AMBER Archive (2006) - By Author

Starting: Sun Jan 01 2006 - 17:31:12 CST
Ending: Sat Dec 30 2006 - 07:20:23 CST

• $B?y?9_at_5F;(B
  • Re: AMBER: post nmanal (Mon Sep 11 2006 - 01:09:28 CDT)
  • AMBER: post nmanal (Sat Sep 09 2006 - 01:03:47 CDT)
• 3Dsig06
  • AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil (Mon May 22 2006 - 17:03:45 CDT)
• a a
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 22:48:32 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 00:11:59 CST)
  • AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 02:11:38 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Fri Dec 01 2006 - 04:26:51 CST)
  • AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 04:35:31 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Thu Nov 30 2006 - 00:45:04 CST)
  • AMBER: DNA helix end stable? (Tue Nov 28 2006 - 21:35:11 CST)
  • AMBER: How to apply a force to some atom in a residues? (Tue Nov 28 2006 - 21:36:15 CST)
  • Re: AMBER: nmode output with ptraj (Tue Nov 28 2006 - 21:18:32 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Mon Nov 27 2006 - 04:29:42 CST)
  • AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it? (Mon Nov 27 2006 - 02:50:12 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Fri Nov 24 2006 - 20:27:26 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 03:29:26 CST)
  • AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 00:13:38 CST)
  • AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 11:51:36 CST)
  • AMBER: Parameters for Nickel (Wed Oct 11 2006 - 04:05:15 CDT)
  • AMBER: Steered molecular dynamics with Amber 8.0 (Tue Oct 10 2006 - 04:44:56 CDT)
  • AMBER: Potential of Mean Force calculation or Steered molecular dynamics (Mon Oct 09 2006 - 01:07:25 CDT)
  • Re: AMBER: RMSD: is it related to flexibility? (Thu Oct 05 2006 - 21:50:43 CDT)
  • Re: AMBER: RMSD: is it related to flexibility? (Wed Oct 04 2006 - 23:15:20 CDT)
  • AMBER: RMSD: is it related to flexibility? (Wed Oct 04 2006 - 04:42:12 CDT)
  • AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp (Tue Aug 29 2006 - 05:15:07 CDT)
  • AMBER: Can I run RED/RESP for Platinum Complexes? (Thu Aug 24 2006 - 04:50:42 CDT)
  • AMBER: (no subject) (Tue Aug 15 2006 - 05:13:49 CDT)
  • RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Tue Aug 15 2006 - 00:48:49 CDT)
  • AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Mon Aug 14 2006 - 06:25:31 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? (Sun Aug 13 2006 - 23:29:59 CDT)
  • Re: AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 21:38:47 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 21:39:54 CDT)
  • AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 04:26:01 CDT)
  • AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 04:22:27 CDT)
  • AMBER: FIX conformation of a ligand (Wed Jul 05 2006 - 21:17:23 CDT)
  • RE: AMBER: fixing residues (Mon Jul 03 2006 - 21:47:08 CDT)
  • AMBER: Tutorial 4-section 4 DIHE in frcmod file. (Mon Jul 03 2006 - 21:13:04 CDT)
  • AMBER: Tutorial 4-section 4 - VDW parameters (Mon Jul 03 2006 - 04:49:31 CDT)
  • AMBER: Tutorial 4-section 4 (plc.frcmod) (Mon Jul 03 2006 - 04:41:44 CDT)
  • Re: AMBER: R.E.D II (Mon Jul 03 2006 - 04:35:35 CDT)
  • AMBER: Minizsation strange error message! Please help. (Mon Jun 26 2006 - 05:38:35 CDT)
  • AMBER: Can we submit jobs in sequences to amber? (Mon Jun 26 2006 - 02:14:05 CDT)
  • AMBER: Tutorial 2: Minimise and equlibrium error NaN (Fri Jun 23 2006 - 05:05:05 CDT)
  • AMBER: kill job command? (Thu Jun 22 2006 - 02:47:51 CDT)
  • AMBER: Tutorial 2: Production MD. (Wed Jun 21 2006 - 05:19:05 CDT)
  • AMBER: Antechamber : +ve charge species (Tue May 30 2006 - 05:04:05 CDT)
  • AMBER: ESP calculations. (Tue May 30 2006 - 05:10:41 CDT)
  • AMBER: Pt containing complex: antechamber (Sun May 28 2006 - 22:42:31 CDT)
  • AMBER: Pt containing complex: xleap (Sun May 28 2006 - 22:30:48 CDT)
  • RE: AMBER: trajin and rms (Wed May 24 2006 - 05:49:05 CDT)
  • RE: AMBER: trajin and rms (Mon May 22 2006 - 03:55:03 CDT)
  • AMBER: trajin and rms (Sun May 21 2006 - 23:18:37 CDT)
  • AMBER: xmgr error (Fri May 19 2006 - 04:50:25 CDT)
  • AMBER: process_mdout.perl error (Fri May 19 2006 - 04:35:20 CDT)
  • AMBER: Tutorial one : xaLeap command not found. (Wed May 17 2006 - 05:12:53 CDT)
  • AMBER: Tutorial one : libsvml.so error (Wed May 17 2006 - 01:01:26 CDT)
  • RE: AMBER: Amber install on RedHat Linux (Thu May 04 2006 - 02:37:34 CDT)
  • AMBER: Amber install on RedHat Linux (Wed May 03 2006 - 21:17:14 CDT)
  • AMBER: Workshops (Wed Jan 11 2006 - 08:27:59 CST)
• A Box
  • AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 22:06:52 CST)
• A D
  • AMBER: rms processing (Mon Mar 06 2006 - 18:21:01 CST)
  • AMBER: script advice (Mon Feb 13 2006 - 20:35:35 CST)
  • Re: AMBER: basic minimize question (Wed Feb 01 2006 - 17:35:38 CST)
  • AMBER: basic minimize question (Wed Feb 01 2006 - 16:50:53 CST)
• Aaron J. Greenwood
  • Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster (Fri Feb 03 2006 - 09:57:30 CST)
  • AMBER: Amber8 parallel compilation problems on an OSCAR Cluster (Thu Feb 02 2006 - 16:18:59 CST)
• Abd Ghani Abd Aziz
  • Re: AMBER: installation problem (Tue Mar 28 2006 - 21:50:08 CST)
  • Re: AMBER: amber8 error installation (Tue Mar 28 2006 - 10:27:37 CST)
  • Re: AMBER: amber8 error installation (Tue Mar 28 2006 - 09:44:42 CST)
  • AMBER: amber8 error installation (Tue Mar 28 2006 - 09:14:59 CST)
  • Re: AMBER: failed to save prm and xyz using ff96 (Wed Mar 01 2006 - 01:49:57 CST)
  • AMBER: failed to save prm and xyz using ff96 (Tue Feb 28 2006 - 09:32:49 CST)
  • RE: AMBER: amber 8 problem (Mon Feb 20 2006 - 22:55:27 CST)
  • Re: AMBER: amber 8 problem (Mon Feb 20 2006 - 10:17:37 CST)
  • AMBER: amber 8 problem (Mon Feb 20 2006 - 09:08:12 CST)
• Abhilash
  • AMBER: have problems with restrained minimization (Fri Sep 15 2006 - 13:10:50 CDT)
  • AMBER: Problems with a restrained minimization approach (Fri Sep 15 2006 - 14:35:34 CDT)
  • AMBER: how to do a molecular dynamic study on a trimer (Fri Aug 11 2006 - 10:05:44 CDT)
  • AMBER: GB tutorials and disulphide bonds (Mon Jul 31 2006 - 15:41:30 CDT)
• Abhilash Mohan
  • AMBER: problems with cpinutil.pl (Fri Jun 23 2006 - 12:00:36 CDT)
  • AMBER: problems with cpinutil.pl (Wed Jun 21 2006 - 16:06:05 CDT)
  • AMBER: constant pH simulation (Thu Mar 16 2006 - 13:14:47 CST)
• Adam Pelzer
  • AMBER: Temperature not rising enough during simulated annealing (Thu Sep 14 2006 - 22:30:12 CDT)
  • AMBER: Calculating energy for specific part of system (Tue Jul 18 2006 - 17:32:34 CDT)
  • Re: AMBER: trouble adding mdcrd files together (Sat Jun 03 2006 - 19:40:28 CDT)
  • AMBER: trouble adding mdcrd files together (Fri Jun 02 2006 - 17:22:46 CDT)
  • AMBER: RE: trouble stripping waters with ptraj (Mon May 29 2006 - 17:20:23 CDT)
  • AMBER: RE: trouble stripping waters with ptraj (Thu May 25 2006 - 23:50:53 CDT)
  • AMBER: RE: trouble stripping waters with ptraj (Sat May 20 2006 - 11:00:12 CDT)
  • AMBER: trouble stripping waters with ptraj (Tue May 16 2006 - 15:09:30 CDT)
• Adrian Roitberg
  • Re: AMBER: Unit of force (Wed Nov 08 2006 - 06:57:00 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 07:00:40 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 13:01:38 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 11:22:14 CST)
  • Re: AMBER: Closest(closest water) (Mon Oct 30 2006 - 07:12:13 CST)
  • Re: AMBER: md and implicit solvation (Tue Oct 24 2006 - 19:19:34 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 23 2006 - 18:44:46 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 12:41:31 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:46:48 CDT)
  • Re: AMBER: generalized born model for organic solvent (Wed Oct 11 2006 - 19:11:33 CDT)
  • Re: AMBER: the RMSD of MD (Sun Sep 24 2006 - 12:49:52 CDT)
  • Re: AMBER: Temperature fluctuation with Langevin Temperature control (Sun Aug 27 2006 - 16:07:07 CDT)
  • Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 (Fri Aug 11 2006 - 15:23:10 CDT)
  • Re: AMBER: Re: Confusion re AMBER SMD output (Tue Aug 01 2006 - 06:07:03 CDT)
  • Re: AMBER: Replica Exchange (Fri Jul 21 2006 - 08:37:26 CDT)
  • Re: AMBER: Replica exchange with Amber9 (Fri Jul 14 2006 - 08:00:14 CDT)
  • Re: AMBER: question about QM/MM in amber9 (Thu May 25 2006 - 05:57:25 CDT)
  • Re: AMBER: increase in computational time with LES (Sun Apr 23 2006 - 17:26:20 CDT)
  • Re: AMBER: Charges on atoms in protein :AMBER (Thu Feb 02 2006 - 13:50:54 CST)
  • Re: AMBER: Values of Spring Constants (Wed Feb 01 2006 - 07:05:14 CST)
  • Re: AMBER: minimalization prior to nmode analysis, is it necessary? (Thu Jan 05 2006 - 20:38:51 CST)
• Ahammadunny Pathiaseril
  • AMBER: IGB=10 (Wed Jan 18 2006 - 09:53:25 CST)
• aini_at_umdnj.edu
  • AMBER: question about solvatecap commander (Tue Mar 07 2006 - 20:46:41 CST)
• aixiaoli
  • AMBER: question about QM/MM in amber9 (Thu May 25 2006 - 03:37:10 CDT)
  • AMBER: vlimit exceeded (Thu May 18 2006 - 03:14:29 CDT)
• Akshay Patny
  • RE: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:46:45 CST)
  • AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 10:04:00 CST)
  • AMBER: Renumber residues in LEAP (Tue Dec 19 2006 - 15:55:57 CST)
  • RE: AMBER: LEAP error (Test Case) (Mon Oct 09 2006 - 10:37:18 CDT)
  • Re: AMBER: LEAP error (Fri Oct 06 2006 - 18:17:05 CDT)
  • AMBER: LEAP error (Fri Oct 06 2006 - 11:49:42 CDT)
  • RE: AMBER: water prmtop/inpcrd problem (Fri Oct 06 2006 - 09:49:22 CDT)
  • AMBER: water prmtop/inpcrd problem (Thu Oct 05 2006 - 20:08:59 CDT)
  • AMBER: VMD PDB into LEAP Readable PDB (Wed Oct 04 2006 - 20:07:11 CDT)
  • AMBER: Which POPC Bilayer to start? (Wed Sep 20 2006 - 16:48:42 CDT)
  • AMBER: GPCR-membrane issue (Wed Sep 20 2006 - 12:30:24 CDT)
  • AMBER: DPPC Bilayer size (Thu Sep 14 2006 - 13:47:45 CDT)
  • RE: AMBER: GAFF parameters: DPPC Bilayer (Wed Aug 09 2006 - 16:08:00 CDT)
  • AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 14:53:49 CDT)
• Alex Tzanov
  • Re: AMBER: compiling errors (Mon Apr 24 2006 - 21:04:10 CDT)
  • AMBER: compiling errors (Mon Apr 24 2006 - 19:17:50 CDT)
• alexandra.marques_at_fc.up.pt
  • AMBER: MMPBSA (Tue Mar 21 2006 - 03:58:35 CST)
  • AMBER: MD and MMPBSA (Wed Mar 08 2006 - 22:29:23 CST)
  • AMBER: NAD parameters (Mon Jan 30 2006 - 10:04:43 CST)
  • AMBER: parameters for C=S (Mon Jan 09 2006 - 08:53:30 CST)
• alexandratm_at_sapo.pt
  • AMBER: amber (Mon Jan 09 2006 - 05:31:56 CST)
• Alfredo Quevedo
  • AMBER: Installing Delphi to perform mm_pbsa analysis? (Wed Apr 19 2006 - 12:39:13 CDT)
  • AMBER: How to evaluate the binding energy of a ligand? (Tue Apr 11 2006 - 12:53:50 CDT)
  • AMBER: Obtaining an average structure from a trajectory (Tue Apr 04 2006 - 18:11:02 CDT)
• alfredoq_at_fcq.unc.edu.ar
  • Re: AMBER: mm-pbsa output (Thu Sep 21 2006 - 06:29:51 CDT)
  • Re: AMBER: strange mm_pbsa output (Sun May 14 2006 - 09:22:14 CDT)
  • Re: AMBER: strange mm_pbsa output (Sat May 13 2006 - 15:43:53 CDT)
  • AMBER: strange mm_pbsa output (Sat May 13 2006 - 10:44:58 CDT)
  • AMBER: About mm_pbsa calculation setting up (Thu May 11 2006 - 21:19:03 CDT)
  • AMBER: Compiler with AMD 64 bit support (Tue May 09 2006 - 12:10:30 CDT)
  • AMBER: Performing Simulated Annealing? (Fri Apr 28 2006 - 11:58:31 CDT)
• Alik Widge
  • AMBER: Re: Confusion re AMBER SMD output (Mon Jul 31 2006 - 17:54:59 CDT)
  • Re: AMBER: process_mdout.perl's output is empty (Tue Jul 25 2006 - 10:19:44 CDT)
  • AMBER: Confusion re AMBER SMD output (Mon Jul 24 2006 - 15:31:34 CDT)
  • Re: AMBER: remlog option changed in amber9? (Wed Jun 28 2006 - 16:24:07 CDT)
  • AMBER: remlog option changed in amber9? (Wed Jun 28 2006 - 14:36:47 CDT)
• Amanda Jonsson
  • AMBER: DNA tutorial xleap help (Wed Feb 08 2006 - 12:56:32 CST)
• amanda.mccook_at_gatech.edu
  • AMBER: DNA tutorial, in vacuo minimization (Fri Apr 14 2006 - 14:15:31 CDT)
  • AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? (Thu Mar 23 2006 - 22:32:39 CST)
• Amarda Shehu
  • Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:56:31 CDT)
  • AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:27:24 CDT)
• Amber admin
  • Re: AMBER: problem with calcpka.pl (Tue Oct 31 2006 - 18:33:09 CST)
  • Re: AMBER: increase force constants (Thu Aug 24 2006 - 19:15:24 CDT)
  • RE: AMBER: compiling parallel amber 9 in linux (Thu Aug 24 2006 - 19:10:57 CDT)
  • AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 14:00:08 CDT)
  • Re: AMBER: pmemd_parallel_ins_prob (Thu Jun 15 2006 - 14:08:46 CDT)
  • AMBER: separating LES copies in moil view (Thu Apr 13 2006 - 12:28:02 CDT)
  • AMBER: m4 error with Amber8 on SUN (Wed Feb 15 2006 - 16:51:38 CST)
  • Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type (Fri Jan 06 2006 - 15:36:19 CST)
• amere swathi
  • AMBER: problem with saving the parameters file (Wed Jul 05 2006 - 03:50:40 CDT)
• amit_at_mbu.iisc.ernet.in
  • AMBER: Having trouble with Nucgen for generating pdb more than 16 bps (Sun Jul 30 2006 - 13:51:05 CDT)
  • AMBER: QMMM simulation (Thu Jul 13 2006 - 13:38:48 CDT)
  • Re: AMBER: Problem with bcc flag of antechamber..continued (Fri Jul 07 2006 - 05:09:32 CDT)
  • AMBER: AMBER9 compilation error on IBM Cluster (Mon May 15 2006 - 06:11:50 CDT)
  • RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 (Wed May 10 2006 - 02:06:46 CDT)
  • AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 (Tue May 09 2006 - 13:32:52 CDT)
  • AMBER: Amber9 test error on SGI Altix (Mon May 08 2006 - 12:14:19 CDT)
• Ananda Rama Krishnan Selvaraj
  • Re: AMBER: calculating box dimensions during MD (Tue Jun 06 2006 - 09:31:32 CDT)
  • Re: AMBER: Please reply (Fri May 26 2006 - 14:36:26 CDT)
  • AMBER: Error in the MD run (Tue Apr 18 2006 - 01:13:04 CDT)
  • Re: AMBER: Calculation of g(r) from PTRAJ (Mon Apr 17 2006 - 12:45:39 CDT)
  • AMBER: Calculation of g(r) from PTRAJ (Sun Apr 16 2006 - 05:33:25 CDT)
  • Re: AMBER: Strange minimization output problem (Sat Feb 04 2006 - 10:12:19 CST)
• Andrea Bortolato
  • AMBER: TI vlimit exceeded (Thu Aug 24 2006 - 08:42:21 CDT)
  • AMBER: dummy atoms in MMPBSA (Thu Jul 27 2006 - 03:10:50 CDT)
  • AMBER: residue and atom number (Mon Jul 10 2006 - 07:57:05 CDT)
  • AMBER: MM-PBSA and first solvation shell (Mon Jun 05 2006 - 04:42:39 CDT)
  • AMBER: different TI calculations starting from the same state (Fri May 26 2006 - 05:12:12 CDT)
  • AMBER: different TI calculations starting from the same state (Fri May 26 2006 - 08:56:47 CDT)
• andrea carotti
  • AMBER: Re: Problems installing antechamber 1.27 (Tue Oct 31 2006 - 02:17:49 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 06:06:22 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:13:37 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 03:17:11 CST)
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 05:39:08 CDT)
  • Re: AMBER: Maximum system size in simulated annealing (Thu Aug 03 2006 - 04:23:13 CDT)
  • Re: AMBER: Gb Na+ ions DNA (Fri Jul 21 2006 - 04:22:21 CDT)
  • Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 (Fri Jul 14 2006 - 05:38:10 CDT)
  • Re: AMBER: Namot on AMD 64 possible (Wed Jul 05 2006 - 13:08:44 CDT)
  • Re: AMBER: Can you use VMD to measure bond angles/lengths (Tue Jul 04 2006 - 11:09:21 CDT)
  • Re: AMBER: NAMOT (Mon Jul 03 2006 - 06:02:57 CDT)
  • RE: AMBER: SHAKE, TIP3P and 2fs Timesteps (Wed May 31 2006 - 13:38:29 CDT)
  • Re: AMBER: Problems compiling amber9 (Mon May 22 2006 - 14:01:09 CDT)
  • Re: AMBER: amber8 compiled erro on opteron with 64 bit (Tue May 16 2006 - 05:53:14 CDT)
  • Re: AMBER: Xleap 64 bit installation problem (Tue Mar 14 2006 - 06:16:47 CST)
  • Re: AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 10:35:16 CST)
  • Re: AMBER: amber 8 problem (Mon Feb 20 2006 - 10:20:28 CST)
  • Re: AMBER: Strange minimization output problem (Sun Feb 05 2006 - 09:23:03 CST)
  • Re: AMBER: Amber 8 install problem (Wed Jan 18 2006 - 05:10:38 CST)
• Andres Palencia
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 14:13:39 CST)
  • AMBER: Amber H-bond print? (Thu Nov 09 2006 - 03:07:46 CST)
  • AMBER: error GRID command in ptraj (Thu Oct 26 2006 - 12:39:19 CDT)
  • Re: AMBER: how to select the problematic residues(atoms) in VMD (Thu Oct 26 2006 - 06:56:31 CDT)
  • AMBER: residence time& hydration density (Wed Oct 25 2006 - 09:16:53 CDT)
• Andrew Box
  • AMBER: Dynamics and Restraint problem (Mon Jul 17 2006 - 18:49:51 CDT)
  • AMBER: (no subject) (Sun Jul 09 2006 - 17:49:02 CDT)
  • Re: AMBER: Sander NOE violations (Thu Jul 06 2006 - 20:32:21 CDT)
  • AMBER: Sander NOE violations (Thu Jul 06 2006 - 18:55:59 CDT)
  • AMBER: MPICH and Sander (Thu Jun 15 2006 - 21:07:11 CDT)
  • AMBER: Shared libraries error (Tue May 02 2006 - 22:14:38 CDT)
  • AMBER: Amber 8 install problem (Tue Jan 17 2006 - 22:50:21 CST)
• andy ng
  • Re: AMBER: NGL error when creating snapshots for MM/PB(GB)SA (Fri Apr 07 2006 - 01:20:16 CDT)
  • AMBER: NGL error when creating snapshots for MM/PB(GB)SA (Fri Apr 07 2006 - 01:05:50 CDT)
  • Re: AMBER: Phosphorylated amino acid (Mon Feb 20 2006 - 23:55:55 CST)
  • AMBER: Phosphorylated amino acid (Sun Feb 19 2006 - 17:51:41 CST)
  • AMBER: Strange minimization output problem (Sat Feb 04 2006 - 06:39:31 CST)
• Andy Purkiss
  • Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names (Tue May 30 2006 - 13:18:58 CDT)
  • Re: AMBER: is there any relationship between RMSD and B-factor? (Thu Jan 19 2006 - 07:19:06 CST)
  • Re: AMBER: Trimming ptraj output (Fri Jan 13 2006 - 12:03:54 CST)
  • AMBER: Trimming ptraj output (Fri Jan 13 2006 - 11:29:00 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:01:09 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 08:52:14 CST)
• Andy Purkiss-Trew
  • RE: AMBER: ibelly not work (Thu Dec 07 2006 - 06:33:24 CST)
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 13:38:28 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 13:34:52 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 06:58:53 CST)
  • Re: AMBER: resolving a bad initial model (Tue Sep 19 2006 - 09:51:01 CDT)
• Angelo
  • Re: AMBER: MM-PBSA (Mon Dec 18 2006 - 10:30:00 CST)
  • AMBER: Biomolecular Simulation 2007 (Thu Nov 09 2006 - 10:03:43 CST)
  • Re: AMBER: PCA results with explicit Vs Implicit solvation (Mon Nov 06 2006 - 11:14:47 CST)
  • Re: AMBER: leap usage (Thu Nov 02 2006 - 10:39:57 CST)
  • Re: AMBER: mm_pbsa: binding energy calculation (Mon Oct 30 2006 - 03:36:25 CST)
  • AMBER: mm_pbsa reference (Fri Oct 27 2006 - 07:47:07 CDT)
  • Re: AMBER: mm_pbsa: binding energy calculation (Thu Oct 26 2006 - 08:04:18 CDT)
  • Re: AMBER: residence time of water molecules (Thu Sep 14 2006 - 03:57:38 CDT)
  • Re: AMBER: Curves and Average Structures (Tue Jun 27 2006 - 03:57:47 CDT)
  • Re: AMBER: offset? (Thu Jun 01 2006 - 04:39:20 CDT)
  • Re: AMBER: Zoom (Thu Mar 16 2006 - 11:04:05 CST)
  • Re: AMBER: Zoom (Thu Mar 16 2006 - 09:57:32 CST)
  • AMBER: Zoom (Thu Mar 16 2006 - 04:24:39 CST)
• Angelo Pugliese
  • AMBER: Free energy perturbation (Wed Feb 22 2006 - 10:42:06 CST)
  • Re: AMBER: Distortion in parallelploied (Mon Feb 13 2006 - 09:40:40 CST)
• Ann Vilan Tran
  • AMBER: Gromos to Amber (Thu Mar 30 2006 - 13:29:07 CST)
• Anna Bowman
  • AMBER: Calculating native contacts for mdcrd files (Thu Oct 26 2006 - 10:20:50 CDT)
• anna ferrari
  • Re: AMBER: MM-PBSA and gaff atom types (Wed Jun 28 2006 - 11:43:41 CDT)
  • AMBER: MM-PBSA and gaff atom types (Tue Jun 27 2006 - 04:28:03 CDT)
• anna.schrey_at_gmx.de
  • AMBER: xleap problems (Mon Dec 04 2006 - 05:45:07 CST)
  • AMBER: Confusion about PBC (Wed Nov 29 2006 - 10:26:04 CST)
  • AMBER: Problems with carnal (Amber7) (Tue Oct 31 2006 - 09:24:29 CST)
  • AMBER: problems with ptraj (Thu Aug 03 2006 - 09:49:39 CDT)
  • AMBER: Problems with restart file from pmemd sim. (Sat Jun 17 2006 - 07:30:56 CDT)
• Anthony Cruz
  • AMBER: GB simulation problem (Fri Jun 30 2006 - 11:49:53 CDT)
  • Re: AMBER: Implicit solvent question (Thu Jun 29 2006 - 11:44:54 CDT)
  • AMBER: Implicit solvent question (Fri Jun 23 2006 - 08:49:22 CDT)
• Arjen-Joachim Jakobi
  • Re: AMBER: "average" command in ptraj (Mon Apr 10 2006 - 13:50:34 CDT)
  • AMBER: "average" command in ptraj (Mon Apr 10 2006 - 07:15:16 CDT)
• Arvind Marathe
  • Re: AMBER: 'lastrst' error for amber8 (Mon Sep 18 2006 - 12:44:11 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Mon Sep 18 2006 - 11:25:33 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Mon Sep 18 2006 - 01:50:41 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Sun Sep 17 2006 - 07:02:09 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Fri Sep 15 2006 - 15:01:43 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Thu Sep 14 2006 - 08:08:08 CDT)
  • AMBER: 'lastrst' error for amber8 (Wed Sep 13 2006 - 07:52:07 CDT)
  • AMBER: regarding diffusion command output (Tue Aug 01 2006 - 05:45:21 CDT)
  • AMBER: amber9 serial compilation error (Thu May 04 2006 - 11:55:39 CDT)
• Asim Okur
  • Re: AMBER: REM test failures on IA-64 architecture (Wed Jun 28 2006 - 15:09:08 CDT)
  • Re: AMBER: RE: trouble stripping waters with ptraj (Mon May 22 2006 - 11:49:46 CDT)
  • Re: AMBER: trouble stripping waters with ptraj (Tue May 16 2006 - 15:17:32 CDT)
• asli ertekin
  • Re: AMBER: force fiels for a-rna (Fri Oct 13 2006 - 18:20:32 CDT)
  • AMBER: force fiels for a-rna (Fri Oct 13 2006 - 17:28:58 CDT)
  • AMBER: addions default settings. (Thu Sep 14 2006 - 10:37:47 CDT)
• Atilio I Anzellotti/O/VCU
  • AMBER: MD of oligomer sequences (Thu Feb 02 2006 - 16:53:28 CST)
• Atro Tossavainen
  • Re: AMBER: nmode memory problem (Fri Aug 25 2006 - 05:10:50 CDT)
  • Re: AMBER: combining different versions of AMBER (Mon Jul 24 2006 - 00:44:10 CDT)
  • Re: AMBER: SGI compiler problems (Wed Jun 21 2006 - 06:30:00 CDT)
  • Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system (Mon May 08 2006 - 06:48:29 CDT)
  • Re: AMBER: compiling errors (Wed Apr 26 2006 - 02:49:23 CDT)
• Atsutoshi Okabe
  • AMBER: Volume of ucell too big (Sat Dec 16 2006 - 02:41:43 CST)
  • AMBER: Error message in methane solvent system (Thu Dec 07 2006 - 21:19:04 CST)
  • AMBER: To create methanol solvent box (Wed Oct 18 2006 - 01:31:02 CDT)
  • RE: AMBER: Grid command of ptraj (Tue Oct 17 2006 - 23:19:13 CDT)
  • RE: AMBER: Grid command of ptraj (Mon Oct 16 2006 - 04:26:55 CDT)
  • AMBER: Grid command of ptraj (Sat Oct 14 2006 - 02:31:01 CDT)
  • AMBER: Picking up water molecules around one molecule (Sat Sep 23 2006 - 03:26:12 CDT)
  • RE: AMBER: Replica exchange with Amber9 (Wed Jul 19 2006 - 11:22:49 CDT)
  • RE: AMBER: Replica exchange with Amber9 (Mon Jul 17 2006 - 03:20:25 CDT)
  • AMBER: Replica exchange with Amber9 (Fri Jul 14 2006 - 01:20:21 CDT)
  • RE: AMBER: Replica exchange (Tue Jul 11 2006 - 23:13:38 CDT)
  • RE: AMBER: Replica exchange (Mon Jul 10 2006 - 21:43:17 CDT)
  • AMBER: Replica exchange (Mon Jul 10 2006 - 06:38:17 CDT)
  • AMBER: 2-D free energy surface using WHAM (Mon Jul 03 2006 - 07:08:01 CDT)
  • RE: AMBER: Umbrella sampling (Sun Jun 18 2006 - 05:14:10 CDT)
  • AMBER: Umbrella sampling (Sat Jun 10 2006 - 05:42:34 CDT)
  • AMBER: Replica exchage: about exchange interval (Wed May 31 2006 - 07:36:27 CDT)
  • RE: AMBER: A dummy atom on the center of solute molecule (Mon May 29 2006 - 00:51:49 CDT)
  • RE: AMBER: A dummy atom on the center of solute molecule (Tue May 23 2006 - 20:46:35 CDT)
  • AMBER: A dummy atom on the center of solute molecule (Mon May 22 2006 - 06:49:23 CDT)
  • AMBER: "The system has extended beyond" error message (Thu May 18 2006 - 00:04:31 CDT)
  • AMBER: About WHAM (Tue Feb 21 2006 - 00:22:01 CST)
  • AMBER: Gibbs PMF Calculation (Fri Feb 03 2006 - 02:38:55 CST)
  • AMBER: Gibbs PMF Calculation (Wed Feb 01 2006 - 06:31:12 CST)
  • AMBER: Gibbs pmf calculation (Wed Jan 11 2006 - 04:14:30 CST)
• Austin B. Yongye
  • AMBER: Ptraj: diffusion rate (Tue Nov 21 2006 - 15:03:52 CST)
  • AMBER: Ptraj: correlation time (Tue Nov 21 2006 - 15:05:52 CST)
  • Re: AMBER: GLYCAM and ff98 atom-types] (Thu Nov 16 2006 - 13:53:03 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 13:02:27 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:50:01 CST)
  • AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:10:39 CST)
  • Re: AMBER: Interbox interactions (Tue Oct 17 2006 - 11:03:18 CDT)
  • AMBER: Interbox interactions (Mon Oct 16 2006 - 12:15:04 CDT)
  • AMBER: REMD: Hybrid topology file (Wed Aug 30 2006 - 09:30:34 CDT)
  • Re: AMBER: Replica Exchange (Fri Jul 21 2006 - 08:29:08 CDT)
  • AMBER: Replica Exchange (Thu Jul 20 2006 - 21:07:46 CDT)
  • Re: AMBER: Replica exchange (Wed Jul 19 2006 - 12:23:47 CDT)
  • AMBER: Replica exchange (Wed Jul 19 2006 - 10:04:44 CDT)
  • Re: AMBER: Replica exchange (Mon Jul 17 2006 - 17:22:51 CDT)
  • AMBER: Replica exchange (Mon Jul 17 2006 - 07:31:09 CDT)
  • AMBER: Ewald and ibelly (Sun Mar 19 2006 - 10:36:53 CST)
• AYTUG TUNCEL
  • AMBER: error about the number of snapshots (Tue Nov 07 2006 - 15:11:24 CST)
  • AMBER: nmode memory allocation error (Fri Sep 08 2006 - 03:41:35 CDT)
  • AMBER: nmode: number of atoms limitation (Mon Aug 28 2006 - 18:15:04 CDT)
  • AMBER: mm_pbsa calculation allocation error (Mon Aug 21 2006 - 08:15:31 CDT)
  • AMBER: input conversion error mm_pbsa (Tue Aug 15 2006 - 17:23:28 CDT)
  • AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 04:08:50 CDT)
  • AMBER: pdb error (Tue Aug 01 2006 - 14:36:39 CDT)
  • AMBER: leap error (Wed Jul 26 2006 - 18:29:35 CDT)
• backy
  • AMBER: EGB term decomposition (Sat Sep 09 2006 - 03:57:43 CDT)
  • AMBER: EGB term decomposition (Sat Sep 09 2006 - 04:01:34 CDT)
  • AMBER: EGB term decomposition (Sat Sep 09 2006 - 04:00:08 CDT)
  • Re: AMBER: DIELC? (Sat Aug 19 2006 - 03:04:14 CDT)
  • AMBER: DIELC? (Sat Aug 12 2006 - 07:16:47 CDT)
  • AMBER: Could mm_pbsa decompose energy only for the receptor ? (Fri Aug 11 2006 - 09:10:52 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Thu Aug 10 2006 - 01:47:37 CDT)
  • AMBER: Energy differecnes as using igb=1 and igb=0 (Wed Aug 09 2006 - 09:46:56 CDT)
• Baird, Jamie \(bairdje\)
  • AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 11:33:00 CST)
• Baker, Bo-Yang
  • AMBER: Distance between two regions (Mon Jul 31 2006 - 19:16:02 CDT)
  • AMBER: convert chemical structure to pdb file (Fri Jul 07 2006 - 13:44:25 CDT)
  • RE: AMBER: antechamber problem (Mon Jan 02 2006 - 18:23:40 CST)
• bala
  • AMBER: splitting LES with ptraj in amber9 (Tue Oct 24 2006 - 00:18:16 CDT)
  • AMBER: Missing values for MM VDW (Thu Oct 05 2006 - 06:33:14 CDT)
  • AMBER: polarizable ff for ligand (Mon Sep 25 2006 - 08:53:02 CDT)
  • AMBER: pmemd error (Thu Sep 14 2006 - 10:34:12 CDT)
  • AMBER: output file not generated (Fri Sep 01 2006 - 10:35:40 CDT)
  • AMBER: parallel pmemd with intel 9 fc (Sat Aug 12 2006 - 10:56:15 CDT)
  • AMBER: average struct.problem (Thu Jun 22 2006 - 04:11:15 CDT)
  • AMBER: question on distance calculation (Mon May 08 2006 - 05:09:23 CDT)
  • AMBER: carnal prob (Thu May 04 2006 - 02:44:53 CDT)
  • AMBER: nucgen error (Tue Mar 14 2006 - 09:35:11 CST)
  • AMBER: sander problem (Thu Feb 16 2006 - 09:57:43 CST)
• Baldoni Hector Armando
  • AMBER: 2D-topology (Mon Feb 13 2006 - 15:50:11 CST)
• Barbault Florent
  • AMBER: MMPBSA entropy question (Tue Oct 31 2006 - 03:08:55 CST)
  • Re: AMBER: ff for drug-dna complex and drug atom types assignment (Mon Oct 23 2006 - 13:37:53 CDT)
• BAUVAIS_at_itodys.jussieu.fr
  • AMBER: "atom number exceeds the MAXATOM" (Wed May 17 2006 - 00:54:24 CDT)
• Benjamin Juhl
  • Re: AMBER: problem with calcpka.pl (Mon Oct 30 2006 - 07:57:42 CST)
  • AMBER: problem with calcpka.pl (Tue Oct 24 2006 - 06:58:27 CDT)
  • Re: AMBER: faulty ambpdb compilation? (Thu Mar 16 2006 - 12:51:47 CST)
  • AMBER: faulty ambpdb compilation? (Thu Mar 16 2006 - 12:16:12 CST)
• bertrand russell
  • AMBER: .crd file (Tue Dec 26 2006 - 03:16:53 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 02:25:10 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Thu Dec 21 2006 - 23:51:48 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 23:09:48 CST)
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 22:16:22 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 22:13:03 CST)
  • AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 05:22:37 CST)
  • AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 04:47:03 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 11:35:16 CST)
  • AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 04:03:53 CST)
  • AMBER: LEaP problem (Mon Dec 11 2006 - 23:10:48 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 04:39:46 CST)
  • AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 10:41:23 CST)
• Bill Ross
  • Re: AMBER: tree name generated by tleap is different from the input PREP parameter file (Fri Dec 29 2006 - 21:00:26 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 15:12:50 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 13:51:07 CST)
  • Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 12:51:25 CST)
  • Re: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 13:06:49 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 13:47:48 CST)
  • Re: AMBER: LEaP problem (Tue Dec 12 2006 - 00:24:33 CST)
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 12:58:11 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:55:00 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 13:06:25 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 12:54:50 CST)
  • Re: AMBER: Restraints of the strand-endings? (Tue Nov 14 2006 - 16:19:06 CST)
  • Re: AMBER: PTRAJ: radius of gyration (Fri Nov 10 2006 - 13:04:06 CST)
  • Re: AMBER: Problems with carnal (Amber7) (Tue Oct 31 2006 - 11:09:57 CST)
  • Re: AMBER: HBON in frcmod file (Sat Oct 21 2006 - 14:57:48 CDT)
  • Re: AMBER: HBON in frcmod file (Sat Oct 21 2006 - 02:41:55 CDT)
  • Re: AMBER: problem of installing carnal on macosx (Fri Oct 20 2006 - 13:50:19 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:26:18 CDT)
  • Re: AMBER: puzzles about solvatoct or solvatebox (Tue Oct 17 2006 - 11:13:58 CDT)
  • Re: AMBER: General Coding Problem (Mon Oct 16 2006 - 19:56:37 CDT)
  • Re: AMBER: puzzles about solvatoct or solvatebox (Thu Oct 12 2006 - 12:43:38 CDT)
  • RE: AMBER: some puzzles in equilibration MD (Mon Oct 09 2006 - 22:14:39 CDT)
  • Re: AMBER: on rst file (Wed Oct 04 2006 - 12:17:10 CDT)
  • Re: AMBER: mdcrd file (Mon Oct 02 2006 - 21:46:15 CDT)
  • Re: AMBER: mdcrd file (Mon Oct 02 2006 - 19:23:18 CDT)
  • Re: AMBER: addions default settings. (Thu Sep 14 2006 - 12:14:18 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:17:10 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:05:27 CDT)
  • Re: AMBER: how to limit the simulation space (Mon Aug 28 2006 - 20:04:39 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 18:21:57 CDT)
  • Re: AMBER: How to create a modified NA in leap (Sat Aug 26 2006 - 19:21:41 CDT)
  • Re: AMBER: How to create a modified NA in leap (Fri Aug 25 2006 - 16:52:40 CDT)
  • Re: AMBER: Carnal: Internal error: stream file name 2 out of range (Wed Aug 23 2006 - 16:16:16 CDT)
  • Re: AMBER: holding a pair of residues fixed during minimization (Wed Aug 23 2006 - 15:45:13 CDT)
  • Re: AMBER: amber naming conventions for structure files (Tue Aug 22 2006 - 17:00:10 CDT)
  • Re: AMBER: Execution time discrepancies (Thu Aug 17 2006 - 20:24:13 CDT)
  • Re: AMBER: help with leap (Wed Aug 16 2006 - 19:51:56 CDT)
  • Re: AMBER: loading torsion parameters (Mon Jul 31 2006 - 15:49:38 CDT)
  • Re: AMBER: Having trouble with Nucgen for generating pdb more than 16 bps (Mon Jul 31 2006 - 13:53:11 CDT)
  • Re: AMBER: Can't open xleap (Thu Jul 27 2006 - 12:21:39 CDT)
  • Re: AMBER: Creating an Intercalation site (Mon Jul 17 2006 - 14:49:20 CDT)
  • Re: AMBER: Ring of dna (Mon Jul 17 2006 - 14:19:49 CDT)
  • Re: AMBER: Ring of dna (Mon Jul 17 2006 - 14:15:10 CDT)
  • Re: AMBER: Ring of dna (Sat Jul 15 2006 - 12:55:07 CDT)
  • Re: AMBER: Ring of dna (Fri Jul 14 2006 - 12:23:07 CDT)
  • Re: AMBER: working with large strained system (Thu Jul 06 2006 - 12:06:57 CDT)
  • Re: AMBER: PTRAJ OUTPUT (Wed Jul 05 2006 - 18:43:57 CDT)
  • Re: AMBER: problem with saving the parameters file (Wed Jul 05 2006 - 13:23:05 CDT)
  • Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! (Fri Jun 30 2006 - 13:42:53 CDT)
  • Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! (Thu Jun 29 2006 - 18:46:17 CDT)
  • Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names (Mon May 29 2006 - 15:26:56 CDT)
  • Re: AMBER: use_pme=0 problem (Fri May 26 2006 - 15:32:35 CDT)
  • Re: AMBER: amber .off file format question (Mon May 22 2006 - 13:17:26 CDT)
  • Re: AMBER: carnal prob (Thu May 04 2006 - 12:31:22 CDT)
  • Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] (Wed May 03 2006 - 17:00:58 CDT)
  • Re: AMBER: Question bonds and angles in frcmod and lib files (Wed May 03 2006 - 11:28:08 CDT)
  • Re: AMBER: a question about "solvateoct" in AMBER 8 (Fri Apr 21 2006 - 13:48:01 CDT)
  • Re: AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 13:38:17 CDT)
  • Re: AMBER: saltcon with explicit water? (Wed Apr 12 2006 - 18:26:05 CDT)
  • Re: AMBER: united atoms (Tue Mar 28 2006 - 11:02:01 CST)
  • Re: AMBER: nucgen error (Tue Mar 14 2006 - 11:06:16 CST)
  • Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group (Sat Mar 11 2006 - 12:37:16 CST)
  • Re: Re: Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 13:24:57 CST)
  • Re: AMBER: modeling a non-standard molecule. (Wed Mar 08 2006 - 15:47:50 CST)
  • Re: AMBER: modeling a non-standard molecule. (Wed Mar 08 2006 - 15:19:21 CST)
  • Re: AMBER: converting .lib files (Wed Mar 08 2006 - 10:30:17 CST)
  • Re: AMBER: CARNAL: H-BOND Specifying side chains only (Tue Feb 21 2006 - 15:41:25 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Thu Feb 16 2006 - 12:53:10 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Thu Feb 16 2006 - 12:49:20 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Wed Feb 15 2006 - 11:25:21 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Tue Feb 14 2006 - 14:35:19 CST)
  • Re: AMBER: DNA tutorial xleap help (Wed Feb 08 2006 - 13:56:25 CST)
  • RE: AMBER: Charges on atoms in protein :AMBER (Thu Feb 02 2006 - 13:31:28 CST)
  • RE: AMBER: Charges on atoms in protein :AMBER (Thu Feb 02 2006 - 12:43:23 CST)
  • Re: AMBER: problem in center command (Fri Jan 20 2006 - 19:40:51 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 18:39:12 CST)
  • Re: AMBER: Ligand charge (Thu Jan 05 2006 - 12:24:18 CST)
  • Re: AMBER: Leap (Wed Jan 04 2006 - 16:02:20 CST)
• Bing Liu
  • AMBER: MM_PBSA problem (No values for MM_GAS ) (Mon Feb 13 2006 - 08:40:47 CST)
• biolabadmin_at_ibt.lt
  • Re: AMBER: install error (Fri Mar 03 2006 - 03:47:11 CST)
  • Re: AMBER: install error (Thu Mar 02 2006 - 06:48:17 CST)
  • AMBER: install error (Wed Mar 01 2006 - 05:13:12 CST)
• Biswa Ranjan Meher
  • AMBER: klambda for TI method. (Tue Nov 07 2006 - 06:59:15 CST)
  • Re: AMBER: Trouble with Leap (Thu Oct 19 2006 - 00:28:46 CDT)
  • Re: AMBER: Trouble with Leap (Wed Oct 18 2006 - 00:35:48 CDT)
  • AMBER: Trouble with Leap (Mon Oct 09 2006 - 09:28:28 CDT)
  • AMBER: TI-FEP : strange result for different clambda values (Fri Sep 22 2006 - 10:26:30 CDT)
  • AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 00:26:22 CDT)
  • AMBER: Different results for TI calculation (Wed May 31 2006 - 02:25:13 CDT)
• Björn C-G. Karlsson
  • AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 01:17:56 CDT)
  • AMBER: Calculate interaction energy between small organic molecules (Mon Aug 21 2006 - 01:37:24 CDT)
• Bob Johnson
  • RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag (Fri Jul 07 2006 - 12:35:59 CDT)
  • AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag (Fri Jul 07 2006 - 09:55:32 CDT)
• Bonnet, Pascal [PRDBE]
  • RE: AMBER: problem to center solvateshell (Tue Oct 03 2006 - 01:30:53 CDT)
  • AMBER: problem to center solvateshell (Fri Sep 29 2006 - 04:30:49 CDT)
• Brent Krueger
  • Re: AMBER: mdcrd file (Thu Sep 07 2006 - 21:55:27 CDT)
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 15:08:57 CDT)
  • AMBER: pmemd9 issue (Sat Jul 01 2006 - 22:45:11 CDT)
• Brian Stupi
  • Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations (Tue Mar 07 2006 - 13:55:13 CST)
  • Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations (Tue Mar 07 2006 - 13:30:59 CST)
  • AMBER: Problem taking the PDB to the Amber coordinates for calculations (Mon Mar 06 2006 - 17:17:22 CST)
  • AMBER: process_mdout.perl (Thu Feb 16 2006 - 16:02:06 CST)
  • RE: AMBER: sander problem (Thu Feb 16 2006 - 14:44:11 CST)
  • Re: AMBER: Error when installing (Mon Feb 13 2006 - 14:40:46 CST)
  • AMBER: Error when installing (Mon Feb 13 2006 - 14:19:19 CST)
  • AMBER: What Viewer is best (Sat Feb 04 2006 - 23:59:29 CST)
• brmeher_at_iitg.ernet.in
  • AMBER: Difference in results for TI calculation (Mon May 29 2006 - 09:23:45 CDT)
  • AMBER: Difference in results for TI calculation (Mon May 29 2006 - 08:53:41 CDT)
  • AMBER: problem with the output file for free energy perturbation calculation (Mon Jan 09 2006 - 23:15:30 CST)
• Burkhard Heil
  • AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 04:54:00 CST)
• bybaker_at_itsa.ucsf.edu
  • AMBER: Ligand charge (Wed Jan 04 2006 - 12:51:57 CST)
• Cameron Abrams
  • AMBER: proposed patch for ptraj/evec.c (Amber 9.0) (Thu Sep 21 2006 - 12:26:35 CDT)
• Cao Tran
  • RE: AMBER: Ask for your help to install Amber8 software (Fri Feb 10 2006 - 03:01:38 CST)
  • AMBER: Ask for your help to install Amber8 software (Wed Feb 08 2006 - 07:53:11 CST)
• caoch_at_cherry.bio.titech.ac.jp
  • AMBER: how to combine NEB method with QM/MM approach (Mon Oct 09 2006 - 11:23:07 CDT)
• CaoTran
  • RE: AMBER: Ask for your help to install Amber8 software (Wed Feb 08 2006 - 09:03:51 CST)
• Carles Jaime Cardiel
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 12:25:02 CST)
• carlos
  • Re: AMBER: RMS (Mon Apr 03 2006 - 16:18:24 CDT)
  • Re: AMBER: LES error (Sat Apr 01 2006 - 12:04:46 CST)
• Carlos Silva Lopez
  • Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster (Tue Feb 28 2006 - 16:27:07 CST)
  • AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster (Tue Feb 28 2006 - 11:30:42 CST)
• Carlos Simmerling
  • Re: AMBER: sander ntc=2 ntf=1 (Tue Dec 19 2006 - 05:39:38 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:54:37 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 07:22:04 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 06:32:16 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 07:48:56 CST)
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 06:23:24 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Thu Nov 30 2006 - 06:13:42 CST)
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Wed Nov 29 2006 - 13:02:20 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Wed Nov 29 2006 - 06:26:19 CST)
  • Re: AMBER: DNA helix end stable? (Wed Nov 29 2006 - 06:24:14 CST)
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:03:18 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 08:07:18 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 06:11:51 CST)
  • Re: AMBER: helices in GB simulations (Mon Nov 27 2006 - 12:12:02 CST)
  • Re: AMBER: problem of the REMD with nmr constraints (Fri Nov 24 2006 - 08:35:25 CST)
  • Re: AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 11:25:31 CST)
  • Re: Fwd: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 06:38:52 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 08:58:26 CST)
  • Re: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 07:26:16 CST)
  • Re: AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 12:14:21 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 12:35:21 CST)
  • Re: AMBER: simulating a small chain protein in water box (Wed Nov 08 2006 - 11:50:59 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 11:46:27 CST)
  • Re: AMBER: question about the topology file (Wed Nov 08 2006 - 06:18:58 CST)
  • Re: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:32:35 CST)
  • Re: AMBER: Zn metal library (Mon Nov 06 2006 - 06:26:52 CST)
  • Re: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 12:05:22 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 05:48:06 CST)
  • Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 (Thu Nov 02 2006 - 14:28:33 CST)
  • Re: AMBER: CARNAL: carnal source code (Wed Oct 25 2006 - 18:06:08 CDT)
