AMBER Archive (2009) - By Author

Starting: Thu Jan 01 2009 - 21:37:45 CST
Ending: Mon Nov 23 2009 - 13:51:08 CST

• . ..
  • [AMBER] hydrogen bond (Wed Mar 04 2009 - 05:12:33 CST)
  • RE: [AMBER] DM complexation (Tue Feb 17 2009 - 09:36:01 CST)
  • [AMBER] DM complexation (Tue Feb 17 2009 - 09:10:49 CST)
  • [AMBER] lmod calculation for complexe (Wed Feb 11 2009 - 03:09:04 CST)
  • [AMBER] Resp charge (Fri Feb 06 2009 - 11:34:12 CST)
  • [AMBER] out error (Tue Feb 03 2009 - 12:58:46 CST)
• A. Gomez-Sicilia
  • Re: [AMBER] TWO restraints with different force constants (Wed Aug 05 2009 - 07:20:54 CDT)
• Abdul Rehman Gani
  • Re: [AMBER] XServe cluster (Thu Oct 22 2009 - 14:40:11 CDT)
  • [AMBER] XServe cluster (Thu Oct 22 2009 - 14:14:36 CDT)
  • Re: [AMBER] AMBER on a Mac Mini cluster PoC - solved (Mon Aug 17 2009 - 09:44:07 CDT)
  • Re: [AMBER] AMBER on a Mac Mini cluster PoC (Mon Aug 17 2009 - 07:31:37 CDT)
  • Re: [AMBER] AMBER on a Mac Mini cluster PoC (Mon Aug 17 2009 - 03:13:38 CDT)
  • [AMBER] AMBER on a Mac Mini cluster PoC (Sun Aug 16 2009 - 10:51:44 CDT)
• ABEL Stephane 175950
  • RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] (Tue Feb 10 2009 - 08:39:17 CST)
  • RE : [AMBER] script to convert GLYCAM ff in CHARMM format (Fri Feb 06 2009 - 09:03:19 CST)
  • [AMBER] script to convert GLYCAM ff in CHARMM format (Fri Feb 06 2009 - 08:39:04 CST)
• Abhishek Banerjee
  • Re: [AMBER]Amber10 + g95 (Sat Nov 07 2009 - 21:41:54 CST)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Thu Oct 15 2009 - 10:51:56 CDT)
  • Re: [AMBER] DMF solvent box (Thu Oct 08 2009 - 22:41:02 CDT)
  • Re: [AMBER] DMF solvent box (Tue Oct 06 2009 - 23:10:22 CDT)
  • Re: [AMBER] Problem in compiling AMBER9 in parallel ! (Tue Sep 29 2009 - 12:25:36 CDT)
  • Re: [AMBER] DMF solvent box (Sat Sep 19 2009 - 00:24:08 CDT)
  • Re: [AMBER] DMF solvent box (Thu Sep 17 2009 - 01:15:53 CDT)
  • Re: [AMBER] DMF solvent box (Tue Sep 15 2009 - 23:33:23 CDT)
  • Re: [AMBER] DMF solvent box (Mon Sep 14 2009 - 08:18:30 CDT)
  • Re: [AMBER] DMF solvent box (Sun Sep 13 2009 - 09:24:04 CDT)
  • Re: [AMBER] DMF solvent box (Sun Sep 13 2009 - 03:56:18 CDT)
  • Re: [AMBER] DMF solvent box (Sun Sep 13 2009 - 00:33:39 CDT)
  • [AMBER] DMF solvent box (Thu Sep 10 2009 - 21:40:21 CDT)
• Abhishek Singh
  • [AMBER] Problem regarding Hbond analysis (Tue Sep 22 2009 - 14:43:50 CDT)
  • [AMBER] RNA and polarizable force field (Wed Jun 10 2009 - 10:30:29 CDT)
• abi ghanem
  • [AMBER] rescaling velocities (Thu Jun 04 2009 - 11:39:02 CDT)
• aditya chhikara
  • Re: [AMBER] installing resp on linux 64bit (Thu Mar 26 2009 - 16:36:50 CDT)
  • [AMBER] installing resp on linux 64bit (Thu Mar 26 2009 - 12:24:27 CDT)
• Adrian Roitberg
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Thu Nov 12 2009 - 07:30:53 CST)
  • Re: [AMBER] Gly -> Ala mutation (Mon Nov 09 2009 - 10:13:11 CST)
  • Re: [AMBER] error in distance restraint (Wed Oct 28 2009 - 09:01:07 CDT)
  • Re: [AMBER] the criterion of equilibrium (Sat Oct 24 2009 - 13:22:25 CDT)
  • Re: [AMBER] pmemd and internal dielectric (Fri Sep 25 2009 - 11:44:56 CDT)
  • Re: [AMBER] Problem on PMEMD (Mon Sep 14 2009 - 20:40:35 CDT)
  • Re: [AMBER] Ki and G (Mon Sep 14 2009 - 09:28:57 CDT)
  • Re: [AMBER] How to denature DNA (Tue Sep 08 2009 - 12:12:00 CDT)
  • Re: [AMBER] How to denature DNA (Tue Sep 08 2009 - 11:46:51 CDT)
  • Re: [AMBER] How to denature DNA (Tue Sep 08 2009 - 09:04:30 CDT)
  • Re: [AMBER] Changing pH of the system (Sun Aug 30 2009 - 11:18:32 CDT)
  • Re: [AMBER] Changing pH of the system (Sun Aug 30 2009 - 10:26:01 CDT)
  • Re: [AMBER] SCC-DFTB MD for mercury ions in proteins (Thu Aug 27 2009 - 11:51:21 CDT)
  • Re: [AMBER] Meaning of GMAX (Mon Aug 24 2009 - 10:05:36 CDT)
  • Re: [AMBER] Gaussian network model (GNM) (Fri Aug 21 2009 - 19:49:04 CDT)
  • Re: [AMBER] Protonated or not (Fri Jul 31 2009 - 12:32:50 CDT)
  • Re: [AMBER] average torsional energy (Sun Jun 07 2009 - 11:09:14 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 15:56:14 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:44:08 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:38:23 CDT)
  • Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. (Sat May 09 2009 - 13:07:08 CDT)
  • Re: [AMBER] IG not change at each restart of NPT simulation (Thu Mar 19 2009 - 08:30:10 CDT)
  • Re: [AMBER] SMD in Amber10 (Fri Mar 13 2009 - 10:01:31 CDT)
  • Re: [AMBER] SMD in Amber10 (Fri Mar 13 2009 - 08:45:39 CDT)
  • Re: [AMBER] SMD in Amber10 (Thu Mar 12 2009 - 13:46:14 CDT)
  • Re: [AMBER] A good way to use an Amber force field with NAMD? (Tue Mar 03 2009 - 18:11:49 CST)
  • Re: [AMBER] Problem with NVT and NPT (Fri Feb 20 2009 - 07:14:23 CST)
  • Re: [AMBER] IG not change at each restart of NPT simulation (Wed Feb 18 2009 - 08:46:36 CST)
  • Re: [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation (Tue Feb 17 2009 - 12:57:56 CST)
  • Re: [AMBER] density and volume in NVT ensamble (Fri Feb 06 2009 - 08:31:24 CST)
  • Re: [AMBER] Any link to a major QM code? (Sun Feb 15 2009 - 20:59:01 CST)
  • Re: [AMBER] non bonded parameteters index (Thu Feb 12 2009 - 18:15:33 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 19:03:45 CST)
  • Re: [AMBER] second derivative matrix (Mon Feb 09 2009 - 08:29:51 CST)
  • Re: [AMBER] DFT SK parameter for P atom (Mon Feb 02 2009 - 14:24:00 CST)
  • Re: [AMBER] precision in the trajectory files (Mon Feb 02 2009 - 08:46:49 CST)
• Adrien Delmont
  • [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 09:37:40 CDT)
  • [AMBER] problem about trajectory analysis (Wed Feb 25 2009 - 08:24:41 CST)
  • [AMBER] install Amber 10 to Macbook (Sat Feb 14 2009 - 05:06:50 CST)
  • [AMBER] analysis (Tue Jan 20 2009 - 11:03:16 CST)
• Age.Skjevik_at_biomed.uib.no
  • Re: [AMBER] Hbond analysis: Direction of the hydrogen (Tue Sep 08 2009 - 16:56:50 CDT)
  • [AMBER] Hbond analysis: Direction of the hydrogen (Tue Sep 08 2009 - 14:45:19 CDT)
• Ahammadunny Pathiaseril
  • Re: [AMBER] glycopeptide Parametrization (Wed Jun 10 2009 - 15:25:21 CDT)
• ahmed said
  • [AMBER] force field choice (Fri Jun 26 2009 - 03:21:16 CDT)
• Akansha Saxena
  • [AMBER] New atom type with 7 bonds (Fri Feb 13 2009 - 17:56:47 CST)
  • [AMBER] "bad atom type" (Fri Jan 09 2009 - 11:15:11 CST)
• AL Olson
  • [AMBER] vlimit error after heating restart (Fri Jul 17 2009 - 09:26:05 CDT)
• Alan
  • [AMBER] AmberTools 1.3 has a likely release date? (Thu Nov 19 2009 - 12:15:30 CST)
  • Re: [AMBER] about divcon (Wed Nov 18 2009 - 11:07:44 CST)
  • [AMBER] about divcon (Wed Nov 18 2009 - 10:24:51 CST)
  • Re: [AMBER] ambertools and Snow Leopard 64 bits kernel (Wed Sep 23 2009 - 09:21:30 CDT)
  • Re: [AMBER] ambertools and Snow Leopard 64 bits kernel (Tue Sep 22 2009 - 16:41:18 CDT)
  • [AMBER] ambertools and Snow Leopard 64 bits kernel (Tue Sep 22 2009 - 08:55:25 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 03:28:09 CDT)
  • Re: [AMBER] AMBER on a Mac Mini cluster PoC (Mon Aug 17 2009 - 05:50:30 CDT)
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Thu Jul 30 2009 - 08:39:03 CDT)
  • [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Wed Jul 29 2009 - 11:00:42 CDT)
  • [AMBER] Re: bugfix 10 failing for ambertools1.2 (Mon Jul 20 2009 - 03:25:55 CDT)
  • [AMBER] bugfix 10 failing for ambertools1.2 (Mon Jul 20 2009 - 03:14:16 CDT)
  • [AMBER] different results for antechamber/mopac for the same input (Wed Jul 15 2009 - 17:05:07 CDT)
  • Re: [AMBER] antechamber (Thu Jul 02 2009 - 05:16:55 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 06:37:40 CDT)
  • [AMBER] a method or program to try to guess the net charge of a small molecule (Fri Jun 26 2009 - 05:00:48 CDT)
  • [AMBER] guessing the charge of a small molecule (Tue Jun 23 2009 - 03:06:51 CDT)
  • Re: [AMBER] max atoms for antechamber (Mon Jun 22 2009 - 08:00:48 CDT)
  • [AMBER] max atoms for antechamber (Mon Jun 22 2009 - 07:37:39 CDT)
  • [AMBER] reclaiming space from amber10 installation (Sun Jun 21 2009 - 17:04:53 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Sat Jun 13 2009 - 13:37:54 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Thu Jun 11 2009 - 06:14:42 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Wed Jun 10 2009 - 11:26:13 CDT)
  • [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Wed Jun 10 2009 - 09:47:00 CDT)
  • [AMBER] Completed installation of AmberTools, version 1.1 (Wed Jun 10 2009 - 08:13:37 CDT)
  • Re: [AMBER] Warning: No sp2 improper torsion term for (Mon Jun 08 2009 - 09:54:50 CDT)
  • [AMBER] Warning: No sp2 improper torsion term for (Fri Jun 05 2009 - 07:26:55 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Thu Jun 04 2009 - 13:05:27 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Thu Jun 04 2009 - 09:19:28 CDT)
  • Re: [AMBER] spc.itp for the Amber force field (Wed Jun 03 2009 - 10:38:56 CDT)
  • [AMBER] ligand QM/semi-empirical coords optmisation (Tue May 26 2009 - 05:55:09 CDT)
  • [AMBER] Re: About Amber installations (Tue May 26 2009 - 04:53:37 CDT)
  • [AMBER] antechamber and wrong net charge with gasteiger method (Tue Apr 14 2009 - 12:41:30 CDT)
  • Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm (Sun Apr 12 2009 - 10:58:18 CDT)
  • [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm (Sun Apr 12 2009 - 04:30:15 CDT)
  • [AMBER] zwitterionic form of ARG and antechamber (Mon Apr 06 2009 - 07:33:31 CDT)
  • [AMBER] testing RRR with antechamber (Mon Apr 06 2009 - 07:10:27 CDT)
  • [AMBER] NALA-ALA-CALA peptide with antechamber (Fri Apr 03 2009 - 11:33:17 CDT)
  • [AMBER] Announcing NMR validation web interface iCing (Mon Mar 30 2009 - 11:55:00 CDT)
  • Re: [AMBER] sleap and check (Wed Mar 18 2009 - 16:23:51 CDT)
  • [AMBER] sleap and check (Wed Mar 18 2009 - 06:18:27 CDT)
  • Re: [AMBER] to understand multiplicity in antechamber (Fri Mar 13 2009 - 17:43:28 CDT)
  • [AMBER] to understand multiplicity in antechamber (Fri Mar 13 2009 - 09:43:45 CDT)
  • [AMBER] to understand multiplicity in antechamber (Fri Mar 13 2009 - 07:06:45 CDT)
• albert albert
  • Re: [AMBER] Segmentation fault in antechamber (Mon Nov 23 2009 - 09:23:00 CST)
  • Re: [AMBER] Segmentation fault in antechamber (Tue Nov 17 2009 - 11:04:46 CST)
  • Re: [AMBER] Segmentation fault in antechamber (Mon Nov 16 2009 - 10:23:02 CST)
  • [AMBER] Segmentation fault in antechamber (Mon Nov 16 2009 - 09:28:20 CST)
  • Re: [AMBER] loading a following attached protein in amber 10 (Tue Sep 08 2009 - 12:43:55 CDT)
  • [AMBER] loading a following attached protein in amber 10 (Tue Sep 08 2009 - 12:09:09 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Fri Jul 31 2009 - 14:27:02 CDT)
  • [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 01:57:20 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Wed Jul 08 2009 - 06:10:43 CDT)
  • [AMBER] unsolved verbosity when running minimization (Mon Jul 06 2009 - 14:09:02 CDT)
• Aldo Humberto Romero
  • [AMBER] Amber10, Serial compilation with ifort (Sun Jul 12 2009 - 15:57:40 CDT)
• alegil_at_fq.uh.cu
  • [AMBER] PARMSCAN (Tue Jun 02 2009 - 17:41:54 CDT)
  • [AMBER] PARMSCAN (Tue Jun 02 2009 - 17:26:42 CDT)
• Alessandro Contini
  • RE: [AMBER] PCA analysis with ptraj (Tue Nov 10 2009 - 06:03:48 CST)
  • [AMBER] PCA analysis with ptraj (Mon Nov 09 2009 - 11:00:19 CST)
• Alessandro Nascimento
  • Re: [AMBER] software to hydrate protein pockets (Fri Oct 23 2009 - 07:50:05 CDT)
  • [AMBER] Fe and Mn simulations (Tue Jun 30 2009 - 15:22:14 CDT)
  • Re: [AMBER] Analysis of the solt-bridge (Mon Jun 29 2009 - 07:58:49 CDT)
  • Re: [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 13:28:26 CDT)
  • [AMBER] antechamber & multiple low-energy conformations (Fri Apr 03 2009 - 07:01:39 CDT)
  • Re: [AMBER] Failure to compile amber9 serial ifort gcc (Wed Apr 01 2009 - 06:09:42 CDT)
  • Re: [AMBER] non bonded parameteters index (Thu Feb 12 2009 - 18:14:44 CST)
• Alessandro S. Nascimento
  • [AMBER] TI in Amber9/10 (Tue Sep 08 2009 - 10:47:26 CDT)
  • Re: [AMBER] hbond-error in amber9 (Thu Apr 30 2009 - 05:46:02 CDT)
• Alexander Boncheff
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Wed Nov 04 2009 - 10:02:50 CST)
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Tue Nov 03 2009 - 16:29:00 CST)
  • [AMBER] AMBER: segmentation fault when running parmchk (Tue Nov 03 2009 - 13:41:55 CST)
• Alexander Schierholt
  • [AMBER] Micelles set-up?? (Tue Feb 03 2009 - 04:09:52 CST)
  • [AMBER] thioglycoside (Mon Jan 26 2009 - 08:46:28 CST)
• Alexander Seifert
  • [AMBER] GB and Atom Type (Wed Nov 18 2009 - 02:58:32 CST)
• Alireza Shaneh
  • [AMBER] Problem with memory in nmode analysis (Tue Oct 06 2009 - 10:23:55 CDT)
  • [AMBER] Dummy atoms and MM-PBSA (Fri Sep 04 2009 - 11:48:16 CDT)
• Alison Saunders
  • [AMBER] Error in Sander Output File (Tue Jul 28 2009 - 12:00:12 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:43:40 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:06:12 CDT)
  • [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 12:07:28 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:47:59 CDT)
  • [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:19:44 CDT)
• Amire-Brahimi Benjamin
  • [AMBER] combining parameter files of ligand and enzyme (Tue Nov 17 2009 - 16:31:32 CST)
• amirhossein taghavi
  • RE: [AMBER] Xleap - solvatebox - counterions (Sat Jan 31 2009 - 11:34:10 CST)
• amit
  • Re: [AMBER] Protein with HETATM, am I doing the (Mon May 25 2009 - 10:26:15 CDT)
• Amit Bajaj
  • Re: [AMBER] Protein with HETATM, am I doing the (Thu May 21 2009 - 00:26:49 CDT)
  • AMBER: reg sander crashing on more than 32 cores over IB (Mon Jan 05 2009 - 00:33:15 CST)
• amit jain
  • [AMBER] AMBER: chiral restraint on protein (Tue Feb 10 2009 - 18:48:12 CST)
• amoreno_at_wesleyan.edu
  • [AMBER] Replacing DNA base with analog (Thu Jul 23 2009 - 09:20:08 CDT)
• Ananda Rama Krishnan Selvaraj
  • [AMBER] Installation error - Amber10 (Thu Jan 29 2009 - 05:47:44 CST)
• Andreas Svrcek-Seiler
  • Re: [AMBER] NAB syntax (Thu Sep 17 2009 - 10:21:51 CDT)
  • Re: [AMBER] Problems using nmode in NAB (Thu Jun 25 2009 - 08:03:15 CDT)
  • Re: [AMBER] Problems using nmode in NAB (Wed Jun 24 2009 - 03:52:30 CDT)
  • RE: [AMBER] Question about NAB module (Mon Mar 02 2009 - 03:23:52 CST)
  • Re: [AMBER] Installation error - Amber10 (Thu Jan 29 2009 - 05:52:44 CST)
  • Re: [AMBER] NAB entropy calcualtion (Fri Jan 09 2009 - 03:28:48 CST)
• Andrei Neamtu
  • [AMBER] R.E.D. too small charges (Fri Nov 13 2009 - 02:57:04 CST)
  • [AMBER] divcon question (Mon Aug 31 2009 - 06:31:35 CDT)
• Andrew Olson
  • Re: [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 13:23:31 CDT)
  • [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 10:23:01 CDT)
  • [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 10:14:38 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 12:10:18 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 10:53:11 CDT)
  • [AMBER] ligand/protein minimization (Fri Jul 10 2009 - 16:00:26 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 08:33:09 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 12:00:19 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 10:22:18 CDT)
  • [AMBER] Antechamber prep question (Thu Jul 09 2009 - 09:39:25 CDT)
  • [AMBER] (no subject) (Thu Feb 19 2009 - 13:46:24 CST)
  • [AMBER] linux install problem (Thu Feb 19 2009 - 12:44:14 CST)
  • [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory (Wed Feb 18 2009 - 11:08:57 CST)
• Andrew Purkiss-Trew
  • Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? (Wed Oct 14 2009 - 07:19:43 CDT)
  • RE: [AMBER] ambertools for NAMD (Thu May 07 2009 - 10:16:40 CDT)
  • Re: [AMBER] ambertools for NAMD (Thu May 07 2009 - 09:30:14 CDT)
  • Re: [AMBER] density and volume in NVT ensamble (Mon Feb 16 2009 - 08:45:25 CST)
  • Re: [AMBER] density and volume in NVT ensamble (Mon Feb 16 2009 - 08:14:40 CST)
  • Re: [AMBER] parameter files for D-amino acid (Thu Feb 05 2009 - 09:02:25 CST)
• Andrew Voronkov
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 11:38:28 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 10:35:51 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 09:44:45 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 06:35:55 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 10:02:57 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 09:25:30 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 09:07:26 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 05:35:31 CST)
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Wed Nov 18 2009 - 09:33:54 CST)
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Wed Nov 18 2009 - 09:32:11 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Wed Nov 18 2009 - 07:19:58 CST)
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Wed Nov 18 2009 - 07:09:52 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 10:34:33 CST)
  • [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 09:47:12 CST)
  • Re: [AMBER] Task is running on supercomputer without any output (Thu Nov 12 2009 - 07:24:56 CST)
  • [AMBER] MD snapshots of most probable protein conformations in Amber (Thu Nov 12 2009 - 07:23:22 CST)
  • [AMBER] Task is running on supercomputer without any output (Mon Nov 09 2009 - 06:39:36 CST)
  • [AMBER] sander.mpi. mdfil: Error unknown flag: sander (Mon Nov 09 2009 - 06:24:17 CST)
  • [AMBER] Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) (Sun Aug 23 2009 - 08:48:07 CDT)
  • [AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift (Sun Aug 23 2009 - 06:55:01 CDT)
  • Re: [AMBER] protein-ligand binding simulation times (Sat Aug 22 2009 - 05:32:42 CDT)
  • [AMBER] ambpdb water removal for rst files (Sat Aug 22 2009 - 01:53:14 CDT)
  • [AMBER] protein-ligand binding simulation times (Sat Aug 22 2009 - 00:09:54 CDT)
  • Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations (Sat Aug 01 2009 - 09:14:49 CDT)
  • [AMBER] Timescales and restraints for protein-small ligands movement simulations (Sat Aug 01 2009 - 01:23:19 CDT)
  • Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Tue Jul 28 2009 - 23:19:41 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Tue Jul 28 2009 - 01:12:15 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Mon Jul 27 2009 - 11:41:27 CDT)
  • [AMBER] amino acids caps for truncated proteins (Thu Jul 16 2009 - 11:31:18 CDT)
  • Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) (Wed Jul 08 2009 - 05:05:52 CDT)
  • [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) (Wed Jul 08 2009 - 04:39:03 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 14:26:48 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 12:00:32 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Wed Jun 03 2009 - 06:52:13 CDT)
  • [AMBER] only ff94 and ff99 for GBSA? (Wed Jun 03 2009 - 05:28:15 CDT)
  • [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 04:28:52 CDT)
  • [AMBER] Papers on Amber package usage (Sun Apr 26 2009 - 00:07:42 CDT)
  • Re: [AMBER] divcon error during antechamber run, convergence problem (Sat Mar 07 2009 - 09:58:19 CST)
  • Re: [AMBER] divcon error during antechamber run, convergence problem (Fri Mar 06 2009 - 12:04:55 CST)
• aneesh cna
  • Re: [AMBER] conversion of kelvin to kcal/mol (Mon Nov 09 2009 - 00:56:36 CST)
  • [AMBER] conversion of kelvin to kcal/mol (Sun Nov 08 2009 - 23:08:33 CST)
  • [AMBER] Pentane UA model (Tue Sep 22 2009 - 01:23:35 CDT)
  • [AMBER] Regarding united atom force field (Mon Sep 21 2009 - 05:17:20 CDT)
  • [AMBER] Regarding Hbond interactions (Wed Jul 22 2009 - 01:30:10 CDT)
  • [AMBER] Problem with radial distribution function (Fri Jun 26 2009 - 03:56:09 CDT)
  • Re: [AMBER] converting vibrational frequency (Mon Jun 01 2009 - 11:53:22 CDT)
  • [AMBER] converting vibrational frequency (Mon Jun 01 2009 - 06:22:01 CDT)
  • Re: [AMBER] High energy during minimization (Wed May 06 2009 - 00:58:00 CDT)
  • [AMBER] High energy during minimization (Sat May 02 2009 - 23:26:16 CDT)
  • [AMBER] dipole autocorrelation functions (Tue Apr 28 2009 - 01:23:05 CDT)
  • [AMBER] problem with antechamber (Wed Apr 08 2009 - 01:32:32 CDT)
  • [AMBER] calculation of Pi-Pi interaction energy (Wed Apr 01 2009 - 07:01:51 CDT)
  • Re: [AMBER] Regarding leap (Wed Mar 04 2009 - 22:29:17 CST)
  • [AMBER] Regarding leap (Wed Mar 04 2009 - 05:43:52 CST)
  • [AMBER] hbond analysis (Mon Feb 09 2009 - 11:55:25 CST)
  • [AMBER] strip frames from crd file (Mon Feb 02 2009 - 03:35:11 CST)
  • [AMBER] strip frames from crd file (Mon Feb 02 2009 - 03:33:16 CST)
• anna berteotti
  • RE: [AMBER] 8Mureabox (Wed Mar 11 2009 - 03:45:03 CDT)
  • [AMBER] 8Mureabox (Mon Mar 09 2009 - 05:07:52 CDT)
• Anselm Horn
  • Re: [AMBER] Phosphothreonine (Thu Nov 05 2009 - 07:17:59 CST)
  • Re: [AMBER] Error running sander.MPI (Tue Feb 17 2009 - 04:28:47 CST)
• Antonija Tomić
  • [AMBER] mm_pbsa- Decomposition: bad atom type (Tue Oct 06 2009 - 08:53:25 CDT)
  • RE: [AMBER] mm_pbsa-Binding and Stability tests? (Wed Aug 26 2009 - 04:15:54 CDT)
  • RE: [AMBER] mm_pbsa-Binding and Stability tests? (Mon Aug 24 2009 - 04:51:28 CDT)
  • [AMBER] mm_pbsa-Binding and Stability tests? (Fri Aug 21 2009 - 05:04:35 CDT)
  • Re: [AMBER] problems with ptraj option IMAGE (Mon Jun 29 2009 - 10:27:54 CDT)
  • [AMBER] problems with ptraj option IMAGE (Mon Jun 29 2009 - 09:48:54 CDT)
  • RE: [AMBER] Problems with running two separate jobs in the same time (Thu Apr 09 2009 - 05:33:03 CDT)
  • [AMBER] Problems with running two separate jobs in the same time (Tue Apr 07 2009 - 03:08:53 CDT)
• Antonio Morreale
  • [AMBER] Van der Waals atom types (Thu Apr 16 2009 - 09:39:14 CDT)
• Antonios Samiotakis
  • [AMBER] Question about improper torsions... (Fri Feb 13 2009 - 16:57:03 CST)
  • [AMBER] Langevin dynamics (Mon Feb 02 2009 - 11:54:31 CST)
• Aravind S
  • Re: [AMBER] problem with the results in the .out file! (Thu Apr 02 2009 - 00:49:19 CDT)
  • Re: [AMBER] .rst file generation problem. (Tue Mar 31 2009 - 03:49:17 CDT)
  • [AMBER] problem with the results in the .out file! (Tue Mar 31 2009 - 00:30:57 CDT)
  • Re: [AMBER] .rst file generation problem. (Mon Mar 30 2009 - 01:32:12 CDT)
  • [AMBER] .rst file generation problem. (Mon Mar 30 2009 - 00:48:55 CDT)
• archana sonawani
  • [AMBER] sander not working (Thu Jan 15 2009 - 23:52:48 CST)
  • [AMBER] Error in xleap (Thu Jan 15 2009 - 01:39:16 CST)
  • [AMBER] errorin sander---Amber10 (Tue Jan 13 2009 - 03:27:43 CST)
  • [AMBER] error in sander (Amber10) (Tue Jan 13 2009 - 02:21:09 CST)
  • AMBER: error in amber 10 (Tue Jan 06 2009 - 01:19:03 CST)
• Arnaud
  • [AMBER] Umbrella test (Thu Apr 02 2009 - 04:51:01 CDT)
  • [AMBER] PMF calculation (Tue Feb 17 2009 - 12:10:18 CST)
  • [AMBER] Xleap - solvatebox - counterions (Fri Jan 30 2009 - 04:44:58 CST)
• Arturas Ziemys
  • Re: [AMBER] large resp charges for non-natural amino acid (Sat Jan 31 2009 - 11:03:44 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Sat Jan 31 2009 - 11:03:09 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Thu Jan 29 2009 - 15:38:12 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Thu Jan 29 2009 - 09:10:50 CST)
  • [AMBER] large resp charges for non-natural amino acid (Tue Jan 27 2009 - 16:40:49 CST)
  • [AMBER] non-natural amino acids (Thu Jan 22 2009 - 11:32:11 CST)
• Arvind Marathe
  • Re: [AMBER] Regarding principal component analysis using ptraj (Fri Aug 28 2009 - 06:56:53 CDT)
  • Re: [AMBER] Regarding principal component analysis using ptraj (Fri Aug 28 2009 - 06:04:22 CDT)
  • [AMBER] Regarding principal component analysis using ptraj (Fri Aug 28 2009 - 01:54:40 CDT)
• Ashish Runthala
  • Re: [AMBER] Cygwin Home Directory (Sat Sep 19 2009 - 21:51:11 CDT)
  • Re: [AMBER] LINMIN failure notice (Fri Sep 18 2009 - 05:46:09 CDT)
  • [AMBER] What is the Optimum Ph for solvating a protein (Sun Sep 13 2009 - 08:08:40 CDT)
  • Re: [AMBER] input file (Thu Sep 10 2009 - 09:05:32 CDT)
  • Re: [AMBER] Leap warning (Wed Sep 09 2009 - 02:21:03 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Tue Sep 08 2009 - 10:14:46 CDT)
  • Re: [AMBER] loadpdb (Mon Sep 07 2009 - 22:00:47 CDT)
  • Re: [AMBER] How to find a protein's energy (Sun Sep 06 2009 - 07:30:26 CDT)
  • [AMBER] How to find a protein's energy (Sat Sep 05 2009 - 22:48:01 CDT)
  • [AMBER] What should be the standard input file when imin=5 (Thu Sep 03 2009 - 02:25:49 CDT)
  • [AMBER] How to consider the off centre charges (Wed Sep 02 2009 - 10:28:40 CDT)
  • [AMBER] What is dual topology (Wed Sep 02 2009 - 10:25:19 CDT)
  • Re: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input (Tue Aug 25 2009 - 00:45:33 CDT)
  • Re: [AMBER] Meaning of GMAX (Mon Aug 24 2009 - 10:38:46 CDT)
  • Re: [AMBER] Meaning of GMAX (Mon Aug 24 2009 - 09:59:53 CDT)
  • Re: [AMBER] PMEMD 10 overflow issues (Fri Aug 21 2009 - 21:52:55 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 21:53:04 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 10:03:19 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 08:56:59 CDT)
  • [AMBER] Can i link and refine the modeled domains with different proteins bound on it (Tue Aug 18 2009 - 06:13:23 CDT)
  • Re: [AMBER] box problem (Mon Aug 17 2009 - 22:08:28 CDT)
  • Re: [AMBER] Conference or workshop on AMBER? (Mon Aug 17 2009 - 22:04:12 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Mon Aug 17 2009 - 22:02:43 CDT)
  • [AMBER] Can i link and refine two domains of a single protein (Mon Aug 17 2009 - 10:32:33 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Mon Aug 17 2009 - 01:21:45 CDT)
  • Re: Re: Re: [AMBER] box problem (Sun Aug 16 2009 - 09:00:50 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Sat Aug 15 2009 - 22:59:11 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 09:39:56 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 04:57:48 CDT)
  • Re: [AMBER] sourcing leap commands in log file (Sat Aug 15 2009 - 01:50:31 CDT)
  • Re: [AMBER] Strange QM/MM Divcon - help me out (Sat Aug 15 2009 - 01:42:38 CDT)
  • Re: Re: [AMBER] box problem (Sat Aug 15 2009 - 01:12:10 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Sat Aug 15 2009 - 01:05:53 CDT)
  • Re: [AMBER] suggestions pls (Tue Aug 11 2009 - 21:40:40 CDT)
  • [AMBER] Regarding Minimization maxcyc (Sun Aug 09 2009 - 09:09:58 CDT)
  • Re: [AMBER] Regd : gaff force field (Sat Aug 08 2009 - 07:17:37 CDT)
  • Re: [AMBER] (no subject) (Fri Aug 07 2009 - 08:27:04 CDT)
  • Re: [AMBER] Regd : gaff force field (Fri Aug 07 2009 - 04:08:43 CDT)
  • Re: [AMBER] implicit solvent simulation (Thu Aug 06 2009 - 00:00:50 CDT)
  • Re: [AMBER] Protein Activity (Tue Aug 04 2009 - 22:42:11 CDT)
  • Re: [AMBER] optimization step length (Mon Aug 03 2009 - 09:26:28 CDT)
  • Re: [AMBER] Showing error in energy minimization (Sun Aug 02 2009 - 22:05:06 CDT)
  • Re: [AMBER] Re: query (Sat Aug 01 2009 - 07:21:47 CDT)
  • Re: [AMBER] problem from xleap (Fri Jul 31 2009 - 22:33:10 CDT)
  • Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Fri Jul 31 2009 - 20:39:54 CDT)
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 20:28:42 CDT)
  • Re: [AMBER] query (Fri Jul 31 2009 - 20:23:07 CDT)
  • Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Thu Jul 30 2009 - 22:40:45 CDT)
  • Re: [AMBER] ambpdb problem (Thu Jul 30 2009 - 22:44:10 CDT)
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 22:44:59 CDT)
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 20:35:09 CDT)
  • Re: [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 20:26:19 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 09:33:02 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 08:08:48 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 05:28:40 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 04:09:23 CDT)
  • Re: [AMBER] DNA + intercalator (Fri Jul 24 2009 - 22:12:27 CDT)
• Ashveen Seenauth
  • Re: [AMBER] Installation issue (Wed Sep 23 2009 - 10:54:27 CDT)
  • Re: [AMBER] Installation issue (Wed Sep 23 2009 - 10:41:53 CDT)
  • Re: [AMBER] Installation issue (Wed Sep 23 2009 - 10:28:55 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 12:59:46 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 12:25:12 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 11:45:13 CDT)
  • [AMBER] Installation issue (Tue Sep 22 2009 - 11:17:49 CDT)
• Astrid Maaß
  • Re: [AMBER] Help with torsions in parm99.dat file (Mon Mar 09 2009 - 08:27:30 CDT)
  • [AMBER] extra torsion terms in tleap.top-file (Thu Feb 26 2009 - 08:32:30 CST)
• Atro Tossavainen
  • Re: [AMBER] Installation directory (Mon May 25 2009 - 03:10:34 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 18:39:30 CDT)
  • Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 18:36:53 CDT)
  • Re: [AMBER] Failures of tests (Wed Apr 08 2009 - 17:43:08 CDT)
  • Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 17:25:54 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 17:24:52 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 06:20:27 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 04:35:17 CDT)
  • Re: [AMBER] errors while testing (Tue Apr 07 2009 - 05:18:08 CDT)
  • Re: [AMBER] ssh and make test.parallel (Mon Apr 06 2009 - 15:21:07 CDT)
  • Re: [AMBER] ssh and make test.parallel (Mon Apr 06 2009 - 05:33:21 CDT)
  • Re: [AMBER] parallel installation of amber on sun (Fri Apr 03 2009 - 17:33:52 CDT)
  • Re: [AMBER] parallel installation of amber on sun (Fri Apr 03 2009 - 16:40:42 CDT)
  • Re: [AMBER] parallel installation of amber on sun (Fri Apr 03 2009 - 04:39:25 CDT)
  • Re: [AMBER] parallel installation of amber on sun (Thu Apr 02 2009 - 15:23:05 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 05:18:58 CDT)
  • Re: [AMBER] Problem build pmemd (Sat Mar 14 2009 - 14:10:53 CDT)
  • Re: [AMBER] problems compiling ambertool (Sat Mar 14 2009 - 14:09:36 CDT)
  • Re: [AMBER] error in executing sander.MPI in amber9 (Thu Feb 05 2009 - 05:08:59 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Thu Feb 05 2009 - 01:50:12 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Wed Feb 04 2009 - 06:33:25 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Mon Feb 02 2009 - 17:06:49 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Sun Feb 01 2009 - 01:10:30 CST)
• Aurum Bai
  • [AMBER] About the "FATAL: Atom err"! (Mon Jun 22 2009 - 05:14:20 CDT)
  • [AMBER] About the "FATAL: Atom err!" (Mon Jun 22 2009 - 05:12:23 CDT)
  • [AMBER] About the Amber tutorial (Mon Jun 22 2009 - 05:03:49 CDT)
• Aust, Susanne
  • AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? (Mon Oct 19 2009 - 04:01:27 CDT)
  • AW: [AMBER] Conference or workshop on AMBER? (Wed Aug 19 2009 - 03:16:21 CDT)
  • AW: AW: [AMBER] Any Comment, please (Tue Aug 11 2009 - 03:36:34 CDT)
  • AW: [AMBER] Any Comment, please (Tue Aug 11 2009 - 03:17:18 CDT)
  • AW: [AMBER] TWO restraints with different force constants (Wed Aug 05 2009 - 07:31:38 CDT)
  • AW: [AMBER] Steered MD---more than one pair of atoms (Wed Jul 08 2009 - 01:47:56 CDT)
  • [AMBER] analysis of QM/MM - LCOD (Fri Jul 03 2009 - 04:51:34 CDT)
  • AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 07:05:10 CDT)
  • AW: AW: AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 06:44:58 CDT)
  • AW: AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 06:27:19 CDT)
  • AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 04:24:07 CDT)
  • [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 01:49:48 CDT)
  • AW: [AMBER] 2 restraints with different force constants (Fri Jun 19 2009 - 07:39:34 CDT)
  • AW: [AMBER] 2 restraints with different force constants (Fri Jun 19 2009 - 06:51:21 CDT)
  • [AMBER] 2 restraints with different force constants (Fri Jun 19 2009 - 02:14:50 CDT)
  • AW: [AMBER] zinc coordination of benzimidazole (Fri Jun 12 2009 - 01:13:19 CDT)
  • [AMBER] zinc coordination of benzimidazole (Thu Jun 11 2009 - 02:09:59 CDT)
• Aydin, Cihan
  • [AMBER] Citing AMBER Tools... (Sat Jan 31 2009 - 23:08:36 CST)
• B. Nandy
  • [AMBER] MM_PBSA decomp problem (Tue Sep 22 2009 - 07:29:23 CDT)
• babak minoofar
  • [AMBER] Low frequency Raman spectra (Sat Nov 07 2009 - 06:53:37 CST)
  • [AMBER] CH3Hg+ parameters (Thu Sep 24 2009 - 07:08:12 CDT)
• backy
  • Re: [AMBER] to unsubscribe email (Wed Jun 17 2009 - 03:22:19 CDT)
  • [AMBER] to unsubscribe email (Wed Jun 17 2009 - 02:13:02 CDT)
• Baifan Wang
  • Re: [AMBER] problem when doing mm/pbsa: bad atom type Br (Mon Sep 28 2009 - 02:26:06 CDT)
  • [AMBER] problem when doing mm/pbsa: bad atom type Br (Sun Sep 27 2009 - 21:50:46 CDT)
• Bala subramanian
