AMBER Archive (2007) - Jul 2007 By Author

Starting: Sun Jul 01 2007 - 08:10:09 CDT
Ending: Tue Jul 31 2007 - 16:34:12 CDT

• Adrian Roitberg
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:44:01 CDT)
  • Re: AMBER: xleap and amber7 (Mon Jul 02 2007 - 09:20:28 CDT)
• Alessandro Nascimento
  • AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1) (Tue Jul 31 2007 - 16:34:12 CDT)
• Andrew Borgert
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 11:27:44 CDT)
  • AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 11:18:05 CDT)
• Anela Ivanova
  • AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field (Wed Jul 04 2007 - 07:26:02 CDT)
• Anju Sharma
  • AMBER: Problem while creating input files in antechamber (Tue Jul 31 2007 - 00:33:12 CDT)
  • AMBER: Problem while saving .top and .crd files. (Mon Jul 30 2007 - 22:47:39 CDT)
• Anna Díaz Cirac
  • AMBER: secstruct command (Thu Jul 19 2007 - 12:35:42 CDT)
• Austin B. Yongye
  • Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a (Tue Jul 17 2007 - 01:22:12 CDT)
• AYTUG TUNCEL
  • AMBER: corrected reaction field energy and PBCAL (Sun Jul 08 2007 - 19:40:53 CDT)
• Barbault Florent
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 13:54:36 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 09:59:03 CDT)
• Beale, John
  • AMBER: Linux install (Tue Jul 31 2007 - 06:55:34 CDT)
• Benjamin Juhl
  • Re: AMBER: Problem while creating input files in antechamber (Tue Jul 31 2007 - 02:08:35 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:18:28 CDT)
  • Re: AMBER: Can t open PDB file in xleap (Mon Jul 16 2007 - 05:53:16 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 02:17:31 CDT)
  • Re: AMBER: xleap and amber7 (Mon Jul 09 2007 - 02:08:57 CDT)
• Bill Ross
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 18:38:26 CDT)
  • Re: SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 14:49:45 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 13:48:28 CDT)
  • Re: AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 16:05:53 CDT)
• Carlos Simmerling
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 11:10:49 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:44:53 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:23:30 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 06:29:48 CDT)
  • Re: AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:28:33 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 12:41:42 CDT)
  • Re: AMBER: not getting topology and restraint file (Wed Jul 25 2007 - 05:16:02 CDT)
  • Re: AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 09:46:49 CDT)
  • Re: AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 14:44:35 CDT)
  • Re: AMBER: regarding distance restraints (Mon Jul 23 2007 - 06:26:27 CDT)
  • Re: AMBER: offending restraint (Sun Jul 22 2007 - 06:32:51 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 09:34:35 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:57:13 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:34:03 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 06:44:36 CDT)
  • Re: AMBER: secstruct command (Thu Jul 19 2007 - 12:46:30 CDT)
  • Re: AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 11:57:27 CDT)
  • Re: AMBER: potential energy calculation (Mon Jul 16 2007 - 20:34:01 CDT)
  • Re: AMBER: convergence in classical MD (Mon Jul 16 2007 - 06:37:09 CDT)
  • Re: AMBER: MPI script (Fri Jul 13 2007 - 17:15:36 CDT)
  • Re: AMBER: related to new amber force field (Fri Jul 13 2007 - 11:33:12 CDT)
  • Re: AMBER: Multiple residues position (Fri Jul 13 2007 - 11:20:19 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 10:32:54 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:28:29 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 06:34:08 CDT)
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 12:08:23 CDT)
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 04:28:56 CDT)
  • Re: AMBER: extract protein energy from MD trajectory (Wed Jul 11 2007 - 03:34:31 CDT)
  • Re: AMBER: extract protein energy from MD trajectory (Tue Jul 10 2007 - 17:08:32 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 14:09:51 CDT)
  • Re: AMBER: tgtrmsmask and tgtfitmask (Tue Jul 10 2007 - 06:26:08 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 05:33:44 CDT)
  • Re: AMBER: surface area over the trajectory (Mon Jul 09 2007 - 17:30:54 CDT)
