Amber Archive Feb 2004: By Thread

AMBER: DNA Beale, John (Mon Feb 02 2004 - 05:31:51 PST)
- Re: AMBER: DNA David A. Case (Mon Feb 02 2004 - 08:58:26 PST)
AMBER: convert restart to mdcrd? Karin Schleinkofer (Mon Feb 02 2004 - 06:39:40 PST)
- Re: AMBER: convert restart to mdcrd? Dr. Yong Duan (Mon Feb 02 2004 - 08:48:55 PST)
  - Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 08:07:12 PST)
  - Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 08:07:49 PST)
    - Re: AMBER: convert restart to mdcrd? Dr. Yong Duan (Mon Feb 02 2004 - 09:27:41 PST)
- Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 07:33:35 PST)
- Re: AMBER: convert restart to mdcrd? Teletchéa Stéphane (Mon Feb 02 2004 - 08:17:30 PST)
AMBER: ptraj & LES Vlad Cojocaru (Mon Feb 02 2004 - 08:46:08 PST)
- Re: AMBER: ptraj & LES Michael Trieb (Mon Feb 02 2004 - 09:11:08 PST)
  - Re: AMBER: ptraj & LES Vlad Cojocaru (Mon Feb 02 2004 - 09:22:09 PST)
AMBER: LEaP- Error reading frcmod parameters. Miguel de Federico (Mon Feb 02 2004 - 10:03:00 PST)
- Re: AMBER: LEaP- Error reading frcmod parameters. David A. Case (Mon Feb 02 2004 - 10:20:43 PST)
Re: AMBER: NVE&polarizable force field Martina Roeselova (Mon Feb 02 2004 - 09:33:17 PST)
- AMBER: cell dimensions Dave S Walker (Mon Feb 02 2004 - 13:46:54 PST)
  - Re: AMBER: cell dimensions David A. Case (Thu Feb 05 2004 - 10:00:41 PST)
- Re: AMBER: NVE&polarizable force field Byungchan Kim (Tue Feb 03 2004 - 09:54:55 PST)
Re: AMBER: ANAL problem. David A. Case (Mon Feb 02 2004 - 10:51:02 PST)
AMBER: TI, angle parameters for nitrogen, frcmod Carsten Detering (Mon Feb 02 2004 - 12:38:59 PST)
- Re: AMBER: TI, angle parameters for nitrogen, frcmod David A. Case (Thu Feb 05 2004 - 09:51:39 PST)
AMBER: nucleic acid bases nonplanar during LES sim Vlad Cojocaru (Mon Feb 02 2004 - 13:17:09 PST)
- Re: AMBER: nucleic acid bases nonplanar during LES sim Carlos Simmerling (Mon Feb 02 2004 - 13:56:00 PST)
  - AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang (Mon Feb 02 2004 - 14:54:05 PST)
    - RE: AMBER: temperature in DelPhi for MM-PBSA calculation S. Frank Yan (Mon Feb 02 2004 - 15:18:22 PST)
    - RE: AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang (Mon Feb 02 2004 - 16:58:54 PST)
    - Re: AMBER: temperature in DelPhi for MM-PBSA calculation rluo.uci.edu (Mon Feb 02 2004 - 18:45:52 PST)
AMBER: leap - orientation of sequenced residues Sarah Wittkopp (Mon Feb 02 2004 - 17:58:33 PST)
- Re: AMBER: leap - orientation of sequenced residues David A. Case (Tue Feb 03 2004 - 09:44:50 PST)
AMBER: Installing Amber on IBM AIX cluster Wayne Dawson (Mon Feb 02 2004 - 22:11:49 PST)
AMBER: xleap & antechamber L Jin (Tue Feb 03 2004 - 01:46:54 PST)
- Re: AMBER: xleap & antechamber David A. Case (Thu Feb 05 2004 - 09:46:02 PST)
AMBER: protonation Nikolai Smolin (Tue Feb 03 2004 - 01:50:23 PST)
AMBER: the uses for Amber FFs a b (Tue Feb 03 2004 - 06:48:24 PST)
- Re: AMBER: the uses for Amber FFs Vlad Cojocaru (Tue Feb 03 2004 - 06:56:26 PST)
AMBER: What does this error message mean? nie beining (Tue Feb 03 2004 - 07:58:41 PST)
- Re: AMBER: What does this error message mean? David A. Case (Tue Feb 03 2004 - 08:12:48 PST)
- Re: AMBER: What does this error message mean? Carlos Simmerling (Tue Feb 03 2004 - 08:30:56 PST)
- Re: AMBER: What does this error message mean? Martina Roeselova (Tue Feb 03 2004 - 11:55:22 PST)
AMBER: Carnal Herbert Georg (Tue Feb 03 2004 - 08:11:28 PST)
Re: AMBER: Carnal Bill Ross (Tue Feb 03 2004 - 10:14:02 PST)
- Re: AMBER: Carnal Herbert Georg (Tue Feb 03 2004 - 11:30:33 PST)