  • Re: AMBER: Not getting proper structure after minimization (Wed Oct 25 2006 - 08:45:38 CDT)
  • Re: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 16:06:14 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 23 2006 - 17:38:22 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:33:40 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:10:52 CDT)
  • Re: AMBER: force fiels for a-rna (Fri Oct 13 2006 - 17:41:21 CDT)
  • Re: AMBER: amber force field (Wed Oct 11 2006 - 13:33:36 CDT)
  • Re: AMBER: RMSD: is it related to flexibility? (Wed Oct 04 2006 - 06:40:04 CDT)
  • Re: AMBER: Electrostatic Energy Constant (Fri Sep 29 2006 - 15:20:24 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 13:33:01 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 13:26:35 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 12:59:33 CDT)
  • Re: AMBER: structure from MD (Tue Sep 26 2006 - 11:43:58 CDT)
  • Re: AMBER: center of mass dihedral restraints (Mon Sep 25 2006 - 06:43:49 CDT)
  • Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS (Mon Sep 25 2006 - 06:30:57 CDT)
  • Re: AMBER: one question on MD (Sat Sep 23 2006 - 20:32:46 CDT)
  • Re: AMBER: Temperature fluctuation BIG with ntt=3 (Thu Sep 21 2006 - 19:48:07 CDT)
  • Re: AMBER: resolving a bad initial model (Tue Sep 19 2006 - 09:53:47 CDT)
  • Re: AMBER: restraints and constant pressure (Sun Sep 17 2006 - 09:01:54 CDT)
  • AMBER: new article on Amber force fields (Fri Sep 15 2006 - 14:47:34 CDT)
  • Re: AMBER: mdcrd file (Fri Sep 08 2006 - 15:54:34 CDT)
  • Re: AMBER: leap - how to recognize my structure (Thu Sep 07 2006 - 17:34:09 CDT)
  • Re: AMBER: trajout (Thu Sep 07 2006 - 06:04:02 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:18:09 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:23:26 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:15:23 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:22:13 CDT)
  • Re: AMBER: REMD: Hybrid topology file (Wed Aug 30 2006 - 09:48:20 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 15:40:05 CDT)
  • Re: AMBER: TI, mutation (Mon Aug 28 2006 - 07:18:56 CDT)
  • Re: AMBER: missing values in md.out (Fri Aug 25 2006 - 07:53:26 CDT)
  • Re: AMBER: missing values in md.out (Thu Aug 24 2006 - 11:24:28 CDT)
  • Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Wed Aug 23 2006 - 07:18:03 CDT)
  • Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 09:19:10 CDT)
  • AMBER: Re: Simulated annealing (Thu Aug 10 2006 - 06:40:24 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Thu Aug 10 2006 - 05:09:23 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Wed Aug 09 2006 - 10:01:27 CDT)
  • Re: AMBER: Format of mdcrd files (Wed Aug 09 2006 - 09:24:35 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:43:47 CDT)
  • Re: AMBER: Problem with restarting MD simulation (Tue Aug 08 2006 - 06:08:27 CDT)
  • Re: AMBER: SURFTEN in GB (mm_pbsa calculations) (Thu Aug 03 2006 - 14:38:59 CDT)
  • Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms (Thu Aug 03 2006 - 10:33:34 CDT)
  • AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 05:59:11 CDT)
  • Re: AMBER: Maximum system size in simulated annealing (Thu Aug 03 2006 - 05:26:58 CDT)
  • Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 13:13:07 CDT)
  • Re: AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 12:43:04 CDT)
  • Re: AMBER: Harmonic restraint along z-axis (Thu Jul 27 2006 - 11:15:18 CDT)
  • Re: AMBER: library for 8oxoguanine (Mon Jul 24 2006 - 16:12:38 CDT)
  • Re: AMBER: converting from parm to parm7 (Sat Jul 22 2006 - 06:27:10 CDT)
  • Re: AMBER: Replica Exchange (Thu Jul 20 2006 - 21:51:19 CDT)
  • Re: AMBER: Replica exchange (Thu Jul 20 2006 - 07:32:07 CDT)
  • Re: AMBER: Replica exchange (Wed Jul 19 2006 - 11:29:33 CDT)
  • Re: AMBER: temperature regulation (Tue Jul 18 2006 - 06:41:18 CDT)
  • Re: AMBER: PhosphoThreonine Parms for use with ff03 (Tue Jul 18 2006 - 06:28:20 CDT)
  • Re: AMBER: Replica exchange (Mon Jul 17 2006 - 09:44:55 CDT)
  • Re: AMBER: center molecule using iwrap=1? (Thu Jul 13 2006 - 14:43:37 CDT)
  • Re: AMBER: center molecule using iwrap=1? (Thu Jul 13 2006 - 14:00:59 CDT)
  • Re: AMBER: Replica exchange (Wed Jul 12 2006 - 09:25:14 CDT)
  • Re: AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 14:05:48 CDT)
  • Re: AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 10:09:21 CDT)
  • Re: AMBER: Replica exchange (Tue Jul 11 2006 - 07:49:20 CDT)
  • Re: AMBER: Replica exchange (Mon Jul 10 2006 - 07:13:48 CDT)
  • Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? (Thu Jul 06 2006 - 20:51:58 CDT)
  • Re: AMBER: working with large strained system (Thu Jul 06 2006 - 08:41:39 CDT)
  • Re: AMBER: remlog option changed in amber9? (Wed Jun 28 2006 - 16:37:54 CDT)
  • Re: AMBER: remlog option changed in amber9? (Wed Jun 28 2006 - 16:11:22 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 20:54:51 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 19:19:10 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 19:18:21 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 18:10:48 CDT)
  • Re: AMBER: Post-MD minimization (Mon Jun 19 2006 - 09:27:37 CDT)
  • AMBER: GB and protein backbone parameters (Thu Jun 08 2006 - 11:27:47 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Wed Jun 07 2006 - 21:02:34 CDT)
  • Re: AMBER: trouble adding mdcrd files together (Fri Jun 02 2006 - 18:45:16 CDT)
  • Re: AMBER: trouble adding mdcrd files together (Fri Jun 02 2006 - 17:37:54 CDT)
  • Re: AMBER: Programes to calculate ligand RMSD (Fri Jun 02 2006 - 06:45:17 CDT)
  • Re: AMBER: Replica exchage: about exchange interval (Wed May 31 2006 - 08:02:32 CDT)
  • Re: AMBER: which time should I use to calculate the number of "ps/Day" (Mon May 29 2006 - 04:50:31 CDT)
  • Re: AMBER: md error : sander (Sun May 28 2006 - 15:06:21 CDT)
  • Re: AMBER: Saving RMSD values in VMD (Fri May 26 2006 - 10:45:17 CDT)
  • Re: AMBER: RMSd error (Fri May 26 2006 - 07:58:42 CDT)
  • Re: AMBER: RE: trouble stripping waters with ptraj (Fri May 26 2006 - 06:28:35 CDT)
  • Re: AMBER: RMSd error (Fri May 26 2006 - 06:27:18 CDT)
  • Re: AMBER: alpha helix preference problem (Thu May 25 2006 - 20:35:10 CDT)
  • Re: AMBER: RMSd error (Mon May 22 2006 - 07:02:02 CDT)
  • Re: AMBER: trajin and rms (Mon May 22 2006 - 06:58:04 CDT)
  • Re: AMBER: RE: trouble stripping waters with ptraj (Sat May 20 2006 - 12:10:24 CDT)
  • Re: AMBER: Fw: RMSd calculations (Fri May 19 2006 - 08:00:50 CDT)
  • Re: AMBER: fail to execute addles (Tue May 16 2006 - 08:47:37 CDT)
  • Re: AMBER: fail to execute addles (Mon May 15 2006 - 11:59:29 CDT)
  • Re: AMBER: fail to execute addles (Mon May 15 2006 - 07:43:31 CDT)
  • Re: AMBER: Error while running test.serial in Amber9 (Wed May 03 2006 - 06:50:37 CDT)
  • Re: AMBER: proper restart procedure? (Wed May 03 2006 - 06:48:25 CDT)
  • Re: AMBER: Amber 9, sander imin = 5, -y flag (Mon May 01 2006 - 08:35:56 CDT)
  • Re: AMBER: about the execuation of REMD with sander of amber9 (Sat Apr 29 2006 - 08:45:24 CDT)
  • Re: AMBER: about the execuation of REMD with sander of amber9 (Sat Apr 29 2006 - 08:43:46 CDT)
  • Re: AMBER: Performing Simulated Annealing? (Fri Apr 28 2006 - 12:16:43 CDT)
  • Re: AMBER: heating process (Fri Apr 28 2006 - 06:06:03 CDT)
  • Re: AMBER: LES copies (Mon Apr 24 2006 - 06:14:20 CDT)
  • Re: AMBER: increase in computational time with LES (Sun Apr 23 2006 - 18:00:20 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 13:28:42 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 11:41:04 CDT)
  • Re: AMBER: separating LES copies in moil view (Thu Apr 13 2006 - 18:45:35 CDT)
  • Re: AMBER: Input conversion error. (Sat Mar 11 2006 - 13:23:29 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Mon Mar 06 2006 - 18:33:14 CST)
  • Re: AMBER: AMBER 8 VS AMBER 7 (Thu Mar 02 2006 - 15:04:09 CST)
  • Re: AMBER: GAFF + AM1BCC & small-molecule aggregation (Wed Mar 01 2006 - 16:00:40 CST)
  • Re: AMBER: GAFF + AM1BCC & small-molecule aggregation (Wed Mar 01 2006 - 15:34:06 CST)
  • Re: AMBER: replica exchange hangs (Wed Mar 01 2006 - 12:37:04 CST)
  • Re: AMBER: replica exchange hangs (Wed Mar 01 2006 - 12:37:40 CST)
  • Re: AMBER: failed to save prm and xyz using ff96 (Tue Feb 28 2006 - 11:24:23 CST)
  • Re: AMBER: AMBER force field with namd (Thu Feb 23 2006 - 07:41:31 CST)
  • Re: AMBER: paralelization and sander problems (Tue Feb 21 2006 - 06:57:10 CST)
  • Re: AMBER: Error in RST files in long simulations! (Tue Feb 21 2006 - 07:02:58 CST)
  • Re: AMBER: Error in RST files in long simulations! (Mon Feb 20 2006 - 14:32:13 CST)
  • Re: AMBER: paralelization and sander problems (Fri Feb 17 2006 - 05:59:44 CST)
  • Re: AMBER: sander problem (Thu Feb 16 2006 - 10:25:20 CST)
  • Re: AMBER: paralelization and sander problems (Tue Feb 14 2006 - 07:59:43 CST)
  • Re: AMBER: EAMBER (Thu Feb 09 2006 - 22:15:21 CST)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 13:21:31 CST)
  • Re: AMBER: dihedral parameters (Mon Feb 06 2006 - 06:22:03 CST)
  • Re: AMBER: dihedral parameters (Sat Feb 04 2006 - 11:30:27 CST)
  • Re: AMBER: AMBER 7 and cutoff's (Fri Feb 03 2006 - 13:20:30 CST)
  • Re: AMBER: Gibbs PMF Calculation (Fri Feb 03 2006 - 05:52:56 CST)
  • Re: AMBER: Values of Spring Constants (Thu Feb 02 2006 - 05:34:30 CST)
  • Re: AMBER: protein ligand complex (Wed Feb 01 2006 - 12:26:10 CST)
  • Re: AMBER: protein ligand complex (Wed Feb 01 2006 - 11:53:06 CST)
  • Re: AMBER: Gibbs PMF Calculation (Wed Feb 01 2006 - 06:54:33 CST)
  • Re: AMBER: Values of Spring Constants (Wed Feb 01 2006 - 06:52:50 CST)
  • Re: AMBER: is there any relationship between RMSD and B-factor? (Thu Jan 19 2006 - 06:59:39 CST)
  • Re: AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 21:53:26 CST)
  • AMBER: Re: RE£ºAMBER: the problem of mdcrd (Tue Jan 17 2006 - 06:56:58 CST)
  • Re: AMBER: base-base interaction (Fri Jan 13 2006 - 12:07:57 CST)
  • Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 16:10:58 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:04:45 CST)
  • Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 07:04:46 CST)
• Carra, Claudio \(JSC-SK\)[USRA]
  • AMBER: library for 8oxoguanine (Mon Jul 24 2006 - 14:50:59 CDT)
  • RE: AMBER: change atom in a DNA double strand (Mon Jul 10 2006 - 14:24:02 CDT)
  • AMBER: change atom in a DNA double strand (Wed Jul 05 2006 - 16:09:23 CDT)
• Cenk Andac
  • AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 05:17:28 CST)
  • Re: AMBER: xleap problems (Mon Dec 04 2006 - 09:46:34 CST)
  • Re: AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 11:32:50 CST)
  • AMBER: LogP (Sat Dec 02 2006 - 04:44:06 CST)
  • Re: AMBER: NAD ?? (Mon Nov 13 2006 - 08:46:47 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 17:20:53 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 17:27:35 CST)
  • Re: AMBER: NAD ?? (Wed Nov 08 2006 - 09:55:38 CST)
  • Re: AMBER: problem with NAD+ parameters (Mon Nov 06 2006 - 16:05:52 CST)
  • Re: AMBER: DIST_RST (Tue Oct 24 2006 - 05:51:01 CDT)
  • Re: AMBER: Amber 9 installation problem (Thu Oct 19 2006 - 14:13:58 CDT)
  • Re: AMBER: Amber 9 installation problem (Thu Oct 19 2006 - 12:55:54 CDT)
  • AMBER: Amber 9 installation problem (Thu Oct 19 2006 - 10:43:02 CDT)
  • Re: AMBER: regarding PBCAL in MM-PBSA (Mon Oct 16 2006 - 20:15:20 CDT)
  • AMBER: regarding PBCAL in MM-PBSA (Mon Oct 16 2006 - 18:11:33 CDT)
  • Re: AMBER: nmode memory allocation error (Mon Sep 11 2006 - 04:48:30 CDT)
  • Re: AMBER: nmode: number of atoms limitation (Wed Aug 30 2006 - 08:01:58 CDT)
  • Re: AMBER: How to calculate binding free energy using MM-PBSA (Fri Jun 30 2006 - 07:22:08 CDT)
  • Re: AMBER: How to calculate binding free energy using MM-PBSA (Thu Jun 29 2006 - 05:38:11 CDT)
  • AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering (Wed Jun 28 2006 - 05:46:49 CDT)
  • AMBER: Langevin mode error?? (Fri Apr 28 2006 - 06:52:02 CDT)
  • AMBER: Question about interpretation of sander.QMMM results (Thu Apr 06 2006 - 14:10:09 CDT)
  • Re: AMBER: question capping helix ends (Fri Mar 24 2006 - 03:09:11 CST)
  • Re: AMBER: dynamic memory allocation problem in nmode (Sun Mar 19 2006 - 03:10:22 CST)
  • AMBER: Xleap 64 bit installation problem (Tue Mar 14 2006 - 05:37:18 CST)
  • Re: AMBER: the total energy is not converge as the cutoff increase (Mon Mar 06 2006 - 07:28:04 CST)
  • AMBER: G95, SGI and Amber8 (Fri Mar 03 2006 - 01:30:44 CST)
  • AMBER: transition metals and the parmcal of the antechamber module (Thu Mar 02 2006 - 05:09:44 CST)
  • Re: AMBER: dynamic memory allocation problem in nmode (Sun Feb 26 2006 - 03:26:23 CST)
  • AMBER: dynamic memory allocation problem in nmode (Sun Feb 26 2006 - 02:58:14 CST)
  • RE: AMBER: Problem with file size of sander outputs (Thu Feb 23 2006 - 01:23:02 CST)
  • AMBER: Problem with file size of sander outputs (Wed Feb 22 2006 - 01:54:24 CST)
  • RE: AMBER: Ask for your help to install Amber8 software (Fri Feb 10 2006 - 04:46:12 CST)
  • Re: AMBER: Ask for your help to install Amber8 software (Wed Feb 08 2006 - 08:44:30 CST)
• Changge Ji
  • AMBER: Charge fitting in Amber (Tue Nov 28 2006 - 10:50:20 CST)
  • AMBER: how can i treat with long "mask" in ptraj analysis. (Sun Nov 26 2006 - 10:22:00 CST)
  • Re: Re: AMBER: PBSA calculation fail .... (Thu Oct 05 2006 - 21:36:34 CDT)
  • AMBER: PBSA calculation fail .... (Thu Oct 05 2006 - 08:42:39 CDT)
  • Re: Re: AMBER: nmode: number of atoms limitation (Tue Aug 29 2006 - 01:33:27 CDT)
  • AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? (Wed Jul 12 2006 - 01:03:30 CDT)
• Charlisa Daniels
  • AMBER: Ptraj problems (Thu Oct 12 2006 - 15:01:30 CDT)
• Cheng Luo, Ph.D.
  • AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 (Fri Aug 11 2006 - 15:41:32 CDT)
  • AMBER: Ask for help in pbsa error in AMBER9 (Thu Jun 08 2006 - 11:08:10 CDT)
• Chengwen Chen
  • AMBER: AMBER complile problem (Fri Dec 29 2006 - 01:41:21 CST)
  • Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Wed Dec 13 2006 - 01:01:03 CST)
  • AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Thu Nov 30 2006 - 02:07:28 CST)
  • AMBER: How to run MD simulation of a silicon containing complex with AMBER9? (Thu Nov 30 2006 - 01:06:54 CST)
  • AMBER: parameters for silicon atom (Mon Nov 20 2006 - 01:45:07 CST)
  • AMBER: what to do with the counter ions when minimizing average structure of DNA? (Tue Nov 14 2006 - 05:09:25 CST)
  • AMBER: problems of running sander.MPI of amber9 on remote node (Mon Jul 24 2006 - 01:29:20 CDT)
  • AMBER: error on running parallel sander on remote node- amber9 (Wed Jul 05 2006 - 02:46:11 CDT)
  • Re: AMBER: problems about compiling a parallel version of AMBER 9 (Tue Jul 04 2006 - 23:29:38 CDT)
  • Re: AMBER: problems about compiling a parallel version of AMBER 9 (Mon Jun 26 2006 - 23:41:05 CDT)
  • AMBER: problems about compiling a parallel version of AMBER 9 (Thu Jun 22 2006 - 02:25:11 CDT)
  • Re: AMBER: a question about "solvateoct" in AMBER 8 (Sun Apr 23 2006 - 23:13:30 CDT)
  • AMBER: a question about "solvateoct" in AMBER 8 (Fri Apr 21 2006 - 01:48:14 CDT)
  • AMBER: Which one is the best force field for DNA? (Wed Apr 12 2006 - 22:11:14 CDT)
  • AMBER: the best force field for DNA (Mon Apr 10 2006 - 23:15:25 CDT)
• Chng Choon-Peng
  • Re: AMBER: Can't open xleap (Thu Jul 27 2006 - 05:45:58 CDT)
  • Re: AMBER: xleap (Thu Jul 27 2006 - 05:14:58 CDT)
  • Re: AMBER: process_mdout.perl's output is empty (Mon Jul 24 2006 - 20:02:57 CDT)
  • Re: AMBER: Ptraj: Hbond time series (Tue Jul 11 2006 - 18:56:20 CDT)
  • Re: AMBER: Related to RESTRAINT_WT (Wed Mar 22 2006 - 18:16:13 CST)
  • Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue (Mon Mar 06 2006 - 02:51:13 CST)
  • Re: AMBER: Which PTRAJ distribution to use? (Thu Mar 02 2006 - 18:27:15 CST)
  • AMBER: Which PTRAJ distribution to use? (Thu Mar 02 2006 - 01:30:49 CST)
• Chris Moth
  • Re: AMBER: Frozen at Minimization (Tue Dec 19 2006 - 09:01:16 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:35:13 CST)
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:27:17 CST)
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:25:03 CST)
  • AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 08:21:11 CST)
  • top2mol2.c scanf format string bug (Mon Nov 06 2006 - 18:19:36 CST)
  • Re: AMBER: error estimate for free energy perturbation calculation (Wed Oct 25 2006 - 11:58:14 CDT)
  • Re: AMBER: RESP charges of iron-porphyrin system (Thu Oct 19 2006 - 11:39:24 CDT)
  • AMBER: Missing LES reference in Amber 9 manual (Tue Aug 29 2006 - 13:43:12 CDT)
  • Re: AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 14:23:01 CDT)
  • Re: AMBER: angle between planes (Fri Apr 07 2006 - 16:19:26 CDT)
  • Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7 (Tue Feb 07 2006 - 08:10:07 CST)
• Christian Roth
  • RE: AMBER: error in tleap test (Wed Nov 15 2006 - 12:18:07 CST)
  • AMBER: error in tleap test (Tue Nov 14 2006 - 18:40:24 CST)
• Christophe Deprez
  • Re: AMBER: problems for running sander.MPI (Mon Oct 30 2006 - 12:27:12 CST)
  • Re: AMBER: problems for running sander.MPI (Thu Oct 12 2006 - 08:54:41 CDT)
• Christophe Guilbert
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 13:51:18 CST)
  • AMBER: antechamber charge calculation very sensitive to conformations ? (Wed Aug 23 2006 - 20:59:08 CDT)
  • AMBER: program to calculate net charge of a ligand for Antechamber (Mon Jul 10 2006 - 20:30:39 CDT)
  • AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? (Thu Jul 06 2006 - 19:51:49 CDT)
  • Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. (Wed Jul 05 2006 - 21:50:24 CDT)
  • Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. (Wed Jul 05 2006 - 18:55:49 CDT)
  • AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. (Thu Jun 29 2006 - 20:28:31 CDT)
  • Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! (Thu Jun 29 2006 - 20:06:29 CDT)
  • AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! (Thu Jun 29 2006 - 16:48:31 CDT)
  • AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected (Mon Jun 19 2006 - 20:00:29 CDT)
  • AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand (Fri Jun 16 2006 - 23:32:12 CDT)
• Christopher Gaughan
  • Re: AMBER: Problem with mask when using distance in ptraj (Sun Nov 26 2006 - 08:28:29 CST)
  • AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 13:36:23 CST)
• Chunhu Tan
  • Re: AMBER: A question about Dynamics. (Mon Sep 18 2006 - 16:24:22 CDT)
  • RE: AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 16:10:44 CDT)
  • AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 12:46:35 CDT)
  • AMBER: ´ð¸´: AMBER: pmf input files (Thu Aug 17 2006 - 11:36:30 CDT)
  • AMBER: ´ð¸´: AMBER: Review. (Mon Jun 26 2006 - 16:46:29 CDT)
  • AMBER: Review. (Mon Jun 26 2006 - 14:37:22 CDT)
  • AMBER: Problem of Ptraj in AMBER9 (Tue Jun 13 2006 - 17:24:26 CDT)
• Claire Zerafa
  • AMBER: PARAMETERISATION PROBLEM (Wed Sep 06 2006 - 09:12:04 CDT)
  • Fw: AMBER: HBOND ANALYSIS (Sat Aug 05 2006 - 14:45:10 CDT)
  • AMBER: HBOND ANALYSIS (Fri Aug 04 2006 - 09:35:50 CDT)
  • AMBER: hbond analysis2 (Tue Jul 04 2006 - 09:00:35 CDT)
  • AMBER: Dihedral analysis (Mon Jul 03 2006 - 16:25:33 CDT)
  • AMBER: hbond analysis (Mon Jul 03 2006 - 16:06:22 CDT)
  • Re: AMBER: RMSd error (Sun May 28 2006 - 11:26:14 CDT)
  • Re: AMBER: RMSd error (Fri May 26 2006 - 08:30:57 CDT)
  • Re: AMBER: RMSd error (Fri May 26 2006 - 07:26:06 CDT)
  • AMBER: RMSd error (Thu May 25 2006 - 23:37:54 CDT)
  • AMBER: RMSd error (Mon May 22 2006 - 03:52:34 CDT)
  • AMBER: Fw: RMSd calculations (Fri May 19 2006 - 07:07:30 CDT)
  • AMBER: RMSd calculations (Thu May 18 2006 - 14:25:57 CDT)
  • AMBER: (Wed Apr 05 2006 - 08:33:39 CDT)
  • AMBER: Ptraj & pca (Fri Mar 31 2006 - 08:23:05 CST)
  • AMBER: Average pdb (Thu Mar 23 2006 - 15:17:33 CST)
  • AMBER: h bond analysis (Mon Mar 06 2006 - 23:39:52 CST)
  • AMBER: mask issues (Tue Feb 28 2006 - 06:46:12 CST)
  • AMBER: ACTIVE SITE (Mon Jan 16 2006 - 08:06:52 CST)
• Claudia Steinert
  • AMBER: LES copies (Mon Apr 24 2006 - 03:28:06 CDT)
  • AMBER: LES error (Fri Mar 31 2006 - 01:59:36 CST)
• Come On
  • AMBER: to do tutorial 4 using tleap (Fri Aug 04 2006 - 11:50:53 CDT)
• Conn O'Rourke
  • AMBER: Gb Na+ ions DNA (Thu Jul 20 2006 - 10:16:05 CDT)
• Cporteli
  • AMBER: PTRAJ OUTPUT (Wed Jul 05 2006 - 18:02:47 CDT)
• Craig Gough
  • AMBER: Correlation matrix used in quasih (Amber 7) (Thu May 18 2006 - 02:06:03 CDT)
• cristian obiol
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Fri Nov 24 2006 - 04:24:28 CST)
  • Re: AMBER: parameters !!?? (Wed Oct 25 2006 - 05:29:42 CDT)
  • Re: AMBER: NAD parameters (Thu Sep 28 2006 - 08:56:43 CDT)
  • AMBER: counterions and particle-mesh-ewald (Tue Aug 29 2006 - 03:06:20 CDT)
  • AMBER: nmode different units (Wed Apr 05 2006 - 05:47:04 CDT)
  • Re: AMBER: paralelization and sander problems (Mon Feb 20 2006 - 06:13:58 CST)
  • Re: AMBER: paralelization and sander problems (Fri Feb 17 2006 - 04:07:37 CST)
  • AMBER: paralelization and sander problems (Tue Feb 14 2006 - 04:24:18 CST)
• Daniel Lee
  • Re: AMBER: cyclic AMP off and frcmod files? (Sun Sep 17 2006 - 21:10:28 CDT)
  • AMBER: cyclic AMP off and frcmod files? (Thu Sep 14 2006 - 22:52:33 CDT)
• Daniel Oehme
  • AMBER: Mass wieghted Covariance Matrix (Wed Apr 12 2006 - 02:16:32 CDT)
  • AMBER: Entropy calculations with Nmode and ptraj (Tue Apr 04 2006 - 02:24:39 CDT)
• darden
  • Re: AMBER: too big EEL values in the minimisation output (Thu Nov 02 2006 - 13:13:29 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Wed Nov 01 2006 - 12:08:27 CST)
  • Re: AMBER: PKDIV lone pair dihedrals (Mon Oct 23 2006 - 16:05:37 CDT)
  • Re: AMBER: counterions and particle-mesh-ewald (Wed Aug 30 2006 - 17:59:32 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 09:34:47 CDT)
  • Re: AMBER: Force units in forcedump.dat (Wed May 31 2006 - 12:53:34 CDT)
  • Re: AMBER: a quetion (Mon Apr 24 2006 - 09:57:59 CDT)
  • Re: AMBER: Constant P for non-orthorhombic cells (Wed Apr 12 2006 - 07:41:14 CDT)
• Dave S Walker
  • Re: AMBER: NONB values adjusted? (Tue Nov 28 2006 - 13:48:36 CST)
  • AMBER: NONB values adjusted? (Tue Nov 28 2006 - 01:37:28 CST)
• Dave, Sonya
  • AMBER: simulating a small chain protein in water box (Wed Nov 08 2006 - 10:03:46 CST)
  • RE: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 13:20:55 CST)
  • AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 11:54:06 CST)
  • RE: AMBER: How do we simulate deletion mutations (Thu Oct 26 2006 - 13:05:01 CDT)
  • RE: AMBER: How do we simulate deletion mutations (Wed Oct 25 2006 - 16:41:48 CDT)
  • AMBER: How do we simulate deletion mutations (Wed Oct 25 2006 - 13:47:38 CDT)
  • RE: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 17:46:45 CDT)
  • AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 15:50:04 CDT)
  • RE: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 13:14:44 CDT)
  • RE: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 12:10:03 CDT)
  • RE: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 12:17:59 CDT)
  • AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:03:59 CDT)
• David A. Case
  • Re: AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 10:56:06 CST)
  • Re: AMBER: bad connectivity - more detail (Fri Dec 29 2006 - 02:15:16 CST)
  • Re: AMBER: problems with Calcium ions treatment in GB run (Fri Dec 29 2006 - 01:56:25 CST)
  • Re: AMBER: AMBER complile problem (Fri Dec 29 2006 - 01:51:49 CST)
  • Re: AMBER: chirality.c line 121 (Wed Dec 27 2006 - 16:46:21 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 12:31:58 CST)
  • Re: AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 12:30:10 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 10:52:41 CST)
  • Re: AMBER: Error compiling amber on parallel (MPICH) (Wed Dec 27 2006 - 10:41:21 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 15:45:54 CST)
  • Re: AMBER: Sander--NMR refinement (Tue Dec 26 2006 - 12:44:46 CST)
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Mon Dec 25 2006 - 16:32:11 CST)
  • Re: AMBER: MM_PBSA (Mon Dec 25 2006 - 16:15:26 CST)
  • Re: AMBER: Renumber residues in LEAP (Mon Dec 25 2006 - 16:11:34 CST)
  • Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Sat Dec 23 2006 - 20:58:29 CST)
  • Re: AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 23:54:56 CST)
  • Re: AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 17:24:00 CST)
  • Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 11:48:49 CST)
  • Re: AMBER: setBox with buffer in leap (Tue Dec 12 2006 - 10:30:25 CST)
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 14:08:58 CST)
  • Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 18:34:15 CST)
  • Re: AMBER: Compiling Amber 9 on SGI with gcc (Sat Dec 09 2006 - 10:55:20 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 20:10:36 CST)
  • Re: AMBER: RDC refinement (Fri Dec 08 2006 - 17:52:11 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 17:47:39 CST)
  • Re: AMBER: description of prep file (Fri Dec 08 2006 - 16:52:30 CST)
  • Re: AMBER: Error message in methane solvent system (Fri Dec 08 2006 - 10:41:49 CST)
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 17:54:33 CST)
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 15:51:53 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 11:06:17 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Thu Dec 07 2006 - 00:14:44 CST)
  • Re: AMBER: parameter definitions (Wed Dec 06 2006 - 13:00:34 CST)
  • Re: AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 12:22:37 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 09:59:43 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 15:24:37 CST)
  • Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 11:45:11 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 10:33:02 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 10:23:15 CST)
  • Re: AMBER: xleap problems (Mon Dec 04 2006 - 10:26:20 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 16:06:10 CST)
  • Re: AMBER: problem at the start of heating up (using extra-point) (Sun Dec 03 2006 - 16:04:25 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 11:52:44 CST)
  • Re: AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 18:24:44 CST)
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 17:54:08 CST)
  • Re: AMBER: How to recompile sander for single-processor use in AMBER 8? (Thu Nov 30 2006 - 17:19:10 CST)
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 10:50:47 CST)
  • Re: AMBER: nmode output with ptraj (Tue Nov 28 2006 - 20:36:33 CST)
  • Re: AMBER: Periodic simulations with net charge (Tue Nov 28 2006 - 20:03:22 CST)
  • Re: AMBER: xleap (Tue Nov 28 2006 - 10:02:13 CST)
  • Re: AMBER: (Tue Nov 28 2006 - 09:53:48 CST)
  • Re: AMBER: minimization of Hydrogens with xLeaP (Mon Nov 27 2006 - 20:19:48 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Mon Nov 27 2006 - 19:56:14 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Sat Nov 25 2006 - 02:51:06 CST)
  • Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 (Fri Nov 24 2006 - 18:43:20 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 01:02:21 CST)
  • Re: AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 21:58:34 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 16:24:44 CST)
  • Re: AMBER: Ptraj syntax change Amber8->Amber9 ? (Wed Nov 22 2006 - 15:22:37 CST)
  • Re: AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 15:07:29 CST)
  • AMBER: Re: installation instructions (Wed Nov 22 2006 - 10:48:17 CST)
  • Re: AMBER: Combining Residues in LEaP for Lipid Bilayers (Tue Nov 21 2006 - 10:16:06 CST)
  • Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0 (Tue Nov 21 2006 - 00:09:28 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 11:33:25 CST)
  • Re: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:35:04 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 12:59:28 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 12:39:39 CST)
  • Re: AMBER: pqr file (Thu Nov 16 2006 - 10:53:46 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 10:20:32 CST)
  • Re: AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 19:24:34 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 10:46:58 CST)
  • Re: AMBER: how to remove the rotation of system in periodic condition? (Wed Nov 15 2006 - 10:34:01 CST)
  • Re: Fwd: AMBER: sander error: rst file crash (Sun Nov 12 2006 - 20:44:48 CST)
  • Re: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 15:11:15 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 10:34:45 CST)
  • Re: AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 12:13:05 CST)
  • Re: AMBER: (Thu Nov 09 2006 - 12:11:55 CST)
  • Re: AMBER: problem in calculating EGB using sander for ligand containing F atom (Thu Nov 09 2006 - 10:14:06 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 15:35:10 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 10:48:01 CST)
  • Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion (Wed Nov 08 2006 - 10:35:24 CST)
  • Re: AMBER: NAD ?? (Wed Nov 08 2006 - 08:49:31 CST)
  • Re: AMBER: leap - compilation error (Tue Nov 07 2006 - 20:25:37 CST)
  • Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) (Tue Nov 07 2006 - 19:51:48 CST)
  • Re: AMBER: top2mol2.c scanf format string bug (Tue Nov 07 2006 - 10:18:43 CST)
  • Re: AMBER: klambda for TI method. (Tue Nov 07 2006 - 10:06:21 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 01:26:13 CST)
  • Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7? (Sun Nov 05 2006 - 21:26:02 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:42:23 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 11:30:50 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 10:56:07 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 10:54:06 CST)
  • Re: AMBER: MMPBSA entropy question (Tue Oct 31 2006 - 19:04:29 CST)
  • Re: AMBER: solvation and His protonation (Tue Oct 31 2006 - 09:57:53 CST)
  • Re: AMBER: ff99SB vs ff02 (ff02pol.rl) (Mon Oct 30 2006 - 20:57:48 CST)
  • Re: AMBER: solvation and His protonation (Mon Oct 30 2006 - 18:34:05 CST)
  • Re: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 10:32:56 CST)
  • Re: AMBER: ff02 force fields (Sun Oct 29 2006 - 23:17:44 CST)
  • Re: AMBER: problem with calcpka.pl (Sun Oct 29 2006 - 22:33:54 CST)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Fri Oct 27 2006 - 23:42:08 CDT)
  • Re: AMBER: where to set bondi radii for halogens (Fri Oct 27 2006 - 19:24:12 CDT)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 15:46:07 CDT)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 14:12:35 CDT)
  • Re: AMBER: where to set bondi radii for halogens (Fri Oct 27 2006 - 13:58:04 CDT)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 11:45:36 CDT)
  • Re: AMBER: how to add hydrogen molecules in the protein (Thu Oct 26 2006 - 19:57:22 CDT)
  • Re: AMBER: error estimate for free energy perturbation calculation (Wed Oct 25 2006 - 13:40:47 CDT)
  • Re: AMBER: Shake&Lone Pairs (Wed Oct 25 2006 - 13:21:02 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 24 2006 - 20:56:14 CDT)
  • Re: AMBER: md and implicit solvation (Tue Oct 24 2006 - 20:47:18 CDT)
  • Re: AMBER: md and implicit solvation (Tue Oct 24 2006 - 20:26:15 CDT)
  • Re: AMBER: load charges to antechamber calculations (Tue Oct 24 2006 - 17:55:29 CDT)
  • Re: AMBER: PKDIV lone pair dihedrals (Mon Oct 23 2006 - 15:26:58 CDT)
  • Re: AMBER: HBON in frcmod file (Mon Oct 23 2006 - 00:11:58 CDT)
  • Re: Re: Re: AMBER: Question about sander code (Fri Oct 20 2006 - 17:55:05 CDT)
  • Re: Re: AMBER: Question about sander code (Fri Oct 20 2006 - 16:47:50 CDT)
  • Re: AMBER: Question about sander code (Fri Oct 20 2006 - 13:37:51 CDT)
  • Re: AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai (Fri Oct 20 2006 - 12:27:50 CDT)
  • Re: AMBER: Probelm with running Amber 9 parallelly (Fri Oct 20 2006 - 10:24:16 CDT)
  • Re: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Thu Oct 19 2006 - 14:22:47 CDT)
  • Re: AMBER: Amber 9 installation problem (Thu Oct 19 2006 - 13:43:35 CDT)
  • Re: AMBER: sander/topology problem (Tue Oct 17 2006 - 12:31:25 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 17 2006 - 11:41:24 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 17 2006 - 10:38:07 CDT)
  • Re: AMBER: How did the coordinates change in xleap? (Tue Oct 17 2006 - 10:28:52 CDT)
  • Re: AMBER: Amber8: problem related to antechamber (Tue Oct 17 2006 - 10:10:43 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 16 2006 - 19:33:54 CDT)
  • Re: AMBER: General Coding Problem (Mon Oct 16 2006 - 19:27:56 CDT)
  • Re: AMBER: How to find equillibration time for my system in a generalised born solvation model (Mon Oct 16 2006 - 17:33:14 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 16 2006 - 17:24:34 CDT)
  • Re: AMBER: Density calculation (Mon Oct 16 2006 - 17:26:49 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 16 2006 - 11:41:31 CDT)
  • Re: AMBER: Amber8: problem related to antechamber (Mon Oct 16 2006 - 10:29:19 CDT)
  • Re: AMBER: angle between two vectors (Thu Oct 12 2006 - 13:14:14 CDT)
  • Re: AMBER: generalized born model for organic solvent (Thu Oct 12 2006 - 13:00:00 CDT)
  • Re: AMBER: generalized born model for organic solvent (Wed Oct 11 2006 - 18:53:49 CDT)
  • Re: AMBER: adding polar hydrogens (Wed Oct 11 2006 - 13:28:11 CDT)
  • Re: AMBER: partial charges (Wed Oct 11 2006 - 11:17:48 CDT)
  • Re: AMBER: adding polar hydrogens (Wed Oct 11 2006 - 11:14:29 CDT)
  • Re: AMBER: generalized born model for organic solvent (Wed Oct 11 2006 - 11:16:23 CDT)
  • Re: AMBER: LEAP error (Sun Oct 08 2006 - 23:28:36 CDT)
  • Re: AMBER: question about building molecules (Sun Oct 08 2006 - 11:31:27 CDT)
  • Re: AMBER: (no subject) (Fri Oct 06 2006 - 11:20:03 CDT)
  • Re: AMBER: water prmtop/inpcrd problem (Thu Oct 05 2006 - 21:01:22 CDT)
  • Re: AMBER: Building polymer with sequence command (Thu Oct 05 2006 - 19:31:36 CDT)
  • Re: AMBER: VMD PDB into LEAP Readable PDB (Thu Oct 05 2006 - 10:13:41 CDT)
  • Re: Re: AMBER: Pressure problem with restraint (Wed Oct 04 2006 - 17:19:50 CDT)
  • Re: AMBER: Pressure problem with restraint (Wed Oct 04 2006 - 13:03:45 CDT)
  • Re: AMBER: RMSD: is it related to flexibility? (Wed Oct 04 2006 - 10:08:32 CDT)
  • Re: AMBER: Pressure problem with restraint (Wed Oct 04 2006 - 10:06:38 CDT)
  • Re: AMBER: problem to center solvateshell (Mon Oct 02 2006 - 11:01:44 CDT)
  • Re: AMBER: proposed patch for ptraj/evec.c (Amber 9.0) (Mon Oct 02 2006 - 10:51:53 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 02 2006 - 10:28:25 CDT)
  • Re: AMBER: RE: Amber8: problem related to antechamber (Sun Oct 01 2006 - 08:34:45 CDT)
  • Re: AMBER: chemical shift restrains (Sun Oct 01 2006 - 08:35:01 CDT)
  • Re: AMBER: Multiple Timestep MD (Sun Oct 01 2006 - 08:35:25 CDT)
  • Re: AMBER: RE: Amber8: problem related to antechamber (Sun Oct 01 2006 - 08:35:55 CDT)
  • Re: AMBER: missing benchmark files (Wed Sep 27 2006 - 01:50:49 CDT)
  • Re: AMBER: bad atom type: Li (Wed Sep 27 2006 - 01:03:56 CDT)
  • Re: AMBER: build a polymer with sequence command (Mon Sep 25 2006 - 16:37:54 CDT)
  • Re: AMBER: leap can't assign CALA (Fri Sep 22 2006 - 19:53:29 CDT)
  • Re: RE: Re: AMBER: A question about Dynamics. (Fri Sep 22 2006 - 19:57:46 CDT)
  • Re: AMBER: build a polymer with sequence command (Fri Sep 22 2006 - 19:03:35 CDT)
  • Re: AMBER: build a polymer with sequence command (Fri Sep 22 2006 - 16:01:27 CDT)
  • Re: AMBER: Amber8: problem related to antechamber (Fri Sep 22 2006 - 09:52:35 CDT)
  • Re: AMBER: Temperature fluctuation BIG with ntt=3 (Thu Sep 21 2006 - 20:39:46 CDT)
  • Re: AMBER: Parmchk problems (parm99.dat) (Wed Sep 20 2006 - 23:22:56 CDT)
  • Re: AMBER: coordinate files (Wed Sep 20 2006 - 20:22:47 CDT)
  • Re: AMBER: Problems using rst distance constraints in Amber 8 (Wed Sep 20 2006 - 14:12:20 CDT)
  • Re: AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? (Tue Sep 19 2006 - 12:29:51 CDT)
  • Re: AMBER: A question about Dynamics. (Mon Sep 18 2006 - 15:55:47 CDT)
  • Re: AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 14:09:46 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Mon Sep 18 2006 - 11:41:56 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Mon Sep 18 2006 - 10:44:49 CDT)
  • Re: AMBER: improper torsion angle problem (Sun Sep 17 2006 - 18:52:38 CDT)
  • Re: AMBER: energy data for limited part of system (Sun Sep 17 2006 - 18:56:23 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Sat Sep 16 2006 - 11:50:31 CDT)
  • Re: AMBER: Problems with a restrained minimization approach (Fri Sep 15 2006 - 19:41:04 CDT)
  • Re: AMBER: About Lennard-Jones Parameters (Fri Sep 15 2006 - 19:07:35 CDT)
  • Re: AMBER: acidifying a water box (Thu Sep 14 2006 - 17:21:01 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Thu Sep 14 2006 - 10:05:25 CDT)
  • Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package (Thu Sep 14 2006 - 00:53:50 CDT)
  • Re: AMBER: Error in reading RDC data (Wed Sep 13 2006 - 16:44:14 CDT)
  • Re: AMBER: MAXM in nmode (Wed Sep 13 2006 - 16:17:29 CDT)
  • Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package (Wed Sep 13 2006 - 11:32:39 CDT)
  • Re: AMBER: RDC refinement (Wed Sep 13 2006 - 10:35:07 CDT)
  • Re: AMBER: Installing AMBER9 on cygwin (WinXP) (Tue Sep 12 2006 - 10:01:41 CDT)
  • Re: AMBER: set a trucated octahedron box in Leap (Tue Sep 12 2006 - 10:03:24 CDT)
  • Re: AMBER: Parallel compile: ld: cannot find -lfmpi (Mon Sep 11 2006 - 13:19:12 CDT)
  • Re: AMBER: System in polarizable waters (Mon Sep 11 2006 - 13:12:04 CDT)
  • Re: AMBER: Error in Running Sander (Mon Sep 11 2006 - 10:59:45 CDT)
  • Re: AMBER: set a trucated octahedron box in Leap (Mon Sep 11 2006 - 10:56:59 CDT)
  • Re: AMBER: seg fault during test.serial (Mon Sep 11 2006 - 10:54:43 CDT)
  • Re: AMBER: cAMP ligand charge (Mon Sep 11 2006 - 10:35:53 CDT)
  • Re: AMBER: nmode memory allocation error (Sat Sep 09 2006 - 23:17:54 CDT)
  • Re: AMBER: pmf with respect to a surface (Sat Sep 09 2006 - 23:14:30 CDT)
  • Re: AMBER: post nmanal (Sat Sep 09 2006 - 11:54:34 CDT)
  • Re: AMBER: a ligand file (Fri Sep 08 2006 - 20:53:18 CDT)
  • Re: AMBER: seg fault during test.serial (Fri Sep 08 2006 - 20:19:16 CDT)
  • Re: AMBER: mdcrd file (Fri Sep 08 2006 - 00:27:54 CDT)
  • AMBER: Re: FF problem: RG residue minimizes to non-planar structure (Thu Sep 07 2006 - 13:53:33 CDT)
  • Re: AMBER: a ligand file (Wed Sep 06 2006 - 16:40:30 CDT)
  • Re: AMBER: Question about using PMEMD and GB (Wed Sep 06 2006 - 12:58:59 CDT)
  • Re: AMBER: Implicit Water - Force field parameters (Wed Sep 06 2006 - 10:54:15 CDT)
  • Re: AMBER: PARAMETERISATION PROBLEM (Wed Sep 06 2006 - 10:20:43 CDT)
  • Re: AMBER: help with antechamber - creating ligand (Tue Sep 05 2006 - 21:11:52 CDT)
  • Re: AMBER: a ligand file (Tue Sep 05 2006 - 15:55:26 CDT)
  • Re: AMBER: ligand file (Mon Sep 04 2006 - 14:02:34 CDT)
  • Re: AMBER: Amber9: Free Energy (Sun Sep 03 2006 - 20:57:50 CDT)
  • Re: AMBER: Question about LEAP and twisting a dihedral angle (Sun Sep 03 2006 - 10:55:16 CDT)
  • Re: AMBER: Question about LEAP and twisting a dihedral angle (Sun Sep 03 2006 - 00:06:04 CDT)
  • Re: AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c (Fri Sep 01 2006 - 09:34:10 CDT)
  • Re: AMBER: Question about free energy with mm_pbsa (Fri Sep 01 2006 - 00:32:54 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:43:50 CDT)
  • Re: AMBER: counterions and particle-mesh-ewald (Wed Aug 30 2006 - 15:14:40 CDT)
  • Re: AMBER: Missing LES reference in Amber 9 manual (Wed Aug 30 2006 - 11:03:34 CDT)
  • Re: AMBER: (Tue Aug 29 2006 - 10:09:23 CDT)
  • Re: AMBER: nmode: number of atoms limitation (Tue Aug 29 2006 - 00:55:53 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 19:17:42 CDT)
  • Re: AMBER: preparing ligand/rna structure for MD (Mon Aug 28 2006 - 19:11:34 CDT)
  • Re: AMBER: Temperature fluctuation with Langevin Temperature control (Mon Aug 28 2006 - 12:32:08 CDT)
  • Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine (Sun Aug 27 2006 - 11:03:54 CDT)
  • Re: AMBER: TI vlimit exceeded (Sat Aug 26 2006 - 12:38:58 CDT)
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 11:39:40 CDT)
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 10:41:49 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 10:03:10 CDT)
  • Re: AMBER: increase force constants (Thu Aug 24 2006 - 17:56:33 CDT)
  • Re: AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 17:47:50 CDT)
  • Re: AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 10:15:44 CDT)
