16 CST)
  • Re: AMBER: Ewald troubles when running very big boxes (Mon Nov 24 2008 - 20:09:23 CST)
  • Re: AMBER: AMBER10 failing to compile PMEMD (Sat Nov 22 2008 - 16:42:50 CST)
  • Re: AMBER: pmemd (Thu Nov 20 2008 - 10:40:36 CST)
  • Re: AMBER: PMEMD with AMOEBA parms including a lone pair site (Tue Nov 18 2008 - 20:50:14 CST)
  • Re: AMBER: SPCFW temperature oscillations (Tue Nov 18 2008 - 07:16:27 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 13:58:18 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:34:50 CST)
  • Re: AMBER: Query on restart file (Thu Oct 30 2008 - 21:14:40 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 21:02:05 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 17:30:07 CDT)
  • Re: AMBER: Setting GROUP for pmemd (Thu Oct 30 2008 - 14:29:27 CDT)
  • Re: AMBER: Optimal compiling of amber on XT3 (Thu Oct 30 2008 - 00:59:21 CDT)
  • Re: AMBER: Optimal compiling of amber on XT3 (Thu Oct 30 2008 - 00:31:49 CDT)
  • Re: AMBER: Problem installing PMEMD with intel mpi, ifort (Tue Oct 28 2008 - 20:12:17 CDT)
  • Re: AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 12:12:20 CDT)
  • Re: AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 07:57:03 CDT)
  • Re: AMBER: Non bond list error (Fri Oct 24 2008 - 14:04:53 CDT)
  • Re: AMBER: Non bond list error (Fri Oct 24 2008 - 13:47:33 CDT)
  • Re: AMBER: Non bond list error (Fri Oct 24 2008 - 11:40:24 CDT)
  • Fw: AMBER: Non bond list error (Fri Oct 24 2008 - 08:20:29 CDT)
  • Re: AMBER: Non bond list error (Thu Oct 23 2008 - 15:44:29 CDT)
  • Re: AMBER: Non bond list error (Thu Oct 23 2008 - 15:14:13 CDT)
  • AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL (Tue Oct 07 2008 - 12:02:51 CDT)
  • Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL (Fri Oct 03 2008 - 10:43:22 CDT)
  • Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL (Thu Oct 02 2008 - 17:39:28 CDT)
  • AMBER: Support for intel mpi in pmemd 10; better support for intel MKL (Thu Oct 02 2008 - 15:56:07 CDT)
  • Re: AMBER: Amber GB problems on PMEMD !! (Thu Sep 25 2008 - 07:22:06 CDT)
  • Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support (Wed Sep 24 2008 - 14:39:30 CDT)
  • Re: AMBER: PMEMD and sander.MPI (Tue Sep 09 2008 - 09:14:52 CDT)
  • Re: AMBER: PMEMD installation problem. (Mon Sep 08 2008 - 07:20:15 CDT)
  • Re: AMBER: Critical patch for pmemd 10 extra points code (Sun Aug 31 2008 - 11:48:56 CDT)
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 17:05:05 CDT)
  • AMBER: Critical patch for pmemd 10 extra points code (Thu Aug 28 2008 - 10:20:59 CDT)
  • Re: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 07:34:44 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 22:17:29 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 14:49:18 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:59:34 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 23:38:40 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 23:22:44 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 22:38:13 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 10:45:03 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 07:40:03 CDT)
  • Re: AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 07:54:43 CDT)
  • Re: AMBER: minimization stops or does not write anything (Thu Aug 14 2008 - 07:39:01 CDT)
  • Re: AMBER: PMEND 9 compilation problems (Wed Jul 30 2008 - 09:40:00 CDT)
  • Re: AMBER: PMEND 9 compilation problems (Tue Jul 29 2008 - 12:41:54 CDT)
  • Re: AMBER: Amber 10 on the BlueGene (Mon Jul 28 2008 - 12:17:18 CDT)
  • Re: AMBER: amber10: pmemd gfortran (Fri Jul 25 2008 - 14:01:27 CDT)
  • Re: AMBER: amber 10: sander and pmemd performance (Fri Jul 25 2008 - 11:06:41 CDT)
  • Re: AMBER: amber 10: sander and pmemd performance (Fri Jul 25 2008 - 09:31:30 CDT)
  • Re: AMBER: the pmemd problem (Fri Jul 25 2008 - 08:46:24 CDT)
  • Re: AMBER: timing info output from pmemd (Fri Jul 11 2008 - 08:41:21 CDT)
  • Re: AMBER: configure_amber (10) for pg compilers (Fri Jul 11 2008 - 07:27:02 CDT)
  • Re: AMBER: timing info output from pmemd (Fri Jul 11 2008 - 07:14:29 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 08:44:19 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 08:12:25 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 19:06:22 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 19:00:07 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:36:12 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:29:52 CDT)
  • Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:28:10 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 13:00:38 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 11:24:10 CDT)
  • Re: AMBER: (no subject) (Mon Jun 30 2008 - 11:43:11 CDT)
  • Re: AMBER: wrapping a restart file (Mon Jun 30 2008 - 11:34:54 CDT)
  • Re: AMBER: Constrained group (Mon Jun 30 2008 - 11:03:15 CDT)
  • Re: AMBER: Amber 10 timing (Fri Jun 20 2008 - 16:29:00 CDT)
  • Re: AMBER: amber10 installation problem (Tue Jun 10 2008 - 17:02:54 CDT)
  • Re: AMBER: Vaccum Simulations in PMEMD !! (Thu Jun 05 2008 - 09:17:13 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 10:28:24 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 09:50:36 CDT)
  • Re: AMBER: Sander instead of PMEMD (Fri May 30 2008 - 09:13:20 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Thu May 29 2008 - 15:16:39 CDT)
  • Re: AMBER: Installing PMEMD with Amber10 (Thu May 29 2008 - 09:44:38 CDT)
  • Re: AMBER: Which is best temperature controlling method (Thu May 29 2008 - 07:19:22 CDT)
  • Re: AMBER: massively parallel computation (Wed May 21 2008 - 12:37:34 CDT)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 09:46:34 CDT)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 09:32:22 CDT)
  • Re: AMBER: massively parallel computation (Tue May 20 2008 - 09:22:56 CDT)
  • Re: AMBER: STEERED MD (Sat May 17 2008 - 08:21:10 CDT)
  • Re: AMBER: STEERED MD (Fri May 16 2008 - 12:29:29 CDT)
  • Re: AMBER: STEERED MD (Fri May 16 2008 - 12:15:40 CDT)
  • Re: AMBER: Compilation of PMEMD (Thu May 08 2008 - 07:17:43 CDT)
  • Re: AMBER: Dose AMBER 10 pmemd support openmpi? (Wed Apr 30 2008 - 10:40:44 CDT)
  • Re: AMBER: Dose AMBER 10 pmemd support openmpi? (Wed Apr 30 2008 - 10:16:58 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Fri Apr 25 2008 - 17:04:58 CDT)
  • Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" (Thu Apr 24 2008 - 14:45:31 CDT)
  • Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" (Thu Apr 24 2008 - 10:04:31 CDT)
  • Re: AMBER: Short trajectory segments / frequent restarts causes explosion (Thu Apr 17 2008 - 16:52:55 CDT)
  • Re: AMBER: Performance issues on Ethernet clusters (Thu Apr 17 2008 - 15:14:32 CDT)
  • Re: AMBER: installing pmemd with fftw (Sun Apr 13 2008 - 08:57:36 CDT)
  • Re: AMBER: MPI run problem (Thu Apr 03 2008 - 15:57:33 CDT)
  • Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? (Mon Mar 10 2008 - 08:24:21 CDT)
  • Re: AMBER: Amber: shared memory vs cluster (Wed Feb 27 2008 - 15:20:56 CST)
  • Re: AMBER: Amber: shared memory vs cluster (Wed Feb 27 2008 - 12:37:31 CST)
  • Re: AMBER: compiling PMEMD with MKL10.0 (Tue Feb 26 2008 - 07:22:04 CST)
  • Re: AMBER: twin cut-off radii (Mon Feb 04 2008 - 10:55:06 CST)
  • Re: AMBER: problem to compile PMEMD? (Tue Jan 29 2008 - 20:10:49 CST)
  • Re: AMBER: problem to compile PMEMD? (Tue Jan 29 2008 - 20:11:57 CST)
  • Re: AMBER: problem to compile PMEMD? (Tue Jan 29 2008 - 17:09:05 CST)
  • Re: AMBER: Amber parallel version on CPU power of 2 only (Tue Jan 29 2008 - 12:43:03 CST)
  • Re: AMBER: pmemd 9.0 compilation error (Mon Jan 14 2008 - 09:19:51 CST)
  • Re: AMBER: About RAMD (Sat Jan 05 2008 - 11:05:55 CST)
• Robert Hanson
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Wed Oct 29 2008 - 06:50:35 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 17:42:19 CDT)
  • Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 13:21:59 CDT)
  • AMBER: antechamber bug? produces incorrect NEWPDB.PDB file (Tue Oct 28 2008 - 11:46:08 CDT)
  • Re: AMBER: changing pdb structure (Thu Oct 09 2008 - 22:23:48 CDT)
  • Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Thu Oct 09 2008 - 18:12:52 CDT)
  • Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Thu Oct 09 2008 - 11:30:32 CDT)
  • Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Thu Oct 09 2008 - 08:59:20 CDT)
  • Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Wed Oct 08 2008 - 15:55:26 CDT)
  • AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files (Wed Oct 08 2008 - 13:16:55 CDT)
  • Re: AMBER: coordinate file question (Tue Sep 30 2008 - 12:24:47 CDT)
  • Re: AMBER: coordinate file question (Tue Sep 30 2008 - 08:30:21 CDT)
  • AMBER: coordinate file question (Mon Sep 29 2008 - 22:16:25 CDT)
• Rogelio Hernández
  • AMBER: Addions in GB Mode? (Sun Oct 19 2008 - 12:04:32 CDT)
  • AMBER: about NMR refinement in explicit solvent (Tue Sep 09 2008 - 14:15:19 CDT)
• Ross Walker
  • RE: AMBER: mwcovar limit? (Wed Dec 31 2008 - 22:44:33 CST)
  • RE: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 11:09:54 CST)
  • RE: AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 19:20:38 CST)
  • RE: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 11:46:58 CST)
  • RE: AMBER: (Mon Dec 22 2008 - 10:41:23 CST)
  • RE: AMBER: AMBER minimization problems (Thu Dec 18 2008 - 11:46:45 CST)
  • RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 11:28:21 CST)
  • RE: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 11:01:37 CST)
  • RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 10:36:14 CST)
  • RE: AMBER: AMBER minimization problems (Wed Dec 17 2008 - 10:18:06 CST)
  • RE: AMBER: solvent box again (Tue Dec 16 2008 - 12:57:01 CST)
  • RE: AMBER: AMBER 10 PMEMD / SGI_MIPS (Tue Dec 16 2008 - 10:16:11 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 11:36:27 CST)
  • RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Mon Dec 15 2008 - 09:18:04 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 13:04:49 CST)
  • RE: AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 11:06:22 CST)
  • RE: AMBER: RESP GAUSSIAN AMBER (Thu Dec 11 2008 - 22:00:27 CST)
  • RE: AMBER: forrtl severe(174) error with minimization and md (Wed Dec 10 2008 - 09:57:42 CST)
  • RE: AMBER: (no subject) (Tue Dec 09 2008 - 09:07:18 CST)
  • RE: AMBER: reg-adding ions (Tue Dec 09 2008 - 09:05:04 CST)
  • AMBER: RE: bugfix 11 & 12 (Mon Dec 08 2008 - 15:12:42 CST)
  • RE: AMBER: reg-adding ions (Mon Dec 08 2008 - 10:33:18 CST)
  • RE: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:26:30 CST)
  • RE: AMBER: QM/MM and unpaired spin (Tue Dec 02 2008 - 21:42:37 CST)
  • RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 10:44:57 CST)
  • RE: AMBER: QM/MM and unpaired spin (Mon Dec 01 2008 - 10:40:20 CST)
  • RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 20:11:49 CST)
  • RE: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 10:57:06 CST)
  • RE: AMBER: Problem running NEB in AMBER10 (Wed Nov 26 2008 - 13:04:55 CST)
  • RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Wed Nov 26 2008 - 11:28:51 CST)
  • RE: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 10:39:30 CST)
  • RE: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 10:30:42 CST)
  • RE: AMBER: Fully QM periodic runs (Tue Nov 25 2008 - 10:54:24 CST)
  • RE: AMBER: Gradual releasing of position restraints (Tue Nov 25 2008 - 10:48:13 CST)
  • RE: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:21:22 CST)
  • RE: AMBER: RE: About restart amber (Sat Nov 22 2008 - 11:18:57 CST)
  • RE: AMBER: QM/MM simulation (Sat Nov 22 2008 - 10:59:49 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 18:20:56 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 16:33:30 CST)
  • AMBER: RE: About restart amber (Fri Nov 21 2008 - 15:45:16 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 15:36:20 CST)
  • RE: AMBER: pmemd (Thu Nov 20 2008 - 10:36:51 CST)
  • RE: AMBER: Restraints (Thu Nov 13 2008 - 13:11:53 CST)
  • RE: AMBER: Your "bellymask-patch" (Thu Nov 13 2008 - 12:17:58 CST)
  • RE: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 15:16:03 CST)
  • RE: AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 15:00:39 CST)
  • RE: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 09:21:59 CST)
  • AMBER: RE: problems about TMD in your tutorial (Mon Nov 10 2008 - 02:20:18 CST)
  • RE: AMBER: using "EP" for dummy atom (Thu Nov 06 2008 - 20:05:22 CST)
  • AMBER: RE: problems about TMD in your tutorial (Thu Nov 06 2008 - 13:32:58 CST)
  • AMBER: RE: Problem with the NEB tutorial (Thu Nov 06 2008 - 13:24:30 CST)
  • RE: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: QUERRY? (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query (Thu Nov 06 2008 - 02:18:22 CST)
  • RE: AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 19:41:27 CST)
  • RE: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:46:17 CST)
  • RE: AMBER: process_mdout modify (Tue Nov 04 2008 - 09:41:33 CST)
  • RE: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 18:06:07 CST)
  • RE: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 15:47:06 CST)
  • RE: AMBER: error message of xleap (Mon Nov 03 2008 - 11:05:54 CST)
  • RE: AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system (Fri Oct 31 2008 - 13:22:13 CDT)
  • RE: AMBER: minimization (Fri Oct 31 2008 - 10:44:49 CDT)
  • RE: AMBER: how to ger resp charge for a residue? (Thu Oct 30 2008 - 23:46:43 CDT)
  • RE: AMBER: error message of xleap (Thu Oct 30 2008 - 23:09:47 CDT)
  • RE: AMBER: minimization (Thu Oct 30 2008 - 13:48:11 CDT)
  • RE: AMBER: Optimal compiling of amber on XT3 (Thu Oct 30 2008 - 00:33:35 CDT)
  • RE: AMBER: Problem installing PMEMD with intel mpi, ifort (Tue Oct 28 2008 - 19:41:39 CDT)
  • RE: AMBER: Conversion between truncated octahedron and orthorohombic box (Sun Oct 26 2008 - 11:56:50 CDT)
  • RE: AMBER: Restraining with PMEMD 10 (Sat Oct 25 2008 - 12:25:08 CDT)
  • RE: AMBER: problem with amber8 installation (Fri Oct 24 2008 - 09:57:52 CDT)
  • RE: AMBER: Non bond list error (Fri Oct 24 2008 - 01:12:20 CDT)
  • RE: AMBER: Non bond list error (Thu Oct 23 2008 - 23:56:32 CDT)
  • RE: AMBER: Non bond list error (Thu Oct 23 2008 - 13:38:09 CDT)
  • RE: AMBER: HOLD fixed vs restraint mask (Tue Oct 21 2008 - 13:33:32 CDT)
  • RE: AMBER: Again: Installation problem of AMBER on cluster (Tue Oct 21 2008 - 11:49:50 CDT)
  • RE: AMBER: Heme cysteine (Tue Oct 21 2008 - 10:17:08 CDT)
  • RE: AMBER: scyld beowulf --amber10--openmpi (Mon Oct 20 2008 - 20:38:04 CDT)
  • RE: AMBER: cnstph test case failure or expected divergence? (Mon Oct 20 2008 - 15:41:27 CDT)
  • RE: AMBER: NAD+ parameters problem using tleap (Fri Oct 17 2008 - 13:16:41 CDT)
  • RE: AMBER: Using charmm force field in amber (Thu Oct 16 2008 - 16:44:30 CDT)
  • RE: AMBER: Clarification re qmmask (Thu Oct 16 2008 - 13:14:04 CDT)
  • RE: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 09:53:29 CDT)
  • RE: AMBER: Origin of periodic box (Wed Oct 15 2008 - 20:57:47 CDT)
  • RE: AMBER: Amber dipole printout. (Tue Oct 14 2008 - 15:05:38 CDT)
  • RE: AMBER: amber10 installation problem in cygwin (Tue Oct 14 2008 - 11:32:06 CDT)
  • RE: AMBER: Segmentation fault (Tue Oct 14 2008 - 09:53:08 CDT)
  • RE: AMBER: changing pdb structure (Thu Oct 09 2008 - 22:29:24 CDT)
  • RE: AMBER: saveamberparm error (Wed Oct 08 2008 - 10:23:12 CDT)
  • RE: AMBER: ptraj average structure (Sat Oct 04 2008 - 09:55:51 CDT)