AMBER: Amber on Redhat Enterprise Mingfeng Yang (Tue Feb 03 2004 - 10:23:44 PST)
Re: AMBER: What does this error message mean? Bill Ross (Tue Feb 03 2004 - 10:40:15 PST)
AMBER: A general question aini.UMDNJ.EDU (Tue Feb 03 2004 - 15:49:06 PST)
- Re: AMBER: A general question Carlos Simmerling (Tue Feb 03 2004 - 16:13:09 PST)
  - Re: AMBER: A general question aini.UMDNJ.EDU (Tue Feb 03 2004 - 17:39:44 PST)
    - Re: AMBER: questions parm94/99 ff secondary structure Wayne Dawson (Thu Feb 05 2004 - 23:50:07 PST)
    - Re: AMBER: questions parm94/99 ff secondary structure Carlos Simmerling (Fri Feb 06 2004 - 04:58:45 PST)
AMBER: NMODE for protein via MM-PBSA-cntd ML (Wed Feb 04 2004 - 08:09:57 PST)
- Re: AMBER: NMODE for protein via MM-PBSA-cntd David A. Case (Wed Feb 04 2004 - 08:32:37 PST)
  - Re: AMBER: NMODE for protein via MM-PBSA-cntd ML (Wed Feb 04 2004 - 09:18:12 PST)
AMBER: rstdip Martina Roeselova (Wed Feb 04 2004 - 09:57:18 PST)
- Re: AMBER: rstdip Scott Brozell (Wed Feb 04 2004 - 10:19:45 PST)
Re: AMBER: sander and mpich (which compilers/mpich work) Viktor Hornak (Wed Feb 04 2004 - 11:13:13 PST)
AMBER: carnal Herbert Georg (Wed Feb 04 2004 - 11:18:37 PST)
Re: AMBER: carnal Bill Ross (Wed Feb 04 2004 - 11:40:31 PST)
- AMBER: How to remove Cl- ions Do Anh Tuan (Fri Feb 06 2004 - 02:38:41 PST)
  - Re: AMBER: How to remove Cl- ions Itziar Maestre Asenjo (Fri Feb 06 2004 - 02:58:05 PST)
  - Re: AMBER: How to remove Cl- ions Vlad Cojocaru (Fri Feb 06 2004 - 03:09:52 PST)
  - AMBER: How to remove Cl- ions Wayne Dawson (Fri Feb 06 2004 - 03:19:33 PST)
- Re: AMBER: carnal Bill Ross (Mon Feb 16 2004 - 10:37:54 PST)
- Re: AMBER: carnal Bill Ross (Tue Feb 24 2004 - 09:49:16 PST)
AMBER: antechamber + mopac error Carsten Detering (Wed Feb 04 2004 - 18:57:48 PST)
- RE: AMBER: antechamber + mopac error Meg McCarrick (Thu Feb 05 2004 - 09:12:42 PST)
- Re: AMBER: antechamber + mopac error David A. Case (Thu Feb 05 2004 - 09:21:11 PST)
AMBER: ptraj Julien Pecher (Thu Feb 05 2004 - 00:46:09 PST)
Re: AMBER: ptraj Bill Ross (Thu Feb 05 2004 - 01:43:59 PST)
AMBER: PMEMD and nmropt=1 aldo jongejan (Thu Feb 05 2004 - 03:52:29 PST)
- Re: AMBER: PMEMD and nmropt=1 Robert Duke (Thu Feb 05 2004 - 04:39:58 PST)
- RE: AMBER: PMEMD and nmropt=1 Kristina Furse (Thu Feb 05 2004 - 13:19:52 PST)
  - Re: AMBER: PMEMD and nmropt=1 Robert Duke (Thu Feb 05 2004 - 13:45:07 PST)
  - Re: AMBER: PMEMD and nmropt=1 David A. Case (Thu Feb 05 2004 - 17:29:41 PST)
Re: AMBER: Re: ANAL problem David A. Case (Thu Feb 05 2004 - 09:36:05 PST)
- Re: AMBER: Re: ANAL problem Bill Ross (Thu Feb 05 2004 - 10:07:58 PST)
AMBER: antechamber error in test / differences in prmtop files Carsten Detering (Thu Feb 05 2004 - 12:07:07 PST)
- Re: AMBER: antechamber error in test / differences in prmtop files David A. Case (Thu Feb 05 2004 - 13:11:53 PST)
AMBER: ptraj and dipoles Herbert Georg (Thu Feb 05 2004 - 13:40:24 PST)
- Re: AMBER: ptraj and dipoles David A. Case (Thu Feb 05 2004 - 23:11:50 PST)
  - Re: AMBER: ptraj and dipoles Herbert Georg (Fri Feb 06 2004 - 03:47:12 PST)
    - AMBER: ptraj and dipoles.... Herbert Georg (Fri Feb 06 2004 - 13:12:10 PST)
AMBER: MCSS Chen, Ya (Thu Feb 05 2004 - 20:33:48 PST)
- Re: AMBER: MCSS David A. Case (Thu Feb 05 2004 - 23:12:47 PST)
AMBER: water as a "ligand" in GBSA and MM-PBSA? Giulio Rastelli (Fri Feb 06 2004 - 09:41:50 PST)
AMBER: How to remove Cl- ions Do Anh Tuan (Fri Feb 06 2004 - 05:24:10 PST)
Re: AMBER: How to remove Cl- ions Bill Ross (Fri Feb 06 2004 - 08:35:27 PST)
AMBER: off-subject ROCKS/Qbank James W. Caldwell (Fri Feb 06 2004 - 12:03:09 PST)