  • [AMBER] symbol lookup error (Tue Sep 01 2009 - 03:43:51 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 10:01:27 CDT)
  • [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 08:24:56 CDT)
  • Re: [AMBER] amber9 in fedora10 (Thu Jul 02 2009 - 03:05:55 CDT)
  • Re: [AMBER] amber9 in fedora10 (Thu Jul 02 2009 - 02:02:54 CDT)
  • [AMBER] amber9 in fedora10 (Wed Jul 01 2009 - 09:09:15 CDT)
  • Re: [AMBER] making leap to recognize 5' phosphate (Tue Jun 23 2009 - 03:49:05 CDT)
  • [AMBER] making leap to recognize 5' phosphate (Mon Jun 22 2009 - 08:45:43 CDT)
  • [AMBER] secstruct with ptraj (Fri May 15 2009 - 05:19:54 CDT)
  • Re: [OFFLIST] Re: [AMBER] amber9 in fedora10 (Thu May 14 2009 - 03:18:07 CDT)
  • [AMBER] amber9 in fedora10 (Wed May 13 2009 - 04:50:25 CDT)
  • [AMBER] ptraj netcdf (Tue May 12 2009 - 07:04:00 CDT)
  • Re: [AMBER] basepair (Tue Apr 14 2009 - 06:09:21 CDT)
  • Re: [AMBER] How to delete the frames at specific intervals (Fri Apr 03 2009 - 04:55:35 CDT)
  • Re: [AMBER] How to find out residence time of water molecules (Fri Apr 03 2009 - 01:12:18 CDT)
  • [AMBER] explicit ion with igb=1 (Thu Apr 02 2009 - 08:39:10 CDT)
  • Re: [AMBER] helical parameters (Mon Mar 23 2009 - 13:14:29 CDT)
  • Re: [AMBER] adding chain id to ptraj pdb output (Mon Mar 23 2009 - 06:37:43 CDT)
  • Re: [AMBER] analysing DNA trajectory (Fri Mar 20 2009 - 03:06:08 CDT)
  • Re: [AMBER] temperature rises with igb=1 (Thu Mar 19 2009 - 06:24:45 CDT)
  • [AMBER] temperature rises with igb=1 (Tue Mar 17 2009 - 11:35:41 CDT)
  • [AMBER] removing center of mass (Tue Mar 17 2009 - 10:21:28 CDT)
  • Re: [AMBER] minimisation with igb=10 (Mon Mar 16 2009 - 10:56:48 CDT)
  • [AMBER] minimisation with igb=10 (Mon Mar 16 2009 - 10:43:10 CDT)
  • [AMBER] suggestions for PB simulation (Sat Mar 14 2009 - 11:41:19 CDT)
  • Re: [AMBER] using Gromacs for analysis (Fri Feb 27 2009 - 12:16:46 CST)
  • Re: [AMBER] hbond analysis (Mon Feb 09 2009 - 12:33:39 CST)
  • Re: [AMBER] amber9 in fedora10 (Tue Jan 13 2009 - 12:16:19 CST)
  • [AMBER] amber9 in fedora10 (Tue Jan 13 2009 - 11:51:49 CST)
  • Re: [AMBER] RE: AMBER: xleap problem (Wed Jan 07 2009 - 08:54:44 CST)
  • Re: [AMBER] RE: AMBER: xleap problem (Wed Jan 07 2009 - 07:34:43 CST)
  • Re: [AMBER] RE: AMBER: xleap problem (Wed Jan 07 2009 - 04:53:24 CST)
  • Re: AMBER: xleap problem (Tue Jan 06 2009 - 13:43:00 CST)
  • AMBER: xleap problem (Tue Jan 06 2009 - 12:57:53 CST)
• balaji nagarajan
  • [AMBER] implicit_run_error (Thu Nov 19 2009 - 12:37:21 CST)
  • [AMBER] reg. GBA (Thu Nov 12 2009 - 06:06:30 CST)
  • [AMBER] minimization error (Fri Oct 02 2009 - 06:42:54 CDT)
  • [AMBER] xleap problem ! (Wed Sep 30 2009 - 13:40:58 CDT)
  • RE: [AMBER] How to denature DNA (Wed Sep 09 2009 - 12:14:37 CDT)
  • RE: [AMBER] How to denature DNA (Tue Sep 08 2009 - 23:01:55 CDT)
  • RE: [AMBER] How to denature DNA (Tue Sep 08 2009 - 11:58:36 CDT)
  • RE: [AMBER] How to denature DNA (Tue Sep 08 2009 - 11:29:57 CDT)
  • [AMBER] How to denature DNA (Tue Sep 08 2009 - 09:00:43 CDT)
  • RE: [AMBER] unit of force constant (Tue Sep 08 2009 - 08:41:37 CDT)
  • [AMBER] unit of force constant (Tue Sep 08 2009 - 08:16:08 CDT)
  • [AMBER] unit of force constant (Wed Sep 02 2009 - 11:57:25 CDT)
  • [AMBER] how to give force values in TMD (Wed Sep 02 2009 - 05:03:41 CDT)
  • [AMBER] how to pull a dna (Tue Sep 01 2009 - 09:24:29 CDT)
  • [AMBER] how to pull a dna (Mon Aug 31 2009 - 21:39:10 CDT)
  • RE: [AMBER] rmsd_ptraj (Thu Jul 09 2009 - 00:50:10 CDT)
  • [AMBER] rmsd_ptraj (Wed Jul 08 2009 - 23:19:56 CDT)
  • RE: [AMBER] rmsd_dna (Wed Jul 08 2009 - 20:55:53 CDT)
  • [AMBER] rmsd_dna (Wed Jul 08 2009 - 11:15:02 CDT)
  • [AMBER] to check basepair in ptraj (Mon Jun 15 2009 - 09:23:28 CDT)
  • [AMBER] ptraj_hbond_problem (Thu Jun 04 2009 - 17:08:24 CDT)
  • [AMBER] mol2 file to amber pdb file format (Thu Jun 04 2009 - 11:32:06 CDT)
  • [AMBER] hbond_DNAtraj (Mon Jun 01 2009 - 12:08:15 CDT)
  • [AMBER] hbond_ptraj (Mon May 25 2009 - 15:05:12 CDT)
  • [AMBER] hbond-error in amber9 (Wed Apr 29 2009 - 21:09:17 CDT)
  • RE: [AMBER] reg-TMD (Wed Apr 29 2009 - 20:44:32 CDT)
  • RE: [AMBER] reg-TMD (Wed Apr 29 2009 - 06:54:59 CDT)
  • RE: [AMBER] reg-TMD (Wed Apr 29 2009 - 06:25:50 CDT)
  • RE: [AMBER] reg-TMD (Tue Apr 28 2009 - 23:16:17 CDT)
  • [AMBER] reg-TMD (Tue Apr 28 2009 - 10:23:34 CDT)
  • [AMBER] help_me to know the reason (Fri Apr 17 2009 - 23:30:07 CDT)
  • RE: [AMBER] help- regarding - TMD (Thu Apr 16 2009 - 12:01:39 CDT)
  • RE: [AMBER] help- regarding - TMD (Thu Apr 16 2009 - 00:21:26 CDT)
  • [AMBER] help- regarding - TMD (Wed Apr 15 2009 - 11:19:59 CDT)
  • [AMBER] hbond_ptraj_eror (Wed Apr 15 2009 - 01:53:29 CDT)
  • [AMBER] problem with explicit solvent in TMD (Mon Apr 13 2009 - 06:37:21 CDT)
  • [AMBER] basepair (Fri Apr 10 2009 - 00:30:57 CDT)
  • RE: [AMBER] problem in input (Thu Apr 02 2009 - 15:23:18 CDT)
  • [AMBER] problem in input (Thu Apr 02 2009 - 05:29:39 CDT)
  • [AMBER] helical parameters (Mon Mar 23 2009 - 11:21:04 CDT)
  • [AMBER] analysing DNA trajectory (Fri Mar 20 2009 - 00:09:10 CDT)
  • RE: [AMBER] TMD (Wed Mar 18 2009 - 06:15:55 CDT)
  • [AMBER] TMD (Tue Mar 17 2009 - 23:58:37 CDT)
  • [AMBER] need- help-for TMD (Tue Mar 17 2009 - 00:16:34 CDT)
  • [AMBER] doubt-reg_ Targeted molecular dynamics (Fri Mar 13 2009 - 11:20:41 CDT)
  • RE: [AMBER] reg.targeted molecular dynamics (Fri Feb 27 2009 - 04:28:02 CST)
  • RE: [AMBER] reg.targeted molecular dynamics (Wed Feb 25 2009 - 03:34:57 CST)
  • RE: [AMBER] reg.targeted molecular dynamics (Wed Feb 25 2009 - 03:18:10 CST)
  • RE: [AMBER] reg.targeted molecular dynamics (Mon Feb 23 2009 - 00:45:18 CST)
  • RE: [AMBER] reg.targeted molecular dynamics (Sun Feb 22 2009 - 08:45:29 CST)
  • [AMBER] reg.targeted molecular dynamics (Fri Feb 20 2009 - 23:10:50 CST)
  • RE: [AMBER] reg.Targeted molecular dynamics (Wed Feb 18 2009 - 08:07:09 CST)
  • [AMBER] reg.Targeted molecular dynamics (Tue Feb 17 2009 - 23:26:49 CST)
  • [AMBER] parallel run error (Tue Feb 17 2009 - 02:19:23 CST)
  • [AMBER] reg . run TMD (Tue Feb 10 2009 - 11:36:28 CST)
  • [AMBER] adding MG2 problem (Fri Jan 30 2009 - 03:45:58 CST)
  • [AMBER] reg.Targeted molecular dynamics (Tue Jan 27 2009 - 07:57:01 CST)
  • [AMBER] reg.Targeted molecular dynamics (Tue Jan 27 2009 - 07:56:54 CST)
  • [AMBER] reg: targeted molecular dynamics (Tue Jan 27 2009 - 07:02:03 CST)
  • [AMBER] reg.parallel.run.error (Sat Jan 24 2009 - 09:09:49 CST)
  • [AMBER] reg.parallel.run error (Fri Jan 23 2009 - 19:59:21 CST)
  • [AMBER] reg.error in parallel run (Fri Jan 23 2009 - 04:05:21 CST)
  • [AMBER] reg.parallel run error (Thu Jan 22 2009 - 12:41:25 CST)
  • [AMBER] reg . parallel run (Wed Jan 21 2009 - 23:34:03 CST)
• Balazs Jojart
  • Re: [AMBER] How to prepare the acetate ion file in leap? (Tue Oct 13 2009 - 02:36:03 CDT)
• Barbault Florent
  • Re: [AMBER] How to derive charges from the output (Mon Aug 31 2009 - 02:38:09 CDT)
  • Re: [AMBER] Problem with MM-PBSA energy calculation (Mon May 25 2009 - 13:57:19 CDT)
  • Re: [AMBER] The PDB file was not recognized by Amber, what can i do? (Wed Apr 29 2009 - 01:56:09 CDT)
  • Re: [AMBER] The PDB file was not recognized by Amber, what can i do? (Tue Apr 28 2009 - 18:00:55 CDT)
  • Re: [AMBER] amber question (Sun Apr 26 2009 - 03:48:31 CDT)
  • Re: [AMBER] binding free energy (Sun Mar 01 2009 - 06:20:39 CST)
  • Re: [AMBER] glycam and solvateoct command (Tue Feb 17 2009 - 14:13:58 CST)
  • Re: [AMBER] Beginner question (Fri Feb 13 2009 - 15:25:13 CST)
  • Re: [AMBER] atomic charge (Thu Jan 29 2009 - 02:24:48 CST)
• Beale, John
  • [AMBER] Segmentation Fault (Thu Nov 05 2009 - 12:04:52 CST)
  • [AMBER] Phosphothreonine (Thu Nov 05 2009 - 07:03:58 CST)
  • [AMBER] Phosphorylated Threonine (Tue Nov 03 2009 - 10:31:09 CST)
  • [AMBER] Large File Support (Thu Oct 15 2009 - 07:40:27 CDT)
  • [AMBER] ptraj and prmtop (Wed Oct 14 2009 - 07:46:11 CDT)
  • [AMBER] Teragrid (Thu Sep 24 2009 - 07:08:56 CDT)
  • [AMBER] (no subject) (Fri Aug 07 2009 - 07:16:58 CDT)
  • [AMBER] (no subject) (Mon Jul 13 2009 - 12:35:46 CDT)
  • [AMBER] NOE (Thu Jun 11 2009 - 07:30:36 CDT)
  • [AMBER] sander error (Mon Jun 08 2009 - 09:43:24 CDT)
  • [AMBER] radius of gyration (Fri Apr 17 2009 - 06:39:31 CDT)
  • [AMBER] Contour plot (Thu Apr 02 2009 - 14:31:22 CDT)
  • [AMBER] secstruct (Thu Mar 05 2009 - 07:54:20 CST)
  • [AMBER] H-Bonds (Thu Feb 26 2009 - 08:38:04 CST)
  • [AMBER] ptraj analyze (Wed Feb 25 2009 - 10:56:59 CST)
  • [AMBER] (no subject) (Tue Feb 24 2009 - 05:59:51 CST)
  • [AMBER] secstruct (Thu Feb 19 2009 - 07:22:20 CST)
  • [AMBER] (no subject) (Tue Feb 17 2009 - 07:02:25 CST)
  • [AMBER] H-bond information (Thu Feb 12 2009 - 09:32:30 CST)
  • [AMBER] Radius of Gyration (Mon Feb 02 2009 - 11:34:35 CST)
  • [AMBER] Alpha helix plot (Thu Jan 29 2009 - 14:10:11 CST)
  • [AMBER] lone pairs on CYX and MET (Thu Jan 08 2009 - 12:08:42 CST)
  • [AMBER] MD (Wed Jan 07 2009 - 08:40:07 CST)
• Ben Roberts
  • Re: [AMBER] Gaussian log file error (Mon Nov 02 2009 - 09:16:23 CST)
  • Re: [AMBER] man pages? (Tue Oct 20 2009 - 12:33:16 CDT)
  • [AMBER] OpenMP (Mon Oct 12 2009 - 12:35:35 CDT)
  • Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac (Fri Oct 02 2009 - 09:20:47 CDT)
  • [AMBER] Compiling Amber with gfortran-4.5.0 on a mac (Tue Sep 29 2009 - 16:37:31 CDT)
  • Re: [AMBER] charge not zero on group: RESP (Sat Jul 18 2009 - 07:45:10 CDT)
  • Re: [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 14:18:41 CDT)
  • Re: [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 14:17:12 CDT)
  • [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 10:24:14 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 14:12:07 CDT)
  • [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 11:11:15 CDT)
• ben rodriguez
  • [AMBER] Centering and reimaging with ptraj- stop rotating. (Mon Oct 19 2009 - 22:00:26 CDT)
  • [AMBER] Is iwrap mapping water molecules to my protein cavity? (Mon Oct 12 2009 - 13:55:23 CDT)
  • RE: [AMBER] PMEMD 10 overflow issues (Fri Aug 21 2009 - 16:17:36 CDT)
  • [AMBER] PMEMD 10 overflow issues (Fri Aug 21 2009 - 15:38:05 CDT)
  • [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' (Fri May 15 2009 - 17:09:44 CDT)
  • [AMBER] Amber 9 Install - AMBERBUILDFLAGS error (Mon Feb 16 2009 - 21:39:14 CST)
  • [AMBER] Normal errors on job kill? (Mon Feb 16 2009 - 20:35:43 CST)
  • [AMBER] How to calculate cavity volume from MD structures? (Tue Jan 20 2009 - 16:21:43 CST)
• Benjamin Roberts
  • [AMBER] Segmentation faults (Wed Mar 04 2009 - 18:17:50 CST)
  • Re: [AMBER] Compilation and qmmm_div (Wed Mar 04 2009 - 18:15:37 CST)
  • [AMBER] Compilation and qmmm_div (Wed Mar 04 2009 - 09:48:16 CST)
• BERGY
  • [AMBER] High RMSD for DNA: A to B transition study (Fri Mar 06 2009 - 01:26:57 CST)
  • Re: [AMBER] DNA simulation: Problem with RMSD (Fri Mar 06 2009 - 00:20:00 CST)
  • [AMBER] DNA simulation: Problem with RMSD (Wed Mar 04 2009 - 21:44:26 CST)
• Beroza, Paul
  • [AMBER] decomposing energies (Thu Oct 01 2009 - 11:15:07 CDT)
• bharat lakhani
  • Re: [AMBER] enquiry regarding parameter file to be used (Thu Nov 19 2009 - 23:35:14 CST)
  • Re: [AMBER] enquiry regarding parameter file to be used (Fri Nov 13 2009 - 23:52:58 CST)
  • [AMBER] enquiry regarding parameter file to be used (Fri Nov 13 2009 - 07:35:30 CST)
  • Re: [AMBER] How to derive charges from the output (Tue Sep 01 2009 - 03:46:12 CDT)
  • Re: [AMBER] How to derive charges from the output (Mon Aug 31 2009 - 08:43:15 CDT)
  • [AMBER] How to derive charges from the output (Mon Aug 31 2009 - 00:33:21 CDT)
  • [AMBER] Need you help (Wed Aug 26 2009 - 08:41:17 CDT)
  • [AMBER] Epsilon value for Iron (Tue Aug 25 2009 - 07:24:10 CDT)
  • [AMBER] query (Fri Aug 07 2009 - 04:11:42 CDT)
  • [AMBER] Re: showing error when creating topology and coordinate file (Mon Aug 03 2009 - 23:54:36 CDT)
  • [AMBER] showing error when creating topology and coordinate file (Mon Aug 03 2009 - 02:19:59 CDT)
  • [AMBER] Showing error in energy minimization (Sun Aug 02 2009 - 01:22:30 CDT)
  • [AMBER] Showing error (Sat Aug 01 2009 - 08:12:00 CDT)
  • [AMBER] Re: query (Sat Aug 01 2009 - 07:07:24 CDT)
  • [AMBER] query (Fri Jul 31 2009 - 02:42:04 CDT)
  • [AMBER] Normal mode analysis of water (Thu Jul 30 2009 - 04:27:19 CDT)
  • Re: [AMBER] command for RESP fitting (Mon Jul 20 2009 - 02:01:23 CDT)
  • [AMBER] command for RESP fitting (Thu Jul 16 2009 - 02:10:33 CDT)
  • [AMBER] Please help me out (Wed Jul 15 2009 - 05:43:21 CDT)
  • [AMBER] calculating the hydrogen bonding energy between the two molecule (Wed Jun 24 2009 - 04:19:01 CDT)
  • [AMBER] how to add ions (Tue Jun 02 2009 - 02:25:46 CDT)
  • [AMBER] how to add charge on metal ions (Thu Apr 30 2009 - 01:44:46 CDT)
  • [AMBER] please read this mail (Sat Apr 18 2009 - 02:38:12 CDT)
  • [AMBER] please help me out (Thu Apr 16 2009 - 01:41:08 CDT)
  • Re: [AMBER] how to add charge in metal ion (Tue Apr 14 2009 - 07:49:44 CDT)
  • [AMBER] please help me out (Thu Apr 09 2009 - 00:10:22 CDT)
  • [AMBER] please help me out (Wed Apr 08 2009 - 04:18:41 CDT)
  • [AMBER] how to add charge in metal ion (Tue Apr 07 2009 - 04:11:23 CDT)
  • [AMBER] please help me out (Thu Apr 02 2009 - 05:13:48 CDT)
  • Re: [AMBER] please help me out (Tue Mar 24 2009 - 08:57:18 CDT)
  • Re: [AMBER] please help me out (Mon Mar 23 2009 - 02:58:52 CDT)
  • Re: [AMBER] please help me out (Sat Mar 14 2009 - 06:04:37 CDT)
  • Re: [AMBER] please help me out (Thu Mar 12 2009 - 01:04:00 CDT)
  • Re: [AMBER] please help me out (Mon Mar 09 2009 - 03:43:08 CDT)
  • Re: [AMBER] please help me out (Mon Mar 09 2009 - 00:04:45 CDT)
  • Re: [AMBER] please help me out (Thu Mar 05 2009 - 05:16:45 CST)
  • [AMBER] please help me out (Thu Mar 05 2009 - 02:35:44 CST)
  • [AMBER] Fwd: please help me out (Wed Mar 04 2009 - 22:42:06 CST)
• Bill K
  • Re: [AMBER] Stability of a long NPT md trajectory? (Tue Feb 10 2009 - 13:39:22 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Tue Feb 10 2009 - 01:37:31 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 14:56:53 CST)
  • [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 01:07:24 CST)
• Bill Kowallis
  • [AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? (Wed Feb 18 2009 - 19:55:47 CST)
• Bill Ross
  • Re:Re: [AMBER] read substrate into leap (Wed Nov 18 2009 - 19:59:33 CST)
  • Re: [AMBER] Asking help for parallel installation of Amber9 (Wed Nov 18 2009 - 11:48:51 CST)
  • Re: [AMBER] have a question (Tue Nov 17 2009 - 20:02:45 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 19:04:48 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 11:51:08 CST)
  • Re: [AMBER] slope {no reply} (Mon Nov 16 2009 - 11:48:22 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Wed Nov 11 2009 - 11:54:01 CST)
  • Re: [AMBER] LJ parameters for HO and HW (Mon Nov 09 2009 - 11:29:40 CST)
  • Re: [AMBER] unable to find mopac charges in mopac.out (Fri Nov 06 2009 - 19:22:22 CST)
  • Re: [AMBER] zeros in excluded atom list in topology file (Fri Nov 06 2009 - 18:09:39 CST)
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Wed Nov 04 2009 - 12:39:32 CST)
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Tue Nov 03 2009 - 17:15:00 CST)
  • RE: [AMBER] vlimit (Wed Oct 28 2009 - 16:55:55 CDT)
  • Re: [AMBER] error in AMBer distance constraint (Sun Oct 25 2009 - 22:03:19 CDT)
  • Re: [AMBER] the criterion of equilibrium (Sat Oct 24 2009 - 12:19:09 CDT)
  • Re: [AMBER] xleap not reconizing inhibitor prepin (Fri Oct 23 2009 - 13:33:44 CDT)
  • Re: [AMBER] inhibitor prepin not recognized in xleap (Fri Oct 23 2009 - 13:32:03 CDT)
  • Re: [AMBER] [Fwd: problem with minimization] (Fri Oct 23 2009 - 12:40:57 CDT)
  • Re: [AMBER] [Fwd: problem with minimization] (Thu Oct 22 2009 - 11:49:45 CDT)
  • Re: [AMBER] translate multiple residues (Wed Oct 21 2009 - 17:40:51 CDT)
  • Re: [AMBER] translate multiple residues (Wed Oct 21 2009 - 15:53:20 CDT)
  • Re: [AMBER] question with hbond in carnal (Tue Oct 20 2009 - 11:32:56 CDT)
  • Re: [AMBER] Centering and reimaging with ptraj- stop rotating. (Tue Oct 20 2009 - 00:14:10 CDT)
  • Re: [AMBER] question with pucker in six member ring (Mon Oct 19 2009 - 12:54:03 CDT)
  • Re: [AMBER] question with pucker in six member ring (Fri Oct 16 2009 - 14:48:04 CDT)
  • Re: [AMBER] question with pucker in six member ring (Fri Oct 16 2009 - 13:43:56 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Thu Oct 15 2009 - 11:28:26 CDT)
  • Re: Re: Re: 回å¤�： [Amber]AMBER: MM_PBSA problemsin AMBER10 (Wed Oct 14 2009 - 11:56:41 CDT)
  • Re: [AMBER] mean square displacment (Tue Oct 13 2009 - 19:09:49 CDT)
  • Re: [AMBER] Simulating transmembrane protein. (Mon Oct 12 2009 - 17:37:50 CDT)
  • Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? (Mon Oct 12 2009 - 14:12:19 CDT)
  • Re: [AMBER] Simulating transmembrane protein. (Mon Oct 12 2009 - 14:04:36 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 09 2009 - 19:24:47 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 09 2009 - 12:52:01 CDT)
  • Re: [AMBER] DG improper torsion problem, two missing parameters (Fri Oct 09 2009 - 12:25:30 CDT)
  • Re: [AMBER] Fwd: Group specification (Thu Oct 08 2009 - 15:22:54 CDT)
  • Re: [AMBER] Fwd: Group specification (Thu Oct 08 2009 - 15:15:44 CDT)
  • Re: [AMBER] Missing X11 Libraries (Thu Oct 08 2009 - 12:25:32 CDT)
  • Re: [AMBER] Missing X11 Libraries (Wed Oct 07 2009 - 17:28:34 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Wed Oct 07 2009 - 11:59:21 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 17:18:01 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 16:19:29 CDT)
  • Re: [AMBER] Environment Variables in Cygwin Don't Remain (Thu Oct 01 2009 - 13:57:43 CDT)
  • Re: [AMBER] Installation issue (Wed Sep 23 2009 - 11:36:59 CDT)
  • Re: [AMBER] Installation issue (Wed Sep 23 2009 - 11:29:28 CDT)
  • Re: [AMBER] Problem regarding Hbond analysis (Tue Sep 22 2009 - 15:00:55 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 13:28:43 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 12:59:22 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 12:55:34 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 12:50:28 CDT)
  • Re: [AMBER] Installation issue (Tue Sep 22 2009 - 11:31:47 CDT)
  • Re: [AMBER] Cygwin Home Directory (Mon Sep 21 2009 - 12:45:02 CDT)
  • Re: [AMBER] combining MD runs for post-MD analysis (Mon Sep 21 2009 - 12:32:53 CDT)
  • Re: [AMBER] Cygwin Home Directory (Sat Sep 19 2009 - 12:29:59 CDT)
  • Re: [AMBER] Cygwin Home Directory (Fri Sep 18 2009 - 15:56:17 CDT)
  • Re: [AMBER] Cygwin Home Directory (Fri Sep 18 2009 - 13:19:44 CDT)
  • Re: [AMBER] LINMIN failure notice (Fri Sep 18 2009 - 11:18:41 CDT)
  • Re: [AMBER] PES QM and MM (Thu Sep 17 2009 - 11:08:35 CDT)
  • RE: [AMBER] database (Wed Sep 16 2009 - 12:54:47 CDT)
  • Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? (Tue Sep 15 2009 - 17:15:38 CDT)
  • Re: [AMBER] input file (Thu Sep 10 2009 - 11:51:10 CDT)
  • Re: [AMBER] parameterization of protein-ligand complex (Wed Sep 09 2009 - 12:12:28 CDT)
  • Re: [AMBER] Leap warning (Wed Sep 09 2009 - 11:49:05 CDT)
  • RE: [AMBER] How to denature DNA (Wed Sep 09 2009 - 11:38:04 CDT)
  • Re: [AMBER] loadpdb (Tue Sep 08 2009 - 21:53:32 CDT)
  • RE: [AMBER] How to denature DNA (Tue Sep 08 2009 - 12:33:09 CDT)
  • Re: [AMBER] loadpdb (Tue Sep 08 2009 - 11:58:12 CDT)
  • Re: [AMBER] loadpdb (Tue Sep 08 2009 - 11:53:03 CDT)
  • Re: [AMBER] Creating new counterions (Tue Sep 01 2009 - 14:58:55 CDT)
  • Re: [AMBER] Single Adenine (Wed Aug 26 2009 - 14:28:31 CDT)
  • Re: [AMBER] ambpdb water removal for rst files (Sat Aug 22 2009 - 09:45:30 CDT)
  • RE: [AMBER] box volume not understood? (Fri Aug 21 2009 - 11:15:51 CDT)
  • RE: [AMBER] box volume not understood? (Thu Aug 20 2009 - 21:53:52 CDT)
  • Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? (Tue Aug 18 2009 - 17:59:12 CDT)
  • Re: [AMBER] AMBER is running silently (Mon Aug 17 2009 - 18:04:02 CDT)
  • Re: [AMBER] drying of solvent possible ? (Thu Aug 13 2009 - 11:21:35 CDT)
  • Re: [AMBER] sourcing leap commands in log file (Wed Aug 12 2009 - 19:47:57 CDT)
  • Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Mon Aug 10 2009 - 20:30:07 CDT)
  • Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Mon Aug 10 2009 - 20:17:05 CDT)
  • Re: [AMBER] Protein Activity (Tue Aug 04 2009 - 14:59:40 CDT)
  • Re: [AMBER] Protein Activity (Tue Aug 04 2009 - 14:19:32 CDT)
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 21:39:48 CDT)
  • Re: [AMBER] residues lacking connect0/connect1 (Mon Jul 27 2009 - 11:40:31 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 11:17:29 CDT)
  • Re: [AMBER] DNA + intercalator (Fri Jul 24 2009 - 18:03:06 CDT)
  • Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" (Wed Jul 15 2009 - 11:53:41 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 18:13:09 CDT)
  • Re: AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 11:42:01 CDT)
  • Re: [AMBER] NAB memory increase (Thu Jun 25 2009 - 11:34:58 CDT)
  • Re: [AMBER] SANDER BOMB in subroutine nonbond_list (Tue Jun 23 2009 - 11:54:30 CDT)
  • Re: [Barracuda SPAM] Re: [AMBER] Atom Type List (Mon Jun 22 2009 - 11:43:39 CDT)
  • Re: [AMBER] Residues (Thu Jun 18 2009 - 16:13:53 CDT)
  • Re: [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 14:25:55 CDT)
  • Re: [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 12:56:26 CDT)
  • Re: [AMBER] GLYCAM: warnings by writing topology (Wed Jun 17 2009 - 12:32:43 CDT)
  • Re: [AMBER] GLYCAM: warnings by writing topology (Wed Jun 17 2009 - 03:01:28 CDT)
  • Re: [AMBER] Seg-fault when creating residue (Wed Jun 17 2009 - 02:51:02 CDT)
  • Re: [AMBER] improper torsion problem (Wed Jun 17 2009 - 02:47:12 CDT)
  • Re: [AMBER] connecting residues (Tue Jun 16 2009 - 11:39:02 CDT)
  • Re: [AMBER] connecting residues (Tue Jun 16 2009 - 11:37:33 CDT)
  • Re: [AMBER] Distance-covariance and PCA questions... (Tue Jun 16 2009 - 11:18:40 CDT)
  • Re: [AMBER] Re: connect (Mon Jun 15 2009 - 15:39:32 CDT)
  • Re: [AMBER] Residues (Fri Jun 12 2009 - 14:49:09 CDT)
  • Re: [AMBER] entangle-less building (Wed Jun 10 2009 - 17:38:31 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 16:17:03 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 14:04:02 CDT)
  • Re: [AMBER] creating bond (Wed Jun 03 2009 - 16:40:09 CDT)
  • Re: [AMBER] creating bond (Wed Jun 03 2009 - 13:40:52 CDT)
  • Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Thu May 28 2009 - 10:42:13 CDT)
  • Re: [AMBER] problem with MM-PBSA (Wed May 27 2009 - 19:52:19 CDT)
  • Re: [AMBER] Modification of His (Mon May 18 2009 - 15:06:16 CDT)
  • RE: [AMBER] What is the purpose to do the bond constraints? (Mon May 18 2009 - 14:39:42 CDT)
  • Re: [AMBER] High energy during minimization (Sun May 03 2009 - 13:00:32 CDT)
  • RE: [AMBER] Nonterminal, was not found in name map (Wed Apr 29 2009 - 00:05:12 CDT)
  • Re: [AMBER] ANAL problems (Tue Apr 28 2009 - 15:40:59 CDT)
  • Re: [AMBER] Restraining counterions? (Tue Apr 28 2009 - 13:59:52 CDT)
  • Re: [AMBER] Best rms fit for correlation and covariance analysis (Tue Apr 28 2009 - 11:57:10 CDT)
  • Re: [AMBER] Problem with RNA hairpin unwinding in explicit water (Thu Apr 23 2009 - 12:53:40 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Wed Apr 22 2009 - 11:19:20 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 15:42:14 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 11:42:36 CDT)
  • Re: [AMBER] Sander and multiple residues (Thu Apr 09 2009 - 15:12:10 CDT)
  • Re: [AMBER] change in protein ligand order (Tue Mar 24 2009 - 13:07:42 CDT)
  • Re: [AMBER] Metal in MD simulation (Thu Mar 19 2009 - 16:22:12 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen (Tue Mar 17 2009 - 17:47:07 CDT)
  • Re: [AMBER] problems compiling ambertool (Tue Mar 17 2009 - 12:24:48 CDT)
  • Re: [AMBER] Unit 5 Error on OPEN: nan.in (Tue Mar 17 2009 - 12:12:07 CDT)
  • Re: [AMBER] problems compiling ambertool (Tue Mar 17 2009 - 12:10:01 CDT)
  • Re: [AMBER] Re: join two units in amber9 or amber10 (Mon Mar 16 2009 - 17:56:01 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 17:50:44 CDT)
  • Re: [AMBER] solvent and counter ions (Thu Mar 05 2009 - 17:29:50 CST)
  • Re: [AMBER] solvent and counter ions (Wed Mar 04 2009 - 18:20:45 CST)
  • RE: [AMBER] Compiling Carnal Amber7 in Amber9 (Thu Feb 12 2009 - 14:32:29 CST)
  • RE: [AMBER] Compiling Carnal Amber7 in Amber9 (Wed Feb 11 2009 - 13:04:53 CST)
  • Re: [AMBER] Irregularity in box during md (Tue Feb 10 2009 - 11:24:12 CST)
  • Re: [AMBER] extract frames from a .mdcrd (Fri Feb 06 2009 - 13:13:27 CST)
  • Re: [AMBER] production run terminates due to (*) symbols in xxx.rst (Thu Feb 05 2009 - 11:42:55 CST)
  • Re: [AMBER] Compiling Carnal Amber7 in Amber9 (Thu Feb 05 2009 - 11:36:00 CST)
  • Re: [AMBER] Xleap - solvatebox - counterions (Fri Jan 30 2009 - 12:40:07 CST)
  • Re: [AMBER] Duplicate residues (Mon Jan 19 2009 - 13:20:01 CST)
  • Re: [AMBER] ambpdb is changing atom names, a feature or bug? (Fri Jan 09 2009 - 11:53:23 CST)
  • Re: [AMBER] problem building AmberTools/sleap on AIX (Fri Jan 09 2009 - 11:45:55 CST)
• Binbin Liu
  • [AMBER] contradictive hydrogen bonds using ptraj (Mon Oct 26 2009 - 11:42:20 CDT)
• Biswaranjan Meher
  • [AMBER] Error in equilibration: file _ew_box.f (Fri Aug 07 2009 - 15:39:00 CDT)
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 18:12:59 CDT)
  • [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 16:54:58 CDT)
• Bo Baker
  • Re: [AMBER] Re: AMBER: ligand parameter (Sun Jan 11 2009 - 18:52:19 CST)
  • Re: [AMBER] Re: AMBER: ligand parameter (Sun Jan 11 2009 - 18:20:08 CST)
  • Re: [AMBER] Re: AMBER: ligand parameter (Wed Jan 07 2009 - 20:18:02 CST)
  • Re: [AMBER] Re: AMBER: ligand parameter (Tue Jan 06 2009 - 23:05:00 CST)
  • [AMBER] Re: AMBER: ligand parameter (Tue Jan 06 2009 - 21:59:19 CST)
  • AMBER: ligand parameter (Mon Jan 05 2009 - 16:05:18 CST)
• Bokun Cho
  • Re: [AMBER] xleap installation error (Mon Aug 03 2009 - 00:18:00 CDT)
  • [AMBER] Re: Ambertools 1.2 installation error (Mon Jul 27 2009 - 01:51:49 CDT)
  • Re: [AMBER] RE: Listing gaff parameters in frcmod (Fri May 08 2009 - 00:00:47 CDT)
  • [AMBER] RE: Listing gaff parameters in frcmod (Thu May 07 2009 - 23:20:46 CDT)
• Brad Dickson
  • [AMBER] Re: force units (Fri Jun 19 2009 - 08:22:40 CDT)
  • [AMBER] Re: force units (Thu Jun 18 2009 - 04:31:16 CDT)
  • [AMBER] force units (Thu Jun 18 2009 - 02:14:31 CDT)
  • [AMBER] force.f routine (Wed Jun 10 2009 - 07:56:39 CDT)
• Bradshaw, Richard
  • [AMBER] MM-PBSA and NetCDF (Wed May 27 2009 - 10:38:13 CDT)
  • [AMBER] MM-PBSA decomp by residue and snapshot? (Thu Mar 05 2009 - 11:55:05 CST)
• Brent Krueger
  • Re: [AMBER] "extra points" incompatibility with pmemd (Wed Oct 21 2009 - 07:28:58 CDT)
  • Re: [AMBER] CY3 dye parameters (Sat Apr 25 2009 - 14:33:40 CDT)
• Brothers, Michael Charles
  • RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Fri Jul 31 2009 - 12:36:10 CDT)
  • [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Thu Jul 30 2009 - 17:28:43 CDT)
  • [AMBER] Syntax Bellymask (Fri Jul 10 2009 - 18:59:01 CDT)
  • RE: [AMBER] Tleap input error, atom not found in residue template (Tue Jul 07 2009 - 11:08:00 CDT)
  • [AMBER] Tleap input error, atom not found in residue template (Mon Jul 06 2009 - 20:25:00 CDT)
  • RE: [AMBER] problem with parametrization (Wed Jun 24 2009 - 13:34:16 CDT)
  • RE: [AMBER] RED Geometry Calculation Error (Fri Jun 19 2009 - 16:10:12 CDT)
  • [AMBER] RED Geometry Calculation Error (Fri Jun 19 2009 - 13:52:37 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Fri Jun 19 2009 - 12:46:25 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Thu Jun 18 2009 - 16:01:52 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Thu Jun 18 2009 - 12:38:53 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Wed Jun 10 2009 - 14:40:21 CDT)
  • [AMBER] Generating LeAP file for helix containing non-standard amino acid (Wed Jun 10 2009 - 13:26:32 CDT)
• Brut Marie
  • Re: [AMBER] Computing an Hessian matrix using NAB (Tue Oct 13 2009 - 14:00:53 CDT)
  • Re: [AMBER] Computing an Hessian matrix using NAB (Tue Oct 13 2009 - 13:56:19 CDT)
  • [AMBER] Computing an Hessian matrix using NAB (Mon Oct 12 2009 - 17:12:44 CDT)
• C Liu
  • [AMBER] QM/MM assigns Cd to C, Se to S (Sat May 02 2009 - 21:09:27 CDT)
• Carina Backtorp
  • [AMBER] RESP charges for Fe in heme (Mon Jan 19 2009 - 07:48:11 CST)
• Carlos P Sosa
  • Re: [AMBER] pmemd on BlueGene/P? (Thu Feb 05 2009 - 14:48:57 CST)
• Carlos Simmerling
  • Re: [AMBER] enquiry regarding parameter file to be used (Fri Nov 20 2009 - 05:20:05 CST)
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Wed Nov 18 2009 - 11:14:50 CST)
  • Re: [AMBER] MD snapshots of most probable protein conformations in Amber (Wed Nov 18 2009 - 07:53:14 CST)
  • Re: [AMBER] Can I get an average trajectory? (Wed Nov 18 2009 - 06:08:59 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 17:49:39 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 05:11:23 CST)
  • Re: [AMBER] slope (Tue Nov 17 2009 - 05:10:35 CST)
  • Re: [AMBER] enquiry regarding parameter file to be used (Mon Nov 16 2009 - 05:40:49 CST)
  • Re: [AMBER] Etot positive (Mon Nov 16 2009 - 05:13:55 CST)
  • Re: [AMBER] slope (Mon Nov 16 2009 - 05:11:46 CST)
  • Re: [AMBER] slope {no reply} (Sun Nov 15 2009 - 13:07:02 CST)
  • Re: [AMBER] How to split mdcrd files (Sun Nov 15 2009 - 11:56:48 CST)
  • Re: [AMBER] How to split mdcrd files (Sun Nov 15 2009 - 11:28:06 CST)
  • Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj (Sat Nov 14 2009 - 10:00:39 CST)
  • Re: [AMBER] enquiry regarding parameter file to be used (Fri Nov 13 2009 - 07:41:50 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Fri Nov 13 2009 - 07:35:28 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 16:29:13 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 08:22:08 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Wed Nov 11 2009 - 15:14:24 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Wed Nov 11 2009 - 11:52:55 CST)
  • Re: [AMBER] High-temperature simulation ? (Wed Nov 11 2009 - 11:26:15 CST)
  • Re: [AMBER] Gly -> Ala mutation (Mon Nov 09 2009 - 09:13:08 CST)
  • Re: [AMBER] zeros in excluded atom list in topology file (Thu Nov 05 2009 - 18:39:56 CST)
  • Re: [AMBER] Is it the way to do simulation in vacuum (Fri Oct 30 2009 - 11:10:22 CDT)
  • Re: [AMBER] SPC/E HOH angle (Fri Oct 30 2009 - 08:47:18 CDT)
  • Re: [AMBER] Is it the way to do simulation in vacuum (Fri Oct 30 2009 - 08:26:20 CDT)
  • Re: [AMBER] Is it the way to do simulation in vacuum (Fri Oct 30 2009 - 05:21:49 CDT)
  • Re: [AMBER] rms fit of mutant with respect to wild type structure (Thu Oct 29 2009 - 09:03:35 CDT)
  • Re: [AMBER] pairwise per-residue decomposition (Thu Oct 29 2009 - 05:20:55 CDT)
  • Re: Re: [AMBER] error in distance restraint (Thu Oct 29 2009 - 05:20:13 CDT)
  • Re: [AMBER] error in distance restraint (Wed Oct 28 2009 - 15:48:13 CDT)
  • Re: [AMBER] Simulated annealing (Wed Oct 28 2009 - 05:51:41 CDT)
  • Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! (Tue Oct 27 2009 - 18:22:43 CDT)
  • Re: Re: [AMBER] error in AMBer distance constraint (Tue Oct 27 2009 - 06:28:22 CDT)
  • Re: [AMBER] error in AMBer distance constraint (Sun Oct 25 2009 - 21:38:23 CDT)
  • Re: [AMBER] Question about distance restraint ? (Fri Oct 23 2009 - 05:56:24 CDT)
  • Re: [AMBER] Time scale of the Protein domain motion ? (Sat Oct 17 2009 - 14:42:01 CDT)
  • Re: [AMBER] Time scale of the Protein domain motion ? (Sat Oct 17 2009 - 14:23:34 CDT)
  • Re: [AMBER] LES and NEB problem (Thu Oct 15 2009 - 13:09:34 CDT)
  • Re: [AMBER] LES and NEB problem (Thu Oct 15 2009 - 11:54:18 CDT)
  • Re: [AMBER] Simulated annealing (Thu Oct 15 2009 - 06:43:56 CDT)
  • Re: [AMBER] part of the protein escaped from the water box (Thu Oct 15 2009 - 06:39:40 CDT)
  • Re: [AMBER] LES and NEB problem (Wed Oct 14 2009 - 09:14:04 CDT)
  • Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? (Wed Oct 14 2009 - 08:49:00 CDT)
  • Re: [AMBER] ptraj and prmtop (Wed Oct 14 2009 - 08:41:04 CDT)
  • Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? (Mon Oct 12 2009 - 14:28:12 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Sat Oct 10 2009 - 06:36:35 CDT)
  • Re: [AMBER] Some queries about pH simulation (Fri Oct 09 2009 - 13:59:17 CDT)
