AMBER Archive (2004) - May 2004 By Author

Starting: Sat May 01 2004 - 07:26:57 CDT
Ending: Mon May 31 2004 - 23:42:39 CDT

• A. Hungie
  • AMBER: Amber 8 compilation (Wed May 26 2004 - 11:23:07 CDT)
  • AMBER: Installation AMber 8: "cannot find -lU77" (Tue May 25 2004 - 08:21:09 CDT)
• Adrian E. Roitberg
  • Re: AMBER: amber 8 under windows XP (Thu May 27 2004 - 08:09:51 CDT)
  • AMBER: amber 8 under windows XP (Wed May 26 2004 - 13:50:02 CDT)
• aini_at_UMDNJ.EDU
  • AMBER: question about mm-pbsa (Mon May 10 2004 - 19:10:05 CDT)
• Amber admin
  • AMBER: problems with mpich (Fri May 28 2004 - 09:55:25 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 12:25:03 CDT)
  • Re: AMBER: antechamber (Wed May 05 2004 - 15:51:22 CDT)
• Amber Administration
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 16:15:14 CDT)
• Andreas Svrcek-Seiler
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:21:40 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 07:13:56 CDT)
  • Re: AMBER: any program or tool (Mon May 03 2004 - 07:11:50 CDT)
• Annette Höglund
  • AMBER: FEP error/early termination - why? (Mon May 31 2004 - 08:23:27 CDT)
• anshul_at_imtech.res.in
  • AMBER: instalation of RES (Thu May 20 2004 - 13:22:08 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Sun May 16 2004 - 15:01:55 CDT)
  • AMBER: antechamber (Sat May 15 2004 - 11:43:48 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Wed May 12 2004 - 10:07:49 CDT)
  • AMBER: Charges and atom type (Sat May 08 2004 - 16:06:25 CDT)
  • Re: AMBER: xleap don't recognize formaldehyde? (Sat May 08 2004 - 14:44:33 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 18:14:53 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 18:01:33 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 17:51:32 CDT)
  • AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 16:50:35 CDT)
  • AMBER: Implicit solvents (Wed May 05 2004 - 15:10:20 CDT)
  • AMBER: H Bonds (Wed May 05 2004 - 15:07:01 CDT)
  • AMBER: methane box (Wed May 05 2004 - 13:57:16 CDT)
• atobak_at_eden.rutgers.edu
  • AMBER: ligand minimization (Sat May 08 2004 - 16:13:21 CDT)
• Beale, John
  • AMBER: dihedral driver (Wed May 12 2004 - 08:58:35 CDT)
• Ben Cossins
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Thu May 13 2004 - 04:22:21 CDT)
• Bill Ross
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 17:16:56 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:28:27 CDT)
  • Re: Re[4]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 16:15:01 CDT)
  • Re: Re[2]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 13:34:08 CDT)
  • Re: AMBER: rmsd over residues using ptraj (Tue May 18 2004 - 19:57:54 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Tue May 18 2004 - 14:08:13 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 19:10:36 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:42:25 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 17:47:24 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 17:05:55 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 13:16:11 CDT)
  • Re: AMBER: H Bonds (Wed May 05 2004 - 16:18:22 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:35:49 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:24:41 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 11:44:16 CDT)
  • Re: AMBER: ptraj: radius of gyration (Sun May 02 2004 - 15:12:23 CDT)
• by way of riccardo nifosi
  • AMBER: SHAKE in thermodynamic integration (Thu May 20 2004 - 05:38:21 CDT)
• bybaker_at_itsa.ucsf.edu
  • Re: AMBER: Sander went through (Sat May 29 2004 - 06:51:26 CDT)
  • AMBER: Sander went through (Fri May 28 2004 - 19:19:02 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 17:05:22 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:22:00 CDT)