  • Re: AMBER: 0 steps the same as 1 step? (Wed Aug 23 2006 - 20:14:53 CDT)
  • Re: AMBER: holding a pair of residues fixed during minimization (Wed Aug 23 2006 - 15:05:25 CDT)
  • Re: AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 15:01:35 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Tue Aug 22 2006 - 01:14:15 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 13:21:10 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 12:10:24 CDT)
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 13:35:04 CDT)
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 12:50:32 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 13:01:45 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 11:04:22 CDT)
  • Re: AMBER: reading ff file into XLeap (Wed Aug 16 2006 - 12:21:47 CDT)
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 11:59:22 CDT)
  • Re: AMBER: MM_PBSA : Question about Stability? (Wed Aug 16 2006 - 11:24:48 CDT)
  • Re: AMBER: MMPBSA: positive energies during nmode (Wed Aug 16 2006 - 11:10:29 CDT)
  • Re: AMBER: TI tutorial (Tue Aug 15 2006 - 18:34:58 CDT)
  • Re: AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 18:14:41 CDT)
  • Re: AMBER: (Another) Question about using antechamber with G03 (Tue Aug 15 2006 - 18:09:56 CDT)
  • Re: AMBER: input conversion error mm_pbsa (Tue Aug 15 2006 - 17:47:19 CDT)
  • Re: AMBER: Question about using antechamber with G03 (Tue Aug 15 2006 - 16:15:26 CDT)
  • Re: AMBER: amber9 Test Failer (Tue Aug 15 2006 - 10:05:54 CDT)
  • Re: AMBER: Problem with sander in Linux (Mon Aug 14 2006 - 11:49:53 CDT)
  • Re: AMBER: klambda (Mon Aug 14 2006 - 11:48:30 CDT)
  • Re: AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:45:48 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Sun Aug 13 2006 - 11:37:03 CDT)
  • Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file (Sun Aug 13 2006 - 11:49:27 CDT)
  • Re: AMBER: DIELC? (Sun Aug 13 2006 - 11:43:58 CDT)
  • Re: AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 13:30:46 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Fri Aug 11 2006 - 11:05:12 CDT)
  • Re: AMBER: Leap adds hydrogens but cannot resolve their type. (Thu Aug 10 2006 - 15:15:16 CDT)
  • Re: AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 11:07:09 CDT)
  • Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 15:45:42 CDT)
  • Re: AMBER: how to reassign charges (Wed Aug 09 2006 - 15:43:07 CDT)
  • Re: AMBER: Amber Installation Help (Tue Aug 08 2006 - 10:25:49 CDT)
  • Re: AMBER: Info regarding reduced cysteines (Mon Aug 07 2006 - 10:02:57 CDT)
  • Re: AMBER: question on chargning free energy in solvent vs vacuum (Fri Aug 04 2006 - 11:18:53 CDT)
  • Re: AMBER: problems with ptraj (Thu Aug 03 2006 - 11:46:19 CDT)
  • Re: AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 11:43:44 CDT)
  • Re: AMBER: about Silica's polarizability (Thu Aug 03 2006 - 11:16:40 CDT)
  • Re: AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 09:48:23 CDT)
  • Re: AMBER: any work-around for 80 character mask string limit? (Tue Aug 01 2006 - 16:37:36 CDT)
  • Re: AMBER: GB tutorials and disulphide bonds (Tue Aug 01 2006 - 12:14:20 CDT)
  • Re: AMBER: Using a trajectory and some PDB files as input for PCA (Tue Aug 01 2006 - 12:10:29 CDT)
  • Re: AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 12:17:38 CDT)
  • Re: AMBER: Zinc-coordinating histidine protonation state (Mon Jul 31 2006 - 10:50:16 CDT)
  • Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . (Fri Jul 28 2006 - 09:27:44 CDT)
  • Re: AMBER: Dynamics and Restraint problem (Thu Jul 27 2006 - 18:08:16 CDT)
  • Re: AMBER: parallel installation of amber8 on HP cluster (Thu Jul 27 2006 - 10:57:41 CDT)
  • Re: AMBER: Harmonic restraint along z-axis (Thu Jul 27 2006 - 09:32:52 CDT)
  • Re: AMBER: leap error (Thu Jul 27 2006 - 09:34:17 CDT)
  • Re: AMBER: Can't open xleap (Thu Jul 27 2006 - 08:53:16 CDT)
  • Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap (Wed Jul 26 2006 - 12:44:58 CDT)
  • Re: AMBER: parallel installation of amber8 on HP cluster (Wed Jul 26 2006 - 10:00:53 CDT)
  • Re: AMBER: Hybridization in leap (Tue Jul 25 2006 - 15:37:30 CDT)
  • Re: AMBER: Fwd: difficulties with antechamber: tests dont even run (Tue Jul 25 2006 - 10:11:22 CDT)
  • Re: AMBER: Long line of input (Mon Jul 24 2006 - 14:37:20 CDT)
  • Re: AMBER: Amber 8.0 MM_PBSA Stability : question about methodology (Mon Jul 24 2006 - 14:36:30 CDT)
  • Re: AMBER: saltcon variable (Mon Jul 24 2006 - 14:38:53 CDT)
  • Re: AMBER: converting from parm to parm7 (Sun Jul 23 2006 - 09:47:05 CDT)
  • Re: AMBER: Simulating an "average" DNA sequence (Sun Jul 23 2006 - 09:47:15 CDT)
  • Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 (Mon Jul 17 2006 - 22:00:36 CDT)
  • Re: AMBER: Compiling Leap problem (Fri Jul 14 2006 - 17:57:31 CDT)
  • Re: AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 (Fri Jul 14 2006 - 10:00:26 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Thu Jul 13 2006 - 13:14:20 CDT)
  • Re: AMBER: Ringof dna (Thu Jul 13 2006 - 11:54:07 CDT)
  • Re: AMBER: problem about Distance Restraints. (Wed Jul 12 2006 - 18:33:54 CDT)
  • Re: AMBER: iso command and a cubic box (Wed Jul 12 2006 - 14:00:25 CDT)
  • Re: AMBER: applying restraints on pre-defined planes (Tue Jul 11 2006 - 18:34:52 CDT)
  • Re: AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 13:55:16 CDT)
  • Re: AMBER: Question about NSCM (Tue Jul 11 2006 - 10:02:11 CDT)
  • Re: AMBER: small bug in ambmask (amber9) (Mon Jul 10 2006 - 10:39:38 CDT)
  • Re: AMBER: about restraint format. (Mon Jul 10 2006 - 10:10:11 CDT)
  • Re: AMBER: residue and atom number (Mon Jul 10 2006 - 10:09:29 CDT)
  • Re: AMBER: (no subject) (Sun Jul 09 2006 - 18:20:30 CDT)
  • Re: AMBER: igb=2 and "bad atom type" conflict (Fri Jul 07 2006 - 16:42:09 CDT)
  • Re: AMBER: AMBER 8: Problem with MPI_Finalize (Fri Jul 07 2006 - 16:29:10 CDT)
  • Re: AMBER: Error in loading molecule in tleap (Fri Jul 07 2006 - 16:11:15 CDT)
  • Re: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag (Fri Jul 07 2006 - 16:06:34 CDT)
  • Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? (Thu Jul 06 2006 - 20:48:12 CDT)
  • Re: AMBER: Sander NOE violations (Thu Jul 06 2006 - 20:41:28 CDT)
  • Re: AMBER: Sander NOE violations (Thu Jul 06 2006 - 20:01:19 CDT)
  • Re: AMBER: change atom in a DNA double strand (Thu Jul 06 2006 - 11:57:12 CDT)
  • Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Thu Jul 06 2006 - 11:43:36 CDT)
  • Re: AMBER: Units for Leonard-Jones potential parameters (Thu Jul 06 2006 - 11:45:00 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 10:16:11 CDT)
  • Re: AMBER: FIX conformation of a ligand (Thu Jul 06 2006 - 09:30:01 CDT)
  • Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. (Wed Jul 05 2006 - 20:54:38 CDT)
  • Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Wed Jul 05 2006 - 17:22:42 CDT)
  • Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. (Wed Jul 05 2006 - 16:31:14 CDT)
  • Re: AMBER: problem with saving the parameters file (Wed Jul 05 2006 - 13:09:12 CDT)
  • Re: AMBER: problems about compiling a parallel version of AMBER 9 (Wed Jul 05 2006 - 13:06:08 CDT)
  • Re: AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging (Wed Jul 05 2006 - 12:50:52 CDT)
  • Re: AMBER: manual/prmtop/missing bonds section (Wed Jul 05 2006 - 11:09:06 CDT)
  • Re: AMBER: Second derivative matrix (Tue Jun 27 2006 - 03:36:57 CDT)
  • Re: AMBER: help creating RNA (Thu Jun 22 2006 - 16:08:45 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 16:36:49 CDT)
  • Re: AMBER: second derivative matrix (Tue Jun 20 2006 - 16:37:01 CDT)
  • Re: AMBER: RMS FLUCTUATIONS (Thu Jun 15 2006 - 23:09:53 CDT)
  • Re: AMBER: MPICH and Sander (Thu Jun 15 2006 - 22:47:36 CDT)
  • Re: AMBER: parmchk error (Wed Jun 14 2006 - 22:28:20 CDT)
  • Re: AMBER: saveamberparams error in Amber9 (Wed Jun 14 2006 - 22:15:05 CDT)
  • Re: AMBER: How to strip waters in trajectorie ? (Mon Jun 12 2006 - 15:06:19 CDT)
  • Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? (Sat Jun 10 2006 - 13:24:29 CDT)
  • Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? (Sat Jun 10 2006 - 12:06:49 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Fri Jun 09 2006 - 16:58:02 CDT)
  • Re: AMBER: charmm force field in amber9 (Fri Jun 09 2006 - 09:02:03 CDT)
  • Re: AMBER: save coordinates during SANDER minimisation (Thu Jun 08 2006 - 17:39:01 CDT)
  • Re: AMBER: software to visualize normal modes (Thu Jun 08 2006 - 12:46:38 CDT)
  • Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. (Wed Jun 07 2006 - 17:22:41 CDT)
  • Re: AMBER: compiler error for Amber9 (Wed Jun 07 2006 - 10:52:14 CDT)
  • Re: AMBER: Amber: Can't get sander to run (Tue Jun 06 2006 - 15:31:56 CDT)
  • Re: AMBER: individual torsion/bond energies from a minimization (Mon Jun 05 2006 - 09:21:40 CDT)
  • Re: AMBER: NMR restraint (Fri Jun 02 2006 - 19:28:16 CDT)
  • Re: AMBER: some questions and problems about antechamber and divcon (Fri Jun 02 2006 - 19:12:42 CDT)
  • Re: AMBER: trouble adding mdcrd files together (Fri Jun 02 2006 - 18:30:20 CDT)
  • Re: AMBER: Namelists in input files (Fri Jun 02 2006 - 15:48:42 CDT)
  • Re: AMBER: Installation of Amber8 on Fedora Core 5. . (Fri Jun 02 2006 - 14:27:59 CDT)
  • AMBER: bugfix for frcmod.ff03 in Amber 9 (Fri Jun 02 2006 - 11:45:29 CDT)
  • Re: AMBER: Different results for TI calculation (Thu Jun 01 2006 - 09:33:32 CDT)
  • Re: AMBER: Difference in results for TI calculation (Tue May 30 2006 - 13:01:49 CDT)
  • Re: AMBER: Pt containing complex: antechamber (Tue May 30 2006 - 12:39:20 CDT)
  • Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names (Tue May 30 2006 - 12:36:37 CDT)
  • Re: AMBER: Installing / Compiling Question (Sat May 27 2006 - 23:50:54 CDT)
  • Re: AMBER: Please reply (Fri May 26 2006 - 14:39:02 CDT)
  • Re: AMBER: use_pme=0 problem (Fri May 26 2006 - 14:30:01 CDT)
  • Re: AMBER: use_pme=0 problem (Fri May 26 2006 - 12:34:39 CDT)
  • Re: AMBER: different TI calculations starting from the same state (Fri May 26 2006 - 10:16:19 CDT)
  • Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) (Thu May 25 2006 - 15:33:33 CDT)
  • Re: AMBER: use_pme=0 problem (Thu May 25 2006 - 12:56:56 CDT)
  • Re: AMBER: use_pme=0 problem (Wed May 24 2006 - 19:33:53 CDT)
  • Re: AMBER: use_pme=0 problem (Wed May 24 2006 - 18:50:56 CDT)
  • Re: AMBER: problem with prepfile (Wed May 24 2006 - 15:56:08 CDT)
  • Re: AMBER: freeze interval vibrations (Wed May 24 2006 - 14:00:35 CDT)
  • Re: AMBER: amber8 bugfix effects (Wed May 24 2006 - 09:38:39 CDT)
  • Re: AMBER: error in AMBER 9.0 (Wed May 24 2006 - 00:19:47 CDT)
  • Re: AMBER: amber .off file format question (Tue May 23 2006 - 01:21:33 CDT)
  • Re: AMBER: Problems compiling amber9 (Mon May 22 2006 - 13:46:09 CDT)
  • Re: AMBER: problem loading forcefield leaprc.ff86 (Fri May 19 2006 - 10:45:33 CDT)
  • Re: AMBER: "The system has extended beyond" error message (Thu May 18 2006 - 07:38:58 CDT)
  • Re: AMBER: Correlation matrix used in quasih (Amber 7) (Thu May 18 2006 - 07:31:00 CDT)
  • Re: AMBER: vlimit exceeded (Thu May 18 2006 - 07:24:49 CDT)
  • Re: AMBER: distance dependent dielectric constant (Wed May 17 2006 - 06:59:41 CDT)
  • Re: AMBER: "atom number exceeds the MAXATOM" (Wed May 17 2006 - 06:53:58 CDT)
  • Re: AMBER: amber compilation on Red Hat 8 with MPICH (Wed May 17 2006 - 06:52:55 CDT)
  • Re: AMBER: fail to execute addles (Mon May 15 2006 - 11:46:28 CDT)
  • Re: AMBER: strange mm_pbsa output (Sat May 13 2006 - 17:44:14 CDT)
  • Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? (Fri May 12 2006 - 12:01:05 CDT)
  • Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? (Fri May 12 2006 - 10:39:37 CDT)
  • Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? (Thu May 11 2006 - 09:43:28 CDT)
  • Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why (Wed May 10 2006 - 15:12:52 CDT)
  • Re: AMBER: problem with prep file (Wed May 10 2006 - 11:12:59 CDT)
  • Re: AMBER: Hexahydrated Counterions (Wed May 10 2006 - 10:32:31 CDT)
  • Re: AMBER: bug in ambpdb (AMBER8) (Wed May 10 2006 - 10:10:08 CDT)
  • Re: AMBER: xleap not recognizing residue (Tue May 09 2006 - 17:42:14 CDT)
  • Re: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 (Tue May 09 2006 - 15:16:30 CDT)
  • Re: AMBER: Amber9 test error on SGI Altix (Mon May 08 2006 - 13:45:30 CDT)
  • Re: AMBER: Amber9 test error on SGI Altix (Mon May 08 2006 - 13:07:17 CDT)
  • Re: AMBER: xleap not recognizing residue (Sun May 07 2006 - 20:50:06 CDT)
  • Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system (Sun May 07 2006 - 09:27:56 CDT)
  • Re: AMBER: Problem with shared libraries: libimf.so (Sat May 06 2006 - 16:17:51 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 20:31:13 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 14:19:31 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 13:46:29 CDT)
  • Re: AMBER: molsurf.c error (Fri May 05 2006 - 12:34:32 CDT)
  • Re: AMBER: molsurf.c error (Thu May 04 2006 - 15:21:28 CDT)
  • Re: AMBER: amber9 serial compilation error (Thu May 04 2006 - 12:36:53 CDT)
  • Re: AMBER: Amber install on RedHat Linux (Thu May 04 2006 - 10:17:08 CDT)
  • Re: AMBER: Error while running test.serial in Amber9 (Thu May 04 2006 - 01:13:06 CDT)
  • Re: AMBER: Question bonds and angles in frcmod and lib files (Wed May 03 2006 - 10:23:12 CDT)
  • Re: AMBER: proper restart procedure? (Wed May 03 2006 - 10:18:43 CDT)
  • Re: AMBER: How does amber calculate HB? (Tue May 02 2006 - 01:20:31 CDT)
  • AMBER: some new tutorials (Mon May 01 2006 - 18:55:19 CDT)
  • Re: AMBER: internal coordinates (Mon May 01 2006 - 15:50:10 CDT)
  • Re: AMBER: Amber 9, sander imin = 5, -y flag (Sun Apr 30 2006 - 23:08:24 CDT)
  • Re: AMBER: Did these differences come from so-called "different machines" ? (Sun Apr 30 2006 - 23:09:35 CDT)
  • Re: AMBER: internal coordinates (Sun Apr 30 2006 - 11:09:52 CDT)
  • Re: AMBER: Setting box dimensions in leap (Sun Apr 30 2006 - 00:42:48 CDT)
  • Re: AMBER: Langevin mode error?? (Fri Apr 28 2006 - 15:13:31 CDT)
  • Re: AMBER: Antechamber & atom types (Fri Apr 21 2006 - 10:22:45 CDT)
  • Re: AMBER: Problems compiling amber9 (Fri Apr 21 2006 - 10:03:37 CDT)
  • Re: AMBER: Error when compiling amber9 ptraj (Fri Apr 21 2006 - 07:08:15 CDT)
  • Re: AMBER: RE: Respgen segemtation fault (Thu Apr 20 2006 - 06:49:34 CDT)
  • Re: AMBER: Installing Delphi to perform mm_pbsa analysis? (Wed Apr 19 2006 - 14:43:46 CDT)
  • Re: AMBER: Could not find atom type. (Wed Apr 19 2006 - 14:37:33 CDT)
  • Re: AMBER: Could not find atom type. (Tue Apr 18 2006 - 18:06:21 CDT)
  • Re: AMBER: probable bug in antechamber (Mon Apr 17 2006 - 19:33:35 CDT)
  • Re: AMBER: Could not find atom type. (Mon Apr 17 2006 - 11:40:05 CDT)
  • Re: AMBER: Calculation of g(r) from PTRAJ (Mon Apr 17 2006 - 11:45:27 CDT)
  • Re: AMBER: amber memory usage (Fri Apr 14 2006 - 19:30:44 CDT)
  • AMBER: How I wasted a rainy Friday in San Diego (Fri Apr 14 2006 - 19:24:00 CDT)
  • Re: AMBER: compile error: can't locate file for: -lcrt1.o (Fri Apr 14 2006 - 17:58:33 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 12:53:50 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 10:27:52 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Thu Apr 13 2006 - 16:41:03 CDT)
  • Re: AMBER: Respgen segemtation fault (Thu Apr 13 2006 - 13:46:55 CDT)
  • Re: AMBER: saltcon with explicit water? (Wed Apr 12 2006 - 14:25:38 CDT)
  • Re: AMBER: Nmode memory allocation error ? (Tue Apr 11 2006 - 14:09:26 CDT)
  • Re: AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 (Tue Apr 11 2006 - 13:19:59 CDT)
  • Re: AMBER: protocols for NMR protein refinement with AMBER (Mon Apr 10 2006 - 15:55:43 CDT)
  • Re: AMBER: mm-pbsa: distant-dependent dielectric constant (Sun Apr 09 2006 - 01:11:49 CDT)
  • Re: AMBER: mm-pbsa: distant-dependent dielectric constant (Sun Apr 09 2006 - 00:23:15 CDT)
  • Re: AMBER: Umbrella sampling (Fri Apr 07 2006 - 15:56:48 CDT)
  • Re: AMBER: POPC parameters (Fri Apr 07 2006 - 11:14:53 CDT)
  • Re: AMBER: Restarting constant pressure sims with restraints (Wed Apr 05 2006 - 13:24:38 CDT)
  • Re: AMBER: (Wed Apr 05 2006 - 09:46:18 CDT)
  • Re: AMBER: how to restrain the intramolecular hydrogen bond (Tue Apr 04 2006 - 17:52:52 CDT)
  • Re: AMBER: Entropy calculations with Nmode and ptraj (Tue Apr 04 2006 - 17:50:55 CDT)
  • AMBER: Using XML for Amber files (Tue Apr 04 2006 - 17:42:35 CDT)
  • Re: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? (Tue Apr 04 2006 - 17:11:51 CDT)
  • Re: AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! (Mon Apr 03 2006 - 09:57:36 CDT)
  • Re: AMBER: Announcement: Amber 9 is now available (Sat Apr 01 2006 - 11:21:52 CST)
  • Re: AMBER: what is the integration scheme for langevin dynamic used in amber8 (Sat Apr 01 2006 - 11:18:57 CST)
  • Re: AMBER: chirality.c error in xleap (Fri Mar 31 2006 - 19:41:53 CST)
  • Re: AMBER: Announcement: Amber 9 is now available (Fri Mar 31 2006 - 11:29:54 CST)
  • Re: AMBER: Announcement: Amber 9 is now available (Fri Mar 31 2006 - 10:56:48 CST)
  • Re: AMBER: Problem with setbox command... (Thu Mar 30 2006 - 10:06:04 CST)
  • Re: AMBER: hessian calculation (Wed Mar 29 2006 - 18:08:34 CST)
  • Re: AMBER: Impropers definition (Wed Mar 29 2006 - 11:10:27 CST)
  • AMBER: Announcement: Amber 9 is now available (Wed Mar 29 2006 - 10:43:59 CST)
  • Re: AMBER: hessian calculation (Tue Mar 28 2006 - 20:15:58 CST)
  • Re: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) (Tue Mar 28 2006 - 20:13:44 CST)
  • Re: AMBER: hessian calculation (Tue Mar 28 2006 - 17:52:14 CST)
  • Re: AMBER: anal: dihedral error (Sat Mar 25 2006 - 14:48:36 CST)
  • Re: AMBER: Related to RESTRAINT_WT (Wed Mar 22 2006 - 18:15:29 CST)
  • Re: AMBER: (Tue Mar 21 2006 - 00:36:09 CST)
  • Re: AMBER: a challenge: a periodic box that cuts through a monomer (Tue Mar 21 2006 - 00:29:33 CST)
  • Re: AMBER: Ewald and ibelly (Mon Mar 20 2006 - 00:26:17 CST)
  • Re: AMBER: NTT for production run (Thu Mar 16 2006 - 12:00:54 CST)
  • Re: AMBER: amber 8 install problem (Wed Mar 15 2006 - 16:00:08 CST)
  • Re: AMBER: amber 8 install problem (Wed Mar 15 2006 - 14:33:08 CST)
  • Re: AMBER: NTT for production run (Wed Mar 15 2006 - 14:21:52 CST)
  • Re: AMBER: Xleap 64 bit installation problem (Tue Mar 14 2006 - 20:06:30 CST)
  • Re: AMBER: NTT for production run (Tue Mar 14 2006 - 19:49:46 CST)
  • Re: AMBER: amber 8 install problem (Mon Mar 13 2006 - 12:44:40 CST)
  • Re: AMBER: (Mon Mar 13 2006 - 12:40:19 CST)
  • Re: AMBER: prepin format (Fri Mar 10 2006 - 00:49:22 CST)
  • Re: AMBER: Power Mac G5 (Thu Mar 09 2006 - 18:14:54 CST)
  • Re: AMBER: Cosine content calculation (Thu Mar 09 2006 - 10:33:53 CST)
  • Re: AMBER: Cosine content calculation (Wed Mar 08 2006 - 14:09:54 CST)
  • Re: AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed (Wed Mar 08 2006 - 10:46:55 CST)
  • Re: AMBER: NADP(H) parameters (Wed Mar 08 2006 - 10:26:04 CST)
  • Re: AMBER: converting .lib files (Wed Mar 08 2006 - 10:06:38 CST)
  • Re: AMBER: question about solvatecap commander (Tue Mar 07 2006 - 21:32:12 CST)
  • Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations (Tue Mar 07 2006 - 13:47:30 CST)
  • Re: AMBER: Amber 8 under Solaris 9 compilation failed (Tue Mar 07 2006 - 10:35:35 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Tue Mar 07 2006 - 10:23:21 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Tue Mar 07 2006 - 10:26:23 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Mon Mar 06 2006 - 20:05:31 CST)
  • Re: AMBER: How to patch the configure script (macosx) (Mon Mar 06 2006 - 12:25:16 CST)
  • Re: AMBER: Amber 9. (Fri Mar 03 2006 - 11:29:25 CST)
  • Re: AMBER: AMBER 8 VS AMBER 7 (Thu Mar 02 2006 - 14:42:39 CST)
  • Re: AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 12:07:05 CST)
  • Re: AMBER: N-H and C-H Residual Dipolar Coupling (Wed Mar 01 2006 - 16:38:09 CST)
  • Re: AMBER: Nmode vs QM Freq Calculation (Wed Mar 01 2006 - 12:54:12 CST)
  • Re: AMBER: Angle restraint (Tue Feb 28 2006 - 17:54:40 CST)
  • Re: AMBER: ptraj warning while loading reference (Mon Feb 27 2006 - 10:44:52 CST)
  • Re: AMBER: dynamic memory allocation problem in nmode (Sun Feb 26 2006 - 22:21:02 CST)
  • Re: AMBER: Constant pressure - restart - Amber8 (Fri Feb 24 2006 - 15:18:58 CST)
  • Re: AMBER: Constant pressure - restart - Amber8 (Fri Feb 24 2006 - 11:34:46 CST)
  • Re: AMBER: entropic energy (Fri Feb 24 2006 - 10:36:49 CST)
  • Re: AMBER: Ti calculations in dmso solvent (Thu Feb 23 2006 - 12:01:26 CST)
  • Re: AMBER: NMR restraints and LES (Mon Feb 20 2006 - 20:26:17 CST)
  • Re: AMBER: amber 8 problem (Mon Feb 20 2006 - 10:33:01 CST)
  • Re: AMBER: charge redistribution in .prep files (Mon Feb 20 2006 - 10:29:41 CST)
  • Re: AMBER: m4 error with Amber8 on SUN (Wed Feb 15 2006 - 17:56:06 CST)
  • Re: AMBER: negative T_solv values (Wed Feb 15 2006 - 10:18:25 CST)
  • Re: AMBER: Istallation AMBER8 (Wed Feb 15 2006 - 00:57:13 CST)
  • Re: AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 (Wed Feb 15 2006 - 00:12:42 CST)
  • Re: AMBER: 2D-topology (Tue Feb 14 2006 - 15:57:45 CST)
  • Re: AMBER: Xleap crash (Tue Feb 14 2006 - 13:51:53 CST)
  • Re: AMBER: Xleap crash (Tue Feb 14 2006 - 11:36:21 CST)
  • Re: AMBER: paralelization and sander problems (Tue Feb 14 2006 - 10:32:59 CST)
  • Re: AMBER: Problem in running umbrella sampling (Sun Feb 12 2006 - 23:11:48 CST)
  • Re: AMBER: Distortion in parallelploied (Fri Feb 10 2006 - 11:04:13 CST)
  • Re: AMBER: non bond list overflow (Tue Feb 07 2006 - 13:00:54 CST)
  • Re: AMBER: Hessian matrix (Tue Feb 07 2006 - 10:40:37 CST)
  • Re: AMBER: non bond list overflow (Tue Feb 07 2006 - 00:37:59 CST)
  • Re: AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 17:37:56 CST)
  • Re: AMBER: Strange minimization output problem (Sat Feb 04 2006 - 14:20:17 CST)
  • Re: AMBER: bugfix for impropers in parmchk (Sat Feb 04 2006 - 12:50:15 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Fri Feb 03 2006 - 18:31:32 CST)
  • Re: AMBER: Values of Spring Constants (Fri Feb 03 2006 - 17:51:22 CST)
  • Re: AMBER: (Fri Feb 03 2006 - 17:46:28 CST)
  • Re: AMBER: positional restraints & constant pressure (Fri Feb 03 2006 - 10:40:53 CST)
  • Re: AMBER: MD of oligomer sequences (Thu Feb 02 2006 - 20:08:42 CST)
  • Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster (Thu Feb 02 2006 - 19:49:39 CST)
  • Re: AMBER: Amber8 parallel compilation problems on EM64T system (Thu Feb 02 2006 - 14:28:27 CST)
  • Re: AMBER: MM-PBSA (Thu Feb 02 2006 - 13:00:23 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Wed Feb 01 2006 - 18:05:58 CST)
  • Re: AMBER: basic minimize question (Wed Feb 01 2006 - 18:09:11 CST)
  • Re: AMBER: Values of Spring Constants (Wed Feb 01 2006 - 10:38:13 CST)
  • Re: AMBER: lifetimes (Wed Feb 01 2006 - 10:20:56 CST)
  • Re: AMBER: anal vs sander (Fri Jan 27 2006 - 17:28:51 CST)
  • Re: AMBER: About the unit of the projection onto eigenvectors (Fri Jan 27 2006 - 16:20:17 CST)
  • Re: AMBER: atom type "O3" not recognized by XLeap (Fri Jan 27 2006 - 16:01:43 CST)
  • Re: AMBER: anal vs sander (Fri Jan 27 2006 - 15:33:57 CST)
  • Re: AMBER: Charges from NMR spin densities (Fri Jan 27 2006 - 10:57:32 CST)
  • Re: AMBER: AMBER 7 and restrained bonds. (Thu Jan 26 2006 - 10:26:42 CST)
  • Re: AMBER: AMBER 8.0 : Octane Implicit Solvent? (Tue Jan 24 2006 - 13:09:32 CST)
  • Re: AMBER: bugfix for impropers in parmchk (Wed Jan 18 2006 - 20:04:36 CST)
  • Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 12:52:51 CST)
  • Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 10:30:51 CST)
  • Re: AMBER: problem in saving parameter file for non-standard residue (Mon Jan 16 2006 - 13:44:22 CST)
  • Re: AMBER: heme improper torsions (Mon Jan 16 2006 - 10:46:47 CST)
  • Re: AMBER: Problem in Antechamber (Thu Jan 12 2006 - 19:40:50 CST)
  • Re: AMBER: Na+ with GB/SA? (Thu Jan 12 2006 - 16:24:17 CST)
  • Re: AMBER: amber atom type -> length of name (Thu Jan 12 2006 - 01:59:48 CST)
  • Re: AMBER: regarding Hydrogen bond analysis (Tue Jan 10 2006 - 02:45:50 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 16:59:46 CST)
  • Re: AMBER: parameters for C=S (Mon Jan 09 2006 - 17:04:52 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Fri Jan 06 2006 - 19:26:55 CST)
  • Re: AMBER: minimalization prior to nmode analysis, is it necessary? (Thu Jan 05 2006 - 19:56:26 CST)
  • Re: AMBER: requirement of delphi for mm_pbsa (Wed Jan 04 2006 - 10:22:53 CST)
• David Case
  • Re: AMBER: OSX 10.4 G4 xlf90 compilation errors (Mon Mar 27 2006 - 14:18:27 CST)
  • Re: AMBER: simulated annealing run--temp won't rise (Fri Feb 03 2006 - 00:46:00 CST)
  • AMBER: Re: Force Decomposition for MTS in AMBER 8. (Fri Feb 03 2006 - 00:34:23 CST)
  • Re: AMBER: Cannot successfully assign bond type for this molecule? (Wed Feb 01 2006 - 15:49:55 CST)
  • Re: AMBER: antechamber (Thu Jan 26 2006 - 17:48:55 CST)
• David E. Konerding
  • Re: AMBER: Curves and Average Structures (Mon Jun 26 2006 - 14:42:05 CDT)
  • Re: AMBER: Announcement: Amber 9 is now available (Fri Mar 31 2006 - 10:38:06 CST)
• David LeBard
  • Re: AMBER: Two different HIS ligands (Thu Oct 26 2006 - 18:16:42 CDT)
  • AMBER: Two different HIS ligands (Thu Oct 26 2006 - 16:16:09 CDT)
  • AMBER: Multiple Timestep MD (Wed Sep 27 2006 - 20:03:35 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 16:01:16 CDT)
  • Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Mon Jul 03 2006 - 13:15:50 CDT)
  • Re: AMBER: AMD 64 Installation / configuration clarification (Thu Jun 08 2006 - 18:52:57 CDT)
  • Re: AMBER: AMD 64 Installation / configuration clarification (Thu Jun 08 2006 - 14:57:18 CDT)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 14:10:29 CST)
  • Re: AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 17:23:16 CST)
  • AMBER: Charges from NMR spin densities (Thu Jan 26 2006 - 17:33:50 CST)
• David Mathews
  • Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU (Sun Jan 01 2006 - 17:29:40 CST)
  • Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU (Sun Jan 01 2006 - 17:08:17 CST)
• David McGiven
  • Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test (Wed Jun 21 2006 - 10:54:44 CDT)
  • AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test (Wed Jun 21 2006 - 05:46:40 CDT)
• David Mobley
  • Re: AMBER: single or dual topology for TI? (Sat Oct 21 2006 - 15:58:41 CDT)
  • Re: AMBER: single or dual topology for TI? (Sat Oct 21 2006 - 14:17:50 CDT)
  • Re: AMBER: charge models in antechamber (Thu Oct 19 2006 - 12:48:14 CDT)
  • Re: AMBER: WHAT IF CHeck after MD (Thu Sep 28 2006 - 17:58:32 CDT)
  • AMBER: question on Lennard-Jones fitting in FF94 and 96 (Mon Sep 25 2006 - 12:07:45 CDT)
  • Re: AMBER: TI-FEP : strange result for different clambda values (Fri Sep 22 2006 - 11:38:19 CDT)
  • Re: AMBER: antechamber charge calculation very sensitive to conformations ? (Fri Aug 25 2006 - 10:08:44 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 15:07:57 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Mon Aug 21 2006 - 09:20:42 CDT)
  • AMBER: Re: antechamber failure on FMN (Fri Aug 18 2006 - 13:46:58 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Fri Aug 18 2006 - 11:13:08 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Wed Aug 16 2006 - 16:51:47 CDT)
  • Re: AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 13:16:47 CDT)
  • AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 13:04:42 CDT)
  • Re: AMBER: how to reassign charges (Wed Aug 09 2006 - 15:03:10 CDT)
  • AMBER: antechamber bond typing questions (Mon Aug 07 2006 - 15:14:42 CDT)
  • Re: AMBER: For different ligand conformation (Mon Jul 31 2006 - 17:29:40 CDT)
  • Re: AMBER: program to calculate net charge of a ligand for Antechamber (Mon Jul 10 2006 - 23:18:36 CDT)
  • Re: AMBER: 2-D free energy surface using WHAM (Mon Jul 03 2006 - 09:33:24 CDT)
  • AMBER: manual/prmtop/missing bonds section (Mon Jun 26 2006 - 15:27:39 CDT)
  • AMBER: antechamber and FMN (Tue Jun 06 2006 - 12:47:03 CDT)
  • Re: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 (Fri May 12 2006 - 12:22:41 CDT)
  • Re: AMBER: probable bug in antechamber (Tue Apr 18 2006 - 08:52:13 CDT)
  • AMBER: probable bug in antechamber (Mon Apr 17 2006 - 18:08:06 CDT)
  • Re: AMBER: How to evaluate the binding energy of a ligand? (Tue Apr 11 2006 - 14:27:13 CDT)
  • Re: AMBER: Any difference about RESP or ESP with Chelpg or MK (Tue Apr 04 2006 - 17:13:30 CDT)
  • Re: AMBER: Ti calculations in dmso solvent (Thu Feb 23 2006 - 14:06:43 CST)
  • Re: AMBER: Ti calculations in dmso solvent (Thu Feb 23 2006 - 10:58:17 CST)
  • Re: AMBER: soft-core potential in amber? (Tue Feb 07 2006 - 08:54:33 CST)
  • Re: AMBER: (Sat Feb 04 2006 - 12:06:23 CST)
  • Re: AMBER: bugfix for impropers in parmchk (Fri Jan 20 2006 - 12:23:39 CST)
  • Re: AMBER: bugfix for impropers in parmchk (Fri Jan 20 2006 - 12:21:49 CST)
  • Re: AMBER: Ligand charge (Wed Jan 04 2006 - 13:43:54 CST)
• DAVID P. RANGEL
  • AMBER: Installation of Amber8 on Fedora Core 5 (Wed May 31 2006 - 17:48:11 CDT)
• David Smith
  • AMBER: imaging issue (Sun Oct 29 2006 - 10:26:07 CST)
• dhruva chakravorty
  • AMBER: generating resp input files with antechamber (Thu Oct 05 2006 - 14:53:03 CDT)
• Dmitry Osolodkin
  • AMBER: leap: syntax error when use source command (Wed Mar 01 2006 - 06:27:47 CST)
• Don Harden
  • Re: AMBER: Problems compiling amber9 (Tue May 23 2006 - 14:45:02 CDT)
  • Re: AMBER: Problems compiling amber9 (Mon May 22 2006 - 12:10:15 CDT)
• Don.Bashford_at_stjude.org
  • Re: AMBER: How to set Bondi Radii using xleap. . (Tue Aug 01 2006 - 12:23:51 CDT)
  • Re: AMBER: Installation of Amber8 on Fedora Core 5. . (Thu Jun 01 2006 - 11:23:11 CDT)
  • AMBER: Restarting constant pressure sims with restraints (Wed Apr 05 2006 - 13:08:41 CDT)
• Douali, Latifa
  • AMBER: software to visualize normal modes (Thu Jun 08 2006 - 12:03:26 CDT)
  • RE: AMBER: xmgr error (Fri May 19 2006 - 12:07:01 CDT)
  • RE: AMBER: force field parameters (Thu May 18 2006 - 13:40:53 CDT)
  • AMBER: force field parameters (Thu May 18 2006 - 12:33:35 CDT)
  • AMBER: MM-PBSA (Wed Jan 25 2006 - 17:03:06 CST)
  • AMBER: base-base interaction (Fri Jan 13 2006 - 11:54:32 CST)
• Dr.Rudolf Friedemann
  • AMBER: Istallation AMBER8 (Tue Feb 14 2006 - 04:41:39 CST)
• Dror
  • AMBER: (Wed Mar 08 2006 - 04:09:28 CST)
  • AMBER: Amber 8 under Solaris 9 compilation failed (Tue Mar 07 2006 - 01:03:03 CST)
  • AMBER: Amber 8 under Solaris 9 compilation failed (Tue Mar 07 2006 - 01:12:19 CST)
• Ed Pate
  • AMBER: problems trying to modify Amber8 (Thu Dec 28 2006 - 16:41:33 CST)
  • AMBER: amber 9 installation problem (Wed Dec 13 2006 - 18:34:19 CST)
  • AMBER: parameter definitions (Wed Dec 06 2006 - 12:27:15 CST)
  • AMBER: pmemd installation problem (Fri Nov 03 2006 - 12:51:36 CST)
  • AMBER: coordinate files (Tue Sep 19 2006 - 15:17:26 CDT)
  • AMBER: Gaussian, antechamber, RESP (Sat Sep 02 2006 - 16:42:11 CDT)
  • AMBER: timing estimates (Wed Apr 19 2006 - 18:10:30 CDT)
  • AMBER: amber memory usage (Fri Apr 14 2006 - 17:45:59 CDT)
• egorov
  • AMBER: Impropers definition (Wed Mar 29 2006 - 00:06:40 CST)
• Einar Uggerud
  • AMBER: protonated phosphate (Tue Nov 28 2006 - 01:11:46 CST)
• Elijah Gregory
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 14:33:50 CST)
  • Re: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 18:17:14 CDT)
  • Re: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 18:12:35 CDT)
  • Re: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 16:39:08 CDT)
  • AMBER: General Coding Problem (Mon Oct 16 2006 - 18:53:27 CDT)
• Emilia Sikorska
  • AMBER: chemical shift restrains (Tue Sep 26 2006 - 13:22:05 CDT)
• emilia wu
  • AMBER: optimatized structure is so much different from the original pdb structure (Thu Nov 16 2006 - 23:38:18 CST)
  • AMBER: (Mon Mar 20 2006 - 06:38:17 CST)
• Emilio Xavier Esposito
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 11:13:40 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 11:08:34 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 08:40:39 CDT)
• Eric Hu
  • AMBER: charge models in antechamber (Wed Oct 18 2006 - 17:51:00 CDT)
  • Re: AMBER: generalized born model for organic solvent (Thu Oct 12 2006 - 18:32:16 CDT)
  • Re: AMBER: generalized born model for organic solvent (Thu Oct 12 2006 - 12:47:44 CDT)
  • Re: AMBER: generalized born model for organic solvent (Wed Oct 11 2006 - 18:37:01 CDT)
  • AMBER: generalized born model for organic solvent (Tue Oct 10 2006 - 20:29:12 CDT)
  • AMBER: how to limit the simulation space (Mon Aug 28 2006 - 19:55:11 CDT)
  • Re: AMBER: transition state (Mon Aug 21 2006 - 19:06:22 CDT)
  • Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 16:30:04 CDT)
  • Re: AMBER: transition state (Wed Aug 09 2006 - 14:05:14 CDT)
  • AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 13:06:30 CDT)
  • Re: AMBER: simulate a self-assemble process in vacuum (Thu Jul 20 2006 - 16:43:35 CDT)
  • AMBER: simulate a self-assemble process in vacuum (Wed Jul 12 2006 - 18:22:58 CDT)
  • AMBER: general question about hydrogen bond energy vs electrostatic energy (Thu Jun 29 2006 - 19:58:24 CDT)
  • AMBER: repeat use of a trimer lib file (Thu Jun 15 2006 - 18:35:39 CDT)
  • AMBER: freeze interval vibrations (Wed May 24 2006 - 12:52:47 CDT)
• Eric Shamay
  • Re: AMBER: acidifying a water box (Fri Sep 15 2006 - 03:49:15 CDT)
  • AMBER: acidifying a water box (Thu Sep 14 2006 - 13:36:11 CDT)
• eric.henon_at_univ-reims.fr
  • Re: AMBER: TI, mutation (Tue Aug 29 2006 - 03:43:04 CDT)
  • AMBER: TI, mutation (Mon Aug 28 2006 - 07:39:48 CDT)
• Esther Brugger
  • AMBER: Sander--NMR refinement (Thu Dec 21 2006 - 22:39:48 CST)
  • AMBER: RDF problem (Tue Dec 12 2006 - 13:45:14 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 19:00:48 CST)
  • AMBER: dihedral angle problem (Fri Dec 08 2006 - 16:53:32 CST)
  • AMBER: dihedral calculation problem (Fri Dec 01 2006 - 15:39:23 CST)
  • Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 13:01:25 CST)
  • AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 10:22:44 CST)
  • AMBER: H-bond analysis (Ptraj) (Thu Nov 30 2006 - 19:28:10 CST)
  • Re: AMBER: watershell and image commands (Thu Nov 30 2006 - 18:04:04 CST)
  • AMBER: watershell command (Thu Nov 30 2006 - 17:16:52 CST)
  • AMBER: watershell and image commands (Thu Nov 30 2006 - 16:37:58 CST)
  • AMBER: ptraj----radial output files (Wed Nov 29 2006 - 14:03:20 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 13:10:20 CST)
  • AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 10:59:29 CST)
  • Re: AMBER: Compile AMBER 8 (Mon Oct 30 2006 - 12:14:05 CST)
  • Re: AMBER: Compile AMBER 8 (Mon Oct 30 2006 - 11:24:59 CST)
  • Re: AMBER: Compile AMBER 8 (Mon Oct 30 2006 - 09:28:08 CST)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 15:18:00 CDT)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 13:21:13 CDT)
  • AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 10:44:51 CDT)
• Evan Kelly
  • AMBER: QM/MD energy conservation (Mon Dec 11 2006 - 21:17:59 CST)
  • AMBER: Please DISREGARD previous message (restraint=0.0000) (Thu Aug 03 2006 - 12:57:46 CDT)
  • AMBER: restraint=0.0000 during minimization? (Thu Aug 03 2006 - 12:48:17 CDT)
  • AMBER: PDB from .rst? (Thu Jul 20 2006 - 15:51:09 CDT)
  • Re: AMBER: igb=2 and "bad atom type" conflict (Thu Jul 06 2006 - 17:01:39 CDT)
  • Re: AMBER: igb=2 and "bad atom type" conflict (Thu Jul 06 2006 - 11:21:06 CDT)
  • Re: AMBER: igb=2 and "bad atom type" conflict (Thu Jul 06 2006 - 10:45:10 CDT)
  • AMBER: Addendum: igb=2 and "bad atom type" conflict (Wed Jul 05 2006 - 14:29:10 CDT)
  • AMBER: igb=2 and "bad atom type" conflict (Wed Jul 05 2006 - 14:25:16 CDT)
  • Re: AMBER: parmchk error (Tue Jun 13 2006 - 00:42:16 CDT)
  • AMBER: parmchk error (Sat Jun 10 2006 - 22:30:11 CDT)
  • AMBER: compile error with pgf90 (Fri Jun 02 2006 - 00:33:21 CDT)
  • AMBER: xleap on iMac G5 (Fri May 05 2006 - 23:01:53 CDT)
  • AMBER: Fujitsu frt compiler (Fri Apr 21 2006 - 09:53:40 CDT)
  • AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? (Mon Apr 03 2006 - 17:28:27 CDT)
• f m
  • Re: AMBER: Ring of dna (Tue Jul 18 2006 - 09:30:03 CDT)
  • Re: AMBER: Ring of dna (Mon Jul 17 2006 - 08:48:33 CDT)
  • Re: AMBER: Ring of dna (Mon Jul 17 2006 - 06:32:01 CDT)
  • Re: AMBER: Ring of dna (Sat Jul 15 2006 - 11:37:59 CDT)
  • Re: AMBER: Ring of dna (Fri Jul 14 2006 - 08:27:03 CDT)
  • Re: AMBER: Ringof dna (Thu Jul 13 2006 - 12:00:48 CDT)
• Fabian Alejandro Rodriguez
  • Re: AMBER: Using modified NA bases (Mon Oct 23 2006 - 18:17:41 CDT)
  • AMBER: partial charges (Tue Oct 10 2006 - 11:35:53 CDT)
  • Re: AMBER: change mdcrd file to pdb file (Sun Sep 17 2006 - 11:04:22 CDT)
  • AMBER: improper torsion angle problem (Wed Sep 06 2006 - 16:52:40 CDT)
• Fabian Boes
  • Re: AMBER: amber 9 intel 9.1 ia64 (Tue Aug 15 2006 - 08:59:39 CDT)
  • AMBER: AMBER9 netcdf trajectory with VMD 1.8.4 (Mon Jul 24 2006 - 03:01:46 CDT)
  • AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jul 06 2006 - 03:29:35 CDT)
  • Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jun 29 2006 - 12:53:23 CDT)
  • AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jun 29 2006 - 10:58:26 CDT)
  • Re: AMBER: analysing water behavior during MD (Fri Jan 13 2006 - 10:22:01 CST)
• Fabiana Caporuscio
  • AMBER: kclust (Wed Sep 27 2006 - 03:32:51 CDT)
• Fabien Cailliez
  • AMBER: switching function for electrostatic interactions (Mon Jun 12 2006 - 06:38:22 CDT)
  • AMBER: AMBER force field with namd (Wed Feb 22 2006 - 11:54:23 CST)
• Fabián Alejandro Rodríguez
  • Re: AMBER: from traj to crd (Tue Aug 01 2006 - 10:41:22 CDT)
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 06:39:19 CDT)
  • AMBER: from traj to crd (Mon Jul 31 2006 - 19:58:19 CDT)
• Feng X Zhou
  • Re: AMBER: RMSD: is it related to flexibility? (Fri Oct 06 2006 - 11:28:36 CDT)
  • AMBER: Advice on linux cluster sought (Mon Aug 14 2006 - 13:34:16 CDT)
  • Re: AMBER: Using XML for Amber files (Tue Apr 25 2006 - 10:07:39 CDT)
  • Re: AMBER: Using XML for Amber files (Fri Apr 07 2006 - 13:54:59 CDT)
  • RE: AMBER: Using XML for Amber files (Wed Apr 05 2006 - 10:21:35 CDT)
  • Re: AMBER: Announcement: Amber 9 is now available (Mon Apr 03 2006 - 10:28:48 CDT)
  • RE: AMBER: Problem with file size of sander outputs (Thu Feb 23 2006 - 11:42:22 CST)
• Fenghui Fan
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 00:25:41 CST)
  • Re: AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 22:19:41 CST)
  • Re: AMBER: bad connectivity (Tue Dec 26 2006 - 11:33:57 CST)
  • Re: AMBER: .crd file (Tue Dec 26 2006 - 10:17:33 CST)
  • Re: AMBER: LEaP problem (Tue Dec 12 2006 - 00:32:06 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 19:56:02 CST)
  • Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 20:51:41 CST)
  • Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 20:49:09 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 18:47:32 CST)
  • Re: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 13:56:06 CST)
  • Re: AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:47:19 CST)
  • Re: AMBER: prepin file nan (Tue Nov 28 2006 - 08:48:33 CST)
  • AMBER: prepin file nan (Mon Nov 27 2006 - 21:28:16 CST)
  • AMBER: bond information (Sun Nov 26 2006 - 22:10:42 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 18:42:09 CST)
  • AMBER: ZN prepin (Sun Nov 26 2006 - 16:29:31 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 11:12:01 CST)
  • AMBER: how to get complete prepin file (Sat Nov 25 2006 - 23:02:20 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 21:15:53 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 19:49:58 CST)
  • AMBER: respin file (Sat Nov 25 2006 - 16:23:46 CST)
  • AMBER: resp (Sat Nov 25 2006 - 15:03:00 CST)
  • AMBER: respin file (Sat Nov 25 2006 - 01:06:49 CST)
  • AMBER: bondtype problem (Fri Nov 24 2006 - 18:22:23 CST)
  • AMBER: Antechamber and gaussian questions (Fri Nov 24 2006 - 16:04:40 CST)
  • Re: AMBER: ammonia parameters (Thu Nov 23 2006 - 09:40:05 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:10:21 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 09:06:53 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 07:57:10 CST)
  • Re: AMBER: GLYCAM and ff98 atom-types (Thu Nov 16 2006 - 13:16:34 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 13:22:59 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Tue Nov 14 2006 - 11:40:13 CST)