  • RE: AMBER: thermodynamic integration with Amber9 (Thu Oct 02 2008 - 12:10:57 CDT)
  • RE: AMBER: thermodynamic integration with Amber9 (Thu Oct 02 2008 - 10:24:01 CDT)
  • RE: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE (Tue Sep 30 2008 - 13:18:44 CDT)
  • RE: AMBER: cluster for running amber10 (Tue Sep 30 2008 - 10:25:09 CDT)
  • RE: AMBER: coordinate file question (Tue Sep 30 2008 - 08:55:57 CDT)
  • RE: AMBER: coordinate file question (Mon Sep 29 2008 - 22:33:10 CDT)
  • RE: AMBER: a question (Mon Sep 29 2008 - 09:41:54 CDT)
  • RE: AMBER: Problem In Paralklel Amber (Mon Sep 29 2008 - 09:35:50 CDT)
  • RE: AMBER: a question (Sun Sep 28 2008 - 23:56:00 CDT)
  • RE: AMBER: Location of vdw radii and partial charges for ff99SB (Mon Sep 29 2008 - 09:51:44 CDT)
  • RE: AMBER: Amber GB problems on PMEMD !! (Thu Sep 25 2008 - 10:23:44 CDT)
  • RE: AMBER: to prepare pdb file fro unusual amino acid. (Thu Sep 25 2008 - 09:55:21 CDT)
  • RE: AMBER: solvate without translating (Thu Sep 25 2008 - 09:55:53 CDT)
  • RE: AMBER: how to enlarge the TIP3PBOX size (Thu Sep 25 2008 - 09:55:38 CDT)
  • RE: AMBER: how to enlarge the TIP3PBOX size (Thu Sep 25 2008 - 01:40:21 CDT)
  • RE: AMBER: solvate without translating (Thu Sep 25 2008 - 01:46:52 CDT)
  • RE: AMBER: to prepare pdb file fro unusual amino acid. (Thu Sep 25 2008 - 01:36:08 CDT)
  • RE: AMBER: MD goes wrong (Tue Sep 23 2008 - 23:33:43 CDT)
  • RE: AMBER: increasing temperature smoothly (Fri Sep 19 2008 - 13:29:31 CDT)
  • RE: AMBER: AMBER10 Compilation (SGI Altix) (Mon Sep 15 2008 - 21:15:54 CDT)
  • RE: AMBER: amber 10 parallel cpu utlization (Mon Sep 15 2008 - 21:09:37 CDT)
  • RE: AMBER: problem in installing parallel version of amber10 with lam (Mon Sep 15 2008 - 21:02:48 CDT)
  • RE: AMBER: mulliken charges in QM/MM calculation (Sun Sep 14 2008 - 03:44:00 CDT)
  • RE: AMBER: Cutoff list exceeds largest sphere in unit cell (Wed Sep 10 2008 - 15:08:53 CDT)
  • RE: AMBER: Cutoff list exceeds largest sphere in unit cell (Wed Sep 10 2008 - 11:01:18 CDT)
  • RE: AMBER: Amber10 Compilation (Wed Sep 10 2008 - 07:31:47 CDT)
  • RE: AMBER: PMEMD installation problem. (Mon Sep 08 2008 - 03:21:17 CDT)
  • RE: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 12:02:30 CDT)
  • AMBER: RE: reference paper - pls help (Fri Sep 05 2008 - 11:37:24 CDT)
  • RE: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 11:07:27 CDT)
  • RE: AMBER: error when using tleap with leaprc.ff02EP (Fri Sep 05 2008 - 11:06:13 CDT)
  • RE: AMBER: help...sander "segmentation fault" after 2hours of minimization (Fri Sep 05 2008 - 10:23:42 CDT)
  • RE: AMBER: resp and 99999 (Fri Sep 05 2008 - 09:31:51 CDT)
  • RE: AMBER: (Wed Sep 03 2008 - 16:14:21 CDT)
  • RE: AMBER: AMBER9 installation problen with open mpi (Wed Sep 03 2008 - 10:35:43 CDT)
  • RE: AMBER: tleap and Zn parameter (Wed Sep 03 2008 - 10:31:26 CDT)
  • RE: AMBER: vlimit exceeded (Sat Aug 30 2008 - 13:41:02 CDT)
  • RE: AMBER: compilation problem (Sat Aug 30 2008 - 13:33:13 CDT)
  • RE: AMBER: to understand how frcmod.ff99SB works (Fri Aug 29 2008 - 10:17:27 CDT)
  • RE: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 12:09:38 CDT)
  • RE: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 11:59:09 CDT)
  • AMBER: RE: Personal favor (Thu Aug 28 2008 - 11:39:59 CDT)
  • RE: AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 18:01:59 CDT)
  • RE: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:57:55 CDT)
  • RE: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:39:31 CDT)
  • RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 09:26:25 CDT)
  • RE: AMBER: Initial structure from NMR structures (Tue Aug 19 2008 - 09:05:43 CDT)
  • RE: AMBER: Negative dihedral coefficients in amber99 - Possible? (Mon Aug 18 2008 - 00:15:45 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Fri Aug 15 2008 - 12:36:36 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 19:38:30 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 11:00:02 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Wed Aug 13 2008 - 22:39:47 CDT)
  • RE: AMBER: Querry (Wed Aug 13 2008 - 09:48:19 CDT)
  • RE: AMBER: amber 9 on Intel Harpertown (Wed Aug 13 2008 - 09:24:47 CDT)
  • RE: AMBER: questions about previous posts (Tue Aug 12 2008 - 01:18:49 CDT)
  • RE: AMBER: Minimization methods (Mon Aug 11 2008 - 09:43:47 CDT)
  • RE: AMBER: problem with minimization (Thu Aug 07 2008 - 10:40:46 CDT)
  • RE: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:29:28 CDT)
  • RE: AMBER: Not integral charge increasing with number of lipids (Thu Aug 07 2008 - 10:24:28 CDT)
  • RE: AMBER: Problems with the charge (membrane simulation) (Thu Aug 07 2008 - 10:18:12 CDT)
  • RE: AMBER: Compailation problum in Amber 10 (Wed Aug 06 2008 - 09:50:05 CDT)
  • RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) (Sun Jul 27 2008 - 04:19:41 CDT)
  • RE: AMBER: Query (Sun Jul 27 2008 - 04:04:57 CDT)
  • RE: AMBER: the install problem (Sun Jul 27 2008 - 04:00:59 CDT)
  • RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) (Sat Jul 26 2008 - 08:58:34 CDT)
  • AMBER: RE: AMBER Question (Sat Jul 26 2008 - 08:53:25 CDT)
  • RE: AMBER: AMBER10: Fortran Runtime Error (Fri Jul 25 2008 - 16:22:16 CDT)
  • RE: AMBER: Regarding ff03 forcefield (Fri Jul 25 2008 - 03:16:57 CDT)
  • RE: AMBER: solvate dna in TIP3PBOX 10.0 (Fri Jul 25 2008 - 03:14:26 CDT)
  • RE: AMBER: big molecule numbers (Fri Jul 25 2008 - 03:10:05 CDT)
  • RE: AMBER: Query about the charge of atoms in the parmtop file (Thu Jul 24 2008 - 07:49:03 CDT)
  • RE: AMBER: adding missing residues (Thu Jul 24 2008 - 07:35:41 CDT)
  • RE: AMBER: solvate dna in TIP3PBOX 10.0 (Thu Jul 24 2008 - 07:29:51 CDT)
  • RE: AMBER: Indentifying cluster center structures in trajectory (Wed Jul 23 2008 - 04:14:27 CDT)
  • RE: AMBER: 1.5ns rst file to PDB file Conversion Error (Wed Jul 23 2008 - 04:08:46 CDT)
  • RE: AMBER: a link for Amber ff ported to Charmm (Sat Jul 19 2008 - 17:28:24 CDT)
  • RE: AMBER: Restarting Problem in MD Simulation (Fri Jul 18 2008 - 12:08:46 CDT)
  • RE: AMBER: how to generate psf file using the AMBER topology file (Fri Jul 18 2008 - 11:57:14 CDT)
  • RE: AMBER: The list-directed or NAMELIST READ statement cannot be completed (Thu Jul 17 2008 - 11:55:22 CDT)
  • RE: AMBER: about RMSD per residue (Wed Jul 16 2008 - 11:40:42 CDT)
  • RE: AMBER:Some questions about replica exchan ge (Wed Jul 16 2008 - 09:45:38 CDT)
  • RE: AMBER: about RMSD per residue (Wed Jul 16 2008 - 09:52:38 CDT)
  • RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Tue Jul 15 2008 - 10:50:20 CDT)
  • RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Tue Jul 15 2008 - 11:01:55 CDT)
  • RE: AMBER: Res minimization (Tue Jul 15 2008 - 10:53:46 CDT)
  • RE: AMBER: Tutorial 6 (Mon Jul 14 2008 - 13:48:05 CDT)
  • RE: AMBER: POL3 with gaff and ff02EP (Sun Jul 13 2008 - 23:40:02 CDT)
  • RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop (Sun Jul 13 2008 - 23:35:42 CDT)
  • RE: AMBER: empty output (Sat Jul 12 2008 - 11:54:01 CDT)
  • RE: AMBER: bond command (Thu Jul 10 2008 - 14:15:53 CDT)
  • RE: AMBER: amber9 / difference of igb=0 and igb=6 (Wed Jul 09 2008 - 15:54:54 CDT)
  • RE: AMBER: XLeap Problems (Wed Jul 09 2008 - 13:08:50 CDT)
  • RE: RE: AMBER: about QMMM output (Fri Jul 04 2008 - 14:55:10 CDT)
  • RE: AMBER: about QMMM output (Fri Jul 04 2008 - 11:30:09 CDT)
  • RE: AMBER: PMEMD and polarized force field ff 02 (Thu Jul 03 2008 - 10:02:17 CDT)
  • RE: AMBER: is amber workshop available this summer?? (Wed Jul 02 2008 - 23:19:31 CDT)
  • RE: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? (Wed Jul 02 2008 - 17:30:21 CDT)
  • RE: AMBER: ptraj problem with imaging (Wed Jul 02 2008 - 15:06:42 CDT)
  • RE: AMBER: ptraj problem with centering in the box (Wed Jul 02 2008 - 10:31:51 CDT)
  • RE: AMBER: missing torsion parameters (Mon Jun 30 2008 - 17:46:45 CDT)
  • RE: AMBER: error in reading namelist cntrl (Mon Jun 30 2008 - 15:26:38 CDT)
  • RE: AMBER: pmemd 10 output (Fri Jun 27 2008 - 11:40:48 CDT)
  • RE: AMBER: pmemd 10 output (Fri Jun 27 2008 - 11:16:44 CDT)
  • RE: AMBER: Dihedral Angle Parameters (Thu Jun 26 2008 - 17:18:52 CDT)
  • RE: AMBER: A problem of dihedral angle (Wed Jun 25 2008 - 10:48:56 CDT)
  • RE: AMBER: drawing repeated units (Tue Jun 24 2008 - 16:40:26 CDT)
  • RE: AMBER: Using AMBER forces (Tue Jun 24 2008 - 13:19:13 CDT)
  • RE: AMBER: Using AMBER forces (Tue Jun 24 2008 - 11:22:25 CDT)
  • RE: AMBER: tip3p water and shake (Wed Jun 18 2008 - 16:35:30 CDT)
  • RE: AMBER: program to calculate rmsd (Tue Jun 17 2008 - 03:26:53 CDT)
  • RE: AMBER: amber10 installation problem (Tue Jun 10 2008 - 17:04:51 CDT)
  • RE: AMBER: problem in starting sander (Sun Jun 08 2008 - 17:30:17 CDT)
  • RE: AMBER: 100 short MD runs within a single Sander script? (Sat Jun 07 2008 - 00:22:36 CDT)
  • RE: AMBER: Problems simulating a protein-ligand complex (Sat Jun 07 2008 - 00:15:32 CDT)
  • RE: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 18:34:39 CDT)
  • RE: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 17:55:37 CDT)
  • RE: AMBER: Problem While Installing Amber (Fri Jun 06 2008 - 10:30:26 CDT)
  • AMBER: RE: solvating RNA in 8M urea box (Thu Jun 05 2008 - 19:12:42 CDT)
  • RE: AMBER: amber installation on cluster (Wed Jun 04 2008 - 12:54:36 CDT)
  • RE: AMBER: drawing repeated units (Tue Jun 03 2008 - 18:49:54 CDT)
  • RE: AMBER: drawing repeated units (Tue Jun 03 2008 - 16:50:23 CDT)
  • RE: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 (Tue Jun 03 2008 - 15:43:43 CDT)
  • RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' (Mon Jun 02 2008 - 12:52:33 CDT)
  • RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' (Sat May 31 2008 - 15:57:48 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Fri May 30 2008 - 17:41:51 CDT)
  • AMBER: SANDER and PMEMD with openmpi (Fri May 30 2008 - 17:18:04 CDT)
  • RE: AMBER: igb and ibelly (Fri May 30 2008 - 15:16:11 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 29 2008 - 23:50:30 CDT)
  • RE: AMBER: NTC and NTF (Thu May 29 2008 - 14:30:28 CDT)
  • RE: AMBER: VMD Movie 3 (Thu May 29 2008 - 13:47:52 CDT)
  • RE: AMBER: solvatebox (Thu May 29 2008 - 10:22:53 CDT)
  • RE: AMBER: error when read inpcrd (Tue May 27 2008 - 15:50:23 CDT)
  • RE: AMBER: periodic boundary condition (Fri May 23 2008 - 22:09:39 CDT)
  • RE: AMBER: how to extract energy (Fri May 23 2008 - 22:07:41 CDT)
  • RE: AMBER: ff94 vs. ff03 (Fri May 23 2008 - 21:58:45 CDT)
  • RE: AMBER: Restart MD Simulation (Fri May 23 2008 - 17:28:16 CDT)
  • RE: AMBER: help MD running error (Fri May 23 2008 - 10:30:03 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Thu May 22 2008 - 17:40:54 CDT)
  • RE: AMBER: Force field in water and in vacuum ?? (Thu May 22 2008 - 11:06:36 CDT)
  • RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system (Thu May 22 2008 - 10:54:51 CDT)
  • RE: AMBER: amber10 installation (Thu May 22 2008 - 10:40:20 CDT)
  • RE: AMBER: $AMBERHOME/dat/slko (Thu May 22 2008 - 10:24:47 CDT)
  • RE: AMBER: about hydrogen bond in amber force field (Wed May 21 2008 - 22:32:06 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Wed May 21 2008 - 13:05:20 CDT)
  • AMBER: 3rd Annual CMM Workshop on QM/MM Simulations (Mon May 19 2008 - 18:33:55 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 16:25:45 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 12:19:37 CDT)
  • RE: AMBER: Hybrid REMD amber10 (Mon May 19 2008 - 10:51:13 CDT)
  • RE: Fw: RE: AMBER: MKL libraries/Amber10 (Mon May 19 2008 - 10:41:59 CDT)
  • RE: AMBER: MKL libraries/Amber10 (Fri May 16 2008 - 13:25:36 CDT)
  • RE: AMBER: PGI amber9 problems (Fri May 16 2008 - 13:06:14 CDT)
  • AMBER: about addles:¡°forrtl: severe (71): integer divide by z (Fri May 16 2008 - 13:00:34 CDT)
  • RE: AMBER: MKL libraries/Amber10 (Thu May 15 2008 - 21:59:16 CDT)
  • RE: AMBER: solvatebox error (Thu May 15 2008 - 16:54:08 CDT)
  • AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. (Thu May 15 2008 - 12:37:22 CDT)
  • RE: AMBER: simulate dipole moment (Wed May 14 2008 - 16:25:33 CDT)
  • AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. (Wed May 14 2008 - 11:30:51 CDT)
  • RE: AMBER: Amber10 testing problem (Tue May 13 2008 - 16:20:53 CDT)
  • RE: AMBER: initial velocities of MD (Tue May 13 2008 - 12:05:05 CDT)
  • RE: AMBER: Ligand energy minimization (Tue May 13 2008 - 10:14:53 CDT)
  • RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Tue May 13 2008 - 10:08:08 CDT)
  • RE: AMBER: drawing repeated units (Fri May 09 2008 - 11:03:28 CDT)
  • RE: AMBER: help to install AMBER9 (Fri May 09 2008 - 11:12:53 CDT)
  • RE: AMBER: can amber read .xyz files? (Thu May 08 2008 - 12:23:16 CDT)
  • RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands (Thu May 08 2008 - 12:19:34 CDT)
  • RE: AMBER: Ewald error estimate (Thu May 08 2008 - 10:27:15 CDT)
  • RE: AMBER: reset time and comments (Thu May 08 2008 - 10:24:50 CDT)
  • RE: AMBER: nmode: number of atoms limitation (Wed May 07 2008 - 16:39:44 CDT)
  • RE: AMBER: uninstall of AMBER (Wed May 07 2008 - 12:05:20 CDT)
  • RE: AMBER: Minimization in Octahedric Box (Tue May 06 2008 - 12:22:39 CDT)
  • RE: AMBER: AMBER Parallel test error (Tue May 06 2008 - 10:25:46 CDT)
  • RE: AMBER: AMBER Parallel test error (Mon May 05 2008 - 14:42:09 CDT)
  • RE: AMBER: Installation error on IBM cluster (Mon May 05 2008 - 10:06:11 CDT)
  • RE: RE: AMBER: point charges (Fri May 02 2008 - 18:03:08 CDT)
  • RE: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 16:33:48 CDT)
  • RE: AMBER: point charges (Fri May 02 2008 - 16:32:43 CDT)
  • RE: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 16:18:48 CDT)
  • RE: AMBER: printing dipoles in Amber10 (and earlier) (Fri May 02 2008 - 16:16:08 CDT)
  • RE: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 14:07:10 CDT)
  • RE: AMBER: cfortran.h error with xlf90 compiler (Fri May 02 2008 - 11:58:27 CDT)
  • RE: AMBER: test.parallel.QMMM problem (Fri May 02 2008 - 10:50:31 CDT)
  • RE: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 10:41:48 CDT)
  • RE: AMBER: Amber10 installation error (Fri May 02 2008 - 10:33:43 CDT)
  • RE: AMBER: Amber10 installation error (Thu May 01 2008 - 23:01:02 CDT)
  • RE: AMBER: RE: amber8 files in amber9 (Wed Apr 30 2008 - 11:24:49 CDT)
  • RE: AMBER: regarding segfault during energy minimization (Wed Apr 30 2008 - 00:40:21 CDT)
  • RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Tue Apr 29 2008 - 15:57:21 CDT)
  • RE: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 12:55:02 CDT)
  • RE: AMBER: prmtop spec trivia (Tue Apr 29 2008 - 10:34:04 CDT)
  • RE: AMBER: segmentation fault in SANDER (Tue Apr 29 2008 - 09:15:08 CDT)
  • RE: AMBER: query regarding energy minimization (Tue Apr 29 2008 - 01:16:11 CDT)
  • RE: AMBER: Parrallel computing (Tue Apr 29 2008 - 01:09:44 CDT)
  • RE: RE: AMBER: memory usage (Sun Apr 27 2008 - 11:45:16 CDT)
  • RE: AMBER: memory usage (Sun Apr 27 2008 - 01:07:04 CDT)
  • RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Sun Apr 27 2008 - 00:59:57 CDT)
  • RE: AMBER: Tutorial B5 (Wed Apr 23 2008 - 21:06:42 CDT)
  • RE: AMBER: vlimit-problems after image and restart (Tue Apr 22 2008 - 23:45:29 CDT)
  • AMBER: RE: amber tutorial A3 (Tue Apr 22 2008 - 23:45:29 CDT)
  • RE: AMBER: Average structure (Mon Apr 21 2008 - 21:27:08 CDT)
  • RE: AMBER: hydrogens are flying in replica exchange simulations (Sat Apr 19 2008 - 00:07:54 CDT)