  • Re: AMBER: Cannot read in sander (Thu May 27 2004 - 15:56:12 CDT)
  • Re: AMBER: Cannot read in sander (Wed May 26 2004 - 19:47:30 CDT)
  • AMBER: Cannot read in sander (Tue May 25 2004 - 17:51:48 CDT)
• Carlos Simmerling
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 13:21:41 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:56:24 CDT)
  • Re: AMBER: about amber8, replica exchange (Fri May 28 2004 - 22:55:34 CDT)
  • Re: AMBER: Amber 7 (sander) use of PME (Thu May 27 2004 - 14:47:50 CDT)
  • Re: AMBER: Reproducing the energy during restart in MD! (Wed May 19 2004 - 08:41:17 CDT)
  • Re: AMBER: Removal of rotation: Flying ice cube (Tue May 18 2004 - 19:39:59 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 12:08:56 CDT)
  • Re: AMBER: tmd questions (Thu May 13 2004 - 06:41:31 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 08:24:02 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 06:47:48 CDT)
• carlsonh_at_umich.edu
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 13:40:03 CDT)
• Carsten Detering
  • AMBER: address error (Wed May 19 2004 - 12:09:12 CDT)
  • AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 15:37:42 CDT)
  • Re: AMBER: dummy atom other than H (Wed May 12 2004 - 16:18:23 CDT)
  • AMBER: dummy atom other than H (Tue May 11 2004 - 20:12:22 CDT)
• Chen Yongzhi
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 13:23:48 CDT)
  • AMBER: A problem for compiling amber8 parallel version (Tue May 25 2004 - 15:58:37 CDT)
• Chutintorn Punwong
  • Re: AMBER: segmentation fault when running parmchk (Fri May 28 2004 - 15:08:56 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:37:09 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:01:16 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Mon May 24 2004 - 17:34:11 CDT)
• Craig TOEPFER
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 14:19:01 CDT)
  • AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 13:21:53 CDT)
• Dalmaris, John
  • AMBER: MMPBSA problem (Sun May 30 2004 - 08:22:55 CDT)
• darden
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Wed May 19 2004 - 16:05:59 CDT)
• Dave S Walker
  • AMBER: ntwprt feature in AMBER7 (Thu May 06 2004 - 21:26:51 CDT)
• David A. Case
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:33:08 CDT)
  • Re: AMBER: program compatibility (Mon May 31 2004 - 00:05:15 CDT)
  • Re: AMBER: question about NMODE for RNA (Sun May 30 2004 - 18:14:33 CDT)
  • Re: AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file (Fri May 28 2004 - 16:34:45 CDT)
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 13:43:23 CDT)
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 11:52:56 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 18:47:49 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 18:15:37 CDT)
  • Re: AMBER: types of water atom (Thu May 27 2004 - 15:34:59 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:24:27 CDT)
  • Re: AMBER: xleap solvatebox problem (Thu May 27 2004 - 10:42:48 CDT)
  • Re: AMBER: amber 8 under windows XP (Thu May 27 2004 - 10:34:50 CDT)
  • Re: AMBER: Cannot read in sander (Thu May 27 2004 - 10:11:03 CDT)
  • Re: AMBER: amber 8 under windows XP (Wed May 26 2004 - 15:07:05 CDT)
  • Re: AMBER: A problem for compiling amber8 parallel version (Wed May 26 2004 - 12:08:43 CDT)
  • Re: AMBER: Scaling nb between groups (Tue May 25 2004 - 15:52:30 CDT)
  • Re: AMBER: protein is out of the water box (Wed May 26 2004 - 11:17:00 CDT)
  • Re: AMBER: Cannot read in sander (Wed May 26 2004 - 11:14:52 CDT)
  • Re: AMBER: IOUTFM and binary/unformatted files error (Tue May 25 2004 - 10:01:28 CDT)
  • Re: AMBER: mm_pbsa energy decomposition error (Tue May 25 2004 - 10:20:13 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Mon May 24 2004 - 23:41:14 CDT)