  • Re: [AMBER] Distance Replica Exchange (Fri Oct 09 2009 - 08:40:17 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Fri Oct 09 2009 - 08:09:32 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Fri Oct 09 2009 - 07:45:04 CDT)
  • Re: [AMBER] Fwd: Group specification (Thu Oct 08 2009 - 13:35:43 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 17:30:21 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 10:06:55 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 09:26:38 CDT)
  • Re: [AMBER] Teragrid (Thu Sep 24 2009 - 07:11:41 CDT)
  • Re: [AMBER] solvent accessible surface area (Wed Sep 23 2009 - 14:29:57 CDT)
  • Re: [AMBER] solvent accessible surface area (Wed Sep 23 2009 - 14:20:24 CDT)
  • [AMBER] ACS COMP division awards- Oct 19th deadline (Mon Sep 21 2009 - 12:49:28 CDT)
  • Re: [AMBER] input file (Thu Sep 10 2009 - 06:03:17 CDT)
  • Re: [AMBER] loadpdb (Wed Sep 09 2009 - 06:35:04 CDT)
  • Re: [AMBER] PK zero for specific dihedral and parmchk (Wed Sep 09 2009 - 05:23:31 CDT)
  • Re: [AMBER] loadpdb (Tue Sep 08 2009 - 08:39:12 CDT)
  • Re: [AMBER] unit of force constant (Tue Sep 08 2009 - 08:21:40 CDT)
  • Re: [AMBER] loading PDB of a RNA sequence (Tue Sep 08 2009 - 05:33:57 CDT)
  • Re: [AMBER] general query: implicit solvation (Tue Sep 08 2009 - 05:11:24 CDT)
  • Re: [AMBER] loadpdb (Mon Sep 07 2009 - 13:01:10 CDT)
  • Re: [AMBER] How to find a protein's energy (Sun Sep 06 2009 - 06:49:53 CDT)
  • Re: [AMBER] nmropt option (Sat Sep 05 2009 - 05:59:04 CDT)
  • Re: [AMBER] nmropt option (Fri Sep 04 2009 - 13:15:13 CDT)
  • Re: [AMBER] Simulation short peptide and protein interaction (Thu Sep 03 2009 - 08:34:27 CDT)
  • Re: [AMBER] What should be the standard input file when imin=5 (Thu Sep 03 2009 - 06:55:48 CDT)
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 06:54:13 CDT)
  • Re: [AMBER] Dyndom (Sat Aug 29 2009 - 09:59:23 CDT)
  • Re: [AMBER] Need you help (Wed Aug 26 2009 - 08:48:20 CDT)
  • Re: [AMBER] How to strip water for MM/GBSA calculations? (Fri Aug 21 2009 - 05:53:59 CDT)
  • Re: [AMBER] amber test fails with ICC 11.0.081 (Mon Aug 17 2009 - 10:16:26 CDT)
  • Re: [AMBER] Protein Domain Motion (Fri Aug 14 2009 - 07:17:28 CDT)
  • Re: [AMBER] Protein Domain Motion (Thu Aug 13 2009 - 14:39:39 CDT)
  • Re: [Amber]: REMD using hybrid solvent model (Wed Aug 12 2009 - 18:54:20 CDT)
  • Re: [Amber]: REMD using hybrid solvent model (Wed Aug 12 2009 - 18:52:56 CDT)
  • Re: [AMBER] Amber99SB (Tue Aug 11 2009 - 09:42:44 CDT)
  • Re: [AMBER] Re: implicit solvent simulation with new ligand (Mon Aug 10 2009 - 09:42:33 CDT)
  • Re: [AMBER] Re: implicit solvent simulation with new ligand (Fri Aug 07 2009 - 13:29:46 CDT)
  • Re: [AMBER] parameters for HIV protease inhibitors (Thu Aug 06 2009 - 10:29:39 CDT)
  • Re: [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 16:14:20 CDT)
  • Re: [AMBER] nonbon.f question (Mon Jul 27 2009 - 14:34:20 CDT)
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Fri Jul 24 2009 - 07:01:28 CDT)
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 16:57:44 CDT)
  • Re: [AMBER] IGB=7 vs IGB=5 (Tue Jul 21 2009 - 08:51:22 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 08:51:44 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 06:40:03 CDT)
  • Re: [AMBER] Box shape change (Sat Jul 18 2009 - 20:35:41 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 05:24:23 CDT)
  • Re: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 09:15:39 CDT)
  • Re: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 08:42:35 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:58:15 CDT)
  • Re: [AMBER] problem with energy calculations (Fri Jul 10 2009 - 12:25:56 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:25:10 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:02:39 CDT)
  • TMD: was: Re: [AMBER] charges in topology file (Fri Jul 10 2009 - 11:36:30 CDT)
  • Re: [AMBER] implicit solvent (GB version2) MD simulation (Fri Jul 10 2009 - 10:57:57 CDT)
  • Re: [AMBER] EPtot for Alpha-L- methyl fucose (Fri Jul 10 2009 - 08:57:34 CDT)
  • Re: [AMBER] Restrained backbone conformation MD simulation" (Fri Jul 10 2009 - 06:47:20 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 05:55:51 CDT)
  • Re: [AMBER] Acetylate and Amidate (Thu Jul 09 2009 - 06:52:28 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:22:58 CDT)
  • Re: [AMBER] rmsd_dna (Wed Jul 08 2009 - 13:21:29 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 09:41:25 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Wed Jul 08 2009 - 06:34:20 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Mon Jul 06 2009 - 14:28:08 CDT)
  • Re: [AMBER] The problem of restart file (Wed Jul 01 2009 - 07:49:32 CDT)
  • Re: [AMBER] problems with ptraj option IMAGE (Mon Jun 29 2009 - 10:00:59 CDT)
  • Re: [AMBER] Velocity rescaling and ig... (Sun Jun 28 2009 - 10:35:37 CDT)
  • Re: [AMBER] explicit solvent NMR refinement (Sun Jun 28 2009 - 07:36:42 CDT)
  • Re: [AMBER] REMD (Tue Jun 23 2009 - 05:07:39 CDT)
  • Re: [AMBER] Fix Residue continued... (Thu Jun 18 2009 - 13:56:54 CDT)
  • Re: [AMBER] Sander imin=5 option (Tue Jun 16 2009 - 09:50:43 CDT)
  • Re: [AMBER] Fix the local structure as a rigid body (Tue Jun 16 2009 - 09:13:45 CDT)
  • Re: [AMBER] Fix the local structure as a rigid body (Tue Jun 16 2009 - 08:15:12 CDT)
  • Re: [AMBER] Histidine, which form? (Mon Jun 15 2009 - 09:57:40 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 12:51:40 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 11:28:04 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 10:48:30 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 10:36:50 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 09:38:14 CDT)
  • Re: [AMBER] average torsional energy (Sun Jun 07 2009 - 11:14:17 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 14:20:59 CDT)
  • Re: [AMBER] rescaling velocities (Thu Jun 04 2009 - 11:43:20 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Wed Jun 03 2009 - 05:51:09 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 05:13:23 CDT)
  • Re: [AMBER] Atom names (Tue Jun 02 2009 - 06:39:25 CDT)
  • Re: [AMBER] ask for parm99MOD (Mon Jun 01 2009 - 15:12:47 CDT)
  • Re: [AMBER] Choice of force field (Mon Jun 01 2009 - 06:14:09 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 16:17:05 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 15:52:56 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 15:22:31 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:57:24 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:56:26 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:44:41 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:41:20 CDT)
  • Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Thu May 28 2009 - 13:15:09 CDT)
  • Re: [AMBER] Molecular simulation of a protein using special H2O cluster (Tue May 26 2009 - 19:25:03 CDT)
  • Re: [AMBER] Molecular simulation of a protein using special H2O cluster (Tue May 26 2009 - 06:45:50 CDT)
  • Re: [AMBER] Loading PDB of complex (Thu May 21 2009 - 08:48:06 CDT)
  • Re: [AMBER] loadpdb atom type (Tue May 19 2009 - 12:09:29 CDT)
  • Re: [AMBER] pmemd running very slow in amber10 (Thu May 14 2009 - 05:09:11 CDT)
  • Re: [AMBER] ambertools for NAMD (Thu May 07 2009 - 09:23:25 CDT)
  • Re: [AMBER] ambertools for NAMD (Thu May 07 2009 - 08:36:27 CDT)
  • Re: [AMBER] multiple chain specification in Sander (Thu May 07 2009 - 05:19:09 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Tue May 05 2009 - 12:32:42 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Tue May 05 2009 - 11:39:52 CDT)
  • Re: [AMBER] Charge problem (Tue May 05 2009 - 07:58:31 CDT)
  • Re: [AMBER] Suggestion for restraining chain of a protein (Tue May 05 2009 - 07:27:05 CDT)
  • Re: [AMBER] Charge problem (Tue May 05 2009 - 07:16:32 CDT)
  • Re: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 05:11:43 CDT)
  • Re: [AMBER] Problem in production run (Tue May 05 2009 - 05:07:11 CDT)
  • Re: [AMBER] Suggestion for restraining chain of a protein (Tue May 05 2009 - 05:05:16 CDT)
  • Re: [AMBER] Number of processor in pmemd (Mon May 04 2009 - 12:27:06 CDT)
  • Re: [AMBER] Parameter file not saved (Mon May 04 2009 - 07:19:14 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Sun May 03 2009 - 06:11:07 CDT)
  • Re: [AMBER] Amber FF and Glycam (Fri May 01 2009 - 07:41:35 CDT)
  • Re: [AMBER] Amber FF and Glycam (Thu Apr 30 2009 - 13:36:21 CDT)
  • Re: [AMBER] reg-TMD (Wed Apr 29 2009 - 06:33:40 CDT)
  • Re: [AMBER] reg-TMD (Wed Apr 29 2009 - 05:28:35 CDT)
  • Re: [AMBER] The PDB file was not recognized by Amber, what can i do? (Tue Apr 28 2009 - 17:03:57 CDT)
  • Re: [AMBER] reg-TMD (Tue Apr 28 2009 - 12:48:18 CDT)
  • Re: [AMBER] Error with calculation of the potential energy (Mon Apr 27 2009 - 06:08:47 CDT)
  • Re: [AMBER] Simulated annealing (Fri Apr 24 2009 - 10:44:02 CDT)
  • Re: [AMBER] Simulated annealing (Fri Apr 24 2009 - 09:49:40 CDT)
  • Re: [AMBER] error in output file (Thu Apr 23 2009 - 06:42:02 CDT)
  • Re: [AMBER] Problem with RNA hairpin unwinding in explicit water (Wed Apr 22 2009 - 17:53:33 CDT)
  • Re: [AMBER] Problem with RNA hairpin unwinding in explicit water (Wed Apr 22 2009 - 17:25:47 CDT)
  • Re: [AMBER] help regarding step size (Wed Apr 22 2009 - 06:03:28 CDT)
  • Re: [AMBER] help regarding step size (Wed Apr 22 2009 - 05:13:54 CDT)
  • Re: [AMBER] help- regarding - TMD (Tue Apr 21 2009 - 18:35:42 CDT)
  • Re: [AMBER] Set start timestep for mdcrd traj output (Tue Apr 21 2009 - 18:26:02 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Tue Apr 21 2009 - 16:32:09 CDT)
  • Re: [AMBER] help- regarding - TMD (Tue Apr 21 2009 - 16:23:23 CDT)
  • Re: [AMBER] help- regarding - TMD (Tue Apr 21 2009 - 14:46:41 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Tue Apr 21 2009 - 14:44:03 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Mon Apr 20 2009 - 13:46:41 CDT)
  • Re: [AMBER] help- regarding - TMD (Mon Apr 20 2009 - 10:30:52 CDT)
  • Re: [AMBER] help- regarding - TMD (Mon Apr 20 2009 - 10:12:40 CDT)
  • Re: [AMBER] Atom type error (Sun Apr 19 2009 - 06:06:07 CDT)
  • Re: [AMBER] about saltcon (Sun Apr 19 2009 - 05:49:57 CDT)
  • Re: [AMBER] Backbone restraint (Sat Apr 18 2009 - 06:08:39 CDT)
  • Re: [AMBER] help_me to know the reason (Sat Apr 18 2009 - 05:53:50 CDT)
  • Re: [AMBER] Backbone restraint (Fri Apr 17 2009 - 21:35:26 CDT)
  • Re: [AMBER] Density in MD simulation (Fri Apr 17 2009 - 11:10:51 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Wed Apr 15 2009 - 08:33:00 CDT)
  • Re: [AMBER] problem with explicit solvent in TMD (Mon Apr 13 2009 - 06:41:41 CDT)
  • Re: [AMBER] Sander and multiple residues (Thu Apr 09 2009 - 15:05:23 CDT)
  • Re: [AMBER] Sander and multiple residues (Thu Apr 09 2009 - 14:21:56 CDT)
  • Re: [AMBER] ntwr (Wed Apr 08 2009 - 17:45:57 CDT)
  • Re: [AMBER] ntwr (Wed Apr 08 2009 - 16:47:04 CDT)
  • Re: [AMBER] A question about SMD force constant (Tue Apr 07 2009 - 05:32:09 CDT)
  • Re: Re: [AMBER] sander.MPI parallel run problem (Mon Apr 06 2009 - 06:02:13 CDT)
  • Re: [AMBER] sander.MPI parallel run problem (Mon Apr 06 2009 - 05:09:11 CDT)
  • Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. (Mon Apr 06 2009 - 05:07:09 CDT)
  • Re: [AMBER] Error in trajin and rms (Thu Apr 02 2009 - 14:19:39 CDT)
  • Re: [AMBER] Averaging simulations (Thu Apr 02 2009 - 10:24:28 CDT)
  • Re: [AMBER] explicit ion with igb=1 (Thu Apr 02 2009 - 08:53:54 CDT)
  • Re: [AMBER] Help: An error happened when I calculate mm/pbsa (Thu Apr 02 2009 - 06:19:04 CDT)
  • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 (Wed Apr 01 2009 - 06:01:51 CDT)
  • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 (Tue Mar 31 2009 - 21:24:34 CDT)
  • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 (Tue Mar 31 2009 - 20:41:49 CDT)
  • Re: [AMBER] combine many coord files into trajectory file (Tue Mar 31 2009 - 08:55:58 CDT)
  • Re: [AMBER] .rst file generation problem. (Tue Mar 31 2009 - 06:28:35 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Mon Mar 30 2009 - 06:56:36 CDT)
  • Re: [AMBER] .rst file generation problem. (Mon Mar 30 2009 - 06:30:58 CDT)
  • Re: [AMBER] continuam water (Tue Mar 24 2009 - 08:36:15 CDT)
  • Re: [AMBER] MMGBSA IG Value (Fri Mar 20 2009 - 12:42:14 CDT)
  • Re: [AMBER] MMGBSA IG Value (Fri Mar 20 2009 - 12:25:38 CDT)
  • Re: [AMBER] Help needed in amber parallel installation (Fri Mar 20 2009 - 06:34:31 CDT)
  • Re: [AMBER] problem in running sander (Wed Mar 18 2009 - 10:51:07 CDT)
  • Re: [AMBER] protein protrudes from unit cell (Wed Mar 18 2009 - 10:49:43 CDT)
  • Re: [AMBER] problem in running sander (Wed Mar 18 2009 - 09:58:04 CDT)
  • Re: [AMBER] TMD (Wed Mar 18 2009 - 05:32:14 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen (Tue Mar 17 2009 - 13:53:05 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen (Tue Mar 17 2009 - 13:53:05 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen (Tue Mar 17 2009 - 13:53:05 CDT)
  • Re: [AMBER] temperature rises with igb=1 (Tue Mar 17 2009 - 11:58:05 CDT)
  • Re: [AMBER] temperature rises with igb=1 (Tue Mar 17 2009 - 11:44:32 CDT)
  • Re: [AMBER] minimisation with igb=10 (Mon Mar 16 2009 - 11:04:37 CDT)
  • Re: [AMBER] minimisation with igb=10 (Mon Mar 16 2009 - 10:45:47 CDT)
  • Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in (Mon Mar 16 2009 - 09:32:02 CDT)
  • Re: [AMBER] Problem with REMD (Thu Mar 12 2009 - 06:00:07 CDT)
  • Re: [AMBER] about MD simulation (Wed Mar 11 2009 - 05:56:43 CDT)
  • Re: [AMBER] problem in rmsd (Tue Mar 10 2009 - 05:29:20 CDT)
  • Re: [AMBER] generalized distance restraint (Mon Mar 09 2009 - 11:39:43 CDT)
  • Re: [AMBER] generalized distance restraint (Mon Mar 09 2009 - 10:13:50 CDT)
  • Re: [AMBER] addles segmentation fault (Mon Mar 09 2009 - 06:45:24 CDT)
  • Re: [AMBER] secstruct (Thu Mar 05 2009 - 08:27:18 CST)
  • Re: [AMBER] Regarding leap (Wed Mar 04 2009 - 05:48:30 CST)
  • Re: [AMBER] hydrogen bond (Wed Mar 04 2009 - 05:20:53 CST)
  • Re: [AMBER] Simulated annealing (Thu Feb 26 2009 - 10:27:04 CST)
  • Re: [AMBER] (no subject) (Thu Feb 26 2009 - 10:24:40 CST)
  • Re: [AMBER] Simulated annealing (Thu Feb 26 2009 - 09:55:41 CST)
  • Re: [AMBER] Simulated annealing (Wed Feb 25 2009 - 19:31:30 CST)
  • Re: [AMBER] problem with amber installation (Wed Feb 25 2009 - 05:25:34 CST)
  • Re: [AMBER] reg.targeted molecular dynamics (Wed Feb 25 2009 - 05:21:39 CST)
  • Re: [AMBER] Equilibration Scaling to System Size (Tue Feb 24 2009 - 16:49:10 CST)
  • Re: [AMBER] problem with amber installation (Tue Feb 24 2009 - 05:47:20 CST)
  • Re: [AMBER] PME doesn't work (Mon Feb 23 2009 - 06:08:07 CST)
  • Re: [AMBER] PME doesn't work (Mon Feb 23 2009 - 05:19:27 CST)
  • Re: [AMBER] reg.targeted molecular dynamics (Mon Feb 23 2009 - 05:16:00 CST)
  • Re: [AMBER] reg.targeted molecular dynamics (Sun Feb 22 2009 - 09:06:32 CST)
  • Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation (Sat Feb 21 2009 - 15:33:31 CST)
  • Re: [AMBER] reg.targeted molecular dynamics (Sat Feb 21 2009 - 06:35:05 CST)
  • [AMBER] ACS computational chemistry awards - March 9th deadline (Fri Feb 20 2009 - 10:27:18 CST)
  • Re: [AMBER] Problem with NVT and NPT (Fri Feb 20 2009 - 07:30:26 CST)
  • Re: Re: [AMBER] dipole correlation function (Thu Feb 19 2009 - 11:23:03 CST)
  • Re: [AMBER] secstruct (Thu Feb 19 2009 - 08:45:47 CST)
  • Re: [AMBER] dipole correlation function (Thu Feb 19 2009 - 08:39:16 CST)
  • Re: [AMBER] secstruct (Thu Feb 19 2009 - 07:30:16 CST)
  • Re: [AMBER] distance matrix plot and secondary structure analysis (Thu Feb 19 2009 - 06:48:57 CST)
  • Re: [AMBER] How to constrain the hydrogen bonding distances... (Wed Feb 18 2009 - 08:25:47 CST)
  • Re: [AMBER] IG not change at each restart of NPT simulation (Wed Feb 18 2009 - 08:04:47 CST)
  • Re: Re: [AMBER] MD simulation with a partially flexible system (Wed Feb 18 2009 - 06:35:40 CST)
  • Re: [AMBER] NVT vs NPT (Wed Feb 18 2009 - 06:18:49 CST)
  • Re: [AMBER] protein monomerizartion times and simulation with implicit solvent (Wed Feb 18 2009 - 06:16:00 CST)
  • Re: [AMBER] DM complexation (Tue Feb 17 2009 - 09:59:15 CST)
  • Re: [AMBER] DM complexation (Tue Feb 17 2009 - 09:28:34 CST)
  • Re: [AMBER] MD simulation with a partially flexible system (Tue Feb 17 2009 - 08:45:33 CST)
  • Re: [AMBER] using ptraj (Tue Feb 17 2009 - 08:29:07 CST)
  • Re: [AMBER] using ptraj (Tue Feb 17 2009 - 07:34:33 CST)
  • Re: [AMBER] (no subject) (Tue Feb 17 2009 - 07:10:49 CST)
  • Re: [AMBER] parallel run error (Tue Feb 17 2009 - 06:40:03 CST)
  • Re: [AMBER] using ptraj (Tue Feb 17 2009 - 06:37:15 CST)
  • Re: [AMBER] using ptraj (Mon Feb 16 2009 - 14:41:54 CST)
  • Re: [AMBER] density and volume in NVT ensamble (Mon Feb 16 2009 - 08:30:02 CST)
  • Re: [AMBER] density and volume in NVT ensamble (Mon Feb 16 2009 - 08:04:22 CST)
  • Re: [AMBER] Error running sander.MPI (Mon Feb 16 2009 - 05:51:08 CST)
  • Re: [AMBER] Beginner question (Fri Feb 13 2009 - 15:24:37 CST)
  • Re: [AMBER] array out of bound in Amber10 tests (Fri Feb 13 2009 - 10:38:04 CST)
  • Re: [AMBER] atoms fly out of the box in NVT calculations (Thu Feb 12 2009 - 16:05:10 CST)
  • Re: [AMBER] Optimization problem (Thu Feb 12 2009 - 08:21:28 CST)
  • Re: [AMBER] array out of bound in Amber10 tests (Wed Feb 11 2009 - 10:14:49 CST)
  • Re: [AMBER] Chlorine containing molecule (Wed Feb 11 2009 - 07:48:27 CST)
  • Re: [AMBER] reg . run TMD (Tue Feb 10 2009 - 11:48:22 CST)
  • Re: [AMBER] the output files (Tue Feb 10 2009 - 08:18:34 CST)
  • Re: [AMBER] the output files (Tue Feb 10 2009 - 05:22:04 CST)
  • Re: [AMBER] extract frames from a .mdcrd (Tue Feb 10 2009 - 04:58:12 CST)
  • Re: [AMBER] Irregularity in box during md (Tue Feb 10 2009 - 04:57:02 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 21:10:55 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 18:56:50 CST)
  • Re: [AMBER] hbond analysis (Mon Feb 09 2009 - 12:52:14 CST)
  • Re: [AMBER] the output files (Mon Feb 09 2009 - 07:06:41 CST)
  • Re: [AMBER] Stability of a long NPT md trajectory? (Mon Feb 09 2009 - 06:08:29 CST)
  • Re: [AMBER] extract frames from a .mdcrd (Fri Feb 06 2009 - 05:12:00 CST)
  • Re: [AMBER] parameter files for D-amino acid (Thu Feb 05 2009 - 09:10:18 CST)
  • Re: [AMBER] parameter files for D-amino acid (Thu Feb 05 2009 - 09:06:09 CST)
  • Re: [AMBER] parameter files for D-amino acid (Thu Feb 05 2009 - 07:37:32 CST)
  • Re: [AMBER] Solvation potential and free energies (Thu Feb 05 2009 - 06:33:08 CST)
  • Re: [AMBER] How to build reference coordinate file for targeted MD (Thu Feb 05 2009 - 05:19:12 CST)
  • Re: [AMBER] compiling errors (Wed Feb 04 2009 - 18:35:28 CST)
  • Re: [AMBER] PDB of a specific frame (Wed Feb 04 2009 - 13:52:49 CST)
  • Re: [AMBER] a question about umbrella sampling (US) (Wed Feb 04 2009 - 11:20:46 CST)
  • Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun (Wed Feb 04 2009 - 05:16:34 CST)
  • Re: [AMBER] out error (Tue Feb 03 2009 - 13:18:39 CST)
  • Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun (Tue Feb 03 2009 - 11:39:58 CST)
  • Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun (Tue Feb 03 2009 - 11:17:53 CST)
  • Re: [AMBER] creating a restart file from md.out (Tue Feb 03 2009 - 09:34:44 CST)
  • Re: [AMBER] creating a restart file from md.out (Tue Feb 03 2009 - 07:36:44 CST)
  • Re: [AMBER] creating a restart file from md.out (Tue Feb 03 2009 - 05:30:44 CST)
  • Re: [AMBER] md simulation on parallel PMEMD (Mon Feb 02 2009 - 07:55:44 CST)
  • Re: [AMBER] strip frames from crd file (Mon Feb 02 2009 - 06:12:27 CST)
  • Re: [AMBER] the output files (Sun Feb 01 2009 - 12:11:51 CST)
  • Re: [AMBER] REMD fixed atoms (Sun Feb 01 2009 - 12:00:33 CST)
  • Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? (Sun Feb 01 2009 - 11:55:54 CST)
  • Re: [AMBER] Question on heating for homology based model. (Sun Feb 01 2009 - 11:47:02 CST)
  • Re: [AMBER] Alpha helix plot (Fri Jan 30 2009 - 16:11:10 CST)
  • Re: [AMBER] reg.Targeted molecular dynamics (Wed Jan 28 2009 - 12:01:43 CST)
  • Re: [AMBER] reg: targeted molecular dynamics (Tue Jan 27 2009 - 07:04:57 CST)
  • Re: [AMBER] errors on REMD (Mon Jan 26 2009 - 11:38:39 CST)
  • Re: [AMBER] restraining atoms (Thu Jan 22 2009 - 08:55:35 CST)
  • Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" (Tue Jan 20 2009 - 08:33:55 CST)
  • Re: [AMBER] errors on REMD (Tue Jan 20 2009 - 08:29:07 CST)
  • Re: [AMBER] errors on REMD (Tue Jan 20 2009 - 05:02:06 CST)
  • Re: [AMBER] (no subject) (Sun Jan 18 2009 - 07:08:41 CST)
  • Re: [AMBER] Heat and Equilibrate Hybrid GB solvent? (Fri Jan 16 2009 - 15:21:27 CST)
  • Re: [AMBER] (no subject) (Fri Jan 16 2009 - 12:46:11 CST)
  • Re: [AMBER] (no subject) (Fri Jan 16 2009 - 11:43:26 CST)
  • Re: [AMBER] sander not working (Fri Jan 16 2009 - 09:01:34 CST)
  • Re: [AMBER] restraint of REMD (Fri Jan 16 2009 - 05:57:29 CST)
  • Re: [AMBER] Using a restart file (Thu Jan 15 2009 - 10:45:27 CST)
  • Re: [AMBER] PTRAJ: solvent accessible surface area (Wed Jan 14 2009 - 09:00:59 CST)
  • Re: [AMBER] charges in topology file (Wed Jan 14 2009 - 05:24:52 CST)
  • Re: [AMBER] mm-GBSA from implicit (Sat Jan 10 2009 - 07:25:10 CST)
  • Re: AMBER: RMS plot (Tue Jan 06 2009 - 13:57:50 CST)
  • Re: AMBER: xleap problem (Tue Jan 06 2009 - 13:05:31 CST)
  • Re: AMBER: problem with ptraj image command in Amber 10? (Tue Jan 06 2009 - 11:37:51 CST)
  • Re: AMBER: RMS plot (Fri Jan 02 2009 - 08:08:44 CST)
• Carmen Domene
  • Re: [AMBER] crystal waters (Mon Jan 12 2009 - 14:32:28 CST)
  • [AMBER] crystal waters (Mon Jan 12 2009 - 14:04:24 CST)
• Carra, Claudio (JSC-SK)[USRA]
  • [AMBER] projections of trajectories onto the first 2 principal eigenvectors (Thu Feb 12 2009 - 12:22:20 CST)
  • [AMBER] thermo, entropy by quasiharmonic method (Fri Jan 30 2009 - 15:35:37 CST)
  • [AMBER] principal component vector onto C-alpha (Tue Jan 13 2009 - 14:52:31 CST)
• case
  • Re: [AMBER] implicit_run_error (Fri Nov 20 2009 - 08:53:31 CST)
  • Re: [AMBER] AmberTools 1.3 has a likely release date? (Fri Nov 20 2009 - 08:50:23 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 07:30:54 CST)
  • Re: [AMBER] about divcon (Wed Nov 18 2009 - 10:53:16 CST)
  • Re: [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 22:45:55 CST)
  • Re: [AMBER] Segmentation fault in antechamber (Tue Nov 17 2009 - 22:28:14 CST)
  • Re: [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 14:24:09 CST)
  • Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala (Tue Nov 17 2009 - 11:29:42 CST)
  • Re: [AMBER] Segmentation fault in antechamber (Mon Nov 16 2009 - 09:53:30 CST)
  • Re: [AMBER] is rst file the last structure? (Sun Nov 15 2009 - 08:33:16 CST)
  • Re: [AMBER] reg. GBA (Thu Nov 12 2009 - 07:02:43 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 06:55:18 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Wed Nov 11 2009 - 16:36:59 CST)
  • Re: [AMBER] Creating new residue with tleap. (Wed Nov 11 2009 - 06:37:47 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Tue Nov 10 2009 - 10:28:17 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Mon Nov 09 2009 - 14:41:59 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Mon Nov 09 2009 - 14:02:42 CST)
  • Re: [AMBER] unable to find mopac charges in mopac.out (Mon Nov 09 2009 - 10:47:01 CST)
  • Re: [AMBER] sander.mpi. mdfil: Error unknown flag: sander (Mon Nov 09 2009 - 07:17:23 CST)
  • Re: [AMBER] ff fitting ? (Sun Nov 08 2009 - 11:42:42 CST)
  • Re: [AMBER] varying positional restraints with PMEMD (Sun Nov 08 2009 - 11:37:53 CST)
  • Re: [AMBER] the problem of nucgen.dat (Sun Nov 08 2009 - 10:19:03 CST)
  • Re: [AMBER] Low frequency Raman spectra (Sat Nov 07 2009 - 09:02:02 CST)
  • Re: [AMBER] the problem of nucgen.dat (Sat Nov 07 2009 - 08:51:57 CST)
  • Re: [AMBER] unable to find mopac charges in mopac.out (Sat Nov 07 2009 - 07:59:43 CST)
  • Re: [AMBER] zeros in excluded atom list in topology file (Fri Nov 06 2009 - 16:44:04 CST)
  • Re: [AMBER] Antechamber and Parmchk problems (Wed Nov 04 2009 - 09:26:03 CST)
  • Re: [AMBER] 60 giga output file .mdcrd file (Wed Nov 04 2009 - 06:17:47 CST)
  • Re: [AMBER] errors on leap for a RNA+Adenine pdb structure (Wed Nov 04 2009 - 06:17:53 CST)
  • Re: [AMBER] Some queries about pH simulation (Tue Nov 03 2009 - 05:30:07 CST)
  • Re: [AMBER] SPC/E HOH angle (Fri Oct 30 2009 - 07:51:41 CDT)
  • Re: [AMBER] Is it the way to do simulation in vacuum (Fri Oct 30 2009 - 07:49:46 CDT)
  • Re: [AMBER] Parallel sander & polarisability (Thu Oct 29 2009 - 12:02:28 CDT)
  • Re: [AMBER] building quadruplex with NAB (Tue Oct 27 2009 - 21:23:29 CDT)
  • Re: [AMBER] Preparing distance restraints (Mon Oct 26 2009 - 16:26:26 CDT)
  • Re: [AMBER] units of measures (Thu Oct 22 2009 - 07:42:11 CDT)
  • Re: [AMBER] Circular RNA topology file (Wed Oct 21 2009 - 14:06:17 CDT)
  • Re: [AMBER] "extra points" incompatibility with pmemd (Wed Oct 21 2009 - 07:22:28 CDT)
  • Re: [AMBER] can I run EVB in other ensemble than NVE? (Tue Oct 20 2009 - 12:08:58 CDT)
  • Re: [AMBER] RDC and alignment tensor (Tue Oct 20 2009 - 07:24:45 CDT)
  • Re: [AMBER] Error: unable to find mopac charges in mopac.out (Tue Oct 20 2009 - 06:45:59 CDT)
  • Re: [AMBER] Re: RDC and alignment tensor (Mon Oct 19 2009 - 13:22:47 CDT)
  • Re: [AMBER] RDC and alignment tensor (Mon Oct 19 2009 - 12:36:16 CDT)
  • Re: [AMBER] why is TAUTP scaled by "e" ? (Fri Oct 16 2009 - 08:30:53 CDT)
  • Re: [AMBER] Re: AMBER: periodic bondary condition (Fri Oct 16 2009 - 08:13:49 CDT)
  • Re: [AMBER] AMBER 11. (Thu Oct 15 2009 - 11:52:51 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Thu Oct 15 2009 - 08:45:42 CDT)
  • Re: [AMBER] part of the protein escaped from the water box (Thu Oct 15 2009 - 06:40:53 CDT)
  • Re: [AMBER] installation of Amber on OSX (Wed Oct 14 2009 - 17:10:04 CDT)
  • Re: [AMBER] nab normal mode analysis has imaginary frequencies (Wed Oct 14 2009 - 13:34:05 CDT)
  • Re: [AMBER] How to add a hydrogen to the residue? (Wed Oct 14 2009 - 06:51:08 CDT)
  • Re: [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber (Wed Oct 14 2009 - 06:37:35 CDT)
  • Re: [AMBER] Computing an Hessian matrix using NAB (Tue Oct 13 2009 - 07:13:42 CDT)
  • Re: [AMBER] Simulating transmembrane protein. (Mon Oct 12 2009 - 16:55:42 CDT)
  • Re: [AMBER] xleap-does not work (Sat Oct 10 2009 - 08:53:57 CDT)
  • Re: [AMBER] xleap-does not work (Sat Oct 10 2009 - 07:27:01 CDT)
  • Re: [AMBER] The -c option in Sander (Fri Oct 09 2009 - 20:54:05 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 09 2009 - 15:02:06 CDT)
  • Re: [AMBER] Combine and rename group of residues in xleap (Fri Oct 09 2009 - 08:32:57 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Fri Oct 09 2009 - 08:03:02 CDT)
  • Re: [AMBER] DG improper torsion problem, two missing parameters (Fri Oct 09 2009 - 06:46:34 CDT)
  • Re: [AMBER] The hydrophobic contribution (Thu Oct 08 2009 - 07:41:28 CDT)
  • Re: [AMBER] RMSD vs time and RMSD vs residues (Fri Oct 02 2009 - 14:12:23 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 02 2009 - 13:56:34 CDT)
  • Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac (Fri Oct 02 2009 - 08:19:11 CDT)
  • Re: [AMBER] minimization error (Fri Oct 02 2009 - 07:00:52 CDT)
  • Re: Re: [AMBER] No restrt file (Wed Sep 30 2009 - 07:06:47 CDT)
  • Re: [AMBER] No restrt file (Wed Sep 30 2009 - 05:29:32 CDT)
  • Re: [AMBER] Problem in compiling AMBER9 in parallel ! (Tue Sep 29 2009 - 13:08:41 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 11:50:19 CDT)
  • Re: [AMBER] Attaching a ligand to a protein residue. (Sat Sep 26 2009 - 09:23:18 CDT)
  • Re: [AMBER] pmemd and internal dielectric (Fri Sep 25 2009 - 16:59:56 CDT)
  • Re: [AMBER] Ewald error estimated (Fri Sep 25 2009 - 10:15:31 CDT)
  • Re: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex (Thu Sep 24 2009 - 17:13:39 CDT)
  • Re: [AMBER] ambertools and Snow Leopard 64 bits kernel (Wed Sep 23 2009 - 15:26:16 CDT)
  • Re: [AMBER] problem building sander.apbs (Tue Sep 22 2009 - 14:12:50 CDT)
  • Re: [AMBER] Cygwin Home Directory (Mon Sep 21 2009 - 12:14:59 CDT)
  • Re: [AMBER] problem building sander.apbs (Mon Sep 21 2009 - 09:38:20 CDT)
  • Re: [AMBER] problem building sander.apbs (Mon Sep 21 2009 - 06:39:41 CDT)
  • Re: [AMBER] combining MD runs for post-MD analysis (Sun Sep 20 2009 - 20:35:08 CDT)
  • Re: [AMBER] warning in dispatchToken (Sun Sep 20 2009 - 08:14:49 CDT)
  • Re: [AMBER] Cygwin Home Directory (Sat Sep 19 2009 - 17:11:57 CDT)
  • Re: [AMBER] database (Fri Sep 18 2009 - 21:46:39 CDT)
  • Re: [AMBER] PROBLEM WITH CHCL3BOX pdb (Fri Sep 18 2009 - 17:01:23 CDT)
  • Re: [AMBER] database (Fri Sep 18 2009 - 12:23:08 CDT)
  • Re: [AMBER] PROBLEM WITH CHCL3BOX pdb (Fri Sep 18 2009 - 08:26:40 CDT)
  • Re: [AMBER] LINMIN failure notice (Fri Sep 18 2009 - 06:38:33 CDT)
  • Re: [AMBER] database (Thu Sep 17 2009 - 17:23:30 CDT)
  • Re: [AMBER] NAB syntax (Thu Sep 17 2009 - 10:22:29 CDT)
  • Re: [AMBER] install ambertools (Thu Sep 17 2009 - 08:40:28 CDT)
  • Re: [AMBER] loading RNA sequence in xleap (Thu Sep 17 2009 - 07:13:38 CDT)
  • Re: [AMBER] antechamber error (Wed Sep 16 2009 - 13:43:56 CDT)
  • Re: [AMBER] database (Wed Sep 16 2009 - 11:53:56 CDT)
  • Re: [AMBER] RDC analysis: "No restraint defined" (Wed Sep 16 2009 - 11:47:41 CDT)
  • Re: [AMBER] database (Wed Sep 16 2009 - 10:26:24 CDT)
  • Re: [AMBER] input file / skinnb (Wed Sep 16 2009 - 06:56:01 CDT)
  • Re: Re: [AMBER] Error in minimal (Tue Sep 15 2009 - 17:15:06 CDT)
  • Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? (Tue Sep 15 2009 - 17:12:25 CDT)
  • Re: [AMBER] makeDIST_RST: no map function (Tue Sep 15 2009 - 09:38:23 CDT)
  • Re: [AMBER] Error in minimal (Tue Sep 15 2009 - 06:56:02 CDT)
  • Re: [AMBER] Ki and G (Mon Sep 14 2009 - 15:24:05 CDT)
  • Re: [AMBER] Ki and G (Mon Sep 14 2009 - 12:23:49 CDT)
  • Re: [AMBER] how to calculate correct RMSF? (Mon Sep 14 2009 - 07:33:29 CDT)
  • Re: [AMBER] error xleap: XaLeap_wcl is empty (Mon Sep 14 2009 - 07:02:12 CDT)
  • Re: [AMBER] How to prepare the coordinate and toplogy files in leap ? (Mon Sep 14 2009 - 06:56:08 CDT)
  • Re: [AMBER] re: charge interaction (Sun Sep 13 2009 - 16:37:55 CDT)
  • Re: [AMBER] What is the Optimum Ph for solvating a protein (Sun Sep 13 2009 - 16:19:24 CDT)
  • Re: [AMBER] re: charge interaction (Sun Sep 13 2009 - 16:13:19 CDT)
  • Re: [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 (Sat Sep 12 2009 - 09:17:16 CDT)
  • Re: [AMBER] dihedral force calculation (Sat Sep 12 2009 - 09:04:34 CDT)
  • Re: [AMBER] charge consideration (Sat Sep 12 2009 - 08:59:56 CDT)
  • Re: [AMBER] "nan" in gaussian input files generated by antechamber (Sat Sep 12 2009 - 08:55:14 CDT)
  • Re: [AMBER] amoeba.prm problem? (Sat Sep 12 2009 - 08:46:52 CDT)
  • Re: [AMBER] What is the unit of RMSF? (Sat Sep 12 2009 - 08:37:42 CDT)
  • Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? (Fri Sep 11 2009 - 14:54:39 CDT)
  • Re: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command (Thu Sep 10 2009 - 21:04:53 CDT)
  • Re: [AMBER] Solvate in an alkaline solution (Thu Sep 10 2009 - 07:05:44 CDT)
  • Re: [AMBER] amoeba.prm problem? (Wed Sep 09 2009 - 14:17:39 CDT)
  • Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? (Wed Sep 09 2009 - 13:50:13 CDT)
  • Re: [AMBER] parameterization of protein-ligand complex (Wed Sep 09 2009 - 11:39:05 CDT)
  • Re: [AMBER] gaff.dat questions (Wed Sep 09 2009 - 09:16:23 CDT)
  • Re: [AMBER] PK zero for specific dihedral and parmchk (Wed Sep 09 2009 - 06:32:51 CDT)
  • Re: [AMBER] Leap warning (Wed Sep 09 2009 - 06:31:36 CDT)
  • Re: [AMBER] loading a following attached protein in amber 10 (Tue Sep 08 2009 - 12:27:47 CDT)
  • Re: [AMBER] No sp2 improper torsion term for NB-CA-CB-CB (Tue Sep 08 2009 - 07:58:33 CDT)
  • Re: [AMBER] loading PDB of a RNA sequence (Tue Sep 08 2009 - 06:38:34 CDT)
  • Re: 回å¤�： [AMBER] Problem about adding a small residue to DNA (Sun Sep 06 2009 - 07:30:23 CDT)
  • Re: [AMBER] Antechamber generate a prep file in a wrong order... (Sun Sep 06 2009 - 07:26:02 CDT)
  • Re: 回å¤�： [AMBER] Problem about adding a small residue to DNA (Fri Sep 04 2009 - 15:37:23 CDT)
  • Re: [AMBER] Problem about adding a small residue to DNA (Fri Sep 04 2009 - 14:32:53 CDT)
  • Re: [AMBER] Kinetics (Fri Sep 04 2009 - 14:29:24 CDT)
  • Re: [AMBER] prep file (Fri Sep 04 2009 - 09:09:06 CDT)
  • Re: [AMBER] antechamber bug: output of incorrect bond character (Thu Sep 03 2009 - 11:29:03 CDT)
  • Re: [AMBER] antechamber bug: output of incorrect bond character (Thu Sep 03 2009 - 06:26:19 CDT)