Fwd: Re: AMBER: Lattice structures in xleap Brandon Tefft (Fri Feb 06 2004 - 13:27:50 PST)
- Re: Fwd: Re: AMBER: Lattice structures in xleap David A. Case (Fri Feb 06 2004 - 13:54:07 PST)
- Re: Fwd: Re: AMBER: Lattice structures in xleap Bill Ross (Fri Feb 06 2004 - 14:21:12 PST)
AMBER: antechamber + mopac +scf failed Carsten Detering (Fri Feb 06 2004 - 16:11:22 PST)
AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED Carsten Detering (Fri Feb 06 2004 - 17:50:46 PST)
- Re: AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED David A. Case (Sat Feb 07 2004 - 08:33:48 PST)
AMBER: adding ions to nucleic acids a b (Sun Feb 08 2004 - 02:47:19 PST)
- Re: AMBER: adding ions to nucleic acids Vlad Cojocaru (Sun Feb 08 2004 - 04:25:55 PST)
AMBER: question about the average structure from ptraj aini.UMDNJ.EDU (Sun Feb 08 2004 - 11:33:23 PST)
- Re: AMBER: question about the average structure from ptraj Thomas E. Cheatham, III (Sun Feb 08 2004 - 11:49:23 PST)
Re: AMBER: adding ions to nucleic acids Bill Ross (Sun Feb 08 2004 - 11:40:50 PST)
- Re: AMBER: adding ions to nucleic acids Dr. Yong Duan (Tue Feb 10 2004 - 21:54:58 PST)
Re: AMBER: question about the average structure from ptraj Bill Ross (Sun Feb 08 2004 - 11:47:11 PST)
AMBER: dipole moment in ptraj Herbert Georg (Sun Feb 08 2004 - 10:42:07 PST)
- Re: AMBER: dipole moment in ptraj Thomas E. Cheatham, III (Sun Feb 08 2004 - 15:00:55 PST)
AMBER: Aldo's PMEMD bug Robert Duke (Mon Feb 09 2004 - 05:53:43 PST)
- Re: AMBER: Aldo's PMEMD bug aldo jongejan (Mon Feb 09 2004 - 07:44:39 PST)
AMBER: antechamber error jwfang (Mon Feb 09 2004 - 07:50:17 PST)
- Re: AMBER: antechamber error David A. Case (Mon Feb 09 2004 - 08:22:07 PST)
- Re: AMBER: antechamber error Carsten Detering (Mon Feb 09 2004 - 09:38:41 PST)
- RE: AMBER: antechamber error Fang, Jianwen (Mon Feb 09 2004 - 10:00:28 PST)
AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering (Mon Feb 09 2004 - 11:17:41 PST)
- Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Junmei Wang (Mon Feb 09 2004 - 11:27:02 PST)
  - Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering (Mon Feb 09 2004 - 14:02:10 PST)
  - Re: AMBER: antechamber + FAILED TO ACHIEVE SCF David A. Case (Mon Feb 09 2004 - 14:17:49 PST)
AMBER: Nmode convergence ML (Mon Feb 09 2004 - 23:36:27 PST)
- Re: AMBER: Nmode convergence ML (Tue Feb 10 2004 - 07:26:12 PST)
- Re: AMBER: Nmode convergence David A. Case (Tue Feb 10 2004 - 08:34:17 PST)
  - Re: AMBER: Nmode convergence ML (Wed Feb 11 2004 - 00:14:31 PST)
AMBER: Temperature in Nmode ML (Tue Feb 10 2004 - 07:25:12 PST)
- Re: AMBER: Temperature in Nmode David A. Case (Tue Feb 10 2004 - 08:42:06 PST)
  - Re: AMBER: Temperature in Nmode ML (Tue Feb 10 2004 - 12:46:19 PST)
AMBER: minimization output L Jin (Tue Feb 10 2004 - 08:36:25 PST)
- Re: AMBER: minimization output David A. Case (Tue Feb 10 2004 - 13:05:59 PST)
  - Re: AMBER: minimization output L Jin (Fri Feb 13 2004 - 01:49:52 PST)
- Re: AMBER: minimization output Anna Schrey (Fri Feb 20 2004 - 01:07:40 PST)
  - Re: AMBER: minimization output L Jin (Fri Feb 20 2004 - 02:36:35 PST)
AMBER: LES question Lishan Yao (Tue Feb 10 2004 - 12:47:20 PST)
- Re: AMBER: LES question Vlad Cojocaru (Tue Feb 10 2004 - 13:01:12 PST)
  - Re: AMBER: LES question Lishan Yao (Tue Feb 10 2004 - 13:02:18 PST)
    - Re: AMBER: LES question xiaolin cheng (Tue Feb 10 2004 - 16:14:31 PST)
    - Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 05:48:48 PST)
    - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 06:16:01 PST)
    - Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 09:55:27 PST)
    - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 11:20:54 PST)
    - Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 11:43:58 PST)
    - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 11:52:09 PST)
    - Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 12:03:44 PST)
    - Re: AMBER: LES question Lishan Yao (Thu Feb 12 2004 - 05:59:02 PST)
AMBER: Nitrogen vdw type Terry Downing (Tue Feb 10 2004 - 14:56:37 PST)
AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. Joseph E. Maxwell (Tue Feb 10 2004 - 15:36:26 PST)
- Re: AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. David A. Case (Tue Feb 10 2004 - 15:54:45 PST)
AMBER: Box of mixed solvant FyD (Tue Feb 10 2004 - 20:18:42 PST)
- Re: AMBER: Box of mixed solvant Dr. Yong Duan (Tue Feb 10 2004 - 22:09:28 PST)
AMBER: atom type for GBSA aini.UMDNJ.EDU (Wed Feb 11 2004 - 07:13:04 PST)
- Re: AMBER: atom type for GBSA David A. Case (Wed Feb 11 2004 - 09:33:04 PST)
AMBER: GBSA frequency update Sergio E. Wong (Wed Feb 11 2004 - 15:29:10 PST)
- Re: AMBER: GBSA frequency update David A. Case (Wed Feb 11 2004 - 22:09:34 PST)
AMBER: Run calculations for protein in Amber Ma³gorzata Jaroñczyk (Thu Feb 12 2004 - 01:18:20 PST)
- Re: AMBER: Run calculations for protein in Amber Carlos Simmerling (Thu Feb 12 2004 - 05:18:32 PST)
AMBER: ptraj Karin Schleinkofer (Thu Feb 12 2004 - 02:57:47 PST)
- Re: AMBER: ptraj Vlad Cojocaru (Thu Feb 12 2004 - 03:45:55 PST)
- Re: AMBER: ptraj Thomas E. Cheatham, III (Thu Feb 12 2004 - 10:03:36 PST)
Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Ma³gorzata Jaroñczyk (Thu Feb 12 2004 - 06:28:59 PST)
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Vlad Cojocaru (Thu Feb 12 2004 - 06:34:31 PST)
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function David A. Case (Thu Feb 12 2004 - 08:41:16 PST)
AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 07:04:03 PST)
- Re: AMBER: TER in amber Vlad Cojocaru (Thu Feb 12 2004 - 07:56:04 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 08:17:02 PST)
    - Re: AMBER: TER in amber Vlad Cojocaru (Fri Feb 13 2004 - 00:35:41 PST)
- Re: AMBER: TER in amber David A. Case (Thu Feb 12 2004 - 08:56:45 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 10:08:29 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 09:12:45 PST)
AMBER: MM-PBSA: molecular charges and active site water Anselm Horn (Thu Feb 12 2004 - 07:23:05 PST)
- Re: AMBER: MM-PBSA: molecular charges and active site water David A. Case (Thu Feb 12 2004 - 20:06:56 PST)
  - Re: AMBER: MM-PBSA: molecular charges and active site water ML (Thu Feb 12 2004 - 23:30:23 PST)
AMBER: center of mass in CARNAL Herbert Georg (Thu Feb 12 2004 - 08:15:17 PST)
AMBER: neutrality of charge in AMBER 7 Sichun Yang (Thu Feb 12 2004 - 12:51:51 PST)
- Re: AMBER: neutrality of charge in AMBER 7 David A. Case (Sat Feb 14 2004 - 12:10:22 PST)
AMBER: Re: To David Case Ma³gorzata Jaroñczyk (Fri Feb 13 2004 - 03:25:52 PST)
AMBER: minimizating complex-protein with AMBER susan.costantini.unina2.it (Sun Feb 15 2004 - 01:27:00 PST)
- Re: AMBER: minimizating complex-protein with AMBER David A. Case (Sun Feb 15 2004 - 21:14:02 PST)
AMBER: problem with tleap in Amber donna j (Sun Feb 15 2004 - 18:44:25 PST)
- Re: AMBER: problem with tleap in Amber David A. Case (Sun Feb 15 2004 - 21:10:31 PST)
AMBER: MM-PBSA:??Decomposition of receptor energies?? ML (Mon Feb 16 2004 - 01:18:17 PST)
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke (Mon Feb 16 2004 - 02:09:07 PST)