  • Re: AMBER: Free energies using Sander in Amber8 (Mon May 24 2004 - 23:36:22 CDT)
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 10:37:29 CDT)
  • Re: AMBER: NHE problem (Sun May 23 2004 - 11:14:34 CDT)
  • Re: AMBER: IGR1/grnam1 problem (Sat May 22 2004 - 23:03:16 CDT)
  • Re: AMBER: NHE problem (Sat May 22 2004 - 18:55:52 CDT)
  • Re: AMBER: Problem compiling amber7 (Fri May 21 2004 - 10:23:09 CDT)
  • Re: AMBER: pbsa calculation on part of the molecule & nmode analysis (Thu May 20 2004 - 20:40:10 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 20:33:14 CDT)
  • Re: AMBER: SHAKE in thermodynamic integration (Thu May 20 2004 - 13:01:17 CDT)
  • Re: AMBER: DEBUG and GB (Thu May 20 2004 - 13:34:38 CDT)
  • Re: AMBER: instalation of RES (Thu May 20 2004 - 12:15:35 CDT)
  • Re: AMBER: (Thu May 20 2004 - 12:14:13 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 10:22:26 CDT)
  • Re: AMBER: Does this warning matter? (about improper torsion parameters) (Wed May 19 2004 - 10:00:59 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 17:47:26 CDT)
  • Re: AMBER: NTT=4 (Tue May 18 2004 - 09:57:19 CDT)
  • Re: AMBER: Clean in RESP (Tue May 18 2004 - 09:55:42 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:21:15 CDT)
  • Re: AMBER: sander_classic for cap simulations? (Mon May 17 2004 - 15:18:41 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Mon May 17 2004 - 14:36:41 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Mon May 17 2004 - 14:31:38 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 14:27:30 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Sat May 15 2004 - 11:14:06 CDT)
  • Re: AMBER: install RESP (Sat May 15 2004 - 11:03:57 CDT)
  • Re: AMBER: antechamber (Sat May 15 2004 - 11:02:30 CDT)
  • Re: AMBER: solvents reference. (Fri May 14 2004 - 15:16:06 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Fri May 14 2004 - 14:20:24 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 13:41:18 CDT)
  • Re: AMBER: dummy atom other than H (Wed May 12 2004 - 14:30:26 CDT)
  • Re: AMBER: shake option in sander (Wed May 12 2004 - 14:11:53 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Wed May 12 2004 - 14:09:24 CDT)
  • Re: AMBER: ptraj and LES (Wed May 12 2004 - 10:19:00 CDT)
  • Re: AMBER: what does EAMBER stand for? (Tue May 11 2004 - 12:30:56 CDT)
  • Re: AMBER: some bugfixes (Mon May 10 2004 - 18:10:08 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Mon May 10 2004 - 10:46:06 CDT)
  • Re: AMBER: Solvent accessible surface area(LCPO) computation (Fri May 07 2004 - 10:23:33 CDT)
  • Re: AMBER: solvent cap and eedmeth (Fri May 07 2004 - 10:20:18 CDT)
  • Re: AMBER: Opteron PMEMD (Thu May 06 2004 - 17:09:47 CDT)
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 14:27:10 CDT)
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 13:42:37 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Thu May 06 2004 - 10:29:30 CDT)
  • Re: AMBER: Sander klambda question (Wed May 05 2004 - 18:43:44 CDT)
  • Re: AMBER: How to choose force constant? (Wed May 05 2004 - 17:00:14 CDT)
  • Re: AMBER: H Bonds (Wed May 05 2004 - 11:20:26 CDT)
  • Re: AMBER: Implicit solvents (Wed May 05 2004 - 10:54:56 CDT)
  • Re: AMBER: Normal Mode Analysis possibility (Tue May 04 2004 - 13:25:27 CDT)
  • Re: AMBER: separate the longitudinal and transverse vibrations frequencies (Tue May 04 2004 - 13:15:38 CDT)
  • Re: AMBER: PMF correction factor (Tue May 04 2004 - 13:01:18 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 10:10:36 CDT)
  • AMBER: some bugfixes (Mon May 03 2004 - 13:10:47 CDT)
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 12:14:19 CDT)
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 10:50:44 CDT)
  • Re: Re: AMBER: xleap problem (Mon May 03 2004 - 10:45:34 CDT)