  • Re: AMBER: Problem with running Sander (Sun Jul 08 2007 - 06:28:58 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 11:45:43 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:14:20 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:35:33 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 14:08:31 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 12:53:53 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:45:14 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:04:12 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:25:42 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 09:36:05 CDT)
  • Re: AMBER: Convergence criteria in replica exchange simulations (Thu Jul 05 2007 - 07:26:26 CDT)
  • Re: AMBER: xleap and amber7 (Thu Jul 05 2007 - 07:23:44 CDT)
  • Re: AMBER: testing amber9 for parallel use (Thu Jul 05 2007 - 07:22:20 CDT)
  • Re: AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 05:39:10 CDT)
  • Re: AMBER: About amber7 (Tue Jul 03 2007 - 08:57:14 CDT)
• Cenk Andac
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 20:37:43 CDT)
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 19:51:02 CDT)
  • AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 11:47:45 CDT)
  • AMBER: Question about NAB (Nucleic Acid Builder) (Wed Jul 11 2007 - 03:30:18 CDT)
• Chris Moth
  • Re: AMBER: PCA with ptraj (Sun Jul 29 2007 - 07:27:32 CDT)
• Colby C
  • AMBER: Gaff Charge (Mon Jul 16 2007 - 22:39:15 CDT)
  • Re: AMBER: Sander Error (Mon Jul 09 2007 - 10:39:50 CDT)
  • Re: AMBER: Sander Error (Tue Jul 03 2007 - 13:21:18 CDT)
• Dan Kidger
  • AMBER: bug in nonbond_list.f (nee ew_setup.f) (Mon Jul 02 2007 - 04:42:58 CDT)
• David A. Case
  • Re: AMBER: Linux install (Tue Jul 31 2007 - 10:35:37 CDT)
  • Re: AMBER: errors in SHIFTS execution (Mon Jul 30 2007 - 10:37:26 CDT)
  • Re: AMBER: errors in SHIFTS execution (Sun Jul 29 2007 - 10:44:05 CDT)
  • Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 10:19:49 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:48:55 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 16:32:32 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 14:56:24 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 12:36:43 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 11:09:18 CDT)
  • Re: AMBER: MD simulation error (Tue Jul 24 2007 - 19:55:09 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 10:20:30 CDT)
  • Re: AMBER: Bug report: a bug of xleap associated with NumLock (Tue Jul 24 2007 - 10:16:07 CDT)
  • Re: AMBER: regarding distance restraints (Mon Jul 23 2007 - 09:56:03 CDT)
  • Re: AMBER: using amber to minimize structure obatined from cyana (Mon Jul 23 2007 - 09:52:00 CDT)
  • Re: AMBER: parallel compilation (Mon Jul 23 2007 - 09:55:02 CDT)
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 18:30:06 CDT)
  • Re: AMBER: offending restraint (Sat Jul 21 2007 - 20:35:51 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 11:16:46 CDT)
  • Re: AMBER: DNA RNA recognition problem (Thu Jul 19 2007 - 10:01:17 CDT)
  • Re: AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 23:34:18 CDT)
  • Re: AMBER: General AMBER questions (Wed Jul 18 2007 - 18:12:34 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Tue Jul 17 2007 - 18:15:59 CDT)
  • Re: AMBER: potential energy calculation (Tue Jul 17 2007 - 18:08:54 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 11:49:41 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 09:53:46 CDT)
  • Re: AMBER: Gaff Charge (Tue Jul 17 2007 - 00:18:17 CDT)
  • Re: AMBER: Problems simulating a big system (Mon Jul 16 2007 - 20:44:09 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Mon Jul 16 2007 - 20:32:16 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:25:20 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 19:13:45 CDT)
  • Re: AMBER: help with phosphotyrosine (Mon Jul 16 2007 - 13:11:51 CDT)
  • Re: AMBER: Non bond list overflow (Sun Jul 15 2007 - 18:50:11 CDT)
  • Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 18:03:45 CDT)
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 17:58:30 CDT)
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 14:55:15 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 10:22:35 CDT)
  • Re: AMBER: Question about NAB (Nucleic Acid Builder) (Wed Jul 11 2007 - 18:23:05 CDT)
  • Re: AMBER: question about iwrap (Wed Jul 11 2007 - 18:24:11 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 18:17:56 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 18:04:15 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 17:39:31 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 12:52:10 CDT)