  • RE: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 23:25:19 CDT)
  • RE: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 18:47:03 CDT)
  • RE: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 17:05:26 CDT)
  • RE: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? (Tue Apr 15 2008 - 10:47:53 CDT)
  • RE: AMBER: Whole System Equilibration & Pressure (Mon Apr 14 2008 - 16:37:51 CDT)
  • RE: AMBER: Problems compiling Amber with MKL (Mon Apr 14 2008 - 16:32:49 CDT)
  • RE: AMBER: Amber installation (Fri Apr 11 2008 - 17:45:42 CDT)
  • RE: AMBER: Amber installation (Fri Apr 11 2008 - 13:09:14 CDT)
  • RE: AMBER: Initial Equilibration (Thu Apr 10 2008 - 20:29:30 CDT)
  • RE: AMBER: protein-ligand complex problem (Thu Apr 10 2008 - 18:50:19 CDT)
  • RE: AMBER: Amber 9 run error (Tue Apr 08 2008 - 16:52:30 CDT)
  • AMBER: RE: amber help (Sat Apr 05 2008 - 22:25:19 CDT)
  • RE: AMBER: sander.MPI setup with SGE (Sat Apr 05 2008 - 11:18:45 CDT)
  • RE: AMBER: NAD parameters (Thu Apr 03 2008 - 09:56:45 CDT)
  • RE: AMBER: cntrl namelist error (Sat Mar 22 2008 - 11:01:47 CDT)
  • RE: AMBER: Water Topology (Thu Mar 20 2008 - 10:08:46 CDT)
  • RE: AMBER: Water Topology (Wed Mar 19 2008 - 23:49:43 CDT)
  • RE: AMBER: MNDO parameters for Mg+2 (Wed Mar 19 2008 - 13:10:18 CDT)
  • RE: AMBER: What's making my system lose total energy? (Mon Mar 17 2008 - 21:54:19 CDT)
  • RE: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). (Fri Mar 14 2008 - 11:30:13 CDT)
  • AMBER: RE: Request (Fri Mar 07 2008 - 14:38:25 CST)
  • RE: AMBER: XMGRACE on Linux 64 Bit (Thu Mar 06 2008 - 20:30:44 CST)
  • RE: AMBER: (Thu Mar 06 2008 - 12:37:16 CST)
  • RE: AMBER: missing gaff parameters (Tue Mar 04 2008 - 09:39:03 CST)
  • RE: AMBER: mpd error in submitting parallel job (Thu Feb 14 2008 - 22:11:23 CST)
  • RE: AMBER: (no subject) (Wed Feb 13 2008 - 09:21:52 CST)
  • RE: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 (Wed Feb 13 2008 - 09:20:07 CST)
  • RE: AMBER: Input file for Minimization (Sun Feb 10 2008 - 12:55:34 CST)
  • RE: AMBER: Error while compiling Amber (Sat Feb 09 2008 - 13:40:41 CST)
  • RE: AMBER: Error while compiling Amber (Sat Feb 09 2008 - 11:58:59 CST)
  • RE: AMBER: PB Bomb in pb_atmlist(): maxnba too short (Fri Feb 08 2008 - 10:53:56 CST)
  • RE: AMBER: Which install compiler and flags? (Fri Feb 08 2008 - 10:52:24 CST)
  • RE: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! (Fri Feb 08 2008 - 10:40:25 CST)
  • RE: AMBER: QMMM with printcharges (Thu Feb 07 2008 - 16:12:17 CST)
  • RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program (Wed Feb 06 2008 - 18:35:33 CST)
  • RE: AMBER: Amber compilation with ifort (Wed Feb 06 2008 - 16:06:20 CST)
  • RE: AMBER: Amber 9 installation (Mon Feb 04 2008 - 16:21:41 CST)
  • RE: AMBER: SANDER BOMB in subroutine nonbond_list (Wed Jan 30 2008 - 10:20:51 CST)
  • RE: AMBER: QM/MM Heating (Tue Jan 29 2008 - 08:49:48 CST)
  • RE: AMBER: Amber parallel version on CPU power of 2 only (Tue Jan 29 2008 - 08:39:21 CST)
  • RE: AMBER: QM/MM: input conversion error (Fri Jan 25 2008 - 16:48:49 CST)
  • RE: AMBER: QM/MM: input conversion error (Thu Jan 24 2008 - 18:01:43 CST)
  • RE: AMBER: BCC charges (Tue Jan 22 2008 - 11:16:05 CST)
  • RE: AMBER: QM/MM Heating (Mon Jan 21 2008 - 10:41:31 CST)
  • RE: AMBER: problems with restart of MD (Sat Jan 12 2008 - 20:58:20 CST)
  • RE: AMBER: problems with restart of MD (Fri Jan 11 2008 - 13:56:16 CST)
  • RE: AMBER: Nudged Elastic Band initial heating problem (Tue Jan 08 2008 - 17:00:59 CST)
  • AMBER: FW: AMBER vs Gaussian : zero VDW parameters? (Fri Jan 04 2008 - 11:01:14 CST)
  • RE: AMBER: Combine mdcrd files (Fri Jan 04 2008 - 10:35:23 CST)
• rpaduri_at_chem.wayne.edu
  • Re: AMBER: query regarding energy minimization (Mon Apr 28 2008 - 09:26:25 CDT)
  • Re: AMBER: query about Generalized Born simulation (Fri Apr 11 2008 - 09:31:21 CDT)
  • Re: AMBER: Charge scheme for simulating protonated adenine (Fri Mar 21 2008 - 10:29:18 CDT)
• Ruchi Sachdeva
  • AMBER: how to choose the appropriate ensemble for a given problem (Wed Aug 13 2008 - 23:09:28 CDT)
  • Re: AMBER: Calculate number of ions (Wed May 14 2008 - 02:24:08 CDT)
• Rupesh Nanjunda
  • Re: AMBER: Problem installing PMEMD with intel mpi, ifort (Thu Oct 30 2008 - 10:07:56 CDT)
  • Re: AMBER: Problem installing PMEMD with intel mpi, ifort (Wed Oct 29 2008 - 12:57:06 CDT)
  • AMBER: Problem installing PMEMD with intel mpi, ifort (Tue Oct 28 2008 - 16:07:01 CDT)
• Ryan Pavlovicz
  • AMBER: makeDIST_RST computation of r3 value with IAT < 0 (Wed Dec 03 2008 - 17:13:32 CST)
  • AMBER: makeDIST_RST error -- no map function for HH TYR (Mon Dec 01 2008 - 13:30:01 CST)
  • AMBER: NMR optimization with group averages (IGR1 / IGR2) (Fri Nov 14 2008 - 09:59:36 CST)
  • Re: AMBER: ptraj - closest command (Wed Oct 08 2008 - 15:49:08 CDT)
  • AMBER: ptraj - closest command (Wed Oct 08 2008 - 12:36:17 CDT)
• S.Sundar Raman
  • AMBER: seeking help regrading Zinc protein GBSA minimization (Thu Nov 27 2008 - 06:32:08 CST)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 12:21:44 CDT)
  • Re: AMBER: 3fe-4s cluster parameter file generation (Mon Sep 15 2008 - 07:56:36 CDT)
  • Re: AMBER: solvent interaction in active site (Mon Sep 01 2008 - 09:28:10 CDT)
  • AMBER: Query related to implicit solvent EXTDIEL (Wed Feb 06 2008 - 06:03:02 CST)
• Sadhna Rana
  • RE: AMBER: thermodynamic integration with Amber9 (Thu Oct 02 2008 - 11:08:27 CDT)
  • AMBER: thermodynamic integration with Amber9 (Thu Oct 02 2008 - 10:12:47 CDT)
• sai kumar ramadugu
  • AMBER: EVB allocation problem (Fri Sep 12 2008 - 11:08:41 CDT)
  • AMBER: Emperical Valence Bond (Tue Sep 09 2008 - 16:46:25 CDT)
  • AMBER: Problem in EVB and Trajectory analysis (Fri Sep 05 2008 - 16:20:17 CDT)
  • AMBER: imin = 5 and PBC (Thu Jul 31 2008 - 09:51:21 CDT)
• Saiful Islam
  • Re: AMBER: test sander error in amber7 (Tue Nov 11 2008 - 01:36:30 CST)
  • AMBER: test sander error in amber7 (Mon Nov 10 2008 - 07:43:45 CST)
• Sally Pias
  • AMBER: periodic boundary (Wed Dec 31 2008 - 02:37:25 CST)
  • AMBER: GB offset for proteins (Sun Dec 07 2008 - 23:14:58 CST)
  • Re: AMBER: energy leakage? (Thu Oct 23 2008 - 09:47:28 CDT)
  • AMBER: energy leakage? (Thu Oct 23 2008 - 02:25:59 CDT)
  • Re: AMBER: changing pdb structure (Sun Oct 12 2008 - 00:00:38 CDT)
  • AMBER: MD with NMR restraints (Wed Aug 13 2008 - 23:25:56 CDT)
  • Re: AMBER: trouble interpreting <P2> time correlation function data (Sun Jul 06 2008 - 12:08:18 CDT)
  • AMBER: trouble interpreting <P2> time correlation function data (Sun Jul 06 2008 - 01:59:57 CDT)
  • Re: AMBER: B-factor calculation from data with different write frequencies (Tue May 27 2008 - 22:42:13 CDT)
  • AMBER: B-factor calculation from data with different write frequencies (Mon May 26 2008 - 23:19:42 CDT)
  • Re: AMBER: converting from CNS file format (Fri Apr 11 2008 - 00:04:55 CDT)
  • AMBER: converting from CNS file format (Wed Apr 09 2008 - 00:32:11 CDT)
  • AMBER: temperature spikes (Sun Jan 06 2008 - 00:26:55 CST)
• Sam Danziger
  • AMBER: How to set a ZN atom radius for PB calculations (Tue May 20 2008 - 19:23:30 CDT)
  • Re: AMBER: Amber 10 ambpdb bug? (Sun May 18 2008 - 22:41:43 CDT)
  • AMBER: Amber 10 ambpdb bug? (Sat May 17 2008 - 21:17:44 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Fri May 16 2008 - 13:29:32 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Fri May 16 2008 - 12:41:31 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Fri May 16 2008 - 12:06:05 CDT)
  • AMBER: Problems installing Amber Tools for Amber 10 (Mon May 12 2008 - 13:20:23 CDT)
• Sam Kaye
  • AMBER: Which install compiler and flags? (Fri Feb 08 2008 - 04:07:15 CST)
• Sampath Koppole
  • Re: AMBER: Amber GB problems on PMEMD !! (Thu Sep 25 2008 - 08:02:42 CDT)
  • AMBER: Amber GB problems on PMEMD !! (Thu Sep 25 2008 - 04:09:30 CDT)
  • AMBER: Trouble installing Amber 9 (Wed Aug 20 2008 - 05:28:58 CDT)
  • AMBER: Vaccum Simulations in PMEMD !! (Thu Jun 05 2008 - 07:53:35 CDT)
  • Re: AMBER: Binary restart file !! (Wed Feb 06 2008 - 11:01:43 CST)
  • AMBER: Binary restart file !! (Wed Feb 06 2008 - 08:41:03 CST)
  • Re: AMBER: AMBER installation problem (Mon Jan 28 2008 - 02:36:27 CST)
• Samuel Genheden
  • AMBER: Steered MD and Jarzynski in pulling simulations (Wed Nov 05 2008 - 08:48:33 CST)
• Samuel Genheden (a03samge)
  • RE: AMBER: Bennett acceptance ratio with Amber10 (Wed Aug 27 2008 - 01:04:28 CDT)
  • AMBER: Bennett acceptance ratio with Amber10 (Tue Aug 26 2008 - 06:58:13 CDT)
  • AMBER: TI calculations in Amber10 (Wed Jun 25 2008 - 06:58:28 CDT)
  • SV: SV: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 15:06:17 CDT)
  • SV: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 10:53:29 CDT)
  • RE: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 08:33:46 CDT)
  • RE: AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 08:10:51 CDT)
  • AMBER: Correlation functions from iRED analysis (Thu Jun 19 2008 - 05:22:53 CDT)
  • SV: SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 15:41:31 CDT)
  • SV: SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 07:00:52 CDT)
  • SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 06:02:59 CDT)
  • SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 05:43:21 CDT)
  • AMBER: ptraj, hbond and non-bonded contacts (Thu Mar 13 2008 - 09:54:03 CDT)
  • AMBER: ptraj and non-bonded contacts (Wed Mar 12 2008 - 11:34:44 CDT)
• Samuele Giani
  • Re: AMBER: missing gaff parameters (Tue Mar 04 2008 - 10:42:03 CST)
  • AMBER: missing gaff parameters (Tue Mar 04 2008 - 02:46:38 CST)
• san_amber roy
  • AMBER: minimization (Tue Apr 22 2008 - 09:01:52 CDT)
  • Re: Fwd: AMBER: lastrst problem (Wed Mar 19 2008 - 11:07:26 CDT)
  • Fwd: AMBER: lastrst problem (Wed Mar 12 2008 - 10:19:08 CDT)
  • AMBER: lastrst problem (Wed Mar 12 2008 - 10:07:23 CDT)
  • AMBER: solvate with methanol (Tue Mar 11 2008 - 04:23:40 CDT)
  • AMBER: antechamber run on charged system (Wed Jan 23 2008 - 12:09:34 CST)
• Sandeep Kaushik
  • Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP (Mon Jul 28 2008 - 07:30:16 CDT)
  • AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP (Fri Jul 25 2008 - 05:04:11 CDT)
  • Re: AMBER: querry (Tue Jul 22 2008 - 07:09:08 CDT)
  • AMBER: twin cut-off radii (Mon Feb 04 2008 - 03:17:57 CST)
• sanket.deshmukh_at_ucd.ie
  • AMBER: Amber:unsubscribe amber (Thu Jun 26 2008 - 06:53:22 CDT)
  • AMBER: unsubscribe amber (Tue Jun 24 2008 - 06:07:42 CDT)
• Sara Alexandra Moura
  • Re: AMBER: bye (Tue May 20 2008 - 09:14:51 CDT)
• Sara J
  • AMBER: mbondi radii for gaff atom types (Wed May 28 2008 - 10:03:52 CDT)
• Sasha Buzko
  • AMBER: Simulating peptide linkers with AMBER (Tue Dec 02 2008 - 14:03:42 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 18:53:06 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 14:56:16 CST)
  • AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:14:00 CST)
  • Re: AMBER: changing pdb structure (Thu Oct 09 2008 - 22:48:43 CDT)
  • AMBER: Amber on Infiniband clusters: SDR vs DDR cables? (Thu Sep 25 2008 - 18:06:44 CDT)
  • Re: AMBER: xleap and Sirius on ubuntu 8.04 (Thu Sep 11 2008 - 22:22:38 CDT)
  • Re: AMBER: Help...which commands in ptraj does clustering by RMSD? (Thu Sep 11 2008 - 16:48:14 CDT)
  • Re: AMBER: Help...which commands in ptraj does clustering by RMSD? (Thu Sep 11 2008 - 15:39:44 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Mon Sep 08 2008 - 17:11:04 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Mon Sep 08 2008 - 15:34:22 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:57:07 CDT)
  • AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:45:01 CDT)
  • Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Sat Aug 23 2008 - 15:19:07 CDT)
  • AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Wed Aug 20 2008 - 17:42:01 CDT)
  • Re: AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:50:39 CDT)
  • AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:35:24 CDT)
  • AMBER: Simulating protein conformational changes? (Fri Aug 01 2008 - 17:42:07 CDT)
  • AMBER: Simulating complexes with magnesium atoms (Tue Jun 10 2008 - 16:32:13 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Mon Jun 09 2008 - 12:57:20 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Sat Jun 07 2008 - 00:37:53 CDT)
  • RE: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 18:40:07 CDT)
  • RE: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 18:13:19 CDT)
  • Re: AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 17:16:29 CDT)
  • AMBER: Problems simulating a protein-ligand complex (Fri Jun 06 2008 - 12:55:05 CDT)
  • Re: AMBER: xLeap compilation issues (Wed May 21 2008 - 10:52:00 CDT)
  • AMBER: xLeap compilation issues (Tue May 20 2008 - 18:41:49 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Sat Apr 26 2008 - 16:15:18 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Sat Apr 26 2008 - 15:31:23 CDT)
  • Re: AMBER: AMD Opteron: compiler recommendations? (Fri Apr 25 2008 - 17:14:19 CDT)
  • AMBER: AMD Opteron: compiler recommendations? (Fri Apr 25 2008 - 16:54:57 CDT)
  • Re: AMBER: SiCortex as an alternative to Ethernet and infiniband clusters (Thu Apr 17 2008 - 17:39:46 CDT)
  • Re: AMBER: Performance issues on Ethernet clusters (Thu Apr 17 2008 - 16:18:44 CDT)
  • AMBER: Performance issues on Ethernet clusters (Thu Apr 17 2008 - 13:20:52 CDT)
  • Re: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 23:49:01 CDT)
  • Re: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 19:40:09 CDT)
  • RE: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 19:06:14 CDT)
  • RE: AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 17:43:12 CDT)
  • AMBER: Amber9 with MPICH2 failure at runtime (Wed Apr 16 2008 - 16:43:07 CDT)
  • RE: AMBER: Problems compiling Amber with MKL (Mon Apr 14 2008 - 18:24:05 CDT)
  • RE: AMBER: Problems compiling Amber with MKL (Mon Apr 14 2008 - 17:25:43 CDT)
  • AMBER: Problems compiling Amber with MKL (Mon Apr 14 2008 - 14:13:23 CDT)
  • Re: AMBER: sander.MPI setup with SGE (Mon Apr 07 2008 - 15:51:20 CDT)
  • AMBER: sander.MPI setup with SGE (Fri Apr 04 2008 - 11:59:34 CDT)
• saurabh agrawal
  • Re: AMBER: ff99 (PK/IDIVF) (Tue Dec 16 2008 - 05:47:09 CST)
  • RE: AMBER: ff99 (PK/IDIVF) (Sun Dec 14 2008 - 12:29:39 CST)
  • AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 07:26:58 CST)
  • AMBER: nonbonded parameters for titanium (Mon Nov 24 2008 - 10:57:56 CST)
  • Re: AMBER: AMBER9 installation problen with open mpi (Wed Sep 03 2008 - 09:55:31 CDT)
  • AMBER: AMBER9 installation problen with open mpi (Tue Sep 02 2008 - 06:41:55 CDT)
  • Re: AMBER: coordinate change of pdb structure using xleap (Wed Aug 27 2008 - 02:23:09 CDT)
  • Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Sat Apr 26 2008 - 09:15:38 CDT)
  • RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Mon Apr 28 2008 - 00:18:50 CDT)
  • AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... (Sat Apr 26 2008 - 06:36:13 CDT)
  • AMBER: How to change default radius assigned to an atom (Mon Apr 21 2008 - 23:47:14 CDT)
  • AMBER: How to add radius of an atom (Mon Apr 21 2008 - 00:45:43 CDT)
  • Re: AMBER: Entropy calculations using NMODE (Sat Feb 02 2008 - 07:50:13 CST)
  • AMBER: Entropy calculations using NMODE (Sat Feb 02 2008 - 01:18:24 CST)
  • AMBER: convergence of free energy calculations (Tue Jan 22 2008 - 05:54:28 CST)
• Schwehm, Jeffrey M.