  • Re: [AMBER] how to deal with aromatic nitro group with antechamber (Wed Sep 02 2009 - 21:15:14 CDT)
  • Re: [AMBER] antechamber bug: output of incorrect bond character (Wed Sep 02 2009 - 20:53:37 CDT)
  • Re: [AMBER] How to consider the off centre charges (Wed Sep 02 2009 - 10:50:12 CDT)
  • Re: [AMBER] What is dual topology (Wed Sep 02 2009 - 10:48:51 CDT)
  • Re: [AMBER] Simulation short peptide and protein interaction (Wed Sep 02 2009 - 07:15:06 CDT)
  • Re: [AMBER] Creating new counterions (Tue Sep 01 2009 - 15:03:48 CDT)
  • Re: [AMBER] How to remove Hydrogen using ptraj (Tue Sep 01 2009 - 12:19:51 CDT)
  • Re: [AMBER] cpin error (Tue Sep 01 2009 - 07:23:04 CDT)
  • Re: [AMBER] momentum in MD simulation (Tue Sep 01 2009 - 06:48:52 CDT)
  • Re: [AMBER] Docking with Amber (Mon Aug 31 2009 - 19:58:49 CDT)
  • Re: [AMBER] antechamber bug report (Mon Aug 31 2009 - 12:36:33 CDT)
  • Re: [AMBER] ATP/GTP parameters (Mon Aug 31 2009 - 07:41:22 CDT)
  • Re: [AMBER] divcon question (Mon Aug 31 2009 - 07:34:14 CDT)
  • Re: [AMBER] RDC import from PALES (Fri Aug 28 2009 - 07:01:30 CDT)
  • Re: [AMBER] Chirality error in pdb (Fri Aug 28 2009 - 06:33:41 CDT)
  • Re: [AMBER] Chirality error in pdb (Wed Aug 26 2009 - 06:52:18 CDT)
  • Re: [AMBER] Single Adenine (Wed Aug 26 2009 - 06:48:36 CDT)
  • Re: [AMBER] ZPVE simple question (Wed Aug 26 2009 - 06:41:27 CDT)
  • Re: [AMBER] Single Adenine (Wed Aug 26 2009 - 06:36:09 CDT)
  • Re: [AMBER] problem compiling amber tools with gcc-4.4.1 (Tue Aug 25 2009 - 07:52:35 CDT)
  • Re: [AMBER] ambertools test faied (Tue Aug 25 2009 - 06:39:16 CDT)
  • Re: [AMBER] Meaning of GMAX (Mon Aug 24 2009 - 06:44:34 CDT)
  • [AMBER] update on am1-bcc charge problem in antechamber (Fri Aug 21 2009 - 11:32:30 CDT)
  • Re: [AMBER] RESP charges of Fe4S4 cluster (Fri Aug 21 2009 - 09:13:23 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 06:18:52 CDT)
  • Re: [AMBER] Distance restraint and periodic boundary conditions (Wed Aug 19 2009 - 19:53:15 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 18:55:52 CDT)
  • Re: [AMBER] Distance restraint and periodic boundary conditions (Tue Aug 18 2009 - 21:02:45 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Mon Aug 17 2009 - 21:56:17 CDT)
  • Re: [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues (Sun Aug 16 2009 - 08:14:14 CDT)
  • Re: [AMBER] Can I do DNA bending with AMBER? (Sun Aug 16 2009 - 08:13:05 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 10:40:51 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 08:49:44 CDT)
  • Re: [AMBER] Strange QM/MM Divcon - help me out (Thu Aug 13 2009 - 10:52:34 CDT)
  • Re: [AMBER] NAB optimization (Thu Aug 13 2009 - 08:56:28 CDT)
  • Re: [AMBER] box problem (Thu Aug 13 2009 - 06:50:54 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Thu Aug 13 2009 - 06:46:02 CDT)
  • Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB (Wed Aug 12 2009 - 14:57:33 CDT)
  • Re: [AMBER] parmchk problem (Tue Aug 11 2009 - 08:51:57 CDT)
  • Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Tue Aug 11 2009 - 06:54:43 CDT)
  • Re: [AMBER] Regarding Minimization maxcyc (Mon Aug 10 2009 - 09:43:00 CDT)
  • Re: [AMBER] Re: antechamber am1-bcc issues (Sat Aug 08 2009 - 14:20:44 CDT)
  • [AMBER] Re: antechamber am1-bcc issues (Fri Aug 07 2009 - 18:54:38 CDT)
  • Re: [AMBER] (no subject) (Fri Aug 07 2009 - 18:54:18 CDT)
  • Re: [AMBER] Error in equilibration: file _ew_box.f (Fri Aug 07 2009 - 17:34:29 CDT)
  • Re: [AMBER] pmemd (Fri Aug 07 2009 - 10:18:52 CDT)
  • Re: [AMBER] Extreme optimization problems (Thu Aug 06 2009 - 10:51:23 CDT)
  • Re: [AMBER] ptraj failure to parse psf input (Wed Aug 05 2009 - 12:32:00 CDT)
  • Re: [AMBER] What is the meaning of IED values for PCA analysis? (Wed Aug 05 2009 - 11:39:30 CDT)
  • Re: [AMBER] parmchk problem (Wed Aug 05 2009 - 11:36:27 CDT)
  • Re: [AMBER] problem of mm_pbsa (Wed Aug 05 2009 - 10:42:56 CDT)
  • Re: [AMBER] Showing error in energy minimization (Sun Aug 02 2009 - 09:25:04 CDT)
  • Re: [AMBER] Normal mode analysis of water (Thu Jul 30 2009 - 09:11:23 CDT)
  • Re: [AMBER] error in antechamber (Mon Jul 27 2009 - 23:23:54 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Mon Jul 27 2009 - 12:05:48 CDT)
  • Re: [AMBER] Output forces in Sander (Mon Jul 27 2009 - 10:11:30 CDT)
  • Re: [AMBER] Re: bugfix 10 failing for ambertools1.2 (Mon Jul 27 2009 - 10:03:24 CDT)
  • Re: [AMBER] thymidine monophosphate parametrization (Mon Jul 27 2009 - 09:47:38 CDT)
  • Re: [AMBER] Re: Ambertools 1.2 installation error (Mon Jul 27 2009 - 09:38:28 CDT)
  • Re: [AMBER] cpin error (Fri Jul 24 2009 - 14:41:00 CDT)
  • Re: [AMBER] setting AMBERHOME (Wed Jul 22 2009 - 21:15:34 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Wed Jul 22 2009 - 21:15:50 CDT)
  • Re: [AMBER] Steered MD.....SHAKE error!! (Fri Jul 17 2009 - 07:01:03 CDT)
  • Re: [AMBER] diffusion coeficients (Fri Jul 17 2009 - 06:59:41 CDT)
  • Re: [AMBER] File conversion for from Amber to Charmm (Fri Jul 17 2009 - 06:53:06 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Fri Jul 17 2009 - 06:41:39 CDT)
  • Re: [AMBER] Umbrella Sampling (Thu Jul 16 2009 - 15:03:29 CDT)
  • Re: [AMBER] query regarding FE4S4 (Thu Jul 16 2009 - 06:45:06 CDT)
  • Re: [AMBER] carbonic anhydrase (CA) simulation (Thu Jul 16 2009 - 06:36:17 CDT)
  • Re: [AMBER] different results for antechamber/mopac for the same input (Thu Jul 16 2009 - 06:30:08 CDT)
  • Re: [AMBER] Please help me out (Wed Jul 15 2009 - 14:55:21 CDT)
  • Re: [AMBER] Equilibrium water density (Wed Jul 15 2009 - 14:53:54 CDT)
  • Re: [AMBER] Could not find bond parameter for O2 - ca (Tue Jul 14 2009 - 22:28:02 CDT)
  • Re: [AMBER] Counterion release and Free energy of binding ? (Tue Jul 14 2009 - 22:10:18 CDT)
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 13:10:46 CDT)
  • [AMBER] Re: reference re. size of dt (Mon Jul 13 2009 - 11:56:46 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 11:51:46 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 11:29:06 CDT)
  • Re: [AMBER] Peptide bond broken (Sun Jul 12 2009 - 21:35:35 CDT)
  • Re: [AMBER] ligand/protein minimization (Sun Jul 12 2009 - 21:32:29 CDT)
  • Re: [AMBER] amber dihedral format (Sun Jul 12 2009 - 16:49:12 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 13:54:44 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 11:48:44 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 10:16:17 CDT)
  • Re: [AMBER] charged or not (Thu Jul 09 2009 - 10:10:14 CDT)
  • Re: [AMBER] ff parameters (Thu Jul 09 2009 - 08:23:31 CDT)
  • Re: [AMBER] amber10 installation problem (Thu Jul 09 2009 - 07:38:01 CDT)
  • Re: [AMBER] amber10 installation problem (Wed Jul 08 2009 - 06:56:19 CDT)
  • Re: [AMBER] Installing of amber10 (Wed Jul 08 2009 - 06:42:02 CDT)
  • Re: [AMBER] H-bond vs. VdW (Mon Jul 06 2009 - 12:29:49 CDT)
  • Re: [AMBER] need charges of FE-S cluster (Mon Jul 06 2009 - 07:35:19 CDT)
  • Re: [AMBER] Boundary Condition Problem (Sat Jul 04 2009 - 08:45:45 CDT)
  • Re: [AMBER] default integration scheme in 7 vs. 10 (Thu Jul 02 2009 - 06:37:17 CDT)
  • Re: [AMBER] Steps for NMR structure minimization (Wed Jul 01 2009 - 07:48:13 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:04:02 CDT)
  • Re: [AMBER] Fe-S topology (Tue Jun 30 2009 - 12:45:27 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Tue Jun 30 2009 - 11:19:00 CDT)
  • Re: [AMBER] Compiling and running NAB programs in parallel using MPI (Tue Jun 30 2009 - 11:02:57 CDT)
  • Re: [AMBER] Compiling and running NAB programs in parallel using MPI (Mon Jun 29 2009 - 07:19:10 CDT)
  • Re: [AMBER] RESP (Mon Jun 29 2009 - 06:52:19 CDT)
  • Re: [AMBER] explicit solvent NMR refinement (Sun Jun 28 2009 - 08:19:11 CDT)
  • Re: [AMBER] NAB memory (Fri Jun 26 2009 - 13:42:03 CDT)
  • Re: [AMBER] Compiling and running NAB programs in parallel using MPI (Fri Jun 26 2009 - 08:19:04 CDT)
  • Re: [AMBER] Re: Error on equilibriation of Amber10 (Fri Jun 26 2009 - 07:17:42 CDT)
  • Re: [AMBER] error in tleap of AMBER 10 (Fri Jun 26 2009 - 07:09:58 CDT)
  • Re: [AMBER] PCA for CA of specific resiudes (Thu Jun 25 2009 - 07:27:01 CDT)
  • Re: [AMBER] setting atomic radii for GB version 7 (Thu Jun 25 2009 - 07:20:36 CDT)
  • Re: [AMBER] Re: Error on equilibriation of Amber10 (Thu Jun 25 2009 - 07:07:20 CDT)
  • Re: [AMBER] error in tleap of AMBER 10 (Thu Jun 25 2009 - 06:54:47 CDT)
  • Re: [AMBER] NAB memory increase (Thu Jun 25 2009 - 06:33:03 CDT)
  • Re: [AMBER] Half charge reported during NN ? (Wed Jun 24 2009 - 12:31:45 CDT)
  • Re: [AMBER] Trying to patch amber 9 (Wed Jun 24 2009 - 09:58:48 CDT)
  • Re: [AMBER] re: net charge (Tue Jun 23 2009 - 14:22:28 CDT)
  • Re: [AMBER] net charge (Tue Jun 23 2009 - 09:34:07 CDT)
  • Re: [AMBER] Compiling amber 9 with openMPI (Tue Jun 23 2009 - 09:13:18 CDT)
  • [AMBER] Re: Regd: Fe4S4 (Mon Jun 22 2009 - 13:39:57 CDT)
  • Re: [AMBER] max atoms for antechamber (Mon Jun 22 2009 - 07:48:43 CDT)
  • Re: [AMBER] About the "FATAL: Atom err"! (Mon Jun 22 2009 - 06:47:59 CDT)
  • Re: [AMBER] Atom Type List (Mon Jun 22 2009 - 06:38:24 CDT)
  • Re: [AMBER] Amber10 Parallel Installation (Sat Jun 20 2009 - 17:04:14 CDT)
  • Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9 (Sat Jun 20 2009 - 13:31:40 CDT)
  • Re: [AMBER] Water-molecules (Sun Apr 26 2009 - 17:35:36 CDT)
  • Re: [AMBER] amber tools installation (Mon Mar 30 2009 - 11:28:38 CDT)
  • Re: [AMBER] mm_pbsa problem (Mon Mar 30 2009 - 07:48:05 CDT)
  • Re: [AMBER] Problem with "Atom does not have a type" (Mon Mar 30 2009 - 07:46:59 CDT)
  • Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 (Wed Mar 25 2009 - 13:58:02 CDT)
  • Re: [AMBER] create new crd files from transformed coordinates (Wed Mar 25 2009 - 07:26:29 CDT)
  • Re: [AMBER] pmemd compile error.... (Tue Mar 24 2009 - 07:12:46 CDT)
• Casey,Richard
  • [AMBER] Can we use AMBER? (Thu Jan 08 2009 - 11:25:57 CST)
  • [AMBER] Can we use Amber? (Thu Jan 08 2009 - 11:16:50 CST)
• Catein Catherine
  • RE: [AMBER] how to calculate correct RMSF? (Mon Sep 14 2009 - 19:57:20 CDT)
  • [AMBER] how to calculate correct RMSF? (Mon Sep 14 2009 - 06:21:52 CDT)
  • [AMBER] What is the unit of RMSF? (Sat Sep 12 2009 - 03:13:02 CDT)
  • [AMBER] Enquiry about MM/GBSA output file. (Tue Sep 08 2009 - 02:14:19 CDT)
  • [AMBER] MM-GBAS decomp error (Fri Sep 04 2009 - 05:29:35 CDT)
  • RE: [AMBER] Question regarding PCA analysis. (Thu Sep 03 2009 - 21:55:42 CDT)
  • [AMBER] How to find water-mediated hydrogen bond? (Wed Sep 02 2009 - 09:10:37 CDT)
  • [AMBER] Question regarding PCA analysis. (Tue Sep 01 2009 - 22:53:10 CDT)
  • [AMBER] How to use AMBER 10 for PCA analysis. (Tue Sep 01 2009 - 10:30:56 CDT)
  • RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? (Thu Aug 27 2009 - 05:02:37 CDT)
  • RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? (Thu Aug 27 2009 - 00:58:27 CDT)
  • RE: [AMBER] Re: question_on_MMPBSA (Thu Aug 27 2009 - 00:55:59 CDT)
  • [AMBER] how much % of the total protein motion are described by the first eigenvector? (Wed Aug 26 2009 - 04:05:17 CDT)
  • [AMBER] How to strip water for MM/GBSA calculations? (Fri Aug 21 2009 - 05:38:27 CDT)
  • RE: [AMBER] Conference or workshop on AMBER? Thank you. (Tue Aug 18 2009 - 01:44:45 CDT)
  • [AMBER] Is it the correct procedures to strip water for MM/GBSA calculations? (Tue Aug 18 2009 - 00:06:18 CDT)
  • RE: [AMBER] Conference or workshop on AMBER? (Mon Aug 17 2009 - 21:30:04 CDT)
  • RE: [AMBER] Can I do DNA bending with AMBER? (Mon Aug 17 2009 - 01:00:08 CDT)
  • RE: [AMBER] What is the parameters for Mg2+? (Mon Aug 17 2009 - 00:59:23 CDT)
  • RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Mon Aug 17 2009 - 00:58:49 CDT)
  • [AMBER] Conference or workshop on AMBER? (Mon Aug 17 2009 - 00:56:41 CDT)
  • [AMBER] What is the parameters for Mg2+? (Sat Aug 15 2009 - 23:21:46 CDT)
  • [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues (Sat Aug 15 2009 - 23:18:28 CDT)
  • [AMBER] Can I do DNA bending with AMBER? (Sat Aug 15 2009 - 23:15:26 CDT)
  • RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Sat Aug 15 2009 - 23:12:42 CDT)
  • RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Sat Aug 15 2009 - 21:45:34 CDT)
  • RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Thu Aug 13 2009 - 22:38:02 CDT)
  • RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Wed Aug 12 2009 - 21:23:40 CDT)
  • [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? (Tue Aug 11 2009 - 06:10:09 CDT)
  • [AMBER] What is the meaning of IED values for PCA analysis? (Mon Aug 03 2009 - 09:30:15 CDT)
  • RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Sun Aug 02 2009 - 22:47:07 CDT)
  • [AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues? (Sun Aug 02 2009 - 22:45:19 CDT)
  • [AMBER] What is the meaning of "rms first *" (Thu Jul 30 2009 - 22:49:17 CDT)
  • RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 22:46:49 CDT)
  • [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 05:37:49 CDT)
  • [AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?) (Wed Jul 29 2009 - 04:39:02 CDT)
  • [AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all) (Wed Jul 29 2009 - 00:50:50 CDT)
  • [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 04:30:22 CDT)
  • [AMBER] RE: MM-PBSA test jobs error messages (Tue Jul 28 2009 - 04:24:31 CDT)
  • [AMBER] MM-PBSA cannot finish without error message. (Thu Jul 23 2009 - 04:57:00 CDT)
  • [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation? (Wed Jul 08 2009 - 04:45:41 CDT)
  • [AMBER] correlation motion at production simulation period still changing. Is it normal? (Mon Jun 22 2009 - 04:26:40 CDT)
  • [AMBER] PTRAJ, rms for separated residues. (Mon Jun 22 2009 - 04:20:36 CDT)
  • RE: [AMBER] Re: force units (Thu Jun 18 2009 - 09:01:40 CDT)
  • [AMBER] ptraj correlation (Thu Jun 18 2009 - 08:47:01 CDT)
  • [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? (Mon Jun 15 2009 - 05:04:53 CDT)
  • RE: [AMBER] Is the result of sander same as that of pmemd? (Fri Jun 12 2009 - 21:55:10 CDT)
  • [AMBER] Is the result of sander same as that of pmemd? (Fri Jun 12 2009 - 09:04:38 CDT)
  • [AMBER] ptraj "image" "center" commands (Thu Jun 11 2009 - 04:13:38 CDT)
  • [AMBER] ptraj amber 10 file. (Wed Jun 10 2009 - 11:02:32 CDT)
  • RE: [AMBER] PDMED (Tue Jun 09 2009 - 01:18:59 CDT)
  • [AMBER] PDMED (Mon Jun 08 2009 - 23:28:58 CDT)
  • [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? (Mon Jun 08 2009 - 10:16:23 CDT)
  • RE: [AMBER] Error message? INFO: Old style inpcrd file read (Sun Jun 07 2009 - 22:55:28 CDT)
  • [AMBER] What is the parallel efficiency of amber10 (Sun Jun 07 2009 - 22:19:37 CDT)
  • [AMBER] Error message? INFO: Old style inpcrd file read (Sun Jun 07 2009 - 22:11:27 CDT)
  • RE: [AMBER] parameter for dihedral angle (Sun Jun 07 2009 - 22:08:17 CDT)
  • [AMBER] AMBER 10: sleap diff errors? (Thu Jun 04 2009 - 00:37:35 CDT)
  • [AMBER] AMBER10: error message mdfil flag..... (Wed Jun 03 2009 - 09:14:50 CDT)
  • [AMBER] AMBER for dual core processor? (Thu May 07 2009 - 03:05:17 CDT)
  • [AMBER] Error in parallel run (Wed May 06 2009 - 21:46:02 CDT)
  • [AMBER] Error message in "make test.sander" Is amber compatible with dual processors? (Wed May 06 2009 - 08:08:49 CDT)
  • RE: [AMBER] Error message in "make test.sander" (Wed May 06 2009 - 01:58:04 CDT)
  • RE: [AMBER] Error message in "make test.sander" (Wed May 06 2009 - 00:40:54 CDT)
  • [AMBER] Error message in "make test.sander" (Tue May 05 2009 - 21:52:26 CDT)
  • RE: [AMBER] QM/MM (Tue May 05 2009 - 21:48:44 CDT)
  • [AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"? (Mon May 04 2009 - 10:16:08 CDT)
  • RE: [AMBER] Error message for tutorial 1 (run in parallel) (Mon May 04 2009 - 08:31:05 CDT)
  • [AMBER] Script for parallel runs 2 (Mon May 04 2009 - 04:41:58 CDT)
  • [AMBER] Script for parallel runs (Mon May 04 2009 - 04:17:42 CDT)
  • [AMBER] Error message for tutorial 1 (run in parallel) (Mon May 04 2009 - 04:05:17 CDT)
  • RE: [AMBER] ERROR In Restraint file. (Tue Apr 28 2009 - 18:32:26 CDT)
  • [AMBER] ERROR In Restraint file. (Tue Apr 28 2009 - 10:27:18 CDT)
  • [AMBER] ERROR In Restraint file. (Tue Apr 28 2009 - 10:12:34 CDT)
  • [AMBER] AMBER installation : compilation error (Wed Mar 04 2009 - 20:53:54 CST)
  • [AMBER] How to restart the umbrella sampling jobs? (Mon Mar 02 2009 - 23:52:16 CST)
  • [AMBER] Scientific Linux 5.2 (Wed Feb 18 2009 - 01:13:23 CST)
  • RE: [AMBER] reaction coordinates (Wed Jan 14 2009 - 23:25:31 CST)
  • [AMBER] PTRAJ: solvent accessible surface area (Wed Jan 14 2009 - 01:32:15 CST)
  • [AMBER] mm-GBSA from implicit (Fri Jan 09 2009 - 21:13:28 CST)
  • [AMBER] implicit and explicit simulation: salt effect (Fri Jan 09 2009 - 21:03:35 CST)
• cc cc
  • RE: [AMBER] Any tutorial on the proper way to merge a ligand and protein? (Fri Sep 11 2009 - 13:16:55 CDT)
  • RE: [AMBER] parameterization of protein-ligand complex (Wed Sep 09 2009 - 12:44:17 CDT)
  • RE: [AMBER] parameterization of protein-ligand complex (Wed Sep 09 2009 - 12:41:52 CDT)
  • [AMBER] parameterization of protein-ligand complex (Wed Sep 09 2009 - 11:29:07 CDT)
• Cen Gao
  • Re: [AMBER] GAFF atom type question (Sun Jun 14 2009 - 23:12:19 CDT)
  • Re: [AMBER] GAFF atom type question (Thu Jun 11 2009 - 19:31:25 CDT)
  • [AMBER] GAFF atom type question (Thu Jun 11 2009 - 08:36:52 CDT)
  • [AMBER] GAFF atom type question (Wed Jun 10 2009 - 10:49:00 CDT)
  • Re: [AMBER] Input file of the second stage RESP fitting (Tue Mar 17 2009 - 16:24:24 CDT)
  • [AMBER] Input file of the second stage RESP fitting (Mon Mar 16 2009 - 23:29:17 CDT)
  • [AMBER] Divcon or Mopac (Tue Jan 13 2009 - 17:54:33 CST)
• Cenk \(Jenk\) Andac
  • Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis (Mon Oct 19 2009 - 16:44:42 CDT)
  • Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis (Sat Oct 17 2009 - 02:02:20 CDT)
  • [AMBER] MMTSB cluster analysis versus ptraj cluster analysis (Fri Oct 16 2009 - 07:19:24 CDT)
  • Re: [AMBER] MM - PBSA problem (Mon Jan 26 2009 - 10:20:25 CST)
  • Re: [AMBER] MM - PBSA problem (Mon Jan 26 2009 - 06:14:52 CST)
  • Re: [AMBER] MM - PBSA problem (Sun Jan 25 2009 - 14:38:16 CST)
  • Re: [AMBER] MM - PBSA problem (Fri Jan 23 2009 - 08:34:46 CST)
  • Re: [AMBER] MM - PBSA problem (Thu Jan 22 2009 - 16:00:13 CST)
• cgji
  • [AMBER] Is it possible to simulate transmembrane protein with GB model ? (Mon Nov 02 2009 - 14:52:44 CST)
  • Re: [AMBER] how to choose different comformations for RESP (Tue Jun 02 2009 - 00:14:02 CDT)
  • Re: [AMBER] How to take into account the charge in GAFF parameterization (Fri May 29 2009 - 01:49:44 CDT)
• chaitanya koppisetty
  • Re: [AMBER] normal modes calculation (Thu May 14 2009 - 03:51:28 CDT)
  • Re: [AMBER] nab compile error with -scalapack (Tue Feb 03 2009 - 12:52:54 CST)
  • [AMBER] nab compile error with -scalapack (Tue Feb 03 2009 - 07:23:46 CST)
  • [AMBER] NAB entropy calcualtion (Fri Jan 09 2009 - 03:01:13 CST)
• CHAMI F.
  • [AMBER] radial distribution without normalization (Wed Jun 10 2009 - 10:48:12 CDT)
  • RE: [AMBER] Amber/CHARMM summer school (Thu May 21 2009 - 06:56:23 CDT)
  • [AMBER] POLARIZABLE WATER MODEL (Tue Mar 24 2009 - 13:03:25 CDT)
  • [AMBER] Chlorine containing molecule (Wed Feb 11 2009 - 07:39:19 CST)
• chenquan
  • RE: [AMBER] mean of character in frcmod.ff03 (Wed Apr 15 2009 - 18:36:32 CDT)
  • [AMBER] mean of character in frcmod.ff03 (Wed Apr 15 2009 - 07:26:38 CDT)
  • [AMBER] Could not find angle parameter (Fri Apr 03 2009 - 05:46:47 CDT)
  • [AMBER] (no subject) (Fri Apr 03 2009 - 05:12:14 CDT)
• Chih-Ying Lin
  • [AMBER] The MSD and periodic boundary condition (Thu Nov 19 2009 - 17:30:46 CST)
  • [AMBER] The decreasing MSD of ligand?? (Wed Nov 18 2009 - 15:19:35 CST)
  • [AMBER] MSD of ligand?? (Tue Nov 17 2009 - 13:07:12 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 22:36:07 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 15:59:11 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Wed Nov 11 2009 - 15:08:12 CST)
  • [AMBER] High-temperature simulation ? (Wed Nov 11 2009 - 09:36:16 CST)
  • [AMBER] Increase Temperature to 550 K (Wed Nov 11 2009 - 09:27:41 CST)
  • Re: [AMBER] Time scale of the Protein domain motion ? (Sat Oct 17 2009 - 14:46:37 CDT)
  • Re: [AMBER] Time scale of the Protein domain motion ? (Sat Oct 17 2009 - 14:36:18 CDT)
  • [AMBER] Time scale of the Protein domain motion ? (Sat Oct 17 2009 - 14:18:34 CDT)
  • [AMBER] Gaussian network model (GNM) (Fri Aug 21 2009 - 19:39:07 CDT)
  • Re: [AMBER] Protein Domain Motion (Thu Aug 13 2009 - 20:51:14 CDT)
  • [AMBER] Protein Domain Motion (Thu Aug 13 2009 - 14:20:09 CDT)
  • Re: [AMBER] Protein Activity (Tue Aug 04 2009 - 14:42:42 CDT)
  • [AMBER] Protein Activity (Tue Aug 04 2009 - 12:57:54 CDT)
  • [AMBER] protein molecular weight? (Fri May 29 2009 - 17:44:24 CDT)
  • Re: [AMBER] Why NaCl or KCl solution? (Wed May 27 2009 - 21:11:21 CDT)
  • Re: RE: [AMBER] How to choose the counter ions for proteins? (Sat May 23 2009 - 13:16:49 CDT)
  • [AMBER] Why NaCl or KCl solution? (Sat May 23 2009 - 11:41:33 CDT)
  • [AMBER] How to choose the counter ions for proteins? (Sat May 23 2009 - 00:42:40 CDT)
  • [AMBER] Why does protein carry charges? (Fri May 22 2009 - 23:09:21 CDT)
  • [AMBER] What are the elements to speed up the simulation? (Tue May 19 2009 - 17:17:07 CDT)
  • [AMBER] The protein swell? (Sun May 17 2009 - 17:17:51 CDT)
  • [AMBER] What is the purpose to do the bond constraints? (Sun May 17 2009 - 17:09:04 CDT)
  • [AMBER] How to setup the pH value? (Sat May 16 2009 - 12:29:21 CDT)
  • [AMBER] how to make the different/specific displacement of ligand around protein? (Fri May 15 2009 - 18:55:49 CDT)
  • Re: [AMBER] Protein Docking (Thu May 14 2009 - 23:28:43 CDT)
  • [AMBER] Protein Docking (Mon May 11 2009 - 15:21:45 CDT)
  • [AMBER] protein PDB (Thu Mar 19 2009 - 15:43:15 CDT)
  • [AMBER] What is the default position of the partial charges? (Wed Mar 04 2009 - 15:06:16 CST)
  • [AMBER] NVT vs NPT (Tue Feb 17 2009 - 21:23:05 CST)
  • Re: RE: [AMBER] MD vs scattering (Tue Jan 20 2009 - 15:26:49 CST)
  • [AMBER] MD vs scattering (Tue Jan 20 2009 - 15:10:47 CST)
• Chris Moth
  • Re: [AMBER] Question regarding PCA analysis. (Thu Sep 03 2009 - 09:17:42 CDT)
  • Re: [AMBER] ptraj netcdf (Tue May 12 2009 - 10:46:31 CDT)
  • Re: [AMBER] bintraj and amber 10 (Thu Apr 23 2009 - 12:46:44 CDT)
  • [AMBER] Source of new CYX residue parameters in ff03ua (Tue Apr 14 2009 - 19:42:33 CDT)
  • [AMBER] Source of new CYX residue parameters in ff03ua (Tue Apr 07 2009 - 14:48:46 CDT)
  • Re: [AMBER] amber tools reading netcdf files (Tue Feb 24 2009 - 11:35:22 CST)
• Chris Whittleston
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Oct 13 2009 - 05:02:17 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Mon Oct 12 2009 - 10:56:06 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Fri Oct 09 2009 - 10:16:53 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Thu Oct 08 2009 - 05:47:22 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Wed Oct 07 2009 - 12:48:18 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Wed Oct 07 2009 - 11:57:25 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 05:54:09 CDT)
  • [AMBER] Using idecomp=3 with igb=10 (PB) (Mon Jul 27 2009 - 15:04:14 CDT)
• Christof Jaeger
  • Re: [AMBER] ptraj-radial distribution function (Thu Jul 16 2009 - 03:22:02 CDT)
• Christopher Materese
  • [AMBER] uncharged c and n terminal amino acids (Wed Apr 22 2009 - 13:05:38 CDT)
• Christopher Stiles
  • [AMBER] Carbon Nanotube Library file (CNT) (Mon Sep 14 2009 - 08:59:57 CDT)
• Chunliyan
  • [AMBER] Dyndom (Sat Aug 29 2009 - 09:43:00 CDT)
  • [AMBER] radius for Manganese ion (Sat Aug 29 2009 - 09:43:00 CDT)
  • [AMBER] Manganese bondi radii (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] Manganese bondi radii for mm/pbsa calculation (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] Manganese (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] radius for Manganese ion (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] manganese bondi radii for mm_pbsa calculation (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] Dyndom (Thu Jun 18 2009 - 10:12:44 CDT)
  • [AMBER] re: essential dynamics (Wed May 13 2009 - 12:25:57 CDT)
  • [AMBER] essential dynamics (Wed May 13 2009 - 11:23:23 CDT)
• Cihan Aydin
  • RE: [AMBER] ptraj - cluster (Fri Jul 17 2009 - 09:22:37 CDT)
  • [AMBER] ptraj - cluster (Thu Jul 16 2009 - 00:55:07 CDT)
  • Re: [AMBER] RE: suggestions (Mon Jul 06 2009 - 20:29:22 CDT)
  • Re: [AMBER] H-bond vs. VdW (Mon Jul 06 2009 - 10:13:39 CDT)
  • [AMBER] Leap Questions... (Sat Jul 04 2009 - 20:41:39 CDT)
  • [AMBER] Simulations including RNA-protein complexes... (Sun Jun 28 2009 - 17:29:10 CDT)
  • RE: [AMBER] Velocity rescaling and ig... (Sun Jun 28 2009 - 11:22:29 CDT)
  • Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Sun Jun 28 2009 - 11:19:07 CDT)
  • Re: [AMBER] Velocity rescaling and ig... (Sun Jun 28 2009 - 11:08:32 CDT)
  • [AMBER] Velocity rescaling and ig... (Sun Jun 28 2009 - 09:52:30 CDT)
  • Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Sat Jun 27 2009 - 09:29:21 CDT)
  • [AMBER] Distance-covariance and PCA questions... (Mon Jun 15 2009 - 23:18:58 CDT)
  • Re: [AMBER] MM-PBSA tutorial (Thu May 14 2009 - 20:19:04 CDT)
  • [AMBER] Best rms fit for correlation and covariance analysis (Tue Apr 28 2009 - 00:02:14 CDT)
• Clark, Tiffany D
  • [AMBER] vertex atom mismatch (Fri Jul 31 2009 - 08:14:15 CDT)
• Cojocaru,Vlad
  • RE: [AMBER] amber tools reading netcdf files (Tue Feb 24 2009 - 12:46:27 CST)
• Collins Nganou
  • [AMBER] skip parallel test (Tue May 05 2009 - 08:09:00 CDT)
  • [AMBER] make test.parallel.MM error (Sun May 03 2009 - 16:20:51 CDT)
  • [AMBER] Make parallel test faillure (Thu Apr 30 2009 - 14:36:55 CDT)
  • [AMBER] (no subject) (Thu Apr 30 2009 - 14:34:36 CDT)
  • [AMBER] Request an error (Thu Apr 30 2009 - 12:41:48 CDT)
  • [AMBER] Bad value during integer read by sander (Thu Apr 16 2009 - 10:09:45 CDT)
• Cristina S.D. Sisu
  • Re: [AMBER] catenan simulation problems (Fri Mar 06 2009 - 09:35:46 CST)
• Cristina Sisu
  • [AMBER] PEMD (Mon Oct 26 2009 - 16:44:42 CDT)
  • Re: [AMBER] B-factor (Sat Oct 17 2009 - 05:58:34 CDT)
  • [AMBER] B-factor (Thu Oct 15 2009 - 12:04:25 CDT)
  • Re: [AMBER] catenan simulation problems (Fri Mar 06 2009 - 09:28:00 CST)
  • [AMBER] catenan simulation problems (Fri Mar 06 2009 - 07:16:08 CST)
• Crowley, Michael
  • Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file (Sat Oct 31 2009 - 12:32:12 CDT)
• cyk5056
  • Re: Re: [AMBER] Can I get an average trajectory? (Wed Nov 18 2009 - 10:02:38 CST)
  • [AMBER] Can I get an average trajectory? (Tue Nov 17 2009 - 22:46:25 CST)
  • [AMBER] How to change the input matrix for "analyze matrix" instruction? (Tue Nov 17 2009 - 22:37:43 CST)
  • Re: Re: Re: [AMBER] Antechamber and Parmchk problems (Thu Nov 05 2009 - 12:59:28 CST)
  • Re: Re: [AMBER] Antechamber and Parmchk problems (Wed Nov 04 2009 - 14:37:55 CST)
  • Re: Re: [AMBER] Antechamber and Parmchk problems (Wed Nov 04 2009 - 13:56:32 CST)
  • [AMBER] Antechamber and Parmchk problems (Tue Nov 03 2009 - 20:22:38 CST)
  • [AMBER] Different results for different computers (Sat Oct 31 2009 - 14:39:59 CDT)
• Cyril Falvo
  • [AMBER] Distance restraint and periodic boundary conditions (Tue Aug 18 2009 - 19:58:29 CDT)
• D.J. Cole
  • Re: AMBER: apparent error in closest function in ptraj 10 (Fri Jan 02 2009 - 10:06:01 CST)
• Dan Kaps
  • Re: [AMBER] atom types in pdb files (Mon Apr 13 2009 - 14:29:43 CDT)
  • [AMBER] atom types in pdb files (Mon Apr 13 2009 - 09:23:58 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 12:46:49 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 10:01:08 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 07:57:54 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 07:56:53 CDT)
  • Re: [AMBER] Sander and multiple residues (Thu Apr 09 2009 - 15:02:46 CDT)
  • [AMBER] Sander and multiple residues (Thu Apr 09 2009 - 13:48:55 CDT)
  • Re: [AMBER] test charge (Fri Feb 20 2009 - 10:58:17 CST)
  • Re: [AMBER] test charge (Thu Feb 19 2009 - 20:22:31 CST)
  • [AMBER] test charge (Wed Feb 18 2009 - 20:27:32 CST)
• Daniel Emery
  • Re: [AMBER] Optimization problem (Thu Feb 12 2009 - 08:11:14 CST)
  • [AMBER] Optimization problem (Thu Feb 12 2009 - 04:01:49 CST)
• Daniel Oehme
  • [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 (Thu Mar 26 2009 - 18:44:59 CDT)
• Daniel Roe
  • Re: [AMBER] hbond analysis by ptraj- segmentation fault (Mon Nov 23 2009 - 11:49:23 CST)
  • Re: [AMBER] hbond analysis by ptraj- segmentation fault (Mon Nov 23 2009 - 11:42:49 CST)
• Daniel Smith
  • Re: [AMBER] Solvating the interior of a channel (Sun Feb 15 2009 - 16:40:23 CST)
  • Re: [AMBER] Solvating the interior of a channel (Fri Feb 13 2009 - 15:02:24 CST)
  • [AMBER] Solvating the interior of a channel (Tue Feb 10 2009 - 14:42:09 CST)
  • [AMBER] Solvating inside of a channel (Mon Feb 09 2009 - 15:03:16 CST)
• Darren Yang
  • [AMBER] Setting a constrain in one direction (Thu Aug 27 2009 - 22:15:30 CDT)
• David A. Case
  • Re: [AMBER] 2 restraints with different force constants (Fri Jun 19 2009 - 07:06:18 CDT)
  • Re: [AMBER] 2 restraints with different force constants (Fri Jun 19 2009 - 06:41:01 CDT)
  • Re: [AMBER] Re: force units (Thu Jun 18 2009 - 06:32:18 CDT)
  • Re: [AMBER] Improper dihedrals from .off and .lib files (Thu Jun 18 2009 - 06:28:40 CDT)
  • Re: [AMBER] Specifying improper dihedrals (Wed Jun 17 2009 - 12:56:20 CDT)
  • Re: [AMBER] Antechamber: stuck at bondtype (Wed Jun 17 2009 - 08:28:15 CDT)
  • Re: [AMBER] Fix the local structure as a rigid body (Tue Jun 16 2009 - 10:41:04 CDT)
  • Re: [AMBER] problem in pressure equillibration (Tue Jun 16 2009 - 06:56:34 CDT)
  • Re: [AMBER] QQD psuedoatom restraints (Mon Jun 15 2009 - 07:00:23 CDT)
  • Re: [AMBER] NOE (Thu Jun 11 2009 - 12:29:06 CDT)
  • Re: [AMBER] (no subject) (Thu Jun 11 2009 - 06:54:38 CDT)
  • Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Wed Jun 10 2009 - 14:23:36 CDT)
  • Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Wed Jun 10 2009 - 14:14:49 CDT)
  • Re: [AMBER] POL3 & SHAKE (Wed Jun 10 2009 - 14:11:40 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Wed Jun 10 2009 - 11:54:38 CDT)
  • Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? (Wed Jun 10 2009 - 11:01:26 CDT)
  • Re: [AMBER] GAFF and solvents.lib error (Wed Jun 10 2009 - 10:54:05 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Wed Jun 10 2009 - 10:34:59 CDT)
  • Re: [AMBER] Completed installation of AmberTools, version 1.1 (Wed Jun 10 2009 - 09:10:22 CDT)
  • Re: [AMBER] force.f routine (Wed Jun 10 2009 - 09:09:47 CDT)
  • Re: [AMBER] Improper dihedrals between residues? (Tue Jun 09 2009 - 12:14:57 CDT)
  • Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script (Tue Jun 09 2009 - 08:20:22 CDT)
  • Re: [AMBER] unit of charge in prep files (Tue Jun 09 2009 - 08:07:08 CDT)
  • Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last (Tue Jun 09 2009 - 06:51:42 CDT)
  • Re: [AMBER] (no subject) (Tue Jun 09 2009 - 06:47:59 CDT)
  • Re: [AMBER] Distance restraints between groups of atoms (Tue Jun 09 2009 - 06:45:14 CDT)
  • Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? (Mon Jun 08 2009 - 11:47:54 CDT)
  • Re: [AMBER] Max filename length in Sander? (Mon Jun 08 2009 - 07:36:32 CDT)
  • Re: [AMBER] Max filename length in Sander? (Mon Jun 08 2009 - 07:28:41 CDT)
  • Re: [AMBER] What is the parallel efficiency of amber10 (Mon Jun 08 2009 - 07:23:11 CDT)
  • Re: [AMBER] parameter for dihedral angle (Sat Jun 06 2009 - 07:47:35 CDT)
  • Re: [AMBER] parameter for dihedral angle (Fri Jun 05 2009 - 14:50:03 CDT)
  • Re: [AMBER] atom type (Fri Jun 05 2009 - 07:32:45 CDT)
  • Re: [AMBER] AMBER 10: sleap diff errors? (Thu Jun 04 2009 - 14:19:44 CDT)
  • Re: [AMBER] mol2 file to amber pdb file format (Thu Jun 04 2009 - 11:55:39 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Thu Jun 04 2009 - 10:06:28 CDT)
  • Re: [AMBER] creating bond (Wed Jun 03 2009 - 13:32:57 CDT)
  • Re: [AMBER] Pentavalent Phosphorous and Antechamber (Wed Jun 03 2009 - 11:35:26 CDT)
  • Re: [AMBER] Distance restraints between groups of atoms (Wed Jun 03 2009 - 11:32:33 CDT)
  • Re: [AMBER] problems with EP of TIP4PEW (Wed Jun 03 2009 - 11:29:43 CDT)
  • Re: [AMBER] Atom names (Wed Jun 03 2009 - 11:00:15 CDT)