  • Re: AMBER: Saving (.)prepin file (Tue Jul 10 2007 - 12:45:58 CDT)
  • Re: AMBER: tgtrmsmask and tgtfitmask (Tue Jul 10 2007 - 11:01:27 CDT)
  • Re: AMBER: ????pig5678?????? (Tue Jul 10 2007 - 10:14:45 CDT)
  • Re: AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 13:31:15 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 09:58:51 CDT)
  • Re: AMBER: program bug? (Mon Jul 09 2007 - 09:48:35 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 09:41:23 CDT)
  • Re: AMBER: Problem with running Sander (Sat Jul 07 2007 - 23:59:05 CDT)
  • Re: AMBER: antechamber: mopac charges (Thu Jul 05 2007 - 15:24:09 CDT)
  • Re: AMBER: antechamber: mopac charges (Wed Jul 04 2007 - 18:27:02 CDT)
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 15:31:29 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 15:15:21 CDT)
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 11:15:39 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 10:53:04 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 01:34:13 CDT)
  • Re: AMBER: Slow Processor Loads when Using PMEMD (Mon Jul 02 2007 - 20:24:09 CDT)
  • Re: AMBER: convergence criterion not reached (Mon Jul 02 2007 - 20:14:53 CDT)
  • Re: AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 15:56:57 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:20:27 CDT)
  • Re: AMBER: Problem with leaprc (Mon Jul 02 2007 - 09:44:59 CDT)
• David Mobley
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Thu Jul 05 2007 - 10:56:43 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 14:55:54 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:03:17 CDT)
• Davide Moiani
  • Re: AMBER: refc error (Tue Jul 17 2007 - 16:00:20 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:17:18 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:03:42 CDT)
  • Re: AMBER: manganese ion (Wed Jul 11 2007 - 16:47:18 CDT)
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 11:47:38 CDT)
  • AMBER: manganese ion (Mon Jul 09 2007 - 16:02:31 CDT)
• Du, Shiyu
  • AMBER: Question on TIP4P model (Mon Jul 09 2007 - 19:01:58 CDT)
• Evan Kelly
  • AMBER: Substitute for GAFF (Fri Jul 06 2007 - 12:32:50 CDT)
  • AMBER: QM/MM LJ parameters (Thu Jul 05 2007 - 18:31:35 CDT)
• Fenghui Fan
  • Re: AMBER: adding water molecules in lipid bilayer model (Mon Jul 09 2007 - 18:11:45 CDT)
• Francesco Pietra
  • RE: AMBER: Average potential energies and conformer ratios (Tue Jul 31 2007 - 00:09:02 CDT)
  • RE: AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 12:59:13 CDT)
  • AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 09:08:36 CDT)
  • AMBER: thermodynamic data for conformers (Sun Jul 29 2007 - 12:11:11 CDT)
  • Fwd: Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:01:40 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 15:43:08 CDT)
  • RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 12:07:15 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:44:46 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:00:58 CDT)
  • AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 08:24:10 CDT)
  • AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 01:24:22 CDT)
  • Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Wed Jul 25 2007 - 01:10:17 CDT)
  • Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 10:02:01 CDT)
  • Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 09:07:10 CDT)
  • Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 02:19:58 CDT)
  • Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 02:17:03 CDT)
  • Re: AMBER: parallel compilation (Tue Jul 24 2007 - 01:19:56 CDT)
  • AMBER: md potential energy (Mon Jul 23 2007 - 11:14:48 CDT)
  • AMBER: parallel compilation (Mon Jul 23 2007 - 05:16:35 CDT)
  • AMBER: RE Amber: Simulated Annealing (Sat Jul 21 2007 - 10:13:11 CDT)
  • Fwd: Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 16:52:25 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 16:50:37 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 10:10:42 CDT)
  • RE: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 01:48:59 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 05:14:51 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 01:48:41 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 16:11:48 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 01:26:54 CDT)