  - AMBER: SIGSEGV John (Mon Feb 16 2004 - 02:43:36 PST)
    - Re: AMBER: SIGSEGV David A. Case (Mon Feb 16 2004 - 08:30:18 PST)
    - AMBER: John (Tue Feb 17 2004 - 02:05:22 PST)
  - Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? ML (Mon Feb 16 2004 - 07:59:04 PST)
    - Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke (Mon Feb 16 2004 - 23:24:25 PST)
AMBER: TIP4P Nikolai Smolin (Mon Feb 16 2004 - 02:58:56 PST)
- Re: AMBER: TIP4P David A. Case (Mon Feb 16 2004 - 08:36:37 PST)
AMBER: IFC COMPILER Obdulia Rabal (Mon Feb 16 2004 - 04:54:00 PST)
- Re: AMBER: IFC COMPILER Robert Duke (Mon Feb 16 2004 - 05:18:03 PST)
AMBER: carnal Julien Pecher (Mon Feb 16 2004 - 05:17:33 PST)
AMBER: DIELC L Jin (Mon Feb 16 2004 - 05:51:35 PST)
AMBER: bad crd file John (Mon Feb 16 2004 - 07:30:26 PST)
AMBER: image in ptraj Lishan Yao (Mon Feb 16 2004 - 08:11:25 PST)
AMBER: TIP4P extended Nikolai Smolin (Mon Feb 16 2004 - 09:06:30 PST)
- Re: AMBER: TIP4P extended Sarah Wittkopp (Mon Feb 16 2004 - 09:21:15 PST)
- Re: AMBER: TIP4P extended David A. Case (Mon Feb 16 2004 - 09:37:32 PST)
AMBER: TIP4P extended Nikolai Smolin (Mon Feb 16 2004 - 09:10:19 PST)
Re: AMBER: bad crd file Bill Ross (Mon Feb 16 2004 - 10:51:57 PST)
AMBER: problem with tleap in Amber donna j (Sun Feb 15 2004 - 19:01:27 PST)
AMBER: saveamberparm warning in leap? opitz.che.udel.edu (Mon Feb 16 2004 - 13:24:45 PST)
- Re: AMBER: saveamberparm warning in leap? David A. Case (Mon Feb 16 2004 - 17:04:17 PST)
AMBER: multiple messages on the amber reflector David A. Case (Mon Feb 16 2004 - 15:33:40 PST)
AMBER: moil-view question S. Frank Yan (Mon Feb 16 2004 - 18:43:57 PST)
- Re: AMBER: moil-view question Carlos Simmerling (Tue Feb 17 2004 - 05:38:59 PST)
- Re: AMBER: moil-view question Teletchéa Stéphane (Tue Feb 17 2004 - 05:49:31 PST)
AMBER: flexible water potential Herbert Georg (Tue Feb 17 2004 - 03:22:12 PST)
AMBER: Close contact warnings L Jin (Tue Feb 17 2004 - 06:29:57 PST)
- Re: AMBER: Close contact warnings David A. Case (Tue Feb 17 2004 - 08:39:22 PST)
  - Re: AMBER: Close contact warnings L Jin (Tue Feb 17 2004 - 10:14:37 PST)
    - Re: AMBER: Close contact warnings David A. Case (Tue Feb 17 2004 - 10:37:06 PST)
    - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 02:14:55 PST)
    - Re: AMBER: Close contact warnings Michael George Lerner (Wed Feb 18 2004 - 05:58:50 PST)
    - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 08:55:55 PST)
    - Re: AMBER: Close contact warnings David A. Case (Wed Feb 18 2004 - 11:34:24 PST)
- Re: AMBER: Close contact warnings Bill Ross (Wed Feb 18 2004 - 10:20:38 PST)
  - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 10:56:49 PST)
    - RE: AMBER: Close contact warnings Yong Duan (Wed Feb 18 2004 - 11:07:36 PST)
    - RE: AMBER: Close contact warnings L Jin (Thu Feb 19 2004 - 07:11:54 PST)
    - Re: AMBER: Close contact warnings David A. Case (Thu Feb 19 2004 - 08:30:15 PST)
    - AMBER: prep files for modified bases Wen Li (Thu Feb 19 2004 - 08:58:01 PST)
    - Re: AMBER: prep files for modified bases David A. Case (Thu Feb 19 2004 - 12:23:41 PST)
- Re: AMBER: Close contact warnings Bill Ross (Wed Feb 18 2004 - 11:29:19 PST)
- RE: AMBER: Close contact warnings Bill Ross (Thu Feb 19 2004 - 11:25:33 PST)
  - AMBER: Build a H+ ion in Leap? Xin Chen (Thu Feb 19 2004 - 11:40:40 PST)
AMBER: RESP charges for protein fragment Tom Turner (Tue Feb 17 2004 - 08:20:15 PST)
AMBER: How to add H+ ion in leap? xinchen (Tue Feb 17 2004 - 11:46:10 PST)
Re: AMBER: center of mass in CARNAL Bill Ross (Tue Feb 17 2004 - 12:25:43 PST)