  • Re: AMBER: xleap problem (Sun May 02 2004 - 16:07:20 CDT)
• david.evans_at_ulsop.ac.uk
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:32:18 CDT)
• Do Anh Tuan
  • AMBER: Program error in testing of Amber8 (Sat May 15 2004 - 23:16:44 CDT)
• Dr. Yong Duan
  • Re: AMBER: energy conservation with GB !! (Sun May 16 2004 - 01:58:25 CDT)
  • Re: AMBER: why delete water molecule (Tue May 04 2004 - 09:40:57 CDT)
• Fang, Jianwen
  • AMBER: mm_pbsa energy decomposition error (Tue May 25 2004 - 09:40:32 CDT)
  • AMBER: why EGB = nan (Mon May 17 2004 - 09:54:44 CDT)
  • AMBER: questions on mm_pbsa (Fri May 14 2004 - 13:49:54 CDT)
  • AMBER: ions in mm_pbsa (Thu May 06 2004 - 10:30:12 CDT)
• Feng, Hanqiao (NIH/NCI)
  • AMBER: protein is out of the water box (Tue May 25 2004 - 17:35:01 CDT)
• Fernandez-Carmona Juan
  • Re: AMBER: reference with ptraj (Fri May 07 2004 - 01:27:53 CDT)
• FyD
  • Re: AMBER: Use of RED (Fri May 28 2004 - 15:20:42 CDT)
  • Re: AMBER: pdb in RED (Thu May 27 2004 - 14:16:59 CDT)
  • Re: AMBER: Bug in babel conversion (Tue May 25 2004 - 13:14:55 CDT)
  • Re: AMBER: parametrizacion partial charges (Mon May 17 2004 - 10:37:02 CDT)
  • RE: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 13:01:31 CDT)
  • Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 11:42:31 CDT)
  • Re: AMBER: choosing 3 atoms for reorientaion in R.E.D (Thu May 06 2004 - 17:00:44 CDT)
  • Re: AMBER: reorientation in R.E.D (Wed May 05 2004 - 12:55:51 CDT)
  • Re: AMBER: methane box (Wed May 05 2004 - 10:36:08 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:48:43 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:16:00 CDT)
  • Re: AMBER: resp demo files (Mon May 03 2004 - 16:40:15 CDT)
• Gary Waters
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 15:08:49 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 12:36:16 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:55:14 CDT)
  • AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:00:33 CDT)
  • AMBER: Opteron PMEMD (Thu May 06 2004 - 13:29:56 CDT)
• Guanglei Cui
  • Re: AMBER: about amber8, replica exchange (Fri May 28 2004 - 23:04:33 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:28:39 CDT)
  • Re: AMBER: parallel installation problem (Wed May 19 2004 - 20:54:21 CDT)
  • Re: AMBER: ptraj and LES (Wed May 12 2004 - 14:34:31 CDT)
  • AMBER: ptraj and LES (Tue May 11 2004 - 16:00:12 CDT)
  • AMBER: antechamber (Tue May 04 2004 - 21:49:28 CDT)
• Gustavo Pierdominici Sottile
  • AMBER: Use of RED (Fri May 28 2004 - 13:44:26 CDT)
  • Re: AMBER: types of water atom (Fri May 28 2004 - 13:25:45 CDT)
  • Re: AMBER: types of water atom (Thu May 27 2004 - 14:28:27 CDT)
  • AMBER: pdb in RED (Thu May 27 2004 - 12:29:44 CDT)
  • AMBER: types of water atom (Wed May 26 2004 - 12:06:16 CDT)
  • AMBER: Clean in RESP (Tue May 18 2004 - 06:46:38 CDT)
  • AMBER: (Mon May 17 2004 - 13:38:53 CDT)
  • AMBER: parametrizacion partial charges (Mon May 17 2004 - 08:45:58 CDT)
  • AMBER: installing RESP (Sat May 15 2004 - 06:52:59 CDT)
  • AMBER: install RESP (Sat May 15 2004 - 06:54:41 CDT)
• Harvey, David Richard
  • AMBER: PMF correction factor (Tue May 04 2004 - 08:35:13 CDT)
• Helios Chen
  • AMBER: single amino acid energy (Tue May 18 2004 - 03:15:02 CDT)
  • AMBER: why delete water molecule (Mon May 03 2004 - 23:18:49 CDT)
  • AMBER: any program or tool (Mon May 03 2004 - 05:16:15 CDT)
• Herbert Georg
  • AMBER: solvents reference. (Fri May 14 2004 - 14:56:38 CDT)
• hj zou
  • AMBER: program compatibility (Sun May 30 2004 - 21:07:39 CDT)
  • AMBER: tmd questions (Wed May 12 2004 - 21:07:36 CDT)
  • Re: AMBER: xleap problem (Tue May 04 2004 - 21:44:43 CDT)
  • Re: Re: AMBER: xleap problem (Mon May 03 2004 - 03:02:34 CDT)
  • AMBER: xleap problem (Sun May 02 2004 - 08:49:40 CDT)