  • Re: AMBER: antechamber (Tue Jul 10 2007 - 02:04:39 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 16:57:45 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:31:18 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:22:30 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 15:53:43 CDT)
  • AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 11:56:58 CDT)
  • AMBER: Simulated Annealing - Best way to create randomness (Sat Jul 07 2007 - 09:56:41 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 15:28:31 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 14:02:19 CDT)
  • AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 12:43:43 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 16:08:02 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 11:54:08 CDT)
  • Re: AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 08:13:41 CDT)
  • AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 02:01:58 CDT)
  • AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 01:14:23 CDT)
  • AMBER: antechamber save prmtop inpcrd (Tue Jul 03 2007 - 12:55:11 CDT)
  • Fwd: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 15:50:39 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 09:38:03 CDT)
• FyD
  • Re: AMBER: adding organic molecule to polypeptide residue (Sat Jul 28 2007 - 04:05:18 CDT)
  • Re: AMBER: Re: RED problem (Mon Jul 23 2007 - 07:08:14 CDT)
  • AMBER: ptraj error (Fri Jul 20 2007 - 16:21:17 CDT)
  • Re: AMBER: Non-standard amino acid residue (Thu Jul 19 2007 - 06:26:39 CDT)
  • Re: AMBER: running_RED-III (Wed Jul 18 2007 - 20:33:20 CDT)
  • Re: AMBER: Non-standard amino acid residue (Wed Jul 18 2007 - 09:50:55 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 08:41:57 CDT)
  • Re: AMBER: RESP_compilation (Mon Jul 16 2007 - 17:59:06 CDT)
  • Re: AMBER: RESP_compilation (Mon Jul 16 2007 - 17:55:20 CDT)
  • Re: AMBER: Non-standard amino acid residue (Mon Jul 16 2007 - 11:45:07 CDT)
  • Re: AMBER: Input required for RESP (Wed Jul 11 2007 - 01:21:42 CDT)
  • Re: AMBER: RESP charge generation (Sun Jul 08 2007 - 05:19:16 CDT)
• Geoff Wood
  • Re: AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) (Mon Jul 23 2007 - 12:23:46 CDT)
  • AMBER: Re: amber-developers: -y option in sander (Thu Jul 19 2007 - 08:54:47 CDT)
• Greg Gannon
  • Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 10:55:52 CDT)
  • AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 09:41:46 CDT)
• Guillermo Mulliert Carlín
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 03:39:40 CDT)
• gurpreet singh
  • AMBER: regarding distance restraints (Mon Jul 23 2007 - 05:46:39 CDT)
• Gustavo Seabra
  • RE: AMBER: QMMM to follow reaction involving water (Mon Jul 30 2007 - 14:41:17 CDT)
  • RE: AMBER: FW: MPI error message (Tue Jul 24 2007 - 14:32:52 CDT)
• hadi behzadi
  • AMBER: resp (Tue Jul 31 2007 - 12:15:37 CDT)
  • AMBER: Resp (Tue Jul 31 2007 - 09:15:15 CDT)
  • AMBER: heme force field (Mon Jul 30 2007 - 06:55:07 CDT)
• Hashem Taha
  • Re: AMBER: MPI script (Tue Jul 17 2007 - 15:10:46 CDT)
  • Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 16:45:50 CDT)
  • AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 15:31:59 CDT)
  • AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 12:53:28 CDT)
• Hayden Eastwood
  • AMBER: Setting nonbonded cutoff to 1 (Mon Jul 16 2007 - 12:27:45 CDT)
• Holger Gohlke
  • Re: AMBER: secstruct command (Thu Jul 19 2007 - 13:22:37 CDT)
• Holly Freedman
  • AMBER: tgtrmsmask and tgtfitmask (Mon Jul 09 2007 - 21:03:39 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Wed Jul 04 2007 - 14:53:01 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 12:14:29 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:51:12 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 14:54:11 CDT)
  • AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 14:13:17 CDT)
• Ilyas Yildirim
  • AMBER: Truncated Octahedron box volume (Sun Jul 22 2007 - 21:52:16 CDT)
  • Re: AMBER: xleap and amber7 (Wed Jul 04 2007 - 23:53:37 CDT)
• In Hee Park
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 11:41:47 CDT)
  • AMBER: MPI Quiescence problem in REMD (Tue Jul 10 2007 - 23:03:08 CDT)
• j j
  • AMBER: GDP UNKNOWN ATOM TYPE: O3 warning (Sat Jul 21 2007 - 12:21:32 CDT)
  • Re: AMBER: Slight_error_on_Compiling_Replica_Exchange (Wed Jul 04 2007 - 05:13:22 CDT)
  • AMBER: Slight_error_on_Compiling_Replica_Exchange (Wed Jul 04 2007 - 03:57:28 CDT)
• Jason Whitte
  • AMBER: incoherent intermediate scattering function (Tue Jul 17 2007 - 17:59:21 CDT)
• Jena M