Re: AMBER: How to add H+ ion in leap? Bill Ross (Tue Feb 17 2004 - 12:29:17 PST)
- Re: AMBER: How to add H+ ion in leap? xinchen (Tue Feb 17 2004 - 12:43:18 PST)
- Re: AMBER: How to add H+ ion in leap? Bill Ross (Tue Feb 17 2004 - 13:09:01 PST)
AMBER: (no subject) ThuZar Lwin (Tue Feb 17 2004 - 12:52:40 PST)
Re: AMBER: (no subject) Bill Ross (Tue Feb 17 2004 - 13:17:39 PST)
- Re: AMBER: (no subject) ThuZar Lwin (Tue Feb 17 2004 - 13:33:30 PST)
AMBER: multiple messages on the amber reflector Amber Administration (Tue Feb 17 2004 - 14:27:52 PST)
AMBER: contributed parameters (modified base - PSU) Shau Grossman (Tue Feb 17 2004 - 18:14:16 PST)
- RE: AMBER: contributed parameters (modified base - PSU) S. Frank Yan (Tue Feb 17 2004 - 18:32:56 PST)
- Re: AMBER: contributed parameters FyD (Wed Feb 18 2004 - 09:12:04 PST)
  - Re: AMBER: contributed parameters Shau Grossman (Thu Feb 19 2004 - 18:55:46 PST)
    - AMBER: ions94.lib file Wen Li (Fri Feb 20 2004 - 09:10:06 PST)
    - Re: AMBER: contributed parameters FyD (Fri Feb 20 2004 - 09:08:34 PST)
    - Re: AMBER: contributed parameters Shau Grossman (Fri Feb 20 2004 - 13:46:04 PST)
    - Re: AMBER: contributed parameters FyD (Fri Feb 20 2004 - 16:05:48 PST)
    - AMBER: R.E.D. Shau Grossman (Mon Feb 23 2004 - 17:20:44 PST)
    - Re: AMBER: R.E.D. FyD (Mon Feb 23 2004 - 17:42:13 PST)
    - Re: AMBER: R.E.D. Shau Grossman (Mon Feb 23 2004 - 18:13:43 PST)
    - Re: AMBER: R.E.D. FyD (Tue Feb 24 2004 - 08:16:57 PST)
AMBER: Segmentation fault in SaveAmberParm xinchen (Tue Feb 17 2004 - 19:31:35 PST)
- Re: AMBER: Segmentation fault in SaveAmberParm Xin Chen (Wed Feb 18 2004 - 11:12:53 PST)
AMBER: histidine and its various forms Stern, Julie (Wed Feb 18 2004 - 06:38:31 PST)
- Re: AMBER: histidine and its various forms David A. Case (Wed Feb 18 2004 - 07:58:44 PST)
- Re: AMBER: histidine and its various forms Peter Oelschlaeger (Wed Feb 18 2004 - 10:10:49 PST)
AMBER: sander + ewald bomb Carsten Detering (Wed Feb 18 2004 - 11:20:51 PST)
- Re: AMBER: sander + ewald bomb Michael Crowley (Wed Feb 18 2004 - 13:13:42 PST)
- Re: AMBER: sander + ewald bomb David A. Case (Wed Feb 18 2004 - 14:00:40 PST)
AMBER: GLYCAM web site Scott Brozell (Wed Feb 18 2004 - 12:00:39 PST)
AMBER: MD simulations with 2 molecules Joey Harriman (Wed Feb 18 2004 - 12:32:47 PST)
- Re: AMBER: MD simulations with 2 molecules David A. Case (Wed Feb 18 2004 - 14:15:04 PST)
AMBER: check unit + saveamberparm Carsten Detering (Wed Feb 18 2004 - 18:21:58 PST)
- re: AMBER: check unit + saveamberparm S. Frank Yan (Fri Feb 20 2004 - 16:17:41 PST)
AMBER: tmd question hj zou (Wed Feb 18 2004 - 18:58:45 PST)
- Re: AMBER: tmd question Carlos Simmerling (Thu Feb 19 2004 - 08:17:51 PST)
AMBER: mm_pbsa question hj zou (Wed Feb 18 2004 - 19:22:00 PST)
AMBER: pmf calculation using gibbs. Myunggi Yi (Wed Feb 18 2004 - 21:22:46 PST)
- Re: AMBER: pmf calculation using gibbs. David A. Case (Wed Feb 18 2004 - 20:45:57 PST)
  - Re: AMBER: pmf calculation using gibbs. Myunggi Yi (Thu Feb 19 2004 - 07:13:30 PST)
    - Re: AMBER: pmf calculation using gibbs. David A. Case (Thu Feb 19 2004 - 08:27:33 PST)
Re: AMBER: compiling software(RESP) on MAC G5 Scott Brozell (Wed Feb 18 2004 - 21:36:06 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 FyD (Thu Feb 19 2004 - 08:27:54 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 James W. Caldwell (Thu Feb 19 2004 - 10:50:28 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 David A. Case (Thu Feb 19 2004 - 12:21:39 PST)
  - AMBER: how to add force field parameters Ioana Cozmuta (Thu Feb 19 2004 - 12:27:02 PST)