  • Re: [AMBER] AMBER10: error message mdfil flag..... (Wed Jun 03 2009 - 09:30:08 CDT)
  • Re: [AMBER] Distance restraints between groups of atoms (Wed Jun 03 2009 - 07:27:04 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Wed Jun 03 2009 - 07:24:56 CDT)
  • Re: [AMBER] Error in MM PBSA (Wed Jun 03 2009 - 06:43:54 CDT)
  • Re: 回å¤�： [AMBER] Error in MM PBSA (Tue Jun 02 2009 - 09:36:39 CDT)
  • Re: [AMBER] Error in MM PBSA (Tue Jun 02 2009 - 09:05:09 CDT)
  • Re: [AMBER] help with parameters for ions (Tue Jun 02 2009 - 08:46:40 CDT)
  • Re: [AMBER] minimization to reduce covalent deviation (Tue Jun 02 2009 - 08:38:58 CDT)
  • Re: [AMBER] Atom names (Tue Jun 02 2009 - 06:44:39 CDT)
  • Re: [AMBER] converting vibrational frequency (Mon Jun 01 2009 - 06:39:32 CDT)
  • Re: [AMBER] broken Ligand (Sun May 31 2009 - 07:50:57 CDT)
  • Re: [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically (Sat May 30 2009 - 08:11:59 CDT)
  • Re: [AMBER] QQD psuedoatom restraints (Fri May 29 2009 - 14:26:27 CDT)
  • Re: [AMBER] QQD psuedoatom restraints (Fri May 29 2009 - 10:18:29 CDT)
  • Re: [AMBER] broken Ligand (Fri May 29 2009 - 09:45:20 CDT)
  • Re: [AMBER] ask for parm99MOD (Thu May 28 2009 - 16:52:29 CDT)
  • Re: [AMBER] xleap segmentation fault (Thu May 28 2009 - 15:05:12 CDT)
  • Re: [AMBER] Minimization error on protonated system? Please help. Thanks! (Thu May 28 2009 - 10:17:59 CDT)
  • Re: [AMBER] SANDER BOMB (Thu May 28 2009 - 09:29:50 CDT)
  • Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels (Wed May 27 2009 - 06:57:07 CDT)
  • Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag (Wed May 27 2009 - 06:42:29 CDT)
  • Re: [AMBER] mdfil: Error unknown flag during sander minimization (Tue May 26 2009 - 09:05:37 CDT)
  • Re: [AMBER] problem with program anal within Amber10 (Tue May 26 2009 - 07:03:01 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Tue May 26 2009 - 06:41:25 CDT)
  • Re: [AMBER] problem with MM-PBSA (Tue May 26 2009 - 06:37:31 CDT)
  • Re: [AMBER] file contains 2 atoms not in residue templates (Sun May 24 2009 - 08:12:14 CDT)
  • Re: [AMBER] Protein with HETATM, am I doing the right thing (Sat May 23 2009 - 07:13:01 CDT)
  • Re: [AMBER] Nab units ? (Fri May 22 2009 - 20:33:34 CDT)
  • Re: [AMBER] Installation directory (Thu May 21 2009 - 13:19:28 CDT)
  • Re: [AMBER] Protein with HETATM, am I doing the right thing (Thu May 21 2009 - 07:39:14 CDT)
  • Re: [AMBER] Problem with Nmode (Thu May 21 2009 - 07:29:06 CDT)
  • Re: [AMBER] errors when add ions (Thu May 21 2009 - 07:23:08 CDT)
  • Re: [AMBER] Problem with Nmode (Wed May 20 2009 - 13:02:44 CDT)
  • [AMBER] Amber/CHARMM summer school (Wed May 20 2009 - 07:40:39 CDT)
  • Re: [AMBER] gaff and aromatic compounds (Wed May 20 2009 - 07:04:05 CDT)
  • Re: [AMBER] How to setup the pH value? (Tue May 19 2009 - 14:08:53 CDT)
  • Re: [AMBER] loadpdb atom type (Tue May 19 2009 - 13:19:44 CDT)
  • Re: [AMBER] gaff and aromatic compounds (Tue May 19 2009 - 11:07:29 CDT)
  • Re: [AMBER] Problem with nonstandard residues (Tue May 19 2009 - 10:22:15 CDT)
  • Re: [AMBER] Problem with nonstandard residues (Tue May 19 2009 - 07:54:14 CDT)
  • Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint (Tue May 19 2009 - 07:35:31 CDT)
  • Re: [AMBER] Amber - Leap- SolvateBox help (Tue May 19 2009 - 06:48:39 CDT)
  • Re: [AMBER] problem with parmchk (Mon May 18 2009 - 15:00:07 CDT)
  • Re: [AMBER] problem with parmchk (Mon May 18 2009 - 09:19:54 CDT)
  • Re: [AMBER] Modification of His (Mon May 18 2009 - 07:31:33 CDT)
  • Re: [AMBER] Modification of His (Mon May 18 2009 - 06:58:34 CDT)
  • Re: [AMBER] parallel amber on cluster (Mon May 18 2009 - 06:54:18 CDT)
  • Re: [AMBER] Amber - Leap- SolvateBox help (Fri May 15 2009 - 18:57:00 CDT)
  • Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' (Fri May 15 2009 - 18:56:34 CDT)
  • Re: [AMBER] xleap reading hydrogens giving error (Fri May 15 2009 - 11:25:11 CDT)
  • Re: [AMBER] xleap reading hydrogens giving error (Fri May 15 2009 - 09:17:04 CDT)
  • Re: [AMBER] molecular crystal simulation (Wed May 13 2009 - 17:28:37 CDT)
  • Re: [AMBER] re: essential dynamics (Wed May 13 2009 - 12:48:42 CDT)
  • Re: [AMBER] essential dynamics (Wed May 13 2009 - 12:15:50 CDT)
  • Re: [AMBER] building quadruplex with NAB (Wed May 13 2009 - 06:48:38 CDT)
  • Re: [AMBER] Adding non standard residues (Mon May 11 2009 - 12:30:56 CDT)
  • Re: [AMBER] molsurf and probe radius (Mon May 11 2009 - 10:03:10 CDT)
  • Re: [AMBER] The resonable way to create single strand DNA with NAB ? (Mon May 11 2009 - 06:34:16 CDT)
  • Re: [AMBER] Problems in the result of MM_PBSA (Fri May 08 2009 - 07:45:19 CDT)
  • Re: [AMBER] ambertools for NAMD (Thu May 07 2009 - 09:09:55 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Thu May 07 2009 - 06:33:20 CDT)
  • Re: [AMBER] xleap input pdb problem (Wed May 06 2009 - 21:16:10 CDT)
  • Re: [AMBER] difference in temperature (Wed May 06 2009 - 07:08:01 CDT)
  • Re: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 10:41:54 CDT)
  • Re: [AMBER] skip parallel test (Tue May 05 2009 - 10:34:14 CDT)
  • Re: [AMBER] creating new residue adds none wanted ter (Tue May 05 2009 - 07:07:53 CDT)
  • Re: [AMBER] creating new residue adds none wanted ter (Mon May 04 2009 - 13:27:58 CDT)
  • Re: [AMBER] normal mode analysis (Mon May 04 2009 - 13:06:32 CDT)
  • Re: [AMBER] normal mode analysis (Mon May 04 2009 - 08:37:02 CDT)
  • Re: [AMBER] creating new residue adds none wanted ter (Mon May 04 2009 - 08:35:41 CDT)
  • Re: [AMBER] Error message for tutorial 1 (run in parallel) (Mon May 04 2009 - 07:40:36 CDT)
  • Re: [AMBER] High energy during minimization (Sun May 03 2009 - 08:40:22 CDT)
  • Re: [AMBER] charge of Fe-heme (Fri May 01 2009 - 17:52:45 CDT)
  • Re: [AMBER] (no subject) (Thu Apr 30 2009 - 15:16:35 CDT)
  • Re: [AMBER] chain restrain x TI (Thu Apr 30 2009 - 13:01:13 CDT)
  • Re: [AMBER] Influence about HIS-HIE-HIS-HIP (Thu Apr 30 2009 - 09:27:02 CDT)
  • Re: [AMBER] input error in TI calculation (Wed Apr 29 2009 - 13:48:04 CDT)
  • Re: [AMBER] (no subject) (Wed Apr 29 2009 - 12:56:28 CDT)
  • Re: [AMBER] ERROR In Restraint file. (Tue Apr 28 2009 - 19:05:23 CDT)
  • Re: [AMBER] ERROR In Restraint file. (Tue Apr 28 2009 - 11:17:36 CDT)
  • Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing (Mon Apr 27 2009 - 12:30:55 CDT)
  • Re: [AMBER] Papers on Amber package usage (Sun Apr 26 2009 - 07:48:31 CDT)
  • Re: [AMBER] Unit name with loadMol2 command (Thu Apr 23 2009 - 17:54:02 CDT)
  • [AMBER] NAB bug with parmbsc0 (Thu Apr 23 2009 - 11:25:27 CDT)
  • Re: [AMBER] nmod no run proprely in mmbsa (Thu Apr 23 2009 - 07:47:44 CDT)
  • Re: [AMBER] uncharged c and n terminal amino acids (Wed Apr 22 2009 - 13:16:19 CDT)
  • Re: [AMBER] atom numbers (Tue Apr 21 2009 - 12:26:32 CDT)
  • Re: [AMBER] atom numbers (Tue Apr 21 2009 - 10:52:22 CDT)
  • Re: [AMBER] atom numbers (Tue Apr 21 2009 - 06:54:37 CDT)
  • Re: [AMBER] Atom type error (Sun Apr 19 2009 - 12:41:11 CDT)
  • Re: [AMBER] please read this mail (Sat Apr 18 2009 - 08:01:08 CDT)
  • [AMBER] Amber and CHARMM summer school (Thu Apr 16 2009 - 10:04:18 CDT)
  • Re: [AMBER] 1-4 vdW, GB MM difference (Thu Apr 16 2009 - 09:47:55 CDT)
  • Re: [AMBER] ambertools failed - SMP IA64 (Thu Apr 16 2009 - 09:10:20 CDT)
  • Re: [AMBER] specification of antechamber AC file format? (Thu Apr 16 2009 - 07:29:46 CDT)
  • Re: [AMBER] my FF (Wed Apr 15 2009 - 07:28:16 CDT)
  • Re: [AMBER] hpux sander.serial failure info (Wed Apr 15 2009 - 07:07:45 CDT)
  • Re: [AMBER] water bonding with protein (Wed Apr 15 2009 - 06:58:17 CDT)
  • Re: [AMBER] antechamber and wrong net charge with gasteiger method (Tue Apr 14 2009 - 13:42:14 CDT)
  • Re: [AMBER] restrained minimization (Mon Apr 13 2009 - 21:03:11 CDT)
  • Re: [AMBER] atom types in pdb files (Mon Apr 13 2009 - 15:25:04 CDT)
  • Re: [AMBER] Energy minimisation and NaN (Mon Apr 13 2009 - 14:28:10 CDT)
  • Re: [AMBER] Sander and multiple residues (Fri Apr 10 2009 - 09:03:57 CDT)
  • Re: [AMBER] RST file (Fri Apr 10 2009 - 07:21:19 CDT)
  • Re: [AMBER] igb=0 vs. igb=6 give different answers (Thu Apr 09 2009 - 21:48:31 CDT)
  • Re: [AMBER] antechamber problems (Thu Apr 09 2009 - 13:04:51 CDT)
  • Re: [AMBER] hpux sander.serial failure info (Thu Apr 09 2009 - 06:56:51 CDT)
  • Re: [AMBER] please help me out (Thu Apr 09 2009 - 06:46:12 CDT)
  • Re: [AMBER] please help me out (Wed Apr 08 2009 - 13:10:04 CDT)
  • Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error (Tue Apr 07 2009 - 15:41:21 CDT)
  • Re: [AMBER] prmtop residue format (Tue Apr 07 2009 - 15:35:40 CDT)
  • Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error (Tue Apr 07 2009 - 11:29:18 CDT)
  • Re: [AMBER] missing violations of the covalent geometry (Tue Apr 07 2009 - 06:10:42 CDT)
  • Re: [AMBER] deffision coefficient (Mon Apr 06 2009 - 21:16:39 CDT)
  • Re: [AMBER] Do I need to modify the cap residues (Mon Apr 06 2009 - 13:57:02 CDT)
  • Re: [AMBER] Amber with AMOEBA force-field (Mon Apr 06 2009 - 08:00:47 CDT)
  • Re: [AMBER] Amber with AMOEBA force-field (Mon Apr 06 2009 - 07:47:11 CDT)
  • Re: [AMBER] error in MM PBSA (Sat Apr 04 2009 - 16:16:42 CDT)
  • Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation (Sat Apr 04 2009 - 08:20:28 CDT)
  • Re: [AMBER] Umbrella test (Sat Apr 04 2009 - 08:12:13 CDT)
  • Re: [AMBER] NALA-ALA-CALA peptide with antechamber (Sat Apr 04 2009 - 08:04:32 CDT)
  • Re: [AMBER] amber9 serial compilation issues (Fri Apr 03 2009 - 15:01:02 CDT)
  • Re: [AMBER] (no subject) (Fri Apr 03 2009 - 07:17:36 CDT)
  • Re: [AMBER] please help me out (Thu Apr 02 2009 - 12:48:10 CDT)
  • Re: [AMBER] yacc parser (Thu Apr 02 2009 - 07:03:06 CDT)
  • Re: [AMBER] ambmol2? (Wed Apr 01 2009 - 08:19:00 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) (Sun Mar 29 2009 - 13:41:13 CDT)
  • Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP (Sun Mar 29 2009 - 13:37:35 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) (Sat Mar 28 2009 - 21:26:58 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) (Sat Mar 28 2009 - 16:39:35 CDT)
  • Re: [AMBER] Question (Sat Mar 28 2009 - 08:38:49 CDT)
  • Re: [AMBER] Problem reading PDB file into XLEAP (Sat Mar 28 2009 - 08:28:53 CDT)
  • Re: [AMBER] Problem with "Atom does not have a type" (Sat Mar 28 2009 - 08:25:33 CDT)
  • Re: [AMBER] Problem reading PDB file into XLEAP (Fri Mar 27 2009 - 07:39:26 CDT)
  • Re: [AMBER] Antechamber problem (Fri Mar 27 2009 - 07:29:48 CDT)
  • Re: [AMBER] problem in installing AMBER10 (Fri Mar 27 2009 - 07:05:31 CDT)
  • Re: [AMBER] Problem with "Atom does not have a type" (Fri Mar 27 2009 - 06:44:22 CDT)
  • Re: [AMBER] leap and chirality (Mon Mar 23 2009 - 08:16:14 CDT)
  • Re: [AMBER] problem in installing AMBER10 (Mon Mar 23 2009 - 06:07:17 CDT)
  • Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box (Thu Mar 19 2009 - 12:38:52 CDT)
  • Re: [AMBER] problem in running sander (Thu Mar 19 2009 - 07:13:11 CDT)
  • Re: [AMBER] temperature rises with igb=1 (Thu Mar 19 2009 - 07:04:54 CDT)
  • Re: [AMBER] error for nmode (Thu Mar 19 2009 - 06:31:24 CDT)
  • Re: [AMBER] Mass of LP (Thu Mar 19 2009 - 06:27:48 CDT)
  • Re: [AMBER] mol2 - pdb conversion (Wed Mar 18 2009 - 16:53:06 CDT)
  • Re: [AMBER] problems compiling ambertool (Wed Mar 18 2009 - 07:39:38 CDT)
  • Re: [AMBER] catenan simulation problems (Wed Mar 18 2009 - 06:47:32 CDT)
  • Re: [AMBER] errors about install amber9 on MAC OS (Wed Mar 18 2009 - 06:08:44 CDT)
  • Re: [AMBER] CCL4 simulation (Wed Mar 18 2009 - 06:06:30 CDT)
  • Re: [AMBER] CCL4 simulation (Tue Mar 17 2009 - 21:14:51 CDT)
  • Re: [AMBER] problems compiling ambertool (Tue Mar 17 2009 - 11:13:30 CDT)
  • Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions (Tue Mar 17 2009 - 11:00:19 CDT)
  • Re: [AMBER] mol2 - pdb conversion (Tue Mar 17 2009 - 10:47:53 CDT)
  • Re: [AMBER] problems compiling ambertool (Tue Mar 17 2009 - 07:49:20 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 10:12:40 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 09:27:26 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 08:50:24 CDT)
  • Re: [AMBER] problems compiling ambertool (Mon Mar 16 2009 - 07:13:23 CDT)
  • Re: [AMBER] please help me out (Sat Mar 14 2009 - 08:06:34 CDT)
  • Re: [AMBER] problems compiling ambertool (Fri Mar 13 2009 - 14:54:56 CDT)
  • Re: [AMBER] High RMSD for DNA: A to B transition study (Fri Mar 13 2009 - 07:00:40 CDT)
  • Re: [AMBER] Changing Force Fields in "Midstream" (Wed Mar 11 2009 - 17:36:56 CDT)
  • [AMBER] installing AmberTools on Windows machines (Wed Mar 11 2009 - 15:27:07 CDT)
  • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? (Wed Mar 11 2009 - 06:08:17 CDT)
  • Re: [AMBER] 8Mureabox (Tue Mar 10 2009 - 07:51:08 CDT)
  • Re: [AMBER] Restraint Mask length restriction !! (Mon Mar 09 2009 - 09:30:16 CDT)
  • Re: [AMBER] Restraint Mask length restriction !! (Mon Mar 09 2009 - 08:43:34 CDT)
  • Re: [AMBER] catenan simulation problems (Sat Mar 07 2009 - 17:25:07 CST)
  • Re: [AMBER] divcon error during antechamber run, convergence problem (Fri Mar 06 2009 - 12:33:24 CST)
  • Re: [AMBER] catenan simulation problems (Fri Mar 06 2009 - 08:59:24 CST)
  • Re: [AMBER] High RMSD for DNA: A to B transition study (Fri Mar 06 2009 - 08:57:02 CST)
  • Re: [AMBER] GBSA: dielectric symmetry (Thu Mar 05 2009 - 18:05:51 CST)
  • Re: [AMBER] chemical shift penalty (Thu Mar 05 2009 - 17:59:33 CST)
  • Re: [AMBER] specification of antechamber AC file format? (Wed Mar 04 2009 - 16:39:44 CST)
  • Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? (Tue Mar 03 2009 - 07:39:26 CST)
  • Re: [AMBER] Pseudoatoms (Mon Mar 02 2009 - 17:25:29 CST)
  • Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? (Mon Mar 02 2009 - 08:56:54 CST)
  • Re: [AMBER] Question about NAB module (Sun Mar 01 2009 - 07:52:19 CST)
  • Re: [AMBER] A problem with xleap and pdb file (Fri Feb 27 2009 - 07:56:26 CST)
  • Re: [AMBER] Simulated annealing (Thu Feb 26 2009 - 09:52:18 CST)
  • Re: [AMBER] tleap errors !! (Thu Feb 26 2009 - 07:45:49 CST)
  • Re: [AMBER] problem with amber installation (Wed Feb 25 2009 - 06:45:01 CST)
  • Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer (Tue Feb 24 2009 - 07:15:27 CST)
  • Re: [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs (Sat Feb 21 2009 - 17:51:38 CST)
  • Re: [AMBER] test charge (Thu Feb 19 2009 - 22:48:29 CST)
  • Re: [AMBER] test charge (Wed Feb 18 2009 - 22:24:04 CST)
  • Re: [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error (Wed Feb 18 2009 - 14:35:12 CST)
  • Re: [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory (Wed Feb 18 2009 - 12:11:56 CST)
  • Re: [AMBER] How to constrain the hydrogen bonding distances... (Wed Feb 18 2009 - 08:28:56 CST)
  • Re: [AMBER] problem compiling nmode.c (Tue Feb 17 2009 - 20:45:03 CST)
  • Re: [AMBER] PMF calculation (Tue Feb 17 2009 - 20:23:20 CST)
  • Re: [AMBER] restraint angle (Tue Feb 17 2009 - 11:52:49 CST)
  • Re: [AMBER] Amber 9 Install - AMBERBUILDFLAGS error (Mon Feb 16 2009 - 22:29:41 CST)
  • Re: [AMBER] Normal errors on job kill? (Mon Feb 16 2009 - 22:25:54 CST)
  • Re: [AMBER] New atom type with 7 bonds (Mon Feb 16 2009 - 08:28:25 CST)
  • Re: [AMBER] Error installing Amber (Mon Feb 16 2009 - 08:21:41 CST)
  • Re: [AMBER] install Amber 10 to Macbook (Sat Feb 14 2009 - 17:17:53 CST)
  • Re: [AMBER] Question about improper torsions... (Sat Feb 14 2009 - 07:32:21 CST)
  • Re: [AMBER] Optimization problem (Thu Feb 12 2009 - 08:35:52 CST)
  • Re: [AMBER] nmr refinement of dimer (Thu Feb 12 2009 - 07:08:08 CST)
  • Re: [AMBER] Optimization problem (Thu Feb 12 2009 - 06:58:17 CST)
  • Re: [AMBER] Compiling Carnal Amber7 in Amber9 (Thu Feb 12 2009 - 06:58:03 CST)
  • Re: [AMBER] amber9 installation problem in SMP IA64 (Wed Feb 11 2009 - 07:07:48 CST)
  • Re: [AMBER] nmr refinement of dimer (Wed Feb 11 2009 - 07:02:37 CST)
  • Re: [AMBER] AMBER: chiral restraint on protein (Wed Feb 11 2009 - 06:56:05 CST)
  • Re: [AMBER] array out of bound in Amber10 tests (Tue Feb 10 2009 - 15:30:36 CST)
  • Re: [AMBER] array out of bound in Amber10 tests (Tue Feb 10 2009 - 10:39:43 CST)
  • Re: [AMBER] NAB md function prints strange output (Tue Feb 10 2009 - 06:46:40 CST)
  • Re: [AMBER] amber9 installation problem in SMP IA64 (Tue Feb 10 2009 - 06:41:29 CST)
  • Re: [AMBER] second derivative matrix (Mon Feb 09 2009 - 09:05:18 CST)
  • Re: [AMBER] NAB md function prints strange output (Mon Feb 09 2009 - 06:58:43 CST)
  • Re: [AMBER] distance calculation by reading in the restraint file (Fri Feb 06 2009 - 16:35:55 CST)
  • Re: [AMBER] distance calculation by reading in the restraint file (Fri Feb 06 2009 - 16:03:08 CST)
  • Re: [AMBER] Solvation potential and free energies (Fri Feb 06 2009 - 07:34:25 CST)
  • Re: [AMBER] amber9 installation problem in SMP IA64 (Fri Feb 06 2009 - 07:25:55 CST)
  • Re: [AMBER] second derivative matrix calculation (Fri Feb 06 2009 - 07:19:52 CST)
  • Re: [AMBER] Citing AMBER Tools... (Thu Feb 05 2009 - 09:44:37 CST)
  • Re: [AMBER] nab compile error with -scalapack (Tue Feb 03 2009 - 08:27:24 CST)
  • Re: [AMBER] Langevin dynamics (Mon Feb 02 2009 - 13:24:59 CST)
  • Re: [AMBER] precision in the trajectory files (Mon Feb 02 2009 - 08:55:40 CST)
  • Re: [AMBER] md simulation on parallel PMEMD (Mon Feb 02 2009 - 07:54:58 CST)
  • Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? (Sun Feb 01 2009 - 12:35:03 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Sat Jan 31 2009 - 20:49:22 CST)
  • Re: [AMBER] thermo, entropy by quasiharmonic method (Fri Jan 30 2009 - 17:40:38 CST)
  • Re: [AMBER] Dr. Ramesh here (Fri Jan 30 2009 - 10:08:43 CST)
  • Re: [AMBER] Xleap - solvatebox - counterions (Fri Jan 30 2009 - 10:04:23 CST)
  • Re: [AMBER] Compilation and usage of NAB in parallel ? (Fri Jan 30 2009 - 09:51:31 CST)
  • Re: [AMBER] AmberTools 1.2 (Fri Jan 30 2009 - 06:04:41 CST)
  • Re: [AMBER] failure to run antechamber with amber 10 (Thu Jan 29 2009 - 16:45:53 CST)
  • Re: [AMBER] GAFF conjugated ring system dihedrals (Thu Jan 29 2009 - 12:37:24 CST)
  • Re: [AMBER] Installation error - Amber10 (Thu Jan 29 2009 - 12:33:33 CST)
  • Re: [AMBER] Compilation and usage of NAB in parallel ? (Thu Jan 29 2009 - 07:22:08 CST)
  • Re: [AMBER] Atome Type (Thu Jan 29 2009 - 07:08:09 CST)
  • Re: [AMBER] generating top file using antechmaber (Thu Jan 29 2009 - 06:51:56 CST)
  • Re: [AMBER] Watercap... some querries (Wed Jan 28 2009 - 09:01:46 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 09:33:57 CST)
  • Re: [AMBER] antechamber : missed atoms (Tue Jan 27 2009 - 09:23:27 CST)
  • Re: [AMBER] RE:xleap problem (Tue Jan 27 2009 - 09:18:53 CST)
  • Re: [AMBER] atom types (Tue Jan 27 2009 - 09:13:30 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 08:59:47 CST)
  • Re: [AMBER] xleap problem (Sun Jan 25 2009 - 17:30:47 CST)
  • Re: [AMBER] MM - PBSA problem (Sun Jan 25 2009 - 08:26:07 CST)
  • Re: [AMBER] MM - PBSA problem (Sun Jan 25 2009 - 08:21:33 CST)
  • Re: [AMBER] xleap problem (Sun Jan 25 2009 - 07:57:41 CST)
  • Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Sat Jan 24 2009 - 08:37:31 CST)
  • Re: [AMBER] error on open distatance restraint (Fri Jan 23 2009 - 21:18:17 CST)
  • Re: [AMBER] charge derivation for ATP molecule using antechamber (Fri Jan 23 2009 - 10:51:49 CST)
  • Re: [AMBER] how to use those water models off the list in amber? (Thu Jan 22 2009 - 07:29:41 CST)
  • Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Wed Jan 21 2009 - 08:52:33 CST)
  • Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Tue Jan 20 2009 - 14:53:48 CST)
  • Re: [AMBER] Duplicate residues (Mon Jan 19 2009 - 07:16:28 CST)
  • Re: [AMBER] (no subject) (Sat Jan 17 2009 - 20:48:25 CST)
  • Re: [AMBER] Parallelepiped periodic box (Fri Jan 16 2009 - 13:50:32 CST)
  • Re: [AMBER] (no subject) (Fri Jan 16 2009 - 13:10:33 CST)
  • Re: [AMBER] nab conjgrad min problem (Fri Jan 16 2009 - 09:33:01 CST)
  • Re: [AMBER] sander not working (Fri Jan 16 2009 - 08:58:50 CST)
  • Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) (Wed Jan 14 2009 - 07:13:18 CST)
  • Re: [AMBER] reaction coordinates (Wed Jan 14 2009 - 07:00:59 CST)
  • Re: [AMBER] errorin sander---Amber10 (Tue Jan 13 2009 - 07:22:36 CST)
  • Re: [AMBER] Writing out trajectory in NAB (Mon Jan 12 2009 - 11:22:58 CST)
  • Re: [AMBER] Amber 9 installation problem on Ubuntu (Mon Jan 12 2009 - 06:01:31 CST)
  • Re: [AMBER] implicit and explicit simulation: salt effect (Sat Jan 10 2009 - 10:26:45 CST)
  • Re: [AMBER] implicit and explicit simulation: salt effect (Sat Jan 10 2009 - 10:23:08 CST)
  • Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? (Sat Jan 10 2009 - 10:02:53 CST)
  • Re: [AMBER] ambpdb is changing atom names, a feature or bug? (Fri Jan 09 2009 - 12:58:20 CST)
  • Re: [AMBER] NAB entropy calcualtion (Fri Jan 09 2009 - 07:13:32 CST)
  • Re: [AMBER] ambpdb is changing atom names, a feature or bug? (Fri Jan 09 2009 - 07:01:54 CST)
  • Re: [AMBER] how many processors for parallel test (Thu Jan 08 2009 - 07:44:52 CST)
  • Re: [AMBER] how many processors for parallel test (Thu Jan 08 2009 - 06:08:06 CST)
  • Re: [AMBER] Using GAFF with a covalently bound ligand or label (Wed Jan 07 2009 - 20:42:27 CST)
  • Re: [AMBER] PHOSPHOTHREONINE (Wed Jan 07 2009 - 13:29:35 CST)
  • Re: [AMBER] four prepin/frcmod files be read simultaneously by leap (Wed Jan 07 2009 - 12:39:56 CST)
  • Re: [AMBER] RE: AMBER: xleap problem (Wed Jan 07 2009 - 07:43:16 CST)
  • Re: [AMBER] Re: AMBER: ligand parameter (Wed Jan 07 2009 - 07:08:27 CST)
  • Re: [AMBER] RE: AMBER: xleap problem (Wed Jan 07 2009 - 07:06:19 CST)
  • [AMBER] Re: AMBER: questions about equilibram (Wed Jan 07 2009 - 06:54:10 CST)
  • Re: AMBER: Re: nmode error: bad nonbon (amber 10) (Tue Jan 06 2009 - 08:32:48 CST)
  • Re: AMBER: error in amber 10 (Tue Jan 06 2009 - 06:28:54 CST)
  • Re: AMBER: error in amber 10 (Tue Jan 06 2009 - 06:18:23 CST)
  • Re: AMBER: CHCl3 solvent box (Mon Jan 05 2009 - 07:48:44 CST)
  • Re: AMBER: reg sander crashing on more than 32 cores over IB (Mon Jan 05 2009 - 06:47:01 CST)
  • Re: AMBER: a question about ff03ua (Fri Jan 02 2009 - 10:35:15 CST)
  • Re: AMBER: energy jumps during molecule minimization (Fri Jan 02 2009 - 06:48:23 CST)
• David Dubins
  • [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. (Mon Sep 21 2009 - 18:02:47 CDT)
  • [AMBER] Installing Amber10 on Ubuntu (Wed Jul 29 2009 - 13:50:12 CDT)
• David LeBard
  • Re: [AMBER] implicit and explicit simulation: salt effect (Fri Jan 09 2009 - 22:23:24 CST)
• David Mobley
  • Re: [AMBER] Re: antechamber am1-bcc issues (Thu Aug 13 2009 - 08:25:52 CDT)
  • [AMBER] antechamber am1-bcc issues (Fri Aug 07 2009 - 13:19:53 CDT)
  • [AMBER] Re: bug in antechamber (Mon Jul 13 2009 - 12:41:01 CDT)
  • [AMBER] bug in antechamber (Wed Jul 08 2009 - 11:19:12 CDT)
  • [AMBER] paper of interest for FF development/solvent models (Thu Feb 19 2009 - 09:15:04 CST)
• David Patiño
  • Re: [AMBER] Error installing Amber (Tue Feb 17 2009 - 08:58:05 CST)
  • [AMBER] Error installing Amber (Mon Feb 16 2009 - 06:02:31 CST)
• David Watson
  • Re: [AMBER] standard way to upload a lipid bilayer (Sat Nov 21 2009 - 07:06:29 CST)
  • Re: [AMBER] Asking help for parallel installation of Amber9 (Wed Nov 18 2009 - 12:04:38 CST)
  • Re: [AMBER] Asking help for parallel installation of Amber9 (Wed Nov 18 2009 - 07:23:17 CST)
  • Re: [AMBER] Asking help for parallel installation of Amber9 (Wed Nov 18 2009 - 06:36:03 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Wed Nov 11 2009 - 10:56:01 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Mon Nov 09 2009 - 18:25:12 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Mon Nov 09 2009 - 16:35:32 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Mon Nov 09 2009 - 13:28:31 CST)
  • Re: [AMBER] amber9 compilation (Fri Nov 06 2009 - 10:16:58 CST)
  • Re: [AMBER] amber9 compilation (Fri Nov 06 2009 - 09:19:31 CST)
  • Re: [AMBER] installation of Amber on OSX (Wed Oct 14 2009 - 17:03:51 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Wed Oct 07 2009 - 10:53:26 CDT)
  • Re: [AMBER] loading a following attached protein in amber 10 (Tue Sep 08 2009 - 12:26:19 CDT)
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Thu Jul 30 2009 - 14:10:39 CDT)
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Wed Jul 29 2009 - 11:21:50 CDT)
  • [AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc (Thu Jul 23 2009 - 15:03:59 CDT)
  • Re: [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 19:30:12 CDT)
  • [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 (Tue Jul 21 2009 - 16:20:36 CDT)
  • Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error (Fri Jun 26 2009 - 06:31:26 CDT)
  • Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error (Thu Jun 25 2009 - 21:51:11 CDT)
  • Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error (Thu Jun 25 2009 - 21:28:22 CDT)
  • Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error (Thu Jun 25 2009 - 13:53:16 CDT)
  • Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi (Thu Jun 11 2009 - 07:43:28 CDT)
  • [AMBER] molsurf and probe radius (Sat May 09 2009 - 12:32:43 CDT)
  • Re: [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 15:00:39 CDT)
  • Re: [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 10:02:55 CDT)
  • Re: [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 09:54:57 CDT)
  • Re: [AMBER] Re: Antechamber (Fri Feb 27 2009 - 16:01:49 CST)
  • Re: [AMBER] Re: Antechamber (Fri Feb 27 2009 - 08:26:30 CST)
  • Re: [AMBER] install Amber 10 to Macbook (Sun Feb 15 2009 - 13:52:36 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 09:34:25 CST)
  • Re: [AMBER] Antechamber Connectivity (Mon Jan 26 2009 - 13:59:58 CST)
  • [AMBER] AmberTools and ptraj clustering on Mac OS X (Sat Jan 24 2009 - 15:41:04 CST)
  • Re: [AMBER] multisander error (Mon Jan 12 2009 - 16:15:26 CST)
  • Re: [AMBER] Re: AMBER: ligand parameter (Sun Jan 11 2009 - 18:39:02 CST)
  • Re: [AMBER] implicit and explicit simulation: salt effect (Fri Jan 09 2009 - 21:49:48 CST)
• david.lisgarten_at_canterbury.ac.uk
  • RE: [AMBER] (no subject) (Thu Jun 11 2009 - 03:28:56 CDT)
  • RE: [AMBER] (no subject) (Tue Jun 09 2009 - 08:56:32 CDT)
  • [AMBER] (no subject) (Tue Jun 09 2009 - 05:23:57 CDT)
• Dean Cuebas
  • [AMBER] -np not 2^x a problem w/ sander??? update (Fri Nov 06 2009 - 13:46:39 CST)
  • [AMBER] -np not 2^x a problem w/ sander??? (Fri Nov 06 2009 - 13:27:48 CST)
  • [AMBER] new process_mdout.pl script???? (Mon Oct 05 2009 - 13:11:49 CDT)
  • [AMBER] File format for reading in charges in antechamber (Sun Oct 04 2009 - 15:20:42 CDT)
  • Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? (Wed Sep 09 2009 - 14:12:00 CDT)
  • [AMBER] Any tutorial on the proper way to merge a ligand and protein? (Wed Sep 09 2009 - 13:26:02 CDT)
• decastro_at_physics.usyd.edu.au
  • [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? (Sun Sep 27 2009 - 23:52:20 CDT)
• Dechang Li
  • Re: [AMBER] J coupling constant calculation (Fri May 29 2009 - 00:31:06 CDT)
  • Re: [AMBER] how to plot this kind of map? (Thu Apr 09 2009 - 03:46:16 CDT)
  • Re: Re: Re: [AMBER] sander.MPI parallel run problem (Mon Apr 06 2009 - 06:09:04 CDT)
  • Re: Re: [AMBER] sander.MPI parallel run problem (Mon Apr 06 2009 - 05:56:53 CDT)
  • [AMBER] sander.MPI parallel run problem (Mon Apr 06 2009 - 02:44:12 CDT)
  • [AMBER] error for nmode (Thu Mar 19 2009 - 06:00:09 CDT)
• deepti nayar
  • [AMBER] atom types (Tue Jan 27 2009 - 03:47:12 CST)
  • [AMBER] prot-DNA simulation (Wed Jan 21 2009 - 05:16:09 CST)
• dhacademic
  • Re: Re: [AMBER] momentum in MD simulation (Wed Sep 02 2009 - 12:37:50 CDT)
  • [AMBER] momentum in MD simulation (Mon Aug 31 2009 - 09:37:42 CDT)
  • [AMBER] center of mass (Thu Aug 20 2009 - 15:50:47 CDT)
• Dharmik Meghana shankar
  • RE: [AMBER] Conference or workshop on AMBER? (Tue Aug 18 2009 - 00:25:25 CDT)
  • [AMBER] radial distribution function (Sat Aug 01 2009 - 00:33:58 CDT)
• Diddo Diddens
  • [AMBER] Scaling of dipole interactions (Tue Feb 10 2009 - 08:33:18 CST)
• Dmitri Nilov
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Thu Nov 05 2009 - 08:55:16 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Thu Nov 05 2009 - 08:38:32 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Thu Nov 05 2009 - 07:39:59 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Tue Nov 03 2009 - 08:06:11 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Tue Nov 03 2009 - 07:20:17 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Mon Nov 02 2009 - 07:11:15 CST)
  • [AMBER] MPI process terminated unexpectedly after cluster upgrade (Mon Nov 02 2009 - 03:17:19 CST)
  • Re: [AMBER] Equilibrium bond lengths and angle values (Tue Apr 28 2009 - 05:56:38 CDT)
  • [AMBER] Equilibrium bond lengths and angle values (Fri Apr 24 2009 - 08:19:56 CDT)
  • [AMBER] Actual force constant in SMD (Mon Mar 16 2009 - 13:07:09 CDT)
  • Re: [AMBER] SMD in Amber10 (Fri Mar 13 2009 - 10:17:44 CDT)
  • Re: [AMBER] SMD in Amber10 (Fri Mar 13 2009 - 09:54:07 CDT)
  • Re: [AMBER] SMD in Amber10 (Fri Mar 13 2009 - 03:52:26 CDT)
  • [AMBER] SMD in Amber10 (Thu Mar 12 2009 - 13:12:13 CDT)
  • [AMBER] formate parameters (Tue Feb 10 2009 - 08:47:31 CST)
• Dmitry Osolodkin
  • [AMBER] MM-PBSA results (Fri Aug 07 2009 - 09:31:48 CDT)
  • Re: [AMBER] MM-PBSA nmode statistics (Mon Jun 01 2009 - 08:12:15 CDT)
  • Re: [AMBER] MM-PBSA nmode statistics (Sat May 30 2009 - 12:25:46 CDT)
  • Re: [AMBER] MM-PBSA nmode statistics (Fri May 29 2009 - 05:53:27 CDT)
  • [AMBER] MM-PBSA nmode statistics (Thu May 28 2009 - 06:54:18 CDT)
  • [AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations (Mon May 04 2009 - 04:24:59 CDT)
  • [AMBER] Protein motions comparison (Thu Feb 19 2009 - 05:58:24 CST)
• Don.Bashford_at_stjude.org
  • Re: [AMBER] binding free energy (Sun Mar 01 2009 - 11:18:39 CST)
• Donald Keidel
  • [AMBER] RESP using antechamber with Se atom (Thu Nov 05 2009 - 13:21:37 CST)
  • Re: [AMBER] amber parameter file creation and usage (Wed Nov 04 2009 - 11:53:23 CST)
  • [AMBER] amber parameter file creation and usage (Tue Nov 03 2009 - 22:47:36 CST)
  • [AMBER] ambr parameter file creation and usage (Tue Nov 03 2009 - 22:39:38 CST)
  • [AMBER] sourcing leap commands in log file (Wed Aug 12 2009 - 19:32:31 CDT)
  • [AMBER] create new crd files from transformed coordinates (Tue Mar 24 2009 - 20:49:03 CDT)
  • [AMBER] Warning: name change in pdb file residue (Thu Mar 05 2009 - 13:25:38 CST)
• Dong Xu
  • [AMBER] MM-GBSA energy decomposition and pairwise decomposition question (Fri May 15 2009 - 17:05:52 CDT)
  • [AMBER] LCPO or Molsurf? (Sat May 02 2009 - 22:14:55 CDT)
  • [AMBER] MM-PBSA energy decomposition (Wed Apr 29 2009 - 21:03:34 CDT)
  • [AMBER] Amber FF and Glycam (Wed Apr 29 2009 - 20:42:55 CDT)
  • [AMBER] restraint constant (Sat Apr 25 2009 - 17:15:22 CDT)
  • Re: [AMBER] Disulfide bond (Tue Apr 21 2009 - 21:41:02 CDT)
  • [AMBER] Disulfide bond (Tue Apr 21 2009 - 20:37:46 CDT)
  • Re: [AMBER] Set start timestep for mdcrd traj output (Tue Apr 21 2009 - 18:44:50 CDT)
  • [AMBER] Flexible ring simulation (Tue Apr 21 2009 - 18:04:55 CDT)
• Dr. Debaprasad Giri
  • Re: [AMBER] problem in installing AMBER10 (Sat Apr 04 2009 - 07:13:46 CDT)
  • Re: [AMBER] problem in installing AMBER10 (Fri Mar 27 2009 - 05:16:47 CDT)
  • [AMBER] problem in installing AMBER10 (Mon Mar 23 2009 - 05:31:26 CDT)
• drugdesign
  • [AMBER] divcon error during antechamber run, convergence problem (Thu Mar 05 2009 - 07:53:59 CST)
  • [AMBER] protein monomerizartion times and simulation with implicit solvent (Wed Feb 18 2009 - 04:27:17 CST)
  • Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun (Tue Feb 03 2009 - 23:46:19 CST)
  • [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun (Tue Feb 03 2009 - 11:03:20 CST)
  • [AMBER] Question on heating for homology based model. (Sat Jan 31 2009 - 12:43:06 CST)
  • [AMBER] Use of Amber in distributed calculations (Sat Jan 17 2009 - 01:33:55 CST)
  • [AMBER] Amber 9 installation problem on Ubuntu (Mon Jan 12 2009 - 00:26:34 CST)
• Duggan, Brendan M.
  • RE: [AMBER] makeDIST_RST: no map function (Tue Sep 15 2009 - 08:40:00 CDT)
  • [AMBER] RE: DCCM (Mon Jul 20 2009 - 09:29:46 CDT)
  • RE: [AMBER] DCCM (Wed Jul 15 2009 - 11:06:57 CDT)
  • RE: [AMBER] Warning: name change in pdb file residue (Thu Mar 05 2009 - 14:42:21 CST)
  • RE: AMBER: RMS plot (Tue Jan 06 2009 - 13:54:04 CST)
• E.M.