  • AMBER: methods to approach two atoms (Thu Jul 26 2007 - 08:53:09 CDT)
  • AMBER: offending restraint (Sat Jul 21 2007 - 19:15:42 CDT)
  • AMBER: convergence criterion not reached (Mon Jul 02 2007 - 18:53:22 CDT)
• Jianyin Shao
  • Re: AMBER: ptraj: RMS per residues and per time (Fri Jul 06 2007 - 02:54:06 CDT)
• Johnson Agbo
  • AMBER: Saving (.)prepin file (Mon Jul 09 2007 - 13:22:40 CDT)
  • AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 15:35:00 CDT)
• Jonathan Suever
  • AMBER: Slow Processor Loads when Using PMEMD (Mon Jul 02 2007 - 19:28:48 CDT)
• Jordi Camps
  • Re: AMBER: Problems simulating a big system (Tue Jul 17 2007 - 04:57:13 CDT)
  • AMBER: Problems simulating a big system (Mon Jul 16 2007 - 06:55:55 CDT)
• Julien Michel
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 17:42:53 CDT)
• Kailee
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:55:06 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:17:32 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 05:55:28 CDT)
  • AMBER: question about iwrap (Wed Jul 11 2007 - 08:17:29 CDT)
• Karl Kirschner
  • Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein (Tue Jul 17 2007 - 08:39:43 CDT)
• Karol Kaszuba
  • AMBER: running_RED-III (Wed Jul 18 2007 - 14:02:10 CDT)
  • Re: AMBER: RESP_compilation_IT_WORKS (Tue Jul 17 2007 - 03:32:59 CDT)
  • AMBER: RESP_compilation (Mon Jul 16 2007 - 14:14:32 CDT)
• Lili Peng
  • AMBER: adding organic molecule to polypeptide residue (Thu Jul 26 2007 - 17:36:29 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 13:21:24 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 12:38:10 CDT)
  • AMBER: MD simulation error (Tue Jul 24 2007 - 18:53:59 CDT)
  • Re: AMBER: potential energy calculation (Wed Jul 18 2007 - 15:47:57 CDT)
  • AMBER: General AMBER questions (Tue Jul 17 2007 - 17:51:32 CDT)
  • Re: AMBER: potential energy calculation (Tue Jul 17 2007 - 17:46:55 CDT)
  • Re: AMBER: refc error (Tue Jul 17 2007 - 17:40:26 CDT)
  • Re: AMBER: refc error (Tue Jul 17 2007 - 13:35:06 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:08:18 CDT)
  • AMBER: potential energy calculation (Mon Jul 16 2007 - 19:03:55 CDT)
  • AMBER: refc error (Mon Jul 16 2007 - 18:56:11 CDT)
  • AMBER: Basic AMBER question (Wed Jul 11 2007 - 14:15:48 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 18:01:11 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 17:58:22 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 16:50:45 CDT)
  • AMBER: Problem with running Sander (Sat Jul 07 2007 - 18:10:06 CDT)
• Lishan Yao
  • AMBER: Ne van del waals potential (Fri Jul 13 2007 - 11:09:37 CDT)
• M. L. Dodson
  • Re: AMBER: QMMM to follow reaction involving water (Tue Jul 31 2007 - 10:14:57 CDT)
  • AMBER: QMMM to follow reaction involving water (Mon Jul 30 2007 - 13:23:14 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 17:25:17 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 19:08:27 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:09:06 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 12:10:58 CDT)
  • Re: AMBER: adding water molecules in lipid bilayer model (Mon Jul 09 2007 - 07:59:01 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 10:57:05 CDT)
• M. Maeda
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 06:29:03 CDT)
  • Re: AMBER: program bug? (Wed Jul 11 2007 - 23:41:34 CDT)
  • Re: AMBER: program bug? (Wed Jul 11 2007 - 23:47:19 CDT)
  • AMBER: program bug? (Sun Jul 08 2007 - 21:24:58 CDT)
• Marcelo Puiatti
  • Re: AMBER: heme force field (Mon Jul 30 2007 - 08:08:52 CDT)
• Marie Brut
  • AMBER: antechamber (Mon Jul 09 2007 - 06:56:19 CDT)
• Mark Williamson
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:20:37 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 14:19:29 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 10:28:06 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 08:33:35 CDT)
  • Re: AMBER: problem in compiling amber9 and running amber9 (Sat Jul 21 2007 - 09:21:18 CDT)
  • Re: SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 10:18:00 CDT)
  • Re: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 09:52:39 CDT)
• Mathy Froeyen
  • Re: AMBER: Nucleic acid : nonplanarity (Wed Jul 04 2007 - 08:57:08 CDT)
• Mattias Blomberg
  • AMBER: modelling substrate binding (Mon Jul 16 2007 - 08:53:15 CDT)
• Melinda Layten
  • Re: AMBER: Basic AMBER question (Wed Jul 11 2007 - 15:05:11 CDT)
  • Re: AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 13:05:39 CDT)
