AMBER Archive (2009) - May 2009 By Author

Starting: Fri May 01 2009 - 03:33:34 CDT
Ending: Sun May 31 2009 - 15:39:13 CDT

• Adrian Roitberg
  • 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)
• Alan
  • [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)
• Alessandro Nascimento
  • Re: [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 13:28:26 CDT)
• 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)
• Andrew Purkiss-Trew
  • 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)
• aneesh cna
  • 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)
• Atro Tossavainen
  • Re: [AMBER] Installation directory (Mon May 25 2009 - 03:10:34 CDT)
• Bala subramanian
  • [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)
• balaji nagarajan
  • [AMBER] hbond_ptraj (Mon May 25 2009 - 15:05:12 CDT)
• Barbault Florent
  • Re: [AMBER] Problem with MM-PBSA energy calculation (Mon May 25 2009 - 13:57:19 CDT)
• ben rodriguez
  • [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' (Fri May 15 2009 - 17:09:44 CDT)
• Bill Ross
  • 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)
• Bokun Cho
  • 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)
• Bradshaw, Richard
  • [AMBER] MM-PBSA and NetCDF (Wed May 27 2009 - 10:38:13 CDT)
• C Liu
  • [AMBER] QM/MM assigns Cd to C, Se to S (Sat May 02 2009 - 21:09:27 CDT)
• Carlos Simmerling
  • 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)
• Catein Catherine
  • [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)
• cgji
  • 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)
• CHAMI F.
  • RE: [AMBER] Amber/CHARMM summer school (Thu May 21 2009 - 06:56:23 CDT)
• Chih-Ying Lin
  • [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)
• Chris Moth
  • Re: [AMBER] ptraj netcdf (Tue May 12 2009 - 10:46:31 CDT)
• Chunliyan
  • [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] MM-PBSA tutorial (Thu May 14 2009 - 20:19:04 CDT)
• 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)
• David A. Case
  • 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)
• David Watson
  • [AMBER] molsurf and probe radius (Sat May 09 2009 - 12:32:43 CDT)
• Dechang Li
  • Re: [AMBER] J coupling constant calculation (Fri May 29 2009 - 00:31:06 CDT)
• Dmitry Osolodkin
  • 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)
• 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)
• E.M.
  • [AMBER] anal output: Entalphy or Free Energy? (Tue May 12 2009 - 17:25:41 CDT)
• Edward M
  • [AMBER] anal output: Entalphy or Free Energy? (Tue May 12 2009 - 19:14:37 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)
• Fernando Martín García
  • 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)
• fmgarcia_at_cbm.uam.es
  • RE: [AMBER] dftb_disper problem (Fri May 08 2009 - 11:27:30 CDT)
• FyD
  • 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)
• Gabriel Urquiza
  • [AMBER] Targeted MD and QM/MM (Fri May 29 2009 - 15:09:31 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)
• Gustavo Seabra
  • 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)
• Haizhen Zhong
  • [AMBER] Minimization error on protonated system? Please help. Thanks! (Thu May 28 2009 - 09:58:49 CDT)
• Hannes Loeffler
  • 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)
• 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)
• Hemant Kumar
  • [AMBER] Number of processor in pmemd (Mon May 04 2009 - 12:17:13 CDT)
• Hopkins, Robert
  • 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)