  • AMBER: XLeap Problems (Wed Jul 09 2008 - 11:26:14 CDT)
• Scott Brozell
  • Re: AMBER: installation amber9 in fedora9 (Mon Dec 22 2008 - 23:41:22 CST)
  • Re: AMBER: xleap (measureGeom) (Mon Dec 22 2008 - 16:10:46 CST)
  • RE: AMBER: (no subject) (Tue Dec 09 2008 - 09:17:06 CST)
  • Re: AMBER: installing amber on new linux (Wed Oct 22 2008 - 18:53:50 CDT)
  • Re: AMBER: Installation Error (Wed Oct 15 2008 - 03:05:48 CDT)
  • Re: Fwd: AMBER: LEaP problem with LEU first residue? (Tue Oct 14 2008 - 16:46:36 CDT)
  • Re: AMBER: value of Pi in Amber (Tue Aug 26 2008 - 17:07:49 CDT)
  • Re: AMBER: PDB files in Amber10 (Mon Aug 25 2008 - 16:32:16 CDT)
  • RE: AMBER: amber10: pmemd gfortran (Thu Jul 31 2008 - 22:16:45 CDT)
  • Re: AMBER: # of ligands and receptors in mmpbsa (Thu Jul 31 2008 - 21:14:50 CDT)
  • Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap (Thu Jul 31 2008 - 17:40:43 CDT)
  • RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 (Thu Jul 31 2008 - 17:04:55 CDT)
  • Re: AMBER: compile amber10 on Mac (Thu Jul 03 2008 - 20:38:19 CDT)
  • Re: AMBER: Problems installing Amber Tools for Amber 10 (Tue May 27 2008 - 12:17:19 CDT)
  • Re: AMBER: error in compilation elsize.cc (Mon May 05 2008 - 13:55:49 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 15:33:49 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 15:15:29 CDT)
  • AMBER: Re: Amber: parameters for Silicon (Mon Mar 10 2008 - 18:57:29 CDT)
  • Re: AMBER: parameters for silicon atom (Fri Feb 29 2008 - 02:31:03 CST)
  • Re: AMBER: parameters for silicon atom (Mon Feb 25 2008 - 20:24:03 CST)
  • Re: AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 15:32:11 CST)
• Scott Pendley
  • Re: AMBER: mm_pbsa error (Fri Apr 04 2008 - 11:29:16 CDT)
• Sean Johnston
  • Re: AMBER: drug/protein interaction modeling setup (Fri Oct 31 2008 - 14:31:56 CDT)
  • AMBER: drug/protein interaction modeling setup (Mon Oct 20 2008 - 15:10:52 CDT)
• Sebastian Stolzenberg
  • AMBER: 100 short MD runs within a single Sander script? (Fri Jun 06 2008 - 23:55:37 CDT)
• selami ercan
  • Re: AMBER: installation amber on suse11.0 (Wed Aug 27 2008 - 13:50:13 CDT)
  • AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 05:57:12 CDT)
• Sergey Samsonov
  • Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Mon Dec 01 2008 - 02:14:36 CST)
  • AMBER: Problems of MM/MM-GBSA calculations (Thu Nov 27 2008 - 04:53:53 CST)
  • AMBER: Zn2+ Bondi radius value (Tue Oct 07 2008 - 03:50:10 CDT)
  • AMBER: RDF: Segmentation fault (Wed Sep 10 2008 - 03:13:29 CDT)
• Sergio Wong
  • AMBER: Nmode entropy calcs (Sat Jul 12 2008 - 20:09:51 CDT)
  • AMBER: energy decomposition vs ala scan (Mon Apr 14 2008 - 21:05:41 CDT)
  • Re: AMBER: imem keyword using mmpbsa (Thu Apr 03 2008 - 20:18:10 CDT)
  • AMBER: imem keyword using mmpbsa (Thu Apr 03 2008 - 15:43:01 CDT)
  • AMBER: mmpbsa INSTRNG error? (Sun Mar 09 2008 - 00:06:44 CST)
• serhanyigen_at_mail.ege.edu.tr
  • AMBER: Adding New Parameters and Modifying Existing Parameters (Tue Mar 11 2008 - 06:51:18 CDT)
• Servaas Michielssens
  • Re: AMBER: gaff paramters (Sat Feb 23 2008 - 01:06:54 CST)
  • Re: AMBER: gaff paramters (Fri Feb 22 2008 - 15:15:23 CST)
  • AMBER: gaff paramters (Fri Feb 22 2008 - 11:38:53 CST)
• Seth Lilavivat
  • AMBER: bellymask for DNA backbone doesn't seem to work (Thu Jul 03 2008 - 15:13:40 CDT)
  • Re: AMBER: ptraj - read in part of trajectory (Fri Jun 27 2008 - 12:01:03 CDT)
  • AMBER: ptraj - read in part of trajectory (Fri Jun 27 2008 - 11:41:51 CDT)
  • AMBER: Nmode - entropy calculation of receptor - should I apply restraint? (Thu Jun 05 2008 - 12:03:08 CDT)
  • AMBER: ptraj analyze matrix (Wed May 21 2008 - 09:53:28 CDT)
  • AMBER: RESP and Jaguar (Thu May 15 2008 - 15:52:35 CDT)
  • AMBER: Free Energy Calculations - parameters for MM (Tue May 13 2008 - 11:29:23 CDT)
  • Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands (Thu May 08 2008 - 15:01:45 CDT)
  • AMBER: nmode "Atom out of bounds" for min of multiple ligands (Thu May 08 2008 - 09:30:24 CDT)
  • AMBER: mm_pbsa.pl not reading parameters for nmode (Tue May 06 2008 - 12:50:18 CDT)
  • Re: AMBER: Help with NMODE (Mon May 05 2008 - 14:39:06 CDT)
  • Re: AMBER: Help with NMODE (Sun May 04 2008 - 17:15:53 CDT)
  • Re: AMBER: Help with NMODE (Fri May 02 2008 - 13:05:19 CDT)
  • Re: AMBER: Help with NMODE (Fri May 02 2008 - 11:50:35 CDT)
  • AMBER: Help with NMODE (Fri May 02 2008 - 10:24:25 CDT)
  • AMBER: double strand DNA break up (imaging) (Thu Apr 24 2008 - 13:53:44 CDT)
  • AMBER: loadPdb returns extra atoms (Mon Apr 14 2008 - 13:50:32 CDT)
  • AMBER: ptraj / covariance / quasiharmonic approximation / entropy (Wed Apr 02 2008 - 14:18:55 CDT)
  • Re: AMBER: mm-pbsa multiple trajectory approach? (Fri Mar 28 2008 - 10:28:31 CDT)
  • AMBER: mm-pbsa multiple trajectory approach? (Wed Mar 26 2008 - 12:32:54 CDT)
  • AMBER: Convert dcd to mdcrd (Tue Mar 25 2008 - 13:13:22 CDT)
  • AMBER: NMR refinement (Thu Jan 24 2008 - 11:39:08 CST)
  • AMBER: running AMBER in NAMD Trucated Octahedron (Mon Jan 14 2008 - 16:19:05 CST)
  • AMBER: Visualizing Electrostatic Potential (Fri Jan 11 2008 - 13:57:31 CST)
  • AMBER: Combining multiple structures into single pdb (Fri Jan 04 2008 - 14:21:58 CST)
• SeungPyo Hong
  • Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. (Wed Jul 16 2008 - 20:50:31 CDT)
  • AMBER: Ligand force field generation, and its consistency with the force field of the protein. (Wed Jul 16 2008 - 07:15:48 CDT)
• Shaikh Abdul R S Ramaju
  • RE: AMBER: Heme cysteine (Tue Oct 21 2008 - 21:46:09 CDT)
  • AMBER: Heme cysteine (Tue Oct 21 2008 - 02:16:50 CDT)
  • RE: AMBER: saveamberparm error (Thu Oct 09 2008 - 05:53:35 CDT)
  • RE: AMBER: saveamberparm error (Wed Oct 08 2008 - 21:24:58 CDT)
  • AMBER: saveamberparm error (Wed Oct 08 2008 - 06:33:31 CDT)
  • RE: AMBER: Amber heme parameters (Wed Oct 08 2008 - 01:38:59 CDT)
  • AMBER: Amber heme parameters (Tue Oct 07 2008 - 01:31:34 CDT)
• Shen, Lingling
  • AMBER: How to create average structure? (Wed Jun 18 2008 - 23:44:03 CDT)
• Shibasish Chowdhury
  • RE: AMBER: problem in installing parallel version of amber10 with lam (Tue Sep 16 2008 - 05:37:06 CDT)
  • AMBER: problem in installing parallel version of amber10 with lam (Sun Sep 14 2008 - 23:20:12 CDT)
• Shozeb Haider
  • Re: AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 10:37:54 CST)
  • AMBER: ANTECHAMBER NAMING (Thu Jan 10 2008 - 15:19:18 CST)
• shubhra srivastava
  • AMBER: constant ph (cpinutil file) (Wed Aug 27 2008 - 01:46:36 CDT)
  • AMBER: constph (Thu Aug 14 2008 - 06:54:57 CDT)
• Shultz, Jack
  • AMBER: Error runing Addles (Thu Aug 21 2008 - 22:25:17 CDT)
  • RE: AMBER: Amber compile (Tue Aug 19 2008 - 14:25:56 CDT)
  • AMBER: Amber compile (Tue Aug 19 2008 - 13:21:18 CDT)
  • AMBER: Compile Error (Tue Aug 19 2008 - 10:44:25 CDT)
  • AMBER: Proton Parameters (Thu Aug 14 2008 - 15:34:54 CDT)
  • RE: AMBER: Harmonic Force Constant (Thu May 08 2008 - 15:21:00 CDT)
  • AMBER: Harmonic Force Constant (Wed May 07 2008 - 14:32:18 CDT)
  • AMBER: Amber Parameter Schema (Tue May 06 2008 - 19:22:02 CDT)
  • AMBER: GAFF Schema (Sun May 04 2008 - 17:11:37 CDT)
  • AMBER: Deriving Force Field Parameters (Sun May 04 2008 - 16:32:03 CDT)
  • AMBER: JavaGenes (Mon Apr 14 2008 - 14:26:25 CDT)
  • AMBER: RE: Force Field Parameterizing (Mon Mar 24 2008 - 10:31:32 CDT)
• Shun Zhu
  • Re: AMBER: about AM1-BCC in antechamber (Tue Jan 22 2008 - 12:09:49 CST)
  • Re: AMBER: about AM1-BCC in antechamber (Tue Jan 22 2008 - 11:38:01 CST)
  • AMBER: about AM1-BCC in antechamber (Fri Jan 18 2008 - 16:06:30 CST)
• Siddharth Rastogi
  • AMBER: High ESURF (Mon Nov 17 2008 - 02:07:57 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 00:18:59 CST)
  • AMBER: Trajectory file ended and unit 24 error on open inptraj (Sat Nov 15 2008 - 09:33:10 CST)
  • AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm? (Fri Nov 14 2008 - 08:02:34 CST)
  • AMBER: Packing density calculation (Thu Oct 30 2008 - 05:41:58 CDT)
  • AMBER: large number of solvent molecules were added for protein with 221 AA residues (Mon Oct 13 2008 - 23:34:58 CDT)
  • AMBER: High Bfactor values for the terminal residues/atoms (Mon Oct 13 2008 - 23:19:52 CDT)
  • AMBER: Initial structure from NMR structures (Tue Aug 19 2008 - 01:15:44 CDT)
  • AMBER: NMR structure as initial structure (Tue Aug 05 2008 - 01:40:54 CDT)
  • AMBER: Distance diagnolization matrix plot (Wed Jul 09 2008 - 02:04:08 CDT)
  • AMBER: ligand complexed simulation (Fri Jun 20 2008 - 02:14:18 CDT)
  • AMBER: ligand complexed simulation (Tue Jun 17 2008 - 05:56:15 CDT)
• SilasConnor_at_gmx.at
  • AMBER: RESP GAUSSIAN AMBER (Mon Dec 08 2008 - 12:31:24 CST)
• Smriti Sharma
  • Re: AMBER: Discontinuous Constant pH Restarts (Thu May 08 2008 - 06:05:31 CDT)
• snoze pa
  • Re: AMBER: error in compilation elsize.cc (Mon Apr 14 2008 - 13:20:40 CDT)
  • AMBER: error in compilation elsize.cc (Mon Apr 14 2008 - 11:38:07 CDT)
  • AMBER: how to link two different atoms in xLeap (Wed Mar 26 2008 - 15:56:12 CDT)
  • Re: AMBER: help regarding warning message (Tue Mar 25 2008 - 15:23:55 CDT)
  • AMBER: help regarding warning message (Tue Mar 25 2008 - 11:17:43 CDT)
  • AMBER: mol2 save (Tue Feb 26 2008 - 11:09:18 CST)
  • Re: AMBER: leaprc help (Mon Feb 11 2008 - 15:08:14 CST)
  • AMBER: leaprc help (Mon Feb 11 2008 - 11:50:30 CST)
  • Re: AMBER: antechamber run on charged system (Wed Jan 23 2008 - 13:34:04 CST)
  • Re: AMBER: Help in radii (Wed Jan 16 2008 - 11:45:20 CST)
  • AMBER: Help in radii (Wed Jan 16 2008 - 11:08:59 CST)
  • Re: AMBER: Help reg. input file (Wed Jan 02 2008 - 13:50:50 CST)
  • AMBER: Help reg. input file (Wed Jan 02 2008 - 12:34:56 CST)
• sobereva
  • Re: AMBER: installation amber9 in fedora9 (Tue Dec 23 2008 - 03:52:00 CST)
  • Re: AMBER: ptraj - closest command (Wed Oct 08 2008 - 21:49:46 CDT)
  • Re: AMBER: internal energy INT is not zero from MM_GBSA (Tue Oct 07 2008 - 09:22:57 CDT)
  • Re: AMBER: Amber heme parameters (Tue Oct 07 2008 - 09:02:12 CDT)
• Soonmin Jang
  • AMBER: Constant pH simulation force field (Sat Sep 27 2008 - 04:13:51 CDT)
• soumick
  • AMBER: adding missing residues (Thu Jul 24 2008 - 06:09:16 CDT)
• Sreeja Parameswaran
  • Re: AMBER: AMBER parameters for Chlorophyll (Sat Feb 16 2008 - 08:45:32 CST)
  • AMBER: AMBER parameters for Chlorophyll (Wed Feb 13 2008 - 19:31:05 CST)
• srinivas sudani
  • AMBER: Compailation problum in Amber 10 (Wed Aug 06 2008 - 04:24:51 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Mon Aug 04 2008 - 00:41:13 CDT)
  • AMBER: Compailation problum in Amber 10 (Fri Aug 01 2008 - 01:59:00 CDT)
• Starr Hazard
  • AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 10:36:05 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 16:11:58 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 15:10:11 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:53:14 CST)
• steinbrt_at_rci.rutgers.edu
  • Re: AMBER: about mmpbsa out data (Tue Dec 23 2008 - 22:53:02 CST)
  • Re: AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu (Sat Dec 13 2008 - 12:58:18 CST)
  • AMBER: Ewald troubles when running very big boxes (Mon Nov 24 2008 - 14:50:50 CST)
  • Re: AMBER: Amber on linux (Wed Nov 19 2008 - 13:47:45 CST)
  • AMBER: ptraj closest command (Mon Nov 17 2008 - 10:14:11 CST)
  • Re: AMBER: subroutine for torsional potential (Fri Nov 14 2008 - 08:49:25 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:57:33 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:57:33 CST)
  • Re: AMBER: resp charges in parameterization (Wed Nov 12 2008 - 10:44:17 CST)
  • Re: AMBER: How to assign /make the ionion bond? (Fri Oct 17 2008 - 18:06:26 CDT)