• Mikyung
  • Re: AMBER: extract protein energy from MD trajectory (Wed Jul 11 2007 - 01:58:31 CDT)
  • AMBER: extract protein energy from MD trajectory (Tue Jul 10 2007 - 16:47:53 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 11:20:12 CDT)
• ming hui
  • AMBER: Re: how to create an O linked N-acetylglucosamine in a protein (Mon Jul 16 2007 - 22:44:08 CDT)
  • AMBER: how to create an O linked N-acetylglucosamine in a protein (Mon Jul 16 2007 - 22:41:40 CDT)
• mkseo
  • Re: AMBER: surface area over the trajectory (Mon Jul 09 2007 - 17:55:18 CDT)
  • AMBER: surface area over the trajectory (Mon Jul 09 2007 - 16:52:32 CDT)
• n.buis_at_soton.ac.uk
  • AMBER: (no subject) (Thu Jul 19 2007 - 03:58:06 CDT)
• Narayanan Veeraraghavan
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Tue Jul 17 2007 - 17:01:10 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 16:35:53 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 13:02:38 CDT)
  • AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 09:30:44 CDT)
• Neelanjana Sengupta
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 13:58:12 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 13:53:16 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 11:33:39 CDT)
  • AMBER: Known residue, unknown error in teLeap (Mon Jul 16 2007 - 14:19:07 CDT)
  • AMBER: Input required for RESP (Tue Jul 10 2007 - 13:03:54 CDT)
  • AMBER: RESP charge generation (Sat Jul 07 2007 - 18:08:07 CDT)
  • Re: AMBER: antechamber: mopac charges (Thu Jul 05 2007 - 14:26:30 CDT)
  • AMBER: antechamber: mopac charges (Wed Jul 04 2007 - 18:21:02 CDT)
• neetu_at_imtech.res.in
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 23:03:54 CDT)
• neva_at_mmb.pcb.ub.es
  • AMBER: Bad residue/molecule data in prmtop (Wed Jul 25 2007 - 08:03:19 CDT)
• neville forlemu
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Sat Jul 14 2007 - 21:09:36 CDT)
• Nicolas Lux Fawzi
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 17:11:30 CDT)
  • AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 14:26:19 CDT)
• pig5678
  • Re:Re: AMBER: ????pig5678?????? (Thu Jul 12 2007 - 20:36:10 CDT)
  • Re:Re: AMBER: ????pig5678?????? (Tue Jul 10 2007 - 22:27:55 CDT)
  • AMBER: À´×Ôpig5678µÄÓʼþ (Tue Jul 10 2007 - 01:59:22 CDT)
• Prashanth Athri
  • Re: AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 17:51:32 CDT)
  • AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 14:38:12 CDT)
• Prem Prakash Pathak
  • Re: AMBER: not getting topology and restraint file (Wed Jul 25 2007 - 08:45:57 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 23:12:48 CDT)
  • Re: AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 23:11:00 CDT)
  • AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 09:09:40 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 07:30:31 CDT)
  • AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Mon Jul 23 2007 - 10:39:21 CDT)
  • AMBER: using amber to minimize structure obatined from cyana (Mon Jul 23 2007 - 02:27:26 CDT)
  • AMBER: problem in compiling amber9 and running amber9 (Sat Jul 21 2007 - 07:27:18 CDT)
• priya priya
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 10:00:30 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 09:23:08 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:36:12 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:13:32 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:11:17 CDT)
  • AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 05:58:48 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 11:41:05 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:43:13 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:27:27 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:41:22 CDT)
  • AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:33:11 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 07:25:02 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 05:39:58 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 01:58:28 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:40:41 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:57:59 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:10:23 CDT)
  • AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 09:31:03 CDT)
• Rachel
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:52:50 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:38:12 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:08:23 CDT)