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 21:08:02 CDT)
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 01:30:31 CDT)
  • [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 00:29:47 CDT)
  • Re: [AMBER] ATP/GTP parameters (Mon Aug 31 2009 - 23:48:39 CDT)
  • Re: [AMBER] ATP/GTP parameters (Mon Aug 31 2009 - 15:50:09 CDT)
  • Re: [AMBER] radius for Manganese ion (Sun Aug 30 2009 - 18:38:38 CDT)
  • [AMBER] Meaning of GMAX (Mon Aug 24 2009 - 04:05:10 CDT)
  • [AMBER] Re: angle with ptraj (Wed Aug 19 2009 - 14:44:56 CDT)
  • [AMBER] angle with ptraj (Wed Aug 19 2009 - 14:27:29 CDT)
  • [AMBER] RESP fit (Fri Jul 17 2009 - 18:00:08 CDT)
  • [AMBER] Re: Request to mailing list AMBER rejected (Mon Jul 13 2009 - 22:37:46 CDT)
  • [AMBER] NAB memory (Fri Jun 26 2009 - 13:06:41 CDT)
  • Re: [AMBER] Problems using nmode in NAB (Wed Jun 24 2009 - 23:15:38 CDT)
  • [AMBER] NAB memory increase (Wed Jun 24 2009 - 15:12:09 CDT)
  • Re: [AMBER] Problems using nmode in NAB (Wed Jun 24 2009 - 04:09:44 CDT)
  • [AMBER] Problems using nmode in NAB (Wed Jun 24 2009 - 01:05:50 CDT)
  • [AMBER] anal output: Entalphy or Free Energy? (Tue May 12 2009 - 17:25:41 CDT)
  • [AMBER] ANAL problems (Tue Apr 28 2009 - 15:12:04 CDT)
• Ed Pate
  • [AMBER] ambmask question (Mon Apr 06 2009 - 23:36:40 CDT)
  • [AMBER] ptraj problem (Fri Apr 03 2009 - 15:13:37 CDT)
• Edward M
  • [AMBER] AMBER question: bad atom type: MN (Mon Jun 22 2009 - 22:05:51 CDT)
  • [AMBER] bad atom type: MN (Mon Jun 22 2009 - 18:12:09 CDT)
  • [AMBER] bad atom type: MN (Mon Jun 22 2009 - 18:12:09 CDT)
  • [AMBER] bad atom type: MN (Mon Jun 22 2009 - 18:10:54 CDT)
  • [AMBER] anal output: Entalphy or Free Energy? (Tue May 12 2009 - 19:14:37 CDT)
  • Re: [AMBER] ANAL problems (Tue Apr 28 2009 - 18:01:34 CDT)
• Edyta Malolepsza
  • Re: [AMBER] total charge for NPRO in ff03ua (Tue Jun 16 2009 - 04:42:55 CDT)
  • [AMBER] total charge for NPRO in ff03ua (Mon Jun 15 2009 - 05:09:35 CDT)
• Eliana Asciutto
  • Re: [AMBER] RDC and alignment tensor (Fri Oct 23 2009 - 14:19:00 CDT)
  • Re: [AMBER] RDC and alignment tensor (Mon Oct 19 2009 - 14:03:43 CDT)
  • [AMBER] Re: RDC and alignment tensor (Mon Oct 19 2009 - 12:51:50 CDT)
  • Re: [AMBER] RDC and alignment tensor (Mon Oct 19 2009 - 11:50:31 CDT)
  • [AMBER] RDC and alignment tensor (Fri Oct 16 2009 - 15:21:34 CDT)
• Elodie Laine
  • [AMBER] Question about Thermal Integration with Softcore (Wed May 13 2009 - 04:13:22 CDT)
• emiliawu_at_dicp.ac.cn
  • [AMBER] unnatural amino acid (Fri May 29 2009 - 01:56:43 CDT)
• Eric
  • Re: [AMBER] amber9 in fedora10 (Tue Jan 13 2009 - 12:28:33 CST)
• eric johnson
  • [AMBER] Amber99SB (Tue Aug 11 2009 - 09:33:34 CDT)
• Eric Pettersen
  • Re: [AMBER] RESP using antechamber with Se atom (Fri Nov 06 2009 - 10:49:16 CST)
• Eric Shamay
  • [AMBER] Lisp library for amber analysis? (Wed Nov 11 2009 - 15:54:12 CST)
• Faezeh Salehi
  • [AMBER] Question about the debug forces (Wed Sep 02 2009 - 16:30:47 CDT)
• Farly Walsh
  • Re: [AMBER] AmberTools compiling error (Wed Apr 29 2009 - 14:49:27 CDT)
  • [AMBER] AmberTools compiling error (Sun Apr 26 2009 - 19:40:38 CDT)
• felix
  • Re: [AMBER] diffusion coeficients (Fri Jul 17 2009 - 08:41:43 CDT)
  • [AMBER] diffusion coeficients (Fri Jul 17 2009 - 03:15:35 CDT)
• Fernando Martín García
  • Re: [AMBER] 60 giga output file .mdcrd file (Tue Nov 03 2009 - 04:35:41 CST)
  • RE: [AMBER] dftb_disper problem (Mon May 11 2009 - 07:34:01 CDT)
  • Re: [AMBER] dftb_disper problem (Fri May 08 2009 - 07:43:19 CDT)
  • Re: [Barracuda SPAM] Re: [AMBER] dftb_disper problem (Thu May 07 2009 - 08:32:06 CDT)
  • [AMBER] dftb_disper problem (Thu May 07 2009 - 07:30:25 CDT)
• Filip Lankas
  • Re: [AMBER] Circular RNA topology file (Mon Oct 26 2009 - 05:13:46 CDT)
• Floris Buelens
  • [AMBER] GAFF conjugated ring system dihedrals (Wed Jan 28 2009 - 06:04:55 CST)
• fmgarcia_at_cbm.uam.es
  • RE: [AMBER] dftb_disper problem (Fri May 08 2009 - 11:27:30 CDT)
• fohm fohm
  • Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem (Tue Mar 31 2009 - 06:04:10 CDT)
  • [AMBER] pmemd | Compilation problem with ifort and mvapich environment (Wed Jan 14 2009 - 11:23:50 CST)
• Francesca Poletti
  • [AMBER] methyl group at the N-terminal (Fri Jun 19 2009 - 07:03:56 CDT)
• Francesco Pietra
  • [AMBER] coarse-grained MD (Wed Nov 11 2009 - 02:27:27 CST)
  • [AMBER] Getting minimized .pdb file without non-polar hydrogens (Mon Nov 09 2009 - 13:31:40 CST)
  • Re: [AMBER] pmemd failure (Sun Nov 08 2009 - 13:08:53 CST)
  • [AMBER] pmemd failure (Sun Nov 08 2009 - 10:52:28 CST)
  • Re: [AMBER] average torsional energy (Mon Jun 08 2009 - 04:11:52 CDT)
  • [AMBER] Fwd: average torsional energy (Sun Jun 07 2009 - 11:09:37 CDT)
  • [AMBER] average torsional energy (Sat Jun 06 2009 - 11:57:49 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Fri Jun 05 2009 - 13:17:45 CDT)
  • [AMBER] Restraining counterions? (Tue Apr 28 2009 - 12:32:18 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Wed Apr 22 2009 - 13:01:39 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Wed Apr 22 2009 - 05:16:11 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Tue Apr 21 2009 - 16:49:14 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Tue Apr 21 2009 - 16:29:36 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Tue Apr 21 2009 - 13:40:35 CDT)
  • Re: [AMBER] Creating conditions for biased MD (Mon Apr 20 2009 - 12:31:52 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Sun Apr 19 2009 - 09:36:02 CDT)
  • Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 18:20:02 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 18:17:38 CDT)
  • Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 10:23:58 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 10:14:43 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 05:03:09 CDT)
  • Re: [AMBER] ssh and make test.parallel (Wed Apr 08 2009 - 02:19:36 CDT)
  • [AMBER] Testing parallel amber10: no libmkl_lapack.so (Tue Apr 07 2009 - 13:56:25 CDT)
  • Re: [AMBER] ssh and make test.parallel (Mon Apr 06 2009 - 09:29:19 CDT)
  • [AMBER] ssh and make test.parallel (Mon Apr 06 2009 - 04:58:39 CDT)
  • Re: [AMBER] amber9 serial compilation issues (Fri Apr 03 2009 - 17:04:17 CDT)
  • [AMBER] amber9 serial compilation issues (Fri Apr 03 2009 - 13:38:12 CDT)
  • Re: [AMBER] Failure to compile amber9 serial ifort gcc (Thu Apr 02 2009 - 11:00:46 CDT)
  • Re: [AMBER] yacc parser (Thu Apr 02 2009 - 10:37:53 CDT)
  • Re: [AMBER] Failure to compile amber9 serial ifort gcc (Thu Apr 02 2009 - 06:16:36 CDT)
  • [AMBER] Fwd: yacc parser (Wed Apr 01 2009 - 15:53:01 CDT)
  • [AMBER] yacc parser (Wed Apr 01 2009 - 09:58:01 CDT)
  • [AMBER] Failure to compile amber9 serial ifort gcc (Wed Apr 01 2009 - 06:04:18 CDT)
  • [AMBER] Creating conditions for biased MD (Mon Mar 30 2009 - 05:16:54 CDT)
  • [AMBER] Quality/size of HDD for Amber (Fri Mar 06 2009 - 03:26:03 CST)
  • [AMBER] MD simulation at constant pH (Thu Feb 26 2009 - 04:52:47 CST)
  • Re: [AMBER] Any link to a major QM code? (Mon Feb 16 2009 - 08:47:04 CST)
  • [AMBER] Any link to a major QM code? (Sun Feb 15 2009 - 11:58:30 CST)
  • Re: [AMBER] failure to run antechamber with amber 10 (Fri Jan 30 2009 - 02:04:33 CST)
  • [AMBER] failure to run antechamber with amber 10 (Thu Jan 29 2009 - 16:29:18 CST)
  • [AMBER] Off topic. Hardware problem (Sat Jan 10 2009 - 02:26:55 CST)
• Frank X. Vázquez
  • [AMBER] Dihedral energy profile in a single molecule (Fri Oct 16 2009 - 09:55:53 CDT)
  • [AMBER] Output forces in Sander (Tue Jul 21 2009 - 16:58:36 CDT)
• Furia Gargano
  • [AMBER] to remove AMBER list (Sat Jan 17 2009 - 12:02:26 CST)
  • [AMBER] To stop the AMBER's list (Sat Jan 17 2009 - 11:59:48 CST)
• FyD
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 13:50:42 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 11:49:05 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 11:31:31 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 11:22:23 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 10:06:01 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Mon Nov 23 2009 - 07:25:15 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 11:47:00 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 09:40:50 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Fri Nov 20 2009 - 07:42:58 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Wed Nov 18 2009 - 08:29:14 CST)
  • Re: [AMBER] combining parameter files of ligand and enzyme (Wed Nov 18 2009 - 01:49:23 CST)
  • Re: [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 14:18:20 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 14:10:03 CST)
  • Re: [AMBER] R.E.D. too small charges (Fri Nov 13 2009 - 07:06:51 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Fri Nov 13 2009 - 05:43:48 CST)
  • Re: [AMBER] R.E.D. resp error (Thu Nov 12 2009 - 23:36:44 CST)
  • Re: [AMBER] Increase Temperature to 550 K (Thu Nov 12 2009 - 01:51:24 CST)
  • Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber (Wed Nov 04 2009 - 23:42:43 CST)
  • Re: [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber (Wed Nov 04 2009 - 09:28:04 CST)
  • Re: [AMBER] errors on leap for a RNA+Adenine pdb structure (Wed Nov 04 2009 - 07:39:02 CST)
  • Re: [AMBER] Phosphorylated Threonine (Tue Nov 03 2009 - 13:41:49 CST)
  • [AMBER] A bug in LEaP II ? (Sun Oct 25 2009 - 07:58:36 CDT)
  • Re: [AMBER] resp_problem (Sun Oct 25 2009 - 01:12:31 CDT)
  • Re: [AMBER] charges for heme-cys in p450 (Fri Oct 23 2009 - 05:57:43 CDT)
  • Re: [AMBER] too many undefined parameters in frcmod (Thu Oct 22 2009 - 04:37:46 CDT)
  • Re: [AMBER] AMBER FF and NAMD (Fri Oct 16 2009 - 14:19:13 CDT)
  • Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? (Wed Oct 14 2009 - 08:40:09 CDT)
  • [AMBER] A bug in LEaP ? (Sun Oct 11 2009 - 07:08:37 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Sun Oct 11 2009 - 06:42:25 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Sat Oct 10 2009 - 00:52:27 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 09 2009 - 16:06:20 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Fri Oct 09 2009 - 15:38:08 CDT)
  • Re: [AMBER] Missing X11 Libraries (Fri Oct 09 2009 - 15:35:59 CDT)
  • Re: [AMBER] ff03 parameter for GDP and GTP (Fri Oct 09 2009 - 05:37:40 CDT)
  • Re: [AMBER] DMF solvent box (Thu Oct 08 2009 - 23:08:59 CDT)
  • Re: [AMBER] Missing X11 Libraries (Wed Oct 07 2009 - 15:45:34 CDT)
  • Re: [AMBER] DMF solvent box (Wed Oct 07 2009 - 15:34:35 CDT)
  • Re: [AMBER] using RESP program (Wed Oct 07 2009 - 15:04:38 CDT)
  • [AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org (Sun Oct 04 2009 - 09:37:06 CDT)
  • Re: [AMBER] red problem (Thu Oct 01 2009 - 23:48:57 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 23:27:13 CDT)
  • Re: [AMBER] too many missing parameters in frcmod for the prep of my ligand (Wed Sep 30 2009 - 05:30:32 CDT)
  • Re: [AMBER] partial charges in Amber force field (Mon Sep 28 2009 - 13:32:42 CDT)
  • Re: [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol (Mon Sep 28 2009 - 13:23:20 CDT)
  • Re: [AMBER] Parameter Problem (Wed Sep 23 2009 - 03:28:49 CDT)
  • Re: [AMBER] Pentane UA model (Tue Sep 22 2009 - 02:02:50 CDT)
  • Re: [AMBER] Regarding united atom force field (Tue Sep 22 2009 - 01:13:03 CDT)
  • Re: [AMBER] DMF solvent box (Sat Sep 19 2009 - 01:36:20 CDT)
  • RE: [AMBER] database (Fri Sep 18 2009 - 19:49:17 CDT)
  • Re: [AMBER] how to make 50% aqueous TFE box? (Fri Sep 18 2009 - 19:22:35 CDT)
  • Re: [AMBER] database (Fri Sep 18 2009 - 02:28:53 CDT)
  • RE: [AMBER] database (Thu Sep 17 2009 - 16:54:29 CDT)
  • RE: [AMBER] database (Thu Sep 17 2009 - 11:00:22 CDT)
  • Re: [AMBER] loading RNA sequence in xleap (Thu Sep 17 2009 - 04:39:09 CDT)
  • Re: [AMBER] DMF solvent box (Thu Sep 17 2009 - 02:00:06 CDT)
  • RE: [AMBER] database (Wed Sep 16 2009 - 13:58:38 CDT)
  • RE: [AMBER] database (Wed Sep 16 2009 - 13:56:16 CDT)
  • RE: [AMBER] database (Wed Sep 16 2009 - 11:59:30 CDT)
  • Re: [AMBER] DMF solvent box (Wed Sep 16 2009 - 00:09:42 CDT)
  • Re: [AMBER] DMF solvent box (Mon Sep 14 2009 - 10:04:58 CDT)
  • Re: [AMBER] DMF solvent box (Sun Sep 13 2009 - 12:01:13 CDT)
  • Re: [AMBER] DMF solvent box (Sun Sep 13 2009 - 04:25:33 CDT)
  • Re: [AMBER] "nan" in gaussian input files generated by antechamber (Sat Sep 12 2009 - 09:58:52 CDT)
  • Re: [AMBER] RESP RED (Sat Sep 12 2009 - 09:35:16 CDT)
  • Re: [AMBER] DMF solvent box (Sat Sep 12 2009 - 09:07:30 CDT)
  • Re: [AMBER] Problem about adding a small residue to DNA (Mon Sep 07 2009 - 04:53:14 CDT)
  • Re: [AMBER] R.E.D. : Gaussian Error (Mon Sep 07 2009 - 00:07:34 CDT)
  • Re: [AMBER] R.E.D. : Gaussian Error (Sun Sep 06 2009 - 14:41:41 CDT)
  • Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter (Fri Sep 04 2009 - 02:43:00 CDT)
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 04:36:45 CDT)
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 03:35:11 CDT)
  • Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter (Thu Sep 03 2009 - 02:03:45 CDT)
  • Re: [AMBER] ATP and GTP parameters (Thu Sep 03 2009 - 01:15:54 CDT)
  • RE: [AMBER] ATP/GTP parameters (Tue Sep 01 2009 - 11:25:45 CDT)
  • Re: [AMBER] ATP/GTP parameters (Tue Sep 01 2009 - 01:10:41 CDT)
  • Re: [AMBER] How to derive charges from the output (Mon Aug 31 2009 - 15:35:46 CDT)
  • Re: [AMBER] ATP/GTP parameters (Mon Aug 31 2009 - 15:20:50 CDT)
  • Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial (Mon Aug 31 2009 - 15:10:52 CDT)
  • Re: [AMBER] Single Adenine (Thu Aug 27 2009 - 16:20:48 CDT)
  • Re: [AMBER] Single Adenine (Thu Aug 27 2009 - 02:05:54 CDT)
  • Re: [AMBER] Inquiries about antechamber (Thu Aug 27 2009 - 01:15:55 CDT)
  • Re: [AMBER] acetone lib and frcmod files? (Tue Aug 25 2009 - 02:50:57 CDT)
  • Re: [AMBER] acetone lib and frcmod files? (Tue Aug 25 2009 - 02:47:50 CDT)
  • Re: [AMBER] acetone lib and frcmod files? (Mon Aug 24 2009 - 15:13:33 CDT)
  • RE: [AMBER] acetone lib and frcmod files? (Mon Aug 24 2009 - 02:31:40 CDT)
  • Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? (Tue Aug 18 2009 - 19:05:19 CDT)
  • Re: [AMBER] antechamber execution (Tue Aug 18 2009 - 18:59:40 CDT)
  • [AMBER] Re: [q4md-fft] charge calculation (Mon Aug 17 2009 - 18:40:49 CDT)
  • Re: [AMBER] gaussain output (Mon Aug 17 2009 - 17:59:39 CDT)
  • Re: [AMBER] gaussain output (Mon Aug 17 2009 - 04:50:53 CDT)
  • Re: [AMBER] Charge Problem (Sat Aug 15 2009 - 07:06:45 CDT)
  • Re: [AMBER] query regarding fes cluster (Wed Aug 12 2009 - 08:00:37 CDT)
  • Re: [AMBER] parameters for HIV protease inhibitors (Wed Aug 12 2009 - 07:56:18 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 06:59:51 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Tue Jul 28 2009 - 02:32:52 CDT)
  • Re: [AMBER] loading a mol2 file in xleap (Mon Jul 27 2009 - 08:44:50 CDT)
  • Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded (Mon Jul 27 2009 - 00:03:00 CDT)
  • Re: [AMBER] loading a mol2 file in xleap (Fri Jul 24 2009 - 15:00:41 CDT)
  • Re: [AMBER] radical simulation (Fri Jul 24 2009 - 05:27:34 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 23 2009 - 12:49:23 CDT)
  • Re: [AMBER] saquinavir parameterization with antechamber (Thu Jul 23 2009 - 02:29:57 CDT)
  • Re: [AMBER] saquinavir parameterization with antechamber (Wed Jul 22 2009 - 13:41:21 CDT)
  • Re: [AMBER] questions about RESP (Mon Jul 20 2009 - 15:46:04 CDT)
  • Re: [AMBER] RE: charge not zero on group:''''.respin1 attached (Sun Jul 19 2009 - 02:41:17 CDT)
  • Re: [AMBER] RESP fit (Sat Jul 18 2009 - 01:29:56 CDT)
  • Re: [AMBER] amino acids caps for truncated proteins (Thu Jul 16 2009 - 11:58:32 CDT)
  • Re: [AMBER] command for RESP fitting (Thu Jul 16 2009 - 09:34:28 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 16 2009 - 09:27:44 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Thu Jul 16 2009 - 01:25:03 CDT)
  • Re: [AMBER] R.E.D. help please (Wed Jul 15 2009 - 11:35:57 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 14 2009 - 15:01:32 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Tue Jul 14 2009 - 02:40:00 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 14 2009 - 01:47:00 CDT)
  • Re: [AMBER] help needed for HID (Mon Jul 13 2009 - 15:27:13 CDT)
  • Re: [AMBER] R.E.D intra-mcc and reorientation (Sat Jul 11 2009 - 03:05:56 CDT)
  • Re: [AMBER] Peptide bond broken (Sat Jul 11 2009 - 01:58:06 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 10:24:08 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 00:52:12 CDT)
  • Re: [AMBER] Zinc ion, help (Wed Jul 08 2009 - 04:43:26 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 07 2009 - 02:50:09 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 01:45:13 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 01:29:11 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Sun Jul 05 2009 - 04:39:13 CDT)
  • [AMBER] Re: [q4md-fft] Charge calculation or non standard residue (Sun Jul 05 2009 - 03:30:50 CDT)
  • Re: [AMBER] H-bond vs. VdW (Sat Jul 04 2009 - 00:01:58 CDT)
  • [AMBER] Re: Error in REDIII (Fri Jul 03 2009 - 09:59:30 CDT)
  • Re: [AMBER] antechamber (Thu Jul 02 2009 - 01:33:46 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:26:39 CDT)
  • Re: [AMBER] Saccharides chains termini (Tue Jun 30 2009 - 10:47:04 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Tue Jun 30 2009 - 02:31:53 CDT)
  • Re: [AMBER] Regd: parameter Fe4S4 (Mon Jun 29 2009 - 14:03:22 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Mon Jun 29 2009 - 13:28:19 CDT)
  • Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues (Fri Jun 26 2009 - 04:41:52 CDT)
  • Re: [AMBER] installation of RESP programm (Fri Jun 26 2009 - 04:15:39 CDT)
  • Re: AW: [AMBER] atomtypes in gaff (Fri Jun 26 2009 - 01:56:35 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 08:47:31 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 06:52:45 CDT)
  • Re: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 06:45:16 CDT)
  • Re: AW: AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 06:36:20 CDT)
  • Re: AW: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 05:32:33 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 05:04:27 CDT)
  • [AMBER] Re: question about ff (Thu Jun 25 2009 - 04:12:40 CDT)
  • Re: [AMBER] atomtypes in gaff (Thu Jun 25 2009 - 03:55:03 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 00:15:23 CDT)
  • Re: [AMBER] How to build amide bond etween two protein chains (Wed Jun 24 2009 - 01:18:25 CDT)
  • Re: [AMBER] making leap to recognize 5' phosphate (Wed Jun 24 2009 - 01:02:42 CDT)
  • Re: [AMBER] making leap to recognize 5' phosphate (Tue Jun 23 2009 - 04:48:34 CDT)
  • Re: [AMBER] making leap to recognize 5' phosphate (Tue Jun 23 2009 - 02:45:31 CDT)
  • RE: [AMBER] RED Geometry Calculation Error (Sat Jun 20 2009 - 01:41:46 CDT)
  • Re: [AMBER] RED Geometry Calculation Error (Fri Jun 19 2009 - 14:19:00 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 10:54:05 CDT)
  • Re: [AMBER] methyl group at the N-terminal (Fri Jun 19 2009 - 07:12:36 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 04:26:46 CDT)
  • Re: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 (Fri Jun 19 2009 - 03:47:39 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Fri Jun 19 2009 - 00:41:54 CDT)
  • Re: [AMBER] Residues (Thu Jun 18 2009 - 15:24:16 CDT)
  • [AMBER] Re: R.E.D. error message (Thu Jun 18 2009 - 15:13:41 CDT)
  • RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Thu Jun 18 2009 - 14:55:34 CDT)
  • Re: [AMBER] GLYCAM: warnings by writing topology (Wed Jun 17 2009 - 10:40:06 CDT)
  • Re: [AMBER] GLYCAM: warnings by writing topology (Wed Jun 17 2009 - 02:30:26 CDT)
  • RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot (Wed Jun 17 2009 - 01:32:11 CDT)
  • Re: [AMBER] Residues (Mon Jun 15 2009 - 01:51:56 CDT)
  • [AMBER] Re: [Contact q4md] qurey reagarding RED Server (Sat Jun 13 2009 - 03:08:26 CDT)
  • RE: [AMBER] glycopeptide Parametrization (Sat Jun 13 2009 - 02:40:00 CDT)
  • Re: [AMBER] Residues (Fri Jun 12 2009 - 10:36:10 CDT)
  • Re: [AMBER] Residues (Fri Jun 12 2009 - 09:24:35 CDT)
  • Re: [AMBER] glycopeptide Parametrization (Fri Jun 12 2009 - 02:05:51 CDT)
  • Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot (Thu Jun 11 2009 - 13:59:27 CDT)
  • Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid (Thu Jun 11 2009 - 01:48:27 CDT)
  • Re: [AMBER] (no subject) (Mon Jun 08 2009 - 12:14:05 CDT)
  • Re: [AMBER] Pentavalent Phosphorous and Antechamber (Thu Jun 04 2009 - 01:29:59 CDT)
  • Re: [AMBER] different comformations to choose for RESP (Mon Jun 01 2009 - 09:32:21 CDT)
  • [AMBER] sleap and delete (Mon Jun 01 2009 - 02:35:32 CDT)
  • Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP (Sun May 31 2009 - 07:51:50 CDT)
  • Re: [AMBER] unnatural amino acid (Thu May 28 2009 - 13:46:27 CDT)
  • Re: [AMBER] partial charge and topology of intrastrand cross-link DNA (Wed May 27 2009 - 00:27:40 CDT)
  • [AMBER] resp charge (Wed May 20 2009 - 02:42:07 CDT)
  • Re: [AMBER] adding a standard amino acid as ligand (Fri May 15 2009 - 08:39:18 CDT)
  • Re: [AMBER] Can I use only a single point calculation to derive RESP charges? (Sun May 10 2009 - 01:52:12 CDT)
  • Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. (Sun May 10 2009 - 00:49:55 CDT)
  • Re: [AMBER] Can I use only a single point calculation to derive RESP charges? (Sat May 09 2009 - 01:00:36 CDT)
  • Re: [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber (Sat May 02 2009 - 11:06:28 CDT)
  • Re: [AMBER] charge of Fe-heme (Sat May 02 2009 - 11:02:48 CDT)
  • Re: [AMBER] REd program! (Wed Apr 29 2009 - 08:53:12 CDT)
  • Re: [AMBER] CY3 dye parameters (Sat Apr 25 2009 - 01:04:22 CDT)
  • Re: [AMBER] Equilibrium bond lengths and angle values (Fri Apr 24 2009 - 16:05:42 CDT)
  • Re: [AMBER] Amber Sulfate Ion Parameters (Thu Apr 23 2009 - 01:07:40 CDT)
  • Re: [AMBER] Amber Sulfate Ion Parameters (Thu Apr 23 2009 - 00:18:28 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Mon Apr 20 2009 - 09:50:12 CDT)
  • Re: [AMBER] missing amber force field parameters (Thu Apr 16 2009 - 04:41:44 CDT)
  • [AMBER] Release of R.E.D. Server (Thu Apr 09 2009 - 03:31:30 CDT)
  • Re: [AMBER] Problem with CAP residues (Tue Apr 07 2009 - 06:01:35 CDT)
  • Re: [AMBER] LYN again (Mon Apr 06 2009 - 09:26:14 CDT)
  • Re: [AMBER] LYN again (Sun Apr 05 2009 - 14:24:27 CDT)
  • Re: [AMBER] modifying LYN (Tue Mar 31 2009 - 10:41:56 CDT)
  • Re: [AMBER] installing resp on linux 64bit (Thu Mar 26 2009 - 14:37:22 CDT)
  • Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? (Sun Mar 22 2009 - 15:12:17 CDT)
  • Re: [AMBER] Input file of the second stage RESP fitting (Tue Mar 17 2009 - 08:32:58 CDT)
  • Re: [AMBER] please help me out (Mon Mar 09 2009 - 05:05:06 CDT)
  • Re: [AMBER] please help me out (Mon Mar 09 2009 - 03:10:08 CDT)
  • Re: [AMBER] please help me out (Thu Mar 05 2009 - 03:22:20 CST)
  • [AMBER] Re: Fw:How to creat .frcmod file (Thu Mar 05 2009 - 00:22:56 CST)
  • Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? (Tue Mar 03 2009 - 08:12:18 CST)
  • Re: [AMBER] inpcrd and prmtop (Tue Mar 03 2009 - 04:19:43 CST)
  • Re: [AMBER] Ramesh here (Sat Feb 28 2009 - 07:45:39 CST)
  • Re: [AMBER] Re: Antechamber (Fri Feb 27 2009 - 07:12:16 CST)
  • Re: [AMBER] MD simulations on a protein with FAD and NADH (Fri Feb 27 2009 - 02:24:37 CST)
  • Re: [AMBER] Iron 2+ parameters (Mon Feb 16 2009 - 12:25:45 CST)
  • Re: [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] (Tue Feb 10 2009 - 09:05:56 CST)
  • Re: [AMBER] parameter files for D-amino acid (Thu Feb 05 2009 - 09:00:55 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Thu Jan 29 2009 - 15:58:34 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Thu Jan 29 2009 - 14:57:51 CST)
  • Re: [AMBER] large resp charges for non-natural amino acid (Wed Jan 28 2009 - 22:04:11 CST)
  • Re: [AMBER] topology file for GLY with amino and carboxyl group? (Tue Jan 27 2009 - 14:02:14 CST)
  • Re: [AMBER] thioglycoside (Mon Jan 26 2009 - 09:07:37 CST)
  • Re: [AMBER] non-natural amino acids (Thu Jan 22 2009 - 17:25:31 CST)
  • Re: [AMBER] Using GAFF with a covalently bound ligand or label (Fri Jan 16 2009 - 03:13:43 CST)
  • Re: [AMBER] Can't reproduce RESP charges (Tue Jan 13 2009 - 05:52:13 CST)
  • [AMBER] Release of the R.E.D.-III.1 tools (Mon Jan 12 2009 - 05:59:14 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Mon Jan 12 2009 - 01:43:48 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Sun Jan 11 2009 - 01:00:40 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Sat Jan 10 2009 - 02:26:13 CST)
  • Re: AMBER: a question about ff03ua (Fri Jan 02 2009 - 14:20:37 CST)
• Gabriel Urquiza
  • Re: [AMBER] Targeted MD and QM/MM (Tue Jun 02 2009 - 17:08:11 CDT)
  • [AMBER] Targeted MD and QM/MM (Fri May 29 2009 - 15:09:31 CDT)
• Ganesh Kamath
  • [AMBER] question with hbond in carnal (Tue Oct 20 2009 - 08:58:36 CDT)
  • Re: [AMBER] question with pucker in six member ring (Mon Oct 19 2009 - 12:42:17 CDT)
  • Re: [AMBER] question with pucker in six member ring (Fri Oct 16 2009 - 14:31:31 CDT)
  • Re: [AMBER] question with pucker in six member ring (Fri Oct 16 2009 - 13:36:41 CDT)
  • [AMBER] question with pucker in six member ring (Thu Oct 15 2009 - 14:55:45 CDT)
  • [AMBER] six member pucker calculation (Wed Oct 14 2009 - 09:27:24 CDT)
  • Re: [AMBER] using RESP program (Wed Oct 07 2009 - 05:36:13 CDT)
  • [AMBER] pucker calculation for six member rings (Mon Oct 05 2009 - 13:03:15 CDT)
  • [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol (Mon Sep 28 2009 - 12:03:13 CDT)
  • Re: [AMBER] solvent accessible surface area (Wed Sep 23 2009 - 14:26:33 CDT)
  • [AMBER] solvent accessible surface area (Wed Sep 23 2009 - 14:07:23 CDT)
  • [AMBER] question with hbond (Wed Sep 16 2009 - 16:36:18 CDT)
  • [AMBER] radial distribution function in amber (Mon Sep 14 2009 - 09:58:56 CDT)
  • [AMBER] question with radial distribution function (Thu Sep 10 2009 - 17:08:34 CDT)
• Ganesh Krishnan
  • Re: [AMBER] R.E.D intra-mcc and reorientation (Sat Jul 11 2009 - 17:56:18 CDT)
  • [AMBER] R.E.D intra-mcc and reorientation (Fri Jul 10 2009 - 17:00:35 CDT)
• Gard Nelson
  • [AMBER] compiling errors (Wed Feb 04 2009 - 18:30:22 CST)
• Gary Clark
  • Re: [AMBER] Amber Sulfate Ion Parameters (Thu Apr 23 2009 - 14:55:24 CDT)
  • [AMBER] Amber Sulfate Ion Parameters (Wed Apr 22 2009 - 17:31:00 CDT)
• gaurav panwar
  • [AMBER] QM/MM minimization (Thu Sep 10 2009 - 09:05:37 CDT)
  • [AMBER] problem in QM/MM input file (Mon Sep 07 2009 - 12:33:20 CDT)
  • [AMBER] QM/MM simulation (Thu Sep 03 2009 - 15:11:42 CDT)
• George Tzotzos
  • Re: [AMBER] RE: Tutorial 5 (Sun Feb 01 2009 - 15:04:36 CST)
  • Re: [AMBER] failure to run antechamber with amber 10 (Thu Jan 29 2009 - 16:48:50 CST)
  • Re: [AMBER] Building atom and angle parameters (Tue Jan 27 2009 - 12:24:52 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 10:44:06 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 09:43:19 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 09:24:30 CST)
  • Re: [AMBER] Antechamber ligand prep (Tue Jan 27 2009 - 08:48:11 CST)
  • Re: [AMBER] Antechamber Connectivity (Mon Jan 26 2009 - 12:23:58 CST)
  • Re: [AMBER] "Could not find bond parameter" (Fri Jan 23 2009 - 12:16:34 CST)
  • RE: [AMBER] Atom types (Mon Jan 19 2009 - 12:02:42 CST)
  • [AMBER] Atom types (Mon Jan 19 2009 - 08:04:09 CST)
  • RE: [AMBER] Duplicate residues (Mon Jan 19 2009 - 06:54:37 CST)
  • Re: [AMBER] RE: Tutorial 5 (Fri Jan 16 2009 - 14:31:11 CST)
• Germain Vallverdu
  • [AMBER] dihedral force calculation (Fri Sep 11 2009 - 09:35:08 CDT)
  • Re: [AMBER] PTRAJ, rms for separated residues. (Mon Jun 22 2009 - 04:27:43 CDT)
  • Re: [AMBER] Distance restraints between groups of atoms (Tue Jun 09 2009 - 03:39:45 CDT)
  • Re: [AMBER] Distance restraints between groups of atoms (Wed Jun 03 2009 - 09:43:37 CDT)
  • [AMBER] Distance restraints between groups of atoms (Wed Jun 03 2009 - 01:58:57 CDT)
• German Erlenkamp
  • Re: [AMBER] Problems with PMEMD installation for AMBER10 (Thu May 07 2009 - 02:18:36 CDT)
  • Re: [AMBER] Problems with PMEMD installation for AMBER10 (Tue May 05 2009 - 08:07:13 CDT)
  • [AMBER] Problems with PMEMD installation for AMBER10 (Tue May 05 2009 - 07:40:56 CDT)
  • [AMBER] Problems with MM-PBSA Calculation after MD (Thu Mar 12 2009 - 04:28:23 CDT)
• Gert von Helden
  • [AMBER] polarizable force field for 18-crown-6 (Thu Apr 16 2009 - 12:33:15 CDT)
• Giacomo Bastianelli
  • [AMBER] GBSA: dielectric symmetry (Thu Mar 05 2009 - 17:29:50 CST)
• Gianluca Degliesposti
  • [AMBER] Question on ECAVITY term of MM_PBSA (Mon Sep 21 2009 - 06:18:27 CDT)
  • [AMBER] Question on ECAVITY term of MM_PBSA (Mon Sep 14 2009 - 10:28:12 CDT)
• Gijs Schaftenaar
  • [AMBER] Parmchk wrongly calculates missing parameters (fwd) (Fri Feb 20 2009 - 07:16:17 CST)
• gilbert_at_bluemarble.net
  • Re: [AMBER] ambertools and Snow Leopard 64 bits kernel (Tue Sep 22 2009 - 21:18:12 CDT)
  • [AMBER] gaff.dat questions (Wed Sep 09 2009 - 09:02:28 CDT)
  • [AMBER] problem compiling amber tools with gcc-4.4.1 (Mon Aug 24 2009 - 22:07:44 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 07:37:53 CDT)
  • Re: [AMBER] Re: antechamber am1-bcc issues (Sat Aug 08 2009 - 08:55:40 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 08:10:32 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:11:17 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 09:17:09 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 07:57:04 CDT)
  • [AMBER] Antechamber am1bcc questions (Mon Jun 15 2009 - 08:04:19 CDT)
• Giorgio Maccari
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Wed Nov 11 2009 - 10:53:04 CST)
• Giorgos Lamprinidis
  • Re: [AMBER] Need help for PMEMD 10 installation (Tue Jul 14 2009 - 02:29:09 CDT)
  • Re: [AMBER] MM-PBSA problem (Mon Jul 06 2009 - 03:07:14 CDT)
  • [AMBER] MM-PBSA problem (Fri Jul 03 2009 - 08:50:36 CDT)
  • Re: [AMBER] mm_pbsa problem (Wed Apr 01 2009 - 02:36:53 CDT)
  • Re: [AMBER] mm_pbsa problem (Mon Mar 30 2009 - 08:59:55 CDT)
  • [AMBER] mm_pbsa problem (Mon Mar 30 2009 - 05:02:07 CDT)
  • [AMBER] pmemd compile error (Mon Mar 23 2009 - 15:54:37 CDT)
  • [AMBER] pmemd compile error.... (Thu Mar 19 2009 - 10:06:04 CDT)
  • Re: [AMBER] Problem build pmemd (Wed Mar 18 2009 - 08:28:06 CDT)
• Giuseppe De Marco
  • [AMBER] error in reading namelist cntrl (Tue Nov 03 2009 - 13:44:01 CST)
• gmail
  • [AMBER] errors on reading time series file in WHAM calculation (Mon Mar 23 2009 - 19:35:02 CDT)
  • [AMBER] Understanding the all.out file in the MM-PBSA output (Wed Mar 11 2009 - 20:39:10 CDT)
  • [AMBER] addles segmentation fault (Mon Mar 09 2009 - 03:28:56 CDT)
  • Re: [AMBER] How to build reference coordinate file for targeted MD (Thu Feb 05 2009 - 23:20:59 CST)
  • [AMBER] How to build reference coordinate file for targeted MD (Thu Feb 05 2009 - 00:44:22 CST)
  • [AMBER] error on open distatance restraint (Fri Jan 23 2009 - 20:58:27 CST)
• Gregersen, Brent
  • RE: [AMBER] Help with torsions in parm99.dat file (Fri Mar 06 2009 - 20:15:11 CST)
  • [AMBER] Help with torsions in parm99.dat file (Fri Mar 06 2009 - 16:44:17 CST)
• guardiani_at_fi.infn.it
  • [AMBER] IGB=7 vs IGB=5 (Thu Jun 25 2009 - 06:20:15 CDT)
  • Re: [AMBER] glycopeptide Parametrization (Fri Jun 12 2009 - 09:06:24 CDT)
  • [AMBER] glycopeptide Parametrization (Wed Jun 10 2009 - 10:41:14 CDT)
  • [AMBER] Solvation potential and free energies (Thu Feb 05 2009 - 06:27:21 CST)
• Guillermo Mulliert Carlín
  • Re: [AMBER] vertex atom mismatch (Fri Jul 31 2009 - 09:33:46 CDT)
• gunajyoti das
  • [AMBER] using RESP program (Wed Oct 07 2009 - 05:30:27 CDT)
  • [AMBER] loading RNA sequence in xleap (Thu Sep 17 2009 - 03:27:49 CDT)
  • [AMBER] loading PDB of a RNA sequence (Tue Sep 08 2009 - 05:31:47 CDT)
  • [AMBER] (no subject) (Mon Sep 07 2009 - 04:21:45 CDT)
  • [AMBER] (no subject) (Sun Jul 19 2009 - 10:13:01 CDT)
  • [AMBER] (no subject) (Sun Jul 19 2009 - 10:14:20 CDT)
• guntheyp_at_aston.ac.uk
  • [AMBER] (Thu Jun 18 2009 - 06:48:21 CDT)
• Gustaf Olsson (go22bi_at_student.hik.se)
  • [AMBER] Is the integral value from RDF the same as average number of atoms? (Wed Nov 18 2009 - 15:56:31 CST)
• Gustavo Seabra
  • Re: [AMBER] reference re. determining size of timestep (Fri Jul 17 2009 - 11:53:46 CDT)
  • Re: Fw: [AMBER] Re: pls help and suggest (Fri Jul 17 2009 - 11:50:59 CDT)
  • Re: [AMBER] QMMM outupts (Thu Jul 09 2009 - 11:58:30 CDT)
  • [AMBER] Re: pls help and suggest (Thu Jul 09 2009 - 11:14:42 CDT)
  • Re: [AMBER] What is the parallel efficiency of amber10 (Mon Jun 08 2009 - 08:44:26 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 14:18:35 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 10:16:00 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 08:37:42 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 08:28:03 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 21:00:51 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Wed Jun 03 2009 - 08:55:24 CDT)
  • Re: [AMBER] create a simulation box (Tue Jun 02 2009 - 10:08:46 CDT)
  • Re: [AMBER] atom number exceeds the MAXATOM when running antechamber (Tue Jun 02 2009 - 10:04:33 CDT)
  • Re: [AMBER] Choice of force feild (Tue Jun 02 2009 - 09:58:11 CDT)
  • Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy (Tue Jun 02 2009 - 09:53:19 CDT)
  • Re: [AMBER] Targeted MD and QM/MM (Tue Jun 02 2009 - 09:43:35 CDT)
  • Re: [AMBER] J coupling constant calculation (Tue Jun 02 2009 - 09:18:08 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 12:28:35 CDT)
  • Re: [AMBER] dftb_disper problem (Fri May 08 2009 - 11:34:39 CDT)
  • Re: [AMBER] dftb_disper problem (Thu May 07 2009 - 08:01:42 CDT)
  • Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? (Tue May 05 2009 - 12:28:10 CDT)
  • Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? (Tue May 05 2009 - 12:04:37 CDT)
  • Re: [AMBER] Script for parallel runs (Tue May 05 2009 - 11:31:38 CDT)
  • Re: [AMBER] force fields (Wed Apr 15 2009 - 07:43:49 CDT)
  • Re: [AMBER] Contour plot (Thu Apr 02 2009 - 14:47:14 CDT)
  • Re: [AMBER] problem with the results in the .out file! (Tue Mar 31 2009 - 08:01:41 CDT)
  • Re: [AMBER] Quality/size of HDD for Amber (Mon Mar 09 2009 - 12:44:54 CDT)
  • Re: [AMBER] Regarding leap (Thu Mar 05 2009 - 09:32:56 CST)
  • Re: [AMBER] Regarding leap (Wed Mar 04 2009 - 16:05:25 CST)
  • Re: [AMBER] A good way to use an Amber force field with NAMD? (Tue Mar 03 2009 - 18:08:33 CST)
  • Re: [AMBER] How to restart the umbrella sampling jobs? (Tue Mar 03 2009 - 14:41:25 CST)
  • Re: [AMBER] Fail to allocate ff (Tue Mar 03 2009 - 14:36:53 CST)
  • Re: [AMBER] inpcrd and prmtop (Tue Mar 03 2009 - 14:20:38 CST)
  • Re: [AMBER] assigning velocities to each atom without heating the system (Mon Mar 02 2009 - 11:31:09 CST)
  • Re: [AMBER] linux install problem (Thu Feb 19 2009 - 14:47:18 CST)
  • Re: [AMBER] contant force pulling simulation with amber 10 (Mon Feb 16 2009 - 12:11:40 CST)
  • Re: [AMBER] Any link to a major QM code? (Mon Feb 16 2009 - 10:51:03 CST)
  • Re: [AMBER] Any link to a major QM code? (Sun Feb 15 2009 - 18:17:32 CST)
  • Re: [AMBER] Optimization problem (Thu Feb 12 2009 - 08:48:23 CST)
  • Re: [AMBER] error in xleap: ligand binding using MMand QMMM tech (Thu Feb 12 2009 - 08:32:17 CST)
  • Re: [AMBER] solvent mixture (Sat Jan 24 2009 - 20:44:31 CST)
  • Re: [AMBER] AMBER External keyword (Sat Jan 24 2009 - 20:32:10 CST)
  • Re: AMBER: SMD-related questions (Fri Jan 02 2009 - 07:21:53 CST)
• GZ Zhang
  • Re: [AMBER] how to use those water models off the list in amber? (Thu Jan 22 2009 - 14:47:02 CST)
  • [AMBER] how to use those water models off the list in amber? (Wed Jan 21 2009 - 15:39:50 CST)
• GÃœL ALTINBAÅž
  • [AMBER] unit convertion for force constants (Mon Oct 12 2009 - 07:47:42 CDT)
  • [AMBER] unit converter for force constants (Mon Oct 12 2009 - 07:22:00 CDT)
• haifeng yuan
  • [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber (Tue Oct 13 2009 - 02:44:55 CDT)
• Haining Liu
  • Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter (Thu Sep 03 2009 - 16:13:09 CDT)
  • [AMBER] Heme + Fe(II) + O2 + histidine parameter (Wed Sep 02 2009 - 22:36:31 CDT)
• Haizhen Zhong
  • [AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? (Fri Jun 05 2009 - 18:17:01 CDT)
  • [AMBER] bad atom type in mm_pbsa calculation. How to solve it? Thanks! (Wed Jun 03 2009 - 18:00:34 CDT)
  • [AMBER] Minimization error on protonated system? Please help. Thanks! (Thu May 28 2009 - 09:58:49 CDT)
• Han Ming
  • Re: [AMBER] fillratio error in mmpbsa (Wed Apr 01 2009 - 10:06:08 CDT)
• Han Zheng
  • Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! (Tue Oct 27 2009 - 17:47:20 CDT)
  • [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! (Tue Oct 27 2009 - 12:28:16 CDT)
  • [AMBER] [amber10] atom groups used in torsion constrain (Mon Oct 26 2009 - 13:09:07 CDT)
• Hannes Kopitz
  • Re: [AMBER] software to hydrate protein pockets (Fri Oct 23 2009 - 08:11:26 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Mon Oct 12 2009 - 14:51:23 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Sun Oct 11 2009 - 16:13:45 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Thu Oct 08 2009 - 15:30:19 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 07:47:15 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 05:09:01 CDT)
  • Re: [AMBER] question of mm_pbsa (Fri Jul 10 2009 - 04:36:44 CDT)
  • Re: [AMBER] MM-PBSA energy decomposition (Thu Apr 30 2009 - 05:37:35 CDT)
  • Re: [AMBER] Problems with MM-PBSA Calculation after MD (Thu Mar 12 2009 - 06:06:54 CDT)
  • Re: [AMBER] Understanding the all.out file in the MM-PBSA output (Thu Mar 12 2009 - 05:54:27 CDT)
• Hannes Loeffler
  • Re: [AMBER] AMBER FF and NAMD (Fri Oct 16 2009 - 09:45:25 CDT)
  • Re: [AMBER] eigenvalues add up to more than trace of matrix (Fri Oct 16 2009 - 08:50:50 CDT)
  • Re: [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? (Mon Sep 28 2009 - 02:34:12 CDT)
  • Re: [AMBER] PROBLEM WITH CHCL3BOX pdb (Fri Sep 18 2009 - 10:16:06 CDT)
  • Re: [AMBER] How to find water-mediated hydrogen bond? (Thu Sep 03 2009 - 02:53:51 CDT)
  • Re: [AMBER] Regarding principal component analysis using ptraj (Fri Aug 28 2009 - 06:45:05 CDT)
  • Re: [AMBER] Regarding principal component analysis using ptraj (Fri Aug 28 2009 - 02:28:29 CDT)
  • RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? (Thu Aug 27 2009 - 02:21:28 CDT)
  • Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? (Wed Aug 26 2009 - 04:41:31 CDT)
  • RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Fri Jul 31 2009 - 02:27:54 CDT)
  • Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 05:52:48 CDT)
  • Re: [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 05:12:04 CDT)
  • [AMBER] nasty memory bug in calculatePrincipalAxis (Mon Jul 20 2009 - 03:30:38 CDT)
  • Re: [AMBER] Distance-covariance and PCA questions... (Wed Jun 17 2009 - 02:41:42 CDT)
  • Re: [AMBER] ptraj quasiharmonic analysis (Tue Jun 09 2009 - 02:19:23 CDT)
  • Re: [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? (Thu May 07 2009 - 02:47:23 CDT)
  • Re: [AMBER] Amber FF and Glycam (Fri May 01 2009 - 03:33:34 CDT)
  • Re: [AMBER] How to find out residence time of water molecules (Fri Apr 03 2009 - 02:31:32 CDT)
  • Re: [AMBER] change in protein ligand order (Tue Mar 24 2009 - 06:27:24 CDT)
  • Re: [AMBER] lipid bliayers (Wed Mar 18 2009 - 08:17:04 CDT)
  • Re: [AMBER] protein protrudes from unit cell (Wed Mar 18 2009 - 04:08:41 CDT)
  • Re: [AMBER] problem in rmsd (Tue Mar 10 2009 - 03:30:16 CDT)
  • Re: [AMBER] inpcrd and prmtop (Tue Mar 03 2009 - 03:37:16 CST)
  • Re: [AMBER] PMEMD vs GROMACS? (Tue Feb 24 2009 - 02:39:29 CST)
  • Re: [AMBER] Protein motions comparison (Thu Feb 19 2009 - 06:07:47 CST)
  • Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors (Fri Feb 13 2009 - 03:33:19 CST)
  • Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors (Fri Feb 13 2009 - 02:32:20 CST)
  • Re: [AMBER] pmemd on BlueGene/P? (Fri Feb 06 2009 - 03:01:37 CST)
  • [AMBER] pmemd on BlueGene/P? (Thu Feb 05 2009 - 07:09:45 CST)
  • [AMBER] ptraj, CHARMM PSF and CMAP (Wed Jan 14 2009 - 03:45:07 CST)