• steinbrt_at_scripps.edu
  • AMBER: unsubscribe amber (Mon Sep 29 2008 - 09:57:50 CDT)
  • RE: AMBER: Bennett acceptance ratio with Amber10 (Wed Aug 27 2008 - 11:28:13 CDT)
  • Re: AMBER: Bennett acceptance ratio with Amber10 (Tue Aug 26 2008 - 08:45:55 CDT)
• Stephan.Reiling_at_sanofi-aventis.com
  • AMBER: mm_pbsa.pl and Amber10 (Mon Nov 10 2008 - 10:05:27 CST)
• Stephane Abel
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Thu Nov 27 2008 - 05:33:56 CST)
  • AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 05:21:52 CST)
  • AMBER: About antechamber and GAFF (Wed Nov 26 2008 - 05:02:00 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 11:07:07 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:51:25 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:26:10 CST)
  • AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 09:40:17 CST)
  • Re: AMBER: AMBER force field for glycolipid (Thu Oct 09 2008 - 09:08:49 CDT)
  • AMBER: AMBER force field for glycolipid (Wed Oct 08 2008 - 07:25:12 CDT)
• stephane acoca
  • Re: AMBER: artifacts in ptraj avg output (Sat Apr 05 2008 - 04:52:26 CDT)
  • AMBER: artifacts in ptraj avg output (Sat Apr 05 2008 - 03:46:55 CDT)
  • Re: AMBER: mm_pbsa error (Thu Apr 03 2008 - 15:21:29 CDT)
  • AMBER: MM-PBSA problem (Thu Jan 03 2008 - 21:45:10 CST)
• Steve Seibold
  • AMBER: problems with ptraj and strip waters (Thu Sep 18 2008 - 16:19:25 CDT)
  • AMBER: problem with traj and strip waters (Thu Sep 18 2008 - 09:13:38 CDT)
  • AMBER: problem with traj and strip waters (Thu Sep 18 2008 - 08:08:21 CDT)
  • AMBER: matrix correl (Wed Sep 03 2008 - 13:40:28 CDT)
  • AMBER: NMA (Fri Jul 11 2008 - 11:34:00 CDT)
  • AMBER: Water tracking (Fri May 02 2008 - 10:09:35 CDT)
  • AMBER: Water residue tracking (Thu May 01 2008 - 11:19:42 CDT)
  • RE: AMBER: (Thu Mar 06 2008 - 12:27:34 CST)
  • AMBER: (Thu Mar 06 2008 - 12:04:01 CST)
  • RE: AMBER: TERs (Mon Feb 18 2008 - 11:51:51 CST)
  • AMBER: TERs (Mon Feb 18 2008 - 07:19:39 CST)
• Steve Spronk
  • AMBER: Does clustering involve fitting? (Fri Jul 25 2008 - 15:02:09 CDT)
  • AMBER: Problem with box dimension in AmberTools ptraj (Tue Jul 22 2008 - 01:35:47 CDT)
  • RE: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? (Tue Jun 17 2008 - 10:54:04 CDT)
  • AMBER: "Dumping RAW 2D RMS data is not yet implemented"? (Tue Jun 17 2008 - 09:00:08 CDT)
  • RE: AMBER: 2D RMS plot (Thu Jun 12 2008 - 07:42:41 CDT)
  • AMBER: 2D RMS plot (Wed Jun 11 2008 - 14:18:32 CDT)
  • RE: AMBER: loading pdb in leap to create parameter files (Mon Apr 21 2008 - 12:04:34 CDT)
  • RE: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 08:13:12 CDT)
  • RE: AMBER: Protein rotating out of box (Tue Apr 01 2008 - 09:55:20 CDT)
  • RE: AMBER: initial command? (Fri Feb 29 2008 - 08:17:38 CST)
  • RE: AMBER: initial command? (Wed Feb 27 2008 - 12:45:43 CST)
  • RE: AMBER: silica slab (Wed Feb 06 2008 - 13:01:22 CST)
  • RE: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? (Mon Jan 28 2008 - 07:47:39 CST)
• Steven
  • Re: Re: AMBER: questions about gaff (Fri Jun 20 2008 - 09:11:08 CDT)
• Steven Winfield
  • Re: AMBER: regarding rigid molecules (Thu Oct 16 2008 - 06:30:31 CDT)
  • Re: AMBER: Using AMBER forces (Tue Jun 24 2008 - 11:54:49 CDT)
  • AMBER: Using AMBER forces (Tue Jun 24 2008 - 10:44:41 CDT)
  • Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Wed Mar 26 2008 - 10:22:26 CDT)
  • Re: AMBER: mol2 save (Tue Feb 26 2008 - 11:13:23 CST)
  • Re: AMBER: silica slab (Wed Feb 06 2008 - 17:48:59 CST)
  • Re: AMBER: benchmark walltime to ps/day calculation (Thu Jan 31 2008 - 14:34:49 CST)
  • Re: AMBER: QM/MM Heating (Wed Jan 23 2008 - 06:30:11 CST)
  • Re: AMBER: QM/MM Heating (Mon Jan 21 2008 - 07:48:22 CST)
  • AMBER: QM/MM Heating (Mon Jan 14 2008 - 09:22:27 CST)
• Su Nwe
  • AMBER: unsubscribe amber (Tue Nov 25 2008 - 01:12:02 CST)
• Subramanian Arun Kumar
  • AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations. (Thu Jan 24 2008 - 11:14:56 CST)
• Sudha Mani Karra
  • AMBER: Re: reaction coordinate in umbrella sampling (Mon Sep 22 2008 - 10:00:42 CDT)
  • Re: AMBER: Writing pressure in md.out file in NVT simulation (Mon Mar 03 2008 - 14:56:13 CST)
  • AMBER: Writing pressure in md.out file in NVT simulation (Mon Mar 03 2008 - 12:58:46 CST)
  • AMBER: Distance restraints between com of two groups of residues (Thu Feb 14 2008 - 16:20:26 CST)
• sudipta sinha
  • AMBER: Problem in .parmtop file (Mon Jul 28 2008 - 10:30:09 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 13:02:53 CDT)
  • Re: AMBER: Which is best temperature controlling method (Wed May 28 2008 - 01:43:32 CDT)
  • AMBER: Which is best temperature controlling method (Tue May 27 2008 - 05:25:02 CDT)
  • AMBER: Compilation of PMEMD (Thu May 08 2008 - 06:07:28 CDT)
  • Re: AMBER: AMBER Parallel test error (Wed May 07 2008 - 11:09:28 CDT)
  • AMBER: uninstall of AMBER (Wed May 07 2008 - 10:50:37 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 06:24:29 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 04:47:38 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Mon May 05 2008 - 01:52:58 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Sun May 04 2008 - 07:31:22 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Sat May 03 2008 - 00:59:23 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 15:29:38 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 13:29:37 CDT)
  • Re: AMBER: Installation problem of AMBER on cluster (Fri May 02 2008 - 02:39:09 CDT)
  • AMBER: Installation problem of AMBER on cluster (Thu May 01 2008 - 13:16:44 CDT)
• suhaib sh
  • Re: AMBER: Ac-Co Parameters for Amber (Thu Oct 02 2008 - 04:34:08 CDT)
  • Re: AMBER: Ac-Co Parameters for Amber (Wed Oct 01 2008 - 04:05:31 CDT)
  • Re: AMBER: Ac-Co Parameters for Amber (Tue Sep 30 2008 - 17:18:48 CDT)
  • AMBER: Ac-Co Parameters for Amber (Tue Sep 30 2008 - 06:49:41 CDT)
• Surasak Chunsrivirot
  • Re: AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 18:38:07 CST)
  • Re: AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 18:22:38 CST)
  • AMBER: Using antechamber without AMBER program (Mon Feb 04 2008 - 14:58:59 CST)
• Swarup Gupta
  • Re: AMBER: PB Radii (Mon Nov 17 2008 - 05:24:42 CST)
  • Re: AMBER: PB Radii (Sat Nov 15 2008 - 21:44:25 CST)
  • AMBER: PB Radii (Thu Nov 13 2008 - 01:06:34 CST)
  • AMBER: Re: entropy of released water (Thu Aug 07 2008 - 07:40:26 CDT)
  • AMBER: entropy of released water (Thu Aug 07 2008 - 07:36:32 CDT)
  • Re: AMBER: trajout input (Sun Jun 22 2008 - 22:01:31 CDT)
  • Re: AMBER: ligand unit charge is not zero (Thu May 29 2008 - 07:48:13 CDT)
  • Re: AMBER: how to overcome theunusual bonds formation (Thu May 29 2008 - 07:27:36 CDT)
  • AMBER: ff94 vs. ff03 (Fri May 23 2008 - 19:26:46 CDT)
  • Re: AMBER: AMBER entropy calculation (Wed May 14 2008 - 21:20:07 CDT)
  • AMBER: stops writing trajectory (Wed Feb 27 2008 - 03:55:10 CST)
• sychen
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 21:46:20 CST)
  • Re[2]: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 20:18:00 CST)
  • AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 01:50:11 CST)
  • AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? (Wed Jun 04 2008 - 07:27:45 CDT)
  • AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri May 02 2008 - 09:22:50 CDT)
  • AMBER: How to calculate deformability by PTRAJ ? (Thu Mar 13 2008 - 20:44:36 CDT)
• Syed Tarique Moin
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 09:11:12 CST)
  • AMBER: QM/MM simulation (Sat Nov 22 2008 - 02:00:36 CST)
  • AMBER: QM/MM (Fri May 09 2008 - 03:28:06 CDT)
  • AMBER: Negative ligand (Sat Mar 15 2008 - 04:12:09 CDT)
  • Fwd: AMBER: Negative ligand (Peroxide) (Mon Mar 10 2008 - 00:59:43 CDT)
  • AMBER: Negative ligand (Peroxide) (Sat Mar 08 2008 - 05:36:56 CST)
  • AMBER: (no subject) (Fri Feb 22 2008 - 00:10:36 CST)
  • RE: AMBER: (no subject) (Wed Feb 13 2008 - 22:58:56 CST)
  • AMBER: (no subject) (Wed Feb 13 2008 - 04:55:02 CST)
  • Fwd: AMBER: (no subject) (Wed Feb 06 2008 - 02:00:23 CST)
  • AMBER: (no subject) (Mon Feb 04 2008 - 08:07:26 CST)
  • AMBER: (no subject) (Wed Jan 30 2008 - 23:31:24 CST)
  • Re: AMBER: RESP (Thu Jan 10 2008 - 03:15:15 CST)
  • Re: AMBER: RESP (Thu Jan 10 2008 - 00:36:05 CST)
  • AMBER: RESP (Tue Jan 08 2008 - 06:40:03 CST)
  • AMBER: RESP (Tue Jan 08 2008 - 06:41:06 CST)
  • AMBER: RESP (Tue Jan 08 2008 - 06:40:21 CST)
  • AMBER: RESP (Tue Jan 08 2008 - 06:41:56 CST)
  • Re: AMBER: MD of protein-ligand comlex (Mon Jan 07 2008 - 00:18:20 CST)
• TAEJIN KIM
  • AMBER: Antechamber and topology file (Wed Jun 11 2008 - 18:05:14 CDT)
• TaoPaul
  • AMBER: the question about "RADIOPT" option in mm_pbsa (Sat Oct 25 2008 - 06:11:04 CDT)
  • RE: AMBER: something puzzled with mm_pbsa (Fri Oct 24 2008 - 21:08:50 CDT)
  • AMBER: something puzzled with mm_pbsa (Fri Oct 24 2008 - 05:50:04 CDT)
  • AMBER: a question about matrix command? (Tue Sep 02 2008 - 20:01:04 CDT)
  • AMBER: how to get the potential energy of a protein from the system (Thu Jul 31 2008 - 03:29:08 CDT)
• Taufik Al-Sarraj
  • AMBER: Re: (Mon Dec 22 2008 - 12:08:17 CST)
  • AMBER: Materials and methods (Mon Dec 22 2008 - 12:05:22 CST)
  • AMBER: xleap (measureGeom) (Sat Dec 20 2008 - 15:02:56 CST)
  • Re: AMBER: distance restraint between non-bonded molecules] (Sat Dec 20 2008 - 12:44:43 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 09:14:51 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 14:41:05 CST)
  • Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 10:49:51 CST)
  • AMBER: distance restraint between non-bonded molecules (Wed Dec 17 2008 - 18:13:36 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 14:16:18 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 13:34:22 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:52:01 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:15:24 CST)
  • Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 11:44:55 CST)
  • AMBER: distance restraint in minimization (Tue Dec 16 2008 - 16:44:35 CST)
  • Re: AMBER: distance restraint in minimization (Tue Dec 16 2008 - 15:16:43 CST)
  • AMBER: distance restraint in minimization (Tue Dec 16 2008 - 12:46:22 CST)
  • AMBER: unable to open pdb file (Wed Dec 03 2008 - 20:44:09 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 24 2008 - 17:37:24 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 15:10:23 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 14:31:39 CST)
  • AMBER: coot mutation (Thu Nov 06 2008 - 14:19:00 CST)
  • Re: AMBER: pdb structure is only half the molecule. (Fri Oct 24 2008 - 18:15:52 CDT)
  • AMBER: pdb structure is only half the molecule. (Thu Oct 23 2008 - 14:42:24 CDT)
  • AMBER: HOLD fixed vs restraint mask (Tue Oct 21 2008 - 13:02:34 CDT)
  • Re: AMBER: changing pdb structure (Tue Oct 14 2008 - 15:26:33 CDT)
  • Re: AMBER: drawing repeated units (Tue Jun 24 2008 - 17:15:39 CDT)
  • Re: AMBER: QM/MM (Wed Jun 11 2008 - 11:28:34 CDT)
  • AMBER: QM/MM (Wed Jun 11 2008 - 11:09:24 CDT)
  • Re: AMBER: drawing repeated units (Wed Jun 04 2008 - 15:17:57 CDT)
  • Re: AMBER: drawing repeated units (Tue Jun 03 2008 - 18:58:25 CDT)
  • Re: AMBER: drawing repeated units (Tue Jun 03 2008 - 17:25:59 CDT)
  • AMBER: writing a script in amber (Mon Jun 02 2008 - 19:28:39 CDT)
  • Re: AMBER: drawing repeated units (Fri May 09 2008 - 13:10:56 CDT)
  • AMBER: drawing repeated units (Fri May 09 2008 - 10:10:19 CDT)
  • Re: AMBER: xleap (draw using edit) (Thu May 08 2008 - 15:58:24 CDT)
  • AMBER: xleap (draw using edit) (Wed May 07 2008 - 21:31:14 CDT)
  • Re: AMBER: single stranded DNA (Tue May 06 2008 - 19:11:07 CDT)