  • AMBER: The plc.frcmod file in the old version tutorial (Sun Nov 12 2006 - 20:50:29 CST)
  • AMBER: ZN-CYS prepin and frcmd file (Sun Nov 12 2006 - 20:16:37 CST)
  • AMBER: bond command between Zn and a CYM residue in one chain of a protein complex (Fri Nov 10 2006 - 23:25:01 CST)
  • Re: AMBER: antechamber:tutorial (Thu Nov 09 2006 - 13:10:17 CST)
  • Re: AMBER: Building Library (Thu Nov 09 2006 - 12:21:57 CST)
  • Re: AMBER: building a box (Tue Nov 07 2006 - 11:49:54 CST)
  • AMBER: Zn metal library (Sun Nov 05 2006 - 21:51:19 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 18:22:26 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 14:13:57 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 12:30:27 CST)
  • AMBER: trajout script (Sun Nov 05 2006 - 10:23:57 CST)
  • RE: AMBER: Amber: disufide bond (Sun Nov 05 2006 - 08:02:48 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Sun Nov 05 2006 - 00:31:25 CST)
  • AMBER: Amber: disufide bond (Sat Nov 04 2006 - 22:29:57 CST)
  • RE: AMBER: How do we simulate deletion mutations (Wed Oct 25 2006 - 17:43:49 CDT)
  • AMBER: Phosphorylated protein MD simulation (Wed Oct 25 2006 - 16:16:50 CDT)
  • Re: AMBER: error estimate for free energy perturbation calculation (Wed Oct 25 2006 - 15:34:42 CDT)
  • Re: AMBER: How do we simulate deletion mutations (Wed Oct 25 2006 - 15:13:20 CDT)
  • Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? (Sun Oct 15 2006 - 23:36:25 CDT)
  • AMBER: Re: atom nomination in the PDB file produced by Amber (Wed Oct 04 2006 - 10:41:11 CDT)
  • AMBER: atom nomination in the PDB file produced by Amber (Wed Oct 04 2006 - 10:37:45 CDT)
  • AMBER: on rst file (Wed Oct 04 2006 - 09:02:40 CDT)
  • AMBER: Distance between 2 atoms (Wed Oct 04 2006 - 08:52:16 CDT)
  • Re: AMBER: Re: Distance between two atoms (Wed Oct 04 2006 - 01:41:27 CDT)
  • AMBER: Re: Distance between two atoms (Wed Oct 04 2006 - 01:12:06 CDT)
  • AMBER: Distance between two atoms (Tue Oct 03 2006 - 18:59:17 CDT)
  • Re: AMBER: mdcrd file (Mon Oct 02 2006 - 21:17:12 CDT)
  • AMBER: mdcrd file (Mon Oct 02 2006 - 19:09:37 CDT)
  • AMBER: Pressure in MD (Mon Oct 02 2006 - 15:55:16 CDT)
  • Re: AMBER: Electrostatic Energy Constant (Fri Sep 29 2006 - 14:23:03 CDT)
  • AMBER: WHAT IF CHeck after MD (Thu Sep 28 2006 - 17:06:04 CDT)
  • Re: AMBER: running sander on several nodes (Thu Sep 28 2006 - 12:21:26 CDT)
  • AMBER: running sander on several nodes (Thu Sep 28 2006 - 11:45:34 CDT)
  • AMBER: WHATIF Check after MD (Wed Sep 27 2006 - 21:24:39 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 14:44:08 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 12:49:53 CDT)
  • AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 10:14:23 CDT)
  • AMBER: structure from MD (Tue Sep 26 2006 - 11:42:14 CDT)
  • AMBER: from ADP-small protein complex to GTP-protein complex (Mon Sep 25 2006 - 23:00:53 CDT)
  • AMBER: the RMSD of MD (Sun Sep 24 2006 - 12:07:56 CDT)
  • AMBER: one question on MD (Sat Sep 23 2006 - 20:03:11 CDT)
  • Re: AMBER: parameters for Nickel and iron (Mon Sep 18 2006 - 21:45:24 CDT)
  • Re: [UCE]Re: RE: AMBER: potential energy (Mon Sep 18 2006 - 21:41:09 CDT)
  • AMBER: potential energy (Sun Sep 17 2006 - 19:38:44 CDT)
  • Re: AMBER: change mdcrd file to pdb file (Sun Sep 17 2006 - 10:30:02 CDT)
  • AMBER: change mdcrd file to pdb file (Sun Sep 17 2006 - 00:02:54 CDT)
  • AMBER: distance between two atoms (Fri Sep 15 2006 - 15:49:11 CDT)
  • Re: AMBER: cyclic AMP off and frcmod files? (Fri Sep 15 2006 - 08:44:49 CDT)
  • AMBER: on the rst file of the current ruuning (Thu Sep 14 2006 - 22:33:50 CDT)
  • AMBER: Denaturing MD (Thu Sep 14 2006 - 17:58:35 CDT)
  • AMBER: potential energy in the MD result (Thu Sep 14 2006 - 09:39:12 CDT)
  • AMBER: MD on protein-ligand interaction (Thu Sep 14 2006 - 09:04:20 CDT)
  • AMBER: the time length of the restricted MD (Wed Sep 13 2006 - 14:38:59 CDT)
  • AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 (Wed Sep 13 2006 - 09:23:33 CDT)
  • AMBER: about ligand charge (Tue Sep 12 2006 - 22:16:27 CDT)
  • AMBER: cAMP ligand charge (Mon Sep 11 2006 - 10:06:40 CDT)
  • AMBER: How to get the ligand. ac file (Mon Sep 11 2006 - 09:46:54 CDT)
  • AMBER: resp (Sat Sep 09 2006 - 20:03:06 CDT)
  • AMBER: resp (Sat Sep 09 2006 - 20:07:48 CDT)
  • AMBER: protein-ligand interaction (Sat Sep 09 2006 - 11:59:51 CDT)
  • Re: AMBER: a ligand file (Fri Sep 08 2006 - 22:06:49 CDT)
  • AMBER: a ligand file (Fri Sep 08 2006 - 20:31:59 CDT)
  • Re: AMBER: a ligand file (Wed Sep 06 2006 - 16:16:58 CDT)
  • AMBER: a ligand file (Tue Sep 05 2006 - 15:18:51 CDT)
  • Re: AMBER: Implicit Water - Force field parameters (Tue Sep 05 2006 - 15:16:37 CDT)
  • AMBER: cAMP ligand file (Mon Sep 04 2006 - 15:00:47 CDT)
  • AMBER: ligand file (Mon Sep 04 2006 - 13:20:27 CDT)
• ferranna_at_unimo.it
  • AMBER: SURFTEN/SURFOFF values in amber9 (Sat Oct 14 2006 - 02:27:42 CDT)
• fine wu
  • Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly... (Thu Jul 20 2006 - 10:55:55 CDT)
  • AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE (Fri Mar 31 2006 - 16:09:36 CST)
• Flora Mactavish
  • AMBER: Ringof dna (Thu Jul 13 2006 - 08:14:22 CDT)
• Florian Haberl
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 07:11:44 CDT)
• Franck Vendeix
  • Re: AMBER: R.E.D II (Wed Jul 05 2006 - 09:56:24 CDT)
• Franck_Vendeix_at_ncsu.edu
  • Re: AMBER: Using modified NA bases (Tue Oct 24 2006 - 08:03:36 CDT)
  • Re: AMBER: Amber parallel version (Thu Sep 07 2006 - 13:45:47 CDT)
  • AMBER: Amber parallel version (Wed Sep 06 2006 - 01:05:20 CDT)
  • Re: AMBER: Amber9: Free Energy (Sun Sep 03 2006 - 21:27:13 CDT)
  • AMBER: Amber9: Free Energy (Sun Sep 03 2006 - 18:11:44 CDT)
  • Re: AMBER: help with leap (Thu Aug 17 2006 - 09:46:07 CDT)
  • Re: AMBER: R.E.D II (Tue Jul 04 2006 - 23:33:21 CDT)
  • Re: AMBER: R.E.D II (Tue Jul 04 2006 - 09:29:59 CDT)
  • Re: AMBER: R.E.D II (Tue Jul 04 2006 - 01:23:22 CDT)
  • AMBER: R.E.D II (Sun Jul 02 2006 - 21:11:39 CDT)
• Fren T
  • AMBER: monosaccharide residues (Tue Jan 24 2006 - 16:20:03 CST)
• frustrated modeller
  • AMBER: Fwd: difficulties with antechamber: tests dont even run (Wed Jul 19 2006 - 18:30:07 CDT)
  • AMBER: difficulties with antechamber: tests dont even run (Wed Jul 19 2006 - 18:06:36 CDT)
  • Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Wed Jul 05 2006 - 19:29:52 CDT)
  • Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Mon Jul 03 2006 - 13:40:50 CDT)
  • AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux (Mon Jul 03 2006 - 12:51:13 CDT)
• FyD
  • AMBER: Problem with LEaP (Fri Dec 22 2006 - 13:42:13 CST)
  • Re: AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 04:23:09 CST)
  • Re: AMBER: RED - help with installation / config (Thu Dec 21 2006 - 03:24:50 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Wed Dec 20 2006 - 01:21:42 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Tue Dec 19 2006 - 01:44:05 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 00:22:36 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Fri Dec 15 2006 - 02:21:21 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 06:57:56 CST)
  • Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 11:17:54 CST)
  • Re: AMBER: Charge fitting in Amber (Wed Nov 29 2006 - 01:16:38 CST)
  • Re: AMBER: RE: Amber: ZN-complex file (Wed Nov 29 2006 - 01:21:19 CST)
  • Re: AMBER: Ethanol (Wed Nov 22 2006 - 06:22:28 CST)
  • Re: AMBER: Ethanol (Fri Nov 17 2006 - 08:19:15 CST)
  • Re: AMBER: RESP charge fitting (Sat Oct 28 2006 - 01:37:59 CDT)
  • Re: AMBER: Using modified NA bases (Tue Oct 24 2006 - 13:14:54 CDT)
  • Re: AMBER: RESP charges of iron-porphyrin system (Fri Oct 20 2006 - 00:23:14 CDT)
  • Re: AMBER: AMBER minimization vs. Gaussian optimization (Thu Oct 05 2006 - 00:14:07 CDT)
  • Re: AMBER: WHATIF Check after MD (Wed Sep 27 2006 - 23:06:30 CDT)
  • Re: AMBER: resp (Sun Sep 10 2006 - 02:46:11 CDT)
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Mon Aug 21 2006 - 07:28:49 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Sat Aug 12 2006 - 14:09:29 CDT)
  • Re: AMBER: neutral N-terminal amino-acid parameters for ff03 (Sat Aug 05 2006 - 03:16:23 CDT)
  • Re: AMBER: library for 8oxoguanine (Tue Jul 25 2006 - 07:39:27 CDT)
  • Re: AMBER: PhosphoThreonine Parms for use with ff03 (Tue Jul 18 2006 - 02:57:24 CDT)
  • Re: AMBER: R.E.D II (Wed Jul 05 2006 - 01:55:13 CDT)
  • Re: AMBER: R.E.D II (Tue Jul 04 2006 - 11:33:46 CDT)
  • Re: AMBER: R.E.D II (Tue Jul 04 2006 - 02:47:51 CDT)
  • Re: AMBER: R.E.D II (Mon Jul 03 2006 - 05:03:19 CDT)
  • Re: AMBER: R.E.D II (Mon Jul 03 2006 - 01:39:20 CDT)
  • Re: AMBER: Having trouble getting Iron parameters for QM/MM (Thu Jun 29 2006 - 15:55:14 CDT)
  • Re: AMBER: Leap: neutralising the charge (Tue Jun 27 2006 - 06:19:08 CDT)
  • Re: AMBER: how to create 2'-5' RNA (Sat Jun 24 2006 - 01:29:43 CDT)
  • Re: AMBER: RESP charge fitting problems with capping group (Thu Jun 22 2006 - 13:51:13 CDT)
  • Re: AMBER: LEaP error : unbalanced charge (Mon Jun 19 2006 - 02:03:38 CDT)
  • Re: AMBER: LEaP Warning ... when do NH2-neutral fragment (Tue Jun 13 2006 - 14:20:52 CDT)
  • Re: Fwd: AMBER: How to build N-terminal of alanine : NH2 (Fri Jun 09 2006 - 01:45:27 CDT)
  • Re: AMBER: How to build N-terminal of alanine : NH2 (Thu Jun 08 2006 - 03:27:58 CDT)
  • Re: AMBER: ESP calculations. (Tue May 30 2006 - 06:15:31 CDT)
  • Re: AMBER: Qestion about input for RESP program (Thu May 25 2006 - 10:53:28 CDT)
  • Re: AMBER: Qestion about input for RESP program (Thu May 25 2006 - 03:22:13 CDT)
  • Re: AMBER: Fwd: RESP for deprotonated tyrosine and lysine (Thu May 25 2006 - 03:26:15 CDT)
  • Re: AMBER: output of first stage RESP calculation (Thu May 25 2006 - 03:12:12 CDT)
  • Re: AMBER: question about REDII (Fri May 12 2006 - 01:34:48 CDT)
  • AMBER: Antechamber & atom types (Thu Apr 20 2006 - 12:04:17 CDT)
  • Re: AMBER: An issue with the "multimolecule and multiconformational" resp fit (Tue Apr 11 2006 - 14:39:40 CDT)
  • Re: AMBER: RESP problem (Tue Apr 11 2006 - 11:31:12 CDT)
  • Re: AMBER: Any difference about RESP or ESP with Chelpg or MK (Tue Apr 04 2006 - 12:01:40 CDT)
  • Re: AMBER: Announcement: Amber 9 is now available (Mon Apr 03 2006 - 13:00:44 CDT)
  • Re: Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 02:22:05 CST)
  • Re: AMBER: Trouble with combining a non-standard residue with a protein of standard residue (Wed Mar 08 2006 - 23:37:07 CST)
  • Re: AMBER: How to develop charge for my deprotonated glycine (Sat Mar 04 2006 - 03:26:13 CST)
  • Re: AMBER: How to develop charge for my deprotonated glycine (Tue Feb 28 2006 - 23:00:37 CST)
  • Re: AMBER: A problem with Amber force field new parameter derivation (Fri Feb 24 2006 - 00:27:31 CST)
  • Re: AMBER: instructions for making a library file for an unusual residue? (Tue Feb 21 2006 - 07:17:48 CST)
  • Re: AMBER: instructions for making a library file for an unusual residue? (Sun Feb 19 2006 - 11:14:10 CST)
  • Re: AMBER: antechamber for a database of organic molecules (Sun Feb 19 2006 - 09:51:52 CST)
  • Re: AMBER: Charges of enantiomers for Amber8 (Thu Jan 26 2006 - 01:53:43 CST)
  • Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 05:41:47 CST)
  • Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 03:38:36 CST)
  • RE: AMBER: partial charge glycam (Wed Jan 25 2006 - 03:23:06 CST)
  • Re: AMBER: partial charge glycam (Sat Jan 21 2006 - 01:30:37 CST)
  • AMBER: Release of RESP ESP charge DDatabase (Mon Jan 16 2006 - 10:04:47 CST)
• Gabbar S. Daaku
  • Re: AMBER: optimatized structure is so much different from the original pdb structure (Fri Nov 17 2006 - 11:13:04 CST)
  • AMBER: GLYCAM and ff98 atom-types (Thu Nov 16 2006 - 12:11:05 CST)
• german
  • Re: AMBER: "The system has extended beyond" error message (Thu May 18 2006 - 07:27:42 CDT)
  • AMBER: a quetion (Mon Apr 24 2006 - 06:17:34 CDT)
  • AMBER: a question (Fri Apr 21 2006 - 06:04:54 CDT)
  • Re: AMBER: about Br- parameters (Fri Mar 03 2006 - 04:52:50 CST)
  • Re: AMBER: Problem with file size of sander outputs (Wed Feb 22 2006 - 04:49:49 CST)
  • Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation (Thu Feb 16 2006 - 06:04:39 CST)
• Gert Kiss
  • Re: AMBER: AMBER9: MacG5 parallel sander.MPI (Sat Apr 29 2006 - 17:29:51 CDT)
• Giovanni
  • AMBER: problems on mm_pbsa (Wed Jun 14 2006 - 07:05:03 CDT)
• Giulio Rastelli
  • Re: AMBER: where to set bondi radii for halogens (Fri Oct 27 2006 - 16:10:32 CDT)
  • AMBER: where to set bondi radii for halogens (Fri Oct 27 2006 - 11:59:00 CDT)
  • AMBER: halogen bondi radii in mm_pbsa_calceneent.pm (Fri Oct 27 2006 - 03:46:30 CDT)
  • Re: AMBER: amber9: SA Bomb in sa_arc (Thu Oct 26 2006 - 10:58:50 CDT)
  • Re: AMBER: amber9: SA Bomb in sa_arc (Thu Oct 26 2006 - 05:56:43 CDT)
  • Re: AMBER: Not getting proper structure after minimization (Wed Oct 25 2006 - 08:52:48 CDT)
  • AMBER: amber9: SA Bomb in sa_arc (Wed Oct 25 2006 - 06:03:54 CDT)
• Glass, Kevin A
  • AMBER: Execution time discrepancies (Thu Aug 17 2006 - 19:18:20 CDT)
  • AMBER: (Mon Aug 07 2006 - 15:09:02 CDT)
  • AMBER: Amber 9 installation issues (Fri Jul 14 2006 - 18:18:36 CDT)
  • AMBER: REM test failures on IA-64 architecture (Wed Jun 28 2006 - 10:28:07 CDT)
• Gloria T. Anderle
  • AMBER: Residue connection points on prep.in (Fri Aug 04 2006 - 11:10:53 CDT)
• Gobind Bisht
  • AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine (Sun Aug 27 2006 - 00:24:12 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Sat Aug 12 2006 - 12:05:29 CDT)
  • AMBER: Format of mdcrd files (Wed Aug 09 2006 - 08:56:18 CDT)
  • AMBER: Problem with restarting MD simulation (Tue Aug 08 2006 - 00:02:56 CDT)
  • Re: AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 14:17:46 CDT)
  • Re: AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 12:13:36 CDT)
  • AMBER: Amber crashed due to power surge and giving problems.. (Tue Jul 11 2006 - 09:46:54 CDT)
  • AMBER: Error in running MD in sander (Sat Jul 08 2006 - 12:20:10 CDT)
  • Re: AMBER: Error in loading molecule in tleap (Fri Jul 07 2006 - 16:18:08 CDT)
  • AMBER: Error in loading molecule in tleap (Fri Jul 07 2006 - 13:01:45 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 11:39:31 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 10:48:35 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 09:13:37 CDT)
  • AMBER: Problem with bcc flag of antechamber..continued (Thu Jul 06 2006 - 12:08:45 CDT)
  • AMBER: Problem with bcc flag of antechamber (Thu Jul 06 2006 - 12:00:49 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 10:36:28 CDT)
  • AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 00:17:54 CDT)
• Gobind Singh Bisht
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 22:26:16 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 21:11:57 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 09:26:27 CST)
  • AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 04:42:01 CST)
  • AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? (Thu Nov 30 2006 - 01:34:28 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 10:40:53 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 08:34:36 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 07:56:10 CST)
  • AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 05:51:30 CST)
  • AMBER: how to simulate water flow inside a channel? (Wed Oct 18 2006 - 09:33:51 CDT)
  • AMBER: How to find equillibration time for my system in a generalised born solvation model (Mon Oct 16 2006 - 16:34:11 CDT)
  • Re: AMBER: Installing AMBER9 on cygwin (WinXP) (Tue Sep 12 2006 - 06:57:06 CDT)
  • Re: AMBER: Problem with ptraj (Fri Sep 08 2006 - 23:35:28 CDT)
  • AMBER: Problem with ptraj (Fri Sep 08 2006 - 16:00:19 CDT)
  • AMBER: Temperature fluctuation with Langevin Temperature control (Sun Aug 27 2006 - 14:06:49 CDT)
• Gregory Sandala
  • AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 03:12:43 CST)
• gtg549i_at_mail.gatech.edu
  • AMBER: pmemd installation on linux_p3_athlon ifort (Tue Oct 24 2006 - 11:20:30 CDT)
  • AMBER: problem of installing carnal on macosx (Fri Oct 20 2006 - 13:37:39 CDT)
  • AMBER: Building polymer with sequence command (Thu Oct 05 2006 - 11:46:11 CDT)
  • RE: AMBER: Problem about installing amber9 on Mac OS X (Thu Sep 28 2006 - 13:32:18 CDT)
  • AMBER: Problem about installing amber9 on Mac OS X (Thu Sep 28 2006 - 11:28:51 CDT)
  • AMBER: Free energy calculated from mm_pbsa (Thu Jul 13 2006 - 02:26:44 CDT)
• Guanglei Cui
  • Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files (Fri Aug 11 2006 - 08:57:46 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 09:38:06 CDT)
  • Re: AMBER: Distance between two regions (Tue Aug 01 2006 - 10:35:54 CDT)
  • Re: AMBER: from traj to crd (Tue Aug 01 2006 - 10:30:59 CDT)
  • Re: AMBER: How to resume remaining simulation (Mon Jul 24 2006 - 10:19:56 CDT)
  • Re: AMBER: Replica exchange (Wed Jul 19 2006 - 13:24:55 CDT)
  • Re: AMBER: RMS & PCA (Mon Jul 17 2006 - 13:22:56 CDT)
  • Re: AMBER: Replica exchange (Mon Jul 17 2006 - 09:18:57 CDT)
  • Re: AMBER: MD job stopped without any error information? (Mon Feb 27 2006 - 09:55:47 CST)
• Guillaume Bollot
  • AMBER: MM_PBSA : Question about Stability? (Wed Aug 16 2006 - 02:00:15 CDT)
  • AMBER: Amber 8.0 MM_PBSA Stability : question about methodology (Mon Jul 17 2006 - 07:18:41 CDT)
  • AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! (Tue Jul 11 2006 - 06:19:29 CDT)
  • AMBER: Amber8.0 predictied pKa problem for a Lysine! (Fri Jul 07 2006 - 04:38:08 CDT)
  • AMBER: Constant pH simulation : LYS residue (Tue Jul 04 2006 - 06:13:00 CDT)
  • AMBER: Restraint internal coordinates in Amber 8.0 (Thu Jun 22 2006 - 04:00:03 CDT)
  • AMBER: AMBER 8.0 : Octane Implicit Solvent? (Tue Jan 24 2006 - 10:25:42 CST)
• Guowen
  • AMBER: k-space cutoff with standard Ewald (Wed Mar 15 2006 - 10:29:33 CST)
• Gustavo Pierdominici Sottile
  • AMBER: lifetimes (Mon Jan 30 2006 - 09:15:55 CST)
  • AMBER: h-bond (Fri Jan 27 2006 - 08:59:07 CST)
• Gustavo Seabra
  • Re: AMBER: Installation help - SGI Altix 350 (Fri Dec 22 2006 - 19:42:03 CST)
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 09:34:53 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 09:31:01 CST)
  • Re: AMBER: QM/MD energy conservation (Tue Dec 12 2006 - 08:02:39 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 12:31:54 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Thu Nov 30 2006 - 09:46:42 CST)
  • Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Thu Nov 30 2006 - 09:20:00 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 09:18:49 CST)
  • Re: AMBER: <kein Betreff> (Mon Nov 13 2006 - 11:52:55 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 10:50:27 CST)
  • Re: AMBER: Not getting proper structure after minimization (Tue Oct 24 2006 - 16:28:27 CDT)
  • Re: AMBER: RESP charges of iron-porphyrin system (Thu Oct 19 2006 - 08:40:20 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 12:41:43 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:56:23 CDT)
  • Re: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:22:31 CDT)
  • Re: AMBER: RMSD: is it related to flexibility? (Thu Oct 05 2006 - 11:08:05 CDT)
  • Re: AMBER: Problem using antechamber (Fri Sep 29 2006 - 14:06:34 CDT)
  • AMBER: Problem using antechamber (Fri Sep 29 2006 - 11:19:12 CDT)
  • Re: AMBER: Question about using antechamber with G03 (Wed Aug 16 2006 - 08:49:42 CDT)
  • AMBER: (Another) Question about using antechamber with G03 (Tue Aug 15 2006 - 12:51:16 CDT)
  • AMBER: Question about using antechamber with G03 (Tue Aug 15 2006 - 10:58:40 CDT)
  • Re: AMBER: center molecule using iwrap=1? (Thu Jul 13 2006 - 14:49:39 CDT)
  • Re: AMBER: center molecule using iwrap=1? (Thu Jul 13 2006 - 14:07:40 CDT)
  • AMBER: center molecule using iwrap=1? (Thu Jul 13 2006 - 13:21:17 CDT)
  • Re: AMBER: simulate a self-assemble process in vacuum (Thu Jul 13 2006 - 08:22:15 CDT)
  • Re: AMBER: convert chemical structure to pdb file (Fri Jul 07 2006 - 13:56:37 CDT)
  • Re: AMBER: script to extract data from minimization .out file (Fri Jul 07 2006 - 12:35:32 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 11:00:36 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Fri Jul 07 2006 - 09:36:50 CDT)
  • Re: AMBER: Compiling AMBER 9 on windows XP using cygwin (Thu Jul 06 2006 - 10:50:05 CDT)
  • Re: AMBER: Fully QM periodic runs (Wed Jun 14 2006 - 12:44:37 CDT)
  • Re: AMBER: How to strip waters in trajectorie ? (Mon Jun 12 2006 - 14:57:30 CDT)
• H W
  • Re: AMBER: Question about using PMEMD and GB (Wed Sep 06 2006 - 13:31:20 CDT)
  • AMBER: Question about using PMEMD and GB (Wed Sep 06 2006 - 12:41:12 CDT)
• haixiao jin
  • AMBER: MM_PBSA: “Found unknown atflag DELPHI” (Mon Apr 24 2006 - 10:23:23 CDT)
  • Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue (Tue Mar 07 2006 - 02:10:02 CST)
  • AMBER: how to calculate the RMSD and B-factor for all atoms of residue (Mon Mar 06 2006 - 02:13:04 CST)
  • Re: AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 22:58:28 CST)
  • AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 21:30:33 CST)
• Hall, Spencer
  • RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem (Tue May 23 2006 - 16:15:08 CDT)
  • RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem (Tue May 23 2006 - 16:15:12 CDT)
  • AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem (Thu May 18 2006 - 17:44:14 CDT)
• Hannes Barsch
  • AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 (Wed Sep 13 2006 - 08:54:54 CDT)
  • AMBER: save coordinates during SANDER minimisation (Thu Jun 08 2006 - 04:34:51 CDT)
• Hannes Loeffler
  • AMBER: ptraj grid (Sun Nov 26 2006 - 22:05:05 CST)
  • AMBER: ions+proteins (Mon Jun 19 2006 - 20:45:57 CDT)
  • AMBER: which patch for ioutfm = 1 in Amber8? (Thu May 11 2006 - 00:21:25 CDT)
  • Re: AMBER: Cosine content calculation (Thu Mar 09 2006 - 19:02:48 CST)
• HARADA Makoto
  • AMBER: Installing AMBER9 on cygwin (WinXP) (Tue Sep 12 2006 - 04:38:19 CDT)
• harianto
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:03:26 CST)
  • AMBER: pqr from constant pH MD (Wed Sep 13 2006 - 16:43:13 CDT)
  • Re: AMBER: alpha helix preference problem (Fri May 26 2006 - 09:04:30 CDT)
  • AMBER: alpha helix preference problem (Thu May 25 2006 - 16:16:23 CDT)
  • AMBER: Born igb =2 (Mon Apr 24 2006 - 20:27:24 CDT)
  • Re: AMBER: VdW radii in the topology file (Mon Apr 10 2006 - 11:51:55 CDT)
  • Re: AMBER: printing Amber VdW radii as separate column in pdb files (Mon Apr 10 2006 - 10:12:39 CDT)
• Hashem Taha
  • AMBER: xleap problem (Tue Jun 06 2006 - 13:29:31 CDT)
• hayden
  • RE: AMBER: Amber: disufide bond (Sun Nov 05 2006 - 07:03:23 CST)
  • RE: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 (Fri Jul 14 2006 - 05:27:54 CDT)
  • RE: AMBER: amber9 compilation problems on EM64T xeon system (Mon Jul 10 2006 - 11:57:44 CDT)
  • AMBER: amber9 compilation problems on EM64T xeon system (Thu Jul 06 2006 - 13:11:04 CDT)
  • RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . (Thu Jul 06 2006 - 07:02:13 CDT)
  • RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . (Mon Jul 03 2006 - 19:28:37 CDT)
  • AMBER: RESP charge fitting problems with capping group (Thu Jun 22 2006 - 04:51:52 CDT)
  • AMBER: 1st 2 lines of restart files (Thu May 25 2006 - 06:40:03 CDT)
  • AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 12:55:34 CST)
  • AMBER: PTRAJ generating wrong dihedral angles (Tue Jan 10 2006 - 05:40:05 CST)
• Hayden Eastwood
  • RE: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 05:23:37 CST)
  • AMBER: Langevin temperature control vs berendson heat bath (Wed Nov 29 2006 - 12:12:16 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 14:47:09 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 14:33:17 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 13:13:24 CST)
  • RE: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:47:00 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:12:49 CST)
• hbluo
  • AMBER: Performing Interactive Essential Dynamics in Ptraj (Thu Nov 30 2006 - 18:58:11 CST)
  • AMBER: how to choose the parameter for the production/sampling run after the equilibration run (Fri Nov 03 2006 - 19:57:01 CST)
  • AMBER: Silicon related parameters (Sat Jul 22 2006 - 12:52:17 CDT)
  • AMBER: periodic boundary condition in the X and Y dimensions only (Mon Jun 26 2006 - 17:15:51 CDT)
  • AMBER: How to give the specific pressure parameter for NTP=2 (Tue Mar 28 2006 - 11:29:48 CST)
• heaton_at_chem.utah.edu
  • RE: AMBER: Problem with running xleap remotely (Sat May 20 2006 - 15:43:53 CDT)
  • AMBER: Problem with running xleap remotely (Sat May 20 2006 - 14:20:27 CDT)
• Hector A. Baldoni
  • Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product (Sat Apr 29 2006 - 19:08:30 CDT)
• Heike.Meiselbach_at_chemie.uni-erlangen.de
  • Re: AMBER: MMPBSA error (Tue Jun 13 2006 - 10:27:22 CDT)
• HL Eastwood
  • AMBER: ab initio terminology query (Wed Nov 01 2006 - 05:38:24 CST)
  • Re: AMBER: Compile AMBER 8 (Mon Oct 30 2006 - 11:37:22 CST)
  • Re: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 10:52:04 CST)
  • Re: AMBER: Compile AMBER 8 (Mon Oct 30 2006 - 10:43:51 CST)
  • Re: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 09:19:16 CST)
  • AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 08:42:53 CST)
  • AMBER: Amber8 parallel compilation problems on EM64T system (Thu Feb 02 2006 - 13:32:32 CST)
• Holger Gohlke
  • Re: AMBER: questions on mm_pbsa_statitistics.pl (Wed Oct 18 2006 - 13:19:20 CDT)
  • Re: AMBER: questions on mm_pbsa_statitistics.pl (Wed Oct 18 2006 - 02:42:52 CDT)
  • Re: AMBER: about the decomposition energies using mm/pbsa (Fri Apr 21 2006 - 02:25:44 CDT)
  • Re: AMBER: Mass wieghted Covariance Matrix (Wed Apr 12 2006 - 02:46:19 CDT)
  • Re: AMBER: PCA (Tue Apr 11 2006 - 07:27:26 CDT)
  • Re: AMBER: MM-GBSA decomposition (Sun Apr 09 2006 - 13:13:41 CDT)
  • Re: AMBER: PCA (Sun Apr 09 2006 - 13:09:06 CDT)
  • Re: AMBER: about atomic fluctuation & RMSF (Thu Mar 23 2006 - 07:01:14 CST)
  • Re: AMBER: what is unit of the out put of mmpbsa caculation (Thu Mar 23 2006 - 06:53:51 CST)
  • Re: AMBER: mm-pbsa (Thu Mar 16 2006 - 11:33:20 CST)
  • Re: AMBER: ptraj distance matrix (Wed Jan 11 2006 - 02:09:33 CST)
  • Re: AMBER: How to run mm_pbsa_statistics.pl? (Wed Jan 04 2006 - 11:27:05 CST)
  • Re: AMBER: requirement of delphi for mm_pbsa (Wed Jan 04 2006 - 11:09:46 CST)
• Holly Freedman
  • Re: AMBER: mm_pbsa does not terminate (Wed Nov 01 2006 - 13:34:17 CST)
  • Re: AMBER: mm_pbsa does not terminate (Wed Nov 01 2006 - 11:56:28 CST)
  • AMBER: mm_pbsa does not terminate (Tue Oct 31 2006 - 18:51:19 CST)
  • Re: AMBER: single or dual topology for TI? (Sat Oct 21 2006 - 15:32:42 CDT)
  • AMBER: single or dual topology for TI? (Sat Oct 21 2006 - 13:20:51 CDT)
  • Re: AMBER: question about group format (Thu May 04 2006 - 18:16:22 CDT)
  • AMBER: question about group format (Wed May 03 2006 - 14:18:36 CDT)
  • AMBER: ptraj distance matrix (Tue Jan 10 2006 - 16:03:36 CST)
• homeira amirkhani
  • AMBER: San Fransisco Amber users (Tue May 09 2006 - 06:38:06 CDT)
• hornak_at_csb.sunysb.edu
  • Re: AMBER: Long line of input (Wed Jul 19 2006 - 15:37:29 CDT)
• Hui Lei
  • AMBER: simulate proteins with non-standard residues (Wed May 24 2006 - 12:10:08 CDT)
• ian gould
  • Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 02:35:12 CDT)
• Igor Schapiro
  • Re: AMBER: dihedral angle equation (Fri Nov 17 2006 - 08:24:29 CST)
  • Re: AMBER: dihedral angle equation (Fri Nov 17 2006 - 08:15:47 CST)
• Ilyas Yildirim
  • Re: AMBER: AMBER - leap - problems with impose command (Sun Dec 17 2006 - 02:45:13 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 05:17:22 CST)
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:02:39 CST)
  • Re: AMBER: helices in GB simulations (Mon Nov 27 2006 - 16:09:04 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 11:45:20 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 02:03:33 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 20:45:37 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 19:07:04 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 18:05:13 CST)
  • AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 13:28:06 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:38:58 CST)
  • Re: AMBER: error estimate for free energy perturbation calculation (Wed Oct 25 2006 - 18:17:36 CDT)
  • Re: AMBER: HBON in frcmod file (Sat Oct 21 2006 - 03:24:42 CDT)
  • AMBER: HBON in frcmod file (Sat Oct 21 2006 - 00:46:31 CDT)
  • Re: AMBER: Trouble with Leap (Thu Oct 19 2006 - 03:04:59 CDT)
  • Re: AMBER: LEAP error (Fri Oct 06 2006 - 23:26:29 CDT)
  • Re: AMBER: water prmtop/inpcrd problem (Fri Oct 06 2006 - 04:17:11 CDT)
  • Re: AMBER: AMBER minimization vs. Gaussian optimization (Wed Oct 04 2006 - 17:17:51 CDT)
  • AMBER: AMBER minimization vs. Gaussian optimization (Wed Oct 04 2006 - 15:27:48 CDT)
  • Re: AMBER: change mdcrd file to pdb file (Sun Sep 17 2006 - 00:17:21 CDT)
  • Re: AMBER: MD on protein-ligand interaction (Thu Sep 14 2006 - 14:09:14 CDT)
  • Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 (Wed Sep 13 2006 - 12:59:10 CDT)
  • RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file (Tue Sep 12 2006 - 17:49:33 CDT)
  • AMBER: forrtl: severe (64): input conversion error, unit 9, file (Tue Sep 12 2006 - 16:09:34 CDT)
  • Re: AMBER: set a trucated octahedron box in Leap (Tue Sep 12 2006 - 03:48:56 CDT)
  • Re: AMBER: protein-ligand interaction (Sat Sep 09 2006 - 16:58:10 CDT)
  • Re: AMBER: a ligand file (Fri Sep 08 2006 - 23:05:11 CDT)
  • Re: AMBER: a ligand file (Fri Sep 08 2006 - 21:23:48 CDT)
  • Re: AMBER: LEAP - "could not find type: NH" (Fri Sep 08 2006 - 17:42:46 CDT)
  • Re: AMBER: hydronium ion parameters (Fri Sep 08 2006 - 15:41:17 CDT)
  • Re: AMBER: Question about LEAP and twisting a dihedral angle (Wed Sep 06 2006 - 03:46:57 CDT)
  • Re: AMBER: Implicit Water - Force field parameters (Tue Sep 05 2006 - 15:22:13 CDT)
  • Re: AMBER: help with antechamber - creating ligand (Tue Sep 05 2006 - 16:26:11 CDT)
  • Re: AMBER: Question about LEAP and twisting a dihedral angle (Sun Sep 03 2006 - 01:20:27 CDT)
  • AMBER: Question about LEAP and twisting a dihedral angle (Sat Sep 02 2006 - 20:52:45 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 22:37:18 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 18:47:54 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:50:26 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:12:24 CDT)
  • Re: AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 15:27:41 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:14:54 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Thu Aug 17 2006 - 14:28:55 CDT)
  • Re: AMBER: klambda (Mon Aug 14 2006 - 12:31:24 CDT)
  • Re: AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 01:15:10 CDT)
  • Re: AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 13:55:38 CDT)
  • Re: AMBER: pdb error (Tue Aug 01 2006 - 14:23:30 CDT)
  • AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 00:40:15 CDT)
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 00:33:38 CDT)
  • Re: AMBER: dummy atoms in MMPBSA (Thu Jul 27 2006 - 07:18:01 CDT)
  • Re: AMBER: PDB from .rst? (Thu Jul 20 2006 - 16:08:20 CDT)
  • Re: AMBER: Tutorial 4-section 4 DIHE in frcmod file. (Mon Jul 03 2006 - 22:47:22 CDT)
  • Re: AMBER: how to create 2'-5' RNA (Mon Jun 26 2006 - 17:52:10 CDT)
  • Re: AMBER: Can we submit jobs in sequences to amber? (Mon Jun 26 2006 - 02:22:00 CDT)
  • Re: AMBER: help creating RNA (Thu Jun 22 2006 - 14:29:49 CDT)
  • RE: AMBER: Umbrella sampling (Sun Jun 18 2006 - 11:57:09 CDT)
  • Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge (Sun Jun 18 2006 - 02:53:58 CDT)
  • Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand (Sat Jun 17 2006 - 03:28:55 CDT)
  • Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) (Wed Jun 14 2006 - 13:46:22 CDT)
  • Re: AMBER: LEaP Warning ... when do NH2-neutral fragment (Tue Jun 13 2006 - 16:23:18 CDT)
  • Re: AMBER: Difficulty loading a pdb file (Tue Jun 13 2006 - 16:25:27 CDT)
  • Re: AMBER: Umbrella sampling (Sat Jun 10 2006 - 09:53:41 CDT)
  • Re: AMBER: save coordinates during SANDER minimisation (Thu Jun 08 2006 - 05:22:24 CDT)
  • Re: AMBER: xleap problem (Wed Jun 07 2006 - 01:49:04 CDT)
  • Re: AMBER: Thermodynamic integration using the amber 9 (Fri Jun 02 2006 - 15:12:18 CDT)
  • RE: AMBER: A dummy atom on the center of solute molecule (Tue May 30 2006 - 18:06:54 CDT)
  • Re: AMBER: Thermodynamic integration using the amber 9 (Mon May 29 2006 - 09:25:21 CDT)
  • RE: AMBER: A dummy atom on the center of solute molecule (Sun May 28 2006 - 23:26:33 CDT)
  • Re: AMBER: Pt containing complex: xleap (Sun May 28 2006 - 23:00:08 CDT)
  • Re: AMBER: Question about .off file (Fri May 26 2006 - 03:58:19 CDT)
  • Re: AMBER: Qestion about input for RESP program (Wed May 24 2006 - 23:49:11 CDT)
  • RE: AMBER: A dummy atom on the center of solute molecule (Tue May 23 2006 - 21:49:00 CDT)
  • Re: AMBER: amber .off file format question (Tue May 23 2006 - 00:53:19 CDT)
  • Re: AMBER: A dummy atom on the center of solute molecule (Mon May 22 2006 - 06:58:24 CDT)
  • Re: AMBER: amber .off file format question (Mon May 22 2006 - 04:16:39 CDT)
  • AMBER: amber .off file format question (Fri May 19 2006 - 21:30:55 CDT)
  • AMBER: AMBER 8 - dihedral angles when clambda=1 (Thu May 11 2006 - 23:57:37 CDT)
  • AMBER: Force Field Question (Thu Apr 27 2006 - 16:57:58 CDT)
  • Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE (Fri Mar 31 2006 - 18:46:03 CST)
  • Re: AMBER: Problem with setbox command... (Fri Mar 31 2006 - 06:34:33 CST)
  • Re: AMBER: charge constraints in resp (Thu Mar 30 2006 - 18:05:35 CST)
  • Re: AMBER: charge constraints in resp (Thu Mar 30 2006 - 11:03:43 CST)
  • AMBER: Problem with setbox command... (Thu Mar 30 2006 - 01:44:37 CST)
  • AMBER: Solvating the system with specific number of water molecules... (Wed Mar 22 2006 - 23:50:25 CST)
  • Re: AMBER: Zoom (Thu Mar 16 2006 - 13:50:12 CST)
  • Re: AMBER: (Mon Mar 13 2006 - 15:35:30 CST)
  • Re: Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 01:22:17 CST)
  • Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 00:18:29 CST)
  • Re: AMBER: aligning polymer with Z-axis of periodic box (Wed Mar 08 2006 - 16:54:22 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Tue Mar 07 2006 - 07:45:01 CST)
  • Re: AMBER: Different results between serial and parallel runs in AMBER 8 (Tue Mar 07 2006 - 06:51:14 CST)
  • Re: AMBER: rms processing (Mon Mar 06 2006 - 18:41:37 CST)
  • AMBER: Different results between serial and parallel runs in AMBER 8 (Mon Mar 06 2006 - 18:28:14 CST)
  • Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations (Mon Mar 06 2006 - 17:42:29 CST)
  • Re: AMBER: instructions for making a library file for an unusual residue? (Tue Feb 21 2006 - 00:28:49 CST)
  • Re: AMBER: Question about renaming a residue (Fri Feb 17 2006 - 20:05:37 CST)
  • Re: AMBER: lib file (Fri Feb 03 2006 - 19:11:36 CST)
  • Re: AMBER: lib file (Thu Feb 02 2006 - 14:18:28 CST)
  • RE: AMBER: Charges on atoms in protein :AMBER (Thu Feb 02 2006 - 14:14:53 CST)
  • Re: AMBER: lib file (Thu Feb 02 2006 - 13:08:12 CST)
  • Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 05:10:52 CST)
  • Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 04:40:56 CST)
  • Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 16:00:24 CST)
  • AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 01:43:06 CST)
  • Re: AMBER: About preparing Zn.lib (Thu Jan 12 2006 - 01:46:03 CST)
  • Re: AMBER: GLUTATHIONE (Wed Jan 11 2006 - 09:38:56 CST)
  • Re: AMBER: Ligand charge (Thu Jan 05 2006 - 00:02:42 CST)
  • Re: AMBER: water molecules with in 3 angstroms to the solute (Tue Jan 03 2006 - 18:40:07 CST)
  • Re: AMBER: water molecules with in 3 angstroms to the solute (Tue Jan 03 2006 - 03:05:24 CST)
• In Hee Park
  • AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 (Fri Nov 24 2006 - 16:50:54 CST)
  • AMBER: mm_pbsa snapshots for "three-trajectory" (Thu Sep 14 2006 - 18:42:13 CDT)
  • AMBER: sequential execution of number of parallel jobs (Mon May 01 2006 - 15:13:23 CDT)
  • AMBER: AMBER9: MacG5 parallel sander.MPI (Sat Apr 29 2006 - 15:59:28 CDT)
• Ingvar Lagerstedt
  • AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai (Fri Oct 20 2006 - 11:17:08 CDT)
• Ioana Cozmuta
  • Re: AMBER: internal coordinates (Tue May 02 2006 - 13:01:45 CDT)
  • AMBER: internal coordinates (Wed Apr 26 2006 - 16:56:20 CDT)
  • AMBER: two references- I got them, thank you! (Wed Apr 26 2006 - 16:15:11 CDT)
  • AMBER: two references (Wed Apr 26 2006 - 15:18:28 CDT)
  • Re: AMBER: DNA structure (Wed Apr 26 2006 - 14:06:22 CDT)
  • AMBER: DNA structure (Tue Apr 25 2006 - 15:17:12 CDT)
  • AMBER: reconstructing PMF (Mon Apr 10 2006 - 13:15:20 CDT)
  • AMBER: divalent ions (Tue Mar 14 2006 - 13:54:49 CST)
  • AMBER: divalent ions (Sat Mar 11 2006 - 13:04:00 CST)
• Isherwood, James
  • AMBER: Nature of QM scanning protocol for parameter development (Fri Aug 11 2006 - 11:17:01 CDT)
• ivan_at_mmb.pcb.ub.es
  • Re: AMBER: prepi definitions (Wed Feb 01 2006 - 10:33:42 CST)
  • Re: AMBER: NAD parameters (Mon Jan 30 2006 - 10:20:19 CST)
• Ivelin Georgiev
  • AMBER: Solvation Energies (Wed Nov 29 2006 - 08:31:13 CST)
  • AMBER: Electrostatic Energy Constant (Fri Sep 29 2006 - 12:50:03 CDT)
  • AMBER: parm*.dat (Thu Sep 28 2006 - 11:39:23 CDT)
• j j
  • Re: AMBER: coordinate out of bounds (Thu Dec 14 2006 - 04:21:50 CST)
  • Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 16:28:14 CST)
  • AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 11:10:26 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Mon Dec 04 2006 - 06:56:54 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 14:28:24 CST)
  • Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 04:59:59 CST)
  • AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 04:51:06 CST)
  • Re: AMBER: Ring of dna (Fri Jul 14 2006 - 09:25:59 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Fri Jul 14 2006 - 03:48:33 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Fri Jul 14 2006 - 03:40:10 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Thu Jul 13 2006 - 12:59:00 CDT)
  • AMBER: New (small) Topology without solvent from previous one (big) with solvent (Thu Jul 13 2006 - 05:50:55 CDT)
  • AMBER: New (small) Topology without solvent from previous one (big) with solvent (Thu Jul 13 2006 - 05:47:15 CDT)
• J. Zhang
  • AMBER: The VDW correctioin (Sun Dec 03 2006 - 20:29:28 CST)
  • AMBER: About the creation of 1-4 pairs in AMBER program (Sun Dec 03 2006 - 20:17:02 CST)
  • Re: Re: AMBER: question about the topology file (Sun Nov 12 2006 - 19:42:20 CST)
  • AMBER: question about the topology file (Wed Nov 08 2006 - 03:24:10 CST)
• Jahidul Islam
  • AMBER: Xmgr in Windows (Mon Jul 31 2006 - 22:24:19 CDT)
  • Re: AMBER: Can't open xleap (Thu Jul 27 2006 - 06:57:30 CDT)
  • AMBER: Can't open xleap (Thu Jul 27 2006 - 05:16:08 CDT)
• James W
  • Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) (Tue Mar 28 2006 - 21:44:42 CST)
  • AMBER: AMBER : About the kinetic energy and temperature (GBSA model) (Tue Mar 28 2006 - 20:00:46 CST)
• Jan Dohnalek
  • AMBER: passwordless ssh stopped working (Thu Apr 13 2006 - 10:51:50 CDT)
  • AMBER: MPICH on OpenMosix (Mon Jan 16 2006 - 07:21:04 CST)
  • Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 04:32:18 CST)
  • AMBER: mpich Amber7 problem (Tue Jan 10 2006 - 08:31:38 CST)
• Jan Kosinski
  • AMBER: modeling zinc binding site (Mon Apr 24 2006 - 07:28:55 CDT)
• Jardas sucuriba
  • AMBER: PCA analysis (Wed Dec 27 2006 - 23:04:41 CST)
  • AMBER: matrix correl (Tue Nov 21 2006 - 07:05:41 CST)
  • Re: AMBER: solvation and His protonation (Tue Oct 31 2006 - 07:07:24 CST)
  • AMBER: solvation and His protonation (Sat Oct 28 2006 - 09:00:44 CDT)
  • Re: AMBER: md and implicit solvation (Tue Oct 24 2006 - 20:29:35 CDT)
  • AMBER: md and implicit solvation (Tue Oct 24 2006 - 18:57:24 CDT)
  • RE: AMBER: RDF output (Wed Aug 30 2006 - 16:31:08 CDT)
  • AMBER: RDF output (Tue Aug 29 2006 - 09:48:29 CDT)
  • AMBER: waters closest to specific residues (Sat Aug 26 2006 - 10:39:35 CDT)
  • Re: AMBER: missing values in md.out (Fri Aug 25 2006 - 07:36:45 CDT)
  • AMBER: missing values in md.out (Thu Aug 24 2006 - 11:15:40 CDT)
  • AMBER: ptraj script (Fri Aug 18 2006 - 15:08:31 CDT)
• Jarrod Smith