• 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)
• 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)
• jacky zhao
  • Re: [AMBER] Re: About Amber installations (Tue May 26 2009 - 06:18:25 CDT)
• Jayalakshmi Sridhar
  • 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)
• Jia Xu
  • 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)
• john smith
  • 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)
• Jorgen Simonsen
  • 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)
• 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)
• Junmei Wang
  • 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)
• Karen Callahan
  • [AMBER] Question about &dipoles printing in AMBER 8 (Mon May 25 2009 - 18:46:00 CDT)
• Kshatresh Dutta Dubey
  • 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)
• Lachele Foley (Lists)
  • Re: [AMBER] Cyclodextrin forcefield (Fri May 01 2009 - 10:23:37 CDT)
• 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)
• Mahmoud A. A. Ibrahim
  • Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? (Tue May 05 2009 - 12:15:18 CDT)
• Majeed Shaik
  • [AMBER] xleap input pdb problem (Wed May 06 2009 - 13:47:45 CDT)
• manoj singh
  • [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)
• Marek Maly
  • [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)
• Marina Grabar
  • [AMBER] problem with program anal within Amber10 (Tue May 26 2009 - 06:48:38 CDT)
• Mark M Huntress
  • [AMBER] heating advice (Wed May 27 2009 - 15:44:26 CDT)
  • RE: [AMBER] loadpdb atom type (Tue May 19 2009 - 13:15:02 CDT)
  • [AMBER] loadpdb atom type (Tue May 19 2009 - 11:20:20 CDT)
  • [AMBER] RE: xleap, mac number problem (Sat May 09 2009 - 17:29:50 CDT)
  • [AMBER] xleap, mac number problem (Sat May 09 2009 - 14:46:46 CDT)
  • [AMBER] prmtop (Sun May 03 2009 - 18:20:39 CDT)
• Maryam Hamzehee
  • [AMBER] problem with MM-PBSA (Mon May 25 2009 - 23:52:29 CDT)
  • [AMBER] problem with MM-PBSA (Sat May 23 2009 - 23:48:05 CDT)
• mathew k varghese
  • [AMBER] MM-PBSA with explicit water (Fri May 15 2009 - 01:45:23 CDT)
  • [AMBER] Fw: MM-PBSA with explicit water (Fri May 15 2009 - 01:43:46 CDT)
• Matthew Tessier
  • RE: [AMBER] Conformation of sulfated Glucosamine (Wed May 06 2009 - 10:19:22 CDT)
• Matthew Wilce
  • [AMBER] ntf, ntc with softcore potentials and TI in amber10 (Tue May 05 2009 - 20:33:28 CDT)
• moitrayee_at_mbu.iisc.ernet.in
  • Re: [AMBER] Problem with nonstandard residues (Tue May 19 2009 - 11:47:38 CDT)
  • Re: [AMBER] Problem with nonstandard residues (Tue May 19 2009 - 08:10:00 CDT)
  • [AMBER] Problem with nonstandard residues (Tue May 19 2009 - 06:48:33 CDT)
• Musa Ozboyaci
  • [AMBER] MM-PBSA statistics (Sun May 10 2009 - 05:00:19 CDT)
• Myunggi Yi
  • Re: [AMBER] ptraj questions (Fri May 22 2009 - 08:57:08 CDT)
  • Re: [AMBER] lipid membrane(dppc) in amber (Fri May 22 2009 - 08:45:20 CDT)
• Nancy
  • [AMBER] how to use two dimensions periodic boundary ? (Wed May 20 2009 - 20:32:50 CDT)
  • [AMBER] no equilibrium (Mon May 18 2009 - 21:44:03 CDT)
  • [AMBER] no equilibrium (Mon May 18 2009 - 21:32:01 CDT)
  • [AMBER] please help me out (Sun May 10 2009 - 02:56:33 CDT)
• Naser Alijabbari
  • Re: [AMBER] nanoseconds of simulation with nscm=0 (Sun May 24 2009 - 14:56:28 CDT)
  • [AMBER] nanoseconds of simulation with nscm=0 (Sun May 24 2009 - 12:20:18 CDT)
  • Re: [AMBER] difference in temperature (Wed May 06 2009 - 07:29:48 CDT)