• Holger Gohlke
  • Re: AMBER: ptraj bug? (Wed May 19 2004 - 10:31:12 CDT)
  • Re: AMBER: single amino acid energy (Tue May 18 2004 - 10:23:26 CDT)
  • Re: AMBER: questions on mm_pbsa (Tue May 18 2004 - 10:18:24 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Mon May 17 2004 - 13:05:57 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Wed May 12 2004 - 01:40:52 CDT)
  • Re: AMBER: ptraj read in matrix (Tue May 11 2004 - 09:45:11 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Fri May 07 2004 - 07:48:51 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 11:32:23 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 05:28:57 CDT)
  • Re: AMBER: problem with MM/PBSA (Wed May 05 2004 - 05:14:47 CDT)
• Holly Freedman
  • Re: AMBER: ptraj (Wed May 26 2004 - 12:30:07 CDT)
  • Re: AMBER: ptraj (Tue May 25 2004 - 19:45:24 CDT)
  • AMBER: ptraj (Tue May 25 2004 - 11:16:42 CDT)
  • AMBER: average structure from traj (Tue May 18 2004 - 16:30:07 CDT)
• Ian Withers
  • AMBER: ptraj bug? (Wed May 19 2004 - 09:33:38 CDT)
• Ilyas Yildirim
  • AMBER: Surface E&S Potential Mapping (Tue May 25 2004 - 16:14:45 CDT)
  • AMBER: Bug in babel conversion (while following the RED manual in pp.15) (Tue May 25 2004 - 13:00:39 CDT)
  • AMBER: Nonplanar ring systems in nucleic acid (Wed May 19 2004 - 15:14:14 CDT)
• Itziar Maestre Asenjo
  • AMBER: problem with MM/PBSA (Tue May 04 2004 - 11:38:32 CDT)
• J. Zhang, Dr
  • Re: Re: AMBER: about amber8, replica exchange (Sun May 30 2004 - 19:09:24 CDT)
  • AMBER: about amber8, replica exchange (Fri May 28 2004 - 22:45:49 CDT)
  • Re: Re: AMBER: Does this warning matter? (about improper torsion parameters) (Wed May 19 2004 - 20:57:35 CDT)
  • AMBER: Does this warning matter? (about improper torsion parameters) (Tue May 18 2004 - 22:04:32 CDT)
• James W. Caldwell
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 22:02:01 CDT)
• Jeffrey Dyason
  • AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 03:07:12 CDT)
• Jiri Sponer
  • Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:42:27 CDT)
  • Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:09:46 CDT)
  • Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 07:41:12 CDT)
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Thu May 20 2004 - 07:42:16 CDT)
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Thu May 20 2004 - 06:46:41 CDT)
• Jiten
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Mon May 24 2004 - 22:54:40 CDT)
  • AMBER: Free energies using Sander in Amber8 (Mon May 24 2004 - 21:52:52 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 19:49:42 CDT)
  • AMBER: PF6- force field parameters (Thu May 20 2004 - 19:32:29 CDT)
  • AMBER: Amber8 on Tru64 UNIX on Alpha systems (Wed May 19 2004 - 20:28:50 CDT)
  • AMBER: Atom type with/without POL (Thu May 13 2004 - 09:01:38 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 05:58:20 CDT)
• Joachim Reichelt
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:27:59 CDT)
  • Re: AMBER: NTT=4 (Tue May 18 2004 - 12:01:50 CDT)
  • AMBER: NTT=4 (Tue May 18 2004 - 09:30:33 CDT)
• John
  • AMBER: torsion angles (Fri May 28 2004 - 18:02:04 CDT)
  • AMBER: time-averaged restraints (Fri May 14 2004 - 12:04:49 CDT)
  • AMBER: reference with ptraj (Thu May 06 2004 - 14:50:48 CDT)
• Jones, Garth A
  • AMBER: DEBUG and GB (Tue May 18 2004 - 07:02:32 CDT)
• Junmei Wang
  • Re: AMBER: problem in antechamber (Wed May 19 2004 - 17:21:43 CDT)
  • Re: AMBER: Problem : antechamber produces no output (Wed May 12 2004 - 09:40:00 CDT)
  • AMBER: Possible amber8 antechamber PDB parsing bug (Thu May 06 2004 - 12:09:30 CDT)
  • Re: AMBER: some bugfixes (Tue May 04 2004 - 14:23:55 CDT)
• Jyh-Shyong Ho
  • Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64 (Tue May 25 2004 - 19:07:34 CDT)