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 17:32:36 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 16:13:29 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 15:54:18 CST)
  • AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 12:42:06 CST)
• Jason K
  • AMBER: An issue with the "multimolecule and multiconformational" resp fit (Tue Apr 11 2006 - 13:16:57 CDT)
  • AMBER: A few problems on the parameterisation of a Glutamine residue (Wed Jan 18 2006 - 12:12:16 CST)
• JAVIER PEREZ
  • AMBER: energy terms (Mon May 29 2006 - 10:25:31 CDT)
  • AMBER: problems with antechamber (Mon May 29 2006 - 10:04:52 CDT)
  • AMBER: problems with saveamberprep command (Fri Apr 21 2006 - 06:33:48 CDT)
  • AMBER: about Br- parameters (Fri Mar 03 2006 - 04:18:23 CST)
• Jennie Thomas
  • AMBER: Periodic simulations with net charge (Tue Nov 28 2006 - 18:47:32 CST)
  • Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] (Thu May 04 2006 - 17:45:21 CDT)
  • [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] (Wed May 03 2006 - 16:49:19 CDT)
  • Re: AMBER: Question bonds and angles in frcmod and lib files (Wed May 03 2006 - 12:26:55 CDT)
  • Re: AMBER: Question bonds and angles in frcmod and lib files (Wed May 03 2006 - 10:54:43 CDT)
  • AMBER: Question bonds and angles in frcmod and lib files (Wed May 03 2006 - 03:02:55 CDT)
  • AMBER: Simulation of crystal - problem with excluded atom list (Tue May 02 2006 - 12:07:20 CDT)
  • AMBER: Setting box dimensions in leap (Fri Apr 28 2006 - 17:42:38 CDT)
  • Re: AMBER: Constant P for non-orthorhombic cells (Wed Apr 12 2006 - 13:36:47 CDT)
  • AMBER: Constant P for non-orthorhombic cells (Tue Apr 11 2006 - 23:40:00 CDT)
  • Re: AMBER: Constant pressure - restart - Amber8 (Sun Feb 26 2006 - 19:56:59 CST)
  • Re: AMBER: Constant pressure - restart - Amber8 (Fri Feb 24 2006 - 14:18:56 CST)
  • AMBER: Constant pressure - restart - Amber8 (Fri Feb 24 2006 - 10:59:34 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 19:54:09 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 18:07:47 CST)
  • Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 16:38:24 CST)
  • AMBER: SHAKE - ntc = 3 (Fri Jan 06 2006 - 19:05:09 CST)
• Jiang Jianwen
  • RE: AMBER: RMS FLUCTUATIONS (Fri Jun 16 2006 - 02:01:10 CDT)
  • AMBER: RMS FLUCTUATIONS (Thu Jun 15 2006 - 06:37:24 CDT)
  • RE: AMBER: Simulating a periodic crystal (Fri Mar 31 2006 - 05:31:47 CST)
  • AMBER: Simulating a periodic crystal (Wed Mar 29 2006 - 09:01:26 CST)
• Jianhui
  • AMBER: ptraj and mdvel question (Wed Nov 15 2006 - 13:07:06 CST)
  • AMBER: Density calculation (Mon Oct 16 2006 - 16:12:24 CDT)
  • Re: Re: AMBER: Pressure problem with restraint (Wed Oct 04 2006 - 14:24:35 CDT)
  • AMBER: Pressure problem with restraint (Tue Oct 03 2006 - 09:41:46 CDT)
  • Re: AMBER: parm*.dat (Thu Sep 28 2006 - 16:24:49 CDT)
  • Re: AMBER: change mdcrd file to pdb file (Sun Sep 17 2006 - 09:16:29 CDT)
  • AMBER: About Lennard-Jones Parameters (Fri Sep 15 2006 - 16:08:13 CDT)
  • Re: AMBER: Error in Running Sander (Mon Sep 11 2006 - 12:10:55 CDT)
  • AMBER: mdcrd file (Thu Sep 07 2006 - 09:15:45 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:48:28 CDT)
  • AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:08:09 CDT)
  • AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file (Fri Aug 11 2006 - 13:50:54 CDT)
• Jianhui Tian
  • AMBER: ptraj radial problem: Segmentation fault (Mon Oct 23 2006 - 16:48:43 CDT)
  • AMBER: Error in compiling Amber 8 parallel (Wed Sep 27 2006 - 15:28:48 CDT)
  • AMBER: Error in Running Sander (Mon Sep 11 2006 - 08:52:39 CDT)
• Jianyin Shao
  • Re: AMBER: mm_pbsa_statistical.pl (Wed Aug 30 2006 - 12:52:56 CDT)
  • Re: AMBER: error propagation in MM-PBSA binding free energy calculation (Mon May 01 2006 - 12:17:04 CDT)
  • Re: AMBER: error propagation in MM-PBSA binding free energy calculation (Wed Apr 26 2006 - 19:13:48 CDT)
  • Re: AMBER: rms processing (Mon Mar 20 2006 - 16:19:25 CST)
  • Re: AMBER: MM-PBSA (Tue Jan 31 2006 - 11:08:09 CST)
• Jianzhong Liu
  • AMBER: Any difference about RESP or ESP with Chelpg or MK (Tue Apr 04 2006 - 10:51:36 CDT)
  • Re: AMBER: Suitable water box (Mon Mar 13 2006 - 10:20:52 CST)
  • Re: AMBER: How to develop charge for my deprotonated glycine (Sat Mar 04 2006 - 21:05:12 CST)
  • Re: AMBER: How to develop charge for my deprotonated glycine (Fri Mar 03 2006 - 13:05:41 CST)
  • AMBER: How to develop charge for my deprotonated glycine (Tue Feb 28 2006 - 13:58:31 CST)
• Jiapu.Zhang_at_csiro.au
  • AMBER: How to get the VDW contacts' messages from the mdcrd files (Tue Oct 03 2006 - 01:11:03 CDT)
• Jiayun Pang
  • AMBER: SAVEPDB in Xleap could not save 4 character atom names (Mon May 29 2006 - 11:38:22 CDT)
• Jim Paugh
  • AMBER: Opteron vs. Xeon performance (Thu May 11 2006 - 13:47:42 CDT)
• Jing Huang
  • AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files (Fri Aug 11 2006 - 08:35:12 CDT)
• Jingyuan Luke
  • AMBER: CPU utilization with Parallel Sander (Thu Mar 09 2006 - 06:14:01 CST)
  • AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 (Tue Feb 14 2006 - 19:35:37 CST)
• Jiri Sponer
  • Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 11:37:52 CST)
  • Re: AMBER: Quantifying pi-pi interactions (Tue Nov 21 2006 - 10:14:32 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 18:30:48 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 17:20:18 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 16:01:27 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 13:43:13 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:34:57 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:27:44 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 05:59:04 CST)
  • Re: AMBER: force fiels for a-rna (Sat Oct 14 2006 - 02:59:13 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 12:08:34 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 11:59:00 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 11:49:58 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 05:31:24 CDT)
  • Re: AMBER: double stranded polyribocytidylic acid (Wed Feb 15 2006 - 11:46:27 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Wed Feb 15 2006 - 07:16:46 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Tue Feb 14 2006 - 06:56:07 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Tue Feb 14 2006 - 04:54:05 CST)
• Jiten
  • Re: AMBER: hydronium ion parameters (Fri Sep 08 2006 - 10:12:03 CDT)
  • AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c (Fri Sep 01 2006 - 01:55:21 CDT)
  • Re: AMBER: dynamic memory allocation problem in nmode (Sun Feb 26 2006 - 09:07:23 CST)
  • AMBER: mm_pbsa problem in IBM-aix (Sat Feb 18 2006 - 01:36:52 CST)
  • AMBER: nmode calculations error (Tue Jan 17 2006 - 07:58:53 CST)
  • Re: AMBER: Leap compilation issues (Tue Jan 10 2006 - 21:19:14 CST)
• jitrayut jitonnom
  • AMBER: Some warning !!! during SANDER ? (Wed Nov 22 2006 - 02:20:36 CST)
  • Re: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 11:22:20 CST)
  • Fwd: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 05:16:37 CST)
  • Fwd: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 09:52:00 CST)
  • AMBER: sander error: rst file crash (Fri Nov 10 2006 - 06:52:19 CST)
  • AMBER: what is the RMS value in resp charge fitting ? (Tue Oct 31 2006 - 02:46:31 CST)
  • AMBER: mmpbsa: fail to run heat in tutorial A3 (Sun Oct 22 2006 - 12:31:53 CDT)
  • AMBER: bad atom type: Li (Thu Sep 21 2006 - 05:30:24 CDT)
  • AMBER: Fwd: ADL: peptide simulation before docking (Sun Jul 09 2006 - 04:26:59 CDT)
  • AMBER: peptide simulation before docking (Sat Jul 08 2006 - 15:45:28 CDT)
  • Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge (Sun Jun 18 2006 - 08:17:57 CDT)
  • Fwd: Fwd: AMBER: LEaP error : unbalanced charge (Sat Jun 17 2006 - 15:37:46 CDT)
  • AMBER: charge in LEaP step (Sat Jun 17 2006 - 13:14:24 CDT)
  • Fwd: Fwd: AMBER: LEaP error : unbalanced charge (Fri Jun 16 2006 - 12:28:08 CDT)
  • Fwd: AMBER: LEaP error : unbalanced charge (Fri Jun 16 2006 - 11:34:42 CDT)
  • AMBER: LEaP error : unbalanced charge (Fri Jun 16 2006 - 08:52:33 CDT)
  • Fwd: Fwd: AMBER: MMPBSA error (Wed Jun 14 2006 - 06:27:51 CDT)
  • AMBER: LEaP Warning ... when do NH2-neutral fragment (Tue Jun 13 2006 - 13:40:47 CDT)
  • Fwd: AMBER: MMPBSA error (Tue Jun 13 2006 - 11:28:43 CDT)
  • AMBER: MMPBSA error (Tue Jun 13 2006 - 09:52:08 CDT)
  • AMBER: How to strip waters in trajectorie ? (Mon Jun 12 2006 - 14:50:02 CDT)
  • Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 14:15:06 CDT)
  • Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 13:37:49 CDT)
  • AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 11:41:52 CDT)
  • AMBER: MMPBSA problem (Fri Jun 09 2006 - 04:48:50 CDT)
  • AMBER: Problem with Leap (Thu Jun 08 2006 - 23:40:52 CDT)
  • Fwd: AMBER: How to build N-terminal of alanine : NH2 (Thu Jun 08 2006 - 07:32:22 CDT)
  • AMBER: How to build N-terminal of alanine : NH2 (Thu Jun 08 2006 - 02:59:34 CDT)
  • AMBER: md error : sander (Sun May 28 2006 - 13:11:45 CDT)
  • AMBER: check as error: load prepin in tleap (Fri May 26 2006 - 12:13:41 CDT)
  • AMBER: How to build NH2 of amino acid in amber (Wed May 24 2006 - 22:52:25 CDT)
  • AMBER: Fwd: RESP for deprotonated tyrosine and lysine (Wed May 24 2006 - 21:57:45 CDT)
  • AMBER: How to built the deprotonated form of lysine and tyrosine (Wed May 24 2006 - 21:49:04 CDT)
• Joachim Reichelt
  • AMBER: GLUTATHIONE (Wed Jan 11 2006 - 08:40:30 CST)
• Joe Nolan
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Wed Nov 29 2006 - 06:40:58 CST)
• John
  • AMBER: angle between planes (Fri Apr 07 2006 - 11:55:59 CDT)
  • AMBER: angle between planes (Fri Apr 07 2006 - 11:48:38 CDT)
• John Bushnell
  • RE: AMBER: amber8 error installation (Tue Mar 28 2006 - 20:20:42 CST)
• John Chuang²øÂ`»·¦Ñ®v
  • Re: AMBER: transition state (Mon Aug 14 2006 - 17:20:20 CDT)
  • AMBER: transition state (Mon Aug 07 2006 - 11:06:50 CDT)
• John J. Love
  • AMBER: proper restart procedure? (Tue May 02 2006 - 22:33:57 CDT)
• John Jett
  • RE: AMBER: Average pdb (Thu Mar 23 2006 - 16:32:00 CST)
• John Mongan
  • Re: AMBER: Implicit solvent question (Fri Jun 23 2006 - 11:09:49 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Wed Jun 07 2006 - 21:04:59 CDT)
  • Re: AMBER: Born igb =2 (Tue Apr 25 2006 - 12:30:22 CDT)
  • Re: AMBER: constant pH simulation (Tue Mar 21 2006 - 17:51:53 CST)
• John S. Zintsmaster
  • AMBER: Etot has downward drift in 'NVE' ensemble (Wed Jul 12 2006 - 21:01:08 CDT)
• John Vieceli
  • AMBER: C -N -CT-CT torsion parameters (Sun Oct 29 2006 - 19:10:49 CST)
• jojartb_at_pharm.u-szeged.hu
  • Re: AMBER: reading psf file (Sat Nov 18 2006 - 03:40:37 CST)
  • Re: AMBER: reading psf file (Sat Nov 18 2006 - 02:38:26 CST)
  • AMBER: reading psf file (Fri Nov 17 2006 - 17:24:24 CST)
• Jones de Andrade
  • AMBER: parameters for fluoromolecules with more than one single carbon? (Thu Oct 26 2006 - 16:51:27 CDT)
• Jordi Camps
  • AMBER: Parallelization method (Tue Dec 19 2006 - 12:19:40 CST)
  • RE: AMBER: gfortran/gcc versus ifort/icc (Thu Nov 16 2006 - 10:22:55 CST)
  • RE: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 11:50:54 CST)
• Jordi Rodrigo De Losada
  • AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 11:11:18 CST)
• Joseph Fernandez
  • AMBER: Questions (Mon Sep 18 2006 - 13:48:25 CDT)
  • RE: AMBER: Amber9/mpich2 performance (Fri May 12 2006 - 20:09:20 CDT)
  • AMBER: Amber9/mpich2 performance (Thu May 11 2006 - 17:30:03 CDT)
  • AMBER: PMEMD compilation error (Mon May 08 2006 - 14:37:03 CDT)
  • AMBER: restraintmask (Thu May 04 2006 - 13:22:21 CDT)
  • AMBER: Leap (Wed Jan 04 2006 - 15:36:13 CST)
• Joseph Nachman
  • Re: AMBER: mdcrd file (Mon Sep 11 2006 - 13:00:21 CDT)
  • Re: AMBER: mdcrd file (Fri Sep 08 2006 - 12:36:42 CDT)
  • AMBER: ptraj: nofit option for rmsd (Tue Aug 08 2006 - 10:27:41 CDT)
  • Re: AMBER: failed to save prm and xyz using ff96 (Wed Mar 01 2006 - 17:29:18 CST)
  • Re: AMBER: failed to save prm and xyz using ff96 (Wed Mar 01 2006 - 14:51:09 CST)
• Joshua
  • AMBER: strange temperature behavior when changing to constant pressure (Thu Nov 09 2006 - 13:52:33 CST)
  • Re: AMBER: restraints and constant pressure (Fri Oct 13 2006 - 17:46:26 CDT)
  • Re: AMBER: restraints and constant pressure (Fri Sep 15 2006 - 04:09:44 CDT)
  • AMBER: restraints and constant pressure (Fri Sep 15 2006 - 00:44:09 CDT)
• jrd
  • AMBER: AMBER 8: Problem with MPI_Finalize (Fri Jul 07 2006 - 13:24:08 CDT)
• julien
  • Re: AMBER: helix content during my simulation (Mon Feb 06 2006 - 09:04:51 CST)
  • AMBER: helix content during my simulation (Mon Feb 06 2006 - 07:09:38 CST)
• JunJun Liu
  • AMBER: ibelly not work (Wed Dec 06 2006 - 17:22:34 CST)
  • Re: AMBER: change from .rst file to .mdcrd file (Wed Oct 04 2006 - 15:14:22 CDT)
  • Re: AMBER: how to calculate rmsd for non hydrogen at oms? (Tue Oct 03 2006 - 14:10:25 CDT)
  • Re: AMBER: job crashes (Tue Sep 26 2006 - 22:39:52 CDT)
  • Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS (Mon Sep 25 2006 - 14:28:55 CDT)
  • AMBER: parameter for Cd2+? (Fri Aug 04 2006 - 10:50:46 CDT)
  • Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl (Thu Jun 29 2006 - 18:56:34 CDT)
  • Re: AMBER: kill job command? (Thu Jun 22 2006 - 08:13:04 CDT)
  • Re: AMBER: What's the meaning of NTYPES? (Wed Jun 21 2006 - 15:59:23 CDT)
  • AMBER: What's the meaning of NTYPES? (Wed Jun 21 2006 - 15:27:51 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 20:08:32 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 18:45:52 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 17:55:09 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 16:37:52 CDT)
  • AMBER: why has "ELE " a large fluctuation in MMPBSA? (Tue Jun 20 2006 - 08:56:25 CDT)
  • Re: Fwd: AMBER: MMPBSA error (Tue Jun 13 2006 - 10:51:58 CDT)
  • Re: AMBER: Nmode memory allocation problem (Tue Jun 13 2006 - 10:08:25 CDT)
  • AMBER: Nmode memory allocation problem (Mon Jun 12 2006 - 18:45:14 CDT)
  • Re: AMBER: Qestion about input for RESP program (Thu May 25 2006 - 09:01:41 CDT)
  • AMBER: Qestion about input for RESP program (Wed May 24 2006 - 21:44:41 CDT)
  • AMBER: output of first stage RESP calculation (Wed May 24 2006 - 17:23:55 CDT)
  • Re: AMBER: one question about mm_pbsa (Thu Apr 06 2006 - 16:48:20 CDT)
  • Re: AMBER: Problem with file size of sander outputs (Wed Feb 22 2006 - 14:58:00 CST)
  • Re: AMBER: amber 8 problem (Mon Feb 20 2006 - 10:05:53 CST)
  • Re: AMBER: sander problem (Thu Feb 16 2006 - 10:16:34 CST)
  • Re: AMBER: script advice (Wed Feb 15 2006 - 09:35:44 CST)
• Junmei Wang
  • RE: AMBER: Problem about dummy atoms when running antechamber (Thu Dec 07 2006 - 11:14:58 CST)
  • RE: AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:54:56 CST)
  • AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:21:40 CST)
  • RE: AMBER: bond information (Tue Nov 28 2006 - 16:16:03 CST)
  • RE: AMBER: Problem about dummy atoms when running antechamber (Tue Nov 28 2006 - 15:54:42 CST)
  • RE: AMBER: prepin file nan (Tue Nov 28 2006 - 15:47:03 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 13:42:42 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 11:19:27 CST)
  • RE: AMBER: Problem loading peptoid residues with antechamber (Wed Oct 18 2006 - 11:05:24 CDT)
  • RE: AMBER: Problem using antechamber (Fri Sep 29 2006 - 13:17:37 CDT)
  • RE: AMBER: parameters for Nickel and iron (Tue Sep 26 2006 - 16:38:08 CDT)
  • RE: AMBER: Amber8: problem related to antechamber (Tue Sep 26 2006 - 16:15:07 CDT)
  • RE: AMBER: parameters for Nickel and iron (Tue Sep 19 2006 - 11:16:26 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Tue Sep 12 2006 - 15:44:30 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Tue Sep 12 2006 - 13:41:21 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Mon Sep 11 2006 - 15:48:51 CDT)
  • RE: AMBER: antechamber charge calculation very sensitive to conformations ? (Thu Aug 24 2006 - 21:51:07 CDT)
  • AMBER: RE: antechamber failure on FMN (Thu Aug 17 2006 - 18:14:47 CDT)
  • RE: AMBER: antechamber error -> metals (Wed Aug 16 2006 - 21:29:46 CDT)
  • AMBER: RE: antechamber bond typing questions (Mon Aug 07 2006 - 20:43:05 CDT)
  • RE: AMBER: Fwd: difficulties with antechamber: tests dont even run (Tue Jul 25 2006 - 18:00:04 CDT)
  • AMBER: Antechamber 1.26 is released (Wed Jul 12 2006 - 18:42:32 CDT)
  • RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag (Fri Jul 07 2006 - 12:04:00 CDT)
  • RE: AMBER: Problem with bcc flag of antechamber (Thu Jul 06 2006 - 12:53:37 CDT)
  • AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected (Mon Jun 19 2006 - 22:08:56 CDT)
  • RE: AMBER: parmchk error (Thu Jun 15 2006 - 10:16:10 CDT)
  • AMBER: RE: antechamber and FMN (Wed Jun 07 2006 - 15:39:48 CDT)
  • RE: AMBER: Antechamber : +ve charge species (Tue May 30 2006 - 10:31:07 CDT)
  • RE: AMBER: problems with antechamber (Tue May 30 2006 - 10:20:33 CDT)
  • RE: AMBER: problem with prepfile (Thu May 25 2006 - 11:24:51 CDT)
  • RE: AMBER: problem with prep file (Mon May 15 2006 - 16:10:53 CDT)
  • AMBER: Nmode memory allocation error ? (Tue Apr 11 2006 - 13:47:46 CDT)
  • AMBER: Antechamber Package Announcement (Fri Feb 24 2006 - 10:26:52 CST)
  • RE: AMBER: antechamber for a database of organic molecules (Sun Feb 19 2006 - 21:32:22 CST)
  • RE: AMBER: Problem in Antechamber (Thu Jan 19 2006 - 17:02:39 CST)
• Juraj Kotulic Bunta
  • AMBER: Maximum system size in simulated annealing (Wed Aug 02 2006 - 21:03:11 CDT)
• Jyh-Shyong Ho
  • Re: AMBER: Amber parallel version (Wed Sep 06 2006 - 01:43:08 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 21:11:21 CDT)
  • AMBER: building AMBER9 with gfortran/cygwin (Thu Aug 24 2006 - 21:30:02 CDT)
• jz7_at_duke.edu
  • AMBER: error estimate for free energy perturbation calculation (Tue Oct 24 2006 - 23:15:26 CDT)
• K. Yarem
  • AMBER: conflicting types for XawScrolledTableSetLocation (Thu May 04 2006 - 10:43:57 CDT)
  • AMBER: OSX 10.4 G4 xlf90 compilation errors (Mon Mar 27 2006 - 14:06:59 CST)
  • AMBER: How to patch the configure script (macosx) (Mon Mar 06 2006 - 09:40:58 CST)
• Kailee
  • AMBER: EXTRA_PTS: frtype 2 Should not be here (Thu Dec 21 2006 - 12:26:31 CST)
  • Re: AMBER: sander: cannot execute binary file (Tue Dec 19 2006 - 10:13:48 CST)
  • Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 11:06:36 CST)
  • Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 10:41:11 CST)
  • Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 11:25:21 CST)
  • AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 09:53:50 CST)
• kakali sen
  • AMBER: addition of subroutine in pmemd module (Mon Dec 11 2006 - 12:52:37 CST)
  • Re: AMBER: Unit of force (Wed Nov 08 2006 - 07:12:41 CST)
  • AMBER: Unit of force (Wed Nov 08 2006 - 05:06:16 CST)
  • AMBER: Re: Unit of force (Wed Nov 08 2006 - 00:41:30 CST)
• kanazta1_at_yahoo.co.jp
  • AMBER: multiple "restraint_wt" in sander (Mon Jul 03 2006 - 09:12:21 CDT)
• Kara Di Giorgio
  • Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) (Thu Jun 15 2006 - 11:27:45 CDT)
  • Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) (Wed Jun 14 2006 - 12:20:40 CDT)
  • AMBER: Difficulty loading a pdb file (Tue Jun 13 2006 - 13:20:41 CDT)
  • AMBER: Question about renaming a residue (Fri Feb 17 2006 - 17:28:26 CST)
• Karen Callahan
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 13:19:49 CST)
• Kateryna Miroshnychenko
  • AMBER: ff for drug-dna complex and drug atom types assignment (Mon Oct 23 2006 - 11:08:59 CDT)
  • AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Mon Aug 14 2006 - 08:19:46 CDT)
  • AMBER: small bug in ambmask (amber9) (Mon Jul 10 2006 - 09:53:02 CDT)
  • Re: AMBER: problems about compiling a parallel version of AMBER 9 (Tue Jun 27 2006 - 03:41:21 CDT)
  • AMBER: cluster architecture for the best amber performance (Wed May 03 2006 - 07:54:58 CDT)
  • RE:AMBER: leap: syntax error when use source command (Wed Mar 01 2006 - 06:58:22 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Thu Feb 16 2006 - 04:41:52 CST)
  • Re: AMBER: double stranded polyribocytidylic acid (Tue Feb 14 2006 - 06:09:36 CST)
  • AMBER: double stranded polyribocytidylic acid (Tue Feb 14 2006 - 03:44:01 CST)
  • Re: AMBER: bugfix for impropers in parmchk (Mon Feb 06 2006 - 09:09:06 CST)
  • AMBER: positional restraints & constant pressure (Thu Feb 02 2006 - 09:40:30 CST)
  • AMBER: bugfix for impropers in parmchk (Wed Jan 18 2006 - 08:48:55 CST)
  • AMBER: ATCOR.dat format (Thu Jan 12 2006 - 10:43:05 CST)
• kawamura_hiro_at_riken.jp
  • AMBER: amber9 Test Failer (Tue Aug 15 2006 - 07:21:49 CDT)
  • AMBER: amber8 bugfix effects (Wed May 24 2006 - 03:17:32 CDT)
  • AMBER: amber compilation on Red Hat 8 with MPICH (Wed May 17 2006 - 00:38:35 CDT)
• Kay Kunes
  • AMBER: CARNAL: H-BOND Specifying side chains only (Tue Feb 21 2006 - 14:47:14 CST)
• Keerthi Gottipati
  • AMBER: Amber9 installation error (Fri Nov 17 2006 - 18:12:53 CST)
  • AMBER: PCA results with explicit Vs Implicit solvation (Mon Nov 06 2006 - 10:32:16 CST)
  • Re: AMBER: CARNAL: carnal source code (Thu Oct 26 2006 - 07:41:21 CDT)
  • AMBER: CARNAL: carnal source code (Wed Oct 25 2006 - 17:14:41 CDT)
• Ken Merz
  • Re: AMBER: parameters for Nickel and iron (Tue Sep 19 2006 - 15:00:51 CDT)
  • AMBER: (Sat Jul 29 2006 - 10:28:53 CDT)
  • Re: AMBER: Having trouble getting Iron parameters for QM/MM (Thu Jun 29 2006 - 14:54:45 CDT)
  • Re: AMBER: Fully QM periodic runs (Thu Jun 15 2006 - 09:10:13 CDT)
  • Re: AMBER: ESP calculations. (Tue May 30 2006 - 06:59:38 CDT)
  • Re: AMBER: ESP calculations. (Tue May 30 2006 - 06:55:24 CDT)
• Kenley Barrett
  • AMBER: rgbmax--something wrong with my input file? (Tue Jun 27 2006 - 16:10:27 CDT)
  • AMBER: problem with installation, or bug? (Thu May 18 2006 - 05:09:10 CDT)
  • AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed (Wed May 10 2006 - 15:04:16 CDT)
  • Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why (Wed May 10 2006 - 14:54:46 CDT)
  • Re: AMBER: xleap not recognizing residue (Mon May 08 2006 - 12:04:37 CDT)
  • AMBER: xleap not recognizing residue (Sun May 07 2006 - 19:13:13 CDT)
  • AMBER: concatenating .mdcrd files (Wed May 03 2006 - 11:31:59 CDT)
  • Re: AMBER: increase in computational time with LES (Sun Apr 23 2006 - 17:46:56 CDT)
  • AMBER: increase in computational time with LES (Sun Apr 23 2006 - 16:53:29 CDT)
  • Re: AMBER: saltcon with explicit water? (Wed Apr 12 2006 - 18:07:44 CDT)
  • AMBER: saltcon with explicit water? (Wed Apr 12 2006 - 11:36:20 CDT)
  • AMBER: chirality.c error in xleap (Fri Mar 31 2006 - 16:43:33 CST)
  • Re: AMBER: charge constraints in resp (Thu Mar 30 2006 - 13:46:49 CST)
  • AMBER: charge constraints in resp (Thu Mar 30 2006 - 10:22:36 CST)
  • AMBER: a challenge: a periodic box that cuts through a monomer (Mon Mar 20 2006 - 16:06:49 CST)
  • Re: AMBER: aligning polymer with Z-axis of periodic box (Wed Mar 08 2006 - 19:26:12 CST)
  • AMBER: aligning polymer with Z-axis of periodic box (Wed Mar 08 2006 - 15:59:18 CST)
  • AMBER: specifying RSOLV when calculating 2003 force field charges (Fri Feb 24 2006 - 14:50:07 CST)
  • AMBER: does anyone have library file for methylated histidine, 2003 ff? (Tue Feb 21 2006 - 10:27:13 CST)
  • Re: AMBER: instructions for making a library file for an unusual residue? (Mon Feb 20 2006 - 18:22:22 CST)
  • AMBER: instructions for making a library file for an unusual residue? (Sat Feb 18 2006 - 16:02:42 CST)
  • Re: AMBER: non bond list overflow (Tue Feb 07 2006 - 10:32:18 CST)
  • AMBER: non bond list overflow (Mon Feb 06 2006 - 21:43:06 CST)
  • AMBER: simulated annealing run--temp won't rise (Thu Feb 02 2006 - 21:26:52 CST)
  • AMBER: atom type "O3" not recognized by XLeap (Fri Jan 27 2006 - 11:32:48 CST)
• kepa koldo burusco
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 11:45:55 CST)
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Fri Nov 24 2006 - 05:38:06 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 04:27:01 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 05:53:27 CST)
  • AMBER: PTRAJ: radius of gyration (Fri Nov 10 2006 - 11:05:09 CST)
  • Re: AMBER: building a box (Wed Nov 08 2006 - 06:08:32 CST)
  • AMBER: building a box (Tue Nov 07 2006 - 10:52:28 CST)
• Kerry P Donny-Clark
  • AMBER: Trouble with ptraj closestwater in Amber8 (Thu May 04 2006 - 12:29:23 CDT)
• Kevin Kelliher
  • AMBER: G5 OSX serial compile error (Tue Dec 26 2006 - 15:18:56 CST)
• Kevin Murphy
  • RE: AMBER: partial charge glycam (Tue Jan 24 2006 - 06:18:05 CST)
  • AMBER: partial charge glycam (Fri Jan 20 2006 - 05:28:27 CST)
• khn _
  • AMBER: COM (Thu Jun 08 2006 - 19:13:27 CDT)
• Kijeong Kwac
  • RE: RE: Re: Re: AMBER: Question about sander code (Fri Oct 20 2006 - 17:48:07 CDT)
  • RE: Re: Re: AMBER: Question about sander code (Fri Oct 20 2006 - 17:32:00 CDT)
  • RE: Re: AMBER: Question about sander code (Fri Oct 20 2006 - 16:08:17 CDT)
  • AMBER: Question about sander code (Fri Oct 20 2006 - 13:13:49 CDT)
• Kirk Hevener
  • AMBER: Amber Installation Help (Mon Aug 07 2006 - 07:43:25 CDT)
• kkirschn_at_hamilton.edu
  • Re: AMBER: partial charge glycam (Thu Jan 26 2006 - 08:49:35 CST)
  • Re: AMBER: partial charge glycam (Fri Jan 20 2006 - 09:39:14 CST)
• Knut Langsestmo
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 11:17:04 CDT)
• Knut Langsetmo
  • Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) (Wed Jun 14 2006 - 14:55:56 CDT)
• Kristina Furse
  • Re: AMBER: imaging issue (Mon Oct 30 2006 - 12:30:25 CST)
  • Re: AMBER: Two different HIS ligands (Thu Oct 26 2006 - 16:41:49 CDT)
• Lachele Foley (Lists)
  • Re: AMBER: phantom sander8 in dmesg (Mon Dec 04 2006 - 11:21:12 CST)
  • AMBER: phantom sander8 in dmesg (Mon Nov 27 2006 - 15:25:57 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Thu Nov 16 2006 - 14:49:23 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 09:37:27 CST)
  • AMBER: gfortran/gcc versus ifort/icc (Tue Nov 14 2006 - 08:35:21 CST)
  • Re: AMBER: Parallel compile: ld: cannot find -lfmpi (Mon Sep 11 2006 - 15:39:55 CDT)
  • AMBER: Parallel compile: ld: cannot find -lfmpi (Mon Sep 11 2006 - 10:38:00 CDT)
  • Re: AMBER: seg fault during test.serial (Mon Sep 11 2006 - 09:50:57 CDT)
  • AMBER: seg fault during test.serial (Fri Sep 08 2006 - 15:45:05 CDT)
• Lars Packschies
  • AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 (Fri Jul 14 2006 - 05:18:08 CDT)
• laura zanet
  • AMBER: nonplanarity of NH2 groups (Wed Dec 06 2006 - 09:48:33 CST)
• Lauren O'Neil
  • Re: AMBER: center of mass dihedral restraints (Mon Sep 25 2006 - 10:39:19 CDT)
  • AMBER: center of mass dihedral restraints (Fri Sep 22 2006 - 14:03:32 CDT)
  • AMBER: pmf input files (Wed Aug 16 2006 - 12:20:45 CDT)
  • AMBER: Curves and Average Structures (Mon Jun 26 2006 - 12:26:46 CDT)
• Laurent Chiche
  • Re: AMBER: Zoom (Thu Mar 16 2006 - 10:40:42 CST)
  • Re: AMBER: Zoom (Thu Mar 16 2006 - 09:37:38 CST)
• Lee Kyung-koo
  • [RE]AMBER: RE: I got the error meassage in testcase of QMMM (Tue Nov 07 2006 - 10:59:16 CST)
  • [RE]AMBER: RE: I got the error meassage in testcase of QMMM (Tue Nov 07 2006 - 10:46:25 CST)
  • AMBER: I got the error meassage in testcase of QMMM (Fri Nov 03 2006 - 23:33:44 CST)
  • [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 02:53:53 CST)
  • [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 17:25:25 CST)
  • AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 13:50:28 CST)
• Lee, Young-Tae
  • AMBER: RDC refinement (Fri Dec 08 2006 - 14:50:42 CST)
  • AMBER: Error in reading RDC data (Wed Sep 13 2006 - 15:09:42 CDT)
• Lei Wang
  • RE: AMBER: Ask for your help to install Amber8 software (Wed Feb 08 2006 - 09:16:32 CST)
• Lena Dolghih
  • AMBER: Modelling dsDNA less than 10bp (Fri Jul 21 2006 - 08:15:16 CDT)
• lhsong
  • Re: AMBER: error propagation in MM-PBSA binding free energy calculation (Fri Apr 28 2006 - 17:37:42 CDT)
  • AMBER: error propagation in MM-PBSA binding free energy calculation (Tue Apr 25 2006 - 22:22:41 CDT)
  • AMBER: mm-pbsa: distant-dependent dielectric constant (Sat Apr 08 2006 - 13:30:56 CDT)
• Li Su
  • AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 12:28:12 CST)
  • AMBER: How does amber calculate HB? (Mon May 01 2006 - 20:01:05 CDT)
  • AMBER: what is the integration scheme for langevin dynamic used in amber8 (Sat Apr 01 2006 - 07:17:02 CST)
• Lihua Wang
  • RE: AMBER: amber9 compilation error on SGI altix (Sat Apr 22 2006 - 17:48:40 CDT)
  • AMBER: amber9 compilation error on SGI altix (Sat Apr 22 2006 - 12:58:26 CDT)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 14:27:40 CST)
  • AMBER: parameter loading problem (Thu Feb 02 2006 - 15:01:51 CST)
• lily ferreira
  • AMBER: MM_PBSA (Wed Dec 20 2006 - 07:46:00 CST)
  • AMBER: MM_PBSA (Wed Dec 20 2006 - 07:42:20 CST)
  • AMBER: (no subject) (Mon Dec 18 2006 - 02:14:44 CST)
  • Re: AMBER: Charges of enantiomers for Amber8 (Thu Jan 26 2006 - 00:46:53 CST)
  • AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 02:01:24 CST)
• linfu
  • Re: AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 18:54:43 CST)
  • AMBER: charge problem in MM-PBSA (Tue Dec 19 2006 - 19:53:52 CST)
  • Re: AMBER: prepin file nan (Tue Nov 28 2006 - 03:00:30 CST)
  • Re: AMBER: mm_pbsa segmentation faults (Mon Sep 25 2006 - 19:56:08 CDT)
  • AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? (Tue Sep 19 2006 - 01:40:52 CDT)
  • Re: AMBER: Can salt effect be determined in GB medel? (Tue Sep 19 2006 - 01:32:16 CDT)
  • Re: RE: AMBER: potential energy (Mon Sep 18 2006 - 20:44:18 CDT)
  • Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? (Sat Jun 10 2006 - 22:27:20 CDT)
  • AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? (Fri Jun 09 2006 - 22:25:24 CDT)
  • AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. (Mon Jun 05 2006 - 21:24:17 CDT)
  • Re: AMBER: manual docking (Sat Jun 03 2006 - 02:39:44 CDT)
  • Re: AMBER: problems with antechamber (Tue May 30 2006 - 07:01:59 CDT)
  • AMBER: amber7 compiling error (Sun Apr 16 2006 - 10:26:17 CDT)
  • AMBER: parallel problem of amber8 (Mon Feb 20 2006 - 07:01:02 CST)
  • AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ? (Sun Feb 05 2006 - 10:49:32 CST)
  • Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 03:27:57 CST)
  • AMBER: about mmpbsa (Mon Jan 09 2006 - 19:17:15 CST)
  • AMBER: Could you help me about mmpbsa! thank you! (Sun Jan 08 2006 - 03:28:13 CST)
• Lishan Yao
  • AMBER: "vector" command in ptraj (Mon Apr 10 2006 - 13:20:56 CDT)
• litong
  • AMBER: about the decomposition energies using mm/pbsa (Thu Apr 20 2006 - 08:34:11 CDT)
• Lorenzo Gontrani
  • AMBER: Shake&Lone Pairs (Wed Oct 25 2006 - 05:58:59 CDT)
  • AMBER: PKDIV lone pair dihedrals (Mon Oct 23 2006 - 12:16:25 CDT)
  • AMBER: sander/topology problem (Tue Oct 17 2006 - 11:51:39 CDT)
• Lubans, Peter S
  • AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 11:55:19 CDT)
• lucas luquitas
  • AMBER: Again SASA (Mon May 22 2006 - 14:51:22 CDT)
  • Re: AMBER: Error in RST files in long simulations! (Mon Feb 20 2006 - 17:08:38 CST)
  • AMBER: Error in RST files in long simulations! (Mon Feb 20 2006 - 13:59:35 CST)
  • AMBER: mm_pbsa output (Mon Feb 13 2006 - 17:40:28 CST)
• luckyang_at_gmail.com
  • Re: AMBER: use_pme=0 problem (Fri May 26 2006 - 15:19:11 CDT)
  • Re: AMBER: use_pme=0 problem (Fri May 26 2006 - 14:10:19 CDT)
  • Re: AMBER: use_pme=0 problem (Thu May 25 2006 - 20:56:30 CDT)
  • Re: AMBER: use_pme=0 problem (Thu May 25 2006 - 12:09:59 CDT)
  • Re: AMBER: use_pme=0 problem (Wed May 24 2006 - 19:51:10 CDT)
  • Re: AMBER: use_pme=0 problem (Wed May 24 2006 - 19:20:35 CDT)
  • AMBER: use_pme=0 problem (Wed May 24 2006 - 18:18:47 CDT)
  • Re: AMBER: Problem in compiling sander with MMTSB (Fri Feb 03 2006 - 19:21:51 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Wed Feb 01 2006 - 21:26:55 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Wed Feb 01 2006 - 13:39:04 CST)
  • Re: AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 17:51:06 CST)
  • AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 17:09:09 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Tue Jan 31 2006 - 00:10:15 CST)
  • AMBER: Problem in compiling sander with MMTSB (Mon Jan 30 2006 - 20:06:32 CST)
• Luis Gracia
  • Re: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 12:34:36 CST)
• Lwin, ThuZar
  • RE: AMBER: antechamber:tutorial. . (Thu Nov 09 2006 - 14:02:28 CST)
  • AMBER: FW: antechamber:tutorial (Thu Nov 09 2006 - 13:03:46 CST)
  • AMBER: antechamber:tutorial (Thu Nov 09 2006 - 12:48:58 CST)
  • RE: AMBER: angle between two vectors. . (Mon Oct 16 2006 - 15:51:28 CDT)
  • AMBER: angle between two vectors (Thu Oct 12 2006 - 11:51:15 CDT)
  • AMBER: how to reassign charges (Wed Aug 09 2006 - 13:16:01 CDT)
  • RE: AMBER: question on chargning free energy in solvent vs vacuum. . (Fri Aug 04 2006 - 14:02:10 CDT)
  • AMBER: how to take care of toluene system neutrality (Fri Aug 04 2006 - 13:31:53 CDT)
  • AMBER: how to take care of toluene system neutrality (Fri Aug 04 2006 - 13:27:39 CDT)
  • AMBER: question on chargning free energy in solvent vs vacuum (Thu Aug 03 2006 - 12:08:07 CDT)
  • AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms (Thu Aug 03 2006 - 10:14:28 CDT)
  • RE: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . (Thu Jul 27 2006 - 20:35:19 CDT)
  • AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap (Tue Jul 25 2006 - 19:39:32 CDT)
  • RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . (Wed Jul 05 2006 - 18:01:25 CDT)
  • RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . (Mon Jul 03 2006 - 14:02:31 CDT)
  • AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 (Wed Jun 28 2006 - 19:58:14 CDT)
  • AMBER: terms in mm-pbsa (Wed Jun 21 2006 - 10:48:37 CDT)
  • AMBER: lipid bi-layer system (Thu May 04 2006 - 12:41:11 CDT)
• Lydia
  • AMBER: soft-core potential in amber? (Mon Feb 06 2006 - 18:13:14 CST)
  • Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 11:43:03 CST)
  • AMBER: rms in principal component analysis (Tue Jan 17 2006 - 14:54:32 CST)
• M. L. Dodson
  • Re: AMBER: General Question about Abmer (Mon Dec 11 2006 - 08:34:45 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 12:05:33 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 08:37:05 CST)
  • AMBER: gfortran and amber9 success on FreeBSD (Sat Nov 18 2006 - 16:02:16 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 14:14:07 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 14:47:22 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 13:35:34 CST)
  • Re: AMBER: angle between two vectors (Thu Oct 12 2006 - 12:40:35 CDT)
  • Re: AMBER: library for 8oxoguanine (Mon Jul 24 2006 - 15:07:17 CDT)
  • Re: AMBER: Ring of dna (Mon Jul 17 2006 - 09:56:03 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 21:34:07 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 17:00:10 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 13:59:48 CDT)
  • AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 13:37:19 CDT)
• M. Scott Shell
  • Re: AMBER: problem with amber 9 and igb=5 (Sat Jun 10 2006 - 13:40:05 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Fri Jun 09 2006 - 00:15:56 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Thu Jun 08 2006 - 11:05:10 CDT)
  • Re: AMBER: problem with amber 9 and igb=5 (Thu Jun 08 2006 - 10:55:36 CDT)
  • AMBER: problem with amber 9 and igb=5 (Wed Jun 07 2006 - 20:06:02 CDT)
• Maarit Hellman
  • AMBER: deviations from idealized geometry (Wed Apr 12 2006 - 04:02:33 CDT)
• madhumalar_at_bii-sg.org
  • Re: AMBER: Zinc coordinating CYS (Fri Jul 28 2006 - 04:17:36 CDT)
  • Re: AMBER: Zinc coordinating CYS (Thu Jul 27 2006 - 19:37:12 CDT)
  • AMBER: calculating dihedral angles, radius of gyration (Fri Jul 07 2006 - 04:57:14 CDT)
• Magne Olufsen
  • AMBER: ptraj: calculating distances between atoms in charges residues (Fri May 26 2006 - 02:13:48 CDT)
  • AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure (Sun Feb 26 2006 - 13:00:23 CST)
  • AMBER: minimalization prior to nmode analysis, is it necessary? (Wed Jan 04 2006 - 11:42:21 CST)
• Mahalakshmi Sahasranaman
  • AMBER: increase force constants (Thu Aug 24 2006 - 08:45:28 CDT)
  • AMBER: problem loading forcefield leaprc.ff86 (Fri May 19 2006 - 09:27:38 CDT)
  • AMBER: distance dependent dielectric constant (Wed May 17 2006 - 05:36:55 CDT)
  • AMBER: installation problem (Mon May 15 2006 - 13:12:51 CDT)
  • AMBER: Hexahydrated Counterions (Wed May 10 2006 - 08:22:02 CDT)
• mahdi fathi
  • AMBER: bugfix (Sun Dec 03 2006 - 09:17:42 CST)
  • RE: AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 23:46:22 CST)
• Maniopoulou, A \(Mina\)
  • AMBER: Amber: Parallel Installation Problems (Fri Oct 27 2006 - 12:13:56 CDT)
  • RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Tue Oct 24 2006 - 08:59:26 CDT)
  • RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Fri Oct 20 2006 - 05:27:29 CDT)
  • AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Thu Oct 19 2006 - 07:48:08 CDT)
• Manish Datt
  • Re: AMBER: parallel installation of amber8 on HP cluster (Wed Jul 26 2006 - 12:54:51 CDT)
  • AMBER: parallel installation of amber8 on HP cluster (Wed Jul 26 2006 - 05:00:30 CDT)
  • AMBER: charge neutralization with GB (Sun Mar 05 2006 - 11:27:34 CST)
  • AMBER: requirement of delphi for mm_pbsa (Tue Jan 03 2006 - 12:46:53 CST)
• Marcela Madrid
  • AMBER: ptraj (Fri Jun 09 2006 - 16:19:54 CDT)
  • AMBER: ptraj PCA (Thu Jan 19 2006 - 19:04:46 CST)
• Marcelo Puiatti
  • Re: AMBER: RESP charges of iron-porphyrin system (Wed Oct 25 2006 - 12:42:07 CDT)
  • AMBER: Heme parameters (Wed Aug 09 2006 - 17:58:35 CDT)
• Margaret S. Cheung
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 09:23:29 CST)
  • AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 17:16:34 CST)
• Marie Brut
  • AMBER: second derivative matrix (Tue Jun 20 2006 - 07:28:02 CDT)
  • AMBER: Organic molecules (Tue Feb 14 2006 - 10:42:23 CST)
  • AMBER: Hessian matrix (Mon Feb 06 2006 - 06:12:53 CST)
• Marie-Pierre Durrieu
  • AMBER: helices in GB simulations (Mon Nov 27 2006 - 11:43:41 CST)
• Mark H. Schofield
  • AMBER: missing benchmark files (Tue Sep 26 2006 - 17:32:38 CDT)
• Mark Williamson
  • Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 15:04:06 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Fri Nov 24 2006 - 07:54:34 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 16:06:35 CST)
  • Re: AMBER: antechamber:tutorial (Thu Nov 09 2006 - 13:06:24 CST)
  • Re: AMBER: leap usage (Thu Nov 02 2006 - 09:26:42 CST)
  • Re: AMBER: Compile AMBER 8 (Fri Oct 27 2006 - 11:03:07 CDT)
  • Re: AMBER: Amber 9 installation problem (Thu Oct 19 2006 - 11:12:01 CDT)
  • Re: AMBER: mm_pbsa segmentation faults (Tue Sep 26 2006 - 16:41:06 CDT)
  • Re: AMBER: mdcrd file (Thu Sep 07 2006 - 12:39:12 CDT)
  • Re: AMBER: Format of mdcrd files (Wed Aug 09 2006 - 09:32:06 CDT)
  • Re: AMBER: Can you use VMD to measure bond angles/lengths (Tue Jul 04 2006 - 11:06:59 CDT)
  • Re: AMBER: Tutorial 4-section 4 (plc.frcmod) (Mon Jul 03 2006 - 07:46:08 CDT)
  • AMBER: SHAKE, TIP3P and 2fs Timesteps (Wed May 31 2006 - 12:32:56 CDT)
  • Re: AMBER: Tutorial one : libsvml.so error (Wed May 17 2006 - 02:27:05 CDT)
  • Re: AMBER: RE: Respgen segemtation fault - debug attempt (Thu Apr 20 2006 - 11:56:55 CDT)
  • Re: AMBER: RE: Respgen segemtation fault - debug attempt (Thu Apr 20 2006 - 08:23:55 CDT)
  • Re: AMBER: installation problem (Tue Mar 28 2006 - 21:40:27 CST)
  • Re: AMBER: amber8 error installation (Tue Mar 28 2006 - 10:08:46 CST)
  • Re: AMBER: amber8 error installation (Tue Mar 28 2006 - 09:23:28 CST)
  • Re: AMBER: install error (Thu Mar 02 2006 - 05:13:40 CST)
  • AMBER: Nmode vs QM Freq Calculation (Wed Mar 01 2006 - 05:28:57 CST)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 15:00:09 CST)
• Markus Kaukonen
  • AMBER: Ptraj syntax change Amber8->Amber9 ? (Wed Nov 22 2006 - 04:35:26 CST)
  • AMBER: ptraj dumpq feature/bug (Thu Aug 24 2006 - 03:31:51 CDT)
• Markus O Kaukonen
  • AMBER: Truncated octahedral box as triclinic lattice vectors (Mon Feb 20 2006 - 08:42:45 CST)
  • AMBER: negative T_solv values (Wed Feb 15 2006 - 02:25:40 CST)
• Markus Weingarth
  • AMBER: Problems with equilibrating the starting density (Fri Nov 03 2006 - 11:32:20 CST)
• Martin LEPSIK
  • AMBER: System in polarizable waters (Mon Sep 11 2006 - 11:14:24 CDT)
  • AMBER: Ca2+ polarizability (Thu Sep 07 2006 - 04:02:38 CDT)