  • AMBER: single stranded DNA (Tue May 06 2008 - 17:37:41 CDT)
  • AMBER: Si parameters for MD (AMBER9) (Fri Apr 25 2008 - 17:08:44 CDT)
  • Re: AMBER: questions about run MD at different pH (Tue Apr 15 2008 - 17:47:10 CDT)
  • Re: AMBER: questions about run MD at different pH (Tue Apr 15 2008 - 15:06:39 CDT)
  • Re: AMBER: questions about run MD at different pH (Tue Apr 15 2008 - 11:15:28 CDT)
  • Re: AMBER: AMBER 9 testing (Wed Apr 02 2008 - 21:36:57 CDT)
  • Re: AMBER: AMBER 9 testing (Fri Mar 28 2008 - 23:13:31 CDT)
  • AMBER: AMBER 9 testing (Fri Mar 28 2008 - 19:18:30 CDT)
  • AMBER: Amber 9 installation (Tue Feb 05 2008 - 09:14:56 CST)
  • AMBER: Amber 9 installation (Mon Feb 04 2008 - 15:53:23 CST)
• taufik.alsarraj_at_utoronto.ca
  • AMBER: changing pdb structure (Thu Oct 09 2008 - 21:35:07 CDT)
  • Re: AMBER: xleap fails to savemol2 (Wed Oct 08 2008 - 16:57:30 CDT)
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 16:28:52 CDT)
  • AMBER: join two units in amber9 or amber10 (Fri Aug 29 2008 - 16:17:58 CDT)
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 12:28:33 CDT)
  • AMBER: xleap fails to savemol2 (Thu Aug 28 2008 - 17:43:07 CDT)
  • AMBER: saveamberparm (Wed Apr 23 2008 - 19:38:16 CDT)
  • AMBER: saveamberparm (Wed Apr 23 2008 - 19:34:02 CDT)
• Ted Fischer
  • Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits (Tue Apr 15 2008 - 04:09:47 CDT)
  • AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits (Mon Apr 14 2008 - 07:53:42 CDT)
• teresa.ierano_at_unina.it
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 11:39:30 CDT)
  • RE: AMBER: Minimization methods (Mon Aug 11 2008 - 11:30:50 CDT)
  • AMBER: Minimization methods (Mon Aug 11 2008 - 07:11:23 CDT)
  • Re: AMBER: NMR refinement (Thu Jul 03 2008 - 04:37:02 CDT)
  • AMBER: NMR refinement (Wed Jul 02 2008 - 03:38:57 CDT)
  • AMBER: NMR refinement (Mon Jun 30 2008 - 05:37:48 CDT)
• Thomas Cheatham
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 12:43:24 CDT)
  • Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? (Tue Jul 22 2008 - 11:45:12 CDT)
  • Re: AMBER: Problem with box dimension in AmberTools ptraj (Tue Jul 22 2008 - 11:47:42 CDT)
  • Re: AMBER: rdparm help (Fri Jun 20 2008 - 09:35:36 CDT)
  • Re: AMBER: PTRAJ - Segmentation Fault (Wed Jun 11 2008 - 13:15:00 CDT)
  • RE: AMBER: Ewald error estimate (Wed May 07 2008 - 22:51:55 CDT)
  • Re: AMBER: What's making my system lose total energy? (Mon Mar 17 2008 - 22:36:30 CDT)
  • Re: AMBER: Problem running implicit minimization (Tue Mar 04 2008 - 17:47:50 CST)
  • Re: AMBER: "Assuming uniform neutralizing plasma" (Tue Feb 26 2008 - 21:31:39 CST)
  • Re: AMBER: TERs (Mon Feb 18 2008 - 11:18:36 CST)
• Thomas Cheatham III
  • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 11:16:47 CST)
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 16:47:51 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:48:04 CDT)
  • Re: AMBER: test of parallel sander 10 fail (Tue Jul 15 2008 - 12:41:12 CDT)
  • Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap (Thu Jul 10 2008 - 17:20:04 CDT)
  • Re: AMBER: problem with rdparm (Thu Jul 10 2008 - 17:13:35 CDT)
  • Re: AMBER: bellymask for DNA backbone doesn't seem to work (Thu Jul 03 2008 - 15:40:47 CDT)
  • Re: AMBER: Regarding force field ff02 and ion library (Mon Jun 30 2008 - 16:30:05 CDT)
  • Re: AMBER: trajout input (Fri Jun 20 2008 - 12:57:43 CDT)
  • RE: AMBER: Ewald error estimate (Thu May 08 2008 - 12:21:38 CDT)
  • Re: AMBER: Water tracking (Fri May 02 2008 - 11:14:21 CDT)
  • Re: AMBER: double strand DNA break up (imaging) (Thu Apr 24 2008 - 14:43:36 CDT)
  • Re: AMBER: loadPdb returns extra atoms (Mon Apr 14 2008 - 14:19:03 CDT)
  • Re: AMBER: Imaging before HBond analysis? (Fri Apr 11 2008 - 17:52:04 CDT)
  • Re: AMBER: Imaging before HBond analysis? (Fri Apr 11 2008 - 17:24:29 CDT)
  • Re: AMBER: working with unformatted restart files in AMBER9 (Wed Apr 02 2008 - 12:26:00 CDT)
  • Re: AMBER: B-factor (Wed Apr 02 2008 - 12:18:18 CDT)
  • Re: AMBER: Protein rotating out of box (Wed Apr 02 2008 - 11:54:46 CDT)
  • Re: AMBER: LEap error message for parmBSC0 force field (Tue Apr 01 2008 - 18:55:38 CDT)
  • Re: AMBER: atomic posiltional fluctuation (Tue Apr 01 2008 - 11:50:43 CDT)
  • Re: SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 11:51:54 CDT)
  • Re: AMBER: implicit energy calculations (Thu Mar 13 2008 - 12:47:04 CDT)
  • Re: AMBER: ptraj, hbond and non-bonded contacts (Thu Mar 13 2008 - 12:49:14 CDT)
  • Re: AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 10:37:03 CST)
  • Re: AMBER: using hydrogen bond facility to monitor ion pair interaction (Thu Jan 10 2008 - 11:21:10 CST)
• Thomas Exner
  • Re: AMBER: BCC charges (Wed Jan 23 2008 - 04:11:36 CST)
  • AMBER: BCC charges (Tue Jan 22 2008 - 09:47:20 CST)
• Thomas Leonard
  • AMBER: pairwise interaction energies (Mon Oct 13 2008 - 01:12:11 CDT)
  • AMBER: PBCAL in MM_PBSA (Mon Aug 11 2008 - 03:12:51 CDT)
  • AMBER: parameters (Fri Aug 08 2008 - 00:45:09 CDT)
  • AMBER: Res minimization (Tue Jul 15 2008 - 02:34:47 CDT)
  • Re: AMBER: trajout input (Fri Jun 20 2008 - 05:05:55 CDT)
  • AMBER: trajout input (Fri Jun 20 2008 - 04:23:55 CDT)
  • AMBER: How to solve - Missing BELE for MM in 1 in amber. (Mon Jun 16 2008 - 22:06:01 CDT)
  • AMBER: How to solve - Missing BELE for MM in 1 in amber. (Mon Jun 16 2008 - 22:05:59 CDT)
  • Re: AMBER: how to overcome theunusual bonds formation (Thu May 29 2008 - 07:01:43 CDT)
  • AMBER: how to overcome theunusual bonds formation (Thu May 29 2008 - 06:03:29 CDT)
  • AMBER: how to calculate delta G from IC50 (Tue May 20 2008 - 00:12:04 CDT)
  • AMBER: AMBER entropy calculation (Wed May 14 2008 - 18:00:45 CDT)
  • AMBER: AMBER PBSA (Wed May 14 2008 - 04:35:54 CDT)
  • Re: AMBER: FAD and NAD parameters (Thu Apr 10 2008 - 01:43:47 CDT)
  • AMBER: FAD and NAD parameters (Wed Mar 26 2008 - 04:26:52 CDT)
• Thomas Patko
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 16:15:58 CST)
  • Re: AMBER: MKL libraries/Amber10 (Fri May 16 2008 - 16:26:33 CDT)
• Thomas Steinbrecher
  • Re: AMBER: help me for filling a nanotube with water?? (Wed Aug 13 2008 - 11:40:22 CDT)
  • Re: AMBER: free energy (Wed Jul 16 2008 - 11:22:45 CDT)
  • Re: AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 (Mon Jul 07 2008 - 17:56:49 CDT)
  • Re: AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential (Wed Jul 02 2008 - 14:08:40 CDT)
  • Re: AMBER: Protonated Phosphate Problem (Tue Jul 01 2008 - 12:41:55 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 12:36:17 CDT)
  • Re: AMBER: "radius = 0.000" (Tue Jul 01 2008 - 11:39:30 CDT)
  • Re: AMBER: TI calculations in Amber10 (Wed Jun 25 2008 - 11:15:47 CDT)
  • Re: AMBER: how to calculate the interaction energy (Tue Jun 10 2008 - 11:45:16 CDT)
  • Re: AMBER: NON-BONDED parameters (Mon May 05 2008 - 13:14:59 CDT)
  • Re: AMBER: Can sander provide ESP with PBC? (Wed Apr 23 2008 - 13:39:10 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Tue Apr 08 2008 - 15:37:39 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Apr 07 2008 - 12:39:18 CDT)
  • Re: AMBER: Restraintmask and Restraint_WT : Question (Fri Apr 04 2008 - 11:18:17 CDT)
  • Re: AMBER: LJ parameters (Wed Apr 02 2008 - 12:31:57 CDT)
  • Re: AMBER: running minimisation on cis-azobenzene (Mon Mar 31 2008 - 15:14:17 CDT)
  • Re: AMBER: TI: perturbation method (Mon Mar 31 2008 - 11:32:21 CDT)
  • Re: AMBER: umbrella sampling for proton transfer (Tue Mar 25 2008 - 20:11:58 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 16:22:21 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 14:31:03 CDT)
  • Re: AMBER: Heating POL3 Box Troubles (Fri Mar 14 2008 - 14:01:06 CDT)
  • Re: AMBER: Adding New Parameters and Modifying Existing Parameters (Tue Mar 11 2008 - 11:46:33 CDT)
  • Re: AMBER: writing out a distance between two atoms in sander (Mon Mar 10 2008 - 12:17:35 CDT)
  • Re: AMBER: Clarification on error message (Sat Mar 08 2008 - 14:17:35 CST)
  • Re: AMBER: setBox command (Thu Mar 06 2008 - 12:06:32 CST)
  • Re: AMBER: (Thu Mar 06 2008 - 12:13:23 CST)
• Thérèse Malliavin
  • AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 08:04:26 CST)
  • RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 06:57:05 CST)
  • AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Mon Dec 15 2008 - 08:41:55 CST)
• Tim Meyer
  • Re: AMBER: misplacement of TER by leap (Mon May 05 2008 - 08:03:54 CDT)
• tinni sona
  • Re: AMBER: Query about the charge of atoms in the parmtop file (Thu Jul 24 2008 - 02:19:26 CDT)
  • AMBER: Query about the charge of atoms in the parmtop file (Wed Jul 23 2008 - 11:48:19 CDT)
  • Re: AMBER: how to generate psf file using the AMBER topology file (Sun Jul 20 2008 - 00:38:10 CDT)
  • Re: AMBER: how to generate psf file using the AMBER topology file (Fri Jul 18 2008 - 07:08:48 CDT)
  • AMBER: how to generate psf file using the AMBER topology file (Fri Jul 18 2008 - 05:41:11 CDT)
  • AMBER: Temperature controlling method in AMBER (Tue Jun 03 2008 - 04:43:11 CDT)
  • AMBER: atom type in glycam06 (Mon May 19 2008 - 12:06:57 CDT)
• Titus, Jamie (bairdje)
  • AMBER: Gohlke in-house iRED Simulated Order Parameter Script (Thu Aug 21 2008 - 07:53:09 CDT)
• Titus, Jamie \(bairdje\)
  • AMBER: Hydroxyprolines!!! (Wed May 07 2008 - 13:54:03 CDT)
  • AMBER: GBSA SA calculation (Wed May 07 2008 - 13:32:43 CDT)
• Tom Darden
  • Re: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. (Mon Sep 22 2008 - 15:51:53 CDT)
  • Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms (Wed Apr 16 2008 - 16:30:53 CDT)
  • Re: AMBER: Electric field on atoms in equallibrium (Tue Apr 01 2008 - 14:26:32 CDT)
  • Re: AMBER: Electric field on atoms in equallibrium (Tue Apr 01 2008 - 12:59:17 CDT)
  • Re: AMBER: Electric field on atoms in equallibrium (Tue Apr 01 2008 - 12:59:17 CDT)
• Tom McGrory
  • AMBER: 2D-RMSD (Wed Apr 23 2008 - 10:00:57 CDT)
• tri nam Vo
  • AMBER: Running Amber8 - Sander (Mon Nov 24 2008 - 00:28:31 CST)
• trudy_at_uoguelph.ca
  • Re: AMBER: Amber9 Installation Problem (Thu Mar 20 2008 - 17:51:08 CDT)
  • Re: AMBER: Amber9 Installation Problem (Thu Mar 20 2008 - 17:43:48 CDT)
  • AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 11:28:35 CDT)
  • AMBER: Amber9 Installation Problem (Wed Mar 19 2008 - 11:28:35 CDT)
• tushar garud
  • AMBER: equilibration of peptide (Fri Mar 21 2008 - 23:02:25 CDT)
  • AMBER: Temperature Range For REMD (Thu Mar 13 2008 - 10:20:02 CDT)
  • AMBER: Plea for REMD tutorial (Fri Feb 29 2008 - 08:57:41 CST)
  • AMBER: Plea for REMD tutorial (Thu Feb 28 2008 - 07:56:42 CST)
• uccabke_at_ucl.ac.uk
  • Re: AMBER: H atom names in Amber (Thu Apr 17 2008 - 10:49:57 CDT)
  • AMBER: (Thu Apr 17 2008 - 10:02:06 CDT)
• Uma R
  • AMBER: reg molecular dynamics (Fri Mar 07 2008 - 21:17:32 CST)
• umbrita itl
  • AMBER: MD of protein-ligand comlex (Sun Jan 06 2008 - 14:54:47 CST)
• Urszula Uciechowska
  • Re: AMBER: equilibration (Tue Oct 21 2008 - 06:28:17 CDT)
  • Re: AMBER: equilibration (Tue Oct 21 2008 - 06:17:08 CDT)
  • AMBER: equilibration (Tue Oct 21 2008 - 05:44:54 CDT)
  • AMBER: input (Tue Oct 21 2008 - 04:14:28 CDT)
  • AMBER: LES trajectories (Mon Aug 25 2008 - 03:12:23 CDT)
  • AMBER: mmpbsa (Mon Aug 11 2008 - 03:43:17 CDT)
  • AMBER: LES (Fri Aug 08 2008 - 07:31:56 CDT)
  • AMBER: linear interaction energy (Thu Aug 07 2008 - 08:55:18 CDT)
  • AMBER: addles (Tue Aug 05 2008 - 03:30:20 CDT)
  • Re: AMBER: rms (Mon May 12 2008 - 08:41:06 CDT)
  • AMBER: rms (Mon May 12 2008 - 06:19:41 CDT)
  • AMBER: distance (Fri May 09 2008 - 09:36:18 CDT)
  • AMBER: NAD parameters (Thu Apr 03 2008 - 09:30:05 CDT)
  • AMBER: tutorial_8_section_6 (Wed Jan 23 2008 - 11:04:38 CST)
• Vahdati N.