• Kamp, Marc vander
  • AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file (Thu May 27 2004 - 08:01:13 CDT)
• Kazuo Koyano
  • Re: AMBER: mm_pbsa examples; delphi in mm_pbsa (Fri May 14 2004 - 04:35:36 CDT)
• Knut Langsetmo
  • Re: AMBER: amber7, namelist, xlf and osx (Tue May 25 2004 - 08:17:26 CDT)
  • AMBER: amber7, namelist, xlf and osx (Wed May 19 2004 - 17:47:26 CDT)
• koby levy
  • AMBER: Removal of rotation: Flying ice cube (Tue May 18 2004 - 19:23:54 CDT)
• Kristy Mardis
  • AMBER: resp demo files (Mon May 03 2004 - 14:29:45 CDT)
• Linda Prengaman
  • AMBER: Amber 7 (sander) use of PME (Thu May 27 2004 - 14:42:13 CDT)
  • AMBER: Sander klambda question (Wed May 05 2004 - 17:14:22 CDT)
• Lishan Yao
  • AMBER: Ammonia (Thu May 20 2004 - 16:11:43 CDT)
  • AMBER: shake option in sander (Wed May 12 2004 - 08:32:48 CDT)
• M. L. Dodson
  • Re: AMBER: thermodynamic integration of ring opening (Tue May 18 2004 - 07:33:28 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:46:29 CDT)
• Majid moghaddam
  • AMBER: PCA prep file (Tue May 18 2004 - 03:19:26 CDT)
• Marc Perea
  • AMBER: Problem : antechamber produces no output (Tue May 11 2004 - 05:19:52 CDT)
• Marcin Krol
  • AMBER: Scaling nb between groups (Tue May 25 2004 - 10:34:00 CDT)
  • AMBER: IGR1/grnam1 problem (Tue May 18 2004 - 12:40:58 CDT)
  • AMBER: ptraj read in matrix (Mon May 10 2004 - 06:57:25 CDT)
  • AMBER: ptraj analyze matrix entropy (Fri May 07 2004 - 03:01:23 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Thu May 06 2004 - 08:48:02 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 10:07:05 CDT)
  • AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 04:19:32 CDT)
• Mark Williamson
  • AMBER: Possible amber8 antechamber PDB parsing bug (Thu May 06 2004 - 10:16:19 CDT)
• Martin Fabani
  • AMBER: MD with NTR + NMROPT (Mon May 10 2004 - 03:56:28 CDT)
• Martin Mucha
  • AMBER: IOUTFM and binary/unformatted files error (Tue May 25 2004 - 02:18:44 CDT)
• Mengjuei Hsieh
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 14:12:39 CDT)
  • Re: AMBER: NHE problem (Sat May 22 2004 - 19:30:07 CDT)
  • Re: AMBER: amber7, namelist, xlf and osx (Wed May 19 2004 - 19:56:23 CDT)
• Michele Porro
  • AMBER: simulated anealing ...vlimit exceed (Tue May 11 2004 - 02:24:56 CDT)
• Miguel
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 04:54:55 CDT)
  • AMBER: Problem compiling amber7 (Fri May 21 2004 - 04:15:10 CDT)
• Miguel de Federico
  • Re: AMBER: Gibbs and solvent caps (Mon May 03 2004 - 05:28:47 CDT)
• Mikyung Seo
  • AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Tue May 11 2004 - 17:51:01 CDT)
  • AMBER: choosing 3 atoms for reorientaion in R.E.D (Thu May 06 2004 - 16:38:19 CDT)
  • AMBER: reorientation in R.E.D (Wed May 05 2004 - 11:38:01 CDT)
  • AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 12:51:01 CDT)
• Ming Lei
  • AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 (Tue May 25 2004 - 10:27:49 CDT)
• myang
  • AMBER: fit a 3D line to points (Thu May 27 2004 - 16:11:08 CDT)
  • AMBER: Normal Mode Analysis possibility (Tue May 04 2004 - 10:52:05 CDT)
• Narang Manpreet Kaur
  • Re: AMBER: Simulated annealing ...vlimit problem (Tue May 18 2004 - 09:09:31 CDT)
• Obdulia Rabal
  • AMBER: CG maxitn exceeded (Tue May 18 2004 - 11:29:53 CDT)
  • AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 04:32:29 CDT)
• Oliver Hucke
  • Re: AMBER: parallel installation problem (Mon May 24 2004 - 18:57:01 CDT)
  • AMBER: parallel installation problem (Sat May 22 2004 - 19:40:17 CDT)
  • AMBER: parallel installation problem (Wed May 19 2004 - 17:17:08 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 16:07:45 CDT)