  • [AMBER] difference in temperature (Tue May 05 2009 - 19:02:28 CDT)
• Neha Gandhi
  • [AMBER] J coupling constant calculation (Fri May 29 2009 - 00:24:37 CDT)
  • [AMBER] scee term (Fri May 15 2009 - 04:03:48 CDT)
  • [AMBER] normal modes calculation (Wed May 13 2009 - 22:12:13 CDT)
  • [AMBER] Conformation of sulfated Glucosamine (Wed May 06 2009 - 04:54:31 CDT)
• nicholus bhattacharjee
  • Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Thu May 28 2009 - 13:08:52 CDT)
  • [AMBER] how to know that adequate equilibration from rmsd curve of equilibration (Thu May 28 2009 - 08:37:29 CDT)
  • [AMBER] Re: How to know that the md is stable in equilibration run (Mon May 25 2009 - 11:11:39 CDT)
  • [AMBER] How to know that the md is stable in equilibration run (Mon May 25 2009 - 06:54:25 CDT)
  • Re: [AMBER] Protein with HETATM, am I doing the right thing (Thu May 21 2009 - 11:28:52 CDT)
  • [AMBER] Protein with HETATM, am I doing the right thing (Thu May 21 2009 - 06:21:15 CDT)
  • Re: [AMBER] Protein with HETATM, am I doing the (Thu May 21 2009 - 01:43:37 CDT)
  • [AMBER] Protein with HETATM, am I doing the (Wed May 20 2009 - 23:48:42 CDT)
  • Re: [AMBER] Suggestion for restraining chain of a protein (Tue May 05 2009 - 07:20:44 CDT)
  • [AMBER] Suggestion for restraining chain of a protein (Tue May 05 2009 - 01:29:54 CDT)
  • [AMBER] Problem in production run (Tue May 05 2009 - 00:50:07 CDT)
• Niel Henriksen
  • RE: [AMBER] re: essential dynamics (Wed May 13 2009 - 13:28:22 CDT)
• Patrick Gedeon
  • [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? (Wed May 06 2009 - 23:12:39 CDT)
• Peter Gannett
  • Re: [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 14:29:58 CDT)
  • Re: [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 12:46:47 CDT)
• Peter Varnai
  • Re: [AMBER] xmin (Sun May 17 2009 - 19:58:00 CDT)
  • [AMBER] makeDIST_RST: no map function for ambiguous restraint (Sun May 17 2009 - 13:41:24 CDT)
  • [AMBER] xmin (Thu May 14 2009 - 16:29:09 CDT)
  • [AMBER] building quadruplex with NAB (Sun May 10 2009 - 18:27:38 CDT)
• PRADEEP VENKATARAMAN
  • [AMBER] SANDER BOMB (Wed May 27 2009 - 21:39:56 CDT)
• R. A.
  • [AMBER] resp charge (Tue May 19 2009 - 21:35:25 CDT)
• Rajesh Raju
  • Re: [AMBER] Cyclodextrin forcefield (Fri May 01 2009 - 12:21:21 CDT)
  • [AMBER] Cyclodextrin forcefield (Fri May 01 2009 - 09:51:17 CDT)
• Ray Luo
  • RE: [AMBER] MM-PBSA nmode statistics (Sun May 31 2009 - 12:32:49 CDT)
  • RE: [AMBER] MM-PBSA nmode statistics (Fri May 29 2009 - 13:01:36 CDT)
  • RE: [AMBER] Radius for Bromine in MMPBSA calculation (Tue May 26 2009 - 14:02:27 CDT)
  • RE: [AMBER] problem with MM-PBSA (Tue May 26 2009 - 11:44:14 CDT)
  • RE: [AMBER] Radius for Bromine in MMPBSA calculation (Mon May 25 2009 - 16:10:41 CDT)
  • RE: [AMBER] Radius for Bromine in MMPBSA calculation (Thu May 21 2009 - 11:32:41 CDT)
  • RE: [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 12:43:30 CDT)
  • RE: [AMBER] Error in binding energy (MM PBSA) (Mon May 11 2009 - 13:14:20 CDT)
  • RE: [AMBER] Problems in the result of MM_PBSA (Mon May 11 2009 - 12:55:12 CDT)
  • RE: [AMBER] Error in binding energy (MM PBSA) (Sat May 09 2009 - 20:39:05 CDT)
  • RE: [AMBER] Problems in the result of MM_PBSA (Sat May 09 2009 - 20:36:04 CDT)
  • RE: [AMBER] Error in binding energy (MM PBSA) (Fri May 08 2009 - 11:42:58 CDT)
  • RE: [AMBER] Problems in the result of MM_PBSA (Thu May 07 2009 - 21:02:58 CDT)