  • RE: AMBER: analysing normal modes (Thu Jul 10 2008 - 07:49:15 CDT)
  • AMBER: analysing normal modes (Tue Jul 08 2008 - 13:03:39 CDT)
  • RE: AMBER: nmode analysis (Mon Jun 30 2008 - 07:41:40 CDT)
  • RE: AMBER: Equilibration/Heating - Protein fixed -Problem (Wed Jun 11 2008 - 12:38:50 CDT)
• vallespardojl_at_chem.leidenuniv.nl
  • AMBER: Problems for use manganese molecules (Fri Nov 21 2008 - 03:06:37 CST)
• Vasu Chandrasekaran
  • Re: AMBER: MM_PBSA snapshot statistic calc problem (Mon Sep 29 2008 - 14:08:15 CDT)
• Vidana.Epa_at_csiro.au
  • AMBER: RESP calculation on Copper containing molecule (Fri Jul 04 2008 - 02:16:24 CDT)
  • AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member (Wed Feb 06 2008 - 00:08:19 CST)
• Vijay Manickam Achari
  • AMBER: xleap error (Wed Dec 24 2008 - 03:58:17 CST)
  • AMBER: installation amber9 in fedora9 using bash shell (Tue Dec 23 2008 - 22:05:28 CST)
  • AMBER: installation amber9 in fedora9 (Mon Dec 22 2008 - 22:44:12 CST)
  • AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 01:40:03 CDT)
  • AMBER: output file AMBER9_MPI (Thu Jun 26 2008 - 14:06:19 CDT)
  • Re: AMBER: pressure varies in constant pressure membrane simulation (Tue Apr 22 2008 - 23:10:54 CDT)
  • AMBER: pressure varies in constant pressure membrane simulation (Tue Apr 22 2008 - 00:58:29 CDT)
  • AMBER: setBox command (Wed Mar 05 2008 - 23:20:01 CST)
  • AMBER: Visualizing Periodc box (Fri Feb 29 2008 - 01:50:13 CST)
  • AMBER: is that possible fix box size in constant pressure MD (Tue Feb 19 2008 - 23:39:46 CST)
  • Re: AMBER: setting perioding box in AMBER (Tue Feb 19 2008 - 00:00:06 CST)
  • AMBER: setting perioding box in AMBER (Sun Feb 17 2008 - 19:47:17 CST)
  • AMBER: setting periodic box (Tue Jan 29 2008 - 22:22:05 CST)
• Vijay Singh
  • AMBER: paricular atom coordinates? (Thu Jul 17 2008 - 11:13:30 CDT)
  • AMBER: amber9 , ptraj vector commad issue (Sat May 31 2008 - 18:34:23 CDT)
  • Re: AMBER: problems with restart of MD (Sun Jan 13 2008 - 13:53:11 CST)
  • Re: AMBER: problems with restart of MD (Sun Jan 13 2008 - 09:45:25 CST)
  • Re: AMBER: problems with restart of MD (Sat Jan 12 2008 - 03:48:39 CST)
  • Re: AMBER: problems with restart of MD (Fri Jan 11 2008 - 14:04:39 CST)
  • AMBER: problems with restart of MD (Fri Jan 11 2008 - 11:29:31 CST)
• vijayaraj_at_clri.info
  • AMBER: amber10 installation (Thu May 22 2008 - 09:22:47 CDT)
  • Re: AMBER: amber tools installation (Thu May 22 2008 - 03:55:00 CDT)
  • AMBER: amber tools installation (Wed May 21 2008 - 10:22:37 CDT)
• vijayaraj_at_clri.res.in
  • AMBER: amber10 installation problem in cygwin (Tue Oct 14 2008 - 10:21:19 CDT)
• vikky 99
  • AMBER: Error- MM_PBSA calculation (Thu Mar 27 2008 - 03:47:53 CDT)
• Vlad Cojocaru
  • Re: AMBER: AMBER9 installation problen with open mpi (Tue Sep 02 2008 - 07:00:33 CDT)
  • Re: AMBER: compilation problem (Tue Sep 02 2008 - 05:16:13 CDT)
  • Re: AMBER: GPCR membrane simulation, setting surface tension (Tue Aug 12 2008 - 03:45:08 CDT)
  • Re: AMBER: amber 10: sander and pmemd performance (Fri Jul 25 2008 - 10:14:08 CDT)
  • AMBER: amber 10: sander and pmemd performance (Fri Jul 25 2008 - 04:57:45 CDT)
  • AMBER: EVB tests failure (Thu Jul 24 2008 - 03:34:52 CDT)
  • AMBER: Re: amber 10 and mpich2 (got eof on console error message from mpich2) (Thu Jul 17 2008 - 08:33:04 CDT)
  • AMBER: amber 10 and mpich2 (got eof on console error message from mpich2) (Thu Jul 17 2008 - 08:30:24 CDT)
  • Re: AMBER: sleap test failures (Wed Jul 16 2008 - 07:40:12 CDT)
  • Re: AMBER: sleap test failures (Wed Jul 16 2008 - 03:07:48 CDT)
  • AMBER: test of parallel sander 10 fail (Tue Jul 15 2008 - 12:05:51 CDT)
  • AMBER: sleap test failures (Tue Jul 15 2008 - 09:14:23 CDT)
  • AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) (Tue Jul 15 2008 - 08:45:11 CDT)
  • Re: AMBER: timing info output from pmemd (Fri Jul 11 2008 - 08:54:02 CDT)
  • Re: AMBER: timing info output from pmemd (Fri Jul 11 2008 - 07:33:31 CDT)
  • AMBER: configure_amber (10) for pg compilers (Fri Jul 11 2008 - 06:51:47 CDT)
  • AMBER: timing info output from pmemd (Fri Jul 11 2008 - 03:49:28 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 09:18:28 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 08:29:17 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 08:26:01 CDT)
  • Re: AMBER: pmemd 10 output (Thu Jul 10 2008 - 05:19:08 CDT)
  • Re: AMBER: ptraj - read in part of trajectory (Fri Jun 27 2008 - 11:59:14 CDT)
  • Re: AMBER: pmemd 10 output (Fri Jun 27 2008 - 11:34:37 CDT)
  • Re: AMBER: pmemd 10 output (Fri Jun 27 2008 - 11:24:58 CDT)
  • AMBER: pmemd 10 output (Fri Jun 27 2008 - 10:48:35 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Wed Jun 25 2008 - 04:00:10 CDT)
  • Re: AMBER: Compilation of amber8 patched with ramd (Tue Jun 24 2008 - 10:07:03 CDT)
  • Re: AMBER: amber10/dat/leap/cmd/README need update (Mon Jun 23 2008 - 10:12:29 CDT)
  • AMBER: the SPCFW water model (Mon Jun 16 2008 - 11:19:34 CDT)
  • Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Fri Jun 06 2008 - 13:50:55 CDT)
  • Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory (Fri Jun 06 2008 - 04:59:54 CDT)
  • Re: AMBER: ptraj imaging issue (Thu Jun 05 2008 - 09:30:42 CDT)
  • Re: AMBER: ptraj imaging issue (Thu Jun 05 2008 - 03:48:43 CDT)
  • AMBER: ptraj imaging issue (Wed Jun 04 2008 - 14:07:44 CDT)
  • Re: AMBER: ff99 and ff03 forcefield parameters (Fri May 23 2008 - 10:52:03 CDT)
  • Re: AMBER: ff99 and ff03 forcefield parameters (Fri May 23 2008 - 04:43:38 CDT)
  • Re: AMBER: ff99 and ff03 forcefield parameters (Fri May 23 2008 - 04:31:47 CDT)
  • AMBER: pressure regulation methods (Wed May 21 2008 - 11:25:08 CDT)
  • Re: AMBER: rms (Wed May 14 2008 - 09:01:17 CDT)
  • Re: AMBER: rms (Mon May 12 2008 - 07:40:46 CDT)
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 03:42:24 CDT)
  • Re: AMBER: GAFF (Fri Apr 04 2008 - 03:22:30 CDT)
  • AMBER: working with unformatted restart files in AMBER9 (Tue Apr 01 2008 - 08:35:57 CDT)
  • Re: AMBER: Convert dcd to mdcrd (Wed Mar 26 2008 - 04:02:38 CDT)
  • Re: AMBER: compiling AMBER9 with bintraj option on AMD64 (Tue Mar 18 2008 - 04:32:13 CDT)
  • AMBER: compiling AMBER9 with bintraj option on AMD64 (Fri Mar 14 2008 - 12:44:56 CDT)
  • Re: SV: AMBER: ptraj, hbond and non-bonded contacts (Mon Mar 17 2008 - 06:00:41 CDT)
  • Re: AMBER: writing out a distance between two atoms in sander (Mon Mar 10 2008 - 12:35:58 CDT)
  • AMBER: writing out a distance between two atoms in sander (Mon Mar 10 2008 - 08:33:55 CDT)
  • Re: AMBER: Writing pressure in md.out file in NVT simulation (Mon Mar 03 2008 - 13:26:50 CST)
  • AMBER: print distance between atoms during simulation within sander itsself (Fri Feb 15 2008 - 08:06:24 CST)
  • Re: AMBER: ptraj: new mask parser (Thu Jan 24 2008 - 12:19:25 CST)
  • AMBER: ptraj: new mask parser (Wed Jan 23 2008 - 05:59:24 CST)
• Volodymyr Zloy
  • AMBER: 2'-5'-branched RNA (Mon Oct 27 2008 - 11:10:00 CDT)
• waleed zalloum
  • AMBER: (no subject) (Tue Dec 09 2008 - 06:22:39 CST)
• Wang, Xuelin
  • RE: AMBER: NAB to calcuate entropy. . (Thu Feb 21 2008 - 14:00:31 CST)
  • RE: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 18:14:01 CST)
  • RE: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 16:22:16 CST)
  • RE: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 15:21:15 CST)
  • AMBER: NAB to calcuate entropy (Tue Feb 19 2008 - 17:58:15 CST)
  • RE: AMBER: using NAB to calculate normal modes. . (Fri Feb 15 2008 - 16:29:55 CST)
  • AMBER: setbox for solvateoct model (Fri Feb 15 2008 - 09:22:07 CST)
  • AMBER: PKa calculation (Tue Feb 12 2008 - 10:45:16 CST)
  • RE: AMBER: using NAB to calculate entropy. . (Wed Feb 06 2008 - 15:00:46 CST)
  • AMBER: using NAB to calculate entropy (Wed Feb 06 2008 - 11:52:06 CST)
• Wang,Ying
  • AMBER: AMBER forfield choose (Thu Nov 20 2008 - 08:32:24 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:17:45 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:05:28 CST)
  • Re: AMBER: Non bond list error (Thu Oct 23 2008 - 16:58:06 CDT)
  • RE: AMBER: Non bond list error (Thu Oct 23 2008 - 14:26:26 CDT)
  • AMBER: Non bond list error (Thu Oct 23 2008 - 12:19:49 CDT)
  • RE: AMBER: vlimit exceeded (Sat Aug 30 2008 - 18:14:21 CDT)
  • AMBER: vlimit exceeded (Sat Aug 30 2008 - 10:49:03 CDT)
  • Re: AMBER: bond command (Thu Jul 10 2008 - 12:56:01 CDT)
  • RE: AMBER: tip3p water and shake (Wed Jun 18 2008 - 22:44:27 CDT)
  • RE: AMBER: tip3p water and shake (Wed Jun 18 2008 - 20:03:55 CDT)
  • AMBER: tip3p water and shake (Wed Jun 18 2008 - 15:07:13 CDT)
  • Re: AMBER: how to calculate the interaction energy (Tue Jun 10 2008 - 14:12:17 CDT)
  • AMBER: how to calculate the interaction energy (Tue Jun 10 2008 - 09:52:10 CDT)
  • AMBER: tleap error message (Fri May 30 2008 - 11:08:14 CDT)
  • RE: AMBER: error when read inpcrd (Tue May 27 2008 - 16:14:02 CDT)
  • AMBER: error when read inpcrd (Tue May 27 2008 - 15:32:02 CDT)
  • RE: AMBER: periodic boundary condition (Sun May 25 2008 - 08:58:20 CDT)
  • RE: AMBER: how to extract energy (Sun May 25 2008 - 08:57:20 CDT)
  • AMBER: periodic bondary condition (Fri May 23 2008 - 20:16:34 CDT)
  • AMBER: how to extract energy (Fri May 23 2008 - 20:08:13 CDT)
  • AMBER: about hydrogen bond in amber force field (Wed May 21 2008 - 21:24:47 CDT)
  • AMBER: nfft1-3 too large (Mon May 19 2008 - 09:46:51 CDT)
  • AMBER: nfft1-3 too large (Mon May 19 2008 - 09:46:51 CDT)
  • RE: AMBER: solvatebox error (Thu May 15 2008 - 17:16:17 CDT)
  • AMBER: solvatebox error (Thu May 15 2008 - 16:47:06 CDT)
  • AMBER: periodic boundary condition (Tue May 13 2008 - 08:55:00 CDT)
  • Re: AMBER: cannot read big .pdb files (Tue May 13 2008 - 08:40:34 CDT)
  • Re: AMBER: cannot read big .pdb files (Mon May 12 2008 - 14:42:27 CDT)
  • Re: AMBER: Ewald PARAMETER RANGE WRONG (Mon May 12 2008 - 12:06:03 CDT)
  • Re: AMBER: cannot read big .pdb files (Mon May 12 2008 - 09:37:24 CDT)
  • AMBER: Ewald PARAMETER RANGE WRONG (Sun May 11 2008 - 13:01:09 CDT)
  • Re: AMBER: cannot read big .pdb files (Sun May 11 2008 - 08:36:48 CDT)
  • Re: AMBER: cannot read big .pdb files (Sun May 11 2008 - 08:38:41 CDT)
  • AMBER: cannot read big .pdb files (Fri May 09 2008 - 21:00:29 CDT)
  • AMBER: can amber read .xyz files? (Thu May 08 2008 - 10:29:57 CDT)
  • Re: AMBER: about glycam06 (Mon May 05 2008 - 09:30:19 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 21:40:14 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 21:35:05 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 18:57:35 CDT)
  • Re: AMBER: about glycam06 (Sat May 03 2008 - 18:55:11 CDT)
  • AMBER: about glycam06 (Sat May 03 2008 - 18:22:18 CDT)
  • Re: AMBER: about glycam06 (Wed Apr 30 2008 - 14:49:46 CDT)
  • AMBER: about glycam06 (Wed Apr 30 2008 - 11:00:12 CDT)
  • Re: AMBER: a question of ptraj (Wed Jan 02 2008 - 12:04:24 CST)
• wangluohuaxue
  • AMBER: subscribe amber (Wed May 14 2008 - 09:40:04 CDT)
• WanJ Ding
  • AMBER: about resp charges (Mon Jun 16 2008 - 14:44:55 CDT)
• wanjian ding
  • Re: AMBER: about resp charges (Wed Jun 18 2008 - 15:43:35 CDT)
• Waqas Nasir
  • AMBER: Distorted ring... (Thu Dec 11 2008 - 05:48:45 CST)
  • AMBER: Single point energy calculations with explicit solvent. (Thu Sep 18 2008 - 07:48:47 CDT)
  • Re: AMBER: top and crd files without hydrogen (Tue Sep 16 2008 - 05:32:42 CDT)
  • Re: AMBER: top and crd files without hydrogen (Tue Sep 16 2008 - 05:32:42 CDT)
  • AMBER: top and crd files without hydrogen (Tue Sep 16 2008 - 04:18:08 CDT)
  • Re: AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 11:17:04 CDT)
  • Re: AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 10:47:00 CDT)
  • AMBER: Hydrogen bond energies in explicit solvent. (Mon Sep 15 2008 - 09:56:34 CDT)
  • Re: AMBER: Need help... High energies for complex... (Tue Sep 09 2008 - 09:06:18 CDT)
  • Re: AMBER: Need help... High energies for complex... (Tue Sep 09 2008 - 08:16:29 CDT)
  • Re: AMBER: Need help... High energies for complex... (Mon Sep 08 2008 - 11:06:26 CDT)
  • Re: AMBER: Need help... High energies for complex... (Fri Sep 05 2008 - 04:15:59 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 11:14:35 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 10:22:55 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 09:12:21 CDT)
  • AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 05:38:53 CDT)
  • Re: AMBER: Need help... High energies for complex... (Thu Sep 04 2008 - 05:08:49 CDT)
  • AMBER: No bond and angle parameters for - -????? (Thu Sep 04 2008 - 05:15:37 CDT)
  • Re: AMBER: Need help... High energies for complex... (Wed Sep 03 2008 - 06:45:20 CDT)
  • AMBER: Need help... High energies for complex... (Wed Sep 03 2008 - 06:20:01 CDT)
  • Re: AMBER: Set 251 is corrupted, ptraj error... (Tue Aug 05 2008 - 06:23:47 CDT)
  • AMBER: Set 251 is corrupted, ptraj error... (Mon Aug 04 2008 - 09:54:09 CDT)
  • Re: AMBER: High force constant for MD ??? (Thu Jul 24 2008 - 05:42:13 CDT)
  • AMBER: High force constant for MD ??? (Wed Jul 23 2008 - 04:49:46 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Sat Jul 12 2008 - 14:44:13 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Fri Jul 11 2008 - 04:47:36 CDT)
  • Re: AMBER: [amber/glycam] dealing with fucose... (Thu Jul 10 2008 - 07:59:34 CDT)
  • AMBER: [amber/glycam] dealing with fucose... (Tue Jul 08 2008 - 09:56:31 CDT)
• waqasuddin.khan_at_iccs.edu
  • Re: AMBER: how to enlarge the TIP3PBOX size (Thu Sep 25 2008 - 01:01:57 CDT)
  • Re: AMBER: to prepare pdb file fro unusual amino acid. (Thu Sep 25 2008 - 00:55:51 CDT)
  • Re: AMBER: Dihedral: ptraj (Thu Sep 18 2008 - 04:14:50 CDT)
  • AMBER: Dihedral: ptraj (Thu Sep 18 2008 - 01:39:33 CDT)
• Wei Chen
  • Re: AMBER: amber :antechamber problem (Mon Jan 07 2008 - 10:14:53 CST)
• Wei Huang
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 10:41:12 CST)
  • Re: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 09:02:22 CDT)
  • Re: AMBER: about RMSD per residue (Wed Jul 16 2008 - 10:31:24 CDT)
  • RE: AMBER: about RMSD per residue (Wed Jul 16 2008 - 10:08:36 CDT)
  • Re: AMBER: about RMSD per residue (Wed Jul 16 2008 - 09:20:03 CDT)
  • AMBER: MM-PBSA calculation problem (Mon Jun 30 2008 - 11:41:16 CDT)
• Wei Zhang