  • AMBER: GBSA of nonstandard cations (Thu Jun 15 2006 - 17:46:16 CDT)
• Martin Peters
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 11:22:06 CST)
  • Re: AMBER: some questions and problems about antechamber and divcon (Fri Jun 02 2006 - 08:07:03 CDT)
  • Re: AMBER: How to build 1,4-dimethyl benzene with amber9 (Fri Apr 28 2006 - 18:00:29 CDT)
  • AMBER: How to build 1,4-dimethyl benzene with amber9 (Fri Apr 28 2006 - 16:27:09 CDT)
• mathew k varghese
  • AMBER: Free-energy using MM-PBSA (Thu Oct 19 2006 - 03:05:45 CDT)
  • AMBER: manual docking (Fri Jun 02 2006 - 22:39:13 CDT)
  • AMBER: manual docking (Fri Jun 02 2006 - 22:50:03 CDT)
  • Re: AMBER: xmgr error (Fri May 19 2006 - 05:54:00 CDT)
  • RE: AMBER: density (Wed May 17 2006 - 22:24:07 CDT)
  • RE: AMBER: density (Tue May 16 2006 - 23:09:17 CDT)
  • AMBER: density (Mon May 15 2006 - 23:02:51 CDT)
• Mathy Froeyen
  • Re: AMBER: G5 OSX serial compile error (Thu Dec 28 2006 - 05:12:13 CST)
  • Re: AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 06:54:48 CST)
  • AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 (Tue Apr 11 2006 - 12:44:40 CDT)
  • Re: AMBER: about Br- parameters (Fri Mar 03 2006 - 08:38:42 CST)
• matteo filandri
  • Re: AMBER: Cosine content calculation (Thu Mar 09 2006 - 04:01:20 CST)
  • AMBER: Cosine content calculation (Wed Mar 08 2006 - 09:59:58 CST)
• Matthew Tessier
  • AMBER: Solvating a bilayer (Fri Dec 15 2006 - 13:32:25 CST)
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:48:32 CST)
  • AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:09:13 CST)
• mbrut_at_laas.fr
  • Re: AMBER: Hessian matrix (Tue Feb 07 2006 - 11:55:17 CST)
• Md Jahidul Islam
  • AMBER: xleap (Thu Jul 27 2006 - 04:49:36 CDT)
• mdione_at_fcq.unc.edu.ar
  • AMBER: sander testing problem (Mon Feb 27 2006 - 15:53:23 CST)
• Melinda Layten
  • Re: AMBER: Dimer Image Wrapping (Thu Mar 30 2006 - 12:16:06 CST)
  • AMBER: Dimer Image Wrapping (Wed Mar 29 2006 - 17:12:00 CST)
  • Re: AMBER: sander restart problem (Mon Mar 06 2006 - 11:35:01 CST)
  • Re: AMBER: MD job stopped without any error information? (Mon Feb 27 2006 - 09:18:09 CST)
• Melissa Foley
  • AMBER: combining different versions of AMBER (Fri Jul 21 2006 - 14:25:35 CDT)
• Mengjuei Hsieh
  • Re: AMBER: Installing Amber 9 on Mac Pro (Mon Dec 11 2006 - 19:52:07 CST)
  • Re: AMBER: AMBER9: MacG5 parallel sander.MPI (Sun May 07 2006 - 09:33:01 CDT)
  • Re: AMBER: xleap on iMac G5 (Sat May 06 2006 - 00:44:00 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 21:05:41 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 19:30:16 CDT)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 19:24:30 CDT)
  • Re: AMBER: AMBER9: MacG5 parallel sander.MPI (Wed May 03 2006 - 19:32:14 CDT)
• mernst_at_tricity.wsu.edu
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 12:06:07 CDT)
  • AMBER: generate "template" frcmod from standard residues? (Wed Aug 16 2006 - 13:41:02 CDT)
• mfyang
  • Re: AMBER: question about solvatecap commander (Tue Mar 07 2006 - 21:07:08 CST)
• Michael Crowley
  • Re: AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 19:41:32 CST)
  • Re: AMBER: 'lastrst' error for amber8 (Wed Sep 13 2006 - 10:14:08 CDT)
  • Re: AMBER: parallel installation of amber8 on HP cluster (Wed Jul 26 2006 - 13:52:09 CDT)
  • Re: AMBER: parallel installation of amber8 on HP cluster (Wed Jul 26 2006 - 09:42:19 CDT)
  • Re: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem (Mon May 22 2006 - 13:28:58 CDT)
  • Re: AMBER: a question about "solvateoct" in AMBER 8 (Fri Apr 21 2006 - 14:50:52 CDT)
  • Re: AMBER: Constant P for non-orthorhombic cells (Wed Apr 12 2006 - 13:24:05 CDT)
• Michael F. Summers
  • AMBER: N1-protonated adenosine, N-terminal myristyl group (Tue Oct 31 2006 - 14:54:49 CST)
• Michael John Hanby
  • AMBER: PMEMD and OpenMPI, anyone have config options? (Wed Dec 27 2006 - 14:04:50 CST)
  • RE: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 17:13:47 CST)
  • RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 15:52:23 CST)
  • AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 15:47:15 CST)
  • RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 21:31:57 CST)
  • AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 14:09:34 CST)
  • AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 15:26:11 CST)
  • AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 16:13:05 CST)
  • RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 15:43:06 CST)
  • RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 14:59:48 CST)
  • AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 12:06:16 CST)
• Michael Mazanetz
  • Re: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes (Thu Sep 14 2006 - 03:15:43 CDT)
  • AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes (Wed Sep 13 2006 - 15:42:02 CDT)
  • AMBER: prepi definitions (Wed Feb 01 2006 - 09:56:25 CST)
• Michel Becker
  • AMBER: Restraints of the strand-endings? (Tue Nov 14 2006 - 14:22:36 CST)
  • AMBER: <kein Betreff> (Mon Nov 13 2006 - 05:21:58 CST)
  • AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 11:45:05 CST)
• Miguel Ferreira
  • AMBER: coordinate out of bounds (Wed Dec 13 2006 - 19:09:57 CST)
  • AMBER: PCA and projections (Wed Nov 01 2006 - 08:11:57 CST)
  • AMBER: atomifluct (Fri Aug 25 2006 - 06:09:03 CDT)
  • AMBER: MM-PBSA questions (Wed Jun 28 2006 - 20:26:14 CDT)
  • AMBER: Leap: neutralising the charge (Tue Jun 27 2006 - 04:49:36 CDT)
  • AMBER: MD stopped (Sat Jun 10 2006 - 04:33:05 CDT)
  • Re: AMBER: molsurf.c error (Fri May 05 2006 - 06:46:24 CDT)
  • RE: AMBER: molsurf.c error (Thu May 04 2006 - 14:43:41 CDT)
  • AMBER: molsurf.c error (Thu May 04 2006 - 11:00:31 CDT)
  • Re: AMBER: MM-PBSA problem (Mon Apr 17 2006 - 12:24:05 CDT)
  • Re: AMBER: MM-PBSA problem (Fri Apr 14 2006 - 16:07:20 CDT)
  • AMBER: MM-PBSA problem (Fri Apr 14 2006 - 10:27:43 CDT)
• Mike Summers
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 17:34:07 CST)
  • AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 14:46:26 CST)
• Mingfeng Yang
  • Re: AMBER: RESP charge fitting for HFIP (Wed Dec 20 2006 - 12:31:53 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Tue Dec 19 2006 - 01:17:24 CST)
  • AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 20:44:19 CST)
  • Re: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 15:06:18 CST)
  • Re: AMBER: Closest(closest water) (Mon Oct 30 2006 - 14:29:00 CST)
  • AMBER: RESP charge fitting (Fri Oct 27 2006 - 19:35:37 CDT)
  • AMBER: TFE parameters for Amber (Thu Oct 12 2006 - 18:33:21 CDT)
  • Re: AMBER: Temperature fluctuation BIG with ntt=3 (Thu Sep 21 2006 - 23:59:54 CDT)
  • AMBER: Temperature fluctuation BIG with ntt=3 (Thu Sep 21 2006 - 18:14:24 CDT)
  • AMBER: Mixed solvent? (Wed Sep 13 2006 - 14:44:32 CDT)
  • AMBER: TI tutorial (Tue Aug 15 2006 - 17:22:10 CDT)
  • Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 14:06:56 CDT)
  • AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 13:25:19 CDT)
  • AMBER: Myrinet or Gigabit ethernet? (Thu Jul 20 2006 - 08:35:08 CDT)
  • Re: AMBER: ptraj: rms per residue (Wed Jun 14 2006 - 15:28:07 CDT)
  • Re: AMBER: a quetion (Mon Apr 24 2006 - 08:07:30 CDT)
  • Re: AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 15:05:43 CDT)
  • Re: AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 15:00:53 CDT)
  • Re: AMBER: PMEMD MPI_Finalize() error (Fri Feb 10 2006 - 10:07:53 CST)
  • AMBER: PMEMD MPI_Finalize() error (Fri Feb 10 2006 - 08:50:59 CST)
  • AMBER: EAMBER (Thu Feb 09 2006 - 21:56:04 CST)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 14:29:38 CST)
  • Re: AMBER: helix content during my simulation (Mon Feb 06 2006 - 09:39:59 CST)
  • Re: AMBER: helix content during my simulation (Mon Feb 06 2006 - 08:03:32 CST)
• Minwoo Han
  • AMBER: Problem about dummy atoms when running antechamber (Mon Nov 27 2006 - 03:29:29 CST)
• mkseo
  • AMBER: error in AMBER 9.0 (Tue May 23 2006 - 16:43:28 CDT)
  • Re: AMBER: MPI parallel problem in AMBER 8.0 (Tue May 02 2006 - 17:14:16 CDT)
  • AMBER: MPI parallel problem in AMBER 8.0 (Tue May 02 2006 - 16:21:50 CDT)
  • AMBER: distance restraints (Mon May 01 2006 - 16:49:21 CDT)
  • AMBER: distance restraints for umbrella sampling (Thu Apr 27 2006 - 17:21:16 CDT)
• Muhammad Naim Mohmad Rouyan
  • AMBER: Error compiling amber on parallel (MPICH) (Wed Dec 27 2006 - 00:35:47 CST)
  • AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Fri Dec 22 2006 - 01:40:32 CST)
• Myunggi Yi
  • Re: AMBER: A BUG report, "ptraj corrplane" (Sun Dec 10 2006 - 19:32:22 CST)
  • AMBER: A BUG report, "ptraj corrplane" (Tue Dec 05 2006 - 11:42:08 CST)
  • AMBER: ptraj vector corrplane bug (Mon Dec 04 2006 - 14:49:46 CST)
  • Re: AMBER: residence time& hydration density (Thu Oct 26 2006 - 10:27:26 CDT)
  • Re: AMBER: Phosphorylated protein MD simulation (Thu Oct 26 2006 - 10:13:17 CDT)
  • Re: AMBER: Phosphorylated protein MD simulation (Thu Oct 26 2006 - 10:18:26 CDT)
  • Re: AMBER: ptraj atomicfluct (Wed Oct 18 2006 - 14:13:36 CDT)
  • AMBER: ptraj atomicfluct (Wed Oct 18 2006 - 13:59:22 CDT)
  • Re: AMBER: angle between two vectors (Mon Oct 16 2006 - 11:15:59 CDT)
  • AMBER: How to merge two molecules to one (Fri Oct 06 2006 - 13:51:19 CDT)
  • Re: AMBER: leap can't assign CALA (Sat Sep 23 2006 - 10:36:12 CDT)
  • AMBER: leap can't assign CALA (Fri Sep 22 2006 - 17:09:06 CDT)
  • Re: AMBER: restraints and constant pressure (Sun Sep 17 2006 - 09:23:33 CDT)
  • Re: AMBER: restraints and constant pressure (Sun Sep 17 2006 - 01:29:38 CDT)
  • Re: AMBER: restraints and constant pressure (Fri Sep 15 2006 - 14:52:21 CDT)
  • Re: AMBER: hydronium ion parameters (Fri Sep 08 2006 - 11:09:55 CDT)
  • AMBER: hydronium ion parameters (Fri Sep 08 2006 - 09:15:32 CDT)
  • Re: AMBER: hydronium ion parameters (Fri Sep 08 2006 - 09:31:33 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 20:16:49 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 18:13:29 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:22:08 CDT)
  • AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:01:24 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:26:09 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:21:59 CDT)
  • AMBER: reference of ff99 (Thu Aug 31 2006 - 10:59:51 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 21:41:46 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 20:20:47 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 22:20:12 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 22:09:29 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:59:09 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:48:07 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:39:43 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 20:29:58 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 14:00:04 CDT)
  • AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 11:05:50 CDT)
  • AMBER: Harmonic restraint along z-axis (Wed Jul 26 2006 - 19:26:02 CDT)
  • Re: [Fwd: AMBER: Long line of input] (Tue Jul 25 2006 - 11:08:27 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Fri Jul 21 2006 - 08:57:03 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 19:24:34 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 10:04:31 CDT)
  • AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 09:01:07 CDT)
  • Re: AMBER: Long line of input (Wed Jul 19 2006 - 21:03:11 CDT)
  • AMBER: Long line of input (Wed Jul 19 2006 - 15:13:26 CDT)
  • Re: AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! (Tue Jul 11 2006 - 11:00:58 CDT)
  • Re: AMBER: Amber8.0 predictied pKa problem for a Lysine! (Fri Jul 07 2006 - 11:14:42 CDT)
  • Re: AMBER: analysis of ATOMs in ´certain range distance during simulation (Thu Jul 06 2006 - 17:03:12 CDT)
  • Re: AMBER: Amber minimization with multiple restraints (Wed Jun 28 2006 - 14:53:12 CDT)
  • Re: AMBER: Amber minimization with multiple restraints (Wed Jun 28 2006 - 14:56:49 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 16:55:05 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 15:07:36 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 13:20:53 CDT)
  • AMBER: ptraj vector (Tue Jun 20 2006 - 11:13:54 CDT)
  • Re: AMBER: antechamber (Wed Jun 07 2006 - 11:31:46 CDT)
  • Re: AMBER: xleap problem (Wed Jun 07 2006 - 09:22:12 CDT)
  • Re: AMBER: xleap problem (Tue Jun 06 2006 - 18:42:34 CDT)
  • Re: AMBER: xleap problem (Tue Jun 06 2006 - 18:32:16 CDT)
  • Re: AMBER: NMR restraint (Sat Jun 03 2006 - 08:25:26 CDT)
  • Re: AMBER: NMR restraint (Fri Jun 02 2006 - 14:23:28 CDT)
  • Re: AMBER: NMR restraint (Fri Jun 02 2006 - 14:15:41 CDT)
  • AMBER: NMR restraint (Fri Jun 02 2006 - 13:11:51 CDT)
  • AMBER: distance restraints (Fri Jun 02 2006 - 10:06:38 CDT)
• nadiav_at_soton.ac.uk
  • AMBER: nmode output with ptraj (Tue Nov 28 2006 - 09:59:02 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 11:13:22 CST)
  • AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 10:41:18 CST)
  • RE: AMBER: compiling amber9 (Tue Jul 04 2006 - 09:31:02 CDT)
  • AMBER: compiling amber9 (Mon Jul 03 2006 - 03:50:44 CDT)
  • Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? (Fri May 12 2006 - 11:00:21 CDT)
  • AMBER: united atoms (Tue Mar 28 2006 - 05:04:53 CST)
• nag raj
  • AMBER: Non bond list overflow in amber8.0 program. (Sun Jun 18 2006 - 23:54:04 CDT)
  • AMBER: Programes to calculate ligand RMSD (Fri Jun 02 2006 - 05:59:04 CDT)
  • AMBER: Saving RMSD values in VMD (Fri May 26 2006 - 09:33:00 CDT)
  • AMBER: water molecules with in 3 angstroms to the solute (Mon Jan 02 2006 - 22:47:06 CST)
• Natasja Brooijmans
  • Re: AMBER: MMPBSA: magnitude of PB calculation (Mon Feb 06 2006 - 06:52:36 CST)
• Navnit Kumar Mishra
  • Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 03:55:26 CST)
  • Re: AMBER: (no subject) (Tue Aug 15 2006 - 07:51:49 CDT)
  • Re: AMBER: mm_pbsa calculation for calcium (Tue Jun 13 2006 - 12:26:56 CDT)
  • Re: AMBER: mm_pbsa calculation for calcium (Tue Jun 13 2006 - 02:45:32 CDT)
  • AMBER: mm_pbsa calculation for calcium (Mon Jun 12 2006 - 00:59:06 CDT)
  • AMBER: process_mdout (Mon Jun 05 2006 - 07:00:40 CDT)
  • Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? (Mon Jun 05 2006 - 04:22:33 CDT)
  • Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? (Mon Jun 05 2006 - 03:08:12 CDT)
  • AMBER: Water density output (Mon May 22 2006 - 06:02:48 CDT)
  • Re: AMBER: force field parameters (Fri May 19 2006 - 06:01:59 CDT)
  • Re: AMBER: force field parameters (Thu May 18 2006 - 13:21:59 CDT)
  • Re: AMBER: bond information in amber (Fri May 12 2006 - 01:28:00 CDT)
  • Re: AMBER: bond information in amber (Thu May 11 2006 - 12:25:10 CDT)
• Nicolas Lux Fawzi
  • AMBER: sander ntc=2 ntf=1 (Mon Dec 18 2006 - 21:10:42 CST)
  • Re: AMBER: Volume of ucell too big (Sat Dec 16 2006 - 12:37:31 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:32:35 CST)
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 13:16:01 CST)
  • AMBER: ff99SB vs ff02 (ff02pol.rl) (Mon Oct 30 2006 - 19:48:32 CST)
  • AMBER: ACML and MASS/MASSV for sander and pmemd (Tue Sep 19 2006 - 14:36:21 CDT)
• Nikola Trbovic
  • Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 10:46:33 CST)
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 11:06:12 CST)
  • AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 10:31:22 CST)
• Nina Fischer
  • AMBER: entropic energy (Fri Feb 24 2006 - 06:15:17 CST)
• Nitin Bhardwaj
  • AMBER: Coodinates not being unique (Mon Dec 11 2006 - 18:50:41 CST)
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 14:48:53 CST)
  • AMBER: Atoms overlapping (Mon Dec 11 2006 - 13:43:44 CST)
  • AMBER: Atom Exclusion (Tue Nov 07 2006 - 23:44:30 CST)
  • AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) (Tue Nov 07 2006 - 15:08:42 CST)
  • Re: AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 16:27:49 CST)
  • AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 15:40:50 CST)
  • AMBER: Mutual exclusion of atoms (Sun Nov 05 2006 - 23:59:38 CST)
  • Re: AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 14:58:59 CDT)
  • Re: AMBER: loading torsion parameters (Mon Jul 31 2006 - 15:35:18 CDT)
  • AMBER: loading torsion parameters (Mon Jul 31 2006 - 14:47:19 CDT)
  • Re: AMBER: Zinc coordinating CYS (Thu Jul 27 2006 - 23:00:45 CDT)
  • AMBER: Zinc coordinating CYS (Thu Jul 27 2006 - 16:30:45 CDT)
  • AMBER: Zinc-coordinating histidine protonation state (Thu Jul 27 2006 - 15:01:16 CDT)
  • AMBER: Zinc parameters (Thu Jul 27 2006 - 11:35:57 CDT)
  • AMBER: Correction on Zinc parameters (Thu Jul 27 2006 - 11:38:00 CDT)
  • Re: AMBER: modeling a non-standard molecule. (Wed Mar 08 2006 - 15:27:10 CST)
  • AMBER: modeling a non-standard molecule. (Wed Mar 08 2006 - 15:02:50 CST)
  • AMBER: Trouble with combining a non-standard residue with a protein of standard residue (Tue Mar 07 2006 - 15:21:44 CST)
• nkyx_at_sohu.com
  • AMBER: prepin format (Wed Mar 08 2006 - 21:18:15 CST)
  • AMBER: heme improper torsions (Mon Jan 16 2006 - 02:55:38 CST)
• norberto_at_ualberta.ca
  • Re: AMBER: ff02 force fields (Mon Oct 30 2006 - 12:37:57 CST)
  • AMBER: ff02 force fields (Sun Oct 29 2006 - 14:18:25 CST)
  • AMBER: Help with polarization force field (Fri Oct 27 2006 - 18:20:09 CDT)
• Noriaki Okimoto
  • Re: AMBER: question on protein folding simulation (Thu Dec 07 2006 - 06:25:51 CST)
  • Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 20:43:11 CST)
  • Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 20:51:17 CST)
  • AMBER: question on protein folding simulation (Fri Dec 01 2006 - 06:01:27 CST)
  • AMBER: amber force field (Wed Oct 11 2006 - 13:21:03 CDT)
• nur avneet
  • AMBER: How to start a Simulation of a peptide in bilayer (Wed Nov 01 2006 - 03:28:31 CST)
  • Re: AMBER:pls help load peptoid residues in antechamber (Wed Oct 25 2006 - 00:29:55 CDT)
  • RE: AMBER: Problem loading peptoid residues with antechamber (Wed Oct 18 2006 - 23:05:15 CDT)
  • AMBER: Problem loading peptoid residues with antechamber (Wed Oct 18 2006 - 01:23:42 CDT)
  • AMBER: Problem working with Antechamber (Tue Oct 17 2006 - 02:44:54 CDT)
• ohucke_at_lav.boehringer-ingelheim.com
  • AMBER: protocols for NMR protein refinement with AMBER (Mon Apr 10 2006 - 15:43:44 CDT)
• Olayiwola Adekoya
  • AMBER: mmpbsa in parallell (Thu Oct 19 2006 - 02:57:07 CDT)
• opitz_at_che.udel.edu
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 12:27:23 CDT)
  • AMBER: DOTA-Lanthanide complexes in Amber (Tue Aug 15 2006 - 12:48:23 CDT)
  • AMBER: Hybridization in leap (Tue Jul 25 2006 - 13:23:12 CDT)
  • AMBER: Amber7-CHARMM22-TRIPOS force fields (Mon Jun 19 2006 - 10:37:24 CDT)
  • AMBER: Macromodel Amber* vs. Amber7 (Mon May 22 2006 - 07:56:54 CDT)
• Osmar Norberto de Souza
  • Re: AMBER: Machine File for Intel Core 2 Duo E6400 (Thu Sep 28 2006 - 14:22:15 CDT)
  • AMBER: Machine File for Intel Core 2 Duo E6400 (Thu Sep 28 2006 - 13:47:06 CDT)
  • AMBER: Problem with "impose" in leap (Mon May 15 2006 - 06:27:13 CDT)
  • [Fwd: AMBER: Problem with impose in lep] (Wed May 10 2006 - 12:09:48 CDT)
  • AMBER: Problem with impose in lep (Mon May 08 2006 - 12:31:16 CDT)
  • AMBER: Force field for DNA (Mon Apr 17 2006 - 05:50:31 CDT)
• Ozlem Demir
  • AMBER: "noimage" option for radial distribution functions (Sun Jul 16 2006 - 16:14:31 CDT)
• Pan, Yongmei
  • AMBER: another question: is rms 2E-2 good for nmode ntrun=1? (Fri May 12 2006 - 10:22:00 CDT)
  • AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 (Thu May 11 2006 - 13:50:36 CDT)
  • AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? (Thu May 11 2006 - 09:13:02 CDT)
• pang zhao
  • AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory (Fri Jun 09 2006 - 03:56:57 CDT)
  • AMBER: How to analyze the trajectory generated by LES simulation (Fri Jun 02 2006 - 02:08:03 CDT)
  • Re: AMBER: fail to execute addles (Tue May 16 2006 - 09:42:36 CDT)
  • Re: AMBER: fail to execute addles (Tue May 16 2006 - 01:39:28 CDT)
  • Re: AMBER: fail to execute addles (Tue May 16 2006 - 01:17:05 CDT)
  • Re: AMBER: fail to execute addles (Tue May 16 2006 - 01:13:21 CDT)
  • Re: AMBER: fail to execute addles (Mon May 15 2006 - 09:31:19 CDT)
  • AMBER: fail to execute addles (Mon May 15 2006 - 06:59:10 CDT)
  • Re: AMBER: about the execuation of REMD with sander of amber9 (Sun Apr 30 2006 - 03:58:06 CDT)
  • AMBER: about the shake with self-guide LD (Sat Apr 29 2006 - 05:44:39 CDT)
  • Re: AMBER: about the execuation of REMD with sander of amber9 (Sat Apr 29 2006 - 00:12:22 CDT)
  • AMBER: about the execuation of REMD with sander of amber9 (Fri Apr 28 2006 - 22:08:41 CDT)
• Pankaj Daga
  • AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 16:56:58 CST)
• pascal.baillod_at_epfl.ch
  • AMBER: Non-periodic simulations: How is the system kept together? (Thu Apr 20 2006 - 11:13:04 CDT)
• Patricia Hunt
  • AMBER: iso command and a cubic box (Wed Jul 12 2006 - 02:03:03 CDT)
• Paul R Brenner
  • Re: AMBER: Leap adds hydrogens but cannot resolve their type. (Tue Aug 15 2006 - 10:39:08 CDT)
  • AMBER: Leap adds hydrogens but cannot resolve their type. (Thu Aug 10 2006 - 14:23:55 CDT)
• Pawe³ Gruszczyñski
  • AMBER: (Sat Feb 04 2006 - 03:16:10 CST)
• Peng Tao
  • Re: AMBER: How to run mm_pbsa_statistics.pl? (Tue Jan 10 2006 - 09:49:00 CST)
  • Re: AMBER: How to run mm_pbsa_statistics.pl? (Thu Jan 05 2006 - 17:11:42 CST)
  • Re: AMBER: How to run mm_pbsa_statistics.pl? (Thu Jan 05 2006 - 07:39:19 CST)
  • AMBER: How to run mm_pbsa_statistics.pl? (Wed Jan 04 2006 - 07:51:55 CST)
• Peter Anderson
  • AMBER: How to recompile sander for single-processor use in AMBER 8? (Thu Nov 30 2006 - 15:41:27 CST)
• Peter Gannett
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 17:40:18 CST)
  • AMBER: Virus? (Mon Oct 23 2006 - 07:34:29 CDT)
  • AMBER: SGI compiler problems (Tue Jun 13 2006 - 07:46:18 CDT)
  • Re: AMBER: problem with ssh and xleap (Mon Jan 02 2006 - 10:26:18 CST)
• Peter Trodler
  • AMBER: ammonia parameters (Thu Nov 23 2006 - 02:51:39 CST)
• Peter Varnai
  • Re: AMBER: replica exchange hangs (Wed Mar 01 2006 - 12:56:21 CST)
  • AMBER: replica exchange hangs (Wed Mar 01 2006 - 11:29:34 CST)
• Petr Jerabek
  • AMBER: reading ff file into XLeap (Wed Aug 16 2006 - 11:21:00 CDT)
• Petr Kulhanek
  • AMBER: AMBER8 - RDF bug (Fri Aug 11 2006 - 11:00:57 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Fri Jul 14 2006 - 04:24:26 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Fri Jul 14 2006 - 02:44:09 CDT)
  • AMBER: bug in ambpdb (AMBER8) (Wed May 10 2006 - 05:54:55 CDT)
  • Re: AMBER: sequential execution of number of parallel jobs (Tue May 02 2006 - 03:20:51 CDT)
  • Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 03:27:01 CST)
• Philip Cheung
  • AMBER: Re: Fluorine and Bromine Parameters in Amber 9 (Fri Nov 03 2006 - 13:56:52 CST)
• Phineus Markwick
  • AMBER: format of qusaiharmonic eigenvector file in AMBER7 (Tue Feb 07 2006 - 05:10:44 CST)
• Pietro Amodeo
  • RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) (Fri Sep 29 2006 - 04:21:43 CDT)
  • AMBER: Questions/observations about Nudged Elastic Band (NEB) (Thu Sep 28 2006 - 05:56:36 CDT)
• ping jiang
  • AMBER: antechamber (Thu Jan 26 2006 - 17:18:29 CST)
• Piotr Cieplak
  • AMBER: problems with Calcium ions treatment in GB run (Thu Dec 28 2006 - 17:44:23 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sun Dec 17 2006 - 01:20:28 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 01:04:05 CST)
  • AMBER: AMBER - leap - problems with impose command (Fri Dec 15 2006 - 12:18:06 CST)
  • AMBER: description of prep file (Fri Dec 08 2006 - 16:28:29 CST)
  • AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA (Mon Dec 04 2006 - 18:20:02 CST)
  • RE: AMBER: Parmchk problems (parm99.dat) (Wed Sep 20 2006 - 22:46:19 CDT)
  • Re: AMBER: impose command in leap problem (Mon Aug 14 2006 - 15:44:02 CDT)
  • AMBER: impose command in leap problem (Fri Aug 11 2006 - 19:56:40 CDT)
  • RE: AMBER: amber9 (Fri Jul 14 2006 - 18:33:00 CDT)
  • AMBER: amber9 (Fri Jul 14 2006 - 17:02:36 CDT)
  • Re: AMBER: anal vs sander (Fri Jan 27 2006 - 16:59:13 CST)
  • AMBER: anal vs sander (Fri Jan 27 2006 - 14:58:39 CST)
• pkb bioinfo
  • Re: AMBER: mm_pbsa.pl fails to start in linux cluster (Wed Aug 02 2006 - 08:58:48 CDT)
  • AMBER: mm_pbsa.pl fails to start in linux cluster (Wed Aug 02 2006 - 07:07:22 CDT)
  • AMBER: For different ligand conformation (Mon Jul 31 2006 - 08:53:45 CDT)
  • AMBER: How to resume remaining simulation (Mon Jul 24 2006 - 05:05:23 CDT)
  • AMBER: analysis of ATOMs in ´certain range distance during simulation (Wed Jul 05 2006 - 22:37:46 CDT)
  • AMBER: analysis of atoms in a range during simulation (Wed Jul 05 2006 - 07:41:58 CDT)
  • AMBER: How to submit a job in cluster (Tue Jun 06 2006 - 03:46:21 CDT)
  • AMBER: antechamber help needed for FAD (Mon May 29 2006 - 04:38:48 CDT)
• pkmukher
  • Re: AMBER: pmemd_parallel_ins_prob (Thu Jun 08 2006 - 13:09:00 CDT)
  • AMBER: pmemd_parallel_ins_prob (Wed Jun 07 2006 - 16:00:20 CDT)
• Prabhakar. G.
  • Re: AMBER: fixing residues (Wed Jul 05 2006 - 22:57:38 CDT)
  • AMBER: fixing residues (Mon Jul 03 2006 - 07:16:46 CDT)
• Pradipta Bandyopadhyay
  • Re: AMBER: TI, mutation (Mon Aug 28 2006 - 07:46:43 CDT)
  • RE: AMBER: ff02 + POL3 problem ! (Tue May 16 2006 - 09:08:03 CDT)
  • AMBER: ff02 + POL3 problem ! (Mon May 15 2006 - 08:53:20 CDT)
  • AMBER: Compilers and libraries for AMBER in HPC! (Sun May 14 2006 - 08:25:07 CDT)
  • AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! (Mon Apr 03 2006 - 00:23:26 CDT)
  • AMBER: MPICH-1.2.7 compilation problem ! (Fri Feb 03 2006 - 07:49:31 CST)
• Prashanth Athri
  • AMBER: Curve fitting during dihedral parameter calculation (Thu Oct 19 2006 - 14:15:21 CDT)
  • AMBER: (no subject) (Thu Oct 05 2006 - 21:34:47 CDT)
  • AMBER: Calculation of Dihedral constants (Thu Oct 05 2006 - 21:36:15 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Tue Sep 12 2006 - 14:30:02 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Tue Sep 12 2006 - 12:10:55 CDT)
  • RE: AMBER: Parmchk problems (parm99.dat) (Tue Sep 12 2006 - 10:54:08 CDT)
  • AMBER: Parmchk problems (parm99.dat) (Sun Sep 10 2006 - 19:23:25 CDT)
  • AMBER: (no subject) (Sun Sep 10 2006 - 19:23:05 CDT)
  • AMBER: amidine group/ gaff parameters (Fri Aug 18 2006 - 14:00:17 CDT)
  • AMBER: process_mdout.perl's output is empty (Mon Jul 24 2006 - 15:53:04 CDT)
• Pravin_Kumar_at_jubilantbiosys.com
  • AMBER: Issue with installation of Amber v9.0 parallel compilation (Thu Oct 19 2006 - 23:17:51 CDT)
  • AMBER: Issue with installation of Amber v9.0 parallel compilation (Thu Oct 19 2006 - 23:02:42 CDT)
• Priti Hansia
  • RE: AMBER: Question regarding lastrst and taup (Wed Oct 25 2006 - 23:58:10 CDT)
  • AMBER: Question regarding lastrst and taup (Wed Oct 25 2006 - 01:37:09 CDT)
  • RE: AMBER: RE: Intel Compiler. (Wed May 10 2006 - 10:39:04 CDT)
  • AMBER: RE: Intel Compiler. (Tue May 09 2006 - 12:12:18 CDT)
  • AMBER: Amber9 test error on SGI Altix (Tue May 09 2006 - 10:18:02 CDT)
  • Re: AMBER: Intel compiler version 9.0.033 (Mon May 08 2006 - 14:55:37 CDT)
  • Re: AMBER: Problem with shared libraries: libimf.so (Sun May 07 2006 - 00:40:49 CDT)
  • RE: AMBER: Problem with shared libraries: libimf.so (Sat May 06 2006 - 02:01:51 CDT)
  • RE: AMBER: Problem with shared libraries: libimf.so (Fri May 05 2006 - 13:39:50 CDT)
  • AMBER: Problem with shared libraries: libimf.so (Fri May 05 2006 - 12:55:39 CDT)
  • Re: AMBER: Error while running test.serial in Amber9 (Thu May 04 2006 - 10:48:36 CDT)
  • RE: AMBER: Error while running test.serial in Amber9 (Thu May 04 2006 - 00:08:02 CDT)
  • Re: AMBER: Error while running test.serial in Amber9 (Wed May 03 2006 - 07:02:04 CDT)
  • AMBER: Error while running test.serial in Amber9 (Wed May 03 2006 - 06:03:27 CDT)
  • RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 22:29:03 CST)
  • Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 05:50:36 CST)
  • Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 04:51:13 CST)
  • AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 03:58:04 CST)
• priya priya
  • Re: AMBER: Amber8: problem related to antechamber (Tue Oct 17 2006 - 01:49:03 CDT)
  • RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration (Mon Oct 16 2006 - 23:42:15 CDT)
  • AMBER: Amber8: how to do Simulated Annealing and Equilibration (Mon Oct 16 2006 - 03:32:18 CDT)
  • AMBER: Amber8: problem related to antechamber (Mon Oct 16 2006 - 02:00:38 CDT)
  • AMBER: RE: Amber8: problem related to antechamber (Wed Sep 27 2006 - 02:29:01 CDT)
  • AMBER: RE: Amber8: problem related to antechamber (Tue Sep 26 2006 - 22:49:34 CDT)
  • AMBER: Amber8: problem related to antechamber (Thu Sep 21 2006 - 23:11:23 CDT)
  • AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 (Wed Sep 13 2006 - 04:02:33 CDT)
  • RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Tue Aug 22 2006 - 23:16:42 CDT)
  • AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 02:46:29 CDT)
  • Re: AMBER: PDB from .rst? (Thu Jul 20 2006 - 22:24:08 CDT)
  • AMBER: can i use unusual amino acid (Thu Jun 22 2006 - 04:15:55 CDT)
• puneet kacker
  • AMBER: Nucgen Problem (Fri Dec 22 2006 - 02:06:41 CST)
• Qing Zhang
  • Re: AMBER: Simulating proteins with calcium ion (Sat Dec 23 2006 - 01:26:11 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 14:22:53 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 14:17:05 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 13:32:43 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 08 2006 - 18:31:02 CST)
  • AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 18:15:42 CST)
• Qingning Shu
  • Re: RE: Re: AMBER: A question about Dynamics. (Fri Sep 22 2006 - 17:28:54 CDT)
  • Re: Re: AMBER: A question about Dynamics. (Thu Sep 21 2006 - 09:38:47 CDT)
  • AMBER: A question about Dynamics. (Mon Sep 18 2006 - 15:57:17 CDT)
  • AMBER: Question about Streptavidin/Biotin Tutorial. (Mon Sep 18 2006 - 15:39:38 CDT)
  • AMBER: A question about Dynamics. (Mon Sep 18 2006 - 15:40:21 CDT)
  • Re: Re: AMBER: (Tue Aug 29 2006 - 11:26:34 CDT)
  • AMBER: (Tue Aug 29 2006 - 08:01:58 CDT)
  • AMBER: problem about Distance Restraints. (Tue Jul 11 2006 - 22:38:48 CDT)
  • AMBER: about restraint format. (Mon Jul 10 2006 - 08:11:16 CDT)
  • AMBER: Amber minimization with multiple restraints (Mon Jun 26 2006 - 12:23:33 CDT)
• qiwenpeng_at_sinap.ac.cn
  • Re: AMBER: amber 8 install problem (Wed Mar 15 2006 - 08:27:00 CST)
  • AMBER: amber 8 install problem (Mon Mar 13 2006 - 07:22:01 CST)
• Qizhi Cui
  • AMBER: ISTRNG or SALT in MM_PBSA (Wed Dec 13 2006 - 21:23:48 CST)
  • Re: AMBER: Using modified NA bases (Wed Oct 25 2006 - 10:51:32 CDT)
  • AMBER: problems for running sander.MPI (Wed Oct 11 2006 - 15:39:36 CDT)
  • AMBER: prep files for L-sugar residues (Fri Mar 17 2006 - 20:42:56 CST)
• r. a.
  • Re: RE: AMBER: Radius of gyration (Mon Nov 27 2006 - 22:20:32 CST)
  • AMBER: Radius of gyration (Wed Nov 22 2006 - 04:11:14 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 01:41:35 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 00:44:35 CST)
  • AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 02:58:25 CST)
  • AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 02:45:25 CST)
  • AMBER: heating process (Fri Apr 28 2006 - 00:56:06 CDT)
  • AMBER: installation problem (Tue Mar 28 2006 - 21:21:50 CST)
• Rabal Gracia María Obdulia
  • AMBER: MMPBSA & PBCAL (Fri Mar 31 2006 - 09:37:57 CST)
• Rachel
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:01:12 CST)
  • AMBER: Unit 5 Error on OPEN: md.in (Wed Dec 13 2006 - 13:55:58 CST)
  • AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 11:24:24 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 12:35:08 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 11:03:11 CST)
  • AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 09:59:34 CST)
  • AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 09:29:09 CST)
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 13:53:29 CST)
  • AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 11:58:53 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 17:22:06 CST)
  • AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 13:31:55 CST)
  • Re: AMBER: SHAKE problem after minimization (Thu Nov 23 2006 - 12:37:24 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 11:45:04 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 10:37:18 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 07:14:09 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 03:56:53 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 13:37:15 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 12:43:50 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 12:34:19 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 09:42:34 CST)
  • AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 05:39:18 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 04:08:42 CST)
  • AMBER: compile amber8 on IBM-sp4 (Tue Nov 21 2006 - 11:56:13 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:42:10 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 11:18:00 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 08:23:30 CST)
  • AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 06:59:07 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Tue Nov 14 2006 - 16:44:44 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Mon Nov 13 2006 - 11:09:22 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 09:54:26 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 08:42:31 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 11:31:12 CST)
  • AMBER: big bond energy change from minimization and md (heating) (Wed Nov 08 2006 - 10:40:12 CST)
  • AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 06:59:00 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Fri Nov 03 2006 - 06:09:54 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Thu Nov 02 2006 - 12:08:00 CST)
  • AMBER: too big EEL values in the minimisation output (Wed Nov 01 2006 - 11:01:17 CST)
  • AMBER: how to add hydrogen molecules in the protein (Thu Oct 26 2006 - 11:28:16 CDT)
  • AMBER: how to select the problematic residues(atoms) in VMD (Thu Oct 26 2006 - 06:00:21 CDT)
  • AMBER: reinstall amber8 (Wed Oct 25 2006 - 09:57:59 CDT)
  • Re: AMBER: parameters for Nickel and iron (Wed Sep 27 2006 - 08:53:45 CDT)
  • Re: AMBER: parameters for Nickel and iron (Thu Sep 21 2006 - 06:50:23 CDT)
  • Re: AMBER: parameters for Nickel and iron (Tue Sep 19 2006 - 11:00:45 CDT)
  • AMBER: parameters for Nickel and iron (Mon Sep 18 2006 - 08:02:39 CDT)
• Raffaella D'Auria
  • Re: AMBER: converting from parm to parm7 (Tue Jul 25 2006 - 11:00:50 CDT)
  • Re: AMBER: converting from parm to parm7 & L-J coeff A and B (Sat Jul 22 2006 - 10:55:56 CDT)
  • AMBER: converting from parm to parm7 (Fri Jul 21 2006 - 20:26:55 CDT)
  • Re: AMBER: question about REDII (Fri May 12 2006 - 14:12:41 CDT)
  • AMBER: question about REDII (Thu May 11 2006 - 21:04:51 CDT)
  • RE: AMBER: organic molecule - from newbie :) (Mon Apr 10 2006 - 17:12:44 CDT)
  • AMBER: organic molecule - from newbie :) (Thu Apr 06 2006 - 20:55:02 CDT)
• Rafi Ahmad
  • AMBER: Probelm with running Amber 9 parallelly (Thu Nov 09 2006 - 06:59:56 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 03:51:18 CST)
  • AMBER: Probelm with running Amber 9 parallelly (Fri Oct 20 2006 - 09:29:14 CDT)
  • AMBER: Info regarding reduced cysteines (Mon Aug 07 2006 - 09:06:40 CDT)
• Rahaman, Asif
  • AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 18:29:53 CST)
  • AMBER: pmf with respect to a surface (Fri Sep 08 2006 - 17:35:22 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 17:29:25 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 16:34:50 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 15:24:43 CDT)
  • AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 15:24:19 CDT)
• Rajendra P. OJHA
  • AMBER: MM_PBSA (Sat Oct 07 2006 - 11:21:49 CDT)
• Rajesh Murarka
  • AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion (Wed Nov 08 2006 - 09:59:36 CST)
• Rama krishnan
  • AMBER: Unable to find solution for an error - "cannot successfully assign bond type" (Sat Nov 04 2006 - 04:06:51 CST)
• Ramdas Pophale
  • AMBER: Implicit Water - Force field parameters (Tue Sep 05 2006 - 14:22:49 CDT)
• Ravinder Abrol
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 18:58:36 CST)
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:38:23 CST)
  • AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 01:09:08 CST)
• Raviprasad Aduri
  • Re: AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 21:46:05 CST)
  • AMBER: Announcement: Parameters for Modified Nucleosides in RNA (Mon Oct 09 2006 - 16:13:56 CDT)
• Ray Luo
  • RE: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 13:16:32 CST)
  • RE: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 09:55:46 CST)
  • RE: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 15:51:52 CST)
  • Re: AMBER: amber9: SA Bomb in sa_arc (Tue Oct 31 2006 - 02:29:27 CST)
  • Re: AMBER: amber9: SA Bomb in sa_arc (Wed Oct 25 2006 - 04:14:08 CDT)
  • Re: AMBER: amber9: SA Bomb in sa_arc (Tue Oct 24 2006 - 16:55:24 CDT)
  • Re: AMBER: regarding PBCAL in MM-PBSA (Mon Oct 16 2006 - 19:35:42 CDT)
  • Re: AMBER: PBSA calculation fail .... (Fri Oct 06 2006 - 11:22:11 CDT)
  • Re: AMBER: PBSA calculation fail .... (Thu Oct 05 2006 - 11:36:32 CDT)
  • Re: AMBER: mm_pbsa segmentation faults (Tue Sep 26 2006 - 11:29:26 CDT)
  • Re: AMBER: mm_pbsa segmentation faults (Mon Sep 25 2006 - 20:17:54 CDT)
  • Re: AMBER: pbsa segmentation faults (Sun Sep 24 2006 - 01:40:58 CDT)
  • Re: AMBER: mm_pbsa calculation allocation error (Mon Aug 21 2006 - 11:37:14 CDT)
  • Re: AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 07:21:03 CDT)
  • Re: AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? (Thu Jul 13 2006 - 16:21:30 CDT)
  • Re: AMBER: MM/PBSA (Fri Jul 07 2006 - 19:26:28 CDT)
  • AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) (Wed Jul 05 2006 - 12:45:49 CDT)
  • Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl (Thu Jun 29 2006 - 19:47:13 CDT)
  • Re: AMBER: MM-PBSA questions (Fri Jun 30 2006 - 00:56:42 CDT)
  • Re: AMBER: MM-PBSA and gaff atom types (Tue Jun 27 2006 - 21:47:51 CDT)
  • Re: AMBER: problems on mm_pbsa (Wed Jun 14 2006 - 00:04:28 CDT)
  • Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? (Sat Jun 10 2006 - 12:45:17 CDT)
  • Re: AMBER: Ask for help in pbsa error in AMBER9 (Thu Jun 08 2006 - 14:01:06 CDT)
  • Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) (Wed May 24 2006 - 18:14:33 CDT)
  • Re: AMBER: strange mm_pbsa output (Fri May 12 2006 - 19:22:57 CDT)
  • Re: AMBER: Amber9 test error on SGI Altix (Tue May 09 2006 - 07:57:57 CDT)
  • Re: AMBER: questions about mm_pbsa (Wed Apr 26 2006 - 20:03:13 CDT)
  • Re: AMBER: Test Failure during amber9 serial compilation (Wed Apr 26 2006 - 13:29:11 CDT)
  • Re: AMBER: Test Failure during amber9 serial compilation (Tue Apr 25 2006 - 13:01:49 CDT)
  • Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” (Mon Apr 24 2006 - 13:40:28 CDT)
  • Re: AMBER: MM-PBSA problem (Fri Apr 14 2006 - 16:40:45 CDT)
  • Re: AMBER: MM-PBSA problem (Fri Apr 14 2006 - 11:57:52 CDT)
  • Re: AMBER: one question about mm_pbsa (Thu Apr 13 2006 - 10:39:53 CDT)
  • Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short (Sun Apr 09 2006 - 21:44:44 CDT)
  • Re: AMBER: quistions about pbsa cacultaion (Wed Mar 15 2006 - 11:36:56 CST)
  • Re: AMBER: quistions about pbsa cacultaion (Mon Mar 13 2006 - 01:26:53 CST)
  • Re: AMBER: mm_pbsa problem in IBM-aix (Sun Feb 19 2006 - 14:22:01 CST)
  • Re: AMBER: MMPBSA: magnitude of PB calculation (Fri Feb 03 2006 - 01:49:07 CST)
  • Re: AMBER: Q: results from PB solver in example no.3 (Wed Jan 04 2006 - 20:45:28 CST)
• rdauria_at_uci.edu
  • RE: AMBER: ibelly & fix atom (Mon Apr 17 2006 - 23:22:16 CDT)
  • Re: AMBER: ibelly & fix atom (Mon Apr 17 2006 - 22:59:56 CDT)
  • AMBER: ibelly & fix atom (Mon Apr 17 2006 - 22:41:28 CDT)
• rebeca_at_mmb.pcb.ub.es
  • AMBER: minimization of Hydrogens with xLeaP (Mon Nov 27 2006 - 12:38:04 CST)
• Reinhard Klement
  • Re: AMBER: ptraj hbond analysis troubles (Wed Oct 11 2006 - 03:25:27 CDT)
• renyanliang
  • AMBER: amber8 compiled erro on opteron with 64 bit (Tue May 16 2006 - 04:15:24 CDT)
  • AMBER: anal: dihedral error (Mon Mar 20 2006 - 19:27:39 CST)
• Rhoad, Jonathan S.