  • RE: [AMBER] Error in binding energy (MM PBSA) (Thu May 07 2009 - 13:12:18 CDT)
• rebeca
  • Re: [AMBER] gaff and aromatic compounds (Fri May 22 2009 - 04:04:45 CDT)
  • [AMBER] gaff and aromatic compounds (Wed May 20 2009 - 03:54:43 CDT)
  • [AMBER] gaff and aromatic compounds (Tue May 19 2009 - 10:50:02 CDT)
  • Re: [AMBER] problem with parmchk (Mon May 18 2009 - 09:34:31 CDT)
  • [AMBER] problem with parmchk (Mon May 18 2009 - 08:59:51 CDT)
• Remya S R
  • Re: [AMBER] Amber - Leap- SolvateBox help (Tue May 19 2009 - 01:22:12 CDT)
  • Re: [AMBER] Charge problem (Tue May 05 2009 - 07:19:51 CDT)
  • [AMBER] Charge problem (Tue May 05 2009 - 06:43:47 CDT)
  • [AMBER] Parameter file not saved (Mon May 04 2009 - 07:03:08 CDT)
  • [AMBER] Parameter file not saved (Mon May 04 2009 - 01:30:19 CDT)
  • [AMBER] "Parameter file not generated" (Mon May 04 2009 - 01:17:23 CDT)
• Rilei Yu
  • Re: [AMBER] Molecular simulation of a protein using special H2O cluster (Tue May 26 2009 - 19:21:15 CDT)
  • [AMBER] Molecular simulation of a protein using special H2O cluster (Tue May 26 2009 - 03:20:56 CDT)
• Robert Duke
  • Re: [AMBER] pmemd running very slow in amber10 (Thu May 14 2009 - 08:38:29 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 20:26:37 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 19:01:23 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 14:44:08 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:24:35 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:14:12 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:06:17 CDT)
  • Re: [AMBER] Error in PMEMD run (Fri May 08 2009 - 08:29:48 CDT)
  • Re: [AMBER] Error in PMEMD run (Thu May 07 2009 - 19:11:25 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 18:04:10 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 15:40:29 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 15:08:56 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:58:29 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:55:49 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:29:41 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:20:37 CDT)
  • Re: [AMBER] Error in PMEMD run (Wed May 06 2009 - 12:30:43 CDT)
  • Re: [AMBER] Problems with PMEMD installation for AMBER10 (Tue May 05 2009 - 08:48:06 CDT)
  • Re: [AMBER] Problems with PMEMD installation for AMBER10 (Tue May 05 2009 - 08:00:54 CDT)
  • Re: [AMBER] Error in PMEMD run (Mon May 04 2009 - 23:08:37 CDT)
  • Re: [AMBER] Error in PMEMD run (Mon May 04 2009 - 20:35:54 CDT)
  • Re: [AMBER] Number of processor in pmemd (Mon May 04 2009 - 12:28:11 CDT)
• Rose Tamil
  • [AMBER] Error: cannot run prepgen (Tue May 05 2009 - 10:20:52 CDT)
• Ross Walker
  • [AMBER] FW: About Amber10 installation "Possible Failure" (Thu May 28 2009 - 09:06:31 CDT)
  • RE: [AMBER] Changing bond length (Wed May 27 2009 - 23:38:59 CDT)
  • RE: [AMBER] Tutorial 4 Parameter file was not saved (Wed May 27 2009 - 12:31:30 CDT)
  • [AMBER] RE: About Amber10 installation "Possible Failure" (Tue May 26 2009 - 10:38:19 CDT)
  • RE: [AMBER] How to choose the counter ions for proteins? (Sat May 23 2009 - 13:09:27 CDT)
  • RE: [AMBER] Why does protein carry charges? (Sat May 23 2009 - 13:06:57 CDT)
  • [AMBER] RE: add magnesium (Wed May 20 2009 - 16:30:09 CDT)
  • RE: [AMBER] resp charge (Wed May 20 2009 - 10:05:20 CDT)
  • RE: [AMBER] Amber - Leap- SolvateBox help (Wed May 20 2009 - 00:20:50 CDT)
  • RE: [AMBER] What is the purpose to do the bond constraints? (Sun May 17 2009 - 22:38:52 CDT)