• Hannes Wallnoefer
  • Re: [AMBER] normal mode analysis (Mon May 04 2009 - 10:56:11 CDT)
  • [AMBER] normal mode analysis (Mon May 04 2009 - 04:39:16 CDT)
  • [AMBER] input error in TI calculation (Wed Apr 29 2009 - 10:40:58 CDT)
  • Re: [AMBER] TI production runs stop after a certain Step number (Wed Apr 08 2009 - 10:14:32 CDT)
  • Re: [AMBER] TI production runs stop after a certain Step number (Wed Apr 08 2009 - 06:48:31 CDT)
  • [AMBER] TI production runs stop after a certain Step number (Tue Apr 07 2009 - 06:48:45 CDT)
  • Re: [AMBER] change in protein ligand order (Tue Mar 24 2009 - 15:45:16 CDT)
  • Re: [AMBER] change in protein ligand order (Tue Mar 24 2009 - 07:38:18 CDT)
  • [AMBER] change in protein ligand order (Tue Mar 24 2009 - 06:05:36 CDT)
• hannes.loeffler_at_stfc.ac.uk
  • RE: [AMBER] PCA analysis with ptraj (Tue Nov 10 2009 - 02:13:29 CST)
• Harald Lanig
  • [AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st (Thu Aug 06 2009 - 03:39:07 CDT)
  • [AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany (Tue Jul 14 2009 - 09:02:16 CDT)
  • [AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany (Fri Mar 20 2009 - 06:25:09 CDT)
• He Hongqing
  • Re: Re: 回å¤�： [Amber]AMBER: MM_PBSA problemsin AMBER10 (Wed Oct 14 2009 - 03:39:33 CDT)
  • Re: 回å¤�： [Amber]AMBER: MM_PBSA problems in AMBER10 (Wed Oct 14 2009 - 02:32:25 CDT)
  • [Amber]AMBER: MM_PBSA problems in AMBER10 (Tue Oct 13 2009 - 22:43:57 CDT)
• Heath Watts
  • Re: [AMBER] glycam and solvateoct command (Tue Feb 17 2009 - 16:31:35 CST)
  • [AMBER] glycam and solvateoct command (Tue Feb 17 2009 - 13:51:13 CST)
  • Re: [AMBER] Beginner question (Fri Feb 13 2009 - 19:20:46 CST)
  • Re: [AMBER] Beginner question (Fri Feb 13 2009 - 19:19:44 CST)
  • [AMBER] Beginner question (Fri Feb 13 2009 - 15:18:42 CST)
• Hector A. Baldoni
  • Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB (Wed Aug 12 2009 - 15:43:28 CDT)
• helde010_at_umn.edu
  • [AMBER] logdvdl does not work (Tue Sep 08 2009 - 11:53:14 CDT)
• Helena P M Tossavainen
  • Re: [AMBER] missing violations of the covalent geometry (Tue Apr 07 2009 - 07:10:16 CDT)
  • [AMBER] missing violations of the covalent geometry (Tue Apr 07 2009 - 04:36:44 CDT)
• Hemant Gangwar
  • [AMBER] POL3 & SHAKE (Tue Jun 09 2009 - 15:53:27 CDT)
  • Re: [AMBER] error in MM PBSA (Sat Apr 04 2009 - 12:08:08 CDT)
  • [AMBER] problem using amoeba (Fri Mar 27 2009 - 05:41:26 CDT)
  • [AMBER] Solvate Box od amoeba water (Fri Mar 06 2009 - 03:50:01 CST)
• Hemant Kumar
  • [AMBER] MM_PBSA energy per residue (Thu Nov 12 2009 - 08:27:22 CST)
  • [AMBER] SPC/E HOH angle (Fri Oct 30 2009 - 05:36:55 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 12:38:43 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 07:05:04 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 06:00:18 CDT)
  • [AMBER] Box shape change (Sat Jul 18 2009 - 14:38:46 CDT)
  • RE: [AMBER] Umbrella Sampling (Sat Jul 18 2009 - 14:28:19 CDT)
  • [AMBER] Umbrella Sampling (Thu Jul 16 2009 - 13:01:40 CDT)
  • RE: [AMBER] dipole printing (Fri Jun 12 2009 - 14:03:17 CDT)
  • [AMBER] dipole printing (Fri Jun 12 2009 - 10:58:29 CDT)
  • [AMBER] POL3 (Sun Jun 07 2009 - 13:27:29 CDT)
  • [AMBER] Number of processor in pmemd (Mon May 04 2009 - 12:17:13 CDT)
  • Re: [AMBER] error in output file (Thu Apr 23 2009 - 07:20:25 CDT)
  • [AMBER] parameter for amoeba (Sat Apr 04 2009 - 06:46:01 CDT)
  • Re: [AMBER] Solvate Box od amoeba water (Sun Mar 22 2009 - 11:06:01 CDT)
• Hlengisizwe Ndlovu
  • [AMBER] Steered MD.....SHAKE error!! (Fri Jul 17 2009 - 03:50:11 CDT)
  • [AMBER] vlimit exceeded....nscu_SMD!! (Thu Jul 16 2009 - 07:53:50 CDT)
  • [AMBER] Steered MD---more than one pair of atoms (Tue Jul 07 2009 - 08:27:59 CDT)
• Hopkins, Robert
  • RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% (Thu Jul 23 2009 - 15:37:12 CDT)
  • [AMBER] PMEMD in a Cygwin Environment (Tue Jul 14 2009 - 14:48:41 CDT)
  • RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% (Mon Jun 22 2009 - 14:54:17 CDT)
  • [AMBER] Amber10 Parallel Installation (Sat Jun 20 2009 - 14:50:16 CDT)
  • RE: [AMBER] Running PTRAJ command line scripts in background (Mon May 18 2009 - 17:50:06 CDT)
  • RE: [AMBER] Running PTRAJ command line scripts in background (Sun May 17 2009 - 11:55:48 CDT)
  • [AMBER] Running PTRAJ command line scripts in background (Sat May 16 2009 - 19:47:38 CDT)
  • [AMBER] Amber 10 install parallel problem (Sat May 16 2009 - 19:38:16 CDT)
  • RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% (Thu Apr 30 2009 - 19:02:34 CDT)
  • RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP (Wed Apr 01 2009 - 18:10:44 CDT)
  • RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP (Sun Mar 29 2009 - 13:27:09 CDT)
  • RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP (Sat Mar 28 2009 - 18:12:06 CDT)
  • RE: [AMBER] Problem reading PDB file into XLEAP (Fri Mar 27 2009 - 17:09:11 CDT)
  • [AMBER] Problem reading PDB file into XLEAP (Thu Mar 26 2009 - 19:01:26 CDT)
  • RE: [AMBER] IG not change at each restart of NPT simulation (Wed Mar 18 2009 - 18:15:54 CDT)
  • Re: [AMBER] IG not change at each restart of NPT simulation (Wed Mar 18 2009 - 17:55:33 CDT)
  • RE: [AMBER] Changing Force Fields in "Midstream" (Thu Mar 12 2009 - 15:45:46 CDT)
  • RE: [AMBER] Changing Force Fields in "Midstream" (Wed Mar 11 2009 - 16:36:12 CDT)
  • RE: [AMBER] Changing Force Fields in "Midstream" (Tue Mar 10 2009 - 18:29:44 CDT)
  • [AMBER] Changing Force Fields in "Midstream" (Mon Mar 09 2009 - 19:12:27 CDT)
  • [AMBER] Equilibration Scaling to System Size (Tue Feb 24 2009 - 16:31:37 CST)
  • [AMBER] Restarting an MD Simulation (Wed Feb 04 2009 - 18:34:16 CST)
• Houyang Chen
  • RE: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 12:39:18 CDT)
  • RE: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 00:24:39 CDT)
  • [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 00:01:31 CDT)
  • RE: [AMBER] The PDB file was not recognized by Amber, what can i do? (Wed Apr 29 2009 - 17:17:51 CDT)
  • RE: [AMBER] The PDB file was not recognized by Amber, what can i do? (Tue Apr 28 2009 - 22:42:39 CDT)
  • [AMBER] The PDB file was not recognized by Amber, what can i do? (Tue Apr 28 2009 - 17:00:05 CDT)
• Hrvoje Brkiæ
  • [AMBER] Iron 2+ parameters (Mon Feb 16 2009 - 07:53:57 CST)
• Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)]
  • RE: [AMBER] Simulated annealing (Thu Feb 26 2009 - 10:30:47 CST)
  • RE: [AMBER] Simulated annealing (Thu Feb 26 2009 - 10:22:59 CST)
• Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
  • RE: [AMBER] reg-TMD (Wed Apr 29 2009 - 15:56:07 CDT)
  • RE: [AMBER] help- regarding - TMD (Tue Apr 21 2009 - 17:40:36 CDT)
  • RE: [AMBER] help- regarding - TMD (Tue Apr 21 2009 - 15:25:15 CDT)
  • RE: [AMBER] help- regarding - TMD (Mon Apr 20 2009 - 11:21:06 CDT)
  • RE: [AMBER] help- regarding - TMD (Mon Apr 20 2009 - 10:28:30 CDT)
  • RE: [AMBER] help- regarding - TMD (Mon Apr 20 2009 - 10:05:38 CDT)
  • RE: [AMBER] help- regarding - TMD (Thu Apr 16 2009 - 08:30:22 CDT)
  • RE: [AMBER] help- regarding - TMD (Wed Apr 15 2009 - 12:56:07 CDT)
  • [AMBER] Questions on targeted MD with explicit solvent (Tue Apr 14 2009 - 08:51:40 CDT)
• Hugh Heldenbrand
  • Re: [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 13:52:37 CDT)
  • [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 10:16:26 CDT)
  • [AMBER] igb=0 vs. igb=6 give different answers (Thu Apr 09 2009 - 15:51:02 CDT)
  • Re: [AMBER] please help me out (Wed Apr 08 2009 - 10:44:54 CDT)
• Huifang
  • [AMBER] Thermodynamic Integration calculation on an artificial anion receptor (Wed Oct 28 2009 - 23:38:05 CDT)
• Huikuan Chao
  • [AMBER] build up solvate box (Sat Nov 07 2009 - 14:29:50 CST)
• hwu_at_clarku.edu
  • [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 16:06:34 CDT)
• Ian Streeter
  • [AMBER] Parallelepiped periodic box (Mon Jan 12 2009 - 09:57:55 CST)
• Ibrahim Moustafa
  • Re: [AMBER] Density in MD simulation (Fri Apr 17 2009 - 18:26:46 CDT)
  • [AMBER] Density in MD simulation (Fri Apr 17 2009 - 11:09:16 CDT)
  • Re: [AMBER] Simulated annealing (Thu Feb 26 2009 - 10:32:32 CST)
  • Re: [AMBER] Simulated annealing (Thu Feb 26 2009 - 09:28:44 CST)
  • [AMBER] Simulated annealing (Wed Feb 25 2009 - 18:26:37 CST)
• iccy liu
  • RE: [AMBER] Error in trajin and rms (Thu Apr 02 2009 - 14:19:16 CDT)
  • [AMBER] long polymer chain and image command in ptraj (Thu Apr 02 2009 - 14:11:26 CDT)
  • [AMBER] radial distribution function mask (Wed Mar 04 2009 - 12:57:08 CST)
  • RE: [AMBER] atoms fly out of the box in NVT calculations (Sun Feb 15 2009 - 17:34:37 CST)
  • [AMBER] atoms fly out of the box in NVT calculations (Thu Feb 12 2009 - 15:48:24 CST)
  • [AMBER] solvent mixture (Tue Jan 20 2009 - 16:08:34 CST)
• Ignacio J. General
  • Re: [AMBER] Partial interactions (Fri Apr 24 2009 - 12:11:31 CDT)
  • Re: [AMBER] Partial interactions (Fri Apr 24 2009 - 09:49:07 CDT)
  • Re: [AMBER] Partial interactions (Wed Apr 22 2009 - 14:02:00 CDT)
  • Re: [AMBER] Partial interactions (Tue Apr 21 2009 - 09:31:26 CDT)
  • [AMBER] Partial interactions (Mon Apr 20 2009 - 16:07:24 CDT)
  • Re: [AMBER] Thermodynamic Integration and belly (Mon Apr 13 2009 - 12:26:16 CDT)
  • [AMBER] Thermodynamic Integration and belly (Mon Apr 13 2009 - 10:24:15 CDT)
  • [AMBER] Thermodynamic Integration and belly (Wed Apr 08 2009 - 14:52:51 CDT)
• Ilyas Yildirim
  • Re: [AMBER] TI in Amber9/10 (Tue Sep 08 2009 - 13:07:40 CDT)
  • Re: »Ø¸´£º »Ø¸´£º [AMBER] too high in binding energy (MM-PBSA) (Sat Jun 13 2009 - 13:19:09 CDT)
  • Re: [AMBER] TI production runs stop after a certain Step number (Tue Apr 07 2009 - 14:08:31 CDT)
• IN SUK JOUNG
  • Re: [AMBER] Need help with point to plane distance calculation in nab (Thu Jan 08 2009 - 13:41:09 CST)
  • Re: [AMBER] Need help with point to plane distance calculation in nab (Thu Jan 08 2009 - 13:00:20 CST)
• InSuk Joung
  • Re: [AMBER] help with parameters for ions (Tue Jun 02 2009 - 13:14:46 CDT)
  • Re: [AMBER] help with parameters for ions (Tue Jun 02 2009 - 10:28:55 CDT)
• intra\\sa175950
  • RE: [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 10:18:38 CST)
• isaac sugden
  • Re: [AMBER] parmchk problem (Wed Aug 05 2009 - 12:21:53 CDT)
  • [AMBER] parmchk problem (Tue Aug 04 2009 - 09:12:29 CDT)
• Ivan Gladich
  • [AMBER] rectangular box with PME problem (Mon Nov 09 2009 - 16:18:16 CST)
  • Re: [AMBER] amoeba.prm problem? (Fri Sep 18 2009 - 14:57:39 CDT)
  • Re: [AMBER] amoeba.prm problem? (Fri Sep 11 2009 - 15:34:07 CDT)
  • [AMBER] amoeba.prm problem? (Tue Sep 08 2009 - 09:31:43 CDT)
• Ivaylo, Ivanov
  • [AMBER] Postdoc position in biomolecular simulation (Thu Jun 18 2009 - 18:26:05 CDT)
• Jack Colis
  • Re: [AMBER] MMPBSA- interaction energy for every frame (Tue May 05 2009 - 03:22:35 CDT)
  • [AMBER] MMPBSA- interaction energy for every frame (Mon May 04 2009 - 09:38:38 CDT)
• Jack Shultz
  • Re: [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 21:05:41 CST)
  • Re: [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 19:51:38 CST)
  • [AMBER] tleap maximum coordination exceeded (Tue Nov 17 2009 - 10:52:20 CST)
  • Re: [AMBER] Environment Variables in Cygwin Don't Remain (Thu Oct 01 2009 - 12:12:19 CDT)
  • Re: [AMBER] Trying to patch amber 9 (Wed Jun 24 2009 - 10:25:41 CDT)
  • Re: [AMBER] Trying to patch amber 9 (Wed Jun 24 2009 - 10:18:23 CDT)
  • [AMBER] Trying to patch amber 9 (Wed Jun 24 2009 - 08:24:40 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 09:34:33 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 09:21:37 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 08:09:06 CDT)
  • Re: [AMBER] From DLG to Antechamber (Fri Jun 19 2009 - 07:27:20 CDT)
  • [AMBER] From DLG to Antechamber (Thu Jun 18 2009 - 19:04:15 CDT)
  • [AMBER] Antechamber: stuck at bondtype (Wed Jun 17 2009 - 07:50:11 CDT)
• jackie
  • Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? (Thu Aug 27 2009 - 10:52:19 CDT)
  • Re: [AMBER] Inquiries about antechamber (Thu Aug 27 2009 - 10:48:24 CDT)
  • Re: [AMBER] Re: question_on_MMPBSA (Thu Aug 27 2009 - 10:41:28 CDT)
  • [AMBER] Re: question_on_MMPBSA (Wed Aug 26 2009 - 10:08:01 CDT)
• Jackie. J. Shen
  • Re: Re: [AMBER] Backbone restraint (Mon Apr 20 2009 - 20:12:13 CDT)
  • [AMBER] A question about SMD force constant (Mon Apr 06 2009 - 20:40:13 CDT)
• jacky zhao
  • [AMBER] have a question (Tue Nov 17 2009 - 19:54:36 CST)
  • Re: [AMBER]Amber10 + g95 (Tue Nov 17 2009 - 02:26:56 CST)
  • [AMBER] which is the best intel complier for amber 10? (Tue Nov 17 2009 - 02:24:30 CST)
  • Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy (Wed Jun 03 2009 - 08:44:12 CDT)
  • Re: [AMBER] Re: About Amber installations (Tue May 26 2009 - 06:18:25 CDT)
• Jacopo Sgrignani
  • [AMBER] Copper semiempirical parameters (Thu Jun 11 2009 - 08:49:50 CDT)
  • [AMBER] calculation of Pi-Pi interaction energy (Wed Apr 01 2009 - 07:24:28 CDT)
  • [AMBER] QM/MM charges (Fri Mar 20 2009 - 04:38:30 CDT)
  • [AMBER] chemical shift penalty (Thu Mar 05 2009 - 03:47:03 CST)
• Jagadeesh, M.N., Ph.D.
  • Re: [AMBER] Metal in MD simulation (Thu Mar 19 2009 - 09:48:28 CDT)
  • [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" (Mon Jan 19 2009 - 03:03:39 CST)
• Jagan Mohan
  • [AMBER] Box Center (Fri Jun 26 2009 - 03:02:05 CDT)
• Jagdeesh C
  • Re: [AMBER] loadpdb (Tue Sep 08 2009 - 20:55:36 CDT)
  • Re: [AMBER] loadpdb (Mon Sep 07 2009 - 13:31:42 CDT)
  • [AMBER] loadpdb (Mon Sep 07 2009 - 12:36:58 CDT)
• James Moore
  • [AMBER] red problem (Thu Oct 01 2009 - 20:52:46 CDT)
• James W
  • [AMBER] About the croase grainded FF (Tue Feb 24 2009 - 01:58:12 CST)
• James W. Caldwell
  • [AMBER] AmberTools 1.2 (Thu Jan 29 2009 - 18:04:36 CST)
  • Re: [AMBER] RE: AMBER: mail list (Tue Jan 06 2009 - 19:24:12 CST)
• Jan Heyda
  • [AMBER] Polarizable simulation of the slab (Sun Nov 22 2009 - 07:13:16 CST)
• jani sahil
  • Re: [AMBER] Regarding use of PME along with Implict solvation (Mon Mar 23 2009 - 08:04:15 CDT)
  • [AMBER] Regarding use of PME along with Implict solvation (Mon Mar 23 2009 - 05:38:39 CDT)
  • [AMBER] regarding tutorial on united atom force field (Mon Mar 16 2009 - 23:51:16 CDT)
• janzso_at_brc.hu
  • Re: [AMBER] problem with parametrization (Mon Jun 29 2009 - 04:30:50 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 07:04:27 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 06:40:35 CDT)
  • Re: [AMBER] problem with parametrization (Thu Jun 25 2009 - 04:49:50 CDT)
  • [AMBER] problem with parametrization (Wed Jun 24 2009 - 13:24:45 CDT)
• Jason A. Ford-Green
  • Re: [AMBER] Solvating the interior of a channel (Wed Feb 11 2009 - 10:04:24 CST)
  • Re: [AMBER] Resp charge (Fri Feb 06 2009 - 14:38:29 CST)
  • [AMBER] PDB of a specific frame (Wed Feb 04 2009 - 13:46:52 CST)
  • Re: [AMBER] How to calculate cavity volume from MD structures? (Wed Jan 21 2009 - 09:39:57 CST)
  • [AMBER] Heat and Equilibrate Hybrid GB solvent? (Fri Jan 16 2009 - 15:14:41 CST)
  • [AMBER] Ligand Diffusion Studies? (Thu Jan 15 2009 - 11:42:03 CST)
• Jason Swails
  • Re: [AMBER] The MSD and periodic boundary condition (Thu Nov 19 2009 - 18:00:30 CST)
  • Re: Re: [AMBER] read substrate into leap (Wed Nov 18 2009 - 19:35:37 CST)
  • Re: [AMBER] about divcon (Wed Nov 18 2009 - 13:09:43 CST)
  • Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala (Wed Nov 18 2009 - 13:00:09 CST)
  • Re: [AMBER] read substrate into leap (Wed Nov 18 2009 - 12:53:30 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 12:05:05 CST)
  • Re: [AMBER] non standart residue library creation with tleap (Zn atom) (Tue Nov 17 2009 - 09:57:41 CST)
  • Re: [AMBER] About zinc parameters ? (Tue Nov 17 2009 - 09:17:23 CST)
  • Re: [AMBER] compilation problem of amber9 (Tue Nov 17 2009 - 08:55:46 CST)
  • Re: [AMBER] compilation problem of amber (Tue Nov 17 2009 - 08:51:42 CST)
  • Re: [AMBER] How to split mdcrd files (Sun Nov 15 2009 - 11:35:24 CST)
  • Re: [AMBER] is rst file the last structure? (Sat Nov 14 2009 - 11:18:22 CST)
  • Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala (Wed Nov 11 2009 - 16:30:35 CST)
  • Re: [AMBER] error reading namelist cntrl (Wed Nov 11 2009 - 08:01:42 CST)
  • Re: [AMBER] Gly -> Ala mutation (Sun Nov 08 2009 - 14:16:42 CST)
  • Re: [AMBER] Gly -> Ala mutation (Sun Nov 08 2009 - 11:53:29 CST)
  • Re: [AMBER] LJ parameters for HO and HW (Sun Nov 08 2009 - 09:14:45 CST)
  • Re: [AMBER] LJ parameters for HO and HW (Sat Nov 07 2009 - 23:50:03 CST)
  • Re: [AMBER] linux version for Amber10 (Sat Nov 07 2009 - 21:38:41 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Thu Nov 05 2009 - 08:12:39 CST)
  • Re: [AMBER] HB for each snapshot (Wed Nov 04 2009 - 13:35:07 CST)
  • Re: [AMBER] total number of hydrogen bonds of the system as a function of time (Wed Nov 04 2009 - 08:08:21 CST)
  • Re: [AMBER] amber parameter file creation and usage (Tue Nov 03 2009 - 23:29:30 CST)
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Tue Nov 03 2009 - 14:22:10 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Tue Nov 03 2009 - 08:11:48 CST)
  • Re: [AMBER] 60 giga output file .mdcrd file (Tue Nov 03 2009 - 07:49:01 CST)
  • Re: [AMBER] amber 10 test failures... (Mon Nov 02 2009 - 18:19:43 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Mon Nov 02 2009 - 11:04:14 CST)
  • Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade (Mon Nov 02 2009 - 06:15:19 CST)
  • Re: [AMBER] Different results for different computers (Sat Oct 31 2009 - 14:57:34 CDT)
  • Re: [AMBER] surface binding protein (Sat Oct 31 2009 - 07:35:44 CDT)
  • Re: [AMBER] some queries on -states flag in constant pH simulation (Sat Oct 31 2009 - 07:28:22 CDT)
  • Re: [AMBER] [Fwd: ligand exiting a protein cavity] (Fri Oct 30 2009 - 11:23:29 CDT)
  • Re: [AMBER] Is it the way to do simulation in vacuum (Fri Oct 30 2009 - 11:06:14 CDT)
  • Re: [AMBER] Ligand covalent bonds appear to be broken (Fri Oct 30 2009 - 08:11:03 CDT)
  • Re: [AMBER] [Fwd: ligand exiting a protein cavity] (Fri Oct 30 2009 - 08:07:17 CDT)
  • Re: [AMBER] some queries on -states flag in constant pH simulation (Fri Oct 30 2009 - 08:00:37 CDT)
  • Re: [AMBER] [Fwd: ligand exiting a protein cavity] (Thu Oct 29 2009 - 10:17:40 CDT)
  • Re: [AMBER] amber parallel test fail (Fri Oct 23 2009 - 06:58:19 CDT)
  • Re: [AMBER] parameters for O2 molecule (Thu Oct 22 2009 - 09:19:51 CDT)
  • Re: [AMBER] too many undefined parameters in frcmod (Thu Oct 22 2009 - 06:59:55 CDT)
  • Re: [AMBER] Can I use other ntb options in constant pH simulation (Wed Oct 21 2009 - 06:42:42 CDT)
  • Re: [AMBER] simulation blown up (Tue Oct 20 2009 - 21:58:47 CDT)
  • Re: [AMBER] man pages? (Tue Oct 20 2009 - 16:28:56 CDT)
  • Re: [AMBER] GAFF parameter (Tue Oct 20 2009 - 09:57:09 CDT)
  • Re: [AMBER] how to get hold of older versions of MKL ? (Mon Oct 19 2009 - 05:54:45 CDT)
  • Re: [AMBER] Dihedral energy profile in a single molecule (Fri Oct 16 2009 - 10:02:35 CDT)
  • Re: [AMBER] eigenvalues add up to more than trace of matrix (Fri Oct 16 2009 - 08:29:13 CDT)
  • Re: [AMBER] How to introduce the second protein molecule into simulation box? (Fri Oct 16 2009 - 08:15:57 CDT)
  • Re: [AMBER] LES and NEB problem (Thu Oct 15 2009 - 13:09:14 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Thu Oct 15 2009 - 08:01:38 CDT)
  • Re: [AMBER] Re: Fw: Help required in Amber10 Installation (Thu Oct 15 2009 - 07:55:31 CDT)
  • Re: [AMBER] part of the protein escaped from the water box (Thu Oct 15 2009 - 06:43:00 CDT)
  • Re: [AMBER] installation of Amber on OSX (Wed Oct 14 2009 - 17:41:31 CDT)
  • Re: [AMBER] S-S problem-in protein (Mon Oct 12 2009 - 06:23:25 CDT)
  • Re: [AMBER] S-S problem-in protein (Sun Oct 11 2009 - 23:24:51 CDT)
  • Re: [AMBER] S-S problem-in protein (Sun Oct 11 2009 - 21:15:10 CDT)
  • Re: [AMBER] Energy-from-MM/PBSA-VS-experiment (Sun Oct 11 2009 - 09:54:08 CDT)
  • Re: [AMBER] xleap-does not work (Sat Oct 10 2009 - 12:08:08 CDT)
  • Re: [AMBER] Some queries about pH simulation (Fri Oct 09 2009 - 13:48:44 CDT)
• Javier Klett
  • Re: [Barracuda SPAM] Re: [AMBER] Atom Type List (Mon Jun 22 2009 - 11:34:43 CDT)
  • [AMBER] Atom Type List (Mon Jun 22 2009 - 04:54:43 CDT)
• Jayalakshmi Sridhar
  • Re: [AMBER] hbond analysis by ptraj- segmentation fault (Mon Nov 23 2009 - 12:36:25 CST)
  • [AMBER] hbond analysis by ptraj- segmentation fault (Mon Nov 23 2009 - 09:51:00 CST)
  • [AMBER] xleap not reconizing inhibitor prepin (Fri Oct 23 2009 - 11:21:07 CDT)
  • [AMBER] inhibitor prepin not recognized in xleap (Fri Oct 23 2009 - 11:05:46 CDT)
  • [AMBER] inhibitor prepin not recognized in xleap (Fri Oct 23 2009 - 10:56:40 CDT)
  • [AMBER] charges for heme-cys in p450 (Thu Oct 22 2009 - 11:03:08 CDT)
  • RE: [AMBER] xleap editing window icons inactive (Wed Oct 21 2009 - 13:32:46 CDT)
  • [AMBER] xleap editing window icons inactive (Wed Oct 21 2009 - 13:20:01 CDT)
  • Re: [AMBER] Simulating transmembrane protein. (Mon Oct 12 2009 - 14:57:02 CDT)
  • [AMBER] Simulating transmembrane protein. (Mon Oct 12 2009 - 13:42:11 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 11:02:56 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 10:44:39 CDT)
  • Re: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 10:33:51 CDT)
  • [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 09:30:39 CDT)
  • Re: [AMBER] xleap segmentation fault (Fri May 29 2009 - 10:45:25 CDT)
  • [AMBER] xleap segmentation fault (Thu May 28 2009 - 11:29:47 CDT)
  • [AMBER] xleap segmentation fault (Mon May 04 2009 - 10:50:06 CDT)
  • [AMBER] unable to start xleap (Fri May 01 2009 - 13:32:27 CDT)
  • [AMBER] amber tools installation (Mon Mar 30 2009 - 10:44:57 CDT)
• jcmoore_at_student.umass.edu
  • [AMBER] CY3 dye parameters (Thu Apr 23 2009 - 16:42:59 CDT)
• Jeff Schwinefus
  • Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory (Wed Mar 04 2009 - 23:22:34 CST)
  • [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory (Tue Mar 03 2009 - 16:18:25 CST)
• Jeff Yeo
  • [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out (Mon Oct 05 2009 - 18:22:53 CDT)
  • [AMBER] MMPBSA: No radius found for F (Sun Oct 04 2009 - 19:10:12 CDT)
  • [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex (Wed Sep 23 2009 - 18:24:51 CDT)
  • [AMBER] combining MD runs for post-MD analysis (Sun Sep 20 2009 - 19:02:12 CDT)
  • [AMBER] warning in dispatchToken (Sun Sep 20 2009 - 05:30:57 CDT)
  • RE: [AMBER] database (Thu Sep 17 2009 - 16:01:48 CDT)
  • RE: [AMBER] parameterization of protein-ligand complex (Mon Sep 14 2009 - 10:03:25 CDT)
• Jeffrey
  • Re: [AMBER] parameters for O2 molecule (Thu Oct 29 2009 - 08:01:44 CDT)
  • [AMBER] parameters for O2 molecule (Thu Oct 22 2009 - 08:32:07 CDT)
  • [AMBER] generate prmtop file from CHARMM psf file (Mon Sep 21 2009 - 09:34:59 CDT)
  • [AMBER] question about ptraj (Wed Sep 02 2009 - 03:20:12 CDT)
  • Re: [AMBER] radical simulation (Sun Jul 26 2009 - 07:28:39 CDT)
  • [AMBER] radical simulation (Fri Jul 24 2009 - 02:34:53 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 23 2009 - 07:51:34 CDT)
  • Re: [AMBER] questions about RESP (Mon Jul 20 2009 - 02:42:29 CDT)
  • [AMBER] questions about RESP (Thu Jul 16 2009 - 01:57:28 CDT)
  • [AMBER] TMD: solvation and equilibration questions (Fri Jul 10 2009 - 20:07:55 CDT)
  • Re: [AMBER] charges in topology file (Fri Jul 10 2009 - 11:20:01 CDT)
  • Re: [AMBER] The problem of restart file (Wed Jul 01 2009 - 09:07:08 CDT)
  • [AMBER] The problem of restart file (Wed Jul 01 2009 - 07:15:34 CDT)
  • [AMBER] validation of parameters and request suggestions (Tue Mar 24 2009 - 06:52:19 CDT)
  • [AMBER] validation of parameters and request of suggestions (Mon Mar 23 2009 - 21:16:35 CDT)
  • [AMBER] protein protrudes from unit cell (Wed Mar 18 2009 - 03:59:06 CDT)
  • Re: Re: Re: [AMBER] dipole correlation function (Thu Feb 19 2009 - 19:31:08 CST)
  • Re: Re: [AMBER] dipole correlation function (Thu Feb 19 2009 - 10:39:15 CST)
  • [AMBER] dipole correlation function (Thu Feb 19 2009 - 08:18:20 CST)
  • [AMBER] IG not change at each restart of NPT simulation (Wed Feb 18 2009 - 06:49:47 CST)
  • Re: Re: [AMBER] MD simulation with a partially flexible system (Tue Feb 17 2009 - 20:19:47 CST)
  • [AMBER] MD simulation with a partially flexible system (Tue Feb 17 2009 - 08:38:10 CST)
  • [AMBER] How to jude whether the trajectory is stable or not (Thu Feb 12 2009 - 20:33:53 CST)
  • [AMBER] NPT md with PME method for a water box (Wed Jan 14 2009 - 08:41:24 CST)
• Jenny Iskrenova
  • Re: [AMBER] input file (Thu Sep 10 2009 - 08:05:03 CDT)
  • [AMBER] Negative "number of measurements" in PTRAJ (Mon Apr 06 2009 - 12:28:59 CDT)
  • Re: [AMBER] errors on reading time series file in WHAM calculation (Tue Mar 24 2009 - 09:35:51 CDT)
  • Re: [AMBER] Unit 5 Error on OPEN: nan.in (Tue Mar 17 2009 - 07:34:00 CDT)
  • Re: [AMBER] test charge (Fri Feb 20 2009 - 14:32:14 CST)
  • Re: [AMBER] precision in the trajectory files (Tue Feb 03 2009 - 11:07:58 CST)
  • [AMBER] precision in the trajectory files (Mon Feb 02 2009 - 08:43:38 CST)
  • Re: [AMBER] (no subject) (Mon Jan 19 2009 - 12:54:39 CST)
  • Re: [AMBER] (no subject) (Fri Jan 16 2009 - 17:20:46 CST)
  • Re: [AMBER] (no subject) (Fri Jan 16 2009 - 12:42:08 CST)
• Jeremy Harris
  • [AMBER] amber tools reading netcdf files (Tue Feb 24 2009 - 09:54:09 CST)
  • Re: [AMBER] nab conjgrad min problem (Mon Jan 19 2009 - 09:00:30 CST)
  • [AMBER] nab conjgrad min problem (Fri Jan 16 2009 - 09:11:12 CST)
  • [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) (Tue Jan 13 2009 - 15:58:36 CST)
  • AMBER: Re: nmode error: bad nonbon (amber 10) (Tue Jan 06 2009 - 07:37:21 CST)
• Jerome.GOLEBIOWSKI_at_unice.fr
  • Re: [AMBER] ZPVE simple question (Wed Aug 26 2009 - 06:15:00 CDT)
• Jesse Dylan Ziebarth (jziebrth)
  • RE: [AMBER] DNA as well as protein distorted during MD run in sander (Tue Jun 09 2009 - 10:47:34 CDT)
• Jia Xu
  • Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial (Tue Sep 01 2009 - 00:10:50 CDT)
  • [AMBER] problem with 4-Hydroxyl-Proline tutorial (Sun Aug 30 2009 - 02:46:18 CDT)
  • Re: [AMBER] about file format (Sun Aug 30 2009 - 00:32:30 CDT)
  • [AMBER] about file format (Sat Aug 29 2009 - 02:55:49 CDT)
  • Re: [AMBER] ptraj questions (Sun May 24 2009 - 00:06:10 CDT)
  • [AMBER] ptraj questions (Wed May 20 2009 - 09:39:13 CDT)
  • Re: [AMBER] Running PTRAJ command line scripts in background (Sun May 17 2009 - 02:16:49 CDT)
  • Re: [AMBER] antechamber problems (Fri Apr 10 2009 - 09:41:53 CDT)
  • [AMBER] antechamber problems (Thu Apr 09 2009 - 12:12:44 CDT)
  • [AMBER] angle between ligand ring plane and axis (Wed Mar 04 2009 - 05:00:08 CST)
• Jianping Lin
  • Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Mon Aug 10 2009 - 20:23:44 CDT)
  • [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Mon Aug 10 2009 - 18:18:44 CDT)
  • Re: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Fri Aug 07 2009 - 15:32:47 CDT)
  • [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" (Mon Aug 03 2009 - 09:57:28 CDT)
• Jianyin Shao
  • Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis (Mon Oct 19 2009 - 13:16:47 CDT)
  • Re: [AMBER] ptraj cluster - snapshot number of a representative structure (Thu Aug 20 2009 - 10:50:22 CDT)
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 14:02:03 CDT)
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 12:57:23 CDT)
  • Re: [AMBER] hbond_DNAtraj (Wed Jun 03 2009 - 11:52:41 CDT)
• Jifeng Wang
  • [AMBER] Unable to correctly identify element when running QM/MM in amber10 (Thu Oct 22 2009 - 11:20:30 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 09:43:25 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 09:10:50 CDT)
• Jihang Wang
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 17:42:38 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 17:26:24 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 16:28:45 CDT)
  • Re: [AMBER] method used to determine partial charges? (Thu Oct 01 2009 - 15:36:31 CDT)
  • [AMBER] partial charges in Amber force field (Mon Sep 28 2009 - 12:52:28 CDT)
• Jim Parker
  • [AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10 (Sat Apr 11 2009 - 23:47:19 CDT)
  • [AMBER] install and test Amber 10 parallel on Ubuntu 8.10 (Sat Apr 11 2009 - 19:20:25 CDT)
  • Re: [AMBER] Solved-Amber 1.2 tools test suite failure (Sat Apr 11 2009 - 14:29:55 CDT)
  • [AMBER] Amber 1.2 tools test suite failure? (Sat Apr 11 2009 - 12:41:54 CDT)
• Jim Paugh
  • Re: [AMBER] XServe cluster (Thu Oct 22 2009 - 16:10:49 CDT)
  • Re: [AMBER] XServe cluster (Thu Oct 22 2009 - 14:24:37 CDT)
• Jimmy Heimdal
  • [AMBER] 1-4 vdW, GB MM difference (Thu Apr 16 2009 - 06:57:01 CDT)
• Jio M
  • Re: [AMBER] slope {no reply} (Thu Nov 19 2009 - 11:15:25 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 23:09:34 CST)
  • Re: [AMBER] slope {no reply} (Tue Nov 17 2009 - 13:13:06 CST)
  • Re: [AMBER] slope {no reply} (Mon Nov 16 2009 - 23:13:44 CST)
  • [AMBER] Re:Etot positive (Mon Nov 16 2009 - 22:59:26 CST)
  • Re: [AMBER] slope (Mon Nov 16 2009 - 22:07:07 CST)
  • [AMBER] Etot positive (Sun Nov 15 2009 - 23:06:22 CST)
  • Re: [AMBER] slope (Sun Nov 15 2009 - 22:42:52 CST)
  • [AMBER] slope {no reply} (Sun Nov 15 2009 - 13:03:17 CST)
  • [AMBER] slope (Thu Nov 12 2009 - 13:28:02 CST)
  • [AMBER] solvent (Sun Nov 08 2009 - 08:12:34 CST)
  • [AMBER] Re: RESP with -a and witout -a flag (Wed Nov 04 2009 - 00:47:55 CST)
  • [AMBER] Re: RESP with -a and witout -a flag (Sun Nov 01 2009 - 23:58:58 CST)
  • [AMBER] Re: (files attached) RESP with -a and witout -a flag (Sat Oct 31 2009 - 00:17:55 CDT)
  • Re: [AMBER] RESP charges with -a and without -a flag (Sat Oct 31 2009 - 00:13:03 CDT)
  • [AMBER] RESP charges with -a and without -a flag (Fri Oct 30 2009 - 08:36:43 CDT)
  • [AMBER] LINMIN failure notice (Fri Sep 18 2009 - 05:20:18 CDT)
  • [AMBER] re: charge consideration (Mon Sep 14 2009 - 03:38:27 CDT)
  • [AMBER] re: charge interaction (Sun Sep 13 2009 - 09:38:43 CDT)
  • [AMBER] charge consideration (Fri Sep 11 2009 - 15:17:34 CDT)
  • Re: [AMBER] DMF solvent box (Fri Sep 11 2009 - 10:00:40 CDT)
  • [AMBER] general query: implicit solvation (Tue Sep 08 2009 - 04:28:49 CDT)
  • Re: [AMBER] nmropt option (Sat Sep 05 2009 - 00:23:09 CDT)
  • [AMBER] nmropt option (Fri Sep 04 2009 - 13:05:25 CDT)
  • [AMBER] prep file (Fri Sep 04 2009 - 04:24:04 CDT)
  • RE: [AMBER] box volume not understood? (Thu Aug 20 2009 - 23:43:31 CDT)
  • RE: [AMBER] box volume not understood? (Thu Aug 20 2009 - 13:26:41 CDT)
  • [AMBER] box volume not understood? (Thu Aug 20 2009 - 08:54:52 CDT)
  • Re: [AMBER] drying of solvent possible ? (Sat Aug 15 2009 - 00:59:08 CDT)
  • [AMBER] drying of solvent possible ? (Thu Aug 13 2009 - 08:49:00 CDT)
  • Re: [AMBER] suggestions pls (Wed Aug 12 2009 - 08:04:16 CDT)
  • [AMBER] suggestions pls (Tue Aug 11 2009 - 12:44:19 CDT)
  • [AMBER] hydrogen bond? (Sun Aug 09 2009 - 06:29:23 CDT)
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 02:11:32 CDT)
  • [AMBER] ambpdb problem (Thu Jul 30 2009 - 14:12:10 CDT)
  • [AMBER] pdb file no bond and charges (Wed Jul 29 2009 - 01:28:48 CDT)
  • [AMBER] residues lacking connect0/connect1 (Mon Jul 27 2009 - 11:10:06 CDT)
  • [AMBER] -a flag :RESP (Sun Jul 19 2009 - 05:48:20 CDT)
  • [AMBER] RE: charge not zero on group:''''.respin1 attached (Sat Jul 18 2009 - 09:40:18 CDT)
  • [AMBER] charge not zero on group: RESP (Sat Jul 18 2009 - 00:14:58 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Wed Jul 15 2009 - 23:29:08 CDT)
  • [AMBER] GAFF and NME, ACE terminal res (Mon Jul 13 2009 - 15:51:06 CDT)
  • [AMBER] suitable force field (Wed Jul 08 2009 - 02:14:12 CDT)
  • [AMBER] suitable force field (Wed Jul 08 2009 - 05:06:35 CDT)
• Jiri Sponer
  • Re: [AMBER] calculation of Pi-Pi interaction energy (Wed Apr 01 2009 - 07:38:49 CDT)
• Joanna Panecka
  • [AMBER] ptraj image in non-orthorhombic cell (Wed Jun 03 2009 - 15:19:52 CDT)
• Jochen Heil
  • Re: [AMBER] NAB md function prints strange output (Tue Feb 10 2009 - 06:19:56 CST)
  • [AMBER] NAB md function prints strange output (Mon Feb 09 2009 - 05:30:21 CST)
• Jodi Hadden
  • [AMBER] 2-step vs 3-step TI, and softcores question (Tue Jun 23 2009 - 17:00:02 CDT)
  • [AMBER] input coordinates for vdW transition step in Amber 10 TI (Wed Jun 10 2009 - 15:27:16 CDT)
• Joe Krahn
  • Re: [AMBER] adding chain id to ptraj pdb output (Mon Mar 23 2009 - 18:20:30 CDT)
• Johan Sund
  • [AMBER] Improper dihedrals from .off and .lib files (Thu Jun 18 2009 - 05:15:37 CDT)
• John Bennett
  • [AMBER] sander.MPI and pmemd.MPI in Fedora 8 (Sun Mar 15 2009 - 16:23:16 CDT)
• john smith
  • [AMBER] MMPBSA and mm_pbsa_statistics.pl error (Tue Jun 02 2009 - 00:38:54 CDT)
  • Re: [AMBER] Radius for Bromine in MMPBSA calculation (Tue May 26 2009 - 00:00:52 CDT)
  • Re: [AMBER] Radius for Bromine in MMPBSA calculation (Sun May 24 2009 - 23:52:48 CDT)
  • [AMBER] Radius for Bromine in MMPBSA calculation (Thu May 21 2009 - 00:24:05 CDT)
  • Re: [AMBER] pmemd compilation error (Tue May 05 2009 - 06:20:08 CDT)
  • [AMBER] pmemd compilation error (Mon Apr 27 2009 - 22:30:21 CDT)
• Jordan Monnet
  • Re: [AMBER] MM_PBSA not successful (Fri Aug 14 2009 - 19:05:00 CDT)
  • Re: [AMBER] problem of mm_pbsa (Thu Aug 13 2009 - 15:04:37 CDT)
  • Re: [AMBER] problem of mm_pbsa (Mon Aug 10 2009 - 14:37:55 CDT)
  • Re: [AMBER] problem of mm_pbsa (Fri Aug 07 2009 - 18:13:57 CDT)
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 09:30:54 CDT)
  • Re: [AMBER] ambpdb problem (Thu Jul 30 2009 - 14:32:57 CDT)
  • Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ? (Wed Jul 15 2009 - 17:56:12 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 11:03:32 CDT)
  • Re: [AMBER] Strange contacts with water molecules (Wed Jun 17 2009 - 12:00:46 CDT)
  • Re: [AMBER] Strange contacts with water molecules (Tue Jun 09 2009 - 11:01:53 CDT)
  • [AMBER] Strange contacts with water molecules (Mon Jun 08 2009 - 16:39:26 CDT)
• Jordan, Brad
  • [AMBER] RE: Problem with GROUP input (Wed Sep 09 2009 - 19:11:51 CDT)
  • [AMBER] Problem with GROUP input (Wed Sep 09 2009 - 18:58:36 CDT)
  • [AMBER] Docking with Amber (Mon Aug 31 2009 - 15:01:15 CDT)
• Jorgen Simonsen
  • [AMBER] parameter for dihedral angle (Fri Jun 05 2009 - 10:16:56 CDT)
  • Re: [AMBER] creating bond (Wed Jun 03 2009 - 14:56:29 CDT)
  • [AMBER] creating bond (Wed Jun 03 2009 - 12:04:11 CDT)
  • Re: [AMBER] Modification of His (Mon May 18 2009 - 07:16:10 CDT)
  • [AMBER] Modification of His (Mon May 18 2009 - 05:51:50 CDT)
  • Re: [AMBER] xleap reading hydrogens giving error (Fri May 15 2009 - 10:54:17 CDT)
  • [AMBER] xleap reading hydrogens giving error (Fri May 15 2009 - 02:47:10 CDT)
  • Re: [AMBER] Adding non standard residues (Mon May 11 2009 - 16:11:49 CDT)
  • [AMBER] Adding non standard residues (Mon May 11 2009 - 03:54:25 CDT)
  • [AMBER] Modifying a water molecule (Sat May 09 2009 - 08:16:54 CDT)
  • Re: [AMBER] ambertools for NAMD (Thu May 07 2009 - 13:29:41 CDT)
  • [AMBER] ambertools for NAMD (Thu May 07 2009 - 07:35:24 CDT)
  • Re: [AMBER] creating new residue adds none wanted ter (Tue May 05 2009 - 04:57:29 CDT)
  • Re: [AMBER] creating new residue adds none wanted ter (Mon May 04 2009 - 09:09:08 CDT)
  • [AMBER] creating new residue adds none wanted ter (Mon May 04 2009 - 02:49:47 CDT)
  • [AMBER] Regarding syntax for freezing different atoms (Thu Apr 23 2009 - 07:50:43 CDT)
• Jose Borreguero
  • [AMBER] can I run EVB in other ensemble than NVE? (Tue Oct 20 2009 - 11:57:04 CDT)
  • Re: [AMBER] why is TAUTP scaled by "e" ? (Fri Oct 16 2009 - 14:13:42 CDT)
  • [AMBER] why is TAUTP scaled by "e" ? (Thu Oct 15 2009 - 15:49:18 CDT)
  • [AMBER] why should one restrain the position of the counterions? (Mon Sep 28 2009 - 13:28:20 CDT)
  • [AMBER] how to ouput the electrostatic potential at a single atomic position? (Thu Sep 17 2009 - 14:06:54 CDT)
  • Re: [AMBER] acetone lib and frcmod files? (Mon Aug 24 2009 - 16:34:07 CDT)
  • Re: [AMBER] acetone lib and frcmod files? (Mon Aug 24 2009 - 07:56:51 CDT)
  • [AMBER] acetone lib and frcmod files? (Sun Aug 23 2009 - 16:36:43 CDT)
  • Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? (Tue Aug 18 2009 - 17:33:32 CDT)
  • [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? (Tue Aug 18 2009 - 09:37:39 CDT)
  • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? (Wed Mar 11 2009 - 16:56:03 CDT)
  • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? (Wed Mar 11 2009 - 13:46:29 CDT)
  • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? (Wed Mar 11 2009 - 12:28:21 CDT)
  • [AMBER] wrong estimation of hydrogen velocities when using SHAKE? (Tue Mar 10 2009 - 11:09:48 CDT)
  • [AMBER] can ptraj output the trajectory of the residue CM? (Mon Feb 16 2009 - 13:47:34 CST)
  • [AMBER] topology file for GLY with amino and carboxyl group? (Tue Jan 27 2009 - 12:57:45 CST)
• Joseph Nachman
  • Re: [AMBER] Parameters for haloacetates (Mon Aug 10 2009 - 09:54:13 CDT)
  • [AMBER] Parameters for haloacetates (Fri Aug 07 2009 - 13:22:34 CDT)
• Josmar R. da Rocha
  • Re: [AMBER] Can I use only a single point calculation to derive RESP charges? (Sat May 09 2009 - 10:19:07 CDT)
  • [AMBER] Can I use only a single point calculation to derive RESP charges? (Fri May 08 2009 - 19:08:54 CDT)
  • [AMBER] help with RESP tutorial using antechamber and gaussian (Sun May 03 2009 - 12:59:23 CDT)
  • Re: [AMBER] chain restrain x TI (Sat May 02 2009 - 12:09:53 CDT)
  • [AMBER] chain restrain x TI (Wed Apr 29 2009 - 17:04:52 CDT)
• journal.update
  • [AMBER] How to build amide bond etween two protein chains (Tue Jun 23 2009 - 23:36:07 CDT)
• Ju Zhang
  • [AMBER] "loadoff tRNA.lib" in Leap (Tue Jun 23 2009 - 15:55:25 CDT)
• Julian Garrec
  • [AMBER] varying positional restraints with PMEMD (Thu Nov 05 2009 - 18:43:35 CST)
• Jun Dong
  • Re: [AMBER] RE: pmemd parallel (Wed Jul 15 2009 - 10:00:49 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Mon Jul 13 2009 - 13:10:34 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 12:25:03 CDT)
  • [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 11:05:49 CDT)
• Jun Wang
  • RE: [AMBER] total charge for NPRO in ff03ua (Mon Jun 15 2009 - 18:35:39 CDT)
• Junmei Wang
  • Re: [AMBER] RESP using antechamber with Se atom (Thu Nov 05 2009 - 15:39:46 CST)
  • Re: Re: Re: [AMBER] Antechamber and Parmchk problems (Thu Nov 05 2009 - 15:16:51 CST)
  • Re: Re: [AMBER] Antechamber and Parmchk problems (Wed Nov 04 2009 - 15:07:35 CST)
  • Re: [AMBER] AMBER: segmentation fault when running parmchk (Wed Nov 04 2009 - 13:22:54 CST)
  • Re: [AMBER] Antechamber and Parmchk problems (Wed Nov 04 2009 - 13:21:25 CST)
  • Re: [AMBER] Re: RESP with -a and witout -a flag (Mon Nov 02 2009 - 10:48:48 CST)
  • Re: [AMBER] Gaussian log file error (Mon Nov 02 2009 - 09:58:10 CST)
  • Re: [AMBER] RESP charges with -a and without -a flag (Fri Oct 30 2009 - 11:49:00 CDT)
  • Re: [AMBER] Conversion of Gaussian output file into mol2 (Thu Oct 29 2009 - 10:45:27 CDT)
  • Re: [AMBER] xleap not reconizing inhibitor prepin (Mon Oct 26 2009 - 09:51:41 CDT)
  • Re: [AMBER] too many undefined parameters in frcmod (Mon Oct 26 2009 - 09:45:04 CDT)
  • [AMBER] cross correlation analysis with ptraj (Thu Oct 15 2009 - 11:49:29 CDT)
  • [AMBER] nab normal mode analysis has imaginary frequencies (Wed Oct 14 2009 - 11:05:06 CDT)
  • Re: [AMBER] re: net charge (Tue Jun 23 2009 - 15:41:24 CDT)
  • Re: [AMBER] ligand QM/semi-empirical coords optmisation (Fri Jun 05 2009 - 10:01:32 CDT)
  • Re: [AMBER] gaff and aromatic compounds (Tue May 26 2009 - 11:03:53 CDT)
  • Re: [AMBER] gaff and aromatic compounds (Thu May 21 2009 - 20:24:52 CDT)
  • Re: [AMBER] ambmol2? (Tue Mar 31 2009 - 21:41:35 CDT)
  • Re: [AMBER] ambmol2? (Tue Mar 31 2009 - 18:08:25 CDT)
  • Re: [AMBER] Antechamber problem (Fri Mar 27 2009 - 16:21:33 CDT)
• Justine Condo
  • Re: [AMBER] multisander error (Mon Jan 12 2009 - 17:01:41 CST)
  • Re: [AMBER] multisander error (Mon Jan 12 2009 - 16:39:44 CST)
  • Re: [AMBER] multisander error (Mon Jan 12 2009 - 16:32:31 CST)
  • [AMBER] multisander error (Mon Jan 12 2009 - 16:03:37 CST)
• Justine Shaw Condo
  • [AMBER] Partial charges of heme (Tue Jun 30 2009 - 13:28:11 CDT)
• K.R.