  • AMBER: sander_classic for cap simulations? (Thu May 13 2004 - 17:43:36 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Thu May 13 2004 - 11:14:08 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 15:42:50 CDT)
  • AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 14:08:18 CDT)
  • AMBER: solvent cap and eedmeth (Thu May 06 2004 - 18:31:42 CDT)
  • AMBER: cap waters always flexible? (Thu May 06 2004 - 15:41:19 CDT)
  • Re: AMBER: antechamber gives GDP 0 charge (Wed May 05 2004 - 15:46:06 CDT)
  • Re: AMBER: some bugfixes (Tue May 04 2004 - 13:12:53 CDT)
  • Re: AMBER: why delete water molecule (Tue May 04 2004 - 11:23:01 CDT)
  • Re: AMBER: xleap problem (Sun May 02 2004 - 17:53:42 CDT)
• opitz_at_che.udel.edu
  • AMBER: Carnal question (Mon May 10 2004 - 10:08:18 CDT)
• Osman Gani
  • AMBER: FAD cofactor. (Fri May 14 2004 - 04:34:28 CDT)
  • AMBER: Ligand from CCDC. (Thu May 06 2004 - 10:38:16 CDT)
• Peter Gannett
  • AMBER: Re: CCL:Helical parameters extraction from trajectory (Fri May 28 2004 - 06:47:08 CDT)
• Piotr Cieplak
  • Re: AMBER: amber 8 under windows XP (Wed May 26 2004 - 17:08:38 CDT)
  • Re: AMBER: types of water atom (Wed May 26 2004 - 12:28:17 CDT)
  • Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 13:57:20 CDT)
• Pradipta Bandyopadhyay
  • AMBER: Software to visualize normal modes! (Mon May 31 2004 - 23:42:39 CDT)
  • AMBER: Low frequency in quasi-harmonic analysis!! (Sun May 30 2004 - 04:23:50 CDT)
  • AMBER: Reproducing the energy during restart in MD! (Wed May 19 2004 - 01:33:27 CDT)
  • AMBER: energy conservation with GB !! (Sun May 16 2004 - 01:27:01 CDT)
• Qiang Lu
  • Re[4]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 14:19:33 CDT)
  • Re[2]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 12:19:38 CDT)
  • AMBER: rmsd over residues using ptraj (Tue May 18 2004 - 19:41:16 CDT)
  • AMBER: A parm file suit for half beta and half alpha structure (Mon May 10 2004 - 13:51:57 CDT)
  • AMBER: hbond in ptraj (Fri May 07 2004 - 13:43:33 CDT)
• Raik Grünberg
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Mon May 17 2004 - 10:38:17 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Fri May 14 2004 - 05:35:13 CDT)
  • AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 12:57:06 CDT)
  • AMBER: antechamber gives GDP 0 charge (Wed May 05 2004 - 15:17:53 CDT)
• Ray Luo
  • Re: AMBER: pbsa calculation on part of the molecule (Wed May 19 2004 - 15:31:50 CDT)
  • Re: AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 19:54:21 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Mon May 17 2004 - 18:07:17 CDT)
  • Re: AMBER: PB bomb in pb_saarc (Mon May 17 2004 - 17:58:21 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Mon May 17 2004 - 16:43:55 CDT)
  • Re: AMBER: CG maxitn exceeded (Mon May 17 2004 - 14:10:29 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 01:21:06 CDT)
• Rhonda Torres
  • Re: AMBER: Sander went through (Fri May 28 2004 - 19:49:44 CDT)
• Robert Duke
  • Re: AMBER: Opteron PMEMD (Thu May 06 2004 - 15:31:46 CDT)
• Ross Walker
  • RE: AMBER: Cannot read in sander (Thu May 27 2004 - 17:36:10 CDT)
  • RE: AMBER: Cannot read in sander (Wed May 26 2004 - 20:08:48 CDT)
  • RE: AMBER: amber 8 under windows XP (Wed May 26 2004 - 14:03:54 CDT)
  • RE: AMBER: ptraj (Tue May 25 2004 - 12:35:39 CDT)
• Ryan Ye
  • Re: AMBER: NHE problem (Sun May 23 2004 - 10:19:56 CDT)
  • AMBER: NHE problem (Sat May 22 2004 - 00:36:44 CDT)
• S. Frank Yan
  • RE: AMBER: pbsa calculation on part of the molecule & nmode analysis (Thu May 20 2004 - 20:06:11 CDT)
  • AMBER: pbsa calculation on part of the molecule (Thu May 20 2004 - 15:25:46 CDT)
  • RE: AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 18:14:36 CDT)
  • AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 15:41:41 CDT)
  • FW: AMBER: ions in mm_pbsa (Thu May 06 2004 - 12:23:55 CDT)
• Sanjeev B.S.