  • RE: [AMBER] Running PTRAJ command line scripts in background (Sun May 17 2009 - 22:35:09 CDT)
  • RE: [AMBER] scee term (Fri May 15 2009 - 10:02:09 CDT)
  • RE: [AMBER] pmemd running very slow in amber10 (Thu May 14 2009 - 07:57:43 CDT)
  • RE: [AMBER] Amber - Leap- SolvateBox help (Thu May 14 2009 - 07:28:36 CDT)
  • RE: [AMBER] amber9 in fedora10 (Wed May 13 2009 - 18:22:20 CDT)
  • RE: [AMBER] Error in PMEMD run (Fri May 08 2009 - 13:11:19 CDT)
  • RE: [AMBER] dftb_disper problem (Fri May 08 2009 - 10:47:39 CDT)
  • RE: [AMBER] QM/MM assigns Cd to C, Se to S (Fri May 08 2009 - 02:16:09 CDT)
  • RE: [AMBER] RE: Listing gaff parameters in frcmod (Thu May 07 2009 - 23:34:08 CDT)
  • RE: [AMBER] AMBER for dual core processor? (Thu May 07 2009 - 10:26:09 CDT)
  • RE: [AMBER] Error in PMEMD run (Wed May 06 2009 - 16:53:07 CDT)
  • RE: [AMBER] Error in PMEMD run (Wed May 06 2009 - 15:36:36 CDT)
  • RE: [AMBER] Error in PMEMD run (Wed May 06 2009 - 14:41:10 CDT)
  • RE: [AMBER] Error in PMEMD run (Wed May 06 2009 - 12:07:01 CDT)
  • RE: [AMBER] Error message in "make test.sander" (Wed May 06 2009 - 01:28:01 CDT)
  • RE: [AMBER] High energy during minimization (Wed May 06 2009 - 01:24:30 CDT)
  • RE: [AMBER] Error message in "make test.sander" (Tue May 05 2009 - 22:37:28 CDT)
  • RE: [AMBER] QM/MM (Tue May 05 2009 - 17:16:26 CDT)
  • RE: [AMBER] skip parallel test (Tue May 05 2009 - 10:43:34 CDT)
  • RE: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 10:29:23 CDT)
  • RE: [AMBER] A confusion about tutorial B1 (Tue May 05 2009 - 00:18:43 CDT)
  • RE: [AMBER] QM/MM (Mon May 04 2009 - 12:47:21 CDT)
  • RE: [AMBER] Script for parallel runs 2 (Mon May 04 2009 - 10:39:27 CDT)
  • RE: [AMBER] problem with cutoff (Mon May 04 2009 - 10:35:40 CDT)
  • RE: [AMBER] problem with cutoff (Mon May 04 2009 - 00:02:04 CDT)
  • RE: [AMBER] prmtop (Sun May 03 2009 - 21:18:04 CDT)
  • RE: [AMBER] QM/MM assigns Cd to C, Se to S (Sat May 02 2009 - 23:45:41 CDT)
• Rubben Torella
  • [AMBER] Minimization on MM-PBSA (Thu May 28 2009 - 10:23:07 CDT)
  • Re: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber (Tue May 26 2009 - 17:33:18 CDT)
  • Re: [AMBER] Problem with MM-PBSA energy calculation (Tue May 26 2009 - 06:24:56 CDT)
  • [AMBER] Problem with MM-PBSA energy calculation (Mon May 25 2009 - 10:58:41 CDT)
• S.Sundar Raman
  • [AMBER] Issue related to saving the vector in ptraj (Sat May 16 2009 - 07:41:10 CDT)
  • [AMBER] Issue related to vector saving (Fri May 15 2009 - 08:35:01 CDT)
• Scott Brozell
  • Re: [AMBER] xmin (Mon May 18 2009 - 15:30:17 CDT)
  • Re: [AMBER] xmin (Sun May 17 2009 - 15:45:27 CDT)
• Sean Zhao
  • Re: [AMBER] Problems in the result of MM_PBSA (Sun May 10 2009 - 03:23:19 CDT)
  • Re: [AMBER] Problems in the result of MM_PBSA (Fri May 08 2009 - 22:44:29 CDT)
  • [AMBER] Problems in the result of MM_PBSA (Thu May 07 2009 - 20:30:24 CDT)
  • [AMBER] MM_PBSA problem in Amber 9 (Mon May 04 2009 - 04:09:14 CDT)
• Sergey Samsonov
  • Re: [AMBER] AMBER 10 output (Tue May 19 2009 - 09:53:41 CDT)
  • [AMBER] AMBER 10 output (Tue May 19 2009 - 02:33:21 CDT)
• sheerychen
  • [AMBER] adding a standard amino acid as ligand (Fri May 15 2009 - 04:37:51 CDT)
• Shuang Ding
  • [AMBER] partial charge and topology of intrastrand cross-link DNA (Mon May 25 2009 - 21:27:43 CDT)
• Shubhra Gupta
  • Re: [AMBER] broken Ligand (Sat May 30 2009 - 01:35:46 CDT)