  • [AMBER] Dipole moment visualization. (Thu Oct 01 2009 - 16:37:29 CDT)
• Kamali Sripathi
  • Re: [AMBER] Problem with loading PDB into tleap (Tue Sep 08 2009 - 08:49:20 CDT)
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 09:06:15 CDT)
  • [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 08:21:30 CDT)
• Karen Callahan
  • [AMBER] Question about &dipoles printing in AMBER 8 (Mon May 25 2009 - 18:46:00 CDT)
• Karl Kirschner
  • Re: [AMBER] Different optimized structures with HF and B3LYP (Fri Oct 02 2009 - 03:07:08 CDT)
  • [AMBER] install ambertools (Thu Sep 17 2009 - 07:55:22 CDT)
  • Re: [AMBER] Charge Problem (Fri Aug 14 2009 - 03:55:07 CDT)
  • Re: [AMBER] gaussian 98 input/output for antechamber/resp (Thu Aug 13 2009 - 02:26:12 CDT)
  • Re: [AMBER] gaussian 98 input/output for antechamber/resp (Thu Aug 13 2009 - 01:57:41 CDT)
  • Re: [AMBER] Saccharides chains termini (Tue Jun 30 2009 - 09:57:46 CDT)
  • Re: [AMBER] bond length energy (Fri Jun 19 2009 - 04:57:04 CDT)
  • Re: [AMBER] GLYCAM: warnings by writing topology (Wed Jun 17 2009 - 03:33:55 CDT)
  • Re: [AMBER] glycopeptide Parametrization (Fri Jun 12 2009 - 10:06:17 CDT)
  • Re: [AMBER] (no subject) (Mon Jun 08 2009 - 06:38:42 CDT)
  • Re: [AMBER] average torsional energy (Mon Jun 08 2009 - 03:29:05 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Thu Apr 23 2009 - 08:54:14 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Thu Apr 23 2009 - 06:43:31 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Tue Apr 21 2009 - 02:24:18 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Mon Apr 20 2009 - 07:27:45 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Wed Apr 15 2009 - 02:07:00 CDT)
  • Re: [AMBER] long polymer chain and image command in ptraj (Mon Apr 06 2009 - 03:15:00 CDT)
  • Re: [AMBER] FF Parameters Transformations ...? (Mon Apr 06 2009 - 02:39:31 CDT)
  • Re: [AMBER] leap and chirality (Tue Mar 24 2009 - 03:11:38 CDT)
  • Re: [AMBER] leap and chirality (Mon Mar 23 2009 - 09:05:56 CDT)
  • [AMBER] leap and chirality (Mon Mar 23 2009 - 04:54:29 CDT)
• Karol Kaszuba
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Sat Jan 17 2009 - 04:41:22 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Mon Jan 12 2009 - 01:57:50 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Sun Jan 11 2009 - 02:01:07 CST)
  • Re: [AMBER] number-of-EPS-exceeds-MAXESP (Sat Jan 10 2009 - 09:27:08 CST)
  • [AMBER] number-of-EPS-exceeds-MAXESP (Fri Jan 09 2009 - 15:07:13 CST)
• karthik s
  • Re: [AMBER] using binary trajectories from NAMD in PTRAJ (Tue Jan 27 2009 - 00:49:13 CST)
  • [AMBER] using binary trajectories from NAMD in PTRAJ (Mon Jan 26 2009 - 01:11:29 CST)
• Kasprzak, Wojciech (NIH/NCI) [C]
  • [AMBER] Circular RNA topology file (Wed Oct 21 2009 - 13:26:04 CDT)
• Katrina Hill
  • [AMBER] Ptraj Segmentation Fault (Wed Oct 21 2009 - 21:15:31 CDT)
• Katrina Lexa
  • [AMBER] Gap in rst file (Mon Sep 28 2009 - 09:47:43 CDT)
• Kaushik Raha
  • Re: [AMBER] Compiling and running NAB programs in parallel using MPI (Tue Jun 30 2009 - 09:48:11 CDT)
  • Re: [AMBER] Compiling and running NAB programs in parallel using MPI (Fri Jun 26 2009 - 10:12:11 CDT)
  • [AMBER] Compiling and running NAB programs in parallel using MPI (Thu Jun 25 2009 - 16:36:35 CDT)
• Kefa Lu
  • Re: [AMBER] AMBER is running silently (Mon Aug 17 2009 - 20:25:14 CDT)
  • Re: [AMBER] AMBER is running silently (Mon Aug 17 2009 - 18:10:17 CDT)
  • [AMBER] AMBER is running silently (Mon Aug 17 2009 - 17:47:34 CDT)
  • Re: [AMBER] AMBER job restart problem (Sun Aug 16 2009 - 00:09:22 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 23:36:59 CDT)
  • Re: [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 05:12:21 CDT)
  • [AMBER] AMBER job restart problem (Sat Aug 15 2009 - 03:22:08 CDT)
• Keith Van Nostrand
  • [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 (Tue Sep 08 2009 - 14:26:14 CDT)
  • Re: [AMBER] Distance restraint and periodic boundary conditions (Wed Aug 19 2009 - 11:44:49 CDT)
  • Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Wed Jul 22 2009 - 10:58:08 CDT)
  • Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Thu Jul 16 2009 - 16:08:04 CDT)
  • [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Fri Jul 10 2009 - 10:27:12 CDT)
• Kevin Wiehe
  • [AMBER] ptraj fails to recognize binary REMD output (Fri Feb 06 2009 - 11:44:21 CST)
• Khaled Barakat
  • Re: [AMBER] antechamber : missed atoms (Mon Jan 26 2009 - 14:22:14 CST)
  • Re: [AMBER] antechamber : missed atoms (Mon Jan 26 2009 - 13:20:52 CST)
  • Re: [AMBER] antechamber : missed atoms (Mon Jan 26 2009 - 13:15:33 CST)
  • [AMBER] antechamber : missed atoms (Mon Jan 26 2009 - 12:54:07 CST)
  • [AMBER] PHOSPHOTHREONINE (Wed Jan 07 2009 - 13:11:43 CST)
• Khavrutskii, Ilja
  • Re: [AMBER] Re: antechamber am1-bcc issues (Fri Aug 21 2009 - 14:32:34 CDT)
  • Re: [AMBER] Re: antechamber am1-bcc issues (Fri Aug 21 2009 - 11:27:28 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 08:04:44 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 07:03:43 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Thu Aug 20 2009 - 06:37:47 CDT)
  • Re: [AMBER] antechamber am1-bcc issues (Tue Aug 18 2009 - 16:00:03 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Mon Jul 20 2009 - 06:46:38 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Thu Jul 16 2009 - 16:02:10 CDT)
  • [AMBER] Disappearing common atoms in Amber 10 with TI (Thu Jul 16 2009 - 08:38:43 CDT)
• Kijeong Kwac
  • [AMBER] AmberTools compilation error (Wed Apr 01 2009 - 14:04:00 CDT)
• Kipras Redeckas
  • Re: [AMBER] Attaching a ligand to a protein residue. (Sun Sep 27 2009 - 05:23:42 CDT)
  • [AMBER] Attaching a ligand to a protein residue. (Fri Sep 25 2009 - 16:33:58 CDT)
• KIRTANA S
  • Re: [AMBER] Regd : gaff force field (Thu Aug 06 2009 - 17:12:15 CDT)
  • [AMBER] Regd : gaff force field (Thu Aug 06 2009 - 15:09:14 CDT)
  • [AMBER] Regd: parameter Fe4S4 (Mon Jun 29 2009 - 11:11:49 CDT)
  • [AMBER] parameters Fe4S4 cluster (Sun Jun 21 2009 - 21:30:08 CDT)
  • [AMBER] Re: residue (Fri Jun 19 2009 - 10:03:31 CDT)
  • [AMBER] residue (Thu Jun 18 2009 - 14:59:50 CDT)
  • Re: [AMBER] Residues (Thu Jun 18 2009 - 14:57:11 CDT)
  • [AMBER] connecting residues (Tue Jun 16 2009 - 10:59:37 CDT)
  • [AMBER] Re: connect (Mon Jun 15 2009 - 15:18:54 CDT)
  • Re: [AMBER] Residues (Sat Jun 13 2009 - 19:14:31 CDT)
  • [AMBER] Re: Residues (Fri Jun 12 2009 - 20:15:20 CDT)
  • Re: [AMBER] Residues (Fri Jun 12 2009 - 14:41:02 CDT)
  • [AMBER] help (Fri Jun 12 2009 - 08:42:04 CDT)
  • Re: [AMBER] Residues (Fri Jun 12 2009 - 10:07:50 CDT)
  • [AMBER] Residues (Fri Jun 12 2009 - 09:10:39 CDT)
• Kristina Furse
  • RE: [AMBER] Replacing DNA base with analog (Thu Jul 23 2009 - 09:36:26 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 11:27:29 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 08:53:21 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 11:56:26 CDT)
  • RE: [AMBER] ntt=3 and ibelly=1 (Fri Jul 17 2009 - 11:41:29 CDT)
  • [AMBER] ntt=3 and ibelly=1 (Thu Jul 16 2009 - 11:07:23 CDT)
  • RE: [AMBER] atom types in pdb files (Mon Apr 13 2009 - 11:30:05 CDT)
  • RE: [AMBER] Changing Force Fields in "Midstream" (Wed Mar 11 2009 - 16:58:06 CDT)
• kshatresh
  • Re: [AMBER] problem in running sander (Mon Jun 30 2008 - 15:27:42 CDT)
  • [AMBER] problem in running sander (Mon Jun 30 2008 - 14:33:24 CDT)
• Kshatresh Dutta Dubey
  • Re: [AMBER] [Fwd: ligand exiting a protein cavity] (Thu Oct 29 2009 - 09:44:28 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 10:23:29 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 10:14:35 CDT)
  • Re: [AMBER] Problem in test run (Tue Sep 29 2009 - 10:05:13 CDT)
  • [AMBER] Problem in test run (Tue Sep 29 2009 - 09:21:56 CDT)
  • Re: [AMBER] MM-PBSA nmode statistics (Fri May 29 2009 - 00:13:34 CDT)
  • [AMBER] Segmentation error in Ptraj (Fri May 22 2009 - 02:17:27 CDT)
  • Re: [AMBER] Problem with Nmode (Thu May 21 2009 - 00:14:50 CDT)
  • [AMBER] Problem with Nmode (Mon May 18 2009 - 23:25:05 CDT)
  • [AMBER] Problem in Nmode (Mon May 18 2009 - 01:07:52 CDT)
  • Re: [AMBER] Question (Sat Mar 28 2009 - 04:16:03 CDT)
  • [AMBER] Question (Fri Mar 27 2009 - 08:06:09 CDT)
  • Re: [AMBER] problem in running sander (Thu Mar 19 2009 - 02:17:21 CDT)
• ksripath_at_umich.edu
  • Re: [AMBER] Problem with loading PDB into tleap (Wed Aug 19 2009 - 14:00:22 CDT)
• kureeckal ramesh
  • [AMBER] MMTSB tool set PDF (Tue Nov 10 2009 - 08:02:39 CST)
  • [AMBER] error in kclust of MMTB_tool set (Tue Nov 10 2009 - 06:41:31 CST)
  • [AMBER] error in kclust of MMTB_tool set (Sun Nov 08 2009 - 18:10:58 CST)
  • [AMBER] ptraj script for H bond for protein (explicit ) (Sat Nov 07 2009 - 01:38:29 CST)
  • [AMBER] error in kclust of MMTB_tool set (Fri Nov 06 2009 - 01:33:01 CST)
  • [AMBER] error in tleap of AMBER 10 (Fri Jun 26 2009 - 02:10:56 CDT)
  • [AMBER] error in tleap of AMBER 10 (Wed Jun 24 2009 - 00:03:55 CDT)
  • Re: [AMBER] Ramesh here (Sat Feb 28 2009 - 09:36:43 CST)
  • [AMBER] Ramesh here (Fri Feb 27 2009 - 21:20:49 CST)
  • [AMBER] Re: Antechamber (Fri Feb 27 2009 - 06:56:58 CST)
  • [AMBER] Antechamber (Thu Feb 19 2009 - 19:36:03 CST)
  • [AMBER] error in xleap: ligand binding using MMand QMMM tech (Thu Feb 12 2009 - 04:27:41 CST)
  • Re: [AMBER] Dr. Ramesh here (Mon Feb 02 2009 - 08:22:51 CST)
  • Re: [AMBER] Dr. Ramesh here (Thu Jan 29 2009 - 21:18:33 CST)
  • Re: [AMBER] Dr. Ramesh here (Thu Jan 29 2009 - 19:41:17 CST)
  • [AMBER] Dr. Ramesh here (Thu Jan 29 2009 - 04:41:10 CST)
• Lachele Foley (Lists)
  • Re: [AMBER] Saccharides chains termini (Tue Jun 30 2009 - 09:46:09 CDT)
  • Re: [AMBER] Cyclodextrin forcefield (Fri May 01 2009 - 10:23:37 CDT)
  • Re: [AMBER] Amber FF and Glycam (Thu Apr 30 2009 - 12:16:17 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Fri Apr 17 2009 - 13:13:49 CDT)
  • Re: [AMBER] glycam and solvateoct command (Wed Feb 18 2009 - 09:00:34 CST)
  • Re: [AMBER] script to convert GLYCAM ff in CHARMM format (Fri Feb 06 2009 - 08:57:17 CST)
  • Re: [AMBER] thioglycoside (Mon Jan 26 2009 - 09:36:26 CST)
• Lake, Thomas
  • RE: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 08:35:33 CDT)
  • [AMBER] (no subject) (Thu Feb 26 2009 - 10:19:53 CST)
  • [AMBER] (no subject) (Thu Jan 22 2009 - 07:43:59 CST)
  • [AMBER] (no subject) (Fri Jan 16 2009 - 11:38:09 CST)
• Lan JIN
  • Re: [AMBER] amber10 installation problem (Fri Jul 10 2009 - 02:41:34 CDT)
  • Re: [AMBER] amber10 installation problem (Wed Jul 08 2009 - 21:46:22 CDT)
  • [AMBER] amber10 installation problem (Wed Jul 08 2009 - 01:49:05 CDT)
• Larry Layne
  • [AMBER] PBSA: PB bomb in pb_setgrd() (Wed Jan 07 2009 - 09:33:57 CST)
• Lauren Wickstrom
  • Re: [AMBER] how to use those water models off the list in amber? (Wed Jan 21 2009 - 17:58:22 CST)
• lev kantorovich
  • [AMBER] question (Wed Jun 10 2009 - 09:20:08 CDT)
• li hui
  • [AMBER] contant force pulling simulation with amber 10 (Mon Feb 16 2009 - 11:01:36 CST)
• liangchen88_at_ucla.edu
  • Re: [AMBER] linux version for Amber10 (Sat Nov 07 2009 - 21:59:53 CST)
  • Re: [AMBER] the problem of nucgen.dat (Sat Nov 07 2009 - 21:48:54 CST)
  • [AMBER] linux version for Amber10 (Sat Nov 07 2009 - 09:28:05 CST)
  • [AMBER] linux version for Amber10 (Sat Nov 07 2009 - 09:28:05 CST)
  • [AMBER] the problem of nucgen.dat (Sat Nov 07 2009 - 08:41:49 CST)
• Lili Peng
  • [AMBER] Combine and rename group of residues in xleap (Wed Oct 07 2009 - 16:49:23 CDT)
  • Re: [AMBER] Parameters for haloacetates (Fri Aug 07 2009 - 23:43:50 CDT)
  • Re: [AMBER] Coarse grained MD in AMBER ? (Wed Jun 17 2009 - 13:57:58 CDT)
• Lin Xu
  • [AMBER] how to deal with aromatic nitro group with antechamber (Wed Sep 02 2009 - 17:04:13 CDT)
• LIU Huanxiang
  • Re: [AMBER] MM_PBSA: abnormal VDW interaction energy (Tue Oct 06 2009 - 21:54:49 CDT)
  • [AMBER] MM_PBSA: abnormal VDW interaction energy (Mon Oct 05 2009 - 21:43:21 CDT)
• liu junjun
  • Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9 (Tue Apr 28 2009 - 21:18:31 CDT)
  • [AMBER] parallel problem of QM/MM calculation for AMBER 9 (Tue Apr 28 2009 - 16:53:06 CDT)
  • Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? (Mon Feb 02 2009 - 10:25:41 CST)
  • [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? (Sun Feb 01 2009 - 01:51:39 CST)
• liuhui
  • Re: [AMBER] Error running MM _PBSA.pl script (Tue May 19 2009 - 21:20:26 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Tue May 19 2009 - 11:15:24 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Tue May 19 2009 - 09:29:23 CDT)
• lnin_1431_at_sina.com
  • [AMBER] how to plot this kind of map? (Thu Apr 09 2009 - 03:36:45 CDT)
• Loeffler, Hannes (STFC,DL,CSE)
  • [AMBER] PK zero for specific dihedral and parmchk (Wed Sep 09 2009 - 03:00:20 CDT)
  • RE: [AMBER] Dyndom (Sat Aug 29 2009 - 10:18:18 CDT)
• lorenzo
  • [AMBER] units of measures (Thu Oct 22 2009 - 06:20:26 CDT)
• Lorenzo Gontrani
  • Re: [AMBER] g(r) extrapolation (Thu Feb 19 2009 - 03:23:19 CST)
  • [AMBER] g(r) extrapolation (Wed Feb 18 2009 - 09:16:26 CST)
  • Re: [AMBER] Solvation potential and free energies (Thu Feb 05 2009 - 06:34:47 CST)
• Louis-Frédéric Feuillette
  • Re: [AMBER] man pages? (Tue Oct 20 2009 - 15:17:52 CDT)
  • [AMBER] man pages? (Tue Oct 20 2009 - 12:09:09 CDT)
• Lucilla Angeli
  • [AMBER] MM-PBSA: decompose energy error (Mon Apr 06 2009 - 09:35:58 CDT)
• Luis Gracia
  • Re: [AMBER] RMSD vs time and RMSD vs residues (Fri Oct 02 2009 - 13:07:10 CDT)
• m m
  • [AMBER] my FF (Tue Apr 14 2009 - 17:21:38 CDT)
  • [AMBER] compare MMPBSA result (Wed Apr 08 2009 - 01:28:06 CDT)
  • [AMBER] fillratio error in mmpbsa (Wed Apr 01 2009 - 06:42:45 CDT)
  • RE: [AMBER] inpcrd and prmtop (Tue Mar 03 2009 - 04:08:51 CST)
  • [AMBER] inpcrd and prmtop (Tue Mar 03 2009 - 03:27:06 CST)
  • [AMBER] restraint angle (Tue Feb 17 2009 - 11:17:00 CST)
  • [AMBER] atomic charge (Thu Jan 29 2009 - 02:08:47 CST)
• M. L. Dodson
  • [AMBER] Need help with nab code to access the m_prm struct in a molecule (Mon Jun 15 2009 - 14:49:02 CDT)
  • Re: [AMBER] Histidine, which form? (Mon Jun 15 2009 - 11:45:25 CDT)
  • Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so (Wed Apr 08 2009 - 11:06:09 CDT)
  • Re: [AMBER] generalized distance restraint (Mon Mar 09 2009 - 11:51:19 CDT)
  • Re: [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 13:34:03 CDT)
  • Re: [AMBER] nmoldyn2 with Amber (Sun Mar 08 2009 - 13:32:22 CDT)
  • Re: [AMBER] Quality/size of HDD for Amber (Fri Mar 06 2009 - 09:44:45 CST)
  • Re: [AMBER] RE:xleap problem (Thu Jan 29 2009 - 10:22:22 CST)
  • Re: [AMBER] RE:xleap problem (Mon Jan 26 2009 - 14:47:26 CST)
  • Re: [AMBER] Use of Amber in distributed calculations (Sat Jan 17 2009 - 08:01:36 CST)
  • Re: [AMBER] Use of Amber in distributed calculations (Sat Jan 17 2009 - 07:48:42 CST)
  • Re: [AMBER] Need help with point to plane distance calculation in nab (Thu Jan 08 2009 - 13:54:15 CST)
  • Re: [AMBER] Need help with point to plane distance calculation in nab (Thu Jan 08 2009 - 13:16:51 CST)
  • [AMBER] Need help with point to plane distance calculation in nab (Thu Jan 08 2009 - 12:39:16 CST)
  • Re: [AMBER] RE: AMBER: mail list (Wed Jan 07 2009 - 10:04:02 CST)
• Madhurima Jana
  • [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 (Fri Jun 19 2009 - 01:40:43 CDT)
  • [AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine (Thu Jun 18 2009 - 07:39:03 CDT)
  • Re: [AMBER] Fail to allocate ff (Tue Mar 03 2009 - 08:27:41 CST)
  • [AMBER] Fail to allocate ff (Tue Mar 03 2009 - 05:17:57 CST)
  • [AMBER] force-field for cyclic oligosaccharide using leap (Sun Jan 11 2009 - 22:21:23 CST)
  • [AMBER] force-field for cyclic oligosaccharide using leap (Thu Jan 08 2009 - 22:50:18 CST)
• Mag. Thomas Taylor
  • Re: [AMBER] input file / skinnb (Thu Sep 17 2009 - 00:50:16 CDT)
  • Re: [AMBER] input file / skinnb (Wed Sep 16 2009 - 02:49:32 CDT)
  • [AMBER] input file (Thu Sep 10 2009 - 05:48:06 CDT)
  • [AMBER] AmberTools 1.3 / CHAMBER (Tue Sep 08 2009 - 09:29:23 CDT)
• Mahmoud A. A. Ibrahim
  • Re: [AMBER] parameter for manganese (Thu Sep 24 2009 - 07:17:29 CDT)
  • Re: [AMBER] problem with the energetics of the system (Sun Jul 12 2009 - 05:37:37 CDT)
  • [AMBER] problem with the energetics of the system (Sat Jul 11 2009 - 18:23:13 CDT)
  • [AMBER] Zinc ion, help (Tue Jul 07 2009 - 09:26:48 CDT)
  • [AMBER] Reference Correction (Sun Jun 21 2009 - 15:11:34 CDT)
  • Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? (Tue May 05 2009 - 12:15:18 CDT)
  • [AMBER] APS & ff03 (Mon Feb 09 2009 - 08:49:56 CST)
  • [AMBER] Atome Type (Thu Jan 29 2009 - 04:59:42 CST)
  • [AMBER] AMBER External keyword (Wed Jan 21 2009 - 09:59:33 CST)
• Majeed Shaik
  • [AMBER] xleap input pdb problem (Wed May 06 2009 - 13:47:45 CDT)
  • [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error (Wed Feb 18 2009 - 14:09:17 CST)
  • [AMBER] How to constrain the hydrogen bonding distances... (Wed Feb 18 2009 - 08:11:37 CST)
• Manikandan Chandrasekaran
  • Re: [AMBER] Test run on Solaris 10 X 86 (Fri Feb 06 2009 - 11:39:54 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Wed Feb 04 2009 - 12:37:21 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Tue Feb 03 2009 - 14:28:37 CST)
  • Re: [AMBER] Test run on Solaris 10 X 86 (Mon Feb 02 2009 - 13:16:32 CST)
  • [AMBER] Test run on Solaris 10 X 86 (Sat Jan 31 2009 - 12:39:14 CST)
• Manish Kumar
  • Re: [AMBER] Parameter Problem (Wed Sep 23 2009 - 08:28:11 CDT)
  • [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB (Wed Aug 12 2009 - 14:44:37 CDT)
  • Re: [AMBER] Re: implicit solvent simulation with new ligand (Fri Aug 07 2009 - 14:08:59 CDT)
  • [AMBER] Re: implicit solvent simulation with new ligand (Fri Aug 07 2009 - 13:22:57 CDT)
  • [AMBER] implicit solvent simulation with new ligand (Thu Aug 06 2009 - 22:29:37 CDT)
  • Re: [AMBER] implicit solvent simulation (Thu Aug 06 2009 - 01:53:54 CDT)
  • Re: [AMBER] implicit solvent simulation (Thu Aug 06 2009 - 00:19:11 CDT)
  • [AMBER] implicit solvent simulation (Wed Aug 05 2009 - 23:49:30 CDT)
  • Re: [AMBER] Simulation with United atom force field in Implicit solvent. (Sun Jul 26 2009 - 13:22:40 CDT)
  • [AMBER] Simulation with United atom force field in Implicit solvent. (Sat Jul 25 2009 - 22:55:42 CDT)
  • Re: [AMBER] radical simulation (Fri Jul 24 2009 - 02:48:01 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Thu Jul 23 2009 - 02:10:51 CDT)
  • [AMBER] Patching terminal (Tue Jul 21 2009 - 18:53:54 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Mon Jul 20 2009 - 16:11:20 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Sun Jul 19 2009 - 14:36:35 CDT)
  • [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Thu Jul 09 2009 - 22:33:01 CDT)
  • [AMBER] MM-PBSA delphi.crg and delphi.siz (Wed Jul 08 2009 - 16:29:40 CDT)
• Mannan
  • [AMBER] Salt bridge time scale (Sun Oct 25 2009 - 20:57:20 CDT)
  • [AMBER] How to remove Hydrogen using ptraj (Tue Sep 01 2009 - 05:50:44 CDT)
  • [AMBER] Query regarding watershell command (Mon Aug 31 2009 - 05:38:08 CDT)
  • [AMBER] WATERSHELL (Mon Aug 31 2009 - 00:02:51 CDT)
  • [AMBER] Measuring volume of the binding pocket (Tue Aug 11 2009 - 21:31:18 CDT)
  • [AMBER] measuring volume of the binding pocket (Tue Aug 11 2009 - 21:03:49 CDT)
  • [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded (Sun Jul 26 2009 - 22:49:54 CDT)
  • [AMBER] Could not find type: MG Parameter file was not saved. (Sat Jul 25 2009 - 22:41:24 CDT)
  • [AMBER] where to I get the parameters for Mg divalent ion (Wed Jun 17 2009 - 23:11:19 CDT)
  • [AMBER] How to calculate SASA in vmd (Wed Jun 17 2009 - 01:40:05 CDT)
  • [AMBER] How to find out residence time of water molecules (Thu Apr 02 2009 - 20:52:36 CDT)
  • [AMBER] How to delete the frames at specific intervals (Thu Apr 02 2009 - 20:16:49 CDT)
  • [AMBER] continuam water (Mon Mar 23 2009 - 23:11:50 CDT)
  • [AMBER] MD simulations on a protein with FAD and NADH (Thu Feb 26 2009 - 19:11:54 CST)
• manoj singh
  • Re: [AMBER] Gly -> Ala mutation (Mon Nov 09 2009 - 10:26:00 CST)
  • Re: [AMBER] Gly -> Ala mutation (Mon Nov 09 2009 - 10:10:40 CST)
  • Re: [AMBER] conversion of kelvin to kcal/mol (Sun Nov 08 2009 - 23:17:03 CST)
  • Re: [AMBER] Gly -> Ala mutation (Sun Nov 08 2009 - 15:18:37 CST)
  • Re: [AMBER] Gly -> Ala mutation (Sun Nov 08 2009 - 13:14:23 CST)
  • [AMBER] Gly -> Ala mutation (Sun Nov 08 2009 - 11:25:46 CST)
  • Re: [AMBER] MM_PBSA enquiries (Sun Nov 08 2009 - 09:21:12 CST)
  • Re: [AMBER] LJ parameters for HO and HW (Sun Nov 08 2009 - 00:09:13 CST)
  • [AMBER] LJ parameters for HO and HW (Sat Nov 07 2009 - 23:21:22 CST)
  • Re: [AMBER] Is it taking too much time (Mon Nov 02 2009 - 07:50:21 CST)
  • Re: [AMBER] Is it taking too much time (Mon Nov 02 2009 - 01:31:07 CST)
  • Re: [AMBER] pairwise per-residue decomposition (Sat Oct 31 2009 - 23:59:38 CDT)
  • Re: [AMBER] Different results for different computers (Sat Oct 31 2009 - 14:47:36 CDT)
  • Re: [AMBER] pairwise per-residue decomposition (Fri Oct 30 2009 - 13:26:14 CDT)
  • Re: [AMBER] pairwise per-residue decomposition (Fri Oct 30 2009 - 00:46:22 CDT)
  • [AMBER] Analyzing per-residue decomposition data (Thu Oct 29 2009 - 15:18:45 CDT)
  • Re: [AMBER] pairwise per-residue decomposition (Thu Oct 29 2009 - 12:32:38 CDT)
  • [AMBER] pairwise per-residue decomposition (Wed Oct 28 2009 - 23:34:32 CDT)
  • [AMBER] Parameter Problem (Tue Sep 22 2009 - 14:46:59 CDT)
  • [AMBER] Parameter Problem (Tue Sep 22 2009 - 14:35:53 CDT)
  • Re: [AMBER] Cygwin Home Directory (Fri Sep 18 2009 - 14:30:28 CDT)
  • Re: [AMBER] Force Field Fitting (Thu Sep 17 2009 - 14:32:33 CDT)
  • Re: [AMBER] Force Field Fitting (Thu Sep 17 2009 - 12:20:50 CDT)
  • [AMBER] Leap warning (Wed Sep 09 2009 - 00:38:33 CDT)
  • Re: [AMBER] R.E.D. : Gaussian Error (Mon Sep 07 2009 - 00:46:54 CDT)
  • Re: [AMBER] R.E.D. : Gaussian Error (Sun Sep 06 2009 - 23:22:44 CDT)
  • [AMBER] R.E.D. : Gaussian Error (Sun Sep 06 2009 - 13:40:48 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 00:03:27 CDT)
  • [AMBER] RED: Charge derivation of transtion state analogue (Sun Jul 05 2009 - 01:10:57 CDT)
  • Re: [AMBER] PMEMD compilation (Sat Jun 20 2009 - 23:30:17 CDT)
  • Re: [AMBER] PMEMD compilation (Sat Jun 20 2009 - 23:22:01 CDT)
  • Re: [AMBER] PMEMD compilation (Sat Jun 20 2009 - 23:05:44 CDT)
  • [AMBER] PMEMD compilation (Fri Jun 19 2009 - 17:49:31 CDT)
  • [AMBER] Choice of force field (Sun May 31 2009 - 15:39:13 CDT)
  • [AMBER] Choice of force feild (Sun May 31 2009 - 12:12:23 CDT)
  • [AMBER] Parameter file content (Sat May 30 2009 - 20:53:37 CDT)
  • Re: [AMBER] Changing bond length (Thu May 28 2009 - 12:00:14 CDT)
  • [AMBER] Changing bond length (Wed May 27 2009 - 22:47:52 CDT)
• Marc Baaden
  • Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy (Tue Jun 02 2009 - 15:56:29 CDT)
• Marcin Krol
  • [AMBER] HB for each snapshot (Wed Nov 04 2009 - 13:14:41 CST)
  • [AMBER] HBOND analysis (Tue Oct 20 2009 - 10:42:35 CDT)
  • [AMBER] ptraj cluster - snapshot number of a representative structure (Thu Aug 20 2009 - 03:26:09 CDT)
• Marek Maly
  • Re: [AMBER] ff fitting ? (Mon Nov 09 2009 - 06:38:35 CST)
  • Re: [AMBER] pmemd vs sander.MPI (Thu Nov 05 2009 - 17:58:50 CST)
  • [AMBER] ff fitting ? (Thu Nov 05 2009 - 15:38:38 CST)
  • Re: [AMBER] pmemd vs sander.MPI (Thu Nov 05 2009 - 12:47:06 CST)
  • Re: [AMBER] pmemd vs sander.MPI (Thu Nov 05 2009 - 12:34:31 CST)
  • Re: [AMBER] pmemd vs sander.MPI (Thu Nov 05 2009 - 12:03:08 CST)
  • Re: [AMBER] pmemd vs sander.MPI (Thu Nov 05 2009 - 07:36:39 CST)
  • Re: [AMBER] RE: question (Thu Nov 05 2009 - 07:28:03 CST)
  • [AMBER] Re: question (Tue Nov 03 2009 - 14:22:16 CST)
  • Re: [AMBER] Ki and G (Tue Sep 15 2009 - 06:58:07 CDT)
  • Re: [AMBER] Ki and G (Mon Sep 14 2009 - 13:41:33 CDT)
  • Re: [AMBER] Ki and G (Mon Sep 14 2009 - 12:02:36 CDT)
  • Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Fri Jul 17 2009 - 13:37:02 CDT)
  • [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Fri Jul 17 2009 - 11:34:44 CDT)
  • Re: [AMBER] Counterion release and Free energy of binding ? (Fri Jul 17 2009 - 06:10:40 CDT)
  • [AMBER] Counterion release and Free energy of binding ? (Tue Jul 14 2009 - 17:27:18 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Wed Jul 01 2009 - 11:02:29 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Wed Jul 01 2009 - 10:47:04 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Mon Jun 29 2009 - 15:48:52 CDT)
  • [AMBER] Nonstandard molecules simulated with parm99EP ? (Mon Jun 29 2009 - 12:06:27 CDT)
  • Re: [AMBER] Half charge reported during NN ? (Wed Jun 24 2009 - 12:43:26 CDT)
  • [AMBER] Half charge reported during NN ? (Wed Jun 24 2009 - 11:33:54 CDT)
  • [AMBER] PRINCIPAL QUESTION (Thu Jun 11 2009 - 10:41:42 CDT)
  • Re: [AMBER] SOS - too high binding energy (Wed Jun 10 2009 - 14:47:58 CDT)
  • Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? (Wed Jun 10 2009 - 14:47:41 CDT)
  • [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? (Wed Jun 10 2009 - 05:33:59 CDT)
  • [AMBER] SOS - too high binding energy (Tue Jun 09 2009 - 05:49:43 CDT)
  • [AMBER] mm_pbsa_statistics-CALC DELTA parameter ? (Mon Jun 08 2009 - 14:16:19 CDT)
  • [AMBER] MaxRad ? (Sat Jun 06 2009 - 15:56:44 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 14:40:13 CDT)
  • [AMBER] Proper ISTRNG value ? (Fri Jun 05 2009 - 11:24:58 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Fri Jun 05 2009 - 08:49:14 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 15:01:54 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 14:16:50 CDT)
  • Re: [AMBER] use of random seed in multiple runs (Thu Jun 04 2009 - 11:35:57 CDT)
  • [AMBER] PARMCAL calculation ? (Wed May 27 2009 - 09:19:48 CDT)
  • Re: [AMBER] Nab units ? (Fri May 22 2009 - 20:43:41 CDT)
  • [AMBER] Nab units ? (Fri May 22 2009 - 19:20:14 CDT)
• Marek Malý
  • Re: [AMBER] The resonable way to create single strand DNA with NAB ? (Mon May 11 2009 - 07:18:06 CDT)
  • [AMBER] The resonable way to create single strand DNA with NAB ? (Sun May 10 2009 - 12:12:09 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 20:36:49 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 20:05:40 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 18:37:28 CDT)
  • [AMBER] Re: (Fri May 08 2009 - 14:12:39 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 14:10:41 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:27:20 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:02:53 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 12:57:36 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 11:38:27 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 07:54:57 CDT)
  • Re: [AMBER] Error in PMEMD run (Thu May 07 2009 - 18:59:23 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 16:27:17 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 16:25:02 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 15:26:58 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 15:02:11 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:48:26 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 13:51:03 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 13:42:36 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 13:30:43 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 10:58:33 CDT)
  • Re: [AMBER] Error in PMEMD run (Mon May 04 2009 - 21:19:20 CDT)
  • [AMBER] Error in PMEMD run (Mon May 04 2009 - 20:23:33 CDT)
  • [AMBER] Mixing of forcefields in case of covaletly bonded systems (Mon Apr 27 2009 - 07:06:38 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Thu Apr 23 2009 - 09:30:07 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Thu Apr 23 2009 - 08:41:03 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Tue Apr 21 2009 - 21:31:34 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Mon Apr 20 2009 - 22:52:46 CDT)
  • [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail (Mon Apr 20 2009 - 06:52:36 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Thu Apr 16 2009 - 16:25:12 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Tue Apr 14 2009 - 19:40:22 CDT)
  • Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Tue Apr 14 2009 - 18:18:18 CDT)
  • [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? (Mon Apr 13 2009 - 22:29:17 CDT)
  • Re: [AMBER] FF Parameters Transformations ...? (Mon Apr 06 2009 - 15:03:58 CDT)
  • [AMBER] FF Parameters Transformations ...? (Wed Apr 01 2009 - 12:29:26 CDT)
  • [AMBER] Parametrisation of Silicon based molecules for Amber simulations ? (Thu Mar 19 2009 - 18:49:21 CDT)
  • [AMBER] Partial entropy calculations ? (Fri Feb 27 2009 - 12:21:29 CST)
  • Re: [AMBER] MKL error ? (Thu Feb 05 2009 - 14:00:10 CST)
  • Re: [AMBER] MKL error ? (Thu Feb 05 2009 - 06:26:05 CST)
  • [AMBER] MKL error ? (Tue Feb 03 2009 - 17:00:03 CST)
  • Re: [AMBER] -MMTSB instalation flag ? (Tue Feb 03 2009 - 11:15:04 CST)
  • [AMBER] -MMTSB instalation flag ? (Tue Feb 03 2009 - 09:31:38 CST)
  • Re: [AMBER] Compilation and usage of NAB in parallel ? (Fri Jan 30 2009 - 10:01:06 CST)
  • Re: [AMBER] Compilation and usage of NAB in parallel ? (Fri Jan 30 2009 - 08:59:07 CST)
  • [AMBER] Compilation and usage of NAB in parallel ? (Wed Jan 28 2009 - 16:25:24 CST)
  • Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Wed Jan 21 2009 - 16:48:58 CST)
  • Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Tue Jan 20 2009 - 20:48:03 CST)
  • [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. (Tue Jan 20 2009 - 12:24:55 CST)
• Mari Carmen Pérez
  • [AMBER] error xleap: XaLeap_wcl is empty (Mon Sep 14 2009 - 04:59:09 CDT)
• Maria Mirza
  • Re: [AMBER] sander does not print out all residues in range. (Tue Aug 25 2009 - 00:17:59 CDT)
  • [AMBER] NATOM in prmtop and inpcrd files does not agree with the input (Mon Aug 24 2009 - 23:41:39 CDT)
  • [AMBER] sander does not print out all residues in range. (Mon Aug 24 2009 - 23:32:31 CDT)
  • [AMBER] ***PROBLEMS WITH GROUPLRES (Tue Aug 18 2009 - 19:34:41 CDT)
  • Re: [AMBER] MM-PBSA: decompose energy error (Sun Aug 16 2009 - 14:49:06 CDT)
• Marie Brut
  • [AMBER] second derivative matrix (Mon Feb 09 2009 - 02:53:01 CST)
  • [AMBER] second derivative matrix calculation (Fri Feb 06 2009 - 04:47:18 CST)
• Marina Grabar
  • [AMBER] problem with program anal within Amber10 (Tue May 26 2009 - 06:48:38 CDT)
• Marius Retegan
  • Re: [AMBER]