  • AMBER: (Fri Feb 03 2006 - 13:56:37 CST)
• Ricardo J. F. Branco
  • Re: AMBER: references (Fri Jun 23 2006 - 05:47:50 CDT)
  • AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 (Fri Jun 23 2006 - 02:36:44 CDT)
• richard dimelow
  • Re: AMBER: dihedral parameters (Mon Feb 06 2006 - 04:22:08 CST)
  • AMBER: dihedral parameters (Sat Feb 04 2006 - 10:06:41 CST)
• Rita Cassia
  • Re: AMBER: Ethanol (Wed Nov 22 2006 - 03:33:24 CST)
  • AMBER: Ethanol (Fri Nov 17 2006 - 06:13:14 CST)
  • Re: AMBER: question about building molecules (Mon Oct 09 2006 - 10:49:10 CDT)
  • AMBER: question about building molecules (Sun Oct 08 2006 - 06:05:59 CDT)
• rob yang
  • AMBER: alanine scan (mm/pbsa) (Wed Oct 18 2006 - 09:46:47 CDT)
• Robert Duke
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 07:23:10 CST)
  • Re: AMBER: Parallelization method (Tue Dec 19 2006 - 12:29:09 CST)
  • Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 17:42:02 CST)
  • Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 16:12:12 CST)
  • Re: AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 08:16:22 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 16:41:52 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 14:22:23 CST)
  • Re: AMBER: PMEMD scaling (Thu Dec 07 2006 - 08:17:46 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 10:47:23 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 07:56:11 CST)
  • Re: AMBER: pmemd installation problem (Fri Nov 03 2006 - 13:09:52 CST)
  • Re: AMBER: pmemd installation on linux_p3_athlon ifort (Tue Oct 24 2006 - 12:08:58 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 20:55:42 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 13:35:20 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 08:58:50 CDT)
  • Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD (Wed Oct 04 2006 - 12:45:06 CDT)
  • Re: AMBER: Multiple Timestep MD (Sun Oct 01 2006 - 09:22:34 CDT)
  • Re: AMBER: ACML and MASS/MASSV for sander and pmemd (Tue Sep 19 2006 - 15:42:05 CDT)
  • Re: AMBER: ACML and MASS/MASSV for sander and pmemd (Tue Sep 19 2006 - 15:03:00 CDT)
  • Re: AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 13:20:27 CDT)
  • Re: AMBER: lib-4324 : UNRECOVERABLE library error (Sun Sep 17 2006 - 07:30:08 CDT)
  • Re: AMBER: pmemd error (Thu Sep 14 2006 - 11:46:40 CDT)
  • Re: AMBER: pmemd error (Thu Sep 14 2006 - 11:46:30 CDT)
  • Re: AMBER: 'lastrst' error for amber8 (Wed Sep 13 2006 - 10:28:16 CDT)
  • Re: AMBER: parallel pmemd with intel 9 fc (Sat Aug 12 2006 - 13:58:59 CDT)
  • Re: AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 12:33:13 CDT)
  • AMBER: Bugfixes available for pmemd iwrap problem (Wed Aug 02 2006 - 12:05:32 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Fri Jul 21 2006 - 08:34:02 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 16:35:58 CDT)
  • Re: AMBER: Myrinet or Gigabit ethernet? (Thu Jul 20 2006 - 09:45:45 CDT)
  • Re: AMBER: Failure of iwrap in PMEMD (Thu Jul 20 2006 - 09:40:48 CDT)
  • Re: AMBER: PMEMD with NMR restraint and position restraint (Tue Jul 18 2006 - 23:34:35 CDT)
  • Re: AMBER: PMEMD with NMR restraint and position restraint (Tue Jul 18 2006 - 21:03:42 CDT)
  • Re: AMBER: PMEMD with NMR restraint and position restraint (Tue Jul 18 2006 - 15:49:05 CDT)
  • Re: AMBER: PMEMD with NMR restraint and position restraint (Mon Jul 17 2006 - 22:03:29 CDT)
  • Re: AMBER: working with large strained system (Thu Jul 06 2006 - 09:06:48 CDT)
  • Re: AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jul 06 2006 - 07:43:24 CDT)
  • Re: AMBER: pmemd9 issue (Sun Jul 02 2006 - 06:46:21 CDT)
  • Re: AMBER: pmemd9 issue (Sun Jul 02 2006 - 06:12:11 CDT)
  • Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jun 29 2006 - 13:24:14 CDT)
  • Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband (Thu Jun 29 2006 - 11:37:53 CDT)
  • Re: AMBER: Problems with restart file from pmemd sim. (Sat Jun 17 2006 - 08:10:24 CDT)
  • Re: AMBER: pmemd_parallel_ins_prob (Wed Jun 07 2006 - 16:21:28 CDT)
  • Re: AMBER: compiler error for Amber9 (Wed Jun 07 2006 - 10:03:15 CDT)
  • Re: AMBER: which time should I use to calculate the number of "ps/Day" (Mon May 29 2006 - 08:10:04 CDT)
  • AMBER: More Amber 9 Benchmarks available (Mon May 22 2006 - 09:23:15 CDT)
  • Re: AMBER: RE: PMEMD compilation problems (Fri May 19 2006 - 11:20:52 CDT)
  • Re: AMBER: Intel fortran compiler 7? (Fri May 19 2006 - 06:59:43 CDT)
  • Re: AMBER: installation problem (Mon May 15 2006 - 13:25:53 CDT)
  • Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 10:24:43 CDT)
  • Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 07:46:08 CDT)
  • Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 07:29:14 CDT)
  • Re: AMBER: Opteron vs. Xeon performance (Thu May 11 2006 - 21:02:10 CDT)
  • Re: AMBER: Amber9 test error on SGI Altix (Tue May 09 2006 - 11:06:19 CDT)
  • Re: AMBER: PMEMD compilation error (Mon May 08 2006 - 15:18:05 CDT)
  • Re: AMBER: cluster architecture for the best amber performance (Wed May 03 2006 - 12:05:57 CDT)
  • Re: AMBER: a question (Mon Apr 24 2006 - 13:21:34 CDT)
  • Re: AMBER: timing estimates (Wed Apr 19 2006 - 19:06:59 CDT)
  • Re: AMBER: amber memory usage (Fri Apr 14 2006 - 17:56:12 CDT)
  • Re: AMBER: Restarting constant pressure sims with restraints (Wed Apr 05 2006 - 13:30:05 CDT)
  • Re: AMBER: PMEMD MPI_Finalize() error (Fri Feb 10 2006 - 09:15:29 CST)
• Robert Konecny
  • AMBER: ANN: APBS/Amber interface released (Fri Jun 23 2006 - 01:23:35 CDT)
• Roberto Gomperts
  • Re: AMBER: Can we submit jobs in sequences to amber? (Mon Jun 26 2006 - 05:25:03 CDT)
  • Re: AMBER: SGI compiler problems (Wed Jun 21 2006 - 10:09:54 CDT)
  • Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test (Wed Jun 21 2006 - 09:10:44 CDT)
• Robyn Ayscue
  • Re: AMBER: problem with ssh and xleap (Mon Jan 02 2006 - 20:33:13 CST)
• Ross Walker
  • AMBER: RE: protein simulation using AMBER (Sat Dec 30 2006 - 00:51:09 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 23:30:53 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 22:36:10 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 10:38:16 CST)
  • RE: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 13:52:05 CST)
  • RE: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 12:52:53 CST)
  • RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 17:15:46 CST)
  • AMBER: Test Message Please Ignore. (Thu Dec 14 2006 - 15:01:07 CST)
  • AMBER: Test Message Please Ignore (Thu Dec 14 2006 - 15:01:07 CST)
  • RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 10:21:19 CST)
  • RE: AMBER: atome type error (Fri Dec 08 2006 - 09:51:29 CST)
  • RE: AMBER: ibelly not work (Wed Dec 06 2006 - 18:07:45 CST)
  • RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 16:48:51 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 11:59:58 CST)
  • RE: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 11:55:45 CST)
  • RE: AMBER: Some warning !!! during SANDER ? (Wed Nov 22 2006 - 10:48:55 CST)
  • RE: AMBER: Amber9 installation error (Sat Nov 18 2006 - 11:20:39 CST)
  • RE: AMBER: <kein Betreff> (Mon Nov 13 2006 - 10:44:03 CST)
  • RE: AMBER: The plc.frcmod file in the old version tutorial (Mon Nov 13 2006 - 10:29:26 CST)
  • RE: AMBER: Zn metal library (Mon Nov 06 2006 - 00:08:20 CST)
  • AMBER: RE: I got the error meassage in testcase of QMMM (Sat Nov 04 2006 - 12:09:13 CST)
  • AMBER: (Sat Nov 04 2006 - 11:35:43 CST)
  • RE: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 20:04:08 CST)
  • RE: AMBER: Problems with equilibrating the starting density (Fri Nov 03 2006 - 13:41:55 CST)
  • RE: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 12:32:27 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 10:39:22 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 11:17:42 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 11:05:38 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 18:04:28 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 15:36:17 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:51:43 CST)
  • RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 11:21:02 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 10:44:22 CST)
  • RE: AMBER: problems for running sander.MPI (Mon Oct 30 2006 - 12:40:06 CST)
  • RE: AMBER: how to restrain some residues in a NPT MD? (Mon Oct 30 2006 - 10:34:46 CST)
  • RE: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 10:24:26 CST)
  • RE: AMBER: Amber: Parallel Installation Problems (Fri Oct 27 2006 - 12:53:10 CDT)
  • RE: AMBER: amber9: SA Bomb in sa_arc (Thu Oct 26 2006 - 11:35:19 CDT)
  • RE: AMBER: amber9: SA Bomb in sa_arc (Thu Oct 26 2006 - 10:38:05 CDT)
  • RE: AMBER: how to select the problematic residues(atoms) in VMD (Thu Oct 26 2006 - 10:26:22 CDT)
  • RE: AMBER: parameters !!?? (Wed Oct 25 2006 - 10:53:01 CDT)
  • RE: AMBER: Question regarding lastrst and taup (Wed Oct 25 2006 - 10:46:52 CDT)
  • RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Tue Oct 24 2006 - 10:33:45 CDT)
  • RE: AMBER: mmpbsa: fail to run heat in tutorial A3 (Mon Oct 23 2006 - 10:39:26 CDT)
  • RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Fri Oct 20 2006 - 11:06:49 CDT)
  • RE: AMBER: Issue with installation of Amber v9.0 parallel compilation (Thu Oct 19 2006 - 23:55:00 CDT)
  • RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred (Thu Oct 19 2006 - 14:24:43 CDT)
  • RE: AMBER: Unstable RMS trajectory (Tue Oct 17 2006 - 11:40:43 CDT)
  • RE: AMBER: Amber8: problem related to antechamber (Mon Oct 16 2006 - 10:32:20 CDT)
  • RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration (Mon Oct 16 2006 - 10:32:20 CDT)
  • AMBER: Updated Tutorials Page (Fri Oct 13 2006 - 14:17:07 CDT)
  • RE: AMBER: problems for running sander.MPI (Thu Oct 12 2006 - 12:41:19 CDT)
  • RE: AMBER: problems for running sander.MPI (Wed Oct 11 2006 - 17:18:14 CDT)
  • RE: AMBER: some puzzles in equilibration MD (Mon Oct 09 2006 - 17:41:54 CDT)
  • RE: AMBER: how to combine NEB method with QM/MM approach (Mon Oct 09 2006 - 17:33:00 CDT)
  • RE: AMBER: some puzzles in equilibration MD (Mon Oct 09 2006 - 09:53:20 CDT)
  • RE: AMBER: mdcrd file (Mon Oct 02 2006 - 23:31:03 CDT)
  • RE: AMBER: Machine File for Intel Core 2 Duo E6400 (Thu Sep 28 2006 - 14:05:02 CDT)
  • RE: AMBER: Problem about installing amber9 on Mac OS X (Thu Sep 28 2006 - 13:52:30 CDT)
  • RE: AMBER: Problem about installing amber9 on Mac OS X (Thu Sep 28 2006 - 12:40:26 CDT)
  • RE: AMBER: running sander on several nodes (Thu Sep 28 2006 - 12:37:28 CDT)
  • RE: AMBER: Error in compiling Amber 8 parallel (Thu Sep 28 2006 - 10:36:25 CDT)
  • RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) (Thu Sep 28 2006 - 10:29:29 CDT)
  • RE: AMBER: NAD parameters (Thu Sep 28 2006 - 10:32:48 CDT)
  • RE: Re: AMBER: A question about Dynamics. (Thu Sep 21 2006 - 10:58:08 CDT)
  • RE: AMBER: installation error for pmemd in Amber 9/Opteron (Tue Sep 19 2006 - 16:41:11 CDT)
  • RE: AMBER: ACML and MASS/MASSV for sander and pmemd (Tue Sep 19 2006 - 15:24:02 CDT)
  • RE: [UCE]Re: RE: AMBER: potential energy (Mon Sep 18 2006 - 23:01:04 CDT)
  • RE: AMBER: Question about Streptavidin/Biotin Tutorial. (Mon Sep 18 2006 - 17:10:39 CDT)
  • RE: AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 16:57:58 CDT)
  • RE: AMBER: Restart problem on PMEMD with position restraint. (Mon Sep 18 2006 - 13:32:05 CDT)
  • RE: AMBER: on the rst file of the current ruuning (Mon Sep 18 2006 - 10:58:01 CDT)
  • RE: AMBER: potential energy (Mon Sep 18 2006 - 10:52:23 CDT)
  • RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file (Tue Sep 12 2006 - 16:35:47 CDT)
  • RE: AMBER: mdcrd file (Thu Sep 07 2006 - 17:52:28 CDT)
  • RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp (Wed Aug 30 2006 - 21:04:36 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 11:16:13 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 17:08:03 CDT)
  • RE: AMBER: nmode memory problem (Thu Aug 24 2006 - 12:57:12 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 12:23:02 CDT)
  • RE: AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 14:54:39 CDT)
  • RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 10:48:00 CDT)
  • RE: AMBER: GBSA EGB = NaN (Fri Aug 18 2006 - 17:11:52 CDT)
  • RE: AMBER: Execution time discrepancies (Thu Aug 17 2006 - 22:00:29 CDT)
  • RE: AMBER: GBSA EGB = NaN (Thu Aug 17 2006 - 21:57:29 CDT)
  • RE: AMBER: identical high energies (Thu Aug 17 2006 - 21:52:38 CDT)
  • RE: AMBER: loading torsion parameters (Mon Jul 31 2006 - 15:25:08 CDT)
  • RE: AMBER: Zinc parameters (Thu Jul 27 2006 - 12:26:29 CDT)
  • RE: AMBER: Tutorial 8, section 6: best fit before clustering (Mon Jul 24 2006 - 09:45:59 CDT)
  • RE: AMBER: combining different versions of AMBER (Fri Jul 21 2006 - 15:11:44 CDT)
  • RE: AMBER: Failure of iwrap in PMEMD (Fri Jul 21 2006 - 10:33:53 CDT)
  • RE: AMBER: amber9 (Fri Jul 14 2006 - 17:37:19 CDT)
  • RE: AMBER: Error in running MD in sander (Sat Jul 08 2006 - 12:38:15 CDT)
  • RE: AMBER: script to extract data from minimization .out file (Sat Jul 08 2006 - 10:47:17 CDT)
  • RE: AMBER: amber9 compilation problems on EM64T xeon system (Thu Jul 06 2006 - 22:06:15 CDT)
  • RE: AMBER: compiling amber9 (Mon Jul 03 2006 - 05:48:10 CDT)
  • RE: AMBER: Having trouble getting Iron parameters for QM/MM (Fri Jun 30 2006 - 03:54:28 CDT)
  • RE: AMBER: rgbmax--something wrong with my input file? (Tue Jun 27 2006 - 17:52:06 CDT)
  • RE: AMBER: constant pressure equillibration (Fri Jun 23 2006 - 10:53:17 CDT)
  • RE: AMBER: Post-MD minimization (Fri Jun 23 2006 - 07:19:14 CDT)
  • RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 (Fri Jun 23 2006 - 06:34:47 CDT)
  • RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN (Fri Jun 23 2006 - 06:28:17 CDT)
  • RE: AMBER: references (Fri Jun 23 2006 - 06:32:57 CDT)
  • RE: AMBER: Post-MD minimization (Mon Jun 19 2006 - 10:20:25 CDT)
  • RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) (Wed Jun 14 2006 - 15:06:49 CDT)
  • RE: AMBER: Fully QM periodic runs (Wed Jun 14 2006 - 11:41:58 CDT)
  • RE: AMBER: Difficulty loading a pdb file (Wed Jun 14 2006 - 09:05:34 CDT)
  • RE: AMBER: Nmode memory allocation problem (Mon Jun 12 2006 - 20:34:24 CDT)
  • RE: AMBER: MD stopped (Mon Jun 12 2006 - 10:50:34 CDT)
  • RE: AMBER: parmchk error (Mon Jun 12 2006 - 10:31:59 CDT)
  • RE: AMBER: switching function for electrostatic interactions (Mon Jun 12 2006 - 10:28:19 CDT)
  • RE: AMBER: problem with amber 9 and igb=5 (Sat Jun 10 2006 - 14:31:26 CDT)
  • RE: AMBER: software to visualize normal modes (Thu Jun 08 2006 - 12:07:41 CDT)
  • RE: AMBER: antechamber (Wed Jun 07 2006 - 11:56:01 CDT)
  • RE: AMBER: compiler error for Amber9 (Wed Jun 07 2006 - 10:34:20 CDT)
  • RE: AMBER: Amber: Segfault while running sander (Mon Jun 05 2006 - 13:31:35 CDT)
  • RE: AMBER: process_mdout (Mon Jun 05 2006 - 10:19:47 CDT)
  • RE: AMBER: compile error with pgf90 (Fri Jun 02 2006 - 10:15:01 CDT)
  • RE: AMBER: Another Installation Problem (Fri Jun 02 2006 - 00:02:03 CDT)
  • RE: AMBER: Amber 8 QMMM tests fail on AIX (Thu Jun 01 2006 - 11:27:24 CDT)
  • RE: AMBER: SHAKE, TIP3P and 2fs Timesteps (Wed May 31 2006 - 12:56:31 CDT)
  • RE: AMBER: Installing / Compiling Question (Sun May 28 2006 - 00:12:46 CDT)
  • RE: AMBER: Saving RMSD values in VMD (Fri May 26 2006 - 10:27:08 CDT)
  • RE: AMBER: alpha helix preference problem (Fri May 26 2006 - 10:23:27 CDT)
  • RE: AMBER: question about QM/MM in amber9 (Thu May 25 2006 - 10:33:17 CDT)
  • RE: AMBER: trajin and rms (Sun May 21 2006 - 23:43:09 CDT)
  • RE: AMBER: Problem with running xleap remotely (Sat May 20 2006 - 14:37:35 CDT)
  • RE: AMBER: process_mdout.perl error (Fri May 19 2006 - 09:43:25 CDT)
  • RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem (Thu May 18 2006 - 18:37:30 CDT)
  • RE: AMBER: AMBER9 installation error on Compaq machine. (Thu May 18 2006 - 17:32:57 CDT)
  • RE: AMBER: density (Wed May 17 2006 - 23:11:11 CDT)
  • RE: AMBER: Tutorial one : xaLeap command not found. (Wed May 17 2006 - 10:40:12 CDT)
  • RE: AMBER: density (Wed May 17 2006 - 10:31:20 CDT)
  • RE: AMBER: amber compilation on Red Hat 8 with MPICH (Wed May 17 2006 - 10:35:00 CDT)
  • RE: AMBER: AMBER9 compilation error on IBM Cluster (Mon May 15 2006 - 22:28:12 CDT)
  • RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs (Mon May 15 2006 - 00:13:01 CDT)
  • RE: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 10:13:48 CDT)
  • RE: AMBER: Opteron vs. Xeon performance (Thu May 11 2006 - 18:17:12 CDT)
  • RE: AMBER: Amber9/mpich2 performance (Thu May 11 2006 - 18:07:21 CDT)
  • RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 (Tue May 09 2006 - 14:12:09 CDT)
  • RE: AMBER: RE: Intel Compiler. (Tue May 09 2006 - 12:21:43 CDT)
  • RE: AMBER: Compiler with AMD 64 bit support (Tue May 09 2006 - 12:19:18 CDT)
  • AMBER: RE: Intel Compiler. (Tue May 09 2006 - 11:05:28 CDT)
  • AMBER: Intel compiler version 9.0.033 (Mon May 08 2006 - 14:40:23 CDT)
  • AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 (Mon May 08 2006 - 13:13:11 CDT)
  • RE: AMBER: AMBER9 INSTALLATION problem on O2 sgi system (Mon May 08 2006 - 10:17:55 CDT)
  • RE: AMBER: Problem with shared libraries: libimf.so (Sun May 07 2006 - 11:10:54 CDT)
  • RE: AMBER: experiences with compiling amber9 for FreeBSD (Fri May 05 2006 - 16:10:51 CDT)
  • RE: AMBER: Problem with shared libraries: libimf.so (Fri May 05 2006 - 16:08:31 CDT)
  • RE: AMBER: Problem with shared libraries: libimf.so (Fri May 05 2006 - 13:04:10 CDT)
  • RE: AMBER: molsurf.c error (Thu May 04 2006 - 11:28:49 CDT)
  • RE: AMBER: Amber install on RedHat Linux (Thu May 04 2006 - 10:31:56 CDT)
  • RE: AMBER: Amber install on RedHat Linux (Wed May 03 2006 - 21:36:45 CDT)
  • RE: AMBER: concatenating .mdcrd files (Wed May 03 2006 - 11:39:11 CDT)
  • RE: AMBER: cluster architecture for the best amber performance (Wed May 03 2006 - 10:42:19 CDT)
  • RE: AMBER: Error while running test.serial in Amber9 (Wed May 03 2006 - 10:21:42 CDT)
  • RE: AMBER: Shared libraries error (Wed May 03 2006 - 10:13:32 CDT)
  • RE: AMBER: MPI parallel problem in AMBER 8.0 (Tue May 02 2006 - 17:40:37 CDT)
  • RE: AMBER: MPI parallel problem in AMBER 8.0 (Tue May 02 2006 - 16:42:33 CDT)
  • AMBER: AMBER Workshops, London UK 26th - 30th June 2006 (Tue May 02 2006 - 10:45:33 CDT)
  • RE: AMBER: How to build 1,4-dimethyl benzene with amber9 (Fri Apr 28 2006 - 18:46:23 CDT)
  • RE: AMBER: How to build 1,4-dimethyl benzene with amber9 (Fri Apr 28 2006 - 17:10:56 CDT)
  • RE: AMBER: Performing Simulated Annealing? (Fri Apr 28 2006 - 12:13:56 CDT)
  • RE: AMBER: Test Failure during amber9 serial compilation (Wed Apr 26 2006 - 13:49:06 CDT)
  • RE: AMBER: Test Failure during amber9 serial compilation (Tue Apr 25 2006 - 14:30:19 CDT)
  • RE: AMBER: compiling errors (Mon Apr 24 2006 - 19:58:52 CDT)
  • RE: AMBER: rmsd value for organic molecule (Mon Apr 24 2006 - 14:25:23 CDT)
  • RE: AMBER: a quetion (Mon Apr 24 2006 - 09:52:59 CDT)
  • RE: AMBER: amber9 compilation error on SGI altix (Sat Apr 22 2006 - 14:21:24 CDT)
  • RE: AMBER: a question (Fri Apr 21 2006 - 15:35:51 CDT)
  • RE: AMBER: Non-periodic simulations: How is the system kept together? (Thu Apr 20 2006 - 11:35:26 CDT)
  • RE: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight (Wed Apr 19 2006 - 10:16:51 CDT)
  • AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight (Tue Apr 18 2006 - 10:42:41 CDT)
  • RE: AMBER: Error in the MD run (Tue Apr 18 2006 - 10:35:41 CDT)
  • RE: AMBER: ibelly & fix atom (Mon Apr 17 2006 - 23:08:42 CDT)
  • RE: AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 13:28:18 CDT)
  • RE: AMBER: amber memory usage (Fri Apr 14 2006 - 19:28:31 CDT)
  • RE: AMBER: DNA tutorial, in vacuo minimization (Fri Apr 14 2006 - 14:34:32 CDT)
  • RE: AMBER:a problem in parallel compiler (Thu Apr 13 2006 - 10:54:43 CDT)
  • RE: AMBER: RESP problem (Tue Apr 11 2006 - 10:08:25 CDT)
  • RE: AMBER: organic molecule - from newbie :) (Mon Apr 10 2006 - 17:41:56 CDT)
  • RE: AMBER: printing Amber VdW radii as separate column in pdb files (Mon Apr 10 2006 - 11:03:18 CDT)
  • RE: AMBER: organic molecule - from newbie :) (Thu Apr 06 2006 - 21:13:46 CDT)
  • RE: AMBER: Obtaining an average structure from a trajectory (Tue Apr 04 2006 - 19:07:18 CDT)
  • RE: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? (Mon Apr 03 2006 - 18:53:06 CDT)
  • RE: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) (Tue Mar 28 2006 - 22:35:03 CST)
  • RE: AMBER: amber8 error installation (Tue Mar 28 2006 - 22:35:03 CST)
  • RE: AMBER: amber8 error installation (Tue Mar 28 2006 - 10:37:34 CST)
  • RE: AMBER: heating system (Fri Mar 24 2006 - 11:29:32 CST)
  • RE: AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? (Thu Mar 23 2006 - 23:38:24 CST)
  • RE: AMBER: heating system (Wed Mar 22 2006 - 10:58:12 CST)
  • RE: AMBER: heating system (Tue Mar 21 2006 - 17:09:28 CST)
  • RE: AMBER: faulty ambpdb compilation? (Thu Mar 16 2006 - 12:44:23 CST)
  • RE: AMBER: NTT for production run (Wed Mar 15 2006 - 10:21:50 CST)
  • AMBER: RE: hi & question (Thu Mar 09 2006 - 16:14:02 CST)
  • RE: AMBER: CPU utilization with Parallel Sander (Thu Mar 09 2006 - 10:23:08 CST)
  • RE: AMBER: MD and MMPBSA (Wed Mar 08 2006 - 23:26:34 CST)
  • RE: AMBER: the total energy is not converge as the cutoff increase (Mon Mar 06 2006 - 09:39:51 CST)
  • RE: AMBER: generating parameters for the NADH analogue H4NAD (Thu Mar 02 2006 - 17:32:27 CST)
  • RE: AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 10:17:49 CST)
  • RE: AMBER: install error (Wed Mar 01 2006 - 10:08:24 CST)
  • RE: AMBER: failed to save prm and xyz using ff96 (Tue Feb 28 2006 - 10:31:41 CST)
  • RE: AMBER: MD job stopped without any error information? (Mon Feb 27 2006 - 10:22:25 CST)
  • AMBER: RE: about compiling errors for Leap (Mon Feb 27 2006 - 10:17:27 CST)
  • RE: AMBER: TI cal (Thu Feb 23 2006 - 13:25:57 CST)
  • RE: AMBER: generating parameters for the NADH analogue H4NAD (Thu Feb 23 2006 - 13:00:30 CST)
  • RE: AMBER: Problem with file size of sander outputs (Thu Feb 23 2006 - 12:06:30 CST)
  • RE: AMBER: Problem with file size of sander outputs (Wed Feb 22 2006 - 15:16:30 CST)
  • RE: AMBER: amber 8 problem (Mon Feb 20 2006 - 11:05:57 CST)
  • RE: AMBER: parallel problem of amber8 (Mon Feb 20 2006 - 11:00:26 CST)
  • RE: AMBER: sander problem (Thu Feb 16 2006 - 15:20:45 CST)
  • RE: AMBER: sander problem (Thu Feb 16 2006 - 10:51:24 CST)
  • RE: AMBER: minization: outputing intermediate snapshots (Tue Feb 14 2006 - 12:34:30 CST)
  • RE: AMBER: Error when installing (Tue Feb 14 2006 - 12:30:29 CST)
  • RE: AMBER: paralelization and sander problems (Tue Feb 14 2006 - 11:48:06 CST)
  • RE: AMBER: Organic molecules (Tue Feb 14 2006 - 11:44:25 CST)
  • RE: AMBER: Charges on atoms in protein :AMBER (Wed Feb 01 2006 - 22:17:24 CST)
  • RE: AMBER: basic minimize question (Wed Feb 01 2006 - 18:17:57 CST)
  • RE: AMBER: basic minimize question (Wed Feb 01 2006 - 17:06:07 CST)
  • RE: AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 16:03:31 CST)
  • RE: AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 16:04:52 CST)
  • RE: AMBER: NAD parameters (Mon Jan 30 2006 - 10:34:20 CST)
  • RE: AMBER: A few problems on the parameterisation of a Glutamine residue (Wed Jan 18 2006 - 12:32:25 CST)
  • RE: AMBER: problem in saving parameter file for non-standard residue (Mon Jan 16 2006 - 10:44:11 CST)
  • RE: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 10:44:11 CST)
  • RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 10:49:17 CST)
  • RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 10:44:12 CST)
  • RE: AMBER: About tleap (Thu Jan 12 2006 - 14:08:14 CST)
  • RE: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 16:51:01 CST)
  • RE: AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 12:01:39 CST)
  • RE: AMBER: Where to modify the atom type in sander? (Thu Jan 05 2006 - 10:12:34 CST)
• Russell Glavey
  • AMBER: tetrolic acid (Thu Dec 21 2006 - 06:29:35 CST)
• S. Jamal Rahi
  • AMBER: 0 steps the same as 1 step? (Wed Aug 23 2006 - 16:25:44 CDT)
  • AMBER: Simulating an "average" DNA sequence (Fri Jul 21 2006 - 22:20:36 CDT)
• S.Sundar Raman
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Sat Aug 26 2006 - 05:51:04 CDT)
  • AMBER: Details about Gaussian basis set for Cobalt complex (Sun Aug 20 2006 - 09:07:57 CDT)
  • AMBER: compiler requirement for SGI Fuel To install AMBER9 (Wed Jun 14 2006 - 01:45:40 CDT)
  • Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system (Mon May 08 2006 - 06:33:58 CDT)
  • AMBER: AMBER9 INSTALLATION problem on O2 sgi system (Sun May 07 2006 - 02:10:15 CDT)
  • AMBER: regarding Hydrogen bond analysis (Mon Jan 09 2006 - 21:19:15 CST)
• Sai Kumar Ramadugu
  • Re: AMBER: Problem in running umbrella sampling (Sun Feb 12 2006 - 23:22:49 CST)
  • AMBER: Problem in running umbrella sampling (Sun Feb 12 2006 - 22:28:09 CST)
  • Re: AMBER: Values of Spring Constants (Thu Feb 02 2006 - 22:01:44 CST)
  • Re: AMBER: Values of Spring Constants (Wed Feb 01 2006 - 23:00:56 CST)
  • Re: AMBER: Values of Spring Constants (Wed Feb 01 2006 - 09:43:05 CST)
  • AMBER: Values of Spring Constants (Wed Feb 01 2006 - 01:18:44 CST)
  • Re: AMBER: Problem in Antechamber (Thu Jan 26 2006 - 22:46:42 CST)
  • Re: AMBER: Problem in Antechamber (Fri Jan 13 2006 - 00:01:46 CST)
  • AMBER: Problem in Antechamber (Tue Jan 10 2006 - 05:17:53 CST)
• sai vikram
  • Re: AMBER: Simulated Annealing problem... (Sat Dec 30 2006 - 07:12:53 CST)
  • AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 04:33:50 CST)
• Sam
  • AMBER: mm_pbsa: "Missing values for MM ..." (Fri Apr 21 2006 - 08:39:19 CDT)
• Sandro Fornili
  • AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 10:21:01 CST)
• sangeeta
  • AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:11:30 CST)
  • AMBER: H-bonds of peptide with water (Fri Aug 04 2006 - 08:20:13 CDT)
  • RE: AMBER: Tutorial 8, section 6: best fit before clustering (Wed Jul 26 2006 - 08:42:47 CDT)
  • AMBER: Tutorial 8, section 6: best fit before clustering (Mon Jul 24 2006 - 08:18:05 CDT)
• sangeeta_at_bioinfo.ernet.in
  • Re: AMBER: script to extract data from minimization .out file (Sat Jul 08 2006 - 05:41:44 CDT)
  • Re: AMBER: script to extract data from minimization .out file (Sat Jul 08 2006 - 05:23:52 CDT)
  • AMBER:Checkoverlap query (Mon Jun 26 2006 - 07:12:56 CDT)
  • RE: AMBER: Post-MD minimization (Fri Jun 23 2006 - 01:09:31 CDT)
  • AMBER: MMTSB: phi-pdi-based clustering (Wed Jun 21 2006 - 07:37:39 CDT)
  • RE: AMBER: checkoverlap doubt [was: Post-MD minimization] (Tue Jun 20 2006 - 08:21:11 CDT)
  • AMBER: Post-MD minimization (Mon Jun 19 2006 - 06:33:58 CDT)
• Sanya Kryklia
  • AMBER: General Question about Abmer (Mon Dec 11 2006 - 08:23:11 CST)
• Satyan Sharma
  • AMBER: Acetyl CoA (Thu Feb 09 2006 - 11:55:19 CST)
• saurabh agrawal
  • AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 03:41:47 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Thu Dec 14 2006 - 05:38:05 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Thu Dec 14 2006 - 01:18:33 CST)
  • AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 05:39:39 CST)
• Sayandeep Purkayasth
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Thu Nov 02 2006 - 00:48:03 CST)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Fri Oct 27 2006 - 20:25:37 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 16 2006 - 01:32:04 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 09 2006 - 03:59:18 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Mon Oct 09 2006 - 03:11:56 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 08:37:07 CDT)
  • AMBER: ptraj hbond analysis troubles (Wed Oct 04 2006 - 16:14:10 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Wed Oct 04 2006 - 00:14:06 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 02 2006 - 19:30:40 CDT)
  • AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Sun Oct 01 2006 - 21:15:54 CDT)
• Scott Brozell
  • RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 13:19:38 CST)
  • Re: AMBER: Parallelization method (Tue Dec 19 2006 - 12:58:07 CST)
  • Re: AMBER: setBox with buffer in leap (Mon Dec 11 2006 - 23:08:38 CST)
  • Re: AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 21:29:15 CST)
  • Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 15:26:52 CST)
  • Re: AMBER: sander error about fortran (Sat Dec 02 2006 - 01:10:03 CST)
  • Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 13:40:54 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Tue Nov 21 2006 - 12:38:49 CST)
  • Re: AMBER: error in tleap test (Wed Nov 15 2006 - 11:55:07 CST)
  • Re: AMBER: Trouble with Leap (Mon Oct 09 2006 - 20:42:38 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Mon Oct 09 2006 - 20:14:54 CDT)
  • Re: AMBER: LEAP error (Fri Oct 06 2006 - 12:30:34 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Oct 06 2006 - 12:13:15 CDT)
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Wed Oct 04 2006 - 03:16:09 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 01:45:09 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 01:28:35 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:58:20 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 (Thu Aug 24 2006 - 21:57:03 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 20:50:31 CDT)
  • Re: AMBER: antechamber error -> metals (Sun Aug 13 2006 - 16:58:14 CDT)
  • Re: AMBER: impose command in leap problem (Fri Aug 11 2006 - 20:57:21 CDT)
  • Re: AMBER: Amber Installation Help; link woes (Tue Aug 08 2006 - 14:36:32 CDT)
  • Re: AMBER: (Mon Aug 07 2006 - 19:37:19 CDT)
  • AMBER: Re: Problem in compiling sander with MMTSB (Thu Jun 15 2006 - 18:28:27 CDT)
  • AMBER: Re: Problem in compiling sander with MMTSB (Wed Jun 14 2006 - 22:29:57 CDT)
  • Re: AMBER: amber7 compiling error (Sun Apr 16 2006 - 14:30:23 CDT)
  • Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short (Mon Apr 10 2006 - 09:59:46 CDT)
  • Re: AMBER: Amber 8 under Solaris 9 compilation failed (Mon Mar 27 2006 - 01:16:27 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Tue Jan 31 2006 - 23:54:56 CST)
  • Re: AMBER: Problem in compiling sander with MMTSB (Mon Jan 30 2006 - 21:44:06 CST)
• Scott P Brown
  • AMBER: GAFF + AM1BCC & small-molecule aggregation (Wed Mar 01 2006 - 14:00:33 CST)
• Scott Pendley
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:28:48 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:20:43 CST)
  • Re: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:19:31 CDT)
  • Re: AMBER: H-bonds of peptide with water (Mon Aug 07 2006 - 14:56:04 CDT)
  • Re: AMBER: analysis of ATOMs in ´certain range distance during simulation (Thu Jul 06 2006 - 16:47:57 CDT)
  • Re: AMBER: igb=2 and "bad atom type" conflict (Wed Jul 05 2006 - 15:22:43 CDT)
  • Re: AMBER: mm_pbsa calculation for calcium (Tue Jun 13 2006 - 15:03:17 CDT)
  • Re: AMBER: mm_pbsa calculation for calcium (Tue Jun 13 2006 - 11:20:42 CDT)
  • Re: AMBER: mm_pbsa calculation for calcium (Mon Jun 12 2006 - 16:42:59 CDT)
  • Re: AMBER: Another Installation Problem (Fri Jun 02 2006 - 11:21:09 CDT)
  • Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” (Wed Apr 26 2006 - 17:54:53 CDT)
  • Re: AMBER: Dimer Image Wrapping (Thu Mar 30 2006 - 11:29:23 CST)
  • Re: AMBER: mm-pbsa (Mon Mar 20 2006 - 12:06:38 CST)
  • Re: AMBER: mm-pbsa (Fri Mar 17 2006 - 17:41:30 CST)
  • Re: AMBER: Xleap crash (Tue Feb 14 2006 - 12:08:59 CST)
  • Re: AMBER: Xleap crash (Tue Feb 14 2006 - 11:53:37 CST)
  • AMBER: Xleap crash (Tue Feb 14 2006 - 10:55:12 CST)
  • Re: AMBER: (Mon Feb 13 2006 - 15:00:15 CST)
  • Re: AMBER: MM_PBSA problem (No values for MM_GAS ) (Mon Feb 13 2006 - 14:57:27 CST)
• Sean Rathlef
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 24 2006 - 21:29:43 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 24 2006 - 21:30:54 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 24 2006 - 18:47:03 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 23 2006 - 17:19:18 CDT)
  • Re: AMBER: charge models in antechamber (Wed Oct 18 2006 - 18:48:00 CDT)
  • Re: AMBER: charge models in antechamber (Wed Oct 18 2006 - 18:29:02 CDT)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 17 2006 - 11:07:18 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 16 2006 - 20:37:25 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 16 2006 - 17:48:16 CDT)
  • AMBER: modeling of ligand concentrations (Mon Oct 16 2006 - 15:43:51 CDT)
  • Re: AMBER: Grid command of ptraj (Sat Oct 14 2006 - 05:25:59 CDT)
  • AMBER: BioBlade (Thu Oct 12 2006 - 22:12:41 CDT)
  • Re: AMBER: adding polar hydrogens (Wed Oct 11 2006 - 13:35:47 CDT)
  • Re: AMBER: adding polar hydrogens (Wed Oct 11 2006 - 13:02:28 CDT)
  • AMBER: adding polar hydrogens (Tue Oct 10 2006 - 21:43:39 CDT)
• sebnem
  • Re: AMBER: hessian calculation (Thu Mar 30 2006 - 10:22:23 CST)
  • Re: AMBER: hessian calculation (Tue Mar 28 2006 - 20:53:59 CST)
  • Re: AMBER: hessian calculation (Tue Mar 28 2006 - 20:41:52 CST)
  • AMBER: hessian calculation (Tue Mar 28 2006 - 15:48:19 CST)
• sebnem_at_mercury.chem.pitt.edu
  • Re: AMBER: hessian calculation (Wed Mar 29 2006 - 15:48:38 CST)
  • Re: AMBER: hessian calculation (Tue Mar 28 2006 - 18:20:18 CST)
• Seongeun Yang
  • AMBER: Replica exchange rate in REMD (Thu Dec 21 2006 - 05:42:59 CST)
  • AMBER: energy minimizations in amber8 vs. amber9 (Tue Nov 28 2006 - 01:43:35 CST)
• Sergei Smirnov
  • AMBER: water diffusion (Mon Jul 17 2006 - 19:48:59 CDT)
• Sergey Krishtal
  • AMBER: Question about .off file (Fri May 26 2006 - 03:15:06 CDT)
  • Re[2]: AMBER: Could not find atom type. (Tue Apr 18 2006 - 21:56:30 CDT)
  • Re[2]: AMBER: Could not find atom type. (Tue Apr 18 2006 - 05:48:07 CDT)
  • AMBER: Could not find atom type. (Mon Apr 17 2006 - 04:08:19 CDT)
  • AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. (Thu Apr 13 2006 - 22:05:45 CDT)
  • Re[2]: AMBER: Input conversion error. (Mon Mar 13 2006 - 08:52:23 CST)
  • AMBER: Input conversion error. (Sat Mar 11 2006 - 07:46:47 CST)
  • AMBER: Amber 9. (Wed Mar 01 2006 - 21:37:02 CST)
  • Re: AMBER: replica exchange hangs (Wed Mar 01 2006 - 12:15:46 CST)
• Sergey Samsonov
  • Re: AMBER: Is there a way to simulate a box of pure water with amber (Mon Dec 18 2006 - 01:43:27 CST)
  • Re: AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 03:38:46 CST)
  • AMBER: Restarting with new topology (Thu Nov 23 2006 - 10:39:53 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 01:09:15 CST)
  • Re: AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:57:20 CST)
  • AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:39:18 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 10:46:07 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 02:35:28 CST)
  • Re: AMBER: Mass weights (Tue Nov 07 2006 - 02:06:14 CST)
  • AMBER: grid output (Wed Nov 01 2006 - 10:31:34 CST)
  • Re: AMBER: Closest(closest water) (Wed Nov 01 2006 - 02:38:55 CST)
  • AMBER: Mass weights (Wed Nov 01 2006 - 02:41:33 CST)
  • Re: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 09:36:29 CST)
  • Re: AMBER: periodic boundary condition question... (Mon Oct 30 2006 - 09:04:12 CST)
  • Re: AMBER: Closest(closest water) (Mon Oct 30 2006 - 08:27:40 CST)
  • AMBER: Closest(closest water) (Mon Oct 30 2006 - 06:58:11 CST)
  • AMBER: klambda (Fri Oct 13 2006 - 09:49:05 CDT)
  • Re: AMBER: Reducing trajectory (Wed Oct 11 2006 - 02:36:15 CDT)
  • AMBER: Reducind trajectory (Wed Oct 11 2006 - 02:03:49 CDT)
  • Re: AMBER: hbond analysis (Thu Oct 05 2006 - 01:40:59 CDT)
  • Re: AMBER: hbond analysis (Wed Oct 04 2006 - 09:49:35 CDT)
  • AMBER: lifetime and maxocc (Tue Sep 26 2006 - 10:56:26 CDT)
• Sergio Aragon
  • AMBER: zzfft issue resolved -thanks! (Tue Sep 19 2006 - 18:09:25 CDT)
  • AMBER: zzfft error for pmemd in Amber 9/Opteron (Tue Sep 19 2006 - 17:53:10 CDT)
  • AMBER: installation error for pmemd in Amber 9/Opteron (Tue Sep 19 2006 - 16:25:53 CDT)
• Sergio Dall'Angelo
  • Re: AMBER: Xleap compilation problem (Fri May 12 2006 - 10:21:02 CDT)
  • AMBER: Xleap compilation problem (Fri May 12 2006 - 05:19:48 CDT)
• SERGIO MIGUEL FERNANDES DOS SANTOS
  • AMBER: Acetone box (Tue Nov 14 2006 - 12:34:24 CST)
• Seth Lilavivat
  • AMBER: chirality.c line 121 (Wed Dec 27 2006 - 15:43:56 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 13:42:42 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 11:44:29 CST)
  • AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 10:49:32 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 10:26:14 CST)
  • AMBER: bad connectivity (Tue Dec 26 2006 - 11:24:17 CST)
  • AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 12:02:27 CST)
  • AMBER: xleap, generating prep file (Thu Dec 21 2006 - 10:49:56 CST)
  • AMBER: RED - help with installation / config (Wed Dec 20 2006 - 09:18:49 CST)
  • AMBER: ambpdb -pqr (Tue Nov 28 2006 - 14:52:10 CST)
  • AMBER: Modifying a Force Field (Tue Nov 28 2006 - 09:27:08 CST)
  • AMBER: pqr file (Thu Nov 16 2006 - 10:43:55 CST)
  • AMBER: holding a pair of residues fixed during minimization (Tue Aug 22 2006 - 22:22:06 CDT)
  • AMBER: Creating an Intercalation site (Sat Jun 17 2006 - 14:25:59 CDT)
  • AMBER: Compiling / Installing Amber 8 on SUSE 10.1 (Tue Jun 13 2006 - 22:23:25 CDT)
  • AMBER: Another Installation Problem (Thu Jun 01 2006 - 18:01:13 CDT)
  • AMBER: Installing / Compiling Question (Fri May 26 2006 - 22:29:06 CDT)
• sethl_at_gatech.edu
  • AMBER: Using modified NA bases (Mon Oct 23 2006 - 14:59:15 CDT)
  • AMBER: atom type nh vs. n2 (Fri Oct 20 2006 - 16:31:09 CDT)
  • AMBER: Phenyl Ring atom types (Thu Oct 12 2006 - 13:59:24 CDT)
  • AMBER: Parameterization of ethidium - phenyl ring (Thu Sep 28 2006 - 15:02:08 CDT)
  • AMBER: LEAP - "could not find type: NH" (Fri Sep 08 2006 - 16:08:11 CDT)
  • AMBER: leap - how to recognize my structure (Thu Sep 07 2006 - 17:16:06 CDT)
  • AMBER: help with antechamber - creating ligand (Tue Sep 05 2006 - 16:10:08 CDT)
  • AMBER: force fields for proflavine molecule (Fri Sep 01 2006 - 12:49:00 CDT)
  • AMBER: preparing ligand/rna structure for MD (Mon Aug 28 2006 - 13:45:17 CDT)
  • Re: AMBER: How to create a modified NA in leap (Sat Aug 26 2006 - 15:13:10 CDT)
  • AMBER: How to create a modified NA in leap (Fri Aug 25 2006 - 15:20:35 CDT)
  • AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 15:03:59 CDT)
  • AMBER: amber naming conventions for structure files (Tue Aug 22 2006 - 16:36:56 CDT)
  • AMBER: help with leap (Wed Aug 16 2006 - 18:24:42 CDT)
  • AMBER: Building an RNA - Proflavin Complex (Mon Jul 24 2006 - 15:05:49 CDT)
  • AMBER: Compiling Leap problem (Fri Jul 14 2006 - 16:36:38 CDT)
  • AMBER: Namot on AMD 64 possible (Wed Jul 05 2006 - 12:05:26 CDT)
  • AMBER: Can you use VMD to measure bond angles/lengths (Tue Jul 04 2006 - 10:24:49 CDT)
  • AMBER: NAMOT (Fri Jun 30 2006 - 14:17:46 CDT)
  • AMBER: creating RNA, nucgen / leap (Mon Jun 26 2006 - 15:59:46 CDT)
  • Re: AMBER: help creating RNA (Mon Jun 26 2006 - 10:42:00 CDT)
  • AMBER: how to create 2'-5' RNA (Fri Jun 23 2006 - 16:13:57 CDT)
  • AMBER: help creating RNA (Thu Jun 22 2006 - 14:14:06 CDT)
  • AMBER: help with custom RNA molecule (Mon Jun 19 2006 - 13:55:59 CDT)
  • AMBER: best way to customize linkages (Wed Jun 14 2006 - 15:25:07 CDT)
  • Re: AMBER: AMD 64 Installation / configuration clarification (Thu Jun 08 2006 - 15:23:51 CDT)
  • AMBER: AMD 64 Installation / configuration clarification (Thu Jun 08 2006 - 14:09:50 CDT)
  • AMBER: Amber: Can't get sander to run (Tue Jun 06 2006 - 13:15:14 CDT)
  • AMBER: Amber: Segfault while running sander (Mon Jun 05 2006 - 13:19:33 CDT)
• Shafinaz
  • AMBER: Please reply (Fri May 26 2006 - 14:19:42 CDT)
  • AMBER: problem with prepfile (Wed May 24 2006 - 14:50:21 CDT)
• Shan-ho Tsai
  • RE: AMBER: Amber 8 QMMM tests fail on AIX (Thu Jun 01 2006 - 12:31:08 CDT)
  • AMBER: Amber 8 QMMM tests fail on AIX (Thu Jun 01 2006 - 10:08:26 CDT)
• Shawn yy
  • AMBER: ptraj quasiharmonic analysis question (Fri Aug 11 2006 - 09:45:21 CDT)
• Shin Tokumoto
  • Re: AMBER: RESP charges of iron-porphyrin system (Thu Dec 14 2006 - 03:31:13 CST)
  • Re: AMBER: RESP charges of iron-porphyrin system (Thu Oct 19 2006 - 23:45:08 CDT)
  • AMBER: RESP charges of iron-porphyrin system (Wed Oct 18 2006 - 21:50:26 CDT)
• Shin, John Y CONTRACTOR WRAIR-Wash DC
  • RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 15:29:12 CST)
  • RE: AMBER: Error in sysdepend.c? (Mon Dec 18 2006 - 14:27:24 CST)
  • AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 13:44:50 CST)
  • AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 12:46:32 CST)
• Shozeb Haider
  • AMBER: MM-PBSA (Mon Dec 18 2006 - 11:57:17 CST)
  • AMBER: Xleap woes (Thu Nov 16 2006 - 17:07:01 CST)
  • AMBER: High Values in MMPBSA (Thu Oct 12 2006 - 11:55:15 CDT)
  • AMBER: MMPBSA vDW error (Mon Oct 09 2006 - 18:08:27 CDT)
  • AMBER: MM_PBSA error (Tue Oct 03 2006 - 16:04:57 CDT)
• shuli kang
  • Re: AMBER: Problem with file size of sander outputs (Wed Feb 22 2006 - 02:45:21 CST)
  • AMBER: (Mon Feb 13 2006 - 06:26:07 CST)
• Shulin Zhuang
  • Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight (Wed Apr 19 2006 - 00:58:06 CDT)
  • Re: AMBER: about Br- parameters (Fri Mar 03 2006 - 05:04:27 CST)
• Shuting Wei
  • AMBER: DRMS setting for Nmode calculation (Thu Dec 07 2006 - 14:46:54 CST)
  • Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 11:02:52 CST)
  • AMBER: sander error about fortran (Fri Dec 01 2006 - 09:58:25 CST)
  • Re: AMBER: pmemd installation on linux_p3_athlon ifort (Tue Oct 24 2006 - 14:19:31 CDT)
  • Re: AMBER: problem of installing carnal on macosx (Fri Oct 20 2006 - 14:45:03 CDT)
  • RE: AMBER: Problem about installing amber9 on Mac OS X (Fri Sep 29 2006 - 16:08:42 CDT)
  • Re: AMBER: build a polymer with sequence command (Mon Sep 25 2006 - 12:15:10 CDT)
  • Re: AMBER: build a polymer with sequence command (Fri Sep 22 2006 - 16:42:04 CDT)
  • AMBER: build a polymer with sequence command (Fri Sep 22 2006 - 15:41:43 CDT)
  • AMBER: the sequence command in leap (Wed Sep 20 2006 - 10:32:17 CDT)
  • AMBER: Carnal: Internal error: stream file name 2 out of range (Wed Aug 23 2006 - 15:43:31 CDT)
  • AMBER: SURFTEN in GB (mm_pbsa calculations) (Thu Aug 03 2006 - 14:18:10 CDT)
  • AMBER: Power Mac G5 (Thu Mar 09 2006 - 17:32:44 CST)
• simon whitehead
  • Re: AMBER: references (Fri Jun 23 2006 - 06:46:22 CDT)
  • AMBER: constant pressure equillibration (Fri Jun 23 2006 - 04:17:35 CDT)
  • AMBER: references (Fri Jun 23 2006 - 05:35:56 CDT)
  • AMBER: ptraj: rms per residue (Wed Jun 14 2006 - 09:14:28 CDT)
  • Re: AMBER: How to strip waters in trajectorie ? (Tue Jun 13 2006 - 03:24:37 CDT)
  • AMBER: RE: PMEMD compilation problems (Fri May 19 2006 - 10:37:46 CDT)
  • AMBER: Intel fortran compiler 7? (Fri May 19 2006 - 04:47:55 CDT)
  • AMBER: problem with prep file (Wed May 10 2006 - 05:52:32 CDT)
  • RE: AMBER: RE: Respgen segemtation fault - debug attempt (Thu Apr 20 2006 - 11:30:51 CDT)
  • RE: AMBER: RE: Respgen segemtation fault - debug attempt (Thu Apr 20 2006 - 07:48:07 CDT)
  • Re: AMBER: RE: Respgen segemtation fault (Thu Apr 20 2006 - 07:30:48 CDT)
  • AMBER: RE: Respgen segemtation fault (Wed Apr 19 2006 - 12:10:11 CDT)
  • AMBER: Respgen segemtation fault (Thu Apr 13 2006 - 11:38:41 CDT)
  • AMBER: dual xeon mpich compilation problem: sorted (Thu Apr 13 2006 - 07:16:53 CDT)
  • AMBER: Dual Xeon mpich compilation error (Thu Apr 13 2006 - 02:56:47 CDT)
  • AMBER: RESP problem (Tue Apr 11 2006 - 08:44:00 CDT)
  • AMBER: Suitable water box (Mon Mar 13 2006 - 06:07:48 CST)
  • AMBER: converting .lib files (Wed Mar 08 2006 - 04:51:25 CST)
  • AMBER: NADP(H) parameters (Wed Mar 08 2006 - 04:06:45 CST)
  • RE: AMBER: generating parameters for the NADH analogue H4NAD (Thu Mar 02 2006 - 17:17:50 CST)
  • AMBER: generating parameters for the NADH analogue H4NAD (Thu Feb 23 2006 - 12:31:02 CST)
• sishi.tang_at_utoronto.ca
  • Re: AMBER: MM-GBSA decomposition (Sat Apr 15 2006 - 12:54:34 CDT)
  • AMBER: MM-GBSA decomposition (Thu Apr 06 2006 - 15:20:36 CDT)
  • Re: AMBER: MMPBSA: magnitude of PB calculation (Sat Feb 04 2006 - 10:47:21 CST)
  • AMBER: MMPBSA: magnitude of PB calculation (Fri Feb 03 2006 - 17:34:10 CST)
• Sivakolundu, Sivashankar
  • AMBER: NMR restraints and LES (Mon Feb 20 2006 - 19:43:38 CST)
• Smriti Sharma
  • Re: AMBER: To create methanol solvent box (Wed Oct 18 2006 - 03:14:38 CDT)
  • AMBER: simulation of protein in non-aq or organic solvent bath (Sun Oct 15 2006 - 23:06:53 CDT)
• snowyowls
  • AMBER:a problem in parallel compiler (Thu Apr 13 2006 - 03:15:09 CDT)
  • AMBER:a problem in parallel compiler (Wed Apr 12 2006 - 23:27:10 CDT)
  • Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short (Mon Apr 10 2006 - 22:07:40 CDT)
  • Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short (Mon Apr 10 2006 - 22:09:35 CDT)
  • AMBER: PB bomb in pb_atmlist(): MAXNEI too short (Mon Apr 10 2006 - 07:55:12 CDT)
  • AMBER: what is unit of the out put of mmpbsa caculation (Thu Mar 23 2006 - 06:47:52 CST)
  • Re: AMBER: quistions about pbsa cacultaion (Tue Mar 14 2006 - 20:43:46 CST)
  • AMBER: quistions about pbsa cacultaion (Tue Mar 14 2006 - 19:26:12 CST)
  • AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed (Wed Mar 08 2006 - 01:18:02 CST)
  • AMBER: strange result of mm/pbsa (Mon Jan 09 2006 - 22:43:11 CST)
• snoze pa
  • AMBER: openmpi (Wed Jun 21 2006 - 12:28:28 CDT)