  • [AMBER] broken Ligand (Fri May 29 2009 - 08:28:22 CDT)
  • Re: [AMBER] mdfil: Error unknown flag during sander minimization (Tue May 26 2009 - 23:07:25 CDT)
  • Re: [AMBER] Amber - Leap- SolvateBox help (Mon May 18 2009 - 22:54:23 CDT)
  • [AMBER] Amber - Leap- SolvateBox help (Thu May 14 2009 - 00:04:16 CDT)
• Siavoush Dastmalchi
  • [AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... (Sat May 30 2009 - 12:11:55 CDT)
  • [AMBER] ERROR in ptrajInitializeState(): Attempting .... (Sat May 30 2009 - 11:06:51 CDT)
  • [AMBER] parallel amber on cluster (Mon May 18 2009 - 01:04:58 CDT)
• Siddharth Rastogi
  • Re: [AMBER] multiple chain specification in Sander (Thu May 07 2009 - 15:29:28 CDT)
  • [AMBER] multiple chain specification in Sander (Wed May 06 2009 - 22:17:57 CDT)
• Simon Becker
  • Re: [AMBER] Protein Docking (Tue May 12 2009 - 10:23:02 CDT)
• Simona Irrera
  • [AMBER] molecular crystal simulation (Tue May 12 2009 - 06:04:26 CDT)
• steinbrt_at_rci.rutgers.edu
  • Re: [AMBER] Strange high temperature in softcore TI (Sun May 24 2009 - 23:13:38 CDT)
  • Re: [AMBER] Strange high temperature in softcore TI (Sun May 24 2009 - 21:26:28 CDT)
  • Re: [AMBER] AMBER 10 output (Tue May 19 2009 - 08:53:03 CDT)
  • Re: [AMBER] no equilibrium (Mon May 18 2009 - 22:00:40 CDT)
  • Re: [AMBER] MM-PBSA tutorial (Thu May 14 2009 - 12:26:50 CDT)
  • Re: [AMBER] Question about Thermal Integration with Softcore (Wed May 13 2009 - 10:11:16 CDT)
  • Re: [AMBER] Protein Docking (Mon May 11 2009 - 15:33:15 CDT)
  • Re: [AMBER] RE: Listing gaff parameters in frcmod (Fri May 08 2009 - 09:23:45 CDT)
  • Re: [AMBER] ntf, ntc with softcore potentials and TI in amber10 (Tue May 05 2009 - 22:39:02 CDT)
• Sunita Patel
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Thu May 07 2009 - 13:35:59 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Tue May 05 2009 - 12:26:09 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Tue May 05 2009 - 11:33:40 CDT)
  • Re: [AMBER] equilibration stops for dimer simulation with REMD (Sun May 03 2009 - 20:30:05 CDT)
  • [AMBER] equilibration stops for dimer simulation with REMD (Sat May 02 2009 - 15:11:48 CDT)
• sychen
  • [AMBER] Can bond clevage & formation conducted by qm/mm via sander? (Tue May 05 2009 - 08:12:32 CDT)
• Syed Tarique Moin
  • RE: [AMBER] QM/MM (Wed May 06 2009 - 02:12:17 CDT)
  • RE: [AMBER] QM/MM (Wed May 06 2009 - 02:11:54 CDT)
  • RE: [AMBER] QM/MM (Mon May 04 2009 - 17:13:22 CDT)
  • [AMBER] QM/MM (Mon May 04 2009 - 10:32:29 CDT)
• Taufik Al-Sarraj
  • [AMBER] Re: Help with xleap (Tue May 26 2009 - 18:58:00 CDT)
• Thomas Cheatham
  • Re: [AMBER] Why NaCl or KCl solution? (Wed May 27 2009 - 19:50:56 CDT)
  • Re: [AMBER] hbond_ptraj (Wed May 27 2009 - 19:39:15 CDT)
  • Re: [AMBER] problem with MM-PBSA (Wed May 27 2009 - 19:35:30 CDT)
  • Re: [AMBER] nanoseconds of simulation with nscm=0 (Sun May 24 2009 - 15:37:23 CDT)
  • Re: [AMBER] nanoseconds of simulation with nscm=0 (Sun May 24 2009 - 13:27:33 CDT)
• Thomas Cheatham III
  • RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% (Fri May 01 2009 - 13:07:40 CDT)
• Thomas Spraggins
  • Re: [AMBER] Installation directory (Thu May 21 2009 - 14:18:13 CDT)
  • [AMBER] Installation directory (Thu May 21 2009 - 13:02:59 CDT)
• Titus, Jamie (bairdje)
  • RE: [AMBER] QQD psuedoatom restraints (Fri May 29 2009 - 14:01:34 CDT)
  • [AMBER] QQD psuedoatom restraints (Fri May 29 2009 - 09:02:31 CDT)
• todd_at_semichem.com
  • Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. (Sun May 10 2009 - 16:56:24 CDT)
  • Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. (Sat May 09 2009 - 13:36:17 CDT)
  • [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. (Sat May 09 2009 - 11:27:52 CDT)
• Tom Joseph
  • Re: [AMBER] Parameter file content (Sat May 30 2009 - 21:23:48 CDT)
  • Re: [AMBER] protein molecular weight? (Fri May 29 2009 - 18:40:58 CDT)
  • Re: [AMBER] Strange high temperature in softcore TI (Sun May 24 2009 - 22:20:20 CDT)
  • [AMBER] Strange high temperature in softcore TI (Sun May 24 2009 - 20:54:43 CDT)
• Tomasio, Susana
  • [AMBER] AMOEBA and carbon nanotubes + include parameters (Thu May 28 2009 - 05:23:00 CDT)
  • RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels (Wed May 27 2009 - 07:13:58 CDT)
  • [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels (Wed May 27 2009 - 06:25:35 CDT)
  • [AMBER] get typeid of -1, sleap - AMBER with amoeba ff (Tue May 26 2009 - 10:51:18 CDT)
  • [AMBER] ongoing issues using sander with AMOEBA (Wed May 13 2009 - 05:00:00 CDT)
• Vijay Manickam Achari
  • [AMBER] pmemd running very slow in amber10 (Thu May 14 2009 - 00:41:40 CDT)
• vijayaraj_at_clri.res.in
  • [AMBER] MMPBSA extract coordinate (Fri May 22 2009 - 13:00:57 CDT)
• Vikas Sharma
  • Re: [AMBER] Loading PDB of complex (Fri May 22 2009 - 00:56:36 CDT)
  • [AMBER] Loading PDB of complex (Thu May 21 2009 - 08:13:36 CDT)
  • Re: 回å¤�： [AMBER] MM PBSA output (Wed May 20 2009 - 12:54:32 CDT)
  • [AMBER] MM PBSA output (Wed May 20 2009 - 06:53:57 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Wed May 20 2009 - 03:29:42 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Tue May 19 2009 - 13:21:47 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Tue May 19 2009 - 10:02:21 CDT)
  • Re: [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 23:34:18 CDT)
  • Re: 回å¤�： [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 09:06:49 CDT)
  • [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 07:00:13 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Tue May 12 2009 - 00:05:08 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Mon May 11 2009 - 03:08:28 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Sun May 10 2009 - 04:03:07 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Sat May 09 2009 - 02:20:09 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Sat May 09 2009 - 02:19:20 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Fri May 08 2009 - 01:50:40 CDT)
  • [AMBER] Error in binding energy (MM PBSA) (Fri May 08 2009 - 01:44:33 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Fri May 08 2009 - 01:42:32 CDT)
  • Re: [AMBER] Error in binding energy (MM PBSA) (Thu May 07 2009 - 08:29:22 CDT)
  • [AMBER] free enrgy error in MM PBSA (Thu May 07 2009 - 05:11:44 CDT)
  • [AMBER] Error in binding energy (MM PBSA) (Thu May 07 2009 - 00:47:33 CDT)
  • [AMBER] positive value of binding enrgy after MM PBSA (Wed May 06 2009 - 10:07:03 CDT)
  • [AMBER] Error in MM PBSA (Wed May 06 2009 - 03:35:57 CDT)
• Vlad
  • [AMBER] The largest AMBER calculation(s)? (Mon May 18 2009 - 21:58:27 CDT)
• Wei Huang
  • RE: [AMBER] ambertools for NAMD (Thu May 07 2009 - 09:51:06 CDT)
  • RE: [AMBER] MMPBSA- interaction energy for every frame (Mon May 04 2009 - 09:58:26 CDT)
• Wei Zhang
  • Re: [AMBER] please help me out (Sun May 10 2009 - 08:21:06 CDT)
  • Re: [AMBER] unable to start xleap (Fri May 01 2009 - 13:39:03 CDT)