  • Re: AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:43:48 CDT)
  • AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:18:32 CDT)
• Rafi Ahmad
  • SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 10:04:46 CDT)
  • AMBER: Atoms in conatct to a specific atoms during MD (Mon Jul 16 2007 - 08:23:38 CDT)
• Rajendra P. OJHA
  • Re: AMBER: potential energy calculation (Wed Jul 18 2007 - 01:03:55 CDT)
• ravishk kumar
  • AMBER: PCA with ptraj (Sat Jul 28 2007 - 07:02:13 CDT)
  • AMBER: rmsd residue wise (Thu Jul 26 2007 - 08:02:20 CDT)
• Robert Duke
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 11:30:40 CDT)
  • Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 15:55:15 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 12:47:57 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 08:07:36 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 21:21:07 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 16:57:54 CDT)
  • Re: AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 14:35:04 CDT)
• Ross Walker
  • RE: AMBER: QMMM to follow reaction involving water (Mon Jul 30 2007 - 23:49:23 CDT)
  • RE: AMBER: Problem while saving .top and .crd files. (Mon Jul 30 2007 - 23:28:42 CDT)
  • RE: AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 23:11:50 CDT)
  • AMBER: RE: help:- regarding "perl" in analyzing the simulation (Mon Jul 30 2007 - 11:38:33 CDT)
  • RE: AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 10:51:36 CDT)
  • AMBER: RE: Problem with sander.MPI (Mon Jul 30 2007 - 09:12:58 CDT)
  • AMBER: RE: Query (Fri Jul 27 2007 - 10:24:56 CDT)
  • AMBER: RE: A little question (Thu Jul 26 2007 - 09:51:55 CDT)
  • RE: AMBER: MD simulation error (Wed Jul 25 2007 - 12:54:30 CDT)
  • AMBER: RE: Contact TSRI: Ross Walker (Wed Jul 25 2007 - 10:31:53 CDT)
  • RE: AMBER: crg file (Wed Jul 25 2007 - 10:26:28 CDT)
  • RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 10:25:58 CDT)
  • RE: AMBER: Bad residue/molecule data in prmtop (Wed Jul 25 2007 - 09:17:00 CDT)
  • RE: AMBER: MD simulation error (Tue Jul 24 2007 - 20:01:13 CDT)
  • RE: AMBER: FW: MPI error message (Tue Jul 24 2007 - 16:31:12 CDT)
  • RE: AMBER: MPI error message (Mon Jul 23 2007 - 12:56:35 CDT)
  • RE: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Mon Jul 23 2007 - 10:52:00 CDT)
  • AMBER: RE: Query (Mon Jul 23 2007 - 10:13:13 CDT)
  • RE: AMBER: Setting nonbonded cutoff to 1 (Mon Jul 16 2007 - 12:43:28 CDT)
  • RE: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 17:06:56 CDT)
  • RE: AMBER: Basic AMBER question (Wed Jul 11 2007 - 15:07:42 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 16:57:39 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 18:00:38 CDT)
  • RE: AMBER: Problem with running Sander (Tue Jul 10 2007 - 18:09:29 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 13:21:12 CDT)
  • RE: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:38:01 CDT)
  • RE: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 12:26:29 CDT)
  • RE: AMBER: QM/MM LJ parameters (Thu Jul 05 2007 - 19:58:49 CDT)
  • RE: AMBER: Slow Processor Loads when Using PMEMD (Mon Jul 02 2007 - 20:42:01 CDT)
  • RE: AMBER: amber7 and xleap (Sun Jul 01 2007 - 12:32:45 CDT)
  • RE: AMBER: xleap and amber7 (Sun Jul 01 2007 - 12:33:15 CDT)
• Ruchi Sachdeva
  • Re: AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 23:18:30 CDT)
  • AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 11:47:30 CDT)
• Saiful Islam
  • Re: AMBER: xleap and amber7 (Tue Jul 10 2007 - 07:47:00 CDT)
  • Re: AMBER: xleap and amber7 (Fri Jul 06 2007 - 21:23:35 CDT)
  • Re: AMBER: xleap and amber7 (Wed Jul 04 2007 - 22:53:42 CDT)
  • AMBER: About amber7 (Tue Jul 03 2007 - 08:49:28 CDT)
  • Re: AMBER: xleap and amber7 (Mon Jul 02 2007 - 09:05:34 CDT)
  • Re: AMBER: amber7 and xleap (Sun Jul 01 2007 - 08:43:45 CDT)
• Sally Pias
  • AMBER: testing amber9 for parallel use (Thu Jul 05 2007 - 01:47:22 CDT)
• Samantha Kaye
  • Re: AMBER: help with phosphotyrosine (Tue Jul 17 2007 - 08:00:23 CDT)
  • AMBER: help with phosphotyrosine (Mon Jul 16 2007 - 10:45:36 CDT)
• Sascha Rehm
  • AMBER: ptraj: RMS per residues and per time (Tue Jul 03 2007 - 09:03:04 CDT)
• Seongeun Yang
  • AMBER: convergence in classical MD (Mon Jul 16 2007 - 06:23:01 CDT)
  • AMBER: Convergence criteria in replica exchange simulations (Thu Jul 05 2007 - 06:18:17 CDT)
• Sergey Samsonov
  • AMBER: Re: RED problem (Mon Jul 23 2007 - 06:35:32 CDT)
  • Re: AMBER: Non-standard amino acid residue (Thu Jul 19 2007 - 04:45:52 CDT)
