AMBER Archive (2006) - By Date

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Starting: Sun Jan 01 2006 - 17:31:12 CST
Ending: Sat Dec 30 2006 - 07:20:23 CST

Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews (Sun Jan 01 2006 - 17:08:17 CST)
Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews (Sun Jan 01 2006 - 17:29:40 CST)
Re: AMBER: problem with ssh and xleap Peter Gannett (Mon Jan 02 2006 - 10:26:18 CST)
RE: AMBER: antechamber problem Baker, Bo-Yang (Mon Jan 02 2006 - 18:23:40 CST)
Re: AMBER: problem with ssh and xleap Robyn Ayscue (Mon Jan 02 2006 - 20:33:13 CST)
AMBER: water molecules with in 3 angstroms to the solute nag raj (Mon Jan 02 2006 - 22:47:06 CST)
Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim (Tue Jan 03 2006 - 03:05:24 CST)
AMBER: requirement of delphi for mm_pbsa Manish Datt (Tue Jan 03 2006 - 12:46:53 CST)
Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim (Tue Jan 03 2006 - 18:40:07 CST)
AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Wed Jan 04 2006 - 07:51:55 CST)
Re: AMBER: requirement of delphi for mm_pbsa David A. Case (Wed Jan 04 2006 - 10:22:53 CST)
Re: AMBER: requirement of delphi for mm_pbsa Holger Gohlke (Wed Jan 04 2006 - 11:09:46 CST)
Re: AMBER: How to run mm_pbsa_statistics.pl? Holger Gohlke (Wed Jan 04 2006 - 11:27:05 CST)
AMBER: minimalization prior to nmode analysis, is it necessary? Magne Olufsen (Wed Jan 04 2006 - 11:42:21 CST)
AMBER: Ligand charge bybaker_at_itsa.ucsf.edu (Wed Jan 04 2006 - 12:51:57 CST)
Re: AMBER: Ligand charge David Mobley (Wed Jan 04 2006 - 13:43:54 CST)
AMBER: Leap Joseph Fernandez (Wed Jan 04 2006 - 15:36:13 CST)
Re: AMBER: Leap Bill Ross (Wed Jan 04 2006 - 16:02:20 CST)
AMBER: Q: results from PB solver in example no.3 Tomimoto_Masaki_at_takeda.co.jp (Wed Jan 04 2006 - 17:09:42 CST)
Re: AMBER: Q: results from PB solver in example no.3 Ray Luo (Wed Jan 04 2006 - 20:45:28 CST)
Re: AMBER: Ligand charge Ilyas Yildirim (Thu Jan 05 2006 - 00:02:42 CST)
AMBER: Where to modify the atom type in sander? zhli_2000_at_126.com (Thu Jan 05 2006 - 03:21:20 CST)
Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Thu Jan 05 2006 - 07:39:19 CST)
RE: AMBER: Where to modify the atom type in sander? Ross Walker (Thu Jan 05 2006 - 10:12:34 CST)
Re: AMBER: Ligand charge Bill Ross (Thu Jan 05 2006 - 12:24:18 CST)
Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Thu Jan 05 2006 - 17:11:42 CST)
Re: AMBER: minimalization prior to nmode analysis, is it necessary? David A. Case (Thu Jan 05 2006 - 19:56:26 CST)
Re: AMBER: minimalization prior to nmode analysis, is it necessary? Adrian Roitberg (Thu Jan 05 2006 - 20:38:51 CST)
AMBER: creating a RST file from specific set of binpos/crd file Baird, Jamie $bairdje$ (Fri Jan 06 2006 - 11:33:00 CST)
Re: AMBER: creating a RST file from specific set of binpos/crd file Thomas E. Cheatham, III (Fri Jan 06 2006 - 11:53:51 CST)
RE: AMBER: creating a RST file from specific set of binpos/crd file Ross Walker (Fri Jan 06 2006 - 12:01:39 CST)
Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type Amber admin (Fri Jan 06 2006 - 15:36:19 CST)
AMBER: SHAKE - ntc = 3 Jennie Thomas (Fri Jan 06 2006 - 19:05:09 CST)
Re: AMBER: SHAKE - ntc = 3 David A. Case (Fri Jan 06 2006 - 19:26:55 CST)
AMBER: Could you help me about mmpbsa! thank you! linfu (Sun Jan 08 2006 - 03:28:13 CST)
AMBER: amber alexandratm_at_sapo.pt (Mon Jan 09 2006 - 05:31:56 CST)
AMBER: parameters for C=S alexandra.marques_at_fc.up.pt (Mon Jan 09 2006 - 08:53:30 CST)
Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 16:38:24 CST)
RE: AMBER: SHAKE - ntc = 3 Ross Walker (Mon Jan 09 2006 - 16:51:01 CST)
Re: AMBER: parameters for C=S David A. Case (Mon Jan 09 2006 - 17:04:52 CST)
Re: AMBER: SHAKE - ntc = 3 David A. Case (Mon Jan 09 2006 - 16:59:46 CST)
Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 18:07:47 CST)
Re: AMBER: SHAKE - ntc = 3 Bill Ross (Mon Jan 09 2006 - 18:39:12 CST)
AMBER: about mmpbsa linfu (Mon Jan 09 2006 - 19:17:15 CST)
Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 19:54:09 CST)
AMBER: problem with the output file for free energy perturbation calculation brmeher_at_iitg.ernet.in (Mon Jan 09 2006 - 23:15:30 CST)
AMBER: regarding Hydrogen bond analysis S.Sundar Raman (Mon Jan 09 2006 - 21:19:15 CST)
AMBER: strange result of mm/pbsa snowyowls (Mon Jan 09 2006 - 22:43:11 CST)
Re: AMBER: regarding Hydrogen bond analysis David A. Case (Tue Jan 10 2006 - 02:45:50 CST)
AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number? tonglei (Sun Jan 08 2006 - 20:36:30 CST)
AMBER: Problem in Antechamber Sai Kumar Ramadugu (Tue Jan 10 2006 - 05:17:53 CST)
AMBER: PTRAJ generating wrong dihedral angles hayden (Tue Jan 10 2006 - 05:40:05 CST)
AMBER: mpich Amber7 problem Jan Dohnalek (Tue Jan 10 2006 - 08:31:38 CST)
Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Tue Jan 10 2006 - 09:49:00 CST)
Re: AMBER: PTRAJ generating wrong dihedral angles Thomas E. Cheatham, III (Tue Jan 10 2006 - 13:42:42 CST)
AMBER: ptraj distance matrix Holly Freedman (Tue Jan 10 2006 - 16:03:36 CST)
Re: AMBER: Leap compilation issues Jiten (Tue Jan 10 2006 - 21:19:14 CST)
Re: AMBER: ptraj distance matrix Holger Gohlke (Wed Jan 11 2006 - 02:09:33 CST)
Re: AMBER: mpich Amber7 problem linfu (Wed Jan 11 2006 - 03:27:57 CST)
Re: AMBER: mpich Amber7 problem Petr Kulhanek (Wed Jan 11 2006 - 03:27:01 CST)
Re: AMBER: mpich Amber7 problem Jan Dohnalek (Wed Jan 11 2006 - 04:32:18 CST)
AMBER: Gibbs pmf calculation Atsutoshi Okabe (Wed Jan 11 2006 - 04:14:30 CST)
AMBER: Workshops a a (Wed Jan 11 2006 - 08:27:59 CST)
AMBER: GLUTATHIONE Joachim Reichelt (Wed Jan 11 2006 - 08:40:30 CST)
Re: AMBER: GLUTATHIONE Ilyas Yildirim (Wed Jan 11 2006 - 09:38:56 CST)
Re: AMBER: GLUTATHIONE Tim Meyer (Wed Jan 11 2006 - 13:13:11 CST)
AMBER: amber atom type -> length of name Tim Meyer (Wed Jan 11 2006 - 13:22:22 CST)
AMBER: About preparing Zn.lib Varsha Goyal (Wed Jan 11 2006 - 19:21:26 CST)
Re: AMBER: About preparing Zn.lib Ilyas Yildirim (Thu Jan 12 2006 - 01:46:03 CST)
AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim (Thu Jan 12 2006 - 01:43:06 CST)
Re: AMBER: amber atom type -> length of name David A. Case (Thu Jan 12 2006 - 01:59:48 CST)
AMBER: ptraj mask question Vlad Cojocaru (Thu Jan 12 2006 - 04:50:37 CST)
Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling (Thu Jan 12 2006 - 07:04:46 CST)
AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 08:19:17 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss (Thu Jan 12 2006 - 08:52:14 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss (Thu Jan 12 2006 - 09:01:09 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Carlos Simmerling (Thu Jan 12 2006 - 09:04:45 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 09:42:41 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 09:51:57 CST)
AMBER: ATCOR.dat format Kateryna Miroshnychenko (Thu Jan 12 2006 - 10:43:05 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Thomas E. Cheatham, III (Thu Jan 12 2006 - 10:59:35 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 11:13:58 CST)
Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 11:25:56 CST)
AMBER: Na+ with GB/SA? Steve Gwaltney (Thu Jan 12 2006 - 11:59:22 CST)
AMBER: About tleap Varsha Goyal (Thu Jan 12 2006 - 12:28:04 CST)
RE: AMBER: About tleap Ross Walker (Thu Jan 12 2006 - 14:08:14 CST)
Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim (Thu Jan 12 2006 - 16:00:24 CST)
Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling (Thu Jan 12 2006 - 16:10:58 CST)
Re: AMBER: Na+ with GB/SA? David A. Case (Thu Jan 12 2006 - 16:24:17 CST)
Re: AMBER: Problem in Antechamber David A. Case (Thu Jan 12 2006 - 19:40:50 CST)
Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu (Fri Jan 13 2006 - 00:01:46 CST)
AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 03:58:04 CST)
Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim (Fri Jan 13 2006 - 04:40:56 CST)
Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 04:51:13 CST)
Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim (Fri Jan 13 2006 - 05:10:52 CST)
Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 05:50:36 CST)
AMBER: analysing water behavior during MD Vlad Cojocaru (Fri Jan 13 2006 - 09:17:06 CST)
Re: AMBER: analysing water behavior during MD Fabian Boes (Fri Jan 13 2006 - 10:22:01 CST)
RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Fri Jan 13 2006 - 10:44:12 CST)
RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Fri Jan 13 2006 - 10:49:17 CST)
AMBER: Trimming ptraj output Andy Purkiss (Fri Jan 13 2006 - 11:29:00 CST)
Re: AMBER: Trimming ptraj output Thomas E. Cheatham, III (Fri Jan 13 2006 - 11:37:45 CST)
AMBER: base-base interaction Douali, Latifa (Fri Jan 13 2006 - 11:54:32 CST)
Re: AMBER: Trimming ptraj output Andy Purkiss (Fri Jan 13 2006 - 12:03:54 CST)
Re: AMBER: base-base interaction Carlos Simmerling (Fri Jan 13 2006 - 12:07:57 CST)
RE: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 22:29:03 CST)
AMBER: heme improper torsions nkyx_at_sohu.com (Mon Jan 16 2006 - 02:55:38 CST)
AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 03:16:09 CST)
Re: AMBER: heme improper torsions Vlad Cojocaru (Mon Jan 16 2006 - 03:50:50 CST)
Re: AMBER: the problem of mdcrd Vlad Cojocaru (Mon Jan 16 2006 - 03:55:45 CST)
AMBER: MPICH on OpenMosix Jan Dohnalek (Mon Jan 16 2006 - 07:21:04 CST)
AMBER: ACTIVE SITE Claire Zerafa (Mon Jan 16 2006 - 08:06:52 CST)
AMBER: Release of RESP ESP charge DDatabase FyD (Mon Jan 16 2006 - 10:04:47 CST)
Re: AMBER: heme improper torsions David A. Case (Mon Jan 16 2006 - 10:46:47 CST)
RE: AMBER: the problem of mdcrd Ross Walker (Mon Jan 16 2006 - 10:44:11 CST)
RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Mon Jan 16 2006 - 10:44:11 CST)
Re: AMBER: problem in saving parameter file for non-standard residue David A. Case (Mon Jan 16 2006 - 13:44:22 CST)
»Ø¸´£º RE: AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 20:13:53 CST)
»Ø¸´£º Re: AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 20:23:00 CST)
RE£ºAMBER: the problem of mdcrd xiphias xie (Tue Jan 17 2006 - 01:52:03 CST)
AMBER: About the unit of the projection onto eigenvectors zgleo (Tue Jan 17 2006 - 03:58:39 CST)
AMBER: Re: RE£ºAMBER: the problem of mdcrd Vlad Cojocaru (Tue Jan 17 2006 - 06:40:41 CST)
AMBER: Re: RE£ºAMBER: the problem of mdcrd Carlos Simmerling (Tue Jan 17 2006 - 06:56:58 CST)
AMBER: nmode calculations error Jiten (Tue Jan 17 2006 - 07:58:53 CST)
AMBER: rms in principal component analysis Lydia (Tue Jan 17 2006 - 14:54:32 CST)
AMBER: Amber 8 install problem Andrew Box (Tue Jan 17 2006 - 22:50:21 CST)
RE£ºAMBER: the problem of mdcrd xiphias xie (Wed Jan 18 2006 - 02:54:18 CST)
AMBER: Re: RE£ºAMBER: the problem of mdcrd Vlad Cojocaru (Wed Jan 18 2006 - 03:48:36 CST)
Re: AMBER: Amber 8 install problem Andreas Svrcek-Seiler (Wed Jan 18 2006 - 05:10:38 CST)
AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko (Wed Jan 18 2006 - 08:48:55 CST)
AMBER: IGB=10 Ahammadunny Pathiaseril (Wed Jan 18 2006 - 09:53:25 CST)
Re: AMBER: rms in principal component analysis David A. Case (Wed Jan 18 2006 - 10:30:51 CST)
Re: AMBER: rms in principal component analysis Lydia (Wed Jan 18 2006 - 11:43:03 CST)
AMBER: A few problems on the parameterisation of a Glutamine residue Jason K (Wed Jan 18 2006 - 12:12:16 CST)
RE: AMBER: A few problems on the parameterisation of a Glutamine residue Ross Walker (Wed Jan 18 2006 - 12:32:25 CST)
Re: AMBER: rms in principal component analysis David A. Case (Wed Jan 18 2006 - 12:52:51 CST)
Re: AMBER: bugfix for impropers in parmchk David A. Case (Wed Jan 18 2006 - 20:04:36 CST)
AMBER: is there any relationship between RMSD and B-factor? haixiao jin (Wed Jan 18 2006 - 21:30:33 CST)
Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling (Wed Jan 18 2006 - 21:53:26 CST)
Re: AMBER: is there any relationship between RMSD and B-factor? haixiao jin (Wed Jan 18 2006 - 22:58:28 CST)
Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling (Thu Jan 19 2006 - 06:59:39 CST)
Re: AMBER: is there any relationship between RMSD and B-factor? Andy Purkiss (Thu Jan 19 2006 - 07:19:06 CST)
AMBER: ptraj grid output Vlad Cojocaru (Thu Jan 19 2006 - 12:25:49 CST)
Re: AMBER: ptraj grid output Thomas E. Cheatham, III (Thu Jan 19 2006 - 12:47:05 CST)
RE: AMBER: Problem in Antechamber Junmei Wang (Thu Jan 19 2006 - 17:02:39 CST)
AMBER: ptraj PCA Marcela Madrid (Thu Jan 19 2006 - 19:04:46 CST)
AMBER: amber: problem in center command xiphias xie (Thu Jan 19 2006 - 20:36:27 CST)
Re: AMBER: amber: problem in center command Vlad Cojocaru (Fri Jan 20 2006 - 03:48:42 CST)
AMBER: partial charge glycam Kevin Murphy (Fri Jan 20 2006 - 05:28:27 CST)
Re: AMBER: partial charge glycam kkirschn_at_hamilton.edu (Fri Jan 20 2006 - 09:39:14 CST)
Re: AMBER: bugfix for impropers in parmchk David Mobley (Fri Jan 20 2006 - 12:21:49 CST)
Re: AMBER: bugfix for impropers in parmchk David Mobley (Fri Jan 20 2006 - 12:23:39 CST)
Re: AMBER: problem in center command xiphias xie (Fri Jan 20 2006 - 19:30:44 CST)
Re: AMBER: problem in center command Bill Ross (Fri Jan 20 2006 - 19:40:51 CST)
Re: AMBER: problem in center command Thomas Cheatham (Fri Jan 20 2006 - 21:37:49 CST)
Re: AMBER: partial charge glycam FyD (Sat Jan 21 2006 - 01:30:37 CST)
RE: AMBER: partial charge glycam Kevin Murphy (Tue Jan 24 2006 - 06:18:05 CST)
AMBER: ptraj PCA Vlad Cojocaru (Tue Jan 24 2006 - 10:02:20 CST)
AMBER: AMBER 8.0 : Octane Implicit Solvent? Guillaume Bollot (Tue Jan 24 2006 - 10:25:42 CST)
Re: AMBER: AMBER 8.0 : Octane Implicit Solvent? David A. Case (Tue Jan 24 2006 - 13:09:32 CST)
AMBER: monosaccharide residues Fren T (Tue Jan 24 2006 - 16:20:03 CST)
AMBER: Charges of enantiomers for Amber8 lily ferreira (Wed Jan 25 2006 - 02:01:24 CST)
RE: AMBER: partial charge glycam FyD (Wed Jan 25 2006 - 03:23:06 CST)
Re: AMBER: Charges of enantiomers for Amber8 FyD (Wed Jan 25 2006 - 03:38:36 CST)
Re: AMBER: Charges of enantiomers for Amber8 FyD (Wed Jan 25 2006 - 05:41:47 CST)
AMBER: ptraj PCA: projection mask bug?? Vlad Cojocaru (Wed Jan 25 2006 - 07:28:42 CST)
AMBER: MM-PBSA Douali, Latifa (Wed Jan 25 2006 - 17:03:06 CST)
Re: AMBER: Charges of enantiomers for Amber8 lily ferreira (Thu Jan 26 2006 - 00:46:53 CST)
Re: AMBER: Charges of enantiomers for Amber8 FyD (Thu Jan 26 2006 - 01:53:43 CST)
Re: AMBER: partial charge glycam kkirschn_at_hamilton.edu (Thu Jan 26 2006 - 08:49:35 CST)
AMBER: AMBER 7 and restrained bonds. Toomas Kaevand (Thu Jan 26 2006 - 09:27:28 CST)
Re: AMBER: AMBER 7 and restrained bonds. David A. Case (Thu Jan 26 2006 - 10:26:42 CST)
AMBER: antechamber ping jiang (Thu Jan 26 2006 - 17:18:29 CST)
AMBER: Charges from NMR spin densities David LeBard (Thu Jan 26 2006 - 17:33:50 CST)
Re: AMBER: antechamber David Case (Thu Jan 26 2006 - 17:48:55 CST)
Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu (Thu Jan 26 2006 - 22:46:42 CST)
AMBER: h-bond Gustavo Pierdominici Sottile (Fri Jan 27 2006 - 08:59:07 CST)
Re: AMBER: Charges from NMR spin densities David A. Case (Fri Jan 27 2006 - 10:57:32 CST)
AMBER: atom type "O3" not recognized by XLeap Kenley Barrett (Fri Jan 27 2006 - 11:32:48 CST)
AMBER: anal vs sander Piotr Cieplak (Fri Jan 27 2006 - 14:58:39 CST)
Re: AMBER: anal vs sander David A. Case (Fri Jan 27 2006 - 15:33:57 CST)
Re: AMBER: atom type "O3" not recognized by XLeap David A. Case (Fri Jan 27 2006 - 16:01:43 CST)
Re: AMBER: About the unit of the projection onto eigenvectors David A. Case (Fri Jan 27 2006 - 16:20:17 CST)
Re: AMBER: anal vs sander Piotr Cieplak (Fri Jan 27 2006 - 16:59:13 CST)
Re: AMBER: anal vs sander David A. Case (Fri Jan 27 2006 - 17:28:51 CST)
AMBER: lifetimes Gustavo Pierdominici Sottile (Mon Jan 30 2006 - 09:15:55 CST)
AMBER: NAD parameters alexandra.marques_at_fc.up.pt (Mon Jan 30 2006 - 10:04:43 CST)
Re: AMBER: NAD parameters ivan_at_mmb.pcb.ub.es (Mon Jan 30 2006 - 10:20:19 CST)
RE: AMBER: NAD parameters Ross Walker (Mon Jan 30 2006 - 10:34:20 CST)
AMBER: Problem in compiling sander with MMTSB luckyang_at_gmail.com (Mon Jan 30 2006 - 20:06:32 CST)
AMBER: Decomposed GB energy in idecomp=3 option Sukjoon Yoon (Mon Jan 30 2006 - 20:13:27 CST)
Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell (Mon Jan 30 2006 - 21:44:06 CST)
Re: AMBER: Problem in compiling sander with MMTSB luckyang_at_gmail.com (Tue Jan 31 2006 - 00:10:15 CST)
Re: AMBER: MM-PBSA Jianyin Shao (Tue Jan 31 2006 - 11:08:09 CST)
AMBER: About placing counter ions Varsha Goyal (Tue Jan 31 2006 - 12:23:03 CST)
AMBER: parallel compile problems on amber8 hayden (Tue Jan 31 2006 - 12:55:34 CST)
RE: AMBER: parallel compile problems on amber8 Ross Walker (Tue Jan 31 2006 - 16:04:52 CST)
RE: AMBER: parallel compile problems on amber8 Ross Walker (Tue Jan 31 2006 - 16:03:31 CST)
AMBER: Problem in compiling AMBER8 parallel version luckyang_at_gmail.com (Tue Jan 31 2006 - 17:09:09 CST)
Re: AMBER: Problem in compiling AMBER8 parallel version David LeBard (Tue Jan 31 2006 - 17:23:16 CST)
Re: AMBER: Problem in compiling AMBER8 parallel version luckyang_at_gmail.com (Tue Jan 31 2006 - 17:51:06 CST)
Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell (Tue Jan 31 2006 - 23:54:56 CST)
AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 01:18:44 CST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Wed Feb 01 2006 - 06:31:12 CST)
Re: AMBER: Values of Spring Constants Carlos Simmerling (Wed Feb 01 2006 - 06:52:50 CST)
Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Wed Feb 01 2006 - 06:54:33 CST)
Re: AMBER: Values of Spring Constants Adrian Roitberg (Wed Feb 01 2006 - 07:05:14 CST)
Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 09:43:05 CST)
AMBER: prepi definitions Michael Mazanetz (Wed Feb 01 2006 - 09:56:25 CST)
Re: AMBER: lifetimes David A. Case (Wed Feb 01 2006 - 10:20:56 CST)
Re: AMBER: Values of Spring Constants David A. Case (Wed Feb 01 2006 - 10:38:13 CST)
Re: AMBER: prepi definitions ivan_at_mmb.pcb.ub.es (Wed Feb 01 2006 - 10:33:42 CST)
AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 11:21:21 CST)
Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 11:53:06 CST)
Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 12:06:39 CST)
Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 12:26:10 CST)
Re: AMBER: Problem in compiling sander with MMTSB luckyang_at_gmail.com (Wed Feb 01 2006 - 13:39:04 CST)
Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 13:42:11 CST)
AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 14:43:53 CST)
Re: AMBER: Cannot successfully assign bond type for this molecule? David Case (Wed Feb 01 2006 - 15:49:55 CST)
AMBER: basic minimize question A D (Wed Feb 01 2006 - 16:50:53 CST)
Re: AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 17:00:40 CST)
RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 17:06:07 CST)
Re: AMBER: basic minimize question A D (Wed Feb 01 2006 - 17:35:38 CST)
Re: AMBER: basic minimize question David A. Case (Wed Feb 01 2006 - 18:09:11 CST)
Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Wed Feb 01 2006 - 18:05:58 CST)
RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 18:17:57 CST)
AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Wed Feb 01 2006 - 21:00:09 CST)
Re: AMBER: Problem in compiling sander with MMTSB luckyang_at_gmail.com (Wed Feb 01 2006 - 21:26:55 CST)
RE: AMBER: Charges on atoms in protein :AMBER Ross Walker (Wed Feb 01 2006 - 22:17:24 CST)
Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 23:00:56 CST)
Re: AMBER: Values of Spring Constants Carlos Simmerling (Thu Feb 02 2006 - 05:34:30 CST)
AMBER: positional restraints & constant pressure Kateryna Miroshnychenko (Thu Feb 02 2006 - 09:40:30 CST)
AMBER: lib file snoze pa (Thu Feb 02 2006 - 10:55:33 CST)
RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 12:43:23 CST)
Re: AMBER: MM-PBSA David A. Case (Thu Feb 02 2006 - 13:00:23 CST)
Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 13:08:12 CST)
RE: AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Thu Feb 02 2006 - 13:20:59 CST)
RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 13:31:28 CST)
AMBER: Amber8 parallel compilation problems on EM64T system HL Eastwood (Thu Feb 02 2006 - 13:32:32 CST)
Re: AMBER: Charges on atoms in protein :AMBER Adrian Roitberg (Thu Feb 02 2006 - 13:50:54 CST)
RE: AMBER: Charges on atoms in protein :AMBER Ilyas Yildirim (Thu Feb 02 2006 - 14:14:53 CST)
Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 14:18:28 CST)
Re: AMBER: Amber8 parallel compilation problems on EM64T system David A. Case (Thu Feb 02 2006 - 14:28:27 CST)
AMBER: parameter loading problem Lihua Wang (Thu Feb 02 2006 - 15:01:51 CST)
AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Thu Feb 02 2006 - 16:18:59 CST)
AMBER: MD of oligomer sequences Atilio I Anzellotti/O/VCU (Thu Feb 02 2006 - 16:53:28 CST)
Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster David A. Case (Thu Feb 02 2006 - 19:49:39 CST)
Re: AMBER: MD of oligomer sequences David A. Case (Thu Feb 02 2006 - 20:08:42 CST)
AMBER: simulated annealing run--temp won't rise Kenley Barrett (Thu Feb 02 2006 - 21:26:52 CST)
Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Thu Feb 02 2006 - 22:01:44 CST)
AMBER: Re: Force Decomposition for MTS in AMBER 8. David Case (Fri Feb 03 2006 - 00:34:23 CST)
Re: AMBER: simulated annealing run--temp won't rise David Case (Fri Feb 03 2006 - 00:46:00 CST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Fri Feb 03 2006 - 02:38:55 CST)
Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Fri Feb 03 2006 - 05:52:56 CST)
AMBER: MPICH-1.2.7 compilation problem ! Pradipta Bandyopadhyay (Fri Feb 03 2006 - 07:49:31 CST)
Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Fri Feb 03 2006 - 09:57:30 CST)
Re: AMBER: positional restraints & constant pressure David A. Case (Fri Feb 03 2006 - 10:40:53 CST)
AMBER: AMBER 7 and cutoff's Toomas Kaevand (Fri Feb 03 2006 - 11:58:53 CST)
Re: AMBER: AMBER 7 and cutoff's Carlos Simmerling (Fri Feb 03 2006 - 13:20:30 CST)
Re: AMBER: lib file snoze pa (Fri Feb 03 2006 - 13:32:39 CST)
AMBER: Rhoad, Jonathan S. (Fri Feb 03 2006 - 13:56:37 CST)
AMBER: MMPBSA: magnitude of PB calculation sishi.tang_at_utoronto.ca (Fri Feb 03 2006 - 17:34:10 CST)
Re: AMBER: David A. Case (Fri Feb 03 2006 - 17:46:28 CST)
Re: AMBER: Values of Spring Constants David A. Case (Fri Feb 03 2006 - 17:51:22 CST)
Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Fri Feb 03 2006 - 18:31:32 CST)
Re: AMBER: MMPBSA: magnitude of PB calculation Ray Luo (Fri Feb 03 2006 - 01:49:07 CST)
Re: AMBER: lib file Ilyas Yildirim (Fri Feb 03 2006 - 19:11:36 CST)
Re: AMBER: Problem in compiling sander with MMTSB luckyang_at_gmail.com (Fri Feb 03 2006 - 19:21:51 CST)
AMBER: Pawe³ Gruszczyñski (Sat Feb 04 2006 - 03:16:10 CST)
AMBER: Strange minimization output problem andy ng (Sat Feb 04 2006 - 06:39:31 CST)
Re: AMBER: Strange minimization output problem Ananda Rama Krishnan Selvaraj (Sat Feb 04 2006 - 10:12:19 CST)
AMBER: dihedral parameters richard dimelow (Sat Feb 04 2006 - 10:06:41 CST)
Re: AMBER: MMPBSA: magnitude of PB calculation sishi.tang_at_utoronto.ca (Sat Feb 04 2006 - 10:47:21 CST)
Re: AMBER: dihedral parameters Carlos Simmerling (Sat Feb 04 2006 - 11:30:27 CST)
Re: AMBER: David Mobley (Sat Feb 04 2006 - 12:06:23 CST)
Re: AMBER: bugfix for impropers in parmchk David A. Case (Sat Feb 04 2006 - 12:50:15 CST)
Re: AMBER: Strange minimization output problem David A. Case (Sat Feb 04 2006 - 14:20:17 CST)
AMBER: What Viewer is best Brian Stupi (Sat Feb 04 2006 - 23:59:29 CST)
Re: AMBER: Strange minimization output problem Andreas Svrcek-Seiler (Sun Feb 05 2006 - 09:23:03 CST)
AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ? linfu (Sun Feb 05 2006 - 10:49:32 CST)
Re: AMBER: What Viewer is best Vlad Cojocaru (Sun Feb 05 2006 - 11:01:11 CST)
Re: AMBER: MMPBSA: magnitude of PB calculation Thomas Steinbrecher (Mon Feb 06 2006 - 02:54:01 CST)
Re: AMBER: dihedral parameters richard dimelow (Mon Feb 06 2006 - 04:22:08 CST)
AMBER: Hessian matrix Marie Brut (Mon Feb 06 2006 - 06:12:53 CST)
Re: AMBER: dihedral parameters Carlos Simmerling (Mon Feb 06 2006 - 06:22:03 CST)
Re: AMBER: MMPBSA: magnitude of PB calculation Natasja Brooijmans (Mon Feb 06 2006 - 06:52:36 CST)
AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 07:09:38 CST)
Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 08:03:32 CST)
Re: AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 09:04:51 CST)
Re: AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko (Mon Feb 06 2006 - 09:09:06 CST)
Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 09:39:59 CST)
AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 12:55:39 CST)
Re: AMBER: Parallel version of Amber: error message Carlos Simmerling (Mon Feb 06 2006 - 13:21:31 CST)
Re: AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 13:45:48 CST)
Re: AMBER: Parallel version of Amber: error message David LeBard (Mon Feb 06 2006 - 14:10:29 CST)
Re: AMBER: Parallel version of Amber: error message Lihua Wang (Mon Feb 06 2006 - 14:27:40 CST)
Re: AMBER: Parallel version of Amber: error message Mingfeng Yang (Mon Feb 06 2006 - 14:29:38 CST)
Re: AMBER: Parallel version of Amber: error message Mark Williamson (Mon Feb 06 2006 - 15:00:09 CST)
AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 16:47:19 CST)
Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 17:02:22 CST)
Re: AMBER: Parallel error in Amber 8 Wei Zhang (Mon Feb 06 2006 - 17:06:07 CST)
Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 17:18:16 CST)
Re: AMBER: Parallel error in Amber 8 David A. Case (Mon Feb 06 2006 - 17:37:56 CST)
AMBER: soft-core potential in amber? Lydia (Mon Feb 06 2006 - 18:13:14 CST)
Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 18:16:20 CST)
AMBER: non bond list overflow Kenley Barrett (Mon Feb 06 2006 - 21:43:06 CST)
Re: AMBER: non bond list overflow David A. Case (Tue Feb 07 2006 - 00:37:59 CST)
AMBER: format of qusaiharmonic eigenvector file in AMBER7 Phineus Markwick (Tue Feb 07 2006 - 05:10:44 CST)
Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7 Chris Moth (Tue Feb 07 2006 - 08:10:07 CST)
Re: AMBER: soft-core potential in amber? David Mobley (Tue Feb 07 2006 - 08:54:33 CST)
Re: AMBER: non bond list overflow Kenley Barrett (Tue Feb 07 2006 - 10:32:18 CST)
Re: AMBER: Hessian matrix David A. Case (Tue Feb 07 2006 - 10:40:37 CST)
Re: AMBER: Hessian matrix mbrut_at_laas.fr (Tue Feb 07 2006 - 11:55:17 CST)
Re: AMBER: non bond list overflow David A. Case (Tue Feb 07 2006 - 13:00:54 CST)
AMBER: Ask for your help to install Amber8 software Cao Tran (Wed Feb 08 2006 - 07:53:11 CST)
Re: AMBER: Ask for your help to install Amber8 software Cenk Andac (Wed Feb 08 2006 - 08:44:30 CST)
RE: AMBER: Ask for your help to install Amber8 software CaoTran (Wed Feb 08 2006 - 09:03:51 CST)
RE: AMBER: Ask for your help to install Amber8 software Lei Wang (Wed Feb 08 2006 - 09:16:32 CST)
AMBER: DNA tutorial xleap help Amanda Jonsson (Wed Feb 08 2006 - 12:56:32 CST)
AMBER: desc related issue snoze pa (Wed Feb 08 2006 - 13:15:19 CST)
Re: AMBER: DNA tutorial xleap help Wei Zhang (Wed Feb 08 2006 - 13:42:32 CST)
Re: AMBER: DNA tutorial xleap help Bill Ross (Wed Feb 08 2006 - 13:56:25 CST)
AMBER: PMED in AMBER snoze pa (Wed Feb 08 2006 - 19:07:40 CST)
AMBER: Acetyl CoA Satyan Sharma (Thu Feb 09 2006 - 11:55:19 CST)
AMBER: Distortion in parallelploied Varsha Goyal (Thu Feb 09 2006 - 19:39:06 CST)
AMBER: EAMBER Mingfeng Yang (Thu Feb 09 2006 - 21:56:04 CST)
Re: AMBER: EAMBER Carlos Simmerling (Thu Feb 09 2006 - 22:15:21 CST)
RE: AMBER: Ask for your help to install Amber8 software Cao Tran (Fri Feb 10 2006 - 03:01:38 CST)
RE: AMBER: Ask for your help to install Amber8 software Cenk Andac (Fri Feb 10 2006 - 04:46:12 CST)
AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 08:50:59 CST)
Re: AMBER: PMEMD MPI_Finalize() error Robert Duke (Fri Feb 10 2006 - 09:15:29 CST)
Re: AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 10:07:53 CST)
Re: AMBER: Distortion in parallelploied David A. Case (Fri Feb 10 2006 - 11:04:13 CST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 05:49:04 CST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 09:05:59 CST)
AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 22:28:09 CST)
Re: AMBER: Problem in running umbrella sampling David A. Case (Sun Feb 12 2006 - 23:11:48 CST)
Re: AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 23:22:49 CST)
AMBER: shuli kang (Mon Feb 13 2006 - 06:26:07 CST)
AMBER: MM_PBSA problem (No values for MM_GAS ) Bing Liu (Mon Feb 13 2006 - 08:40:47 CST)
Re: AMBER: Distortion in parallelploied Angelo Pugliese (Mon Feb 13 2006 - 09:40:40 CST)
AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 14:19:19 CST)
Re: AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 14:40:46 CST)
Re: AMBER: MM_PBSA problem (No values for MM_GAS ) Scott Pendley (Mon Feb 13 2006 - 14:57:27 CST)
Re: AMBER: Scott Pendley (Mon Feb 13 2006 - 15:00:15 CST)
AMBER: 2D-topology Baldoni Hector Armando (Mon Feb 13 2006 - 15:50:11 CST)
AMBER: mm_pbsa output lucas luquitas (Mon Feb 13 2006 - 17:40:28 CST)
AMBER: script advice A D (Mon Feb 13 2006 - 20:35:35 CST)
AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 03:44:01 CST)
AMBER: Istallation AMBER8 Dr.Rudolf Friedemann (Tue Feb 14 2006 - 04:41:39 CST)
Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 04:54:05 CST)
AMBER: paralelization and sander problems cristian obiol (Tue Feb 14 2006 - 04:24:18 CST)
Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 06:09:36 CST)
Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 06:56:07 CST)
Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 14 2006 - 07:59:43 CST)
Re: AMBER: paralelization and sander problems David A. Case (Tue Feb 14 2006 - 10:32:59 CST)
AMBER: Organic molecules Marie Brut (Tue Feb 14 2006 - 10:42:23 CST)
AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 10:55:12 CST)
Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 11:36:21 CST)
RE: AMBER: Organic molecules Ross Walker (Tue Feb 14 2006 - 11:44:25 CST)
RE: AMBER: paralelization and sander problems Ross Walker (Tue Feb 14 2006 - 11:48:06 CST)
Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 11:53:37 CST)
Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 12:08:59 CST)
RE: AMBER: Error when installing Ross Walker (Tue Feb 14 2006 - 12:30:29 CST)
RE: AMBER: minization: outputing intermediate snapshots Ross Walker (Tue Feb 14 2006 - 12:34:30 CST)
Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 13:51:53 CST)
Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Tue Feb 14 2006 - 14:35:19 CST)
Re: AMBER: 2D-topology David A. Case (Tue Feb 14 2006 - 15:57:45 CST)
AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 Jingyuan Luke (Tue Feb 14 2006 - 19:35:37 CST)
Re: AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 David A. Case (Wed Feb 15 2006 - 00:12:42 CST)
Re: AMBER: Istallation AMBER8 David A. Case (Wed Feb 15 2006 - 00:57:13 CST)
AMBER: negative T_solv values Markus O Kaukonen (Wed Feb 15 2006 - 02:25:40 CST)
Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 07:16:46 CST)
Re: AMBER: script advice JunJun Liu (Wed Feb 15 2006 - 09:35:44 CST)
Re: AMBER: negative T_solv values David A. Case (Wed Feb 15 2006 - 10:18:25 CST)
Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Wed Feb 15 2006 - 11:25:21 CST)
Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 11:46:27 CST)
AMBER: m4 error with Amber8 on SUN Amber admin (Wed Feb 15 2006 - 16:51:38 CST)
Re: AMBER: m4 error with Amber8 on SUN David A. Case (Wed Feb 15 2006 - 17:56:06 CST)
AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation zgleo (Thu Feb 16 2006 - 00:04:47 CST)
Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Thu Feb 16 2006 - 04:41:52 CST)
Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation german (Thu Feb 16 2006 - 06:04:39 CST)
AMBER: sander problem bala (Thu Feb 16 2006 - 09:57:43 CST)
Re: AMBER: sander problem snoze pa (Thu Feb 16 2006 - 10:13:22 CST)
Re: AMBER: sander problem Carlos Simmerling (Thu Feb 16 2006 - 10:25:20 CST)
Re: AMBER: sander problem JunJun Liu (Thu Feb 16 2006 - 10:16:34 CST)
RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 10:51:24 CST)
Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 12:49:20 CST)
Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 12:53:10 CST)
RE: AMBER: sander problem Brian Stupi (Thu Feb 16 2006 - 14:44:11 CST)
RE: AMBER: sander problem Thomas E. Cheatham, III (Thu Feb 16 2006 - 15:12:39 CST)
RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 15:20:45 CST)
AMBER: process_mdout.perl Brian Stupi (Thu Feb 16 2006 - 16:02:06 CST)
Re: AMBER: paralelization and sander problems cristian obiol (Fri Feb 17 2006 - 04:07:37 CST)
Re: AMBER: paralelization and sander problems Carlos Simmerling (Fri Feb 17 2006 - 05:59:44 CST)
AMBER: Torsional restraints for groups of atoms Supat Jiranusornkul (Fri Feb 17 2006 - 06:14:12 CST)
AMBER: Question about renaming a residue Kara Di Giorgio (Fri Feb 17 2006 - 17:28:26 CST)
Re: AMBER: Question about renaming a residue Thomas E. Cheatham, III (Fri Feb 17 2006 - 17:46:27 CST)
Re: AMBER: Question about renaming a residue Ilyas Yildirim (Fri Feb 17 2006 - 20:05:37 CST)
AMBER: mm_pbsa problem in IBM-aix Jiten (Sat Feb 18 2006 - 01:36:52 CST)
AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Sat Feb 18 2006 - 16:02:42 CST)
AMBER: antechamber for a database of organic molecules Yogesh Sabnis (Sun Feb 19 2006 - 09:16:23 CST)
Re: AMBER: antechamber for a database of organic molecules FyD (Sun Feb 19 2006 - 09:51:52 CST)
Re: AMBER: instructions for making a library file for an unusual residue? FyD (Sun Feb 19 2006 - 11:14:10 CST)
Re: AMBER: mm_pbsa problem in IBM-aix Ray Luo (Sun Feb 19 2006 - 14:22:01 CST)
AMBER: Phosphorylated amino acid andy ng (Sun Feb 19 2006 - 17:51:41 CST)
RE: AMBER: antechamber for a database of organic molecules Junmei Wang (Sun Feb 19 2006 - 21:32:22 CST)
Re: AMBER: Phosphorylated amino acid Tim Meyer (Mon Feb 20 2006 - 02:56:36 CST)
Re: AMBER: paralelization and sander problems cristian obiol (Mon Feb 20 2006 - 06:13:58 CST)
AMBER: parallel problem of amber8 linfu (Mon Feb 20 2006 - 07:01:02 CST)
AMBER: charge redistribution in .prep files Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 20 2006 - 06:37:54 CST)
AMBER: Truncated octahedral box as triclinic lattice vectors Markus O Kaukonen (Mon Feb 20 2006 - 08:42:45 CST)
AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 09:08:12 CST)
Re: AMBER: amber 8 problem JunJun Liu (Mon Feb 20 2006 - 10:05:53 CST)
Re: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 10:17:37 CST)
Re: AMBER: amber 8 problem Andreas Svrcek-Seiler (Mon Feb 20 2006 - 10:20:28 CST)
Re: AMBER: charge redistribution in .prep files David A. Case (Mon Feb 20 2006 - 10:29:41 CST)
Re: AMBER: amber 8 problem David A. Case (Mon Feb 20 2006 - 10:33:01 CST)
RE: AMBER: parallel problem of amber8 Ross Walker (Mon Feb 20 2006 - 11:00:26 CST)
RE: AMBER: amber 8 problem Ross Walker (Mon Feb 20 2006 - 11:05:57 CST)
AMBER: Ti calculations in dmso solvent Vitor Manuel Sousa F?x (Mon Feb 20 2006 - 11:55:32 CST)
AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 13:59:35 CST)
Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Mon Feb 20 2006 - 14:32:13 CST)
Re: AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 17:08:38 CST)
Re: AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Mon Feb 20 2006 - 18:22:22 CST)
AMBER: NMR restraints and LES Sivakolundu, Sivashankar (Mon Feb 20 2006 - 19:43:38 CST)
Re: AMBER: NMR restraints and LES David A. Case (Mon Feb 20 2006 - 20:26:17 CST)
RE: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 22:55:27 CST)
Re: AMBER: Phosphorylated amino acid andy ng (Mon Feb 20 2006 - 23:55:55 CST)
Re: AMBER: instructions for making a library file for an unusual residue? Ilyas Yildirim (Tue Feb 21 2006 - 00:28:49 CST)
AMBER: About WHAM Atsutoshi Okabe (Tue Feb 21 2006 - 00:22:01 CST)
Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Tue Feb 21 2006 - 07:02:58 CST)
Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 21 2006 - 06:57:10 CST)
Re: AMBER: instructions for making a library file for an unusual residue? FyD (Tue Feb 21 2006 - 07:17:48 CST)
AMBER: does anyone have library file for methylated histidine, 2003 ff? Kenley Barrett (Tue Feb 21 2006 - 10:27:13 CST)
AMBER: CARNAL: H-BOND Specifying side chains only Kay Kunes (Tue Feb 21 2006 - 14:47:14 CST)
Re: AMBER: CARNAL: H-BOND Specifying side chains only Bill Ross (Tue Feb 21 2006 - 15:41:25 CST)
AMBER: Problem with file size of sander outputs Cenk Andac (Wed Feb 22 2006 - 01:54:24 CST)
Re: AMBER: Problem with file size of sander outputs shuli kang (Wed Feb 22 2006 - 02:45:21 CST)
Re: AMBER: Problem with file size of sander outputs german (Wed Feb 22 2006 - 04:49:49 CST)
AMBER: Free energy perturbation Angelo Pugliese (Wed Feb 22 2006 - 10:42:06 CST)
AMBER: AMBER force field with namd Fabien Cailliez (Wed Feb 22 2006 - 11:54:23 CST)
Re: AMBER: Problem with file size of sander outputs JunJun Liu (Wed Feb 22 2006 - 14:58:00 CST)
RE: AMBER: Problem with file size of sander outputs Ross Walker (Wed Feb 22 2006 - 15:16:30 CST)
RE: AMBER: Problem with file size of sander outputs Cenk Andac (Thu Feb 23 2006 - 01:23:02 CST)
Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 04:11:17 CST)
Re: AMBER: AMBER force field with namd Carlos Simmerling (Thu Feb 23 2006 - 07:41:31 CST)
Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 08:04:51 CST)
Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 10:58:17 CST)
RE: AMBER: Problem with file size of sander outputs Feng X Zhou (Thu Feb 23 2006 - 11:42:22 CST)
Re: AMBER: Ti calculations in dmso solvent David A. Case (Thu Feb 23 2006 - 12:01:26 CST)
RE: AMBER: Problem with file size of sander outputs Ross Walker (Thu Feb 23 2006 - 12:06:30 CST)
AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead (Thu Feb 23 2006 - 12:31:02 CST)
Re: AMBER: generating parameters for the NADH analogue H4NAD Vlad Cojocaru (Thu Feb 23 2006 - 12:53:30 CST)
RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker (Thu Feb 23 2006 - 13:00:30 CST)
AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 13:02:45 CST)
RE: AMBER: TI cal Ross Walker (Thu Feb 23 2006 - 13:25:57 CST)
Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 14:06:43 CST)
RE: AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 14:08:20 CST)
AMBER: A problem with Amber force field new parameter derivation Vidana.Epa_at_csiro.au (Fri Feb 24 2006 - 00:16:04 CST)
Re: AMBER: A problem with Amber force field new parameter derivation FyD (Fri Feb 24 2006 - 00:27:31 CST)
AMBER: entropic energy Nina Fischer (Fri Feb 24 2006 - 06:15:17 CST)
AMBER: Antechamber Package Announcement Junmei Wang (Fri Feb 24 2006 - 10:26:52 CST)
Re: AMBER: entropic energy David A. Case (Fri Feb 24 2006 - 10:36:49 CST)
AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 10:59:34 CST)
Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 11:34:46 CST)
Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 14:18:56 CST)
AMBER: specifying RSOLV when calculating 2003 force field charges Kenley Barrett (Fri Feb 24 2006 - 14:50:07 CST)
Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 15:18:58 CST)
AMBER: How to explain the meaning of the mmpbsa/DC result? zhli_2000_at_126.com (Sun Feb 26 2006 - 01:01:04 CST)
AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 02:58:14 CST)
Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 03:26:23 CST)
Re: AMBER: dynamic memory allocation problem in nmode Jiten (Sun Feb 26 2006 - 09:07:23 CST)
AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure Magne Olufsen (Sun Feb 26 2006 - 13:00:23 CST)
AMBER: Sulfonamides and GAFF Varsha Goyal (Sun Feb 26 2006 - 19:16:18 CST)
Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Sun Feb 26 2006 - 19:56:59 CST)
Re: AMBER: dynamic memory allocation problem in nmode David A. Case (Sun Feb 26 2006 - 22:21:02 CST)
AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 06:45:28 CST)
AMBER: MD job stopped without any error information? ying xiong (Mon Feb 27 2006 - 02:29:50 CST)
Re: AMBER: MD job stopped without any error information? Melinda Layten (Mon Feb 27 2006 - 09:18:09 CST)
Re: AMBER: MD job stopped without any error information? Guanglei Cui (Mon Feb 27 2006 - 09:55:47 CST)
AMBER: RE: about compiling errors for Leap Ross Walker (Mon Feb 27 2006 - 10:17:27 CST)
RE: AMBER: MD job stopped without any error information? Ross Walker (Mon Feb 27 2006 - 10:22:25 CST)
Re: AMBER: ptraj warning while loading reference David A. Case (Mon Feb 27 2006 - 10:44:52 CST)
Re: AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 11:00:43 CST)
AMBER: sander testing problem mdione_at_fcq.unc.edu.ar (Mon Feb 27 2006 - 15:53:23 CST)
AMBER: mask issues Claire Zerafa (Tue Feb 28 2006 - 06:46:12 CST)
Re: AMBER: mask issues Vlad Cojocaru (Tue Feb 28 2006 - 07:03:16 CST)
AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Tue Feb 28 2006 - 09:32:49 CST)
RE: AMBER: failed to save prm and xyz using ff96 Ross Walker (Tue Feb 28 2006 - 10:31:41 CST)
Re: AMBER: failed to save prm and xyz using ff96 Carlos Simmerling (Tue Feb 28 2006 - 11:24:23 CST)
AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 11:30:42 CST)
Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Wei Zhang (Tue Feb 28 2006 - 12:01:34 CST)
AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Tue Feb 28 2006 - 13:58:31 CST)
AMBER: Angle restraint venditti2_at_unisi.it (Tue Feb 28 2006 - 14:00:48 CST)
Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 16:27:07 CST)
Re: AMBER: Angle restraint David A. Case (Tue Feb 28 2006 - 17:54:40 CST)
Re: AMBER: How to develop charge for my deprotonated glycine FyD (Tue Feb 28 2006 - 23:00:37 CST)
Re: AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Wed Mar 01 2006 - 01:49:57 CST)
AMBER: install error biolabadmin_at_ibt.lt (Wed Mar 01 2006 - 05:13:12 CST)
AMBER: Nmode vs QM Freq Calculation Mark Williamson (Wed Mar 01 2006 - 05:28:57 CST)
AMBER: leap: syntax error when use source command Dmitry Osolodkin (Wed Mar 01 2006 - 06:27:47 CST)
RE:AMBER: leap: syntax error when use source command Kateryna Miroshnychenko (Wed Mar 01 2006 - 06:58:22 CST)
RE: AMBER: install error Ross Walker (Wed Mar 01 2006 - 10:08:24 CST)
AMBER: replica exchange hangs Peter Varnai (Wed Mar 01 2006 - 11:29:34 CST)
Re: AMBER: replica exchange hangs Sergey Krishtal (Wed Mar 01 2006 - 12:15:46 CST)
Re: AMBER: replica exchange hangs Carlos Simmerling (Wed Mar 01 2006 - 12:37:40 CST)
Re: AMBER: replica exchange hangs Carlos Simmerling (Wed Mar 01 2006 - 12:37:04 CST)
Re: AMBER: Nmode vs QM Freq Calculation David A. Case (Wed Mar 01 2006 - 12:54:12 CST)
Re: AMBER: replica exchange hangs Peter Varnai (Wed Mar 01 2006 - 12:56:21 CST)
Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman (Wed Mar 01 2006 - 14:51:09 CST)
AMBER: GAFF + AM1BCC & small-molecule aggregation Scott P Brown (Wed Mar 01 2006 - 14:00:33 CST)
Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Thomas E. Cheatham, III (Wed Mar 01 2006 - 15:17:35 CST)
Re: AMBER: failed to save prm and xyz using ff96 Viktor Hornak (Wed Mar 01 2006 - 15:16:13 CST)
Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling (Wed Mar 01 2006 - 15:34:06 CST)
Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman (Wed Mar 01 2006 - 17:29:18 CST)
Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling (Wed Mar 01 2006 - 16:00:40 CST)
AMBER: N-H and C-H Residual Dipolar Coupling thenmalar (Wed Mar 01 2006 - 16:01:52 CST)
Re: AMBER: N-H and C-H Residual Dipolar Coupling David A. Case (Wed Mar 01 2006 - 16:38:09 CST)
Re: AMBER: N-H and C-H Residual Dipolar Coupling thenmalar (Wed Mar 01 2006 - 18:59:34 CST)
AMBER: Amber 9. Sergey Krishtal (Wed Mar 01 2006 - 21:37:02 CST)
AMBER: Which PTRAJ distribution to use? Chng Choon-Peng (Thu Mar 02 2006 - 01:30:49 CST)
Re: AMBER: install error biolabadmin_at_ibt.lt (Thu Mar 02 2006 - 06:48:17 CST)
AMBER: transition metals and the parmcal of the antechamber module Cenk Andac (Thu Mar 02 2006 - 05:09:44 CST)
Re: AMBER: install error Mark Williamson (Thu Mar 02 2006 - 05:13:40 CST)
AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 10:00:00 CST)
RE: AMBER: amber8 and gfortran 4.1.0 Ross Walker (Thu Mar 02 2006 - 10:17:49 CST)
Re: AMBER: amber8 and gfortran 4.1.0 Andreas Svrcek-Seiler (Thu Mar 02 2006 - 10:35:16 CST)
Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 11:55:10 CST)
Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 11:57:59 CST)
Re: AMBER: amber8 and gfortran 4.1.0 David A. Case (Thu Mar 02 2006 - 12:07:05 CST)
AMBER: AMBER 8 VS AMBER 7 venditti2_at_unisi.it (Thu Mar 02 2006 - 13:54:47 CST)
Re: AMBER: AMBER 8 VS AMBER 7 David A. Case (Thu Mar 02 2006 - 14:42:39 CST)
Re: AMBER: AMBER 8 VS AMBER 7 Carlos Simmerling (Thu Mar 02 2006 - 15:04:09 CST)
RE: AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead (Thu Mar 02 2006 - 17:17:50 CST)
RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker (Thu Mar 02 2006 - 17:32:27 CST)
Re: AMBER: Which PTRAJ distribution to use? Thomas Cheatham (Thu Mar 02 2006 - 17:47:51 CST)
Re: AMBER: Which PTRAJ distribution to use? Chng Choon-Peng (Thu Mar 02 2006 - 18:27:15 CST)
AMBER: G95, SGI and Amber8 Cenk Andac (Fri Mar 03 2006 - 01:30:44 CST)
Re: AMBER: install error biolabadmin_at_ibt.lt (Fri Mar 03 2006 - 03:47:11 CST)
AMBER: about Br- parameters JAVIER PEREZ (Fri Mar 03 2006 - 04:18:23 CST)
Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x (Fri Mar 03 2006 - 04:28:40 CST)
Re: AMBER: about Br- parameters german (Fri Mar 03 2006 - 04:52:50 CST)
Re: AMBER: about Br- parameters Shulin Zhuang (Fri Mar 03 2006 - 05:04:27 CST)
Re: AMBER: about Br- parameters Mathy Froeyen (Fri Mar 03 2006 - 08:38:42 CST)
Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x (Fri Mar 03 2006 - 08:48:24 CST)
Re: AMBER: Amber 9. David A. Case (Fri Mar 03 2006 - 11:29:25 CST)
AMBER: from Wei Zhang: flight information Wei Zhang (Fri Mar 03 2006 - 12:45:59 CST)
Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Fri Mar 03 2006 - 13:05:41 CST)
Re: AMBER: How to develop charge for my deprotonated glycine FyD (Sat Mar 04 2006 - 03:26:13 CST)
Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Sat Mar 04 2006 - 21:05:12 CST)
AMBER: sander restart problem Vlad Cojocaru (Sun Mar 05 2006 - 07:31:30 CST)
AMBER: charge neutralization with GB Manish Datt (Sun Mar 05 2006 - 11:27:34 CST)
AMBER: ptraj:hbond question Yam (Sun Mar 05 2006 - 21:09:39 CST)
AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin (Mon Mar 06 2006 - 02:13:04 CST)
Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue Chng Choon-Peng (Mon Mar 06 2006 - 02:51:13 CST)
AMBER: the total energy is not converge as the cutoff increase thanyarat Udom (Mon Mar 06 2006 - 02:51:46 CST)
Re: AMBER: the total energy is not converge as the cutoff increase Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Mar 06 2006 - 03:28:52 CST)
Re: AMBER: the total energy is not converge as the cutoff increase Cenk Andac (Mon Mar 06 2006 - 07:28:04 CST)
AMBER: How to patch the configure script (macosx) K. Yarem (Mon Mar 06 2006 - 09:40:58 CST)
RE: AMBER: the total energy is not converge as the cutoff increase Ross Walker (Mon Mar 06 2006 - 09:39:51 CST)
Re: AMBER: sander restart problem Melinda Layten (Mon Mar 06 2006 - 11:35:01 CST)
Re: AMBER: How to patch the configure script (macosx) David A. Case (Mon Mar 06 2006 - 12:25:16 CST)
AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Mon Mar 06 2006 - 17:17:22 CST)
Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Ilyas Yildirim (Mon Mar 06 2006 - 17:42:29 CST)
Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Thomas Cheatham (Mon Mar 06 2006 - 17:51:08 CST)
AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Mon Mar 06 2006 - 18:28:14 CST)
AMBER: rms processing A D (Mon Mar 06 2006 - 18:21:01 CST)
Re: AMBER: rms processing Ilyas Yildirim (Mon Mar 06 2006 - 18:41:37 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 Carlos Simmerling (Mon Mar 06 2006 - 18:33:14 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Mon Mar 06 2006 - 20:05:31 CST)
AMBER: h bond analysis Claire Zerafa (Mon Mar 06 2006 - 23:39:52 CST)
AMBER: Amber 8 under Solaris 9 compilation failed Dror (Tue Mar 07 2006 - 01:12:19 CST)
AMBER: Amber 8 under Solaris 9 compilation failed Dror (Tue Mar 07 2006 - 01:03:03 CST)
RE: AMBER: the total energy is not converge as the cutoff increase thanyarat Udom (Tue Mar 07 2006 - 01:17:23 CST)
AMBER: ptraj: hbond analysis Yam (Tue Mar 07 2006 - 02:03:08 CST)
Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin (Tue Mar 07 2006 - 02:10:02 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Tue Mar 07 2006 - 06:51:14 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Tue Mar 07 2006 - 07:45:01 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Tue Mar 07 2006 - 10:26:23 CST)
Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Tue Mar 07 2006 - 10:23:21 CST)
Re: AMBER: Amber 8 under Solaris 9 compilation failed David A. Case (Tue Mar 07 2006 - 10:35:35 CST)
Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Tue Mar 07 2006 - 13:30:59 CST)
Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations David A. Case (Tue Mar 07 2006 - 13:47:30 CST)
Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Tue Mar 07 2006 - 13:55:13 CST)
AMBER: Trouble with combining a non-standard residue with a protein of standard residue Nitin Bhardwaj (Tue Mar 07 2006 - 15:21:44 CST)
AMBER: question about solvatecap commander aini_at_umdnj.edu (Tue Mar 07 2006 - 20:46:41 CST)
Re: AMBER: question about solvatecap commander David A. Case (Tue Mar 07 2006 - 21:32:12 CST)
Re: AMBER: question about solvatecap commander mfyang (Tue Mar 07 2006 - 21:07:08 CST)
AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed snowyowls (Wed Mar 08 2006 - 01:18:02 CST)
AMBER: NADP(H) parameters Simon Whitehead (Wed Mar 08 2006 - 04:06:45 CST)
AMBER: Dror (Wed Mar 08 2006 - 04:09:28 CST)
AMBER: converting .lib files Simon Whitehead (Wed Mar 08 2006 - 04:51:25 CST)
AMBER: Cosine content calculation matteo filandri (Wed Mar 08 2006 - 09:59:58 CST)
Re: AMBER: converting .lib files David A. Case (Wed Mar 08 2006 - 10:06:38 CST)
Re: AMBER: NADP(H) parameters David A. Case (Wed Mar 08 2006 - 10:26:04 CST)
Re: AMBER: converting .lib files Bill Ross (Wed Mar 08 2006 - 10:30:17 CST)
Re: AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed David A. Case (Wed Mar 08 2006 - 10:46:55 CST)
Re: AMBER: Cosine content calculation David A. Case (Wed Mar 08 2006 - 14:09:54 CST)
AMBER: modeling a non-standard molecule. Nitin Bhardwaj (Wed Mar 08 2006 - 15:02:50 CST)
Re: AMBER: modeling a non-standard molecule. Bill Ross (Wed Mar 08 2006 - 15:19:21 CST)
Re: AMBER: modeling a non-standard molecule. Nitin Bhardwaj (Wed Mar 08 2006 - 15:27:10 CST)
Re: AMBER: modeling a non-standard molecule. Bill Ross (Wed Mar 08 2006 - 15:47:50 CST)
AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett (Wed Mar 08 2006 - 15:59:18 CST)
Re: AMBER: aligning polymer with Z-axis of periodic box Ilyas Yildirim (Wed Mar 08 2006 - 16:54:22 CST)
Re: AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett (Wed Mar 08 2006 - 19:26:12 CST)
AMBER: bond parameters for positively charged guanidine group Ye Mei (Wed Mar 08 2006 - 20:54:15 CST)
AMBER: prepin format nkyx_at_sohu.com (Wed Mar 08 2006 - 21:18:15 CST)
AMBER: MD and MMPBSA alexandra.marques_at_fc.up.pt (Wed Mar 08 2006 - 22:29:23 CST)
RE: AMBER: MD and MMPBSA Ross Walker (Wed Mar 08 2006 - 23:26:34 CST)
Re: AMBER: Trouble with combining a non-standard residue with a protein of standard residue FyD (Wed Mar 08 2006 - 23:37:07 CST)
Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim (Thu Mar 09 2006 - 00:18:29 CST)
Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Thu Mar 09 2006 - 00:35:51 CST)
Re: Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim (Thu Mar 09 2006 - 01:22:17 CST)
Re: Re: AMBER: bond parameters for positively charged guanidine group FyD (Thu Mar 09 2006 - 02:22:05 CST)
Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Thu Mar 09 2006 - 02:40:14 CST)
Re: AMBER: Cosine content calculation matteo filandri (Thu Mar 09 2006 - 04:01:20 CST)
AMBER: CPU utilization with Parallel Sander Jingyuan Luke (Thu Mar 09 2006 - 06:14:01 CST)
RE: AMBER: CPU utilization with Parallel Sander Ross Walker (Thu Mar 09 2006 - 10:23:08 CST)
Re: AMBER: Cosine content calculation David A. Case (Thu Mar 09 2006 - 10:33:53 CST)
Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross (Thu Mar 09 2006 - 13:24:57 CST)
AMBER: RE: hi & question Ross Walker (Thu Mar 09 2006 - 16:14:02 CST)
AMBER: Power Mac G5 Shuting Wei (Thu Mar 09 2006 - 17:32:44 CST)
Re: AMBER: Power Mac G5 David A. Case (Thu Mar 09 2006 - 18:14:54 CST)
Re: AMBER: Cosine content calculation Hannes Loeffler (Thu Mar 09 2006 - 19:02:48 CST)
Re: AMBER: prepin format David A. Case (Fri Mar 10 2006 - 00:49:22 CST)
AMBER: Antechamber calculations Varsha Goyal (Fri Mar 10 2006 - 13:26:08 CST)
Re: AMBER: Antechamber calculations Vitor Manuel Sousa F?x (Fri Mar 10 2006 - 14:03:53 CST)
Re: AMBER: Antechamber calculations Varsha Goyal (Fri Mar 10 2006 - 17:47:41 CST)
AMBER: error while running sander snoze pa (Fri Mar 10 2006 - 22:23:54 CST)
Re: AMBER: error while running sander Thomas Cheatham (Fri Mar 10 2006 - 22:41:16 CST)
AMBER: Input conversion error. Sergey Krishtal (Sat Mar 11 2006 - 07:46:47 CST)
Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Sat Mar 11 2006 - 11:01:53 CST)
Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross (Sat Mar 11 2006 - 12:37:16 CST)
AMBER: divalent ions Ioana Cozmuta (Sat Mar 11 2006 - 13:04:00 CST)
Re: AMBER: Input conversion error. Carlos Simmerling (Sat Mar 11 2006 - 13:23:29 CST)
AMBER: using MM_PBSA just for binding site, feasible ??? tonglei (Sun Mar 12 2006 - 00:53:44 CST)
AMBER: Suitable water box simon whitehead (Mon Mar 13 2006 - 06:07:48 CST)
AMBER: amber 8 install problem qiwenpeng_at_sinap.ac.cn (Mon Mar 13 2006 - 07:22:01 CST)
AMBER: Steve Seibold (Mon Mar 13 2006 - 08:17:41 CST)
Re[2]: AMBER: Input conversion error. Sergey Krishtal (Mon Mar 13 2006 - 08:52:23 CST)
Re: AMBER: Suitable water box Jianzhong Liu (Mon Mar 13 2006 - 10:20:52 CST)
AMBER: NTT for production run snoze pa (Mon Mar 13 2006 - 12:03:32 CST)
Re: AMBER: David A. Case (Mon Mar 13 2006 - 12:40:19 CST)
Re: AMBER: amber 8 install problem David A. Case (Mon Mar 13 2006 - 12:44:40 CST)
Re: AMBER: Ilyas Yildirim (Mon Mar 13 2006 - 15:35:30 CST)
Re: AMBER: NTT for production run Vlad Cojocaru (Tue Mar 14 2006 - 02:44:35 CST)
AMBER: Xleap 64 bit installation problem Cenk Andac (Tue Mar 14 2006 - 05:37:18 CST)
Re: AMBER: Xleap 64 bit installation problem Andreas Svrcek-Seiler (Tue Mar 14 2006 - 06:16:47 CST)
AMBER: nucgen error bala (Tue Mar 14 2006 - 09:35:11 CST)
Re: AMBER: nucgen error Bill Ross (Tue Mar 14 2006 - 11:06:16 CST)
AMBER: divalent ions Ioana Cozmuta (Tue Mar 14 2006 - 13:54:49 CST)
Re: AMBER: divalent ions Thomas E. Cheatham, III (Tue Mar 14 2006 - 16:10:19 CST)
AMBER: quistions about pbsa cacultaion snowyowls (Tue Mar 14 2006 - 19:26:12 CST)
Re: AMBER: NTT for production run David A. Case (Tue Mar 14 2006 - 19:49:46 CST)
Re: AMBER: Xleap 64 bit installation problem David A. Case (Tue Mar 14 2006 - 20:06:30 CST)
Re: AMBER: quistions about pbsa cacultaion Ray Luo (Mon Mar 13 2006 - 01:26:53 CST)
Re: AMBER: quistions about pbsa cacultaion snowyowls (Tue Mar 14 2006 - 20:43:46 CST)
Re: AMBER: NTT for production run Vlad Cojocaru (Wed Mar 15 2006 - 02:53:46 CST)
Re: AMBER: amber 8 install problem qiwenpeng_at_sinap.ac.cn (Wed Mar 15 2006 - 08:27:00 CST)
RE: AMBER: NTT for production run Ross Walker (Wed Mar 15 2006 - 10:21:50 CST)
AMBER: k-space cutoff with standard Ewald Guowen (Wed Mar 15 2006 - 10:29:33 CST)
Re: AMBER: NTT for production run snoze pa (Wed Mar 15 2006 - 11:03:22 CST)
Re: AMBER: quistions about pbsa cacultaion Ray Luo (Wed Mar 15 2006 - 11:36:56 CST)
Re: AMBER: NTT for production run David A. Case (Wed Mar 15 2006 - 14:21:52 CST)
Re: AMBER: amber 8 install problem David A. Case (Wed Mar 15 2006 - 14:33:08 CST)
Re: AMBER: amber 8 install problem David A. Case (Wed Mar 15 2006 - 16:00:08 CST)
Re: AMBER: NTT for production run Vlad Cojocaru (Thu Mar 16 2006 - 03:56:46 CST)
AMBER: Zoom Angelo (Thu Mar 16 2006 - 04:24:39 CST)
Re: AMBER: Zoom Laurent Chiche (Thu Mar 16 2006 - 09:37:38 CST)
AMBER: mm-pbsa vorasit vongsutilers (Thu Mar 16 2006 - 09:34:33 CST)
Re: AMBER: Zoom Angelo (Thu Mar 16 2006 - 09:57:32 CST)
Re: AMBER: Zoom Laurent Chiche (Thu Mar 16 2006 - 10:40:42 CST)
Re: AMBER: Zoom Angelo (Thu Mar 16 2006 - 11:04:05 CST)
Re: AMBER: mm-pbsa Holger Gohlke (Thu Mar 16 2006 - 11:33:20 CST)
Re: AMBER: NTT for production run David A. Case (Thu Mar 16 2006 - 12:00:54 CST)
AMBER: faulty ambpdb compilation? Benjamin Juhl (Thu Mar 16 2006 - 12:16:12 CST)
RE: AMBER: faulty ambpdb compilation? Ross Walker (Thu Mar 16 2006 - 12:44:23 CST)
Re: AMBER: faulty ambpdb compilation? Benjamin Juhl (Thu Mar 16 2006 - 12:51:47 CST)
AMBER: constant pH simulation Abhilash Mohan (Thu Mar 16 2006 - 13:14:47 CST)
Re: AMBER: Zoom Ilyas Yildirim (Thu Mar 16 2006 - 13:50:12 CST)
Re: AMBER: NTT for production run Vlad Cojocaru (Fri Mar 17 2006 - 03:16:36 CST)
Re: AMBER: mm-pbsa vorasit vongsutilers (Fri Mar 17 2006 - 08:03:15 CST)
Re: AMBER: mm-pbsa Scott Pendley (Fri Mar 17 2006 - 17:41:30 CST)
AMBER: prep files for L-sugar residues Qizhi Cui (Fri Mar 17 2006 - 20:42:56 CST)
Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Mar 19 2006 - 03:10:22 CST)
AMBER: Ewald and ibelly Austin B. Yongye (Sun Mar 19 2006 - 10:36:53 CST)
Re: AMBER: mm-pbsa vorasit vongsutilers (Sun Mar 19 2006 - 11:45:15 CST)
Re: AMBER: Ewald and ibelly David A. Case (Mon Mar 20 2006 - 00:26:17 CST)
AMBER: emilia wu (Mon Mar 20 2006 - 06:38:17 CST)
AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1) Vlad Cojocaru (Mon Mar 20 2006 - 10:40:37 CST)
Re: AMBER: mm-pbsa Scott Pendley (Mon Mar 20 2006 - 12:06:38 CST)
AMBER: a challenge: a periodic box that cuts through a monomer Kenley Barrett (Mon Mar 20 2006 - 16:06:49 CST)
Re: AMBER: rms processing Jianyin Shao (Mon Mar 20 2006 - 16:19:25 CST)
AMBER: anal: dihedral error renyanliang (Mon Mar 20 2006 - 19:27:39 CST)
Re: AMBER: a challenge: a periodic box that cuts through a monomer David A. Case (Tue Mar 21 2006 - 00:29:33 CST)
Re: AMBER: David A. Case (Tue Mar 21 2006 - 00:36:09 CST)
AMBER: MMPBSA alexandra.marques_at_fc.up.pt (Tue Mar 21 2006 - 03:58:35 CST)
AMBER: heating system snoze pa (Tue Mar 21 2006 - 15:58:25 CST)
RE: AMBER: heating system Ross Walker (Tue Mar 21 2006 - 17:09:28 CST)
Re: AMBER: heating system snoze pa (Tue Mar 21 2006 - 17:39:15 CST)
Re: AMBER: constant pH simulation John Mongan (Tue Mar 21 2006 - 17:51:53 CST)
AMBER: About statistics results in MMPBSA_DC pair Àò ÕÅ (Wed Mar 22 2006 - 09:22:17 CST)
RE: AMBER: heating system Ross Walker (Wed Mar 22 2006 - 10:58:12 CST)
AMBER: Related to RESTRAINT_WT snoze pa (Wed Mar 22 2006 - 16:06:04 CST)
Re: AMBER: Related to RESTRAINT_WT David A. Case (Wed Mar 22 2006 - 18:15:29 CST)
Re: AMBER: Related to RESTRAINT_WT Chng Choon-Peng (Wed Mar 22 2006 - 18:16:13 CST)
AMBER: Solvating the system with specific number of water molecules... Ilyas Yildirim (Wed Mar 22 2006 - 23:50:25 CST)
AMBER: about atomic fluctuation & RMSF xueping (Thu Mar 23 2006 - 04:05:03 CST)
AMBER: question capping helix ends Zhuang (Thu Mar 23 2006 - 04:35:21 CST)
Re: AMBER: question capping helix ends Vlad Cojocaru (Thu Mar 23 2006 - 04:48:14 CST)
AMBER: what is unit of the out put of mmpbsa caculation snowyowls (Thu Mar 23 2006 - 06:47:52 CST)
Re: AMBER: what is unit of the out put of mmpbsa caculation Holger Gohlke (Thu Mar 23 2006 - 06:53:51 CST)
Re: AMBER: about atomic fluctuation & RMSF Holger Gohlke (Thu Mar 23 2006 - 07:01:14 CST)
AMBER: Average pdb Claire Zerafa (Thu Mar 23 2006 - 15:17:33 CST)
RE: AMBER: Average pdb John Jett (Thu Mar 23 2006 - 16:32:00 CST)
AMBER: question capping helix ends Zhuang (Thu Mar 23 2006 - 18:21:06 CST)
AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? amanda.mccook_at_gatech.edu (Thu Mar 23 2006 - 22:32:39 CST)
RE: AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? Ross Walker (Thu Mar 23 2006 - 23:38:24 CST)
Re: AMBER: question capping helix ends Cenk Andac (Fri Mar 24 2006 - 03:09:11 CST)
Re: AMBER: question capping helix ends Vlad Cojocaru (Fri Mar 24 2006 - 04:51:24 CST)
RE: AMBER: heating system Ross Walker (Fri Mar 24 2006 - 11:29:32 CST)
Re: AMBER: anal: dihedral error David A. Case (Sat Mar 25 2006 - 14:48:36 CST)
AMBER: negative values of PBSOL and PBCAL in mm_pbsa result tonglei (Sun Mar 26 2006 - 20:07:47 CST)
Re: AMBER: about atomic fluctuation & RMSF xueping (Sun Mar 26 2006 - 20:39:45 CST)
AMBER: temp control snoze pa (Sun Mar 26 2006 - 21:16:20 CST)
To dac --AMBER: anal: dihedral error Àò ÕÅ (Mon Mar 27 2006 - 00:43:22 CST)
Re: AMBER: Amber 8 under Solaris 9 compilation failed Scott Brozell (Mon Mar 27 2006 - 01:16:27 CST)
AMBER: OSX 10.4 G4 xlf90 compilation errors K. Yarem (Mon Mar 27 2006 - 14:06:59 CST)
Re: AMBER: OSX 10.4 G4 xlf90 compilation errors David Case (Mon Mar 27 2006 - 14:18:27 CST)
AMBER: How to give the specific pressure parameter for NTP=2 hbluo (Tue Mar 28 2006 - 11:29:48 CST)
AMBER: united atoms nadiav_at_soton.ac.uk (Tue Mar 28 2006 - 05:04:53 CST)
AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 09:14:59 CST)
Re: AMBER: amber8 error installation Mark Williamson (Tue Mar 28 2006 - 09:23:28 CST)
Re: AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 09:44:42 CST)
Re: AMBER: amber8 error installation Mark Williamson (Tue Mar 28 2006 - 10:08:46 CST)
Re: AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 10:27:37 CST)
RE: AMBER: amber8 error installation Ross Walker (Tue Mar 28 2006 - 10:37:34 CST)
Re: AMBER: united atoms Bill Ross (Tue Mar 28 2006 - 11:02:01 CST)
AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 15:48:19 CST)
Re: AMBER: hessian calculation David A. Case (Tue Mar 28 2006 - 17:52:14 CST)
Re: AMBER: hessian calculation sebnem_at_mercury.chem.pitt.edu (Tue Mar 28 2006 - 18:20:18 CST)
AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W (Tue Mar 28 2006 - 20:00:46 CST)
Re: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) David A. Case (Tue Mar 28 2006 - 20:13:44 CST)
Re: AMBER: hessian calculation David A. Case (Tue Mar 28 2006 - 20:15:58 CST)
RE: AMBER: amber8 error installation John Bushnell (Tue Mar 28 2006 - 20:20:42 CST)
Re: AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 20:41:52 CST)
Re: AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 20:53:59 CST)
AMBER: installation problem r. a. (Tue Mar 28 2006 - 21:21:50 CST)
Re: AMBER: installation problem Mark Williamson (Tue Mar 28 2006 - 21:40:27 CST)
Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W (Tue Mar 28 2006 - 21:44:42 CST)
Re: AMBER: installation problem Abd Ghani Abd Aziz (Tue Mar 28 2006 - 21:50:08 CST)
Re: Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Thomas Cheatham (Tue Mar 28 2006 - 22:32:37 CST)
RE: AMBER: amber8 error installation Ross Walker (Tue Mar 28 2006 - 22:35:03 CST)
RE: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Ross Walker (Tue Mar 28 2006 - 22:35:03 CST)
AMBER: Impropers definition egorov (Wed Mar 29 2006 - 00:06:40 CST)
AMBER: Simulating a periodic crystal Jiang Jianwen (Wed Mar 29 2006 - 09:01:26 CST)
Re: AMBER: Simulating a periodic crystal Thomas Cheatham (Wed Mar 29 2006 - 09:57:10 CST)
AMBER: Announcement: Amber 9 is now available David A. Case (Wed Mar 29 2006 - 10:43:59 CST)
Re: AMBER: Impropers definition David A. Case (Wed Mar 29 2006 - 11:10:27 CST)
Re: AMBER: hessian calculation sebnem_at_mercury.chem.pitt.edu (Wed Mar 29 2006 - 15:48:38 CST)
AMBER: Dimer Image Wrapping Melinda Layten (Wed Mar 29 2006 - 17:12:00 CST)
Re: AMBER: hessian calculation David A. Case (Wed Mar 29 2006 - 18:08:34 CST)
AMBER: post-processing replica exchange trajectory Zhuang (Wed Mar 29 2006 - 17:57:43 CST)
AMBER: Problem with setbox command... Ilyas Yildirim (Thu Mar 30 2006 - 01:44:37 CST)
Re: AMBER: Problem with setbox command... David A. Case (Thu Mar 30 2006 - 10:06:04 CST)
AMBER: charge constraints in resp Kenley Barrett (Thu Mar 30 2006 - 10:22:36 CST)
Re: AMBER: hessian calculation sebnem (Thu Mar 30 2006 - 10:22:23 CST)
Re: AMBER: charge constraints in resp Ilyas Yildirim (Thu Mar 30 2006 - 11:03:43 CST)
Re: AMBER: Dimer Image Wrapping Scott Pendley (Thu Mar 30 2006 - 11:29:23 CST)
Re: AMBER: Dimer Image Wrapping Melinda Layten (Thu Mar 30 2006 - 12:16:06 CST)
AMBER: Gromos to Amber Ann Vilan Tran (Thu Mar 30 2006 - 13:29:07 CST)
Re: AMBER: charge constraints in resp Kenley Barrett (Thu Mar 30 2006 - 13:46:49 CST)
Re: AMBER: charge constraints in resp Ilyas Yildirim (Thu Mar 30 2006 - 18:05:35 CST)
AMBER: LES error Claudia Steinert (Fri Mar 31 2006 - 01:59:36 CST)
RE: AMBER: Simulating a periodic crystal Jiang Jianwen (Fri Mar 31 2006 - 05:31:47 CST)
Re: AMBER: Problem with setbox command... Ilyas Yildirim (Fri Mar 31 2006 - 06:34:33 CST)
AMBER: Ptraj & pca Claire Zerafa (Fri Mar 31 2006 - 08:23:05 CST)
AMBER: MMPBSA & PBCAL Rabal Gracia María Obdulia (Fri Mar 31 2006 - 09:37:57 CST)
Re: AMBER: Announcement: Amber 9 is now available David E. Konerding (Fri Mar 31 2006 - 10:38:06 CST)
Re: AMBER: Announcement: Amber 9 is now available David A. Case (Fri Mar 31 2006 - 10:56:48 CST)
Re: AMBER: Announcement: Amber 9 is now available David A. Case (Fri Mar 31 2006 - 11:29:54 CST)
AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE fine wu (Fri Mar 31 2006 - 16:09:36 CST)
Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Thomas E. Cheatham, III (Fri Mar 31 2006 - 16:18:57 CST)
AMBER: chirality.c error in xleap Kenley Barrett (Fri Mar 31 2006 - 16:43:33 CST)
Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Ilyas Yildirim (Fri Mar 31 2006 - 18:46:03 CST)
Re: AMBER: chirality.c error in xleap David A. Case (Fri Mar 31 2006 - 19:41:53 CST)
AMBER: what is the integration scheme for langevin dynamic used in amber8 Li Su (Sat Apr 01 2006 - 07:17:02 CST)
Re: AMBER: Announcement: Amber 9 is now available Thomas Patko (CSULB) (Sat Apr 01 2006 - 10:29:26 CST)
Re: AMBER: what is the integration scheme for langevin dynamic used in amber8 David A. Case (Sat Apr 01 2006 - 11:18:57 CST)
Re: AMBER: Announcement: Amber 9 is now available David A. Case (Sat Apr 01 2006 - 11:21:52 CST)
Re: AMBER: LES error carlos (Sat Apr 01 2006 - 12:04:46 CST)
AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! Pradipta Bandyopadhyay (Mon Apr 03 2006 - 00:23:26 CDT)
Re: AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! David A. Case (Mon Apr 03 2006 - 09:57:36 CDT)
Re: AMBER: Announcement: Amber 9 is now available Feng X Zhou (Mon Apr 03 2006 - 10:28:48 CDT)
Re: AMBER: Announcement: Amber 9 is now available FyD (Mon Apr 03 2006 - 13:00:44 CDT)
AMBER: RMS Wen Li (Mon Apr 03 2006 - 16:03:29 CDT)
Re: AMBER: RMS carlos (Mon Apr 03 2006 - 16:18:24 CDT)
AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Evan Kelly (Mon Apr 03 2006 - 17:28:27 CDT)
RE: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Ross Walker (Mon Apr 03 2006 - 18:53:06 CDT)
AMBER: Entropy calculations with Nmode and ptraj Daniel Oehme (Tue Apr 04 2006 - 02:24:39 CDT)
AMBER: how to restrain the intramolecular hydrogen bond Ye Mei (Tue Apr 04 2006 - 04:35:42 CDT)
AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? tonglei (Tue Apr 04 2006 - 08:10:59 CDT)
Re: AMBER: RMS Wen Li (Tue Apr 04 2006 - 08:59:04 CDT)
Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 10:02:02 CDT)
Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 10:17:14 CDT)
AMBER: Any difference about RESP or ESP with Chelpg or MK Jianzhong Liu (Tue Apr 04 2006 - 10:51:36 CDT)
Re: AMBER: Any difference about RESP or ESP with Chelpg or MK FyD (Tue Apr 04 2006 - 12:01:40 CDT)
Re: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? David A. Case (Tue Apr 04 2006 - 17:11:51 CDT)
Re: AMBER: Any difference about RESP or ESP with Chelpg or MK David Mobley (Tue Apr 04 2006 - 17:13:30 CDT)
AMBER: Using XML for Amber files David A. Case (Tue Apr 04 2006 - 17:42:35 CDT)
Re: AMBER: Entropy calculations with Nmode and ptraj David A. Case (Tue Apr 04 2006 - 17:50:55 CDT)
Re: AMBER: how to restrain the intramolecular hydrogen bond David A. Case (Tue Apr 04 2006 - 17:52:52 CDT)
AMBER: Obtaining an average structure from a trajectory Alfredo Quevedo (Tue Apr 04 2006 - 18:11:02 CDT)
RE: AMBER: Obtaining an average structure from a trajectory Ross Walker (Tue Apr 04 2006 - 19:07:18 CDT)
AMBER: molsurf or LCPO method in MM_GB/SA? tonglei (Tue Apr 04 2006 - 20:25:37 CDT)
AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Wed Apr 05 2006 - 01:47:06 CDT)
AMBER: nmode different units cristian obiol (Wed Apr 05 2006 - 05:47:04 CDT)
AMBER: Claire Zerafa (Wed Apr 05 2006 - 08:33:39 CDT)
Re: AMBER: David A. Case (Wed Apr 05 2006 - 09:46:18 CDT)
RE: AMBER: Using XML for Amber files Feng X Zhou (Wed Apr 05 2006 - 10:21:35 CDT)
AMBER: Restarting constant pressure sims with restraints Don.Bashford_at_stjude.org (Wed Apr 05 2006 - 13:08:41 CDT)
Re: AMBER: Restarting constant pressure sims with restraints David A. Case (Wed Apr 05 2006 - 13:24:38 CDT)
Re: AMBER: Restarting constant pressure sims with restraints Robert Duke (Wed Apr 05 2006 - 13:30:05 CDT)
AMBER: Question about interpretation of sander.QMMM results Cenk Andac (Thu Apr 06 2006 - 14:10:09 CDT)
AMBER: MM-GBSA decomposition sishi.tang_at_utoronto.ca (Thu Apr 06 2006 - 15:20:36 CDT)
AMBER: PCA venditti2_at_unisi.it (Thu Apr 06 2006 - 15:27:20 CDT)
Re: AMBER: one question about mm_pbsa JunJun Liu (Thu Apr 06 2006 - 16:48:20 CDT)
AMBER: organic molecule - from newbie :) Raffaella D'Auria (Thu Apr 06 2006 - 20:55:02 CDT)
RE: AMBER: organic molecule - from newbie :) Ross Walker (Thu Apr 06 2006 - 21:13:46 CDT)
AMBER: POPC parameters xiaoqin huang (Thu Apr 06 2006 - 22:18:10 CDT)
AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Fri Apr 07 2006 - 01:05:50 CDT)
Re: AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Fri Apr 07 2006 - 01:20:16 CDT)
Re: AMBER: POPC parameters David A. Case (Fri Apr 07 2006 - 11:14:53 CDT)
AMBER: angle between planes John (Fri Apr 07 2006 - 11:48:38 CDT)
AMBER: angle between planes John (Fri Apr 07 2006 - 11:55:59 CDT)
Re: AMBER: Using XML for Amber files Xuebin Qiao (Fri Apr 07 2006 - 12:52:08 CDT)
Re: AMBER: Using XML for Amber files Feng X Zhou (Fri Apr 07 2006 - 13:54:59 CDT)
AMBER: Umbrella sampling venditti2_at_unisi.it (Fri Apr 07 2006 - 15:04:55 CDT)
Re: AMBER: Umbrella sampling David A. Case (Fri Apr 07 2006 - 15:56:48 CDT)
Re: AMBER: angle between planes Chris Moth (Fri Apr 07 2006 - 16:19:26 CDT)
AMBER: mm-pbsa: distant-dependent dielectric constant lhsong (Sat Apr 08 2006 - 13:30:56 CDT)
Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sun Apr 09 2006 - 00:23:15 CDT)
Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sun Apr 09 2006 - 01:11:49 CDT)
Re: AMBER: PCA Holger Gohlke (Sun Apr 09 2006 - 13:09:06 CDT)
Re: AMBER: MM-GBSA decomposition Holger Gohlke (Sun Apr 09 2006 - 13:13:41 CDT)
AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 07:15:16 CDT)
AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 07:55:12 CDT)
AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 09:41:51 CDT)
Re: AMBER: PCA venditti2_at_unisi.it (Mon Apr 10 2006 - 09:57:41 CDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Scott Brozell (Mon Apr 10 2006 - 09:59:46 CDT)
Re: AMBER: printing Amber VdW radii as separate column in pdb files harianto (Mon Apr 10 2006 - 10:12:39 CDT)
Re: AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 10:43:18 CDT)
RE: AMBER: printing Amber VdW radii as separate column in pdb files Ross Walker (Mon Apr 10 2006 - 11:03:18 CDT)
AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 11:14:16 CDT)
Re: AMBER: VdW radii in the topology file harianto (Mon Apr 10 2006 - 11:51:55 CDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Ray Luo (Sun Apr 09 2006 - 21:44:44 CDT)
Re: AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 12:01:33 CDT)
Re: AMBER: "average" command in ptraj Thomas E. Cheatham, III (Mon Apr 10 2006 - 13:06:20 CDT)
AMBER: reconstructing PMF Ioana Cozmuta (Mon Apr 10 2006 - 13:15:20 CDT)
Re: AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 13:50:34 CDT)
AMBER: "vector" command in ptraj Lishan Yao (Mon Apr 10 2006 - 13:20:56 CDT)
AMBER: protocols for NMR protein refinement with AMBER ohucke_at_lav.boehringer-ingelheim.com (Mon Apr 10 2006 - 15:43:44 CDT)
Re: AMBER: protocols for NMR protein refinement with AMBER David A. Case (Mon Apr 10 2006 - 15:55:43 CDT)
RE: AMBER: organic molecule - from newbie :) Raffaella D'Auria (Mon Apr 10 2006 - 17:12:44 CDT)
RE: AMBER: organic molecule - from newbie :) Ross Walker (Mon Apr 10 2006 - 17:41:56 CDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 22:09:35 CDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 22:07:40 CDT)
AMBER: the best force field for DNA Chengwen Chen (Mon Apr 10 2006 - 23:15:25 CDT)
Re: AMBER: PCA Holger Gohlke (Tue Apr 11 2006 - 07:27:26 CDT)
AMBER: RESP problem Simon Whitehead (Tue Apr 11 2006 - 08:44:00 CDT)
RE: AMBER: RESP problem Ross Walker (Tue Apr 11 2006 - 10:08:25 CDT)
Re: AMBER: RESP problem FyD (Tue Apr 11 2006 - 11:31:12 CDT)
AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 Mathy Froeyen (Tue Apr 11 2006 - 12:44:40 CDT)
AMBER: How to evaluate the binding energy of a ligand? Alfredo Quevedo (Tue Apr 11 2006 - 12:53:50 CDT)
Re: AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 David A. Case (Tue Apr 11 2006 - 13:19:59 CDT)
AMBER: An issue with the "multimolecule and multiconformational" resp fit Jason K (Tue Apr 11 2006 - 13:16:57 CDT)
AMBER: Nmode memory allocation error ? Junmei Wang (Tue Apr 11 2006 - 13:47:46 CDT)
Re: AMBER: Nmode memory allocation error ? David A. Case (Tue Apr 11 2006 - 14:09:26 CDT)
Re: AMBER: How to evaluate the binding energy of a ligand? David Mobley (Tue Apr 11 2006 - 14:27:13 CDT)
Re: AMBER: An issue with the "multimolecule and multiconformational" resp fit FyD (Tue Apr 11 2006 - 14:39:40 CDT)
AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Tue Apr 11 2006 - 23:40:00 CDT)
AMBER: Mass wieghted Covariance Matrix Daniel Oehme (Wed Apr 12 2006 - 02:16:32 CDT)
Re: AMBER: Mass wieghted Covariance Matrix Holger Gohlke (Wed Apr 12 2006 - 02:46:19 CDT)
AMBER: deviations from idealized geometry Maarit Hellman (Wed Apr 12 2006 - 04:02:33 CDT)
Re: AMBER: Constant P for non-orthorhombic cells darden (Wed Apr 12 2006 - 07:41:14 CDT)
AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 11:36:20 CDT)
Re: AMBER: Constant P for non-orthorhombic cells Michael Crowley (Wed Apr 12 2006 - 13:24:05 CDT)
Re: AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Wed Apr 12 2006 - 13:36:47 CDT)
Re: AMBER: saltcon with explicit water? David A. Case (Wed Apr 12 2006 - 14:25:38 CDT)
Re: AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 18:07:44 CDT)
Re: AMBER: saltcon with explicit water? Bill Ross (Wed Apr 12 2006 - 18:26:05 CDT)
AMBER: Which one is the best force field for DNA? Chengwen Chen (Wed Apr 12 2006 - 22:11:14 CDT)
AMBER:a problem in parallel compiler snowyowls (Wed Apr 12 2006 - 23:27:10 CDT)
AMBER: Dual Xeon mpich compilation error Simon Whitehead (Thu Apr 13 2006 - 02:56:47 CDT)
Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Thu Apr 13 2006 - 03:11:33 CDT)
AMBER:a problem in parallel compiler snowyowls (Thu Apr 13 2006 - 03:15:09 CDT)
AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Thu Apr 13 2006 - 03:37:50 CDT)
AMBER: dual xeon mpich compilation problem: sorted Simon Whitehead (Thu Apr 13 2006 - 07:16:53 CDT)
Re: AMBER: one question about mm_pbsa Ray Luo (Thu Apr 13 2006 - 10:39:53 CDT)
AMBER: passwordless ssh stopped working Jan Dohnalek (Thu Apr 13 2006 - 10:51:50 CDT)
RE: AMBER:a problem in parallel compiler Ross Walker (Thu Apr 13 2006 - 10:54:43 CDT)
AMBER: Respgen segemtation fault Simon Whitehead (Thu Apr 13 2006 - 11:38:41 CDT)
AMBER: separating LES copies in moil view Amber admin (Thu Apr 13 2006 - 12:28:02 CDT)
Re: AMBER: Respgen segemtation fault David A. Case (Thu Apr 13 2006 - 13:46:55 CDT)
Re: AMBER: Which one is the best force field for DNA? David A. Case (Thu Apr 13 2006 - 16:41:03 CDT)
Re: AMBER: separating LES copies in moil view Carlos Simmerling (Thu Apr 13 2006 - 18:45:35 CDT)
Re: AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Thu Apr 13 2006 - 21:26:49 CDT)
AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Sergey Krishtal (Thu Apr 13 2006 - 22:05:45 CDT)
Re: AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Vlad Cojocaru (Fri Apr 14 2006 - 04:18:41 CDT)
Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 04:57:33 CDT)
Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 05:31:24 CDT)
Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 10:27:52 CDT)
AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 10:27:43 CDT)
Re: AMBER: Which one is the best force field for DNA? Thomas E. Cheatham, III (Fri Apr 14 2006 - 11:01:50 CDT)
Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 11:30:23 CDT)
Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 11:41:04 CDT)
Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 11:49:58 CDT)
Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 11:57:52 CDT)
Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 11:59:00 CDT)
Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 12:01:27 CDT)
Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 12:08:34 CDT)
Re: AMBER: Which one is the best force field for DNA? Thomas Cheatham (Fri Apr 14 2006 - 12:20:14 CDT)
Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 12:53:50 CDT)
Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 13:28:42 CDT)
AMBER: DNA tutorial, in vacuo minimization amanda.mccook_at_gatech.edu (Fri Apr 14 2006 - 14:15:31 CDT)
RE: AMBER: DNA tutorial, in vacuo minimization Ross Walker (Fri Apr 14 2006 - 14:34:32 CDT)
Re: AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 16:07:20 CDT)
Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 16:40:45 CDT)
AMBER: compile error: can't locate file for: -lcrt1.o xyu3 (Fri Apr 14 2006 - 17:37:50 CDT)
AMBER: amber memory usage Ed Pate (Fri Apr 14 2006 - 17:45:59 CDT)
Re: AMBER: amber memory usage Robert Duke (Fri Apr 14 2006 - 17:56:12 CDT)
Re: AMBER: compile error: can't locate file for: -lcrt1.o David A. Case (Fri Apr 14 2006 - 17:58:33 CDT)
AMBER: How I wasted a rainy Friday in San Diego David A. Case (Fri Apr 14 2006 - 19:24:00 CDT)
RE: AMBER: amber memory usage Ross Walker (Fri Apr 14 2006 - 19:28:31 CDT)
Re: AMBER: amber memory usage David A. Case (Fri Apr 14 2006 - 19:30:44 CDT)
AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Sun Apr 16 2006 - 05:33:25 CDT)
AMBER: amber7 compiling error linfu (Sun Apr 16 2006 - 10:26:17 CDT)
Re: AMBER: amber7 compiling error Scott Brozell (Sun Apr 16 2006 - 14:30:23 CDT)
AMBER: Could not find atom type. Sergey Krishtal (Mon Apr 17 2006 - 04:08:19 CDT)
AMBER: Force field for DNA Osmar Norberto de Souza (Mon Apr 17 2006 - 05:50:31 CDT)
Re: AMBER: Calculation of g(r) from PTRAJ David A. Case (Mon Apr 17 2006 - 11:45:27 CDT)
Re: AMBER: Could not find atom type. David A. Case (Mon Apr 17 2006 - 11:40:05 CDT)
RE: AMBER: Could not find atom type. Yong Duan (Mon Apr 17 2006 - 11:45:10 CDT)
Re: AMBER: MM-PBSA problem Miguel Ferreira (Mon Apr 17 2006 - 12:24:05 CDT)
Re: AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Mon Apr 17 2006 - 12:45:39 CDT)
AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 13:20:05 CDT)
RE: AMBER: ambpdb and original PDB Ross Walker (Mon Apr 17 2006 - 13:28:18 CDT)
Re: AMBER: ambpdb and original PDB Bill Ross (Mon Apr 17 2006 - 13:38:17 CDT)
Re: AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 13:48:55 CDT)
Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 15:00:53 CDT)
Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 15:05:43 CDT)
AMBER: probable bug in antechamber David Mobley (Mon Apr 17 2006 - 18:08:06 CDT)
Re: AMBER: probable bug in antechamber David A. Case (Mon Apr 17 2006 - 19:33:35 CDT)
AMBER: ibelly & fix atom rdauria_at_uci.edu (Mon Apr 17 2006 - 22:41:28 CDT)
Re: AMBER: ibelly & fix atom rdauria_at_uci.edu (Mon Apr 17 2006 - 22:59:56 CDT)
RE: AMBER: ibelly & fix atom Ross Walker (Mon Apr 17 2006 - 23:08:42 CDT)
RE: AMBER: ibelly & fix atom rdauria_at_uci.edu (Mon Apr 17 2006 - 23:22:16 CDT)
AMBER: Error in the MD run Ananda Rama Krishnan Selvaraj (Tue Apr 18 2006 - 01:13:04 CDT)
Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 05:48:07 CDT)
Re: AMBER: probable bug in antechamber David Mobley (Tue Apr 18 2006 - 08:52:13 CDT)
Re: AMBER: MM-GBSA decomposition sishi.tang_at_utoronto.ca (Sat Apr 15 2006 - 12:54:34 CDT)
RE: AMBER: Error in the MD run Ross Walker (Tue Apr 18 2006 - 10:35:41 CDT)
AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Tue Apr 18 2006 - 10:42:41 CDT)
Re: AMBER: Could not find atom type. David A. Case (Tue Apr 18 2006 - 18:06:21 CDT)
Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 21:56:30 CDT)
Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Shulin Zhuang (Wed Apr 19 2006 - 00:58:06 CDT)
RE: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Wed Apr 19 2006 - 10:16:51 CDT)
AMBER: RE: Respgen segemtation fault Simon Whitehead (Wed Apr 19 2006 - 12:10:11 CDT)
AMBER: Installing Delphi to perform mm_pbsa analysis? Alfredo Quevedo (Wed Apr 19 2006 - 12:39:13 CDT)
Re: AMBER: Could not find atom type. David A. Case (Wed Apr 19 2006 - 14:37:33 CDT)
Re: AMBER: Installing Delphi to perform mm_pbsa analysis? David A. Case (Wed Apr 19 2006 - 14:43:46 CDT)
AMBER: timing estimates Ed Pate (Wed Apr 19 2006 - 18:10:30 CDT)
Re: AMBER: timing estimates Robert Duke (Wed Apr 19 2006 - 19:06:59 CDT)
Re: AMBER: RE: Respgen segemtation fault David A. Case (Thu Apr 20 2006 - 06:49:34 CDT)
Re: AMBER: RE: Respgen segemtation fault Simon Whitehead (Thu Apr 20 2006 - 07:30:48 CDT)
RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 07:48:07 CDT)
Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 08:23:55 CDT)
AMBER: about the decomposition energies using mm/pbsa litong (Thu Apr 20 2006 - 08:34:11 CDT)
AMBER: Non-periodic simulations: How is the system kept together? pascal.baillod_at_epfl.ch (Thu Apr 20 2006 - 11:13:04 CDT)
RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 11:30:51 CDT)
RE: AMBER: Non-periodic simulations: How is the system kept together? Ross Walker (Thu Apr 20 2006 - 11:35:26 CDT)
Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 11:56:55 CDT)
AMBER: Antechamber & atom types FyD (Thu Apr 20 2006 - 12:04:17 CDT)
AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Fri Apr 21 2006 - 01:48:14 CDT)
Re: AMBER: about the decomposition energies using mm/pbsa Holger Gohlke (Fri Apr 21 2006 - 02:25:44 CDT)
AMBER: Error when compiling amber9 ptraj Thomas Steinbrecher (Fri Apr 21 2006 - 03:19:54 CDT)
AMBER: a question german (Fri Apr 21 2006 - 06:04:54 CDT)
AMBER: problems with saveamberprep command JAVIER PEREZ (Fri Apr 21 2006 - 06:33:48 CDT)
Re: AMBER: Error when compiling amber9 ptraj David A. Case (Fri Apr 21 2006 - 07:08:15 CDT)
AMBER: mm_pbsa: "Missing values for MM ..." Sam (Fri Apr 21 2006 - 08:39:19 CDT)
AMBER: Problems compiling amber9 Thomas Steinbrecher (Fri Apr 21 2006 - 09:27:51 CDT)
AMBER: Fujitsu frt compiler Evan Kelly (Fri Apr 21 2006 - 09:53:40 CDT)
Re: AMBER: Problems compiling amber9 David A. Case (Fri Apr 21 2006 - 10:03:37 CDT)
Re: AMBER: Antechamber & atom types David A. Case (Fri Apr 21 2006 - 10:22:45 CDT)
Re: AMBER: a question about "solvateoct" in AMBER 8 Bill Ross (Fri Apr 21 2006 - 13:48:01 CDT)
Re: AMBER: a question about "solvateoct" in AMBER 8 Michael Crowley (Fri Apr 21 2006 - 14:50:52 CDT)
RE: AMBER: a question Ross Walker (Fri Apr 21 2006 - 15:35:51 CDT)
AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 12:58:26 CDT)
RE: AMBER: amber9 compilation error on SGI altix Ross Walker (Sat Apr 22 2006 - 14:21:24 CDT)
RE: AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 17:48:40 CDT)
AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 16:53:29 CDT)
Re: AMBER: increase in computational time with LES Adrian Roitberg (Sun Apr 23 2006 - 17:26:20 CDT)
Re: AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 17:46:56 CDT)
Re: AMBER: increase in computational time with LES Carlos Simmerling (Sun Apr 23 2006 - 18:00:20 CDT)
Re: AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Sun Apr 23 2006 - 23:13:30 CDT)
AMBER: LES copies Claudia Steinert (Mon Apr 24 2006 - 03:28:06 CDT)
Re: AMBER: LES copies Carlos Simmerling (Mon Apr 24 2006 - 06:14:20 CDT)
AMBER: a quetion german (Mon Apr 24 2006 - 06:17:34 CDT)
AMBER: modeling zinc binding site Jan Kosinski (Mon Apr 24 2006 - 07:28:55 CDT)
Re: AMBER: a quetion Mingfeng Yang (Mon Apr 24 2006 - 08:07:30 CDT)
RE: AMBER: a quetion Ross Walker (Mon Apr 24 2006 - 09:52:59 CDT)
Re: AMBER: a quetion darden (Mon Apr 24 2006 - 09:57:59 CDT)
AMBER: MM_PBSA: “Found unknown atflag DELPHI” haixiao jin (Mon Apr 24 2006 - 10:23:23 CDT)
Re: AMBER: a question Robert Duke (Mon Apr 24 2006 - 13:21:34 CDT)
Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Ray Luo (Mon Apr 24 2006 - 13:40:28 CDT)
AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 14:00:20 CDT)
RE: AMBER: rmsd value for organic molecule Ross Walker (Mon Apr 24 2006 - 14:25:23 CDT)
RE: AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 15:48:59 CDT)
AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 19:17:50 CDT)
RE: AMBER: compiling errors Ross Walker (Mon Apr 24 2006 - 19:58:52 CDT)
AMBER: Born igb =2 harianto (Mon Apr 24 2006 - 20:27:24 CDT)
Re: AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 21:04:10 CDT)
Re: AMBER: Using XML for Amber files Xuebin Qiao (Mon Apr 24 2006 - 22:57:47 CDT)
AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Tue Apr 25 2006 - 09:17:29 CDT)
Re: AMBER: Using XML for Amber files Feng X Zhou (Tue Apr 25 2006 - 10:07:39 CDT)
Re: AMBER: Born igb =2 John Mongan (Tue Apr 25 2006 - 12:30:22 CDT)
Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Tue Apr 25 2006 - 13:01:49 CDT)
RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Tue Apr 25 2006 - 14:30:19 CDT)
AMBER: DNA structure Ioana Cozmuta (Tue Apr 25 2006 - 15:17:12 CDT)
AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Tue Apr 25 2006 - 22:22:41 CDT)
Re: AMBER: compiling errors Atro Tossavainen (Wed Apr 26 2006 - 02:49:23 CDT)
RE: AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Wed Apr 26 2006 - 04:23:24 CDT)
Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Wed Apr 26 2006 - 13:29:11 CDT)
RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Wed Apr 26 2006 - 13:49:06 CDT)
Re: AMBER: DNA structure Ioana Cozmuta (Wed Apr 26 2006 - 14:06:22 CDT)
AMBER: two references Ioana Cozmuta (Wed Apr 26 2006 - 15:18:28 CDT)
AMBER: two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 16:15:11 CDT)
AMBER: internal coordinates Ioana Cozmuta (Wed Apr 26 2006 - 16:56:20 CDT)
Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Scott Pendley (Wed Apr 26 2006 - 17:54:53 CDT)
Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Wed Apr 26 2006 - 19:13:48 CDT)
AMBER: questions about mm_pbsa Weihua Li (Wed Apr 26 2006 - 22:09:45 CDT)
Re: AMBER: questions about mm_pbsa Ray Luo (Wed Apr 26 2006 - 20:03:13 CDT)
AMBER: Force Field Question Ilyas Yildirim (Thu Apr 27 2006 - 16:57:58 CDT)
AMBER: distance restraints for umbrella sampling mkseo (Thu Apr 27 2006 - 17:21:16 CDT)
AMBER: heating process r. a. (Fri Apr 28 2006 - 00:56:06 CDT)
AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Yu Zh.H. (Fri Apr 28 2006 - 05:31:08 CDT)
Re: AMBER: heating process Carlos Simmerling (Fri Apr 28 2006 - 06:06:03 CDT)
AMBER: Langevin mode error?? Cenk Andac (Fri Apr 28 2006 - 06:52:02 CDT)
AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 09:03:22 CDT)
AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 09:13:55 CDT)
AMBER: Performing Simulated Annealing? alfredoq_at_fcq.unc.edu.ar (Fri Apr 28 2006 - 11:58:31 CDT)
RE: AMBER: Performing Simulated Annealing? Ross Walker (Fri Apr 28 2006 - 12:13:56 CDT)
Re: AMBER: Performing Simulated Annealing? Carlos Simmerling (Fri Apr 28 2006 - 12:16:43 CDT)
Re: AMBER: Langevin mode error?? David A. Case (Fri Apr 28 2006 - 15:13:31 CDT)
AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 16:27:09 CDT)
RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 17:10:56 CDT)
AMBER: Setting box dimensions in leap Jennie Thomas (Fri Apr 28 2006 - 17:42:38 CDT)
Re: AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 18:00:29 CDT)
RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 18:46:23 CDT)
Re: AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Fri Apr 28 2006 - 17:37:42 CDT)
AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 22:08:41 CDT)
Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Sat Apr 29 2006 - 00:12:22 CDT)
AMBER: about the shake with self-guide LD pang zhao (Sat Apr 29 2006 - 05:44:39 CDT)
Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 08:43:46 CDT)
Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 08:45:24 CDT)
AMBER: AMBER9: MacG5 parallel sander.MPI In Hee Park (Sat Apr 29 2006 - 15:59:28 CDT)
Re: AMBER: AMBER9: MacG5 parallel sander.MPI Gert Kiss (Sat Apr 29 2006 - 17:29:51 CDT)
Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Hector A. Baldoni (Sat Apr 29 2006 - 19:08:30 CDT)
Re: AMBER: Setting box dimensions in leap David A. Case (Sun Apr 30 2006 - 00:42:48 CDT)
AMBER: Did these differences come from so-called "different machines" ? Zhihong Yu (Sun Apr 30 2006 - 03:47:28 CDT)
Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Sun Apr 30 2006 - 03:58:06 CDT)
Re: AMBER: internal coordinates David A. Case (Sun Apr 30 2006 - 11:09:52 CDT)
AMBER: Amber 9, sander imin = 5, -y flag z3020110_at_student.unsw.edu.au (Sun Apr 30 2006 - 20:08:44 CDT)
Re: AMBER: Did these differences come from so-called "different machines" ? David A. Case (Sun Apr 30 2006 - 23:09:35 CDT)
Re: AMBER: Amber 9, sander imin = 5, -y flag David A. Case (Sun Apr 30 2006 - 23:08:24 CDT)
Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling (Mon May 01 2006 - 08:35:56 CDT)
Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Mon May 01 2006 - 12:17:04 CDT)
AMBER: sequential execution of number of parallel jobs In Hee Park (Mon May 01 2006 - 15:13:23 CDT)
Re: AMBER: internal coordinates David A. Case (Mon May 01 2006 - 15:50:10 CDT)
AMBER: distance restraints mkseo (Mon May 01 2006 - 16:49:21 CDT)
AMBER: some new tutorials David A. Case (Mon May 01 2006 - 18:55:19 CDT)
AMBER: How does amber calculate HB? Li Su (Mon May 01 2006 - 20:01:05 CDT)
Re: AMBER: How does amber calculate HB? David A. Case (Tue May 02 2006 - 01:20:31 CDT)
Re: AMBER: sequential execution of number of parallel jobs Petr Kulhanek (Tue May 02 2006 - 03:20:51 CDT)
AMBER: AMBER Workshops, London UK 26th - 30th June 2006 Ross Walker (Tue May 02 2006 - 10:45:33 CDT)
AMBER: Simulation of crystal - problem with excluded atom list Jennie Thomas (Tue May 02 2006 - 12:07:20 CDT)
Re: AMBER: internal coordinates Ioana Cozmuta (Tue May 02 2006 - 13:01:45 CDT)
AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 16:21:50 CDT)
RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker (Tue May 02 2006 - 16:42:33 CDT)
Re: AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 17:14:16 CDT)
RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker (Tue May 02 2006 - 17:40:37 CDT)
AMBER: Shared libraries error Andrew Box (Tue May 02 2006 - 22:14:38 CDT)
AMBER: proper restart procedure? John J. Love (Tue May 02 2006 - 22:33:57 CDT)
AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 03:02:55 CDT)
AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 06:03:27 CDT)
Re: AMBER: proper restart procedure? Carlos Simmerling (Wed May 03 2006 - 06:48:25 CDT)
Re: AMBER: Error while running test.serial in Amber9 Carlos Simmerling (Wed May 03 2006 - 06:50:37 CDT)
Re: AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 07:02:04 CDT)
AMBER: cluster architecture for the best amber performance Kateryna Miroshnychenko (Wed May 03 2006 - 07:54:58 CDT)
RE: AMBER: Shared libraries error Ross Walker (Wed May 03 2006 - 10:13:32 CDT)
Re: AMBER: proper restart procedure? David A. Case (Wed May 03 2006 - 10:18:43 CDT)
RE: AMBER: Error while running test.serial in Amber9 Ross Walker (Wed May 03 2006 - 10:21:42 CDT)
Re: AMBER: Question bonds and angles in frcmod and lib files David A. Case (Wed May 03 2006 - 10:23:12 CDT)
RE: AMBER: cluster architecture for the best amber performance Ross Walker (Wed May 03 2006 - 10:42:19 CDT)
Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 10:54:43 CDT)
Re: AMBER: Question bonds and angles in frcmod and lib files Bill Ross (Wed May 03 2006 - 11:28:08 CDT)
AMBER: concatenating .mdcrd files Kenley Barrett (Wed May 03 2006 - 11:31:59 CDT)
RE: AMBER: concatenating .mdcrd files Ross Walker (Wed May 03 2006 - 11:39:11 CDT)
Re: AMBER: cluster architecture for the best amber performance Robert Duke (Wed May 03 2006 - 12:05:57 CDT)
Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 12:26:55 CDT)
AMBER: question about group format Holly Freedman (Wed May 03 2006 - 14:18:36 CDT)
[Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Wed May 03 2006 - 16:49:19 CDT)
Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Bill Ross (Wed May 03 2006 - 17:00:58 CDT)
Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh (Wed May 03 2006 - 19:32:14 CDT)
AMBER: Amber install on RedHat Linux a a (Wed May 03 2006 - 21:17:14 CDT)
RE: AMBER: Amber install on RedHat Linux Ross Walker (Wed May 03 2006 - 21:36:45 CDT)
RE: AMBER: Error while running test.serial in Amber9 Priti Hansia (Thu May 04 2006 - 00:08:02 CDT)
Re: AMBER: Error while running test.serial in Amber9 David A. Case (Thu May 04 2006 - 01:13:06 CDT)
RE: AMBER: Amber install on RedHat Linux a a (Thu May 04 2006 - 02:37:34 CDT)
AMBER: carnal prob bala (Thu May 04 2006 - 02:44:53 CDT)
Re: AMBER: carnal prob Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu May 04 2006 - 02:58:18 CDT)
Re: AMBER: Amber install on RedHat Linux David A. Case (Thu May 04 2006 - 10:17:08 CDT)
RE: AMBER: Amber install on RedHat Linux Ross Walker (Thu May 04 2006 - 10:31:56 CDT)
AMBER: conflicting types for XawScrolledTableSetLocation K. Yarem (Thu May 04 2006 - 10:43:57 CDT)
Re: AMBER: Error while running test.serial in Amber9 Priti Hansia (Thu May 04 2006 - 10:48:36 CDT)
AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 11:00:31 CDT)
RE: AMBER: molsurf.c error Ross Walker (Thu May 04 2006 - 11:28:49 CDT)
AMBER: amber9 serial compilation error Arvind Marathe (Thu May 04 2006 - 11:55:39 CDT)
Re: AMBER: conflicting types for XawScrolledTableSetLocation Wei Zhang (Thu May 04 2006 - 12:17:40 CDT)
AMBER: Trouble with ptraj closestwater in Amber8 Kerry P Donny-Clark (Thu May 04 2006 - 12:29:23 CDT)
Re: AMBER: carnal prob Bill Ross (Thu May 04 2006 - 12:31:22 CDT)
Re: AMBER: amber9 serial compilation error David A. Case (Thu May 04 2006 - 12:36:53 CDT)
AMBER: lipid bi-layer system Lwin, ThuZar (Thu May 04 2006 - 12:41:11 CDT)
AMBER: restraintmask Joseph Fernandez (Thu May 04 2006 - 13:22:21 CDT)
Re: AMBER: restraintmask Viktor Hornak (Thu May 04 2006 - 13:41:37 CDT)
Re: AMBER: question about group format Viktor Hornak (Thu May 04 2006 - 13:49:20 CDT)
Re: AMBER: Shared libraries error Viktor Hornak (Thu May 04 2006 - 13:54:26 CDT)
RE: AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 14:43:41 CDT)
Re: AMBER: molsurf.c error David A. Case (Thu May 04 2006 - 15:21:28 CDT)
Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Thu May 04 2006 - 17:45:21 CDT)
Re: AMBER: question about group format Holly Freedman (Thu May 04 2006 - 18:16:22 CDT)
Re: AMBER: molsurf.c error Miguel Ferreira (Fri May 05 2006 - 06:46:24 CDT)
Re: AMBER: molsurf.c error David A. Case (Fri May 05 2006 - 12:34:32 CDT)
AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 12:55:39 CDT)
RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Fri May 05 2006 - 13:04:10 CDT)
AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 13:37:19 CDT)
RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 13:39:50 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 13:46:29 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 13:59:48 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 14:19:31 CDT)
RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Fri May 05 2006 - 16:08:31 CDT)
RE: AMBER: experiences with compiling amber9 for FreeBSD Ross Walker (Fri May 05 2006 - 16:10:51 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 17:00:10 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 19:24:30 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 19:30:16 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 20:31:13 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 21:05:41 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 21:34:07 CDT)
AMBER: xleap on iMac G5 Evan Kelly (Fri May 05 2006 - 23:01:53 CDT)
Re: AMBER: xleap on iMac G5 Mengjuei Hsieh (Sat May 06 2006 - 00:44:00 CDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD Xuebin Qiao (Sat May 06 2006 - 01:31:06 CDT)
RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Sat May 06 2006 - 02:01:51 CDT)
Re: AMBER: Problem with shared libraries: libimf.so David A. Case (Sat May 06 2006 - 16:17:51 CDT)
Re: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Sun May 07 2006 - 00:40:49 CDT)
AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Sun May 07 2006 - 02:10:15 CDT)
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system David A. Case (Sun May 07 2006 - 09:27:56 CDT)
Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh (Sun May 07 2006 - 09:33:01 CDT)
RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Sun May 07 2006 - 11:10:54 CDT)
AMBER: xleap not recognizing residue Kenley Barrett (Sun May 07 2006 - 19:13:13 CDT)
Re: AMBER: xleap not recognizing residue David A. Case (Sun May 07 2006 - 20:50:06 CDT)
AMBER: question on distance calculation bala (Mon May 08 2006 - 05:09:23 CDT)
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Mon May 08 2006 - 06:33:58 CDT)
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Atro Tossavainen (Mon May 08 2006 - 06:48:29 CDT)
RE: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Ross Walker (Mon May 08 2006 - 10:17:55 CDT)
Re: AMBER: xleap not recognizing residue Kenley Barrett (Mon May 08 2006 - 12:04:37 CDT)
AMBER: Amber9 test error on SGI Altix amit_at_mbu.iisc.ernet.in (Mon May 08 2006 - 12:14:19 CDT)
AMBER: Problem with impose in lep Osmar Norberto de Souza (Mon May 08 2006 - 12:31:16 CDT)
Re: AMBER: Amber9 test error on SGI Altix David A. Case (Mon May 08 2006 - 13:07:17 CDT)
AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Mon May 08 2006 - 13:13:11 CDT)
Re: AMBER: Amber9 test error on SGI Altix David A. Case (Mon May 08 2006 - 13:45:30 CDT)
Re: AMBER: Amber9 test error on SGI Altix Ray Luo (Tue May 09 2006 - 07:57:57 CDT)
AMBER: Intel compiler version 9.0.033 Ross Walker (Mon May 08 2006 - 14:40:23 CDT)
AMBER: PMEMD compilation error Joseph Fernandez (Mon May 08 2006 - 14:37:03 CDT)
Re: AMBER: Intel compiler version 9.0.033 Priti Hansia (Mon May 08 2006 - 14:55:37 CDT)
Re: AMBER: PMEMD compilation error Robert Duke (Mon May 08 2006 - 15:18:05 CDT)
AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format wang (Tue May 09 2006 - 01:25:47 CDT)
AMBER: San Fransisco Amber users homeira amirkhani (Tue May 09 2006 - 06:38:06 CDT)
AMBER: Amber9 test error on SGI Altix Priti Hansia (Tue May 09 2006 - 10:18:02 CDT)
AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 11:05:28 CDT)
Re: AMBER: Amber9 test error on SGI Altix Robert Duke (Tue May 09 2006 - 11:06:19 CDT)
AMBER: Compiler with AMD 64 bit support alfredoq_at_fcq.unc.edu.ar (Tue May 09 2006 - 12:10:30 CDT)
AMBER: RE: Intel Compiler. Priti Hansia (Tue May 09 2006 - 12:12:18 CDT)
RE: AMBER: Compiler with AMD 64 bit support Ross Walker (Tue May 09 2006 - 12:19:18 CDT)
RE: AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 12:21:43 CDT)
AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit_at_mbu.iisc.ernet.in (Tue May 09 2006 - 13:32:52 CDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Tue May 09 2006 - 14:12:09 CDT)
Re: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 David A. Case (Tue May 09 2006 - 15:16:30 CDT)
Re: AMBER: xleap not recognizing residue David A. Case (Tue May 09 2006 - 17:42:14 CDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit_at_mbu.iisc.ernet.in (Wed May 10 2006 - 02:06:46 CDT)
AMBER: bug in ambpdb (AMBER8) Petr Kulhanek (Wed May 10 2006 - 05:54:55 CDT)
AMBER: problem with prep file Simon Whitehead (Wed May 10 2006 - 05:52:32 CDT)
AMBER: Hexahydrated Counterions Mahalakshmi Sahasranaman (Wed May 10 2006 - 08:22:02 CDT)
Re: AMBER: bug in ambpdb (AMBER8) David A. Case (Wed May 10 2006 - 10:10:08 CDT)
Re: AMBER: Hexahydrated Counterions David A. Case (Wed May 10 2006 - 10:32:31 CDT)
RE: AMBER: RE: Intel Compiler. Priti Hansia (Wed May 10 2006 - 10:39:04 CDT)
Re: AMBER: problem with prep file David A. Case (Wed May 10 2006 - 11:12:59 CDT)
[Fwd: AMBER: Problem with impose in lep] Osmar Norberto de Souza (Wed May 10 2006 - 12:09:48 CDT)
Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why Kenley Barrett (Wed May 10 2006 - 14:54:46 CDT)
AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed Kenley Barrett (Wed May 10 2006 - 15:04:16 CDT)
Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why David A. Case (Wed May 10 2006 - 15:12:52 CDT)
AMBER: which patch for ioutfm = 1 in Amber8? Hannes Loeffler (Thu May 11 2006 - 00:21:25 CDT)
AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? Pan, Yongmei (Thu May 11 2006 - 09:13:02 CDT)
Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? David A. Case (Thu May 11 2006 - 09:43:28 CDT)
AMBER: bond information in amber snoze pa (Thu May 11 2006 - 11:48:58 CDT)
Re: AMBER: bond information in amber Navnit Kumar Mishra (Thu May 11 2006 - 12:25:10 CDT)
Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 13:36:18 CDT)
Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 13:41:00 CDT)
AMBER: Opteron vs. Xeon performance Jim Paugh (Thu May 11 2006 - 13:47:42 CDT)
AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 Pan, Yongmei (Thu May 11 2006 - 13:50:36 CDT)
Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 14:16:56 CDT)
AMBER: Amber9/mpich2 performance Joseph Fernandez (Thu May 11 2006 - 17:30:03 CDT)
RE: AMBER: Amber9/mpich2 performance Ross Walker (Thu May 11 2006 - 18:07:21 CDT)
RE: AMBER: Opteron vs. Xeon performance Ross Walker (Thu May 11 2006 - 18:17:12 CDT)
Re: AMBER: Opteron vs. Xeon performance Robert Duke (Thu May 11 2006 - 21:02:10 CDT)
AMBER: question about REDII Raffaella D'Auria (Thu May 11 2006 - 21:04:51 CDT)
AMBER: About mm_pbsa calculation setting up alfredoq_at_fcq.unc.edu.ar (Thu May 11 2006 - 21:19:03 CDT)
AMBER: AMBER 8 - dihedral angles when clambda=1 Ilyas Yildirim (Thu May 11 2006 - 23:57:37 CDT)
Re: AMBER: bond information in amber Navnit Kumar Mishra (Fri May 12 2006 - 01:28:00 CDT)
Re: AMBER: question about REDII FyD (Fri May 12 2006 - 01:34:48 CDT)
Re: AMBER: Opteron vs. Xeon performance ian gould (Fri May 12 2006 - 02:35:12 CDT)
Re: AMBER: Opteron vs. Xeon performance Ye Mei (Fri May 12 2006 - 03:04:45 CDT)
AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 05:19:48 CDT)
AMBER: RMSD calculation between ligands Stefan Henrich (Fri May 12 2006 - 07:09:15 CDT)
Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 07:29:14 CDT)
Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 07:46:08 CDT)
Re: Re: AMBER: Opteron vs. Xeon performance Ye Mei (Fri May 12 2006 - 08:23:00 CDT)
RE: AMBER: Opteron vs. Xeon performance Ross Walker (Fri May 12 2006 - 10:13:48 CDT)
Re: AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 10:21:02 CDT)
AMBER: another question: is rms 2E-2 good for nmode ntrun=1? Pan, Yongmei (Fri May 12 2006 - 10:22:00 CDT)
Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 10:24:43 CDT)
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case (Fri May 12 2006 - 10:39:37 CDT)
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? nadiav_at_soton.ac.uk (Fri May 12 2006 - 11:00:21 CDT)
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case (Fri May 12 2006 - 12:01:05 CDT)
Re: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 David Mobley (Fri May 12 2006 - 12:22:41 CDT)
Re: AMBER: question about REDII Raffaella D'Auria (Fri May 12 2006 - 14:12:41 CDT)
AMBER: binpos file Varsha Goyal (Fri May 12 2006 - 15:46:24 CDT)
RE: AMBER: Amber9/mpich2 performance Joseph Fernandez (Fri May 12 2006 - 20:09:20 CDT)
AMBER: strange mm_pbsa output alfredoq_at_fcq.unc.edu.ar (Sat May 13 2006 - 10:44:58 CDT)
Re: AMBER: strange mm_pbsa output Ray Luo (Fri May 12 2006 - 19:22:57 CDT)
Re: AMBER: strange mm_pbsa output alfredoq_at_fcq.unc.edu.ar (Sat May 13 2006 - 15:43:53 CDT)
Re: AMBER: strange mm_pbsa output David A. Case (Sat May 13 2006 - 17:44:14 CDT)
AMBER: Compilers and libraries for AMBER in HPC! Pradipta Bandyopadhyay (Sun May 14 2006 - 08:25:07 CDT)
Re: AMBER: strange mm_pbsa output alfredoq_at_fcq.unc.edu.ar (Sun May 14 2006 - 09:22:14 CDT)
AMBER: PBS script for lemieux Stern, Julie (Sun May 14 2006 - 18:09:30 CDT)
RE: AMBER: Opteron vs. Xeon performance Yong Duan (Sun May 14 2006 - 19:53:55 CDT)
AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Sun May 14 2006 - 22:55:51 CDT)
RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Ross Walker (Mon May 15 2006 - 00:13:01 CDT)
RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Mon May 15 2006 - 04:00:03 CDT)
AMBER: AMBER9 compilation error on IBM Cluster amit_at_mbu.iisc.ernet.in (Mon May 15 2006 - 06:11:50 CDT)
AMBER: Problem with "impose" in leap Osmar Norberto de Souza (Mon May 15 2006 - 06:27:13 CDT)
AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 06:59:10 CDT)
Re: AMBER: fail to execute addles Carlos Simmerling (Mon May 15 2006 - 07:43:31 CDT)
AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Mon May 15 2006 - 08:53:20 CDT)
Re: AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 09:31:19 CDT)
RE: AMBER: ff02 + POL3 problem ! Yong Duan (Mon May 15 2006 - 11:15:02 CDT)
Re: AMBER: fail to execute addles David A. Case (Mon May 15 2006 - 11:46:28 CDT)
Re: AMBER: fail to execute addles Carlos Simmerling (Mon May 15 2006 - 11:59:29 CDT)
AMBER: installation problem Mahalakshmi Sahasranaman (Mon May 15 2006 - 13:12:51 CDT)
Re: AMBER: installation problem Robert Duke (Mon May 15 2006 - 13:25:53 CDT)
RE: AMBER: problem with prep file Junmei Wang (Mon May 15 2006 - 16:10:53 CDT)
RE: AMBER: AMBER9 compilation error on IBM Cluster Ross Walker (Mon May 15 2006 - 22:28:12 CDT)
AMBER: density mathew k varghese (Mon May 15 2006 - 23:02:51 CDT)
RE: AMBER: density Yong Duan (Tue May 16 2006 - 00:37:28 CDT)
Re: AMBER: fail to execute addles pang zhao (Tue May 16 2006 - 01:13:21 CDT)
Re: AMBER: fail to execute addles pang zhao (Tue May 16 2006 - 01:17:05 CDT)
Re: AMBER: fail to execute addles pang zhao (Tue May 16 2006 - 01:39:28 CDT)
AMBER: amber8 compiled erro on opteron with 64 bit renyanliang (Tue May 16 2006 - 04:15:24 CDT)
Re: AMBER: amber8 compiled erro on opteron with 64 bit Andreas Svrcek-Seiler (Tue May 16 2006 - 05:53:14 CDT)
Re: AMBER: fail to execute addles Carlos Simmerling (Tue May 16 2006 - 08:47:37 CDT)
RE: AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Tue May 16 2006 - 09:08:03 CDT)
Re: AMBER: fail to execute addles pang zhao (Tue May 16 2006 - 09:42:36 CDT)
AMBER: trouble stripping waters with ptraj Adam Pelzer (Tue May 16 2006 - 15:09:30 CDT)
RE: AMBER: ff02 + POL3 problem ! Yong Duan (Tue May 16 2006 - 15:06:54 CDT)
Re: AMBER: trouble stripping waters with ptraj Asim Okur (Tue May 16 2006 - 15:17:32 CDT)
RE: AMBER: density mathew k varghese (Tue May 16 2006 - 23:09:17 CDT)
AMBER: amber compilation on Red Hat 8 with MPICH kawamura_hiro_at_riken.jp (Wed May 17 2006 - 00:38:35 CDT)
AMBER: "atom number exceeds the MAXATOM" BAUVAIS_at_itodys.jussieu.fr (Wed May 17 2006 - 00:54:24 CDT)
AMBER: Tutorial one : libsvml.so error a a (Wed May 17 2006 - 01:01:26 CDT)
Re: AMBER: Tutorial one : libsvml.so error Mark Williamson (Wed May 17 2006 - 02:27:05 CDT)
AMBER: Tutorial one : xaLeap command not found. a a (Wed May 17 2006 - 05:12:53 CDT)
AMBER: distance dependent dielectric constant Mahalakshmi Sahasranaman (Wed May 17 2006 - 05:36:55 CDT)
Re: AMBER: amber compilation on Red Hat 8 with MPICH David A. Case (Wed May 17 2006 - 06:52:55 CDT)
Re: AMBER: "atom number exceeds the MAXATOM" David A. Case (Wed May 17 2006 - 06:53:58 CDT)
Re: AMBER: distance dependent dielectric constant David A. Case (Wed May 17 2006 - 06:59:41 CDT)
RE: AMBER: amber compilation on Red Hat 8 with MPICH Ross Walker (Wed May 17 2006 - 10:35:00 CDT)
RE: AMBER: density Ross Walker (Wed May 17 2006 - 10:31:20 CDT)
RE: AMBER: Tutorial one : xaLeap command not found. Ross Walker (Wed May 17 2006 - 10:40:12 CDT)
RE: AMBER: density mathew k varghese (Wed May 17 2006 - 22:24:07 CDT)
RE: AMBER: density Ross Walker (Wed May 17 2006 - 23:11:11 CDT)
AMBER: "The system has extended beyond" error message Atsutoshi Okabe (Thu May 18 2006 - 00:04:31 CDT)
AMBER: Correlation matrix used in quasih (Amber 7) Craig Gough (Thu May 18 2006 - 02:06:03 CDT)
AMBER: AMBER9 installation error on Compaq machine. Soonmin Jang (Thu May 18 2006 - 02:11:46 CDT)
AMBER: vlimit exceeded aixiaoli (Thu May 18 2006 - 03:14:29 CDT)
AMBER: problem with installation, or bug? Kenley Barrett (Thu May 18 2006 - 05:09:10 CDT)
Re: AMBER: vlimit exceeded David A. Case (Thu May 18 2006 - 07:24:49 CDT)
Re: AMBER: "The system has extended beyond" error message german (Thu May 18 2006 - 07:27:42 CDT)
Re: AMBER: Correlation matrix used in quasih (Amber 7) David A. Case (Thu May 18 2006 - 07:31:00 CDT)
Re: AMBER: "The system has extended beyond" error message David A. Case (Thu May 18 2006 - 07:38:58 CDT)
AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 12:33:35 CDT)
Re: AMBER: force field parameters Navnit Kumar Mishra (Thu May 18 2006 - 13:21:59 CDT)
RE: AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 13:40:53 CDT)
AMBER: RMSd calculations Claire Zerafa (Thu May 18 2006 - 14:25:57 CDT)
AMBER: OT: software to support AMBER? Steve Gwaltney (Thu May 18 2006 - 13:37:06 CDT)
RE: AMBER: AMBER9 installation error on Compaq machine. Ross Walker (Thu May 18 2006 - 17:32:57 CDT)
AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Thu May 18 2006 - 17:44:14 CDT)
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Ross Walker (Thu May 18 2006 - 18:37:30 CDT)
AMBER: process_mdout.perl error a a (Fri May 19 2006 - 04:35:20 CDT)
AMBER: Intel fortran compiler 7? Simon Whitehead (Fri May 19 2006 - 04:47:55 CDT)
AMBER: xmgr error a a (Fri May 19 2006 - 04:50:25 CDT)
Re: AMBER: xmgr error mathew k varghese (Fri May 19 2006 - 05:54:00 CDT)
Re: AMBER: force field parameters Navnit Kumar Mishra (Fri May 19 2006 - 06:01:59 CDT)
Re: AMBER: Intel fortran compiler 7? Robert Duke (Fri May 19 2006 - 06:59:43 CDT)
AMBER: Fw: RMSd calculations Claire Zerafa (Fri May 19 2006 - 07:07:30 CDT)
Re: AMBER: Fw: RMSd calculations Carlos Simmerling (Fri May 19 2006 - 08:00:50 CDT)
AMBER: problem loading forcefield leaprc.ff86 Mahalakshmi Sahasranaman (Fri May 19 2006 - 09:27:38 CDT)
RE: AMBER: process_mdout.perl error Ross Walker (Fri May 19 2006 - 09:43:25 CDT)
Re: AMBER: problem loading forcefield leaprc.ff86 David A. Case (Fri May 19 2006 - 10:45:33 CDT)
AMBER: RE: PMEMD compilation problems Simon Whitehead (Fri May 19 2006 - 10:37:46 CDT)
Re: AMBER: RE: PMEMD compilation problems Robert Duke (Fri May 19 2006 - 11:20:52 CDT)
RE: AMBER: xmgr error Douali, Latifa (Fri May 19 2006 - 12:07:01 CDT)
AMBER: amber .off file format question Ilyas Yildirim (Fri May 19 2006 - 21:30:55 CDT)
AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Sat May 20 2006 - 11:00:12 CDT)
Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling (Sat May 20 2006 - 12:10:24 CDT)
AMBER: Problem with running xleap remotely heaton_at_chem.utah.edu (Sat May 20 2006 - 14:20:27 CDT)
RE: AMBER: Problem with running xleap remotely Ross Walker (Sat May 20 2006 - 14:37:35 CDT)
RE: AMBER: Problem with running xleap remotely heaton_at_chem.utah.edu (Sat May 20 2006 - 15:43:53 CDT)
AMBER: trajin and rms a a (Sun May 21 2006 - 23:18:37 CDT)
RE: AMBER: trajin and rms Ross Walker (Sun May 21 2006 - 23:43:09 CDT)
AMBER: RMSd error Claire Zerafa (Mon May 22 2006 - 03:52:34 CDT)
RE: AMBER: trajin and rms a a (Mon May 22 2006 - 03:55:03 CDT)
Re: AMBER: amber .off file format question Ilyas Yildirim (Mon May 22 2006 - 04:16:39 CDT)
AMBER: Water density output Navnit Kumar Mishra (Mon May 22 2006 - 06:02:48 CDT)
AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Mon May 22 2006 - 06:49:23 CDT)
Re: AMBER: trajin and rms Carlos Simmerling (Mon May 22 2006 - 06:58:04 CDT)
Re: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Mon May 22 2006 - 06:58:24 CDT)
Re: AMBER: RMSd error Carlos Simmerling (Mon May 22 2006 - 07:02:02 CDT)
AMBER: Macromodel Amber* vs. Amber7 opitz_at_che.udel.edu (Mon May 22 2006 - 07:56:54 CDT)
AMBER: More Amber 9 Benchmarks available Robert Duke (Mon May 22 2006 - 09:23:15 CDT)
Re: AMBER: RE: trouble stripping waters with ptraj Asim Okur (Mon May 22 2006 - 11:49:46 CDT)
Re: AMBER: Problems compiling amber9 Don Harden (Mon May 22 2006 - 12:10:15 CDT)
Re: AMBER: amber .off file format question Wei Zhang (Mon May 22 2006 - 13:13:12 CDT)
Re: AMBER: amber .off file format question Bill Ross (Mon May 22 2006 - 13:17:26 CDT)
Re: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Michael Crowley (Mon May 22 2006 - 13:28:58 CDT)
Re: AMBER: Problems compiling amber9 David A. Case (Mon May 22 2006 - 13:46:09 CDT)
Re: AMBER: Problems compiling amber9 Andreas Svrcek-Seiler (Mon May 22 2006 - 14:01:09 CDT)
AMBER: Again SASA lucas luquitas (Mon May 22 2006 - 14:51:22 CDT)
AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil 3Dsig06 (Mon May 22 2006 - 17:03:45 CDT)
Re: AMBER: amber .off file format question Ilyas Yildirim (Tue May 23 2006 - 00:53:19 CDT)
Re: AMBER: amber .off file format question David A. Case (Tue May 23 2006 - 01:21:33 CDT)
Re: AMBER: Problems compiling amber9 Don Harden (Tue May 23 2006 - 14:45:02 CDT)
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Tue May 23 2006 - 16:15:12 CDT)
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Tue May 23 2006 - 16:15:08 CDT)
AMBER: error in AMBER 9.0 mkseo (Tue May 23 2006 - 16:43:28 CDT)
RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Tue May 23 2006 - 20:46:35 CDT)
RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Tue May 23 2006 - 21:49:00 CDT)
Re: AMBER: error in AMBER 9.0 David A. Case (Wed May 24 2006 - 00:19:47 CDT)
AMBER: amber8 bugfix effects kawamura_hiro_at_riken.jp (Wed May 24 2006 - 03:17:32 CDT)
RE: AMBER: trajin and rms a a (Wed May 24 2006 - 05:49:05 CDT)
Re: AMBER: amber8 bugfix effects David A. Case (Wed May 24 2006 - 09:38:39 CDT)
AMBER: simulate proteins with non-standard residues Hui Lei (Wed May 24 2006 - 12:10:08 CDT)
AMBER: freeze interval vibrations Eric Hu (Wed May 24 2006 - 12:52:47 CDT)
Re: AMBER: freeze interval vibrations David A. Case (Wed May 24 2006 - 14:00:35 CDT)
AMBER: problem with prepfile Shafinaz (Wed May 24 2006 - 14:50:21 CDT)
Re: AMBER: problem with prepfile David A. Case (Wed May 24 2006 - 15:56:08 CDT)
AMBER: use_pme=0 problem luckyang_at_gmail.com (Wed May 24 2006 - 18:18:47 CDT)
AMBER: output of first stage RESP calculation JunJun Liu (Wed May 24 2006 - 17:23:55 CDT)
Re: AMBER: use_pme=0 problem David A. Case (Wed May 24 2006 - 18:50:56 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Wed May 24 2006 - 19:20:35 CDT)
Re: AMBER: use_pme=0 problem David A. Case (Wed May 24 2006 - 19:33:53 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Wed May 24 2006 - 19:51:10 CDT)
AMBER: How to built the deprotonated form of lysine and tyrosine jitrayut jitonnom (Wed May 24 2006 - 21:49:04 CDT)
AMBER: Fwd: RESP for deprotonated tyrosine and lysine jitrayut jitonnom (Wed May 24 2006 - 21:57:45 CDT)
AMBER: Qestion about input for RESP program JunJun Liu (Wed May 24 2006 - 21:44:41 CDT)
AMBER: How to build NH2 of amino acid in amber jitrayut jitonnom (Wed May 24 2006 - 22:52:25 CDT)
Re: AMBER: Qestion about input for RESP program Ilyas Yildirim (Wed May 24 2006 - 23:49:11 CDT)
Re: AMBER: output of first stage RESP calculation FyD (Thu May 25 2006 - 03:12:12 CDT)
Re: AMBER: Fwd: RESP for deprotonated tyrosine and lysine FyD (Thu May 25 2006 - 03:26:15 CDT)
Re: AMBER: Qestion about input for RESP program FyD (Thu May 25 2006 - 03:22:13 CDT)
AMBER: question about QM/MM in amber9 aixiaoli (Thu May 25 2006 - 03:37:10 CDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Soonmin Jang (Thu May 25 2006 - 05:51:02 CDT)
Re: AMBER: question about QM/MM in amber9 Adrian Roitberg (Thu May 25 2006 - 05:57:25 CDT)
AMBER: 1st 2 lines of restart files hayden (Thu May 25 2006 - 06:40:03 CDT)
Re: AMBER: 1st 2 lines of restart files Steven Winfield (Thu May 25 2006 - 06:50:18 CDT)
Re: AMBER: Qestion about input for RESP program JunJun Liu (Thu May 25 2006 - 09:01:41 CDT)
RE: AMBER: question about QM/MM in amber9 Ross Walker (Thu May 25 2006 - 10:33:17 CDT)
Re: AMBER: Qestion about input for RESP program FyD (Thu May 25 2006 - 10:53:28 CDT)
RE: AMBER: problem with prepfile Junmei Wang (Thu May 25 2006 - 11:24:51 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Thu May 25 2006 - 12:09:59 CDT)
Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo (Wed May 24 2006 - 18:14:33 CDT)
Re: AMBER: use_pme=0 problem David A. Case (Thu May 25 2006 - 12:56:56 CDT)
Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) David A. Case (Thu May 25 2006 - 15:33:33 CDT)
AMBER: alpha helix preference problem harianto (Thu May 25 2006 - 16:16:23 CDT)
Re: AMBER: alpha helix preference problem Carlos Simmerling (Thu May 25 2006 - 20:35:10 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Thu May 25 2006 - 20:56:30 CDT)
AMBER: RMSd error Claire Zerafa (Thu May 25 2006 - 23:37:54 CDT)
AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Thu May 25 2006 - 23:50:53 CDT)
AMBER: ptraj: calculating distances between atoms in charges residues Magne Olufsen (Fri May 26 2006 - 02:13:48 CDT)
AMBER: Question about .off file Sergey Krishtal (Fri May 26 2006 - 03:15:06 CDT)
Re: AMBER: Question about .off file Ilyas Yildirim (Fri May 26 2006 - 03:58:19 CDT)
Re: AMBER: RMSd error Carlos Simmerling (Fri May 26 2006 - 06:27:18 CDT)
Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling (Fri May 26 2006 - 06:28:35 CDT)
Re: AMBER: RMSd error Claire Zerafa (Fri May 26 2006 - 07:26:06 CDT)
Re: AMBER: RMSd error Carlos Simmerling (Fri May 26 2006 - 07:58:42 CDT)
Re: AMBER: RMSd error Claire Zerafa (Fri May 26 2006 - 08:30:57 CDT)
AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 08:56:47 CDT)
Re: AMBER: alpha helix preference problem harianto (Fri May 26 2006 - 09:04:30 CDT)
AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 05:12:12 CDT)
AMBER: Saving RMSD values in VMD nag raj (Fri May 26 2006 - 09:33:00 CDT)
Re: AMBER: different TI calculations starting from the same state David A. Case (Fri May 26 2006 - 10:16:19 CDT)
RE: AMBER: alpha helix preference problem Ross Walker (Fri May 26 2006 - 10:23:27 CDT)
RE: AMBER: Saving RMSD values in VMD Ross Walker (Fri May 26 2006 - 10:27:08 CDT)
Re: AMBER: Saving RMSD values in VMD Carlos Simmerling (Fri May 26 2006 - 10:45:17 CDT)
Re: AMBER: RMSd error Thomas Cheatham (Fri May 26 2006 - 10:59:34 CDT)
Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham (Fri May 26 2006 - 11:04:22 CDT)
Re: AMBER: ptraj: calculating distances between atoms in charges residues Thomas Cheatham (Fri May 26 2006 - 11:12:40 CDT)
AMBER: check as error: load prepin in tleap jitrayut jitonnom (Fri May 26 2006 - 12:13:41 CDT)
Re: AMBER: use_pme=0 problem David A. Case (Fri May 26 2006 - 12:34:39 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Fri May 26 2006 - 14:10:19 CDT)
AMBER: Please reply Shafinaz (Fri May 26 2006 - 14:19:42 CDT)
Re: AMBER: use_pme=0 problem David A. Case (Fri May 26 2006 - 14:30:01 CDT)
Re: AMBER: Please reply Ananda Rama Krishnan Selvaraj (Fri May 26 2006 - 14:36:26 CDT)
Re: AMBER: Please reply David A. Case (Fri May 26 2006 - 14:39:02 CDT)
Re: AMBER: use_pme=0 problem luckyang_at_gmail.com (Fri May 26 2006 - 15:19:11 CDT)
Re: AMBER: use_pme=0 problem Bill Ross (Fri May 26 2006 - 15:32:35 CDT)
AMBER: Installing / Compiling Question Seth Lilavivat (Fri May 26 2006 - 22:29:06 CDT)
Re: AMBER: Installing / Compiling Question David A. Case (Sat May 27 2006 - 23:50:54 CDT)
RE: AMBER: Installing / Compiling Question Ross Walker (Sun May 28 2006 - 00:12:46 CDT)
Re: AMBER: RMSd error Claire Zerafa (Sun May 28 2006 - 11:26:14 CDT)
AMBER: md error : sander jitrayut jitonnom (Sun May 28 2006 - 13:11:45 CDT)
Re: AMBER: md error : sander Carlos Simmerling (Sun May 28 2006 - 15:06:21 CDT)
AMBER: Pt containing complex: xleap a a (Sun May 28 2006 - 22:30:48 CDT)
AMBER: Pt containing complex: antechamber a a (Sun May 28 2006 - 22:42:31 CDT)
Re: AMBER: Pt containing complex: xleap Ilyas Yildirim (Sun May 28 2006 - 23:00:08 CDT)
RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Sun May 28 2006 - 23:26:33 CDT)
RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Mon May 29 2006 - 00:51:49 CDT)
AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 04:32:26 CDT)
AMBER: antechamber help needed for FAD pkb bioinfo (Mon May 29 2006 - 04:38:48 CDT)
Re: AMBER: which time should I use to calculate the number of "ps/Day" Carlos Simmerling (Mon May 29 2006 - 04:50:31 CDT)
Re: AMBER: which time should I use to calculate the number of "ps/Day" Robert Duke (Mon May 29 2006 - 08:10:04 CDT)
AMBER: Thermodynamic integration using the amber 9 Vitor Manuel Sousa F?x (Mon May 29 2006 - 08:41:14 CDT)
AMBER: Difference in results for TI calculation brmeher_at_iitg.ernet.in (Mon May 29 2006 - 08:53:41 CDT)
AMBER: Difference in results for TI calculation brmeher_at_iitg.ernet.in (Mon May 29 2006 - 09:23:45 CDT)
Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Mon May 29 2006 - 09:25:21 CDT)
AMBER: problems with antechamber JAVIER PEREZ (Mon May 29 2006 - 10:04:52 CDT)
AMBER: energy terms JAVIER PEREZ (Mon May 29 2006 - 10:25:31 CDT)
AMBER: SAVEPDB in Xleap could not save 4 character atom names Jiayun Pang (Mon May 29 2006 - 11:38:22 CDT)
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Bill Ross (Mon May 29 2006 - 15:26:56 CDT)
AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Mon May 29 2006 - 17:20:23 CDT)
Re: AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 19:42:01 CDT)
AMBER: ESP calculations. a a (Tue May 30 2006 - 05:10:41 CDT)
AMBER: Antechamber : +ve charge species a a (Tue May 30 2006 - 05:04:05 CDT)
Re: AMBER: ESP calculations. FyD (Tue May 30 2006 - 06:15:31 CDT)
Re: AMBER: ESP calculations. Ken Merz (Tue May 30 2006 - 06:55:24 CDT)
Re: AMBER: ESP calculations. Ken Merz (Tue May 30 2006 - 06:59:38 CDT)
Re: AMBER: problems with antechamber linfu (Tue May 30 2006 - 07:01:59 CDT)
RE: AMBER: problems with antechamber Junmei Wang (Tue May 30 2006 - 10:20:33 CDT)
RE: AMBER: Antechamber : +ve charge species Junmei Wang (Tue May 30 2006 - 10:31:07 CDT)
Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham (Tue May 30 2006 - 12:17:31 CDT)
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names David A. Case (Tue May 30 2006 - 12:36:37 CDT)
Re: AMBER: Pt containing complex: antechamber David A. Case (Tue May 30 2006 - 12:39:20 CDT)
Re: AMBER: Difference in results for TI calculation David A. Case (Tue May 30 2006 - 13:01:49 CDT)
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Andy Purkiss (Tue May 30 2006 - 13:18:58 CDT)
RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Tue May 30 2006 - 18:06:54 CDT)
AMBER: Different results for TI calculation Biswa Ranjan Meher (Wed May 31 2006 - 02:25:13 CDT)
AMBER: Replica exchage: about exchange interval Atsutoshi Okabe (Wed May 31 2006 - 07:36:27 CDT)
Re: AMBER: Replica exchage: about exchange interval Carlos Simmerling (Wed May 31 2006 - 08:02:32 CDT)
AMBER: Force units in forcedump.dat Steven Winfield (Wed May 31 2006 - 08:41:43 CDT)
AMBER: Namelists in input files Steven Winfield (Wed May 31 2006 - 11:42:05 CDT)
AMBER: SHAKE, TIP3P and 2fs Timesteps Mark Williamson (Wed May 31 2006 - 12:32:56 CDT)
Re: AMBER: Force units in forcedump.dat darden (Wed May 31 2006 - 12:53:34 CDT)
RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Ross Walker (Wed May 31 2006 - 12:56:31 CDT)
AMBER: xleap problem and answer Thomas Pochapsky (Wed May 31 2006 - 13:32:32 CDT)
RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Andreas Svrcek-Seiler (Wed May 31 2006 - 13:38:29 CDT)
AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 16:57:22 CDT)
AMBER: Installation of Amber8 on Fedora Core 5 DAVID P. RANGEL (Wed May 31 2006 - 17:48:11 CDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 18:04:53 CDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham (Wed May 31 2006 - 18:27:16 CDT)
AMBER: offset? Tonda March (Thu Jun 01 2006 - 01:12:19 CDT)
AMBER: Bond Force Conctants in Amber Force Fields åÇÏÒÏ× ä.á. (Thu Jun 01 2006 - 00:22:01 CDT)
Re: AMBER: offset? Angelo (Thu Jun 01 2006 - 04:39:20 CDT)
Re: AMBER: Different results for TI calculation David A. Case (Thu Jun 01 2006 - 09:33:32 CDT)
AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 10:08:26 CDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Thu Jun 01 2006 - 10:41:02 CDT)
Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford_at_stjude.org (Thu Jun 01 2006 - 11:23:11 CDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham (Thu Jun 01 2006 - 11:25:19 CDT)
RE: AMBER: Amber 8 QMMM tests fail on AIX Ross Walker (Thu Jun 01 2006 - 11:27:24 CDT)
RE: AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 12:31:08 CDT)
AMBER: Another Installation Problem Seth Lilavivat (Thu Jun 01 2006 - 18:01:13 CDT)
RE: AMBER: Another Installation Problem Ross Walker (Fri Jun 02 2006 - 00:02:03 CDT)
AMBER: compile error with pgf90 Evan Kelly (Fri Jun 02 2006 - 00:33:21 CDT)
AMBER: some questions and problems about antechamber and divcon Zhihong Yu (Fri Jun 02 2006 - 02:11:22 CDT)
AMBER: How to analyze the trajectory generated by LES simulation pang zhao (Fri Jun 02 2006 - 02:08:03 CDT)
AMBER: attachments for my last mail Zhihong Yu (Fri Jun 02 2006 - 02:30:30 CDT)
Re: AMBER: How to analyze the trajectory generated by LES simulation Vlad Cojocaru (Fri Jun 02 2006 - 04:54:20 CDT)
AMBER: Programes to calculate ligand RMSD nag raj (Fri Jun 02 2006 - 05:59:04 CDT)
Re: AMBER: Programes to calculate ligand RMSD Carlos Simmerling (Fri Jun 02 2006 - 06:45:17 CDT)
Re: AMBER: some questions and problems about antechamber and divcon Martin Peters (Fri Jun 02 2006 - 08:07:03 CDT)
AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky (Fri Jun 02 2006 - 08:25:33 CDT)
AMBER: distance restraints Myunggi Yi (Fri Jun 02 2006 - 10:06:38 CDT)
RE: AMBER: compile error with pgf90 Ross Walker (Fri Jun 02 2006 - 10:15:01 CDT)
Re: AMBER: Another Installation Problem Scott Pendley (Fri Jun 02 2006 - 11:21:09 CDT)
AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case (Fri Jun 02 2006 - 11:45:29 CDT)
AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 13:11:51 CDT)
Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 14:15:41 CDT)
Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 14:23:28 CDT)
Re: AMBER: Installation of Amber8 on Fedora Core 5. . David A. Case (Fri Jun 02 2006 - 14:27:59 CDT)
Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Fri Jun 02 2006 - 15:12:18 CDT)
Re: AMBER: Namelists in input files David A. Case (Fri Jun 02 2006 - 15:48:42 CDT)
AMBER: trouble adding mdcrd files together Adam Pelzer (Fri Jun 02 2006 - 17:22:46 CDT)
Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 17:37:54 CDT)
Re: AMBER: trouble adding mdcrd files together David A. Case (Fri Jun 02 2006 - 18:30:20 CDT)
Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 18:45:16 CDT)
Re: AMBER: some questions and problems about antechamber and divcon David A. Case (Fri Jun 02 2006 - 19:12:42 CDT)
Re: AMBER: NMR restraint David A. Case (Fri Jun 02 2006 - 19:28:16 CDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 22:50:03 CDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 22:39:13 CDT)
AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu (Sat Jun 03 2006 - 02:00:23 CDT)
Re: AMBER: manual docking linfu (Sat Jun 03 2006 - 02:39:44 CDT)
Re: AMBER: NMR restraint Myunggi Yi (Sat Jun 03 2006 - 08:25:26 CDT)
Re: AMBER: trouble adding mdcrd files together Adam Pelzer (Sat Jun 03 2006 - 19:40:28 CDT)
Re: AMBER: manual docking snoze pa (Sun Jun 04 2006 - 23:46:05 CDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 03:08:12 CDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu (Mon Jun 05 2006 - 03:57:44 CDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 04:22:33 CDT)
AMBER: MM-PBSA and first solvation shell Andrea Bortolato (Mon Jun 05 2006 - 04:42:39 CDT)
AMBER: process_mdout Navnit Kumar Mishra (Mon Jun 05 2006 - 07:00:40 CDT)
Re: AMBER: individual torsion/bond energies from a minimization David A. Case (Mon Jun 05 2006 - 09:21:40 CDT)
RE: AMBER: process_mdout Ross Walker (Mon Jun 05 2006 - 10:19:47 CDT)
Re: AMBER: MM-PBSA and first solvation shell Thomas Cheatham (Mon Jun 05 2006 - 12:23:58 CDT)
AMBER: Amber: Segfault while running sander sethl_at_gatech.edu (Mon Jun 05 2006 - 13:19:33 CDT)
RE: AMBER: Amber: Segfault while running sander Ross Walker (Mon Jun 05 2006 - 13:31:35 CDT)
AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu (Mon Jun 05 2006 - 21:24:17 CDT)
AMBER: How to submit a job in cluster pkb bioinfo (Tue Jun 06 2006 - 03:46:21 CDT)
AMBER: calculating box dimensions during MD Vlad Cojocaru (Tue Jun 06 2006 - 09:13:14 CDT)
Re: AMBER: calculating box dimensions during MD Ananda Rama Krishnan Selvaraj (Tue Jun 06 2006 - 09:31:32 CDT)
AMBER: antechamber and FMN David Mobley (Tue Jun 06 2006 - 12:47:03 CDT)
AMBER: Amber: Can't get sander to run sethl_at_gatech.edu (Tue Jun 06 2006 - 13:15:14 CDT)
AMBER: xleap problem Hashem Taha (Tue Jun 06 2006 - 13:29:31 CDT)
Re: AMBER: Amber: Can't get sander to run David A. Case (Tue Jun 06 2006 - 15:31:56 CDT)
Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 18:32:16 CDT)
Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 18:42:34 CDT)
Re: AMBER: xleap problem Ilyas Yildirim (Wed Jun 07 2006 - 01:49:04 CDT)
Re: AMBER: xleap problem Myunggi Yi (Wed Jun 07 2006 - 09:22:12 CDT)
AMBER: compiler error for Amber9 Weihua Li (Wed Jun 07 2006 - 09:34:49 CDT)
Re: AMBER: compiler error for Amber9 Robert Duke (Wed Jun 07 2006 - 10:03:15 CDT)
RE: AMBER: compiler error for Amber9 Ross Walker (Wed Jun 07 2006 - 10:34:20 CDT)
Re: AMBER: compiler error for Amber9 David A. Case (Wed Jun 07 2006 - 10:52:14 CDT)
AMBER: antechamber Steve Seibold (Wed Jun 07 2006 - 11:16:47 CDT)
Re: AMBER: antechamber Myunggi Yi (Wed Jun 07 2006 - 11:31:46 CDT)
RE: AMBER: antechamber Ross Walker (Wed Jun 07 2006 - 11:56:01 CDT)
AMBER: RE: antechamber and FMN Junmei Wang (Wed Jun 07 2006 - 15:39:48 CDT)
AMBER: pmemd_parallel_ins_prob pkmukher (Wed Jun 07 2006 - 16:00:20 CDT)
Re: AMBER: pmemd_parallel_ins_prob Robert Duke (Wed Jun 07 2006 - 16:21:28 CDT)
Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. David A. Case (Wed Jun 07 2006 - 17:22:41 CDT)
AMBER: problem with amber 9 and igb=5 M. Scott Shell (Wed Jun 07 2006 - 20:06:02 CDT)
Re: AMBER: problem with amber 9 and igb=5 Carlos Simmerling (Wed Jun 07 2006 - 21:02:34 CDT)
Re: AMBER: problem with amber 9 and igb=5 John Mongan (Wed Jun 07 2006 - 21:04:59 CDT)
AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 02:59:34 CDT)
Re: AMBER: How to build N-terminal of alanine : NH2 FyD (Thu Jun 08 2006 - 03:27:58 CDT)
AMBER: save coordinates during SANDER minimisation Hannes Barsch (Thu Jun 08 2006 - 04:34:51 CDT)
Re: AMBER: save coordinates during SANDER minimisation Ilyas Yildirim (Thu Jun 08 2006 - 05:22:24 CDT)
Fwd: AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 07:32:22 CDT)
AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D. (Thu Jun 08 2006 - 11:08:10 CDT)
Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 10:55:36 CDT)
Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 11:05:10 CDT)
AMBER: GB and protein backbone parameters Carlos Simmerling (Thu Jun 08 2006 - 11:27:47 CDT)
AMBER: software to visualize normal modes Douali, Latifa (Thu Jun 08 2006 - 12:03:26 CDT)
RE: AMBER: software to visualize normal modes Ross Walker (Thu Jun 08 2006 - 12:07:41 CDT)
Re: AMBER: software to visualize normal modes David A. Case (Thu Jun 08 2006 - 12:46:38 CDT)
Re: AMBER: pmemd_parallel_ins_prob pkmukher (Thu Jun 08 2006 - 13:09:00 CDT)
Re: AMBER: Ask for help in pbsa error in AMBER9 Ray Luo (Thu Jun 08 2006 - 14:01:06 CDT)
AMBER: AMD 64 Installation / configuration clarification sethl_at_gatech.edu (Thu Jun 08 2006 - 14:09:50 CDT)
Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 14:57:18 CDT)
Re: AMBER: AMD 64 Installation / configuration clarification sethl_at_gatech.edu (Thu Jun 08 2006 - 15:23:51 CDT)
Re: AMBER: save coordinates during SANDER minimisation David A. Case (Thu Jun 08 2006 - 17:39:01 CDT)
Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 18:52:57 CDT)
AMBER: COM khn _ (Thu Jun 08 2006 - 19:13:27 CDT)
Re: AMBER: COM Thomas Cheatham (Thu Jun 08 2006 - 19:34:03 CDT)
AMBER: Problem with Leap jitrayut jitonnom (Thu Jun 08 2006 - 23:40:52 CDT)
AMBER: charmm force field in amber9 soo (Thu Jun 08 2006 - 23:23:26 CDT)
Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Fri Jun 09 2006 - 00:15:56 CDT)
Re: Fwd: AMBER: How to build N-terminal of alanine : NH2 FyD (Fri Jun 09 2006 - 01:45:27 CDT)
AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao (Fri Jun 09 2006 - 03:56:57 CDT)
AMBER: MMPBSA problem jitrayut jitonnom (Fri Jun 09 2006 - 04:48:50 CDT)
Re: AMBER: charmm force field in amber9 David A. Case (Fri Jun 09 2006 - 09:02:03 CDT)
Re: AMBER: MMPBSA problem Thomas Steinbrecher (Fri Jun 09 2006 - 10:06:34 CDT)
AMBER: ptraj Marcela Madrid (Fri Jun 09 2006 - 16:19:54 CDT)
Re: AMBER: problem with amber 9 and igb=5 David A. Case (Fri Jun 09 2006 - 16:58:02 CDT)
AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 22:03:26 CDT)
AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 21:57:42 CDT)
AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Fri Jun 09 2006 - 22:25:24 CDT)
AMBER: MD stopped Miguel Ferreira (Sat Jun 10 2006 - 04:33:05 CDT)
AMBER: Umbrella sampling Atsutoshi Okabe (Sat Jun 10 2006 - 05:42:34 CDT)
Re: AMBER: Umbrella sampling Ilyas Yildirim (Sat Jun 10 2006 - 09:53:41 CDT)
Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? David A. Case (Sat Jun 10 2006 - 12:06:49 CDT)
Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? Ray Luo (Sat Jun 10 2006 - 12:45:17 CDT)
Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? David A. Case (Sat Jun 10 2006 - 13:24:29 CDT)
Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Sat Jun 10 2006 - 13:40:05 CDT)
RE: AMBER: problem with amber 9 and igb=5 Ross Walker (Sat Jun 10 2006 - 14:31:26 CDT)
AMBER: parmchk error Evan Kelly (Sat Jun 10 2006 - 22:30:11 CDT)
Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Sat Jun 10 2006 - 22:27:20 CDT)
AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Mon Jun 12 2006 - 00:59:06 CDT)
AMBER: switching function for electrostatic interactions Fabien Cailliez (Mon Jun 12 2006 - 06:38:22 CDT)
RE: AMBER: switching function for electrostatic interactions Ross Walker (Mon Jun 12 2006 - 10:28:19 CDT)
RE: AMBER: parmchk error Ross Walker (Mon Jun 12 2006 - 10:31:59 CDT)
RE: AMBER: MD stopped Ross Walker (Mon Jun 12 2006 - 10:50:34 CDT)
Re: AMBER: switching function for electrostatic interactions Thomas Cheatham (Mon Jun 12 2006 - 11:12:28 CDT)
AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 11:41:52 CDT)
Re: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 11:58:33 CDT)
Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 13:37:49 CDT)
Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 13:50:30 CDT)
Re: AMBER: How to calculate the mmpbsa for explicit MD ? Chris Moth (Mon Jun 12 2006 - 14:23:01 CDT)
Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 14:15:06 CDT)
Re: AMBER: How to strip waters in trajectorie ? Gustavo Seabra (Mon Jun 12 2006 - 14:57:30 CDT)
AMBER: How to strip waters in trajectorie ? jitrayut jitonnom (Mon Jun 12 2006 - 14:50:02 CDT)
Re: AMBER: How to strip waters in trajectorie ? David A. Case (Mon Jun 12 2006 - 15:06:19 CDT)
Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Mon Jun 12 2006 - 16:42:59 CDT)
AMBER: Nmode memory allocation problem JunJun Liu (Mon Jun 12 2006 - 18:45:14 CDT)
RE: AMBER: Nmode memory allocation problem Ross Walker (Mon Jun 12 2006 - 20:34:24 CDT)
Re: AMBER: parmchk error Evan Kelly (Tue Jun 13 2006 - 00:42:16 CDT)
Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 02:45:32 CDT)
Re: AMBER: How to strip waters in trajectorie ? simon whitehead (Tue Jun 13 2006 - 03:24:37 CDT)
AMBER: SGI compiler problems Peter Gannett (Tue Jun 13 2006 - 07:46:18 CDT)
AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 09:52:08 CDT)
Re: AMBER: MMPBSA error Heike.Meiselbach_at_chemie.uni-erlangen.de (Tue Jun 13 2006 - 10:27:22 CDT)
Re: AMBER: Nmode memory allocation problem JunJun Liu (Tue Jun 13 2006 - 10:08:25 CDT)
Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 11:20:42 CDT)
Fwd: AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 11:28:43 CDT)
Re: Fwd: AMBER: MMPBSA error JunJun Liu (Tue Jun 13 2006 - 10:51:58 CDT)
Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 12:26:56 CDT)
AMBER: Difficulty loading a pdb file Kara Di Giorgio (Tue Jun 13 2006 - 13:20:41 CDT)
AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom (Tue Jun 13 2006 - 13:40:47 CDT)
Re: AMBER: LEaP Warning ... when do NH2-neutral fragment FyD (Tue Jun 13 2006 - 14:20:52 CDT)
Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 15:03:17 CDT)
Re: AMBER: Difficulty loading a pdb file Ilyas Yildirim (Tue Jun 13 2006 - 16:25:27 CDT)
Re: AMBER: LEaP Warning ... when do NH2-neutral fragment Ilyas Yildirim (Tue Jun 13 2006 - 16:23:18 CDT)
AMBER: Problem of Ptraj in AMBER9 Chunhu Tan (Tue Jun 13 2006 - 17:24:26 CDT)
AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman (Wed Jun 14 2006 - 01:45:40 CDT)
AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu (Wed Jun 14 2006 - 05:43:59 CDT)
Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom (Wed Jun 14 2006 - 06:27:51 CDT)
AMBER: problems on mm_pbsa Giovanni (Wed Jun 14 2006 - 07:05:03 CDT)
AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 08:28:43 CDT)
RE: AMBER: Difficulty loading a pdb file Ross Walker (Wed Jun 14 2006 - 09:05:34 CDT)
AMBER: ptraj: rms per residue simon whitehead (Wed Jun 14 2006 - 09:14:28 CDT)
Re: AMBER: saveamberparams error in Amber9 Thomas Steinbrecher (Wed Jun 14 2006 - 10:07:28 CDT)
AMBER: Fully QM periodic runs Steven Winfield (Wed Jun 14 2006 - 11:03:43 CDT)
RE: AMBER: Fully QM periodic runs Ross Walker (Wed Jun 14 2006 - 11:41:58 CDT)
Re: AMBER: Fully QM periodic runs Wei Zhang (Wed Jun 14 2006 - 11:58:51 CDT)
Re: AMBER: problems on mm_pbsa Ray Luo (Wed Jun 14 2006 - 00:04:28 CDT)
Re: AMBER: Fully QM periodic runs Gustavo Seabra (Wed Jun 14 2006 - 12:44:37 CDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Wed Jun 14 2006 - 12:20:40 CDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ilyas Yildirim (Wed Jun 14 2006 - 13:46:22 CDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Knut Langsetmo (Wed Jun 14 2006 - 14:55:56 CDT)
RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ross Walker (Wed Jun 14 2006 - 15:06:49 CDT)
AMBER: best way to customize linkages sethl_at_gatech.edu (Wed Jun 14 2006 - 15:25:07 CDT)
Re: AMBER: ptraj: rms per residue Mingfeng Yang (Wed Jun 14 2006 - 15:28:07 CDT)
Re: AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 21:15:03 CDT)
Re: AMBER: saveamberparams error in Amber9 David A. Case (Wed Jun 14 2006 - 22:15:05 CDT)
Re: AMBER: parmchk error David A. Case (Wed Jun 14 2006 - 22:28:20 CDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Wed Jun 14 2006 - 22:29:57 CDT)
Re: AMBER: saveamberparams error in Amber9 Weihua Li (Thu Jun 15 2006 - 01:48:52 CDT)
AMBER: RMS FLUCTUATIONS Jiang Jianwen (Thu Jun 15 2006 - 06:37:24 CDT)
Re: AMBER: Fully QM periodic runs Ken Merz (Thu Jun 15 2006 - 09:10:13 CDT)
RE: AMBER: RMS FLUCTUATIONS Yong Duan (Thu Jun 15 2006 - 09:49:16 CDT)
RE: AMBER: parmchk error Junmei Wang (Thu Jun 15 2006 - 10:16:10 CDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Thu Jun 15 2006 - 11:27:45 CDT)
Re: AMBER: pmemd_parallel_ins_prob Amber admin (Thu Jun 15 2006 - 14:08:46 CDT)
AMBER: GBSA of nonstandard cations Martin LEPSIK (Thu Jun 15 2006 - 17:46:16 CDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Thu Jun 15 2006 - 18:28:27 CDT)
AMBER: repeat use of a trimer lib file Eric Hu (Thu Jun 15 2006 - 18:35:39 CDT)
AMBER: MPICH and Sander Andrew Box (Thu Jun 15 2006 - 21:07:11 CDT)
Re: AMBER: MPICH and Sander David A. Case (Thu Jun 15 2006 - 22:47:36 CDT)
Re: AMBER: RMS FLUCTUATIONS David A. Case (Thu Jun 15 2006 - 23:09:53 CDT)
RE: AMBER: RMS FLUCTUATIONS Jiang Jianwen (Fri Jun 16 2006 - 02:01:10 CDT)
AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 08:52:33 CDT)
Re: AMBER: LEaP error : unbalanced charge Thomas Steinbrecher (Fri Jun 16 2006 - 09:59:50 CDT)
Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 11:34:42 CDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 12:28:08 CDT)
AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert (Fri Jun 16 2006 - 23:32:12 CDT)
Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Ilyas Yildirim (Sat Jun 17 2006 - 03:28:55 CDT)
AMBER: Problems with restart file from pmemd sim. anna.schrey_at_gmx.de (Sat Jun 17 2006 - 07:30:56 CDT)
Re: AMBER: Problems with restart file from pmemd sim. Robert Duke (Sat Jun 17 2006 - 08:10:24 CDT)
AMBER: charge in LEaP step jitrayut jitonnom (Sat Jun 17 2006 - 13:14:24 CDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sat Jun 17 2006 - 15:37:46 CDT)
Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge Ilyas Yildirim (Sun Jun 18 2006 - 02:53:58 CDT)
RE: AMBER: Umbrella sampling Atsutoshi Okabe (Sun Jun 18 2006 - 05:14:10 CDT)
Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sun Jun 18 2006 - 08:17:57 CDT)
RE: AMBER: Umbrella sampling Ilyas Yildirim (Sun Jun 18 2006 - 11:57:09 CDT)
AMBER: Non bond list overflow in amber8.0 program. nag raj (Sun Jun 18 2006 - 23:54:04 CDT)
Re: AMBER: LEaP error : unbalanced charge FyD (Mon Jun 19 2006 - 02:03:38 CDT)
AMBER: Post-MD minimization sangeeta_at_bioinfo.ernet.in (Mon Jun 19 2006 - 06:33:58 CDT)
Re: AMBER: Post-MD minimization Carlos Simmerling (Mon Jun 19 2006 - 09:27:37 CDT)
RE: AMBER: Post-MD minimization Ross Walker (Mon Jun 19 2006 - 10:20:25 CDT)
AMBER: Amber7-CHARMM22-TRIPOS force fields opitz_at_che.udel.edu (Mon Jun 19 2006 - 10:37:24 CDT)
AMBER: help with custom RNA molecule sethl_at_gatech.edu (Mon Jun 19 2006 - 13:55:59 CDT)
AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected Christophe Guilbert (Mon Jun 19 2006 - 20:00:29 CDT)
AMBER: ions+proteins Hannes Loeffler (Mon Jun 19 2006 - 20:45:57 CDT)
AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected Junmei Wang (Mon Jun 19 2006 - 22:08:56 CDT)
AMBER: second derivative matrix Marie Brut (Tue Jun 20 2006 - 07:28:02 CDT)
AMBER: why has "ELE " a large fluctuation in MMP BSA? yxiong99 (Tue Jun 20 2006 - 08:47:44 CDT)
RE: AMBER: checkoverlap doubt [was: Post-MD minimization] sangeeta_at_bioinfo.ernet.in (Tue Jun 20 2006 - 08:21:11 CDT)
AMBER: why has "ELE " a large fluctuation in MMPBSA? JunJun Liu (Tue Jun 20 2006 - 08:56:25 CDT)
AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 11:13:54 CDT)
Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 13:20:53 CDT)
Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 14:32:17 CDT)
Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 15:07:36 CDT)
Re: AMBER: second derivative matrix David A. Case (Tue Jun 20 2006 - 16:37:01 CDT)
Re: AMBER: ptraj vector David A. Case (Tue Jun 20 2006 - 16:36:49 CDT)
Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 16:55:05 CDT)
Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 16:59:50 CDT)
Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 17:13:06 CDT)
RE: AMBER: checkoverlap doubt [was: Post-MD minimization] Thomas Cheatham (Tue Jun 20 2006 - 17:28:36 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 16:37:52 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 18:10:48 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Thomas Cheatham (Tue Jun 20 2006 - 18:48:54 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 17:55:09 CDT)
AMBER: amber9 hostfile snoze pa (Tue Jun 20 2006 - 19:12:50 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 19:18:21 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 19:19:10 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 18:45:52 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 20:54:51 CDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 20:08:32 CDT)
AMBER: Tutorial 2: Production MD. a a (Wed Jun 21 2006 - 05:19:05 CDT)
AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 05:46:40 CDT)
Re: AMBER: SGI compiler problems Atro Tossavainen (Wed Jun 21 2006 - 06:30:00 CDT)
Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test Roberto Gomperts (Wed Jun 21 2006 - 09:10:44 CDT)
AMBER: MMTSB: phi-pdi-based clustering sangeeta_at_bioinfo.ernet.in (Wed Jun 21 2006 - 07:37:39 CDT)
Re: AMBER: SGI compiler problems Roberto Gomperts (Wed Jun 21 2006 - 10:09:54 CDT)
Re: AMBER: Tutorial 2: Production MD. Thomas Steinbrecher (Wed Jun 21 2006 - 10:37:51 CDT)
AMBER: terms in mm-pbsa Lwin, ThuZar (Wed Jun 21 2006 - 10:48:37 CDT)
Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 10:54:44 CDT)
AMBER: openmpi snoze pa (Wed Jun 21 2006 - 12:28:28 CDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Wed Jun 21 2006 - 16:06:05 CDT)
AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 15:27:51 CDT)
Re: AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 15:59:23 CDT)
AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Thu Jun 22 2006 - 02:25:11 CDT)
AMBER: kill job command? a a (Thu Jun 22 2006 - 02:47:51 CDT)
AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot (Thu Jun 22 2006 - 04:00:03 CDT)
AMBER: average struct.problem bala (Thu Jun 22 2006 - 04:11:15 CDT)
AMBER: can i use unusual amino acid priya priya (Thu Jun 22 2006 - 04:15:55 CDT)
AMBER: RESP charge fitting problems with capping group hayden (Thu Jun 22 2006 - 04:51:52 CDT)
Re: AMBER: average struct.problem Thomas Cheatham (Thu Jun 22 2006 - 09:35:45 CDT)
Re: AMBER: kill job command? JunJun Liu (Thu Jun 22 2006 - 08:13:04 CDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9 Wei Zhang (Thu Jun 22 2006 - 11:21:32 CDT)
Re: AMBER: What's the meaning of NTYPES? Wei Zhang (Thu Jun 22 2006 - 11:18:38 CDT)
Re: AMBER: RESP charge fitting problems with capping group FyD (Thu Jun 22 2006 - 13:51:13 CDT)
AMBER: help creating RNA sethl_at_gatech.edu (Thu Jun 22 2006 - 14:14:06 CDT)
Re: AMBER: help creating RNA Ilyas Yildirim (Thu Jun 22 2006 - 14:29:49 CDT)
Re: AMBER: help creating RNA David A. Case (Thu Jun 22 2006 - 16:08:45 CDT)
AMBER: ANN: APBS/Amber interface released Robert Konecny (Fri Jun 23 2006 - 01:23:35 CDT)
RE: AMBER: Post-MD minimization sangeeta_at_bioinfo.ernet.in (Fri Jun 23 2006 - 01:09:31 CDT)
AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco (Fri Jun 23 2006 - 02:36:44 CDT)
Re: AMBER: help creating RNA Vlad Cojocaru (Fri Jun 23 2006 - 03:14:24 CDT)
AMBER: Tutorial 2: Minimise and equlibrium error NaN a a (Fri Jun 23 2006 - 05:05:05 CDT)
AMBER: references simon whitehead (Fri Jun 23 2006 - 05:35:56 CDT)
Re: AMBER: references Ricardo J. F. Branco (Fri Jun 23 2006 - 05:47:50 CDT)
RE: AMBER: references Ross Walker (Fri Jun 23 2006 - 06:32:57 CDT)
RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN Ross Walker (Fri Jun 23 2006 - 06:28:17 CDT)
RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ross Walker (Fri Jun 23 2006 - 06:34:47 CDT)
RE: AMBER: Post-MD minimization Ross Walker (Fri Jun 23 2006 - 07:19:14 CDT)
AMBER: constant pressure equillibration simon whitehead (Fri Jun 23 2006 - 04:17:35 CDT)
AMBER: Implicit solvent question Anthony Cruz (Fri Jun 23 2006 - 08:49:22 CDT)
RE: AMBER: constant pressure equillibration Ross Walker (Fri Jun 23 2006 - 10:53:17 CDT)
Re: AMBER: Implicit solvent question John Mongan (Fri Jun 23 2006 - 11:09:49 CDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Fri Jun 23 2006 - 12:00:36 CDT)
AMBER: how to create 2'-5' RNA sethl_at_gatech.edu (Fri Jun 23 2006 - 16:13:57 CDT)
Re: AMBER: references simon whitehead (Fri Jun 23 2006 - 06:46:22 CDT)
Re: AMBER: how to create 2'-5' RNA FyD (Sat Jun 24 2006 - 01:29:43 CDT)
AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 17:15:51 CDT)
AMBER: Can we submit jobs in sequences to amber? a a (Mon Jun 26 2006 - 02:14:05 CDT)
Re: AMBER: Can we submit jobs in sequences to amber? Ilyas Yildirim (Mon Jun 26 2006 - 02:22:00 CDT)
Re: AMBER: Can we submit jobs in sequences to amber? Roberto Gomperts (Mon Jun 26 2006 - 05:25:03 CDT)
AMBER: Minizsation strange error message! Please help. a a (Mon Jun 26 2006 - 05:38:35 CDT)
AMBER:Checkoverlap query sangeeta_at_bioinfo.ernet.in (Mon Jun 26 2006 - 07:12:56 CDT)
Re: AMBER: help creating RNA sethl_at_gatech.edu (Mon Jun 26 2006 - 10:42:00 CDT)
AMBER: Amber minimization with multiple restraints Qingning Shu (Mon Jun 26 2006 - 12:23:33 CDT)
AMBER: Curves and Average Structures Lauren O'Neil (Mon Jun 26 2006 - 12:26:46 CDT)
AMBER: Review. Chunhu Tan (Mon Jun 26 2006 - 14:37:22 CDT)
Re: AMBER: Curves and Average Structures David E. Konerding (Mon Jun 26 2006 - 14:42:05 CDT)
AMBER: manual/prmtop/missing bonds section David Mobley (Mon Jun 26 2006 - 15:27:39 CDT)
AMBER: creating RNA, nucgen / leap sethl_at_gatech.edu (Mon Jun 26 2006 - 15:59:46 CDT)
AMBER: ´ð¸´: AMBER: Review. Chunhu Tan (Mon Jun 26 2006 - 16:46:29 CDT)
Re: AMBER: how to create 2'-5' RNA Ilyas Yildirim (Mon Jun 26 2006 - 17:52:10 CDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Mon Jun 26 2006 - 23:41:05 CDT)
Re: AMBER: Second derivative matrix David A. Case (Tue Jun 27 2006 - 03:36:57 CDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9 Kateryna Miroshnychenko (Tue Jun 27 2006 - 03:41:21 CDT)
Re: AMBER: Curves and Average Structures Angelo (Tue Jun 27 2006 - 03:57:47 CDT)
AMBER: MM-PBSA and gaff atom types anna ferrari (Tue Jun 27 2006 - 04:28:03 CDT)
AMBER: Leap: neutralising the charge Miguel Ferreira (Tue Jun 27 2006 - 04:49:36 CDT)
Re: AMBER: Leap: neutralising the charge FyD (Tue Jun 27 2006 - 06:19:08 CDT)
Re: AMBER: MM-PBSA and gaff atom types Ray Luo (Tue Jun 27 2006 - 21:47:51 CDT)
AMBER: rgbmax--something wrong with my input file? Kenley Barrett (Tue Jun 27 2006 - 16:10:27 CDT)
RE: AMBER: rgbmax--something wrong with my input file? Ross Walker (Tue Jun 27 2006 - 17:52:06 CDT)
AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac (Wed Jun 28 2006 - 05:46:49 CDT)
AMBER: REM test failures on IA-64 architecture Glass, Kevin A (Wed Jun 28 2006 - 10:28:07 CDT)
Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Thomas Cheatham (Wed Jun 28 2006 - 11:22:42 CDT)
Re: AMBER: MM-PBSA and gaff atom types anna ferrari (Wed Jun 28 2006 - 11:43:41 CDT)
Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 14:56:49 CDT)
Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 14:53:12 CDT)
Re: AMBER: REM test failures on IA-64 architecture Asim Okur (Wed Jun 28 2006 - 15:09:08 CDT)
AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 14:36:47 CDT)
Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 16:11:22 CDT)
Re: AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 16:24:07 CDT)
Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 16:37:54 CDT)
Re: AMBER: rgbmax--something wrong with my input file? tmarch_at_coin.org (Wed Jun 28 2006 - 16:37:19 CDT)
AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 Lwin, ThuZar (Wed Jun 28 2006 - 19:58:14 CDT)
AMBER: MM-PBSA questions Miguel Ferreira (Wed Jun 28 2006 - 20:26:14 CDT)
Re: AMBER: MM-PBSA questions Ray Luo (Fri Jun 30 2006 - 00:56:42 CDT)
AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 04:38:58 CDT)
Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Thu Jun 29 2006 - 05:38:11 CDT)
AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 10:58:26 CDT)
Re: AMBER: Implicit solvent question Anthony Cruz (Thu Jun 29 2006 - 11:44:54 CDT)
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 11:37:53 CDT)
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 12:53:23 CDT)
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 13:24:14 CDT)
AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman (Thu Jun 29 2006 - 14:23:06 CDT)
Re: AMBER: Having trouble getting Iron parameters for QM/MM Ken Merz (Thu Jun 29 2006 - 14:54:45 CDT)
Re: AMBER: Having trouble getting Iron parameters for QM/MM FyD (Thu Jun 29 2006 - 15:55:14 CDT)
AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99 (Thu Jun 29 2006 - 15:49:50 CDT)
Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl Ray Luo (Thu Jun 29 2006 - 19:47:13 CDT)
AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 16:48:31 CDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Thu Jun 29 2006 - 18:46:17 CDT)
Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl JunJun Liu (Thu Jun 29 2006 - 18:56:34 CDT)
AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu (Thu Jun 29 2006 - 19:58:24 CDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 20:06:29 CDT)
AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Thu Jun 29 2006 - 20:28:31 CDT)
Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 23:16:48 CDT)
RE: AMBER: Having trouble getting Iron parameters for QM/MM Ross Walker (Fri Jun 30 2006 - 03:54:28 CDT)
Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Fri Jun 30 2006 - 07:22:08 CDT)
AMBER: GB simulation problem Anthony Cruz (Fri Jun 30 2006 - 11:49:53 CDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Fri Jun 30 2006 - 13:42:53 CDT)
AMBER: NAMOT sethl_at_gatech.edu (Fri Jun 30 2006 - 14:17:46 CDT)
Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Fri Jun 30 2006 - 23:39:09 CDT)
AMBER: pmemd9 issue Brent Krueger (Sat Jul 01 2006 - 22:45:11 CDT)
Re: AMBER: pmemd9 issue Robert Duke (Sun Jul 02 2006 - 06:12:11 CDT)
Re: AMBER: pmemd9 issue Robert Duke (Sun Jul 02 2006 - 06:46:21 CDT)
AMBER: R.E.D II Franck_Vendeix_at_ncsu.edu (Sun Jul 02 2006 - 21:11:39 CDT)
Re: AMBER: R.E.D II FyD (Mon Jul 03 2006 - 01:39:20 CDT)
AMBER: compiling amber9 nadiav_at_soton.ac.uk (Mon Jul 03 2006 - 03:50:44 CDT)
Re: AMBER: R.E.D II a a (Mon Jul 03 2006 - 04:35:35 CDT)
AMBER: Tutorial 4-section 4 (plc.frcmod) a a (Mon Jul 03 2006 - 04:41:44 CDT)
AMBER: Tutorial 4-section 4 - VDW parameters a a (Mon Jul 03 2006 - 04:49:31 CDT)
Re: AMBER: R.E.D II FyD (Mon Jul 03 2006 - 05:03:19 CDT)
RE: AMBER: compiling amber9 Ross Walker (Mon Jul 03 2006 - 05:48:10 CDT)
Re: AMBER: NAMOT Andreas Svrcek-Seiler (Mon Jul 03 2006 - 06:02:57 CDT)
AMBER: 2-D free energy surface using WHAM Atsutoshi Okabe (Mon Jul 03 2006 - 07:08:01 CDT)
AMBER: fixing residues Prabhakar. G. (Mon Jul 03 2006 - 07:16:46 CDT)
Re: AMBER: Tutorial 4-section 4 (plc.frcmod) Mark Williamson (Mon Jul 03 2006 - 07:46:08 CDT)
AMBER: multiple "restraint_wt" in sander kanazta1_at_yahoo.co.jp (Mon Jul 03 2006 - 09:12:21 CDT)
Re: AMBER: 2-D free energy surface using WHAM David Mobley (Mon Jul 03 2006 - 09:33:24 CDT)
Re: AMBER: multiple "restraint_wt" in sander Viktor Hornak (Mon Jul 03 2006 - 09:43:44 CDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Mon Jul 03 2006 - 12:51:13 CDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David LeBard (Mon Jul 03 2006 - 13:15:50 CDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Mon Jul 03 2006 - 13:40:50 CDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . Lwin, ThuZar (Mon Jul 03 2006 - 14:02:31 CDT)
AMBER: hbond analysis Claire Zerafa (Mon Jul 03 2006 - 16:06:22 CDT)
Re: AMBER: hbond analysis Thomas Cheatham (Mon Jul 03 2006 - 14:19:57 CDT)
AMBER: Dihedral analysis Claire Zerafa (Mon Jul 03 2006 - 16:25:33 CDT)
Re: AMBER: Dihedral analysis Thomas Cheatham (Mon Jul 03 2006 - 14:47:42 CDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . hayden (Mon Jul 03 2006 - 19:28:37 CDT)
AMBER: Tutorial 4-section 4 DIHE in frcmod file. a a (Mon Jul 03 2006 - 21:13:04 CDT)
RE: AMBER: fixing residues a a (Mon Jul 03 2006 - 21:47:08 CDT)
Re: AMBER: Tutorial 4-section 4 DIHE in frcmod file. Ilyas Yildirim (Mon Jul 03 2006 - 22:47:22 CDT)
Re: AMBER: R.E.D II Franck_Vendeix_at_ncsu.edu (Tue Jul 04 2006 - 01:23:22 CDT)
AMBER: MM-PBSA: Problem when Generating Snapshots Zu Thur Yew (Tue Jul 04 2006 - 02:20:39 CDT)
Re: AMBER: R.E.D II FyD (Tue Jul 04 2006 - 02:47:51 CDT)
AMBER: Constant pH simulation : LYS residue Guillaume Bollot (Tue Jul 04 2006 - 06:13:00 CDT)
AMBER: hbond analysis2 Claire Zerafa (Tue Jul 04 2006 - 09:00:35 CDT)
RE: AMBER: compiling amber9 nadiav_at_soton.ac.uk (Tue Jul 04 2006 - 09:31:02 CDT)
Re: AMBER: R.E.D II Franck_Vendeix_at_ncsu.edu (Tue Jul 04 2006 - 09:29:59 CDT)
AMBER: Can you use VMD to measure bond angles/lengths sethl_at_gatech.edu (Tue Jul 04 2006 - 10:24:49 CDT)
Re: AMBER: Can you use VMD to measure bond angles/lengths Andreas Svrcek-Seiler (Tue Jul 04 2006 - 11:09:21 CDT)
Re: AMBER: Can you use VMD to measure bond angles/lengths Mark Williamson (Tue Jul 04 2006 - 11:06:59 CDT)
Re: AMBER: R.E.D II FyD (Tue Jul 04 2006 - 11:33:46 CDT)
Re: AMBER: R.E.D II Franck_Vendeix_at_ncsu.edu (Tue Jul 04 2006 - 23:33:21 CDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Tue Jul 04 2006 - 23:29:38 CDT)
Re: AMBER: R.E.D II FyD (Wed Jul 05 2006 - 01:55:13 CDT)
AMBER: error on running parallel sander on remote node- amber9 Chengwen Chen (Wed Jul 05 2006 - 02:46:11 CDT)
AMBER: problem with saving the parameters file amere swathi (Wed Jul 05 2006 - 03:50:40 CDT)
AMBER: analysis of atoms in a range during simulation pkb bioinfo (Wed Jul 05 2006 - 07:41:58 CDT)
Re: AMBER: R.E.D II Franck Vendeix (Wed Jul 05 2006 - 09:56:24 CDT)
Re: AMBER: manual/prmtop/missing bonds section David A. Case (Wed Jul 05 2006 - 11:09:06 CDT)
AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging Zu Thur Yew (Wed Jul 05 2006 - 12:03:13 CDT)
AMBER: Namot on AMD 64 possible sethl_at_gatech.edu (Wed Jul 05 2006 - 12:05:26 CDT)
Re: AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging David A. Case (Wed Jul 05 2006 - 12:50:52 CDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo (Wed Jul 05 2006 - 12:45:49 CDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9 David A. Case (Wed Jul 05 2006 - 13:06:08 CDT)
Re: AMBER: Namot on AMD 64 possible Andreas Svrcek-Seiler (Wed Jul 05 2006 - 13:08:44 CDT)
Re: AMBER: problem with saving the parameters file David A. Case (Wed Jul 05 2006 - 13:09:12 CDT)
Re: AMBER: problem with saving the parameters file Bill Ross (Wed Jul 05 2006 - 13:23:05 CDT)
AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 14:25:16 CDT)
AMBER: Addendum: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 14:29:10 CDT)
Re: AMBER: igb=2 and "bad atom type" conflict Scott Pendley (Wed Jul 05 2006 - 15:22:43 CDT)
AMBER: change atom in a DNA double strand Carra, Claudio $JSC-SK$[USRA] (Wed Jul 05 2006 - 16:09:23 CDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. David A. Case (Wed Jul 05 2006 - 16:31:14 CDT)
AMBER: PTRAJ OUTPUT Cporteli (Wed Jul 05 2006 - 18:02:47 CDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David A. Case (Wed Jul 05 2006 - 17:22:42 CDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . Lwin, ThuZar (Wed Jul 05 2006 - 18:01:25 CDT)
Re: AMBER: PTRAJ OUTPUT Bill Ross (Wed Jul 05 2006 - 18:43:57 CDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Wed Jul 05 2006 - 18:55:49 CDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Wed Jul 05 2006 - 19:29:52 CDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. David A. Case (Wed Jul 05 2006 - 20:54:38 CDT)
AMBER: FIX conformation of a ligand a a (Wed Jul 05 2006 - 21:17:23 CDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Wed Jul 05 2006 - 21:50:24 CDT)
AMBER: Units for Leonard-Jones potential parameters Vanessa Oklejas (Wed Jul 05 2006 - 22:02:59 CDT)
AMBER: analysis of ATOMs in ´certain range distance during simulation pkb bioinfo (Wed Jul 05 2006 - 22:37:46 CDT)
Re: AMBER: fixing residues Prabhakar. G. (Wed Jul 05 2006 - 22:57:38 CDT)
AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Thu Jul 06 2006 - 00:17:54 CDT)
AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jul 06 2006 - 03:29:35 CDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . hayden (Thu Jul 06 2006 - 07:02:13 CDT)
Re: AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jul 06 2006 - 07:43:24 CDT)
AMBER: working with large strained system Tanya Johannsen (Wed Jul 05 2006 - 21:29:58 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Thu Jul 06 2006 - 08:40:39 CDT)
Re: AMBER: working with large strained system Carlos Simmerling (Thu Jul 06 2006 - 08:41:39 CDT)
Re: AMBER: working with large strained system Robert Duke (Thu Jul 06 2006 - 09:06:48 CDT)
Re: AMBER: FIX conformation of a ligand David A. Case (Thu Jul 06 2006 - 09:30:01 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin David A. Case (Thu Jul 06 2006 - 10:16:11 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Thu Jul 06 2006 - 10:36:28 CDT)
Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 10:45:10 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Thu Jul 06 2006 - 10:50:05 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Thu Jul 06 2006 - 11:08:34 CDT)
Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 11:21:06 CDT)
Re: AMBER: Units for Leonard-Jones potential parameters David A. Case (Thu Jul 06 2006 - 11:45:00 CDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David A. Case (Thu Jul 06 2006 - 11:43:36 CDT)
Re: AMBER: change atom in a DNA double strand David A. Case (Thu Jul 06 2006 - 11:57:12 CDT)
AMBER: Problem with bcc flag of antechamber Gobind Bisht (Thu Jul 06 2006 - 12:00:49 CDT)
Re: AMBER: working with large strained system Bill Ross (Thu Jul 06 2006 - 12:06:57 CDT)
AMBER: Problem with bcc flag of antechamber..continued Gobind Bisht (Thu Jul 06 2006 - 12:08:45 CDT)
RE: AMBER: Problem with bcc flag of antechamber Junmei Wang (Thu Jul 06 2006 - 12:53:37 CDT)
AMBER: amber9 compilation problems on EM64T xeon system hayden (Thu Jul 06 2006 - 13:11:04 CDT)
RE: AMBER: amber9 compilation problems on EM64T xeon system Yong Duan (Thu Jul 06 2006 - 14:38:05 CDT)
Re: AMBER: analysis of ATOMs in ´certain range distance during simulation Scott Pendley (Thu Jul 06 2006 - 16:47:57 CDT)
Re: AMBER: analysis of ATOMs in ´certain range distance during simulation Myunggi Yi (Thu Jul 06 2006 - 17:03:12 CDT)
Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 17:01:39 CDT)
AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities Thomas Steinbrecher (Thu Jul 06 2006 - 18:02:19 CDT)
AMBER: Sander NOE violations Andrew Box (Thu Jul 06 2006 - 18:55:59 CDT)
AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? Christophe Guilbert (Thu Jul 06 2006 - 19:51:49 CDT)
Re: AMBER: Sander NOE violations David A. Case (Thu Jul 06 2006 - 20:01:19 CDT)
Re: AMBER: Sander NOE violations Andrew Box (Thu Jul 06 2006 - 20:32:21 CDT)
Re: AMBER: Sander NOE violations David A. Case (Thu Jul 06 2006 - 20:41:28 CDT)
Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? David A. Case (Thu Jul 06 2006 - 20:48:12 CDT)
Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? Carlos Simmerling (Thu Jul 06 2006 - 20:51:58 CDT)
RE: AMBER: amber9 compilation problems on EM64T xeon system Ross Walker (Thu Jul 06 2006 - 22:06:15 CDT)
AMBER: Amber8.0 predictied pKa problem for a Lysine! Guillaume Bollot (Fri Jul 07 2006 - 04:38:08 CDT)
AMBER: calculating dihedral angles, radius of gyration madhumalar_at_bii-sg.org (Fri Jul 07 2006 - 04:57:14 CDT)
Re: AMBER: Problem with bcc flag of antechamber..continued amit_at_mbu.iisc.ernet.in (Fri Jul 07 2006 - 05:09:32 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 09:13:37 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Fri Jul 07 2006 - 09:36:50 CDT)
AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Bob Johnson (Fri Jul 07 2006 - 09:55:32 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 10:48:35 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Fri Jul 07 2006 - 11:00:36 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Fri Jul 07 2006 - 11:13:40 CDT)
Re: AMBER: Amber8.0 predictied pKa problem for a Lysine! Myunggi Yi (Fri Jul 07 2006 - 11:14:42 CDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 11:39:31 CDT)
AMBER: script to extract data from minimization .out file Tanya Johannsen (Fri Jul 07 2006 - 11:55:44 CDT)
RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Junmei Wang (Fri Jul 07 2006 - 12:04:00 CDT)
Re: AMBER: script to extract data from minimization .out file Gustavo Seabra (Fri Jul 07 2006 - 12:35:32 CDT)
RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Bob Johnson (Fri Jul 07 2006 - 12:35:59 CDT)
AMBER: Error in loading molecule in tleap Gobind Bisht (Fri Jul 07 2006 - 13:01:45 CDT)
AMBER: AMBER 8: Problem with MPI_Finalize jrd (Fri Jul 07 2006 - 13:24:08 CDT)
AMBER: convert chemical structure to pdb file Baker, Bo-Yang (Fri Jul 07 2006 - 13:44:25 CDT)
Re: AMBER: convert chemical structure to pdb file Gustavo Seabra (Fri Jul 07 2006 - 13:56:37 CDT)
Re: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag David A. Case (Fri Jul 07 2006 - 16:06:34 CDT)
Re: AMBER: Error in loading molecule in tleap David A. Case (Fri Jul 07 2006 - 16:11:15 CDT)
Re: AMBER: Error in loading molecule in tleap Gobind Bisht (Fri Jul 07 2006 - 16:18:08 CDT)
AMBER: MM/PBSA Wei Chen (Fri Jul 07 2006 - 16:20:47 CDT)
Re: AMBER: AMBER 8: Problem with MPI_Finalize David A. Case (Fri Jul 07 2006 - 16:29:10 CDT)
Re: AMBER: igb=2 and "bad atom type" conflict David A. Case (Fri Jul 07 2006 - 16:42:09 CDT)
Re: AMBER: MM/PBSA Ray Luo (Fri Jul 07 2006 - 19:26:28 CDT)
Re: AMBER: script to extract data from minimization .out file sangeeta_at_bioinfo.ernet.in (Sat Jul 08 2006 - 05:23:52 CDT)
Re: AMBER: script to extract data from minimization .out file sangeeta_at_bioinfo.ernet.in (Sat Jul 08 2006 - 05:41:44 CDT)
RE: AMBER: script to extract data from minimization .out file Ross Walker (Sat Jul 08 2006 - 10:47:17 CDT)
AMBER: Error in running MD in sander Gobind Bisht (Sat Jul 08 2006 - 12:20:10 CDT)
RE: AMBER: Error in running MD in sander Ross Walker (Sat Jul 08 2006 - 12:38:15 CDT)
Re: AMBER: MM/PBSA Wei Chen (Sat Jul 08 2006 - 13:29:06 CDT)
AMBER: peptide simulation before docking jitrayut jitonnom (Sat Jul 08 2006 - 15:45:28 CDT)
AMBER: Fwd: ADL: peptide simulation before docking jitrayut jitonnom (Sun Jul 09 2006 - 04:26:59 CDT)
AMBER: (no subject) Andrew Box (Sun Jul 09 2006 - 17:49:02 CDT)
Re: [UCE]AMBER: (no subject) Thomas Cheatham (Sun Jul 09 2006 - 18:18:49 CDT)
Re: AMBER: (no subject) David A. Case (Sun Jul 09 2006 - 18:20:30 CDT)
AMBER: Replica exchange Atsutoshi Okabe (Mon Jul 10 2006 - 06:38:17 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Mon Jul 10 2006 - 07:13:48 CDT)
AMBER: residue and atom number Andrea Bortolato (Mon Jul 10 2006 - 07:57:05 CDT)
AMBER: about restraint format. Qingning Shu (Mon Jul 10 2006 - 08:11:16 CDT)
Re: AMBER: residue and atom number David A. Case (Mon Jul 10 2006 - 10:09:29 CDT)
Re: AMBER: about restraint format. David A. Case (Mon Jul 10 2006 - 10:10:11 CDT)
AMBER: small bug in ambmask (amber9) Kateryna Miroshnychenko (Mon Jul 10 2006 - 09:53:02 CDT)
Re: AMBER: small bug in ambmask (amber9) David A. Case (Mon Jul 10 2006 - 10:39:38 CDT)
RE: AMBER: amber9 compilation problems on EM64T xeon system hayden (Mon Jul 10 2006 - 11:57:44 CDT)
RE: AMBER: change atom in a DNA double strand Carra, Claudio $JSC-SK$[USRA] (Mon Jul 10 2006 - 14:24:02 CDT)
AMBER: program to calculate net charge of a ligand for Antechamber Christophe Guilbert (Mon Jul 10 2006 - 20:30:39 CDT)
RE: AMBER: Replica exchange Atsutoshi Okabe (Mon Jul 10 2006 - 21:43:17 CDT)
Re: AMBER: program to calculate net charge of a ligand for Antechamber David Mobley (Mon Jul 10 2006 - 23:18:36 CDT)
AMBER: Question about NSCM Xiaowei (David) Li (Tue Jul 11 2006 - 03:25:48 CDT)
AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! Guillaume Bollot (Tue Jul 11 2006 - 06:19:29 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Tue Jul 11 2006 - 07:49:20 CDT)
AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 09:46:54 CDT)
Re: AMBER: Question about NSCM David A. Case (Tue Jul 11 2006 - 10:02:11 CDT)
Re: AMBER: Amber crashed due to power surge and giving problems.. Carlos Simmerling (Tue Jul 11 2006 - 10:09:21 CDT)
AMBER: Ptraj: Hbond time series Zu Thur Yew (Tue Jul 11 2006 - 10:19:34 CDT)
AMBER: applying restraints on pre-defined planes Vlad Cojocaru (Tue Jul 11 2006 - 10:34:07 CDT)
Re: AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! Myunggi Yi (Tue Jul 11 2006 - 11:00:58 CDT)
Re: AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 12:13:36 CDT)
Re: AMBER: Amber crashed due to power surge and giving problems.. David A. Case (Tue Jul 11 2006 - 13:55:16 CDT)
Re: AMBER: Amber crashed due to power surge and giving problems.. Carlos Simmerling (Tue Jul 11 2006 - 14:05:48 CDT)
Re: AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 14:17:46 CDT)
Re: AMBER: applying restraints on pre-defined planes David A. Case (Tue Jul 11 2006 - 18:34:52 CDT)
Re: AMBER: Ptraj: Hbond time series Chng Choon-Peng (Tue Jul 11 2006 - 18:56:20 CDT)
AMBER: problem about Distance Restraints. Qingning Shu (Tue Jul 11 2006 - 22:38:48 CDT)
RE: AMBER: Replica exchange Atsutoshi Okabe (Tue Jul 11 2006 - 23:13:38 CDT)
AMBER: iso command and a cubic box Patricia Hunt (Wed Jul 12 2006 - 02:03:03 CDT)
AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? Changge Ji (Wed Jul 12 2006 - 01:03:30 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Wed Jul 12 2006 - 09:25:14 CDT)
Re: AMBER: iso command and a cubic box David A. Case (Wed Jul 12 2006 - 14:00:25 CDT)
AMBER: simulate a self-assemble process in vacuum Eric Hu (Wed Jul 12 2006 - 18:22:58 CDT)
Re: AMBER: problem about Distance Restraints. David A. Case (Wed Jul 12 2006 - 18:33:54 CDT)
AMBER: Antechamber 1.26 is released Junmei Wang (Wed Jul 12 2006 - 18:42:32 CDT)
Re: AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? Ray Luo (Thu Jul 13 2006 - 16:21:30 CDT)
AMBER: Etot has downward drift in 'NVE' ensemble John S. Zintsmaster (Wed Jul 12 2006 - 21:01:08 CDT)
Re: AMBER: Etot has downward drift in 'NVE' ensemble Thomas Cheatham (Wed Jul 12 2006 - 21:43:11 CDT)
AMBER: Free energy calculated from mm_pbsa gtg549i_at_mail.gatech.edu (Thu Jul 13 2006 - 02:26:44 CDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 05:47:15 CDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 05:50:55 CDT)
Re: AMBER: simulate a self-assemble process in vacuum Gustavo Seabra (Thu Jul 13 2006 - 08:22:15 CDT)
AMBER: Ringof dna Flora Mactavish (Thu Jul 13 2006 - 08:14:22 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Thomas Cheatham (Thu Jul 13 2006 - 11:34:00 CDT)
Re: AMBER: Ringof dna David A. Case (Thu Jul 13 2006 - 11:54:07 CDT)
Re: AMBER: Ringof dna f m (Thu Jul 13 2006 - 12:00:48 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent David A. Case (Thu Jul 13 2006 - 13:14:20 CDT)
AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 13:21:17 CDT)
AMBER: QMMM simulation amit_at_mbu.iisc.ernet.in (Thu Jul 13 2006 - 13:38:48 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 12:59:00 CDT)
Re: AMBER: center molecule using iwrap=1? Carlos Simmerling (Thu Jul 13 2006 - 14:00:59 CDT)
Re: AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 14:07:40 CDT)
Re: AMBER: center molecule using iwrap=1? Carlos Simmerling (Thu Jul 13 2006 - 14:43:37 CDT)
Re: AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 14:49:39 CDT)
AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat (Tue Jun 13 2006 - 22:23:25 CDT)
AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Fri Jul 14 2006 - 01:20:21 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Petr Kulhanek (Fri Jul 14 2006 - 02:44:09 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Fri Jul 14 2006 - 03:40:10 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Fri Jul 14 2006 - 03:48:33 CDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Petr Kulhanek (Fri Jul 14 2006 - 04:24:26 CDT)
RE: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 hayden (Fri Jul 14 2006 - 05:27:54 CDT)
AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 Lars Packschies (Fri Jul 14 2006 - 05:18:08 CDT)
Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Andreas Svrcek-Seiler (Fri Jul 14 2006 - 05:38:10 CDT)
Re: AMBER: Replica exchange with Amber9 Adrian Roitberg (Fri Jul 14 2006 - 08:00:14 CDT)
Re: AMBER: Ring of dna f m (Fri Jul 14 2006 - 08:27:03 CDT)
Re: AMBER: Ring of dna j j (Fri Jul 14 2006 - 09:25:59 CDT)
Re: AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 David A. Case (Fri Jul 14 2006 - 10:00:26 CDT)
Re: AMBER: Ring of dna Bill Ross (Fri Jul 14 2006 - 12:23:07 CDT)
AMBER: Compiling Leap problem sethl_at_gatech.edu (Fri Jul 14 2006 - 16:36:38 CDT)
AMBER: amber9 Piotr Cieplak (Fri Jul 14 2006 - 17:02:36 CDT)
Re: AMBER: amber9 Thomas Steinbrecher (Fri Jul 14 2006 - 17:12:13 CDT)
RE: AMBER: amber9 Ross Walker (Fri Jul 14 2006 - 17:37:19 CDT)
Re: AMBER: Compiling Leap problem David A. Case (Fri Jul 14 2006 - 17:57:31 CDT)
AMBER: Amber 9 installation issues Glass, Kevin A (Fri Jul 14 2006 - 18:18:36 CDT)
RE: AMBER: amber9 Piotr Cieplak (Fri Jul 14 2006 - 18:33:00 CDT)
Re: AMBER: Ring of dna f m (Sat Jul 15 2006 - 11:37:59 CDT)
Re: AMBER: Ring of dna Bill Ross (Sat Jul 15 2006 - 12:55:07 CDT)
AMBER: "noimage" option for radial distribution functions Ozlem Demir (Sun Jul 16 2006 - 16:14:31 CDT)
RE: AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Mon Jul 17 2006 - 03:20:25 CDT)
Re: AMBER: Ring of dna f m (Mon Jul 17 2006 - 06:32:01 CDT)
AMBER: Amber 8.0 MM_PBSA Stability : question about methodology Guillaume Bollot (Mon Jul 17 2006 - 07:18:41 CDT)
AMBER: Replica exchange Austin B. Yongye (Mon Jul 17 2006 - 07:31:09 CDT)
Re: AMBER: Ring of dna f m (Mon Jul 17 2006 - 08:48:33 CDT)
Re: AMBER: Replica exchange Guanglei Cui (Mon Jul 17 2006 - 09:18:57 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Mon Jul 17 2006 - 09:44:55 CDT)
Re: AMBER: Ring of dna M. L. Dodson (Mon Jul 17 2006 - 09:56:03 CDT)
AMBER: RMS & PCA Zu Thur Yew (Mon Jul 17 2006 - 09:55:12 CDT)
Re: AMBER: RMS & PCA Guanglei Cui (Mon Jul 17 2006 - 13:22:56 CDT)
AMBER: Obtaining LCPO parameters for F and Fe zachary hartman (Mon Jul 17 2006 - 13:16:54 CDT)
Re: AMBER: Ring of dna Bill Ross (Mon Jul 17 2006 - 14:15:10 CDT)
Re: AMBER: Ring of dna Bill Ross (Mon Jul 17 2006 - 14:19:49 CDT)
AMBER: Creating an Intercalation site Seth Lilavivat (Sat Jun 17 2006 - 14:25:59 CDT)
Re: AMBER: Creating an Intercalation site Bill Ross (Mon Jul 17 2006 - 14:49:20 CDT)
Re: AMBER: Replica exchange Austin B. Yongye (Mon Jul 17 2006 - 17:22:51 CDT)
AMBER: PMEMD with NMR restraint and position restraint Ting Wang (Mon Jul 17 2006 - 18:18:31 CDT)
Re: AMBER: Creating an Intercalation site Thomas Cheatham (Mon Jul 17 2006 - 15:13:54 CDT)
AMBER: Dynamics and Restraint problem Andrew Box (Mon Jul 17 2006 - 18:49:51 CDT)
AMBER: water diffusion Sergei Smirnov (Mon Jul 17 2006 - 19:48:59 CDT)
Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Mon Jul 17 2006 - 22:03:29 CDT)
Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 David A. Case (Mon Jul 17 2006 - 22:00:36 CDT)
AMBER: PhosphoThreonine Parms for use with ff03 Zu Thur Yew (Tue Jul 18 2006 - 00:19:15 CDT)
Re: AMBER: RMS & PCA Zu Thur Yew (Tue Jul 18 2006 - 00:12:35 CDT)
Re: AMBER: water diffusion Thomas Cheatham (Tue Jul 18 2006 - 01:36:36 CDT)
AMBER: temperature regulation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Jul 18 2006 - 03:31:04 CDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03 FyD (Tue Jul 18 2006 - 02:57:24 CDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03 Carlos Simmerling (Tue Jul 18 2006 - 06:28:20 CDT)
Re: AMBER: temperature regulation Carlos Simmerling (Tue Jul 18 2006 - 06:41:18 CDT)
Re: AMBER: Ring of dna f m (Tue Jul 18 2006 - 09:30:03 CDT)
Re: AMBER: PMEMD with NMR restraint and position restraint Ting Wang (Tue Jul 18 2006 - 15:12:41 CDT)
Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 15:49:05 CDT)
AMBER: Calculating energy for specific part of system Adam Pelzer (Tue Jul 18 2006 - 17:32:34 CDT)
Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 21:03:42 CDT)
Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 23:34:35 CDT)
AMBER: Replica exchange Austin B. Yongye (Wed Jul 19 2006 - 10:04:44 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Wed Jul 19 2006 - 11:29:33 CDT)
RE: AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Wed Jul 19 2006 - 11:22:49 CDT)
Re: AMBER: Replica exchange Austin B. Yongye (Wed Jul 19 2006 - 12:23:47 CDT)
Re: AMBER: Replica exchange Guanglei Cui (Wed Jul 19 2006 - 13:24:55 CDT)
AMBER: Long line of input Myunggi Yi (Wed Jul 19 2006 - 15:13:26 CDT)
AMBER: difficulties with antechamber: tests dont even run frustrated modeller (Wed Jul 19 2006 - 18:06:36 CDT)
Re: AMBER: Long line of input hornak_at_csb.sunysb.edu (Wed Jul 19 2006 - 15:37:29 CDT)
AMBER: Fwd: difficulties with antechamber: tests dont even run frustrated modeller (Wed Jul 19 2006 - 18:30:07 CDT)
Re: AMBER: Long line of input Myunggi Yi (Wed Jul 19 2006 - 21:03:11 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Thu Jul 20 2006 - 07:32:07 CDT)
AMBER: Myrinet or Gigabit ethernet? Mingfeng Yang (Thu Jul 20 2006 - 08:35:08 CDT)
AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 09:01:07 CDT)
Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Thu Jul 20 2006 - 09:40:48 CDT)
Re: AMBER: Myrinet or Gigabit ethernet? Robert Duke (Thu Jul 20 2006 - 09:45:45 CDT)
Re: AMBER: Failure of iwrap in PMEMD darden (Thu Jul 20 2006 - 09:34:47 CDT)
Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 10:04:31 CDT)
AMBER: Gb Na+ ions DNA Conn O'Rourke (Thu Jul 20 2006 - 10:16:05 CDT)
Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly... fine wu (Thu Jul 20 2006 - 10:55:55 CDT)
AMBER: saltcon variable Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jul 20 2006 - 14:00:01 CDT)
AMBER: PDB from .rst? Evan Kelly (Thu Jul 20 2006 - 15:51:09 CDT)
Re: AMBER: PDB from .rst? Wei Zhang (Thu Jul 20 2006 - 16:04:58 CDT)
Re: AMBER: PDB from .rst? Ilyas Yildirim (Thu Jul 20 2006 - 16:08:20 CDT)
Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Thu Jul 20 2006 - 16:35:58 CDT)
Re: AMBER: simulate a self-assemble process in vacuum Eric Hu (Thu Jul 20 2006 - 16:43:35 CDT)
Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 19:24:34 CDT)
AMBER: Replica Exchange Austin B. Yongye (Thu Jul 20 2006 - 21:07:46 CDT)
Re: AMBER: Replica Exchange Carlos Simmerling (Thu Jul 20 2006 - 21:51:19 CDT)
Re: AMBER: PDB from .rst? priya priya (Thu Jul 20 2006 - 22:24:08 CDT)
Re: AMBER: Gb Na+ ions DNA Andreas Svrcek-Seiler (Fri Jul 21 2006 - 04:22:21 CDT)
AMBER: Modelling dsDNA less than 10bp Lena Dolghih (Fri Jul 21 2006 - 08:15:16 CDT)
Re: AMBER: Replica Exchange Austin B. Yongye (Fri Jul 21 2006 - 08:29:08 CDT)
Re: AMBER: Replica Exchange Adrian Roitberg (Fri Jul 21 2006 - 08:37:26 CDT)
Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Fri Jul 21 2006 - 08:34:02 CDT)
Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Fri Jul 21 2006 - 08:57:03 CDT)
RE: AMBER: Failure of iwrap in PMEMD Ross Walker (Fri Jul 21 2006 - 10:33:53 CDT)
AMBER: combining different versions of AMBER Melissa Foley (Fri Jul 21 2006 - 14:25:35 CDT)
RE: AMBER: combining different versions of AMBER Ross Walker (Fri Jul 21 2006 - 15:11:44 CDT)
AMBER: converting from parm to parm7 Raffaella D'Auria (Fri Jul 21 2006 - 20:26:55 CDT)
AMBER: Silicon related parameters hbluo (Sat Jul 22 2006 - 12:52:17 CDT)
AMBER: Simulating an "average" DNA sequence S. Jamal Rahi (Fri Jul 21 2006 - 22:20:36 CDT)
Re: AMBER: converting from parm to parm7 Carlos Simmerling (Sat Jul 22 2006 - 06:27:10 CDT)
Re: AMBER: converting from parm to parm7 & L-J coeff A and B Raffaella D'Auria (Sat Jul 22 2006 - 10:55:56 CDT)
Re: AMBER: Simulating an "average" DNA sequence David A. Case (Sun Jul 23 2006 - 09:47:15 CDT)
Re: AMBER: converting from parm to parm7 David A. Case (Sun Jul 23 2006 - 09:47:05 CDT)
Re: AMBER: combining different versions of AMBER Atro Tossavainen (Mon Jul 24 2006 - 00:44:10 CDT)
AMBER: problems of running sander.MPI of amber9 on remote node Chengwen Chen (Mon Jul 24 2006 - 01:29:20 CDT)
AMBER: AMBER9 netcdf trajectory with VMD 1.8.4 Fabian Boes (Mon Jul 24 2006 - 03:01:46 CDT)
AMBER: How to resume remaining simulation pkb bioinfo (Mon Jul 24 2006 - 05:05:23 CDT)
AMBER: Minimization problem: coordinates out of virtual box Zu Thur Yew (Mon Jul 24 2006 - 07:53:19 CDT)
AMBER: Tutorial 8, section 6: best fit before clustering sangeeta (Mon Jul 24 2006 - 08:18:05 CDT)
RE: AMBER: Tutorial 8, section 6: best fit before clustering Ross Walker (Mon Jul 24 2006 - 09:45:59 CDT)
Re: AMBER: How to resume remaining simulation Guanglei Cui (Mon Jul 24 2006 - 10:19:56 CDT)
AMBER: library for 8oxoguanine Carra, Claudio $JSC-SK$[USRA] (Mon Jul 24 2006 - 14:50:59 CDT)
Re: AMBER: saltcon variable David A. Case (Mon Jul 24 2006 - 14:38:53 CDT)
Re: AMBER: Amber 8.0 MM_PBSA Stability : question about methodology David A. Case (Mon Jul 24 2006 - 14:36:30 CDT)
Re: AMBER: Long line of input David A. Case (Mon Jul 24 2006 - 14:37:20 CDT)
AMBER: Building an RNA - Proflavin Complex sethl_at_gatech.edu (Mon Jul 24 2006 - 15:05:49 CDT)
Re: AMBER: library for 8oxoguanine M. L. Dodson (Mon Jul 24 2006 - 15:07:17 CDT)
AMBER: Confusion re AMBER SMD output Alik Widge (Mon Jul 24 2006 - 15:31:34 CDT)
AMBER: process_mdout.perl's output is empty Prashanth Athri (Mon Jul 24 2006 - 15:53:04 CDT)
Re: AMBER: library for 8oxoguanine Carlos Simmerling (Mon Jul 24 2006 - 16:12:38 CDT)
Re: AMBER: process_mdout.perl's output is empty Chng Choon-Peng (Mon Jul 24 2006 - 20:02:57 CDT)
Re: AMBER: library for 8oxoguanine FyD (Tue Jul 25 2006 - 07:39:27 CDT)
Re: AMBER: Fwd: difficulties with antechamber: tests dont even run David A. Case (Tue Jul 25 2006 - 10:11:22 CDT)
Re: AMBER: process_mdout.perl's output is empty Alik Widge (Tue Jul 25 2006 - 10:19:44 CDT)
Re: AMBER: converting from parm to parm7 Raffaella D'Auria (Tue Jul 25 2006 - 11:00:50 CDT)
Re: [Fwd: AMBER: Long line of input] Myunggi Yi (Tue Jul 25 2006 - 11:08:27 CDT)
AMBER: Hybridization in leap opitz_at_che.udel.edu (Tue Jul 25 2006 - 13:23:12 CDT)
Re: AMBER: Hybridization in leap David A. Case (Tue Jul 25 2006 - 15:37:30 CDT)
RE: AMBER: Fwd: difficulties with antechamber: tests dont even run Junmei Wang (Tue Jul 25 2006 - 18:00:04 CDT)
AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap Lwin, ThuZar (Tue Jul 25 2006 - 19:39:32 CDT)
AMBER: parallel installation of amber8 on HP cluster Manish Datt (Wed Jul 26 2006 - 05:00:30 CDT)
RE: AMBER: Tutorial 8, section 6: best fit before clustering sangeeta (Wed Jul 26 2006 - 08:42:47 CDT)
Re: AMBER: parallel installation of amber8 on HP cluster michael crowley (Wed Jul 26 2006 - 09:42:19 CDT)
Re: AMBER: parallel installation of amber8 on HP cluster David A. Case (Wed Jul 26 2006 - 10:00:53 CDT)
Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap David A. Case (Wed Jul 26 2006 - 12:44:58 CDT)
Re: AMBER: parallel installation of amber8 on HP cluster Manish Datt (Wed Jul 26 2006 - 12:54:51 CDT)
Re: AMBER: parallel installation of amber8 on HP cluster Michael Crowley (Wed Jul 26 2006 - 13:52:09 CDT)
AMBER: leap error AYTUG TUNCEL (Wed Jul 26 2006 - 18:29:35 CDT)
AMBER: Harmonic restraint along z-axis Myunggi Yi (Wed Jul 26 2006 - 19:26:02 CDT)
AMBER: dummy atoms in MMPBSA Andrea Bortolato (Thu Jul 27 2006 - 03:10:50 CDT)
AMBER: xleap Md Jahidul Islam (Thu Jul 27 2006 - 04:49:36 CDT)
Re: AMBER: xleap Chng Choon-Peng (Thu Jul 27 2006 - 05:14:58 CDT)
AMBER: Can't open xleap Jahidul Islam (Thu Jul 27 2006 - 05:16:08 CDT)
Re: AMBER: Can't open xleap Chng Choon-Peng (Thu Jul 27 2006 - 05:45:58 CDT)
Re: AMBER: Can't open xleap Jahidul Islam (Thu Jul 27 2006 - 06:57:30 CDT)
Re: AMBER: dummy atoms in MMPBSA Ilyas Yildirim (Thu Jul 27 2006 - 07:18:01 CDT)
Re: AMBER: Can't open xleap David A. Case (Thu Jul 27 2006 - 08:53:16 CDT)
Re: AMBER: leap error David A. Case (Thu Jul 27 2006 - 09:34:17 CDT)
Re: AMBER: Harmonic restraint along z-axis David A. Case (Thu Jul 27 2006 - 09:32:52 CDT)
Re: AMBER: parallel installation of amber8 on HP cluster David A. Case (Thu Jul 27 2006 - 10:57:41 CDT)
Re: AMBER: Harmonic restraint along z-axis Carlos Simmerling (Thu Jul 27 2006 - 11:15:18 CDT)
AMBER: Correction on Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 11:38:00 CDT)
AMBER: Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 11:35:57 CDT)
Re: AMBER: Can't open xleap Bill Ross (Thu Jul 27 2006 - 12:21:39 CDT)
RE: AMBER: Zinc parameters Ross Walker (Thu Jul 27 2006 - 12:26:29 CDT)
AMBER: Zinc-coordinating histidine protonation state Nitin Bhardwaj (Thu Jul 27 2006 - 15:01:16 CDT)
AMBER: Zinc coordinating CYS Nitin Bhardwaj (Thu Jul 27 2006 - 16:30:45 CDT)
Re: AMBER: Dynamics and Restraint problem David A. Case (Thu Jul 27 2006 - 18:08:16 CDT)
Re: AMBER: Zinc coordinating CYS madhumalar_at_bii-sg.org (Thu Jul 27 2006 - 19:37:12 CDT)
RE: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . Lwin, ThuZar (Thu Jul 27 2006 - 20:35:19 CDT)
Re: AMBER: Zinc coordinating CYS Nitin Bhardwaj (Thu Jul 27 2006 - 23:00:45 CDT)
Re: AMBER: Zinc coordinating CYS madhumalar_at_bii-sg.org (Fri Jul 28 2006 - 04:17:36 CDT)
Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . David A. Case (Fri Jul 28 2006 - 09:27:44 CDT)
AMBER: Ken Merz (Sat Jul 29 2006 - 10:28:53 CDT)
AMBER: Having trouble with Nucgen for generating pdb more than 16 bps amit_at_mbu.iisc.ernet.in (Sun Jul 30 2006 - 13:51:05 CDT)
Re: AMBER: Zinc-coordinating histidine protonation state David A. Case (Mon Jul 31 2006 - 10:50:16 CDT)
Re: AMBER: Having trouble with Nucgen for generating pdb more than 16 bps Bill Ross (Mon Jul 31 2006 - 13:53:11 CDT)
AMBER: loading torsion parameters Nitin Bhardwaj (Mon Jul 31 2006 - 14:47:19 CDT)
Re: AMBER: loading torsion parameters Wei Zhang (Mon Jul 31 2006 - 15:13:57 CDT)
RE: AMBER: loading torsion parameters Ross Walker (Mon Jul 31 2006 - 15:25:08 CDT)
Re: AMBER: loading torsion parameters Nitin Bhardwaj (Mon Jul 31 2006 - 15:35:18 CDT)
AMBER: GB tutorials and disulphide bonds Abhilash (Mon Jul 31 2006 - 15:41:30 CDT)
Re: AMBER: loading torsion parameters Bill Ross (Mon Jul 31 2006 - 15:49:38 CDT)
AMBER: For different ligand conformation pkb bioinfo (Mon Jul 31 2006 - 08:53:45 CDT)
AMBER: Using a trajectory and some PDB files as input for PCA Zu Thur Yew (Mon Jul 31 2006 - 05:20:42 CDT)
Re: AMBER: For different ligand conformation David Mobley (Mon Jul 31 2006 - 17:29:40 CDT)
AMBER: Re: Confusion re AMBER SMD output Alik Widge (Mon Jul 31 2006 - 17:54:59 CDT)
AMBER: Distance between two regions Baker, Bo-Yang (Mon Jul 31 2006 - 19:16:02 CDT)
AMBER: from traj to crd Fabián Alejandro Rodríguez (Mon Jul 31 2006 - 19:58:19 CDT)
AMBER: Xmgr in Windows Jahidul Islam (Mon Jul 31 2006 - 22:24:19 CDT)
Re: AMBER: Xmgr in Windows Ilyas Yildirim (Tue Aug 01 2006 - 00:33:38 CDT)
AMBER: How to set Bondi Radii using xleap Ilyas Yildirim (Tue Aug 01 2006 - 00:40:15 CDT)
AMBER: regarding diffusion command output Arvind Marathe (Tue Aug 01 2006 - 05:45:21 CDT)
Re: AMBER: Re: Confusion re AMBER SMD output Adrian Roitberg (Tue Aug 01 2006 - 06:07:03 CDT)
Re: AMBER: Xmgr in Windows Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 06:39:19 CDT)
Re: AMBER: Xmgr in Windows Florian Haberl (Tue Aug 01 2006 - 07:11:44 CDT)
Re: AMBER: from traj to crd Guanglei Cui (Tue Aug 01 2006 - 10:30:59 CDT)
Re: AMBER: Distance between two regions Guanglei Cui (Tue Aug 01 2006 - 10:35:54 CDT)
Re: AMBER: from traj to crd Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 10:41:22 CDT)
Re: AMBER: How to set Bondi Radii using xleap David A. Case (Tue Aug 01 2006 - 12:17:38 CDT)
Re: AMBER: Using a trajectory and some PDB files as input for PCA David A. Case (Tue Aug 01 2006 - 12:10:29 CDT)
Re: AMBER: GB tutorials and disulphide bonds David A. Case (Tue Aug 01 2006 - 12:14:20 CDT)
Re: AMBER: How to set Bondi Radii using xleap. . Don.Bashford_at_stjude.org (Tue Aug 01 2006 - 12:23:51 CDT)
Re: AMBER: How to set Bondi Radii using xleap Carlos Simmerling (Tue Aug 01 2006 - 12:43:04 CDT)
AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 12:55:31 CDT)
Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 13:02:22 CDT)
Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Carlos Simmerling (Tue Aug 01 2006 - 13:13:07 CDT)
AMBER: pdb error AYTUG TUNCEL (Tue Aug 01 2006 - 14:36:39 CDT)
Re: AMBER: pdb error