  - Re: AMBER: compiling software(RESP) on MAC G5 Lifeng Tian.PantherServer (Thu Feb 19 2004 - 12:41:05 PST)
AMBER: LCPO parameters in gbsa Giulio Rastelli (Thu Feb 19 2004 - 08:53:56 PST)
- Re: AMBER: LCPO parameters in gbsa David A. Case (Mon Feb 23 2004 - 10:51:46 PST)
AMBER: distance-aromatic ring John (Thu Feb 19 2004 - 03:03:56 PST)
AMBER: LES Petr Jeøábek (Thu Feb 19 2004 - 10:10:50 PST)
- Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 12:26:21 PST)
  - Re: AMBER: LES Petr Jeøábek (Thu Feb 19 2004 - 13:08:38 PST)
    - Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 13:11:58 PST)
    - Re: AMBER: LES Viktor Hornak (Thu Feb 19 2004 - 13:30:32 PST)
    - Re: AMBER: LES Petr Jeøábek (Thu Feb 19 2004 - 14:10:00 PST)
    - Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 14:13:07 PST)
Re: AMBER: distance-aromatic ring Bill Ross (Thu Feb 19 2004 - 11:41:32 PST)
Re: AMBER: Build a H+ ion in Leap? Bill Ross (Thu Feb 19 2004 - 12:00:38 PST)
- Re: AMBER: Build a H+ ion in Leap? xinchen (Thu Feb 19 2004 - 12:19:20 PST)
- Re: AMBER: Build a H+ ion in Leap? Bill Ross (Thu Feb 19 2004 - 13:22:08 PST)
Re: AMBER: sander output Dave S Walker (Thu Feb 19 2004 - 15:55:59 PST)
- Re: AMBER: sander output David A. Case (Thu Feb 19 2004 - 21:54:32 PST)
  - Re: AMBER: sander output Dave S Walker (Fri Feb 20 2004 - 13:47:24 PST)
AMBER: The charge given by xleap from amber 5 Ben Cossins (Fri Feb 20 2004 - 04:25:55 PST)
AMBER: LES methodology question Vlad Cojocaru (Fri Feb 20 2004 - 04:12:14 PST)
- Re: AMBER: LES methodology question Carlos Simmerling (Fri Feb 20 2004 - 05:01:06 PST)
AMBER: Defining residues opitz.che.udel.edu (Sat Feb 21 2004 - 20:34:56 PST)
- Re: AMBER: Defining residues David A. Case (Mon Feb 23 2004 - 08:49:58 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 10:04:33 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 11:02:58 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 12:44:44 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 12:14:46 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 13:35:44 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 14:19:48 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 13:47:51 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 14:39:48 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 15:39:46 PST)
AMBER: xleap don't recognize my residue/atom scopio (Sun Feb 22 2004 - 03:18:42 PST)
- Re: AMBER: xleap don't recognize my residue/atom Rhonda Torres (Sun Feb 22 2004 - 14:23:59 PST)
AMBER: Can anybody help me with CHARMM Gabbar Daaku (Sun Feb 22 2004 - 19:13:09 PST)
- Re: AMBER: Can anybody help me with CHARMM Tru Huynh (Wed Feb 25 2004 - 05:36:18 PST)
Re: AMBER: Can anybody help me with CHARMM Piotr Cieplak (Sun Feb 22 2004 - 19:49:21 PST)
AMBER: How to add ACE and NME groups? Ma³gorzata Jaroñczyk (Mon Feb 23 2004 - 01:47:00 PST)
- Re: AMBER: How to add ACE and NME groups? David A. Case (Mon Feb 23 2004 - 08:47:05 PST)
- Re: AMBER: How to add ACE and NME groups? Ben Cossins (Tue Feb 24 2004 - 08:47:43 PST)
AMBER: protein - fractional native contacts uddhavesh bhaskar sonavane (Mon Feb 23 2004 - 03:50:06 PST)
AMBER: pka calculation hj zou (Mon Feb 23 2004 - 05:33:00 PST)
AMBER: Thermostat comparison ? MD Tyka, Biochemistry (Mon Feb 23 2004 - 09:41:56 PST)
AMBER: how to use prep file Fang, Jianwen (Mon Feb 23 2004 - 11:15:19 PST)
- RE: AMBER: how to use prep file Kristina Furse (Mon Feb 23 2004 - 12:14:20 PST)
- Re: AMBER: how to use prep file David A. Case (Mon Feb 23 2004 - 12:19:30 PST)