  • AMBER: amber9 hostfile (Tue Jun 20 2006 - 19:12:50 CDT)
  • Re: AMBER: manual docking (Sun Jun 04 2006 - 23:46:05 CDT)
  • Re: AMBER: AMBER mdcrd file bigger than 2GB (Thu Jun 01 2006 - 10:41:02 CDT)
  • Re: AMBER: AMBER mdcrd file bigger than 2GB (Wed May 31 2006 - 18:04:53 CDT)
  • AMBER: AMBER mdcrd file bigger than 2GB (Wed May 31 2006 - 16:57:22 CDT)
  • Re: AMBER: bond information in amber (Thu May 11 2006 - 14:16:56 CDT)
  • Re: AMBER: bond information in amber (Thu May 11 2006 - 13:41:00 CDT)
  • Re: AMBER: bond information in amber (Thu May 11 2006 - 13:36:18 CDT)
  • AMBER: bond information in amber (Thu May 11 2006 - 11:48:58 CDT)
  • Re: AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 13:48:55 CDT)
  • AMBER: ambpdb and original PDB (Mon Apr 17 2006 - 13:20:05 CDT)
  • AMBER: temp control (Sun Mar 26 2006 - 21:16:20 CST)
  • AMBER: Related to RESTRAINT_WT (Wed Mar 22 2006 - 16:06:04 CST)
  • Re: AMBER: heating system (Tue Mar 21 2006 - 17:39:15 CST)
  • AMBER: heating system (Tue Mar 21 2006 - 15:58:25 CST)
  • Re: AMBER: NTT for production run (Wed Mar 15 2006 - 11:03:22 CST)
  • AMBER: NTT for production run (Mon Mar 13 2006 - 12:03:32 CST)
  • AMBER: error while running sander (Fri Mar 10 2006 - 22:23:54 CST)
  • Re: AMBER: sander problem (Thu Feb 16 2006 - 10:13:22 CST)
  • AMBER: PMED in AMBER (Wed Feb 08 2006 - 19:07:40 CST)
  • AMBER: desc related issue (Wed Feb 08 2006 - 13:15:19 CST)
  • Re: AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 18:16:20 CST)
  • Re: AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 17:18:16 CST)
  • Re: AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 17:02:22 CST)
  • AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 16:47:19 CST)
  • Re: AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 13:45:48 CST)
  • AMBER: Parallel version of Amber: error message (Mon Feb 06 2006 - 12:55:39 CST)
  • Re: AMBER: lib file (Fri Feb 03 2006 - 13:32:39 CST)
  • AMBER: lib file (Thu Feb 02 2006 - 10:55:33 CST)
  • Re: AMBER: Cannot successfully assign bond type for this molecule? (Wed Feb 01 2006 - 17:00:40 CST)
  • AMBER: Cannot successfully assign bond type for this molecule? (Wed Feb 01 2006 - 14:43:53 CST)
  • Re: AMBER: protein ligand complex (Wed Feb 01 2006 - 13:42:11 CST)
  • Re: AMBER: protein ligand complex (Wed Feb 01 2006 - 12:06:39 CST)
  • AMBER: protein ligand complex (Wed Feb 01 2006 - 11:21:21 CST)
• soo
  • AMBER: charmm force field in amber9 (Thu Jun 08 2006 - 23:23:26 CDT)
• Soonmin Jang
  • AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) (Thu May 25 2006 - 05:51:02 CDT)
  • AMBER: AMBER9 installation error on Compaq machine. (Thu May 18 2006 - 02:11:46 CDT)
• Stefan Henrich
  • AMBER: RMSD calculation between ligands (Fri May 12 2006 - 07:09:15 CDT)
• Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
  • AMBER: leap usage (Thu Nov 02 2006 - 03:41:34 CST)
  • Re: AMBER: Gaussian, antechamber, RESP (Sun Sep 03 2006 - 07:57:57 CDT)
  • AMBER: saltcon variable (Thu Jul 20 2006 - 14:00:01 CDT)
  • AMBER: temperature regulation (Tue Jul 18 2006 - 03:31:04 CDT)
  • Re: AMBER: carnal prob (Thu May 04 2006 - 02:58:18 CDT)
  • Re: AMBER: the total energy is not converge as the cutoff increase (Mon Mar 06 2006 - 03:28:52 CST)
  • AMBER: charge redistribution in .prep files (Mon Feb 20 2006 - 06:37:54 CST)
• Stefano Pieraccini
  • AMBER: MM-PBSA memory usage (Thu Oct 26 2006 - 07:33:41 CDT)
  • AMBER: mm-pbsa output (Thu Sep 21 2006 - 03:51:28 CDT)
  • Re: AMBER: resolving a bad initial model (Tue Sep 19 2006 - 10:25:46 CDT)
• Stern, Julie
  • AMBER: PBS script for lemieux (Sun May 14 2006 - 18:09:30 CDT)
• Steve Gwaltney
  • AMBER: OT: software to support AMBER? (Thu May 18 2006 - 13:37:06 CDT)
  • AMBER: Na+ with GB/SA? (Thu Jan 12 2006 - 11:59:22 CST)
• Steve Seibold
  • AMBER: Frozen at Minimization (Tue Dec 19 2006 - 08:18:21 CST)
  • AMBER: Building Parameters (Mon Dec 11 2006 - 15:29:15 CST)
  • RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 12:09:05 CST)
  • AMBER: Atom Type problem (Fri Dec 08 2006 - 10:04:29 CST)
  • AMBER: Atom Type problem (Fri Dec 08 2006 - 10:01:23 CST)
  • AMBER: atome type error (Fri Dec 08 2006 - 09:08:35 CST)
  • AMBER: xleap (Tue Nov 28 2006 - 08:33:48 CST)
  • AMBER: Building Library (Thu Nov 09 2006 - 13:40:30 CST)
  • AMBER: (Thu Nov 09 2006 - 11:03:14 CST)
  • AMBER: Building Library (Thu Nov 09 2006 - 10:52:08 CST)
  • AMBER: RMSd vs RMSf (Fri Sep 22 2006 - 08:42:28 CDT)
  • AMBER: (Wed Sep 20 2006 - 11:56:00 CDT)
  • AMBER: ptraj RMSD vs. RMSF (Mon Sep 18 2006 - 14:54:02 CDT)
  • AMBER: checkmask (Wed Aug 16 2006 - 13:14:29 CDT)
  • RE: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:50:16 CDT)
  • AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:05:16 CDT)
  • AMBER: antechamber (Wed Jun 07 2006 - 11:16:47 CDT)
  • AMBER: (Mon Mar 13 2006 - 08:17:41 CST)
  • RE: AMBER: TI cal (Thu Feb 23 2006 - 14:08:20 CST)
  • AMBER: TI cal (Thu Feb 23 2006 - 13:02:45 CST)
• Steven Winfield
  • AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 18:43:58 CST)
  • AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 13:05:22 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 15:53:07 CST)
  • Re: AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 18:10:33 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Tue Nov 07 2006 - 05:26:28 CST)
  • AMBER: Fully QM periodic runs (Wed Jun 14 2006 - 11:03:43 CDT)
  • AMBER: Namelists in input files (Wed May 31 2006 - 11:42:05 CDT)
  • AMBER: Force units in forcedump.dat (Wed May 31 2006 - 08:41:43 CDT)
  • Re: AMBER: 1st 2 lines of restart files (Thu May 25 2006 - 06:50:18 CDT)
• Sukjoon Yoon
  • AMBER: Decomposed GB energy in idecomp=3 option (Mon Jan 30 2006 - 20:13:27 CST)
• Supat Jiranusornkul
  • AMBER: 7-Methylguanine force field parameters (Fri Apr 28 2006 - 09:13:55 CDT)
  • AMBER: 7-Methylguanine force field parameters (Fri Apr 28 2006 - 09:03:22 CDT)
  • AMBER: Torsional restraints for groups of atoms (Fri Feb 17 2006 - 06:14:12 CST)
• Suxin Zheng
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 13:23:17 CDT)
  • AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Wed Aug 16 2006 - 13:23:44 CDT)
• Tanya Johannsen
  • Re: AMBER: ntt=1 in simulated annealing (Tue Nov 14 2006 - 17:59:04 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 18:38:38 CST)
  • AMBER: ntt=1 in simulated annealing (Thu Nov 02 2006 - 21:44:19 CST)
  • AMBER: energy data for limited part of system (Wed Sep 13 2006 - 12:57:15 CDT)
  • AMBER: identical high energies (Thu Aug 17 2006 - 21:22:40 CDT)
  • AMBER: any work-around for 80 character mask string limit? (Tue Aug 01 2006 - 15:12:22 CDT)
  • AMBER: script to extract data from minimization .out file (Fri Jul 07 2006 - 11:55:44 CDT)
  • AMBER: working with large strained system (Wed Jul 05 2006 - 21:29:58 CDT)
• thanyarat Udom
  • RE: AMBER: the total energy is not converge as the cutoff increase (Tue Mar 07 2006 - 01:17:23 CST)
  • AMBER: the total energy is not converge as the cutoff increase (Mon Mar 06 2006 - 02:51:46 CST)
• thenmalar
  • Re: AMBER: N-H and C-H Residual Dipolar Coupling (Wed Mar 01 2006 - 18:59:34 CST)
  • AMBER: N-H and C-H Residual Dipolar Coupling (Wed Mar 01 2006 - 16:01:52 CST)
• Thomas Cheatham
  • Re: AMBER: rdparm (Sat Dec 16 2006 - 21:43:55 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 21:23:26 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 23:14:56 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 16:01:35 CST)
  • Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 12:00:05 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 11:53:50 CST)
  • Re: AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 11:56:57 CST)
  • Re: AMBER: watershell and image commands (Thu Nov 30 2006 - 17:22:59 CST)
  • Re: AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 15:17:12 CST)
  • Re: AMBER: reading psf file (Fri Nov 17 2006 - 18:28:45 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 17:51:36 CST)
  • Re: AMBER: ptraj and mdvel question (Wed Nov 15 2006 - 17:37:13 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 13:17:40 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:34:57 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 10:25:39 CST)
  • Re: AMBER: Mass weights (Mon Nov 06 2006 - 22:58:54 CST)
  • Re: AMBER: grid output (Mon Nov 06 2006 - 22:30:25 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Mon Nov 06 2006 - 22:18:20 CST)
  • Re: AMBER: trajout script (Mon Nov 06 2006 - 14:39:04 CST)
  • AMBER: ACS Chicago potential symposia and OASYS abstracts (Sat Nov 04 2006 - 15:04:47 CST)
  • Re: AMBER: ff99SB vs ff02 (ff02pol.rl) (Mon Oct 30 2006 - 23:07:46 CST)
  • Re: AMBER: ff99SB vs ff02 (ff02pol.rl) (Mon Oct 30 2006 - 20:15:18 CST)
  • Re: AMBER: imaging issue (Mon Oct 30 2006 - 14:54:20 CST)
  • Re: AMBER: md and implicit solvation (Tue Oct 24 2006 - 20:50:43 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 23 2006 - 17:51:28 CDT)
  • Re: AMBER: modeling of ligand concentrations (Mon Oct 23 2006 - 11:38:55 CDT)
  • RE: AMBER: Grid command of ptraj (Mon Oct 23 2006 - 11:24:20 CDT)
  • RE: AMBER: Grid command of ptraj (Tue Oct 17 2006 - 10:40:22 CDT)
  • Re: AMBER: Interbox interactions (Tue Oct 17 2006 - 10:34:50 CDT)
  • Re: AMBER: RDF calculation (Tue Oct 17 2006 - 10:23:05 CDT)
  • Re: AMBER: puzzles about solvatoct or solvatebox (Tue Oct 17 2006 - 10:05:08 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 14:43:37 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Thu Oct 05 2006 - 10:21:40 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Wed Oct 04 2006 - 17:41:55 CDT)
  • Re: AMBER: ptraj hbond analysis troubles (Wed Oct 04 2006 - 16:36:49 CDT)
  • Re: AMBER: hbond analysis (Wed Oct 04 2006 - 16:00:02 CDT)
  • Re: AMBER: AMBER minimization vs. Gaussian optimization (Wed Oct 04 2006 - 15:45:59 CDT)
  • Re: AMBER: hbond analysis (Tue Oct 03 2006 - 11:27:56 CDT)
  • Re: AMBER: hbond analysis (Tue Oct 03 2006 - 11:05:00 CDT)
  • Re: AMBER: Electrostatic Energy Constant (Fri Sep 29 2006 - 14:44:25 CDT)
  • Re: AMBER: Electrostatic Energy Constant (Fri Sep 29 2006 - 13:19:00 CDT)
  • Re: AMBER: A script file for measuring the distance between 2 atoms during MD (Wed Sep 27 2006 - 13:05:25 CDT)
  • Re: RE: AMBER: potential energy (Tue Sep 19 2006 - 11:57:47 CDT)
  • Re: [UCE]Re: RE: AMBER: potential energy (Mon Sep 18 2006 - 21:16:20 CDT)
  • Re: AMBER: restraints and constant pressure (Sat Sep 16 2006 - 23:38:06 CDT)
  • Re: AMBER: restraints and constant pressure (Fri Sep 15 2006 - 01:22:02 CDT)
  • Re: [UCE]AMBER: Temperature not rising enough during simulated annealing (Thu Sep 14 2006 - 23:33:42 CDT)
  • Re: AMBER: Denaturing MD (Thu Sep 14 2006 - 18:55:59 CDT)
  • Re: AMBER: acidifying a water box (Thu Sep 14 2006 - 17:56:32 CDT)
  • Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 (Wed Sep 13 2006 - 10:48:54 CDT)
  • Re: AMBER: Problem with ptraj (Tue Sep 12 2006 - 21:47:46 CDT)
  • Re: AMBER: Question about free energy with mm_pbsa (Fri Sep 01 2006 - 01:23:59 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 23:38:02 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 23:07:40 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 16:50:33 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 15:49:42 CDT)
  • Re: AMBER: RDF output (Wed Aug 30 2006 - 17:18:29 CDT)
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Fri Aug 25 2006 - 13:21:07 CDT)
  • Re: AMBER: ptraj dumpq feature/bug (Thu Aug 24 2006 - 15:16:23 CDT)
  • Re: AMBER: identical high energies (Thu Aug 17 2006 - 21:57:23 CDT)
  • Re: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:32:24 CDT)
  • Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 13:42:52 CDT)
  • Re: AMBER: source code (Mon Aug 14 2006 - 13:31:08 CDT)
  • Re: AMBER: HBOND ANALYSIS (Thu Aug 10 2006 - 18:57:34 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 17:18:00 CDT)
  • Re: AMBER: problems with ptraj (Thu Aug 10 2006 - 14:25:18 CDT)
  • Re: AMBER: water diffusion (Tue Jul 18 2006 - 01:36:36 CDT)
  • Re: AMBER: Creating an Intercalation site (Mon Jul 17 2006 - 15:13:54 CDT)
  • Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent (Thu Jul 13 2006 - 11:34:00 CDT)
  • Re: AMBER: Etot has downward drift in 'NVE' ensemble (Wed Jul 12 2006 - 21:43:11 CDT)
  • Re: [UCE]AMBER: (no subject) (Sun Jul 09 2006 - 18:18:49 CDT)
  • Re: AMBER: Dihedral analysis (Mon Jul 03 2006 - 14:47:42 CDT)
  • Re: AMBER: hbond analysis (Mon Jul 03 2006 - 14:19:57 CDT)
  • Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering (Wed Jun 28 2006 - 11:22:42 CDT)
  • Re: AMBER: average struct.problem (Thu Jun 22 2006 - 09:35:45 CDT)
  • Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 18:48:54 CDT)
  • RE: AMBER: checkoverlap doubt [was: Post-MD minimization] (Tue Jun 20 2006 - 17:28:36 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 17:13:06 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 16:59:50 CDT)
  • Re: AMBER: ptraj vector (Tue Jun 20 2006 - 14:32:17 CDT)
  • Re: AMBER: switching function for electrostatic interactions (Mon Jun 12 2006 - 11:12:28 CDT)
  • Re: AMBER: COM (Thu Jun 08 2006 - 19:34:03 CDT)
  • Re: AMBER: MM-PBSA and first solvation shell (Mon Jun 05 2006 - 12:23:58 CDT)
  • Re: AMBER: AMBER mdcrd file bigger than 2GB (Thu Jun 01 2006 - 11:25:19 CDT)
  • Re: AMBER: AMBER mdcrd file bigger than 2GB (Wed May 31 2006 - 18:27:16 CDT)
  • Re: [UCE]AMBER: RE: trouble stripping waters with ptraj (Tue May 30 2006 - 12:17:31 CDT)
  • Re: AMBER: ptraj: calculating distances between atoms in charges residues (Fri May 26 2006 - 11:12:40 CDT)
  • Re: [UCE]AMBER: RE: trouble stripping waters with ptraj (Fri May 26 2006 - 11:04:22 CDT)
  • Re: AMBER: RMSd error (Fri May 26 2006 - 10:59:34 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 12:20:14 CDT)
  • Re: AMBER: Simulating a periodic crystal (Wed Mar 29 2006 - 09:57:10 CST)
  • Re: Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) (Tue Mar 28 2006 - 22:32:37 CST)
  • Re: AMBER: error while running sander (Fri Mar 10 2006 - 22:41:16 CST)
  • Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations (Mon Mar 06 2006 - 17:51:08 CST)
  • Re: AMBER: Which PTRAJ distribution to use? (Thu Mar 02 2006 - 17:47:51 CST)
  • Re: AMBER: problem in center command (Fri Jan 20 2006 - 21:37:49 CST)
• Thomas E. Cheatham, III
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 11:01:50 CDT)
  • Re: AMBER: "average" command in ptraj (Mon Apr 10 2006 - 13:06:20 CDT)
  • Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE (Fri Mar 31 2006 - 16:18:57 CST)
  • Re: AMBER: divalent ions (Tue Mar 14 2006 - 16:10:19 CST)
  • Re: AMBER: GAFF + AM1BCC & small-molecule aggregation (Wed Mar 01 2006 - 15:17:35 CST)
  • Re: AMBER: Question about renaming a residue (Fri Feb 17 2006 - 17:46:27 CST)
  • RE: AMBER: sander problem (Thu Feb 16 2006 - 15:12:39 CST)
  • Re: AMBER: ptraj grid output (Thu Jan 19 2006 - 12:47:05 CST)
  • Re: AMBER: Trimming ptraj output (Fri Jan 13 2006 - 11:37:45 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 10:59:35 CST)
  • Re: AMBER: PTRAJ generating wrong dihedral angles (Tue Jan 10 2006 - 13:42:42 CST)
  • Re: AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 11:53:51 CST)
• Thomas Patko (CSULB)
  • Re: AMBER: Announcement: Amber 9 is now available (Sat Apr 01 2006 - 10:29:26 CST)
• Thomas Pochapsky
  • AMBER: individual torsion/bond energies from a minimization (Fri Jun 02 2006 - 08:25:33 CDT)
  • AMBER: xleap problem and answer (Wed May 31 2006 - 13:32:32 CDT)
• Thomas Steinbrecher
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 16:11:47 CST)
  • Re: AMBER: Confusion about PBC (Wed Nov 29 2006 - 10:40:05 CST)
  • Re: AMBER: NONB values adjusted? (Tue Nov 28 2006 - 10:31:33 CST)
  • Re: AMBER: MM_PBSA (Thu Nov 16 2006 - 10:21:55 CST)
  • Re: AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 16:02:47 CST)
  • Re: AMBER: modeling of ligand concentrations (Tue Oct 24 2006 - 20:11:05 CDT)
  • Re: AMBER: High Values in MMPBSA (Thu Oct 12 2006 - 10:36:31 CDT)
  • Re: AMBER: Pressure in MD (Mon Oct 02 2006 - 16:24:30 CDT)
  • Re: AMBER: mm_pbsa segmentation faults (Tue Sep 26 2006 - 12:31:34 CDT)
  • AMBER: mm_pbsa segmentation faults (Mon Sep 25 2006 - 13:24:17 CDT)
  • AMBER: pbsa segmentation faults (Fri Sep 22 2006 - 18:46:11 CDT)
  • Re: AMBER: TI-FEP : strange result for different clambda values (Fri Sep 22 2006 - 10:38:10 CDT)
  • Re: AMBER: amber9 (Fri Jul 14 2006 - 17:12:13 CDT)
  • AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities (Thu Jul 06 2006 - 18:02:19 CDT)
  • Re: AMBER: Tutorial 2: Production MD. (Wed Jun 21 2006 - 10:37:51 CDT)
  • Re: AMBER: LEaP error : unbalanced charge (Fri Jun 16 2006 - 09:59:50 CDT)
  • Re: AMBER: saveamberparams error in Amber9 (Wed Jun 14 2006 - 10:07:28 CDT)
  • Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 13:50:30 CDT)
  • Re: AMBER: How to calculate the mmpbsa for explicit MD ? (Mon Jun 12 2006 - 11:58:33 CDT)
  • Re: AMBER: MMPBSA problem (Fri Jun 09 2006 - 10:06:34 CDT)
  • RE: AMBER: Test Failure during amber9 serial compilation (Wed Apr 26 2006 - 04:23:24 CDT)
  • AMBER: Test Failure during amber9 serial compilation (Tue Apr 25 2006 - 09:17:29 CDT)
  • AMBER: Problems compiling amber9 (Fri Apr 21 2006 - 09:27:51 CDT)
  • AMBER: Error when compiling amber9 ptraj (Fri Apr 21 2006 - 03:19:54 CDT)
  • Re: AMBER: MMPBSA: magnitude of PB calculation (Mon Feb 06 2006 - 02:54:01 CST)
• Tim Meyer
  • Re: AMBER: rdparm (Tue Dec 19 2006 - 09:22:45 CST)
  • Re: AMBER: Phosphorylated amino acid (Mon Feb 20 2006 - 02:56:36 CST)
  • AMBER: amber atom type -> length of name (Wed Jan 11 2006 - 13:22:22 CST)
  • Re: AMBER: GLUTATHIONE (Wed Jan 11 2006 - 13:13:11 CST)
• Tim Robinson
  • AMBER: amber 9 intel 9.1 ia64 (Tue Aug 15 2006 - 08:45:16 CDT)
• Ting Wang
  • Re: AMBER: PMEMD with NMR restraint and position restraint (Tue Jul 18 2006 - 15:12:41 CDT)
  • AMBER: PMEMD with NMR restraint and position restraint (Mon Jul 17 2006 - 18:18:31 CDT)
• Tiziano Tuccinardi
  • AMBER: PMEMD scaling (Thu Dec 07 2006 - 02:46:49 CST)
• tmarch_at_coin.org
  • Re: AMBER: rgbmax--something wrong with my input file? (Wed Jun 28 2006 - 16:37:19 CDT)
• Tomas Kubar
  • AMBER: leap - compilation error (Tue Nov 07 2006 - 03:47:33 CST)
• Tomimoto_Masaki_at_takeda.co.jp
  • AMBER: Q: results from PB solver in example no.3 (Wed Jan 04 2006 - 17:09:42 CST)
• Tonda March
  • AMBER: offset? (Thu Jun 01 2006 - 01:12:19 CDT)
• tonglei
  • AMBER: molsurf or LCPO method in MM_GB/SA? (Tue Apr 04 2006 - 20:25:37 CDT)
  • AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? (Tue Apr 04 2006 - 08:10:59 CDT)
  • AMBER: negative values of PBSOL and PBCAL in mm_pbsa result (Sun Mar 26 2006 - 20:07:47 CST)
  • AMBER: using MM_PBSA just for binding site, feasible ??? (Sun Mar 12 2006 - 00:53:44 CST)
  • AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number? (Sun Jan 08 2006 - 20:36:30 CST)
• tongli
  • AMBER: about the std of computational alanine scanning (Fri Dec 01 2006 - 05:50:11 CST)
• Toomas Kaevand
  • AMBER: AMBER 7 and cutoff's (Fri Feb 03 2006 - 11:58:53 CST)
  • AMBER: AMBER 7 and restrained bonds. (Thu Jan 26 2006 - 09:27:28 CST)
• Toshifumi Yui
  • AMBER: Re: AMBER: $B#F#e(B complex$B!!(B(correction) (Tue Oct 10 2006 - 20:41:05 CDT)
  • AMBER: $B#F#e(B complex (Tue Oct 10 2006 - 20:09:36 CDT)
• Tru Huynh
  • Re: AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 11:57:59 CST)
  • Re: AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 11:55:10 CST)
  • AMBER: amber8 and gfortran 4.1.0 (Thu Mar 02 2006 - 10:00:00 CST)
• trudy_at_uoguelph.ca
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Thu Nov 30 2006 - 09:31:02 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Wed Nov 29 2006 - 08:50:51 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Tue Nov 28 2006 - 09:41:07 CST)
  • AMBER: Problem Installing Amber in SGI Irix 6.5 (Mon Nov 27 2006 - 14:29:53 CST)
• uccadco_at_ucl.ac.uk
  • AMBER: (Tue Nov 28 2006 - 08:48:08 CST)
• Uni-Halle
  • AMBER: NAD parameters (Thu Sep 28 2006 - 08:06:06 CDT)
• Urszula Uciechowska
  • Re: AMBER: NAD ?? (Mon Nov 13 2006 - 03:08:45 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 03:36:15 CST)
  • AMBER: NAD ?? (Wed Nov 08 2006 - 07:40:15 CST)
  • AMBER: problem with NAD+ parameters (Mon Nov 06 2006 - 08:27:16 CST)
  • Re: AMBER: parameters !!?? (Wed Oct 25 2006 - 08:32:49 CDT)
  • AMBER: parameters !!?? (Wed Oct 25 2006 - 04:27:22 CDT)
  • AMBER: DIST_RST (Tue Oct 24 2006 - 03:32:03 CDT)
• VANDANA KUMARI
  • AMBER: problem in calculating EGB using sander for ligand containing F atom (Wed Nov 08 2006 - 21:36:52 CST)
• Vanessa Oklejas
  • AMBER: Units for Leonard-Jones potential parameters (Wed Jul 05 2006 - 22:02:59 CDT)
• vanessa wai
  • Re: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 19:33:35 CST)
  • Re: AMBER: MM-PBSA problem (Sun Dec 03 2006 - 19:52:25 CST)
  • Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 03:08:15 CST)
  • Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 03:11:18 CST)
  • AMBER: MM-PBSA problem (Thu Nov 30 2006 - 19:27:06 CST)
• Varsha Goyal
  • Re: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 15:35:27 CST)
  • AMBER: MM_PBSA (Wed Nov 15 2006 - 20:27:15 CST)
  • Re: AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 17:04:12 CST)
  • AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 15:34:28 CST)
  • Re: AMBER: mm_pbsa: binding energy calculation (Sat Oct 28 2006 - 16:41:02 CDT)
  • AMBER: mm_pbsa: binding energy calculation (Wed Oct 25 2006 - 13:51:57 CDT)
  • AMBER: binpos file (Fri May 12 2006 - 15:46:24 CDT)
  • RE: AMBER: rmsd value for organic molecule (Mon Apr 24 2006 - 15:48:59 CDT)
  • AMBER: rmsd value for organic molecule (Mon Apr 24 2006 - 14:00:20 CDT)
  • Re: AMBER: Antechamber calculations (Fri Mar 10 2006 - 17:47:41 CST)
  • AMBER: Antechamber calculations (Fri Mar 10 2006 - 13:26:08 CST)
  • AMBER: Sulfonamides and GAFF (Sun Feb 26 2006 - 19:16:18 CST)
  • AMBER: Distortion in parallelploied (Thu Feb 09 2006 - 19:39:06 CST)
  • RE: AMBER: Charges on atoms in protein :AMBER (Thu Feb 02 2006 - 13:20:59 CST)
  • AMBER: Charges on atoms in protein :AMBER (Wed Feb 01 2006 - 21:00:09 CST)
  • AMBER: About placing counter ions (Tue Jan 31 2006 - 12:23:03 CST)
  • AMBER: About tleap (Thu Jan 12 2006 - 12:28:04 CST)
  • AMBER: About preparing Zn.lib (Wed Jan 11 2006 - 19:21:26 CST)
• Vasu Chandrasekaran
  • Re: AMBER: lib-4324 : UNRECOVERABLE library error (Sun Sep 17 2006 - 12:23:24 CDT)
  • AMBER: lib-4324 : UNRECOVERABLE library error (Sun Sep 17 2006 - 02:36:26 CDT)
• venditti2_at_unisi.it
  • AMBER: rdparm (Fri Dec 15 2006 - 10:08:17 CST)
  • Re: AMBER: center of mass dihedral restraints (Mon Sep 25 2006 - 12:44:01 CDT)
  • AMBER: residence time of water molecules (Wed Sep 13 2006 - 09:56:34 CDT)
  • Re: AMBER: PCA (Mon Apr 10 2006 - 09:57:41 CDT)
  • AMBER: Umbrella sampling (Fri Apr 07 2006 - 15:04:55 CDT)
  • AMBER: PCA (Thu Apr 06 2006 - 15:27:20 CDT)
  • AMBER: AMBER 8 VS AMBER 7 (Thu Mar 02 2006 - 13:54:47 CST)
  • AMBER: Angle restraint (Tue Feb 28 2006 - 14:00:48 CST)
• vic_at_mail.nankai.edu.cn
  • AMBER: A problem with mm_pbsa (Mon Dec 25 2006 - 19:41:41 CST)
• Vidana.Epa_at_csiro.au
  • AMBER: A problem with Amber force field new parameter derivation (Fri Feb 24 2006 - 00:16:04 CST)
• Viktor Hornak
  • Re: AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:50:59 CST)
  • Re: AMBER: how to calculate rmsd for non hydrogen at oms? (Tue Oct 03 2006 - 11:51:53 CDT)
  • Re: AMBER: multiple "restraint_wt" in sander (Mon Jul 03 2006 - 09:43:44 CDT)
  • Re: AMBER: Shared libraries error (Thu May 04 2006 - 13:54:26 CDT)
  • Re: AMBER: question about group format (Thu May 04 2006 - 13:49:20 CDT)
  • Re: AMBER: restraintmask (Thu May 04 2006 - 13:41:37 CDT)
  • Re: AMBER: failed to save prm and xyz using ff96 (Wed Mar 01 2006 - 15:16:13 CST)
• Vitor Manuel Sousa F?x
  • AMBER: dihedral angle equation (Fri Nov 17 2006 - 06:41:25 CST)
  • AMBER: opls_aa in amber (Thu Nov 16 2006 - 08:29:45 CST)
  • Re: AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 16:08:01 CST)
  • AMBER: polarization effects (Sun Oct 01 2006 - 09:08:55 CDT)
  • AMBER: klambda (Mon Aug 14 2006 - 05:45:10 CDT)
  • AMBER: Thermodynamic integration using the amber 9 (Mon May 29 2006 - 08:41:14 CDT)
  • Re: AMBER: Antechamber calculations (Fri Mar 10 2006 - 14:03:53 CST)
  • Re: AMBER: about Br- parameters (Fri Mar 03 2006 - 08:48:24 CST)
  • Re: AMBER: about Br- parameters (Fri Mar 03 2006 - 04:28:40 CST)
  • AMBER: Ti calculations in dmso solvent (Mon Feb 20 2006 - 11:55:32 CST)
• Vlad Cojocaru
  • Re: AMBER: hbond analysis (Wed Oct 04 2006 - 10:26:32 CDT)
  • Re: AMBER: hbond analysis (Tue Oct 03 2006 - 11:35:32 CDT)
  • Re: AMBER: hbond analysis (Tue Oct 03 2006 - 11:18:28 CDT)
  • AMBER: hbond analysis (Tue Oct 03 2006 - 10:45:23 CDT)
  • Re: AMBER: set a trucated octahedron box in Leap (Tue Sep 12 2006 - 03:30:06 CDT)
  • AMBER: set a trucated octahedron box in Leap (Mon Sep 11 2006 - 09:24:44 CDT)
  • Re: AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 09:56:49 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:52:39 CDT)
  • AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:12:37 CDT)
  • Re: AMBER: ff03 and ff99SB force fields (Fri Aug 04 2006 - 03:17:59 CDT)
  • Re: AMBER: PhosphoThreonine Parms for use with ff03 (Thu Aug 03 2006 - 05:07:48 CDT)
  • AMBER: neutral N-terminal amino-acid parameters for ff03 (Wed Aug 02 2006 - 09:21:31 CDT)
  • AMBER: applying restraints on pre-defined planes (Tue Jul 11 2006 - 10:34:07 CDT)
  • Re: AMBER: help creating RNA (Fri Jun 23 2006 - 03:14:24 CDT)
  • AMBER: calculating box dimensions during MD (Tue Jun 06 2006 - 09:13:14 CDT)
  • Re: AMBER: How to analyze the trajectory generated by LES simulation (Fri Jun 02 2006 - 04:54:20 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 12:01:27 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 11:30:23 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Fri Apr 14 2006 - 04:57:33 CDT)
  • Re: AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. (Fri Apr 14 2006 - 04:18:41 CDT)
  • Re: AMBER: Which one is the best force field for DNA? (Thu Apr 13 2006 - 03:11:33 CDT)
  • Re: AMBER: VdW radii in the topology file (Mon Apr 10 2006 - 12:01:33 CDT)
  • AMBER: VdW radii in the topology file (Mon Apr 10 2006 - 11:14:16 CDT)
  • Re: AMBER: printing Amber VdW radii as separate column in pdb files (Mon Apr 10 2006 - 10:43:18 CDT)
  • AMBER: printing Amber VdW radii as separate column in pdb files (Mon Apr 10 2006 - 09:41:51 CDT)
  • Re: AMBER: question capping helix ends (Fri Mar 24 2006 - 04:51:24 CST)
  • Re: AMBER: question capping helix ends (Thu Mar 23 2006 - 04:48:14 CST)
  • AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1) (Mon Mar 20 2006 - 10:40:37 CST)
  • Re: AMBER: NTT for production run (Fri Mar 17 2006 - 03:16:36 CST)
  • Re: AMBER: NTT for production run (Thu Mar 16 2006 - 03:56:46 CST)
  • Re: AMBER: NTT for production run (Wed Mar 15 2006 - 02:53:46 CST)
  • Re: AMBER: NTT for production run (Tue Mar 14 2006 - 02:44:35 CST)
  • AMBER: sander restart problem (Sun Mar 05 2006 - 07:31:30 CST)
  • Re: AMBER: mask issues (Tue Feb 28 2006 - 07:03:16 CST)
  • Re: AMBER: ptraj warning while loading reference (Mon Feb 27 2006 - 11:00:43 CST)
  • AMBER: ptraj warning while loading reference (Mon Feb 27 2006 - 06:45:28 CST)
  • Re: AMBER: generating parameters for the NADH analogue H4NAD (Thu Feb 23 2006 - 12:53:30 CST)
  • Re: AMBER: AMBER force field with namd (Thu Feb 23 2006 - 08:04:51 CST)
  • Re: AMBER: AMBER force field with namd (Thu Feb 23 2006 - 04:11:17 CST)
  • AMBER: minization: outputing intermediate snapshots (Fri Feb 10 2006 - 09:05:59 CST)
  • AMBER: minization: outputing intermediate snapshots (Fri Feb 10 2006 - 05:49:04 CST)
  • Re: AMBER: What Viewer is best (Sun Feb 05 2006 - 11:01:11 CST)
  • AMBER: ptraj PCA: projection mask bug?? (Wed Jan 25 2006 - 07:28:42 CST)
  • AMBER: ptraj PCA (Tue Jan 24 2006 - 10:02:20 CST)
  • Re: AMBER: amber: problem in center command (Fri Jan 20 2006 - 03:48:42 CST)
  • AMBER: ptraj grid output (Thu Jan 19 2006 - 12:25:49 CST)
  • AMBER: Re: RE£ºAMBER: the problem of mdcrd (Wed Jan 18 2006 - 03:48:36 CST)
  • AMBER: Re: RE£ºAMBER: the problem of mdcrd (Tue Jan 17 2006 - 06:40:41 CST)
  • Re: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 03:55:45 CST)
  • Re: AMBER: heme improper torsions (Mon Jan 16 2006 - 03:50:50 CST)
  • AMBER: analysing water behavior during MD (Fri Jan 13 2006 - 09:17:06 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 11:25:56 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 11:13:58 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:51:57 CST)
  • Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:42:41 CST)
  • AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 08:19:17 CST)
  • AMBER: ptraj mask question (Thu Jan 12 2006 - 04:50:37 CST)
• vorasit vongsutilers
  • Re: AMBER: mm-pbsa (Sun Mar 19 2006 - 11:45:15 CST)
  • Re: AMBER: mm-pbsa (Fri Mar 17 2006 - 08:03:15 CST)
  • AMBER: mm-pbsa (Thu Mar 16 2006 - 09:34:33 CST)
• wang
  • AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format (Tue May 09 2006 - 01:25:47 CDT)
• Wang, Xuelin
  • AMBER: load charges to antechamber calculations (Tue Oct 24 2006 - 14:30:24 CDT)
  • AMBER: change from .rst file to .mdcrd file (Wed Oct 04 2006 - 10:52:56 CDT)
  • AMBER: how to run a mm_pbsa on a minimized structure? (Mon Oct 02 2006 - 16:50:02 CDT)
• wang_at_cbs.cnrs.fr
  • AMBER: resolving a bad initial model (Tue Sep 19 2006 - 09:42:11 CDT)
• Wei Chen
  • Re: AMBER: MM/PBSA (Sat Jul 08 2006 - 13:29:06 CDT)
  • AMBER: MM/PBSA (Fri Jul 07 2006 - 16:20:47 CDT)
• Wei Zhang
  • Re: AMBER: reinstall amber8 (Wed Oct 25 2006 - 10:13:01 CDT)
  • Re: AMBER: loading torsion parameters (Mon Jul 31 2006 - 15:13:57 CDT)
  • Re: AMBER: PDB from .rst? (Thu Jul 20 2006 - 16:04:58 CDT)
  • Re: AMBER: problems about compiling a parallel version of AMBER 9 (Thu Jun 22 2006 - 11:21:32 CDT)
  • Re: AMBER: What's the meaning of NTYPES? (Thu Jun 22 2006 - 11:18:38 CDT)
  • Re: AMBER: Fully QM periodic runs (Wed Jun 14 2006 - 11:58:51 CDT)
  • Re: AMBER: amber .off file format question (Mon May 22 2006 - 13:13:12 CDT)
  • Re: AMBER: conflicting types for XawScrolledTableSetLocation (Thu May 04 2006 - 12:17:40 CDT)
  • AMBER: from Wei Zhang: flight information (Fri Mar 03 2006 - 12:45:59 CST)
  • Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster (Tue Feb 28 2006 - 12:01:34 CST)
  • Re: AMBER: DNA tutorial xleap help (Wed Feb 08 2006 - 13:42:32 CST)
  • Re: AMBER: Parallel error in Amber 8 (Mon Feb 06 2006 - 17:06:07 CST)
• Weihua Li
  • AMBER: trajout (Wed Sep 06 2006 - 22:22:28 CDT)
  • Re: AMBER: Heme parameters (Wed Aug 09 2006 - 21:44:15 CDT)
  • Re: AMBER: saveamberparams error in Amber9 (Thu Jun 15 2006 - 01:48:52 CDT)
  • Re: AMBER: saveamberparams error in Amber9 (Wed Jun 14 2006 - 21:15:03 CDT)
  • AMBER: saveamberparams error in Amber9 (Wed Jun 14 2006 - 08:28:43 CDT)
  • AMBER: compiler error for Amber9 (Wed Jun 07 2006 - 09:34:49 CDT)
  • AMBER: questions about mm_pbsa (Wed Apr 26 2006 - 22:09:45 CDT)
• Wen Li
  • Re: AMBER: RMS (fwd) (Tue Apr 04 2006 - 10:17:14 CDT)
  • Re: AMBER: RMS (fwd) (Tue Apr 04 2006 - 10:02:02 CDT)
  • Re: AMBER: RMS (Tue Apr 04 2006 - 08:59:04 CDT)
  • AMBER: RMS (Mon Apr 03 2006 - 16:03:29 CDT)
• wenfei Li
  • Re: AMBER: problem of the REMD with nmr constraints (Thu Dec 07 2006 - 18:55:04 CST)
  • Re: AMBER: problem of the REMD with nmr constraints (Sat Nov 25 2006 - 19:56:05 CST)
  • AMBER: problem of the REMD with nmr constraints (Wed Nov 22 2006 - 19:57:32 CST)
  • AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 (Thu Nov 02 2006 - 06:44:18 CST)
  • AMBER: Oon Modeling the metalloprotein with GB model. (Mon Sep 11 2006 - 02:41:16 CDT)
• Whitney Allen
  • AMBER: Problems using rst distance constraints in Amber 8 (Wed Sep 20 2006 - 13:30:05 CDT)
• William Lianhu Wei
  • AMBER: GBSA EGB = NaN (Thu Aug 17 2006 - 21:30:50 CDT)
• William Wei
  • AMBER: mm_pbsa PBCAL (Tue Oct 03 2006 - 14:23:18 CDT)
  • Re: AMBER: MAXM in nmode (Wed Sep 13 2006 - 16:07:52 CDT)
  • AMBER: MAXM in nmode (Wed Sep 13 2006 - 15:24:14 CDT)
  • Re: AMBER: Question about free energy with mm_pbsa (Fri Sep 01 2006 - 08:32:29 CDT)
  • AMBER: Question about free energy with mm_pbsa (Thu Aug 31 2006 - 13:50:11 CDT)
  • Re: AMBER: mm_pbsa_statistical.pl (Wed Aug 30 2006 - 16:11:51 CDT)
  • AMBER: mm_pbsa_statistical.pl (Tue Aug 29 2006 - 16:02:32 CDT)
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 16:05:55 CDT)
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 12:04:59 CDT)
  • AMBER: nmode memory problem (Thu Aug 24 2006 - 10:29:13 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 13:00:21 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:37:47 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:04:36 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:04:26 CDT)
  • Re: AMBER: GBSA EGB = NaN (Fri Aug 18 2006 - 10:12:10 CDT)
• Wimal
  • AMBER: Problem with sander in Linux (Mon Aug 14 2006 - 03:14:00 CDT)
• Xiaojian Deng
  • Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 13:02:22 CDT)
  • AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 12:55:31 CDT)
• xiaoqin huang
  • AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 18:53:39 CST)
  • AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 10:48:14 CST)
  • AMBER: POPC parameters (Thu Apr 06 2006 - 22:18:10 CDT)
• Xiaowei (David) Li
  • AMBER: the energy and temperature both increasing during the simulation with NTT=0 (Mon Nov 20 2006 - 12:50:00 CST)
  • Re: AMBER: job crashes (Tue Sep 26 2006 - 22:57:18 CDT)
  • AMBER: job crashes (Tue Sep 26 2006 - 22:09:04 CDT)
  • AMBER: Question about NSCM (Tue Jul 11 2006 - 03:25:48 CDT)
• Xioling Chuang
  • AMBER: RDF calculation (Tue Oct 17 2006 - 05:54:02 CDT)
  • Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? (Mon Oct 16 2006 - 03:48:04 CDT)
  • AMBER: How to calculate RDF based on the center of mass of specific solute atoms? (Sun Oct 15 2006 - 23:04:10 CDT)
  • AMBER: Can salt effect be determined in GB medel? (Mon Sep 18 2006 - 23:04:03 CDT)
  • Re: AMBER: How to calculate binding free energy using MM-PBSA (Fri Jun 30 2006 - 23:39:09 CDT)
  • Re: AMBER: How to calculate binding free energy using MM-PBSA (Thu Jun 29 2006 - 23:16:48 CDT)
  • AMBER: How to calculate binding free energy using MM-PBSA (Thu Jun 29 2006 - 04:38:58 CDT)
• xiphias xie
  • Re: AMBER: problem in center command (Fri Jan 20 2006 - 19:30:44 CST)
  • AMBER: amber: problem in center command (Thu Jan 19 2006 - 20:36:27 CST)
  • RE£ºAMBER: the problem of mdcrd (Wed Jan 18 2006 - 02:54:18 CST)
  • RE£ºAMBER: the problem of mdcrd (Tue Jan 17 2006 - 01:52:03 CST)
  • »Ø¸´£º Re: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 20:23:00 CST)
  • »Ø¸´£º RE: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 20:13:53 CST)
  • AMBER: the problem of mdcrd (Mon Jan 16 2006 - 03:16:09 CST)
• Xuebin Qiao
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 22:55:14 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 08:23:36 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 06:26:12 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 06:21:07 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 21:51:57 CST)
  • Re: AMBER: experiences with compiling amber9 for FreeBSD (Sat May 06 2006 - 01:31:06 CDT)
  • Re: AMBER: Using XML for Amber files (Mon Apr 24 2006 - 22:57:47 CDT)
  • Re: AMBER: Using XML for Amber files (Fri Apr 07 2006 - 12:52:08 CDT)
• xueping
  • Re: AMBER: about atomic fluctuation & RMSF (Sun Mar 26 2006 - 20:39:45 CST)
  • AMBER: about atomic fluctuation & RMSF (Thu Mar 23 2006 - 04:05:03 CST)
• xyu3
  • AMBER: compile error: can't locate file for: -lcrt1.o (Fri Apr 14 2006 - 17:37:50 CDT)
• Yam
  • AMBER: ptraj: hbond analysis (Tue Mar 07 2006 - 02:03:08 CST)
  • AMBER: ptraj:hbond question (Sun Mar 05 2006 - 21:09:39 CST)
• Yannick Bomble
  • AMBER: source code (Mon Aug 14 2006 - 13:09:31 CDT)
• Ye Mei
  • Re: AMBER: bugfix (Sun Dec 03 2006 - 09:38:40 CST)
  • Re: Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 08:23:00 CDT)
  • Re: AMBER: Opteron vs. Xeon performance (Fri May 12 2006 - 03:04:45 CDT)
  • AMBER: how to restrain the intramolecular hydrogen bond (Tue Apr 04 2006 - 04:35:42 CDT)
  • Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group (Sat Mar 11 2006 - 11:01:53 CST)
  • Re: Re: Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 02:40:14 CST)
  • Re: Re: AMBER: bond parameters for positively charged guanidine group (Thu Mar 09 2006 - 00:35:51 CST)
  • AMBER: bond parameters for positively charged guanidine group (Wed Mar 08 2006 - 20:54:15 CST)
• ying xiong
  • AMBER: MD job stopped without any error information? (Mon Feb 27 2006 - 02:29:50 CST)
• yipinl_at_umich.edu
  • AMBER: parameters for beta peptides (Thu Nov 16 2006 - 13:29:08 CST)
• Yogesh Sabnis
  • AMBER: antechamber for a database of organic molecules (Sun Feb 19 2006 - 09:16:23 CST)
• Yong Duan
  • RE: AMBER: question on protein folding simulation (Tue Dec 05 2006 - 13:57:45 CST)
  • RE: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 12:32:58 CST)
  • RE: AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 11:41:17 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Tue Nov 14 2006 - 17:05:08 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Mon Nov 13 2006 - 19:56:29 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 15:55:23 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 17:17:43 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:53:39 CST)
  • RE: AMBER: how to reassign charges (Wed Aug 09 2006 - 16:26:10 CDT)
  • RE: AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 15:42:50 CDT)
  • RE: AMBER: ff03 and ff99SB force fields (Fri Aug 04 2006 - 06:58:51 CDT)
  • RE: AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 14:29:51 CDT)
  • RE: AMBER: amber9 compilation problems on EM64T xeon system (Thu Jul 06 2006 - 14:38:05 CDT)
  • RE: AMBER: RMS FLUCTUATIONS (Thu Jun 15 2006 - 09:49:16 CDT)
  • RE: AMBER: ff02 + POL3 problem ! (Tue May 16 2006 - 15:06:54 CDT)
  • RE: AMBER: density (Tue May 16 2006 - 00:37:28 CDT)
  • RE: AMBER: ff02 + POL3 problem ! (Mon May 15 2006 - 11:15:02 CDT)
  • RE: AMBER: Opteron vs. Xeon performance (Sun May 14 2006 - 19:53:55 CDT)
  • RE: AMBER: Could not find atom type. (Mon Apr 17 2006 - 11:45:10 CDT)
• Yongmei Pan
  • AMBER: How the ensemble average calculated in Gibbs, AMBER7? (Wed Nov 01 2006 - 16:06:09 CST)
  • AMBER: question on molsurf (Fri Oct 20 2006 - 17:38:38 CDT)
  • Re: AMBER: Free-energy using MM-PBSA (Thu Oct 19 2006 - 08:20:07 CDT)
  • Re: Re: AMBER: questions on mm_pbsa_statitistics.pl (Wed Oct 18 2006 - 10:12:58 CDT)
  • AMBER: questions on mm_pbsa_statitistics.pl (Tue Oct 17 2006 - 17:57:59 CDT)
  • AMBER: question on mm_pbsa_statistics.pl (Tue Oct 17 2006 - 17:36:23 CDT)
  • AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? (Fri Jun 09 2006 - 21:57:42 CDT)
  • AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? (Fri Jun 09 2006 - 22:03:26 CDT)
• Young-Tae Lee
  • AMBER: RDC refinement (Wed Sep 13 2006 - 10:13:30 CDT)
• Yu Chen
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 13:05:55 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 09:18:35 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 11:02:26 CST)
  • AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 10:22:54 CST)
• Yu Zh.H.
  • AMBER: how to perform parallel MD on a linux cluster with Platform LSF product (Fri Apr 28 2006 - 05:31:08 CDT)
• Yumi Nukusina
  • AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 02:59:36 CST)
• yxiong99
  • AMBER: how to calculate rmsd for non hydrogen at oms? (Tue Oct 03 2006 - 11:43:49 CDT)
  • AMBER: about Silica's polarizability (Thu Aug 03 2006 - 10:20:19 CDT)
  • AMBER: where can I find the force field paramete r for Silica (Wed Aug 02 2006 - 14:53:33 CDT)
  • AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl (Thu Jun 29 2006 - 15:49:50 CDT)
  • AMBER: why has "ELE " a large fluctuation in MMP BSA? (Tue Jun 20 2006 - 08:47:44 CDT)
• z3020110_at_student.unsw.edu.au
  • AMBER: Amber 9, sander imin = 5, -y flag (Sun Apr 30 2006 - 20:08:44 CDT)
• zachary hartman
  • AMBER: Quantifying pi-pi interactions (Tue Nov 21 2006 - 09:51:30 CST)
  • AMBER: Obtaining LCPO parameters for F and Fe (Mon Jul 17 2006 - 13:16:54 CDT)
  • AMBER: Having trouble getting Iron parameters for QM/MM (Thu Jun 29 2006 - 14:23:06 CDT)
• zgleo
  • AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation (Thu Feb 16 2006 - 00:04:47 CST)
  • AMBER: About the unit of the projection onto eigenvectors (Tue Jan 17 2006 - 03:58:39 CST)
• Zhihong Yu
  • AMBER: how to restrain some residues in a NPT MD? (Mon Oct 30 2006 - 09:20:38 CST)
  • AMBER: How did the coordinates change in xleap? (Tue Oct 17 2006 - 10:03:47 CDT)
  • Re: AMBER: puzzles about solvatoct or solvatebox (Tue Oct 17 2006 - 09:42:54 CDT)
  • AMBER: puzzles about solvatoct or solvatebox (Thu Oct 12 2006 - 05:00:08 CDT)
  • RE: AMBER: some puzzles in equilibration MD (Mon Oct 09 2006 - 10:19:15 CDT)
  • AMBER: some puzzles in equilibration MD (Mon Oct 09 2006 - 08:58:06 CDT)
  • Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS (Mon Sep 25 2006 - 20:20:14 CDT)
  • AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS (Sun Sep 24 2006 - 22:03:28 CDT)
  • Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package (Thu Sep 14 2006 - 01:47:07 CDT)
  • Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package (Wed Sep 13 2006 - 22:21:07 CDT)
  • AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package (Wed Sep 13 2006 - 07:57:44 CDT)
  • AMBER: How to simplify this big system rationally to perform MD studies (Wed Jun 14 2006 - 05:43:59 CDT)
  • Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? (Mon Jun 05 2006 - 03:57:44 CDT)
  • AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? (Sat Jun 03 2006 - 02:00:23 CDT)
  • AMBER: attachments for my last mail (Fri Jun 02 2006 - 02:30:30 CDT)
  • AMBER: some questions and problems about antechamber and divcon (Fri Jun 02 2006 - 02:11:22 CDT)
  • Re: AMBER: which time should I use to calculate the number of "ps/Day" (Mon May 29 2006 - 19:42:01 CDT)
  • AMBER: which time should I use to calculate the number of "ps/Day" (Mon May 29 2006 - 04:32:26 CDT)
  • RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs (Mon May 15 2006 - 04:00:03 CDT)
  • AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs (Sun May 14 2006 - 22:55:51 CDT)
  • AMBER: Did these differences come from so-called "different machines" ? (Sun Apr 30 2006 - 03:47:28 CDT)
• zhli_2000_at_126.com
  • AMBER: How to explain the meaning of the mmpbsa/DC result? (Sun Feb 26 2006 - 01:01:04 CST)
  • AMBER: Where to modify the atom type in sander? (Thu Jan 05 2006 - 03:21:20 CST)
• Zhuang
  • AMBER: post-processing replica exchange trajectory (Wed Mar 29 2006 - 17:57:43 CST)
  • AMBER: question capping helix ends (Thu Mar 23 2006 - 18:21:06 CST)
  • AMBER: question capping helix ends (Thu Mar 23 2006 - 04:35:21 CST)
• Zu Thur Yew
  • Re: AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 12:32:14 CDT)
  • AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 08:13:14 CDT)
  • AMBER: MMPBSA: positive energies during nmode (Wed Aug 16 2006 - 09:15:11 CDT)
  • Re: AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 11:42:04 CDT)
  • AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 09:17:31 CDT)
  • AMBER: Using a trajectory and some PDB files as input for PCA (Mon Jul 31 2006 - 05:20:42 CDT)
  • AMBER: Minimization problem: coordinates out of virtual box (Mon Jul 24 2006 - 07:53:19 CDT)
  • Re: AMBER: RMS & PCA (Tue Jul 18 2006 - 00:12:35 CDT)
  • AMBER: PhosphoThreonine Parms for use with ff03 (Tue Jul 18 2006 - 00:19:15 CDT)
  • AMBER: RMS & PCA (Mon Jul 17 2006 - 09:55:12 CDT)
  • AMBER: Ptraj: Hbond time series (Tue Jul 11 2006 - 10:19:34 CDT)
  • AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging (Wed Jul 05 2006 - 12:03:13 CDT)
  • AMBER: MM-PBSA: Problem when Generating Snapshots (Tue Jul 04 2006 - 02:20:39 CDT)
• ²ÜȽ
  • Re:AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:12:05 CST)
  • Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Thu Dec 07 2006 - 19:46:44 CST)
  • AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 19:05:55 CST)
  • AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 19:02:55 CST)
• ¶ÅÓÀ´º
  • Re: AMBER: one question about mm_pbsa (Thu Apr 13 2006 - 21:26:49 CDT)
  • AMBER: one question about mm_pbsa (Thu Apr 13 2006 - 03:37:50 CDT)
  • AMBER: one question about mm_pbsa (Wed Apr 05 2006 - 01:47:06 CDT)
• Àò ÕÅ
  • To dac --AMBER: anal: dihedral error (Mon Mar 27 2006 - 00:43:22 CST)
  • AMBER: About statistics results in MMPBSA_DC pair (Wed Mar 22 2006 - 09:22:17 CST)
• ÇÑ ¹Î¿ì
  • AMBER: Problem about dummy atoms when running antechamber (Mon Nov 27 2006 - 21:30:27 CST)
• ÕÅÓÂ
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 19:02:57 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 18:25:03 CST)
  • AMBER: how to remove the rotation of system in periodic condition? (Tue Nov 14 2006 - 06:10:22 CST)
  • AMBER: angle between helices (Mon Sep 11 2006 - 21:05:51 CDT)
• åÇÏÒÏ× ä.á.
  • AMBER: Bond Force Conctants in Amber Force Fields (Thu Jun 01 2006 - 00:22:01 CDT)