  • Re: AMBER: H Bonds (Fri May 07 2004 - 03:38:24 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 00:09:06 CDT)
• Sarah Wittkopp
  • AMBER: Treating atom type LP the same as EP (Mon May 17 2004 - 14:16:20 CDT)
• scopio
  • Re: AMBER: ptraj (Tue May 25 2004 - 18:49:47 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:15:28 CDT)
  • AMBER: Converting ORAC's topology file to AMBER's prepi file (Fri May 14 2004 - 07:30:32 CDT)
  • AMBER: what does EAMBER stand for? (Mon May 10 2004 - 20:08:35 CDT)
  • Re: AMBER: HIS protonation (Mon May 10 2004 - 06:00:19 CDT)
  • AMBER: what is its file format ? (Sat May 08 2004 - 09:13:21 CDT)
  • Re: AMBER: xleap problem (Mon May 03 2004 - 03:51:03 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sun May 02 2004 - 23:18:31 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sun May 02 2004 - 19:15:58 CDT)
  • AMBER: problem for compiling amber7 by ifc8 (Sat May 01 2004 - 07:26:57 CDT)
• Scott Brozell
  • Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 (Tue May 25 2004 - 14:24:23 CDT)
  • Re: AMBER: Program error in testing of Amber8 (Sun May 16 2004 - 18:17:44 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 14:41:15 CDT)
  • Re: AMBER: what does EAMBER stand for? (Tue May 11 2004 - 12:45:09 CDT)
  • Re: AMBER: antechamber (Wed May 05 2004 - 16:30:17 CDT)
  • Re: AMBER: ptraj: radius of gyration (Sun May 02 2004 - 03:09:12 CDT)
• sebnem
  • AMBER: nmode analysis (Sun May 02 2004 - 19:52:12 CDT)
• sebnem_at_mercury.chem.pitt.edu
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 11:31:18 CDT)
• Seonah Kim
  • AMBER: Install Amber8 under cygwin (Mon May 31 2004 - 20:35:16 CDT)
• Sichun Yang
  • AMBER: ptraj: radius of gyration (Sat May 01 2004 - 21:50:37 CDT)
• Stefano.Pieraccini_at_unimi.it
  • AMBER: gaussian03 output in antechamber (Wed May 12 2004 - 03:46:17 CDT)
  • AMBER: gaussian03 output in antechamber (Tue May 11 2004 - 04:27:46 CDT)
  • AMBER: HIS protonation (Mon May 10 2004 - 04:50:40 CDT)
• Sunil_Koovakkat_at_berlex.com
  • AMBER: Solvent accessible surface area(LCPO) computation (Wed May 05 2004 - 16:51:59 CDT)
• Suwipa saen-oon
  • AMBER: problem in antechamber (Wed May 19 2004 - 03:27:24 CDT)
• Sébastien Osborne
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 13:12:54 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:51:15 CDT)
  • Re: AMBER: some bugfixes (Mon May 03 2004 - 13:14:33 CDT)
  • AMBER: Gibbs and solvent caps (Sat May 01 2004 - 13:59:07 CDT)
• Thomas E. Cheatham, III
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 15:17:33 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 09:24:17 CDT)
  • Re: AMBER: hbond in ptraj (Fri May 07 2004 - 14:15:15 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 17:12:18 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 15:11:58 CDT)
  • Re: AMBER: ions in mm_pbsa (Thu May 06 2004 - 14:07:42 CDT)
• Thomas Steinbrecher
  • AMBER: Decomposition in MMPBSA (Thu May 13 2004 - 19:15:03 CDT)
  • Re: AMBER: question about mm-pbsa (Mon May 10 2004 - 20:10:09 CDT)
• Tomas Kubar
  • AMBER: xleap solvatebox problem (Thu May 27 2004 - 07:33:44 CDT)
• tomjas_at_poczta.onet.pl
  • AMBER: How to choose force constant? (Tue May 04 2004 - 08:48:44 CDT)
• Tru Huynh
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Tue May 25 2004 - 09:31:34 CDT)
  • AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 02:45:39 CDT)
• Ty Curtis
  • RE: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 11:23:50 CDT)
• Venkata S Koppuravuri
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 12:00:44 CDT)
  • AMBER: Simulated annealing ...vlimit problem (Fri May 14 2004 - 09:22:44 CDT)
• Viktor Hornak
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 14:00:15 CDT)
  • Re: AMBER: Amber 8 compilation (Wed May 26 2004 - 12:08:08 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:20:40 CDT)
  • Re: AMBER: Problem compiling amber7 (Mon May 24 2004 - 10:19:04 CDT)
  • Re: AMBER: parallel installation problem (Mon May 24 2004 - 09:38:50 CDT)
  • Re: AMBER: tmd questions (Thu May 13 2004 - 07:16:36 CDT)
  • Re: AMBER: any program or tool (Mon May 03 2004 - 07:18:56 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sat May 01 2004 - 09:11:49 CDT)
• xhu1_at_memphis.edu
  • Re: AMBER: question about NMODE for RNA (Sun May 30 2004 - 20:53:58 CDT)
  • AMBER: question about NMODE for RNA (Sun May 30 2004 - 17:32:22 CDT)
  • AMBER: amber on AMD 64 (Fri May 28 2004 - 13:56:02 CDT)
• Xiao He
  • Re: Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 10:01:28 CDT)
  • Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:29:56 CDT)
  • Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 08:55:05 CDT)
  • AMBER: a question about Van der waals radius (Sat May 22 2004 - 07:07:05 CDT)
• xiaowei li
  • AMBER: separate the longitudinal and transverse vibrations frequencies (Mon May 03 2004 - 23:33:11 CDT)
• Ye Mei
  • Re: Re: Re: Re: Re: AMBER: a question about Van der waals radius (Mon May 24 2004 - 01:54:30 CDT)
  • AMBER: h bond (Mon May 24 2004 - 01:27:37 CDT)
• Ülo Lille
  • AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 05:16:24 CDT)

Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:01 CDT