• Workalemhu Berhanu
  • [AMBER] solutes in a simulation box (Sun May 31 2009 - 11:59:39 CDT)
  • [AMBER] create a simulation box (Sat May 30 2009 - 22:06:24 CDT)
  • [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically (Sat May 30 2009 - 06:20:03 CDT)
  • [AMBER] How to take into account the charge in GAFF parameterization (Thu May 28 2009 - 18:22:07 CDT)
  • [AMBER] Tutorial 4 Parameter file was not saved (Wed May 27 2009 - 11:00:30 CDT)
  • [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber (Tue May 26 2009 - 16:45:55 CDT)
  • [AMBER] Tutorial 4 Please check the total charge and your -nc flag (Tue May 26 2009 - 14:47:07 CDT)
  • [AMBER] mdfil: Error unknown flag during sander minimization (Tue May 26 2009 - 08:57:29 CDT)
  • Re: [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 17:12:00 CDT)
  • [AMBER] Unit 8 Error on OPEN: prmtop (Sun May 24 2009 - 12:27:38 CDT)
  • [AMBER] file contains 2 atoms not in residue templates (Sat May 23 2009 - 19:17:09 CDT)
  • [AMBER] 2 atoms not in residue template (Sat May 23 2009 - 19:11:12 CDT)
  • [AMBER] Tutorial A1 (Tue May 19 2009 - 18:05:15 CDT)
  • [AMBER] Alignment of small molecule on peptide fragment (Sat May 16 2009 - 04:32:38 CDT)
  • [AMBER] Alignment of small molecule on peptide fragment (Sat May 16 2009 - 04:31:08 CDT)
  • Re: [AMBER] MM-PBSA tutorial (Thu May 14 2009 - 13:53:25 CDT)
  • [AMBER] MM-PBSA tutorial (Thu May 14 2009 - 12:16:55 CDT)
• xiaoqin huang
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 16:43:15 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 16:09:26 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 15:32:02 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 15:09:28 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:51:59 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:46:23 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:41:54 CDT)
  • RE: [AMBER] ask for parm99MOD (Thu May 28 2009 - 14:31:14 CDT)
  • [AMBER] ask for parm99MOD (Thu May 28 2009 - 13:16:35 CDT)
• xueqin pang
  • [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy (Sun May 31 2009 - 07:47:57 CDT)
  • [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP (Sun May 31 2009 - 07:43:09 CDT)
  • [AMBER] partial charges of lipid membrane for GPCR system (Tue May 26 2009 - 08:34:34 CDT)
  • [AMBER] lipid membrane(dppc) in amber (Fri May 22 2009 - 04:01:26 CDT)
  • [AMBER] lipid membrane(dppc) in amber (Fri May 22 2009 - 03:42:54 CDT)
• Ye MEI
  • [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber (Sat May 02 2009 - 07:01:20 CDT)
  • [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber (Sat May 02 2009 - 07:00:06 CDT)
• Yunjie Zhao
  • Re: [AMBER] problem with cutoff (Mon May 04 2009 - 07:58:00 CDT)
  • [AMBER] problem with cutoff (Sun May 03 2009 - 22:53:00 CDT)
• zgong.hust
  • [AMBER] errors when add ions (Wed May 20 2009 - 21:51:48 CDT)
• ¶­ê»
  • [AMBER] charge of Fe-heme (Fri May 01 2009 - 14:08:12 CDT)
• Å·ÑôµÂ·½
  • [AMBER] contacts in ptraj (Thu May 28 2009 - 06:55:28 CDT)
• å»–é�’å�Ž
  • [AMBER] decomposition and alanine scanning (Fri May 22 2009 - 09:13:49 CDT)
  • 回å¤�： [AMBER] MM PBSA output (Wed May 20 2009 - 07:15:04 CDT)
  • 回å¤�： 回å¤�： [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 09:41:14 CDT)
  • 回å¤�： [AMBER] Error running MM _PBSA.pl script (Mon May 18 2009 - 07:08:47 CDT)

Last message date: Mon Nov 23 2009 - 13:51:08 CST
Archived on: Mon Nov 23 2009 - 13:51:11 CST