- RE: AMBER: how to use prep file Bill Ross (Mon Feb 23 2004 - 12:30:37 PST)
AMBER: problem with frcmod file donna j (Mon Feb 23 2004 - 13:47:12 PST)
- Re: AMBER: problem with frcmod file David A. Case (Mon Feb 23 2004 - 14:43:59 PST)
- Re: AMBER: problem with frcmod file donna j (Thu Feb 26 2004 - 10:23:25 PST)
  - Re: AMBER: problem with frcmod file James W. Caldwell (Thu Feb 26 2004 - 10:45:44 PST)
    - Re: AMBER: problem with frcmod file donna j (Sun Feb 29 2004 - 11:43:24 PST)
Re: AMBER: problem with frcmod file Bill Ross (Mon Feb 23 2004 - 14:44:08 PST)
AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap? Ma³gorzata Jaroñczyk (Tue Feb 24 2004 - 06:59:46 PST)
AMBER: carnal Youyi Peng (Tue Feb 24 2004 - 08:36:11 PST)
AMBER: add Na+ L Jin (Tue Feb 24 2004 - 10:23:55 PST)
- RE: AMBER: add Na+ Ross Walker (Tue Feb 24 2004 - 10:42:28 PST)
  - RE: AMBER: add Na+ L Jin (Tue Feb 24 2004 - 11:29:36 PST)
    - Re: AMBER: add Na+ David A. Case (Tue Feb 24 2004 - 11:35:06 PST)
- RE: AMBER: add Na+ Bill Ross (Tue Feb 24 2004 - 11:07:07 PST)
- RE: AMBER: add Na+ Bill Ross (Tue Feb 24 2004 - 11:33:34 PST)
  - RE: AMBER: add Na+ L Jin (Wed Feb 25 2004 - 02:33:02 PST)
- RE: AMBER: add Na+ Bill Ross (Wed Feb 25 2004 - 10:31:43 PST)
AMBER: Star like (branching) molecule opitz.che.udel.edu (Tue Feb 24 2004 - 14:54:45 PST)
- Re: AMBER: Star like (branching) molecule John Bushnell (Tue Feb 24 2004 - 15:33:45 PST)
Re: AMBER: Star like (branching) molecule Bill Ross (Tue Feb 24 2004 - 15:40:13 PST)
- Re: AMBER: Star like (branching) molecule Bill Ross (Tue Feb 24 2004 - 15:51:10 PST)
AMBER: PGA Beale, John (Wed Feb 25 2004 - 05:09:46 PST)
AMBER: NMR restraints-Floating point exception John (Wed Feb 25 2004 - 06:44:52 PST)
- Re: AMBER: NMR restraints-Floating point exception David A. Case (Wed Feb 25 2004 - 08:17:46 PST)
- RE: AMBER: NMR restraints-Floating point exception John (Wed Feb 25 2004 - 10:19:25 PST)
AMBER: pmf calculation using gibbs Myunggi Yi (Wed Feb 25 2004 - 08:47:25 PST)
- Re: AMBER: pmf calculation using gibbs David Smith (Thu Feb 26 2004 - 00:57:02 PST)
AMBER: Errors when running tleap Ann P (Wed Feb 25 2004 - 13:13:53 PST)
- RE: AMBER: Errors when running tleap Ann P (Thu Feb 26 2004 - 11:21:03 PST)
- RE: AMBER: Errors when running tleap Bill Ross (Thu Feb 26 2004 - 11:47:05 PST)
Re: AMBER: Errors when running tleap Bill Ross (Wed Feb 25 2004 - 13:31:54 PST)
AMBER: averaged structure with unknown elements Youyi Peng (Wed Feb 25 2004 - 13:32:54 PST)
- Re: AMBER: averaged structure with unknown elements David A. Case (Wed Feb 25 2004 - 14:15:25 PST)
Re: AMBER: averaged structure with unknown elements Bill Ross (Wed Feb 25 2004 - 13:49:40 PST)
AMBER: mmpbsa qustion hj zou (Wed Feb 25 2004 - 17:23:37 PST)
- Re: AMBER: mmpbsa qustion Holger Gohlke (Wed Feb 25 2004 - 23:29:06 PST)
  - Re: AMBER: mmpbsa qustion James W. Caldwell (Thu Feb 26 2004 - 10:06:13 PST)
AMBER: size.h error Emmanuel Giudice (Thu Feb 26 2004 - 13:15:20 PST)
- Re: AMBER: size.h error Surjit Dixit (Thu Feb 26 2004 - 13:53:20 PST)
- Re: AMBER: size.h error David A. Case (Thu Feb 26 2004 - 14:48:29 PST)
AMBER: sander + vlimit exceed... Carsten Detering (Thu Feb 26 2004 - 15:16:31 PST)
AMBER: pka calculation hj zou (Fri Feb 27 2004 - 18:42:34 PST)
- Re: AMBER: pka calculation Florian Barth (Sat Feb 28 2004 - 07:46:04 PST)
AMBER: PB in mm-pbsa Sue Heavner (Sat Feb 28 2004 - 08:30:05 PST)
- Re: AMBER: PB in mm-pbsa Holger Gohlke (Sun Feb 29 2004 - 06:02:29 PST)
AMBER: Problems with xleap Javier Perez Miron (Thu Feb 26 2004 - 17:18:11 PST)

Amber Archive Feb 2004 By Thread