  • Re: AMBER: Error in creating topology file (Mon Oct 20 2008 - 07:34:40 CDT)
  • Re: AMBER: saveamberparm error (Thu Oct 09 2008 - 05:22:45 CDT)
  • Re: AMBER: cannot read big .pdb files (Mon May 12 2008 - 09:34:40 CDT)
  • Re: AMBER: AmberTools on OS X fails tests (Thu May 08 2008 - 14:15:46 CDT)
  • Re: AMBER: How to change default radius assigned to an atom (Wed Apr 23 2008 - 10:29:03 CDT)
  • Re: AMBER: xleap segmentation fault on SaveAmberParm (Tue Apr 15 2008 - 14:32:32 CDT)
  • Re: AMBER: question on antechamber: jaguar ouput (Wed Mar 12 2008 - 13:14:55 CDT)
  • AMBER: question on antechamber: jaguar ouput (Tue Mar 11 2008 - 12:01:55 CDT)
• Wenyong Tong
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 11:13:34 CST)
  • Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 14:32:31 CDT)
  • Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 09:51:31 CDT)
  • Re: AMBER: mask for oligosaccharide (Wed Jul 30 2008 - 23:13:08 CDT)
  • AMBER: mask for oligosaccharide (Wed Jul 30 2008 - 13:23:58 CDT)
  • AMBER: for mask in rms (Tue Jul 29 2008 - 22:35:23 CDT)
  • AMBER: for NMR refinement (Thu Feb 28 2008 - 20:20:08 CST)
  • Re: AMBER: NMR refinement (Fri Jan 18 2008 - 22:18:18 CST)
  • AMBER: NMR refinement (Thu Jan 17 2008 - 20:54:04 CST)
• wfli_at_biophy.nju.edu.cn
  • AMBER: energy pairwise decomposition in GB/SA simulation (Wed May 28 2008 - 05:29:42 CDT)
• Willy Valdivia-Granda
  • AMBER: Position: Postdoctoral Fellow (Mon Sep 22 2008 - 10:50:48 CDT)
• WJ Ding
  • Re: AMBER: problem with zMatrix in tleap (Fri Oct 31 2008 - 10:48:27 CDT)
  • Re: AMBER: how to ger resp charge for a residue? (Fri Oct 31 2008 - 09:26:48 CDT)
  • Re: AMBER: problem with zMatrix in tleap (Fri Oct 31 2008 - 09:23:45 CDT)
  • AMBER: problem with zMatrix in tleap (Thu Oct 30 2008 - 23:40:59 CDT)
  • AMBER: how to ger resp charge for a residue? (Thu Oct 30 2008 - 23:20:05 CDT)
• wl2290_at_columbia.edu
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 16:15:59 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 11:54:58 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 23 2008 - 09:52:39 CST)
  • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Mon Dec 22 2008 - 17:26:10 CST)
  • AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Fri Dec 19 2008 - 12:16:39 CST)
• xiaonan zhang
  • AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange (Wed Aug 20 2008 - 02:25:43 CDT)
  • AMBER: mm_pbsa incorrect complex prmtop file (Thu Jul 10 2008 - 02:44:58 CDT)
  • AMBER: How to confirm atom types of small molecule perceived by antechamber (Mon Jun 23 2008 - 03:39:30 CDT)
  • Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating (Tue Jun 10 2008 - 09:23:15 CDT)
  • AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating (Tue Jun 10 2008 - 07:24:02 CDT)
• Xioling Chuang
  • AMBER: DNA-Gold parameters (Wed Dec 03 2008 - 05:37:55 CST)
  • RE: AMBER: problem of install amber9 (Thu Jun 05 2008 - 04:09:27 CDT)
  • AMBER: problem of install amber9 (Thu Jun 05 2008 - 03:37:27 CDT)
  • AMBER: bugfix (imin=5) in amber9 (Tue May 27 2008 - 23:23:09 CDT)
  • AMBER: sander & imin=5 (Thu Apr 24 2008 - 02:03:09 CDT)
  • AMBER: Topology file format for Amber9 (Wed Apr 23 2008 - 00:41:32 CDT)
• Xu, Huafeng
  • AMBER: saveAmberPrep in internal coordinates (Wed Feb 20 2008 - 11:02:00 CST)
• xwu_at_purdue.edu
  • Re: AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 16:29:19 CDT)
  • Re: AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 16:03:08 CDT)
  • AMBER: problem of use MPICHI2 to run RMED on amber10 (Tue Sep 30 2008 - 15:31:24 CDT)
• Yang, Lee-Wei
  • RE: AMBER: NMODE units and hrmax value for Langevine modes (Wed Jun 04 2008 - 22:55:45 CDT)
  • AMBER: NMODE units and hrmax value for Langevine modes (Wed Jun 04 2008 - 11:27:00 CDT)
  • AMBER: About reading in heme and CO molecule together with myoglobin (Mon May 05 2008 - 13:08:53 CDT)
• Yang, Ping
  • RE: AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 21:57:29 CST)
  • AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 17:44:27 CST)
• YangMingjun
  • Re: Re: AMBER: installing pmemd with fftw (Sun Apr 13 2008 - 20:08:16 CDT)
  • AMBER: installing pmemd with fftw (Sun Apr 13 2008 - 08:07:44 CDT)
• Yannick Monclin
  • AMBER: [success] problem compiling Amber9 on Bull Linux (Thu Mar 13 2008 - 06:56:48 CDT)
  • Re: AMBER: problem bull linux compiling (Mon Feb 25 2008 - 07:16:06 CST)
  • AMBER: problem bull linux compiling (Fri Feb 22 2008 - 05:22:49 CST)
• yavuzturkm_at_prc.boun.edu.tr
  • AMBER: corrupted restart file (Tue Jun 03 2008 - 04:18:25 CDT)
  • AMBER: Amber 8 on Redhat 4 X86_64 (Tue Apr 01 2008 - 00:30:32 CDT)
  • AMBER: memory limitation of Amber 9 (Mon Mar 31 2008 - 13:49:40 CDT)
• Ye Mei
  • AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms (Thu Nov 27 2008 - 09:12:51 CST)
  • AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure? (Sat Oct 25 2008 - 07:32:25 CDT)
  • Re: AMBER: pdb structure is only half the molecule. (Thu Oct 23 2008 - 22:21:59 CDT)
  • Re: Re: AMBER: Installation Error (Wed Oct 15 2008 - 03:54:57 CDT)
  • AMBER: energy terms in hybrid REMD calculation (Mon Sep 29 2008 - 04:28:13 CDT)
  • Re: AMBER: amber 9 install (Tue Sep 16 2008 - 22:26:07 CDT)
  • Re: Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:35:41 CDT)
  • Re: Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 07:11:28 CDT)
  • Re: Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 06:49:08 CDT)
  • Re: Re: AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 06:16:59 CDT)
  • AMBER: replicas trapped in a few low temperatures (Thu Jul 10 2008 - 04:13:25 CDT)
  • Re: AMBER: help to install AMBER9 (Fri May 09 2008 - 09:55:56 CDT)
  • Re: RE: RE: AMBER: memory usage (Mon Apr 28 2008 - 09:06:20 CDT)
  • Re: RE: AMBER: memory usage (Sun Apr 27 2008 - 09:52:42 CDT)
  • AMBER: memory usage (Sat Apr 26 2008 - 08:57:44 CDT)
  • AMBER: a minor bug in RESP (Tue Mar 18 2008 - 02:05:34 CDT)
  • AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit (Wed Mar 05 2008 - 03:30:50 CST)
• Yi-Ming Cheng
  • AMBER: Polarizable force field for divalent ions? (Wed Jul 23 2008 - 05:59:08 CDT)
  • AMBER: Free energy landscape? HOWTO? (Mon Mar 31 2008 - 03:12:05 CDT)
  • Fwd: Re: AMBER: Problem with "trajout pdb" (Sat Feb 23 2008 - 04:21:29 CST)
  • Re: AMBER: Problem with "trajout pdb" (Sat Feb 23 2008 - 04:15:29 CST)
  • Re: AMBER: Problem with "trajout pdb" (Sat Feb 23 2008 - 03:36:24 CST)
  • AMBER: Problem with "trajout pdb" (Wed Feb 20 2008 - 10:53:32 CST)
• Yicun Ni
  • AMBER: A problem of installing Amber10 (Thu Jun 05 2008 - 10:55:53 CDT)
• Yong Duan
  • RE: AMBER: all & united atoms force field (Fri Aug 22 2008 - 19:39:23 CDT)
  • RE: AMBER: Regarding ff03 forcefield (Fri Jul 25 2008 - 11:24:19 CDT)
  • RE: AMBER: change in secondary structure during MD (Wed Feb 27 2008 - 20:13:11 CST)
  • RE: AMBER: Has anyone seen a protein fall apart due to PBCs? (Tue Jan 22 2008 - 21:20:41 CST)
  • AMBER: RE: »Ø¸´£º RE: AMBER: A problem to loadup the molecular in the xleap (Sat Jan 19 2008 - 14:44:25 CST)
  • RE: AMBER: A problem to loadup the molecular in the xleap (Sat Jan 19 2008 - 00:17:35 CST)
  • AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Wed Jan 16 2008 - 10:13:15 CST)
  • AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Tue Jan 15 2008 - 22:16:10 CST)
  • AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Tue Jan 15 2008 - 01:40:39 CST)
  • AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Mon Jan 14 2008 - 22:14:26 CST)
  • RE: AMBER: Disturb you for help! (Mon Jan 14 2008 - 14:06:11 CST)
  • RE: AMBER: problems with restart of MD (Mon Jan 14 2008 - 12:16:24 CST)
  • RE: AMBER: problems with restart of MD (Sun Jan 13 2008 - 12:08:52 CST)
  • RE: AMBER: About RAMD (Sat Jan 05 2008 - 13:24:53 CST)
• yongleli
  • AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 (Mon Jul 07 2008 - 17:04:53 CDT)
  • AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential (Wed Jul 02 2008 - 13:19:03 CDT)
  • Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 (Thu May 15 2008 - 21:40:51 CDT)
  • Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 (Thu May 15 2008 - 23:03:41 CDT)
  • Re: AMBER: MKL libraries/Amber10 (Thu May 15 2008 - 21:03:57 CDT)
  • Re: Re: AMBER: Prepgen (Thu May 15 2008 - 11:18:31 CDT)
  • AMBER: Amber10:Compiling with gcc 2.4.1 (Thu May 15 2008 - 10:36:29 CDT)
• Yongmei Pan
  • Re: AMBER: problem when running energy minimization with polarizable potential (Tue Sep 09 2008 - 15:36:33 CDT)
  • AMBER: energy decomposition with sander? (Mon Sep 08 2008 - 16:32:32 CDT)
  • AMBER: who can give a sample input file regarding the energy decomposition with sander? (Mon Sep 08 2008 - 15:41:37 CDT)
  • AMBER: problem when running energy minimization with polarizable potential (Mon Sep 08 2008 - 10:32:30 CDT)
  • AMBER: error when using tleap with leaprc.ff02EP (Fri Sep 05 2008 - 10:49:38 CDT)
• Yu Chen
  • Re: AMBER: unable to compile AmberTools 1.0 (Mon May 05 2008 - 14:06:26 CDT)
  • Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error (Wed Apr 23 2008 - 13:50:54 CDT)
  • AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error (Wed Apr 23 2008 - 13:03:13 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 22:21:34 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 14:52:16 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 13:47:06 CDT)
  • Re: AMBER: AmberTools on OS X Leopard with Intel compilers (Mon Apr 21 2008 - 09:30:10 CDT)
  • AMBER: AmberTools on OS X Leopard with Intel compilers (Fri Apr 18 2008 - 14:17:37 CDT)
  • Re: AMBER: Amber 9 installation (Mon Feb 04 2008 - 16:10:37 CST)
• yuan li
  • AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER (Tue May 13 2008 - 21:53:10 CDT)
• Yunierkis Perez Castillo
  • AMBER: side chain expression (Thu Dec 04 2008 - 10:43:14 CST)
  • AMBER: about SASA and AMBER (Mon Oct 20 2008 - 10:58:06 CDT)
  • RE: AMBER: question about pression (Mon Oct 13 2008 - 10:33:45 CDT)
  • AMBER: question about pression (Mon Oct 13 2008 - 09:45:38 CDT)
  • AMBER: ptraj average structure (Sat Oct 04 2008 - 08:25:42 CDT)
• yuri pomè
  • AMBER: problem with nmod (Fri Mar 28 2008 - 11:42:54 CDT)
• yzhao
  • AMBER: questions about gaff (Wed Jun 18 2008 - 21:01:45 CDT)
• Z Insepov
  • Re: AMBER: diblock copolymer (Tue Jan 22 2008 - 23:23:39 CST)
  • AMBER: collision with surface (Tue Jan 22 2008 - 18:25:55 CST)
  • AMBER: PEO-PLA/PCE (Thu Jan 17 2008 - 14:19:47 CST)
  • AMBER: diblock copolymer (Thu Jan 17 2008 - 09:27:47 CST)
• Z. Nevin Gerek
  • Re: AMBER: NAB to calcuate entropy. . (Wed Feb 20 2008 - 15:34:33 CST)
  • Re: AMBER: NAB to calcuate entropy (Wed Feb 20 2008 - 14:38:28 CST)
  • AMBER: using NAB to calculate normal modes (Fri Feb 15 2008 - 14:24:50 CST)
• zachary hartman
  • RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Wed Apr 09 2008 - 09:00:45 CDT)
• Zhan Chen
  • Re: AMBER: Lennard-Jones parameters (Wed Feb 27 2008 - 20:59:26 CST)
  • AMBER: Lennard-Jones parameters (Thu Feb 28 2008 - 01:41:02 CST)
• Zhao, Zhen (zhaozh)
  • AMBER: Amber dipole printout. (Tue Oct 14 2008 - 12:25:40 CDT)
  • AMBER: How to set up a water slab in Amber? (Tue Sep 30 2008 - 16:23:06 CDT)
  • RE: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. (Tue Sep 23 2008 - 09:11:23 CDT)
  • AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. (Mon Sep 22 2008 - 14:02:27 CDT)
  • AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? (Sat Sep 20 2008 - 15:01:59 CDT)
  • AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10. (Mon Aug 25 2008 - 10:04:34 CDT)
  • AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. (Tue Aug 19 2008 - 15:20:00 CDT)
• Zhenwei Lu
  • AMBER: problem with Mg2+ during MD (Thu Apr 03 2008 - 11:48:13 CDT)
  • AMBER: flexible molecule parameterization (Fri Jan 25 2008 - 09:36:46 CST)
  • Re: AMBER: using hydrogen bond facility to monitor ion pair interaction (Thu Jan 10 2008 - 12:16:57 CST)
  • AMBER: using hydrogen bond facility to monitor ion pair interaction (Thu Jan 10 2008 - 11:09:09 CST)
• ³ÉÈ«
  • AMBER: RE: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by z (Fri May 16 2008 - 01:56:34 CDT)
  • AMBER: RE: AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. (Wed May 14 2008 - 19:18:05 CDT)
  • AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. (Wed May 14 2008 - 09:57:25 CDT)
• ÀÌë Óæ
  • »Ø¸´£º RE: AMBER: A problem to loadup the molecular in the xleap (Sat Jan 19 2008 - 10:31:05 CST)
  • AMBER: A problem to loadup the molecular in the xleap (Fri Jan 18 2008 - 23:28:02 CST)
  • »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Thu Jan 17 2008 - 09:33:28 CST)
  • »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Wed Jan 16 2008 - 08:55:37 CST)
  • »Ø¸´£º AMBER: RE: »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Tue Jan 15 2008 - 19:24:30 CST)
  • »Ø¸´£º AMBER: RE: »Ø¸´£º RE: AMBER: Disturb you for help !?= (Mon Jan 14 2008 - 23:33:49 CST)
  • »Ø¸´£º RE: AMBER: Disturb you for help !?= (Mon Jan 14 2008 - 18:12:27 CST)
  • AMBER: Disturb you for help! (Mon Jan 14 2008 - 10:16:37 CST)
  • AMBER: A problem about antechamber (Tue Jan 08 2008 - 10:03:49 CST)
  • AMBER: Problem about antechamber (Tue Jan 08 2008 - 10:09:03 CST)
• Å·ÑôµÂ·½
  • RE: AMBER: MM_PBSA problems in AMBER9 (Tue Oct 07 2008 - 00:19:54 CDT)
  • RE: AMBER: MM_PBSA problems in AMBER9 (Tue Oct 07 2008 - 00:19:54 CDT)
  • AMBER: MM_PBSA problems in AMBER9 (Sun Oct 05 2008 - 16:30:12 CDT)
  • AMBER: the plot of the groove width versus time for RNA (Thu Jul 17 2008 - 18:35:31 CDT)
  • AMBER: A-prime RNA input file (Tue Jun 24 2008 - 06:16:27 CDT)
  • AMBER: SIZE.h problems (Sat Jun 21 2008 - 07:33:49 CDT)
  • RE: AMBER: Ewald error estimate (Thu May 08 2008 - 00:04:05 CDT)
  • RE: AMBER: Ewald error estimate (Wed May 07 2008 - 22:38:18 CDT)
  • AMBER: build RNA by nucgen (Sat Jan 12 2008 - 20:26:44 CST)
• ÇØæ©æ©
  • Re: Re: AMBER: improper dihedral in ff03 united atom forcefield (Wed Jul 23 2008 - 00:14:11 CDT)
  • AMBER: improper dihedral in ff03 united atom forcefield (Tue Jul 22 2008 - 20:49:28 CDT)
• ÕÅÓÂ
  • Re:AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 08:32:30 CDT)
  • Re:AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 08:32:30 CDT)
• 欧阳德方
  • AMBER: Ewald error estimate (Wed May 07 2008 - 03:25:22 CDT)