  • Re: AMBER: Non-standard amino acid residue (Wed Jul 18 2007 - 09:19:42 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 10:37:03 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 07:30:14 CDT)
  • AMBER: Non-standard amino acid residue (Mon Jul 16 2007 - 09:44:32 CDT)
• Sergio Wong
  • AMBER: computational Ala scan (Wed Jul 11 2007 - 18:36:58 CDT)
• Seth Lilavivat
  • AMBER: Verifying Bond Angles (Wed Jul 18 2007 - 16:32:30 CDT)
  • AMBER: Belly Restraints and Distance Restraints (Wed Jul 11 2007 - 14:13:04 CDT)
  • Re: AMBER: Simulated Annealing - Best way to create randomness (Mon Jul 09 2007 - 10:03:29 CDT)
• snoze pa
  • AMBER: Multiple residues position (Fri Jul 13 2007 - 11:04:59 CDT)
  • AMBER: related to new amber force field (Fri Jul 13 2007 - 10:57:38 CDT)
• Sophie Barbe
  • AMBER: Nucleic acid : nonplanarity (Wed Jul 04 2007 - 07:37:26 CDT)
  • AMBER: Nucleic acid : nonplanarity (Tue Jul 03 2007 - 10:48:07 CDT)
• steinbrt_at_scripps.edu
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Wed Jul 04 2007 - 07:51:08 CDT)
• Steve Seibold
  • AMBER: DNA RNA recognition problem (Thu Jul 19 2007 - 08:51:43 CDT)
• Steven Winfield
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Mon Jul 23 2007 - 10:43:17 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:32:07 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:36:06 CDT)
• Syed Tarique Moin
  • RE: AMBER: problem in installing amber9 (Sat Jul 21 2007 - 00:18:05 CDT)
• Sébastien Kozlowskyj
  • AMBER: Problems during compilation (Wed Jul 18 2007 - 04:26:06 CDT)
• Taryn Hartley
  • AMBER: FW: MPI error message (Tue Jul 24 2007 - 14:00:25 CDT)
  • AMBER: MPI error message (Mon Jul 23 2007 - 12:39:27 CDT)
  • AMBER: MPI script (Fri Jul 13 2007 - 17:06:45 CDT)
• Thomas Cheatham
  • Re: AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 14:49:49 CDT)
• Thomas Cheatham III
  • Re: AMBER: MPI script (Fri Jul 13 2007 - 17:19:37 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:17:23 CDT)
• Thomas Pochapsky
  • Re: AMBER: errors in SHIFTS execution (Mon Jul 30 2007 - 12:06:04 CDT)
  • Re: AMBER: errors in SHIFTS execution (Mon Jul 30 2007 - 09:06:19 CDT)
  • Re: AMBER: errors in SHIFTS execution (Mon Jul 30 2007 - 08:49:47 CDT)
• Thomas Steinbrecher
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Fri Jul 06 2007 - 12:55:32 CDT)
• Tim Meyer
  • Re: AMBER: secstruct command (Fri Jul 20 2007 - 08:55:47 CDT)
• Tom Pochapsky
  • AMBER: errors in SHIFTS execution (Sat Jul 28 2007 - 06:58:57 CDT)
• tonglei
  • AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA? (Sun Jul 29 2007 - 22:45:24 CDT)
• Toshifumi Yui
  • AMBER: O-acetylated sugar (Tue Jul 03 2007 - 07:26:12 CDT)
• umbrita itl
  • RE: AMBER:charge file (Wed Jul 25 2007 - 10:36:11 CDT)
  • AMBER: crg file (Wed Jul 25 2007 - 09:43:17 CDT)
• Vijay Manickam Achari
  • AMBER: Can't open PDB file in xleap (Mon Jul 16 2007 - 04:43:16 CDT)
  • AMBER: can open PDB file in xleap (Sun Jul 15 2007 - 20:44:17 CDT)
  • Re: AMBER: adding water molecules in lipid bilayer model (Tue Jul 10 2007 - 21:00:30 CDT)
  • AMBER: adding water molecules in lipid bilayer model (Sun Jul 08 2007 - 22:22:46 CDT)
• WANG,YING
  • AMBER: Who has the structure file of beta-chitin? (Tue Jul 03 2007 - 13:19:11 CDT)
• Wei Chen
  • AMBER: bound magnesium ions in proteins with GBSA (Wed Jul 18 2007 - 11:01:26 CDT)
• Ye Mei
  • Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 21:27:04 CDT)
  • Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 09:26:26 CDT)
  • Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 05:15:28 CDT)
  • Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 05:07:31 CDT)
  • Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 01:44:43 CDT)
  • AMBER: Bug report: a bug of xleap associated with NumLock (Tue Jul 24 2007 - 01:15:27 CDT)
  • AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water (Mon Jul 23 2007 - 08:00:34 CDT)
  • Re: AMBER: Slight_error_on_Compiling_Replica_Exchange (Wed Jul 04 2007 - 04:30:09 CDT)
• yen li
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 13:21:22 CDT)
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 07:23:49 CDT)
  • Re: AMBER: Problem with leaprc (Sun Jul 01 2007 - 12:36:14 CDT)
  • Re: AMBER: Problem with leaprc (Sun Jul 01 2007 - 08:10:09 CDT)
• ÇÑÀç¹ü
  • AMBER: How to use antechamber properly? (Tue Jul 03 2007 - 00:57:33 CDT)

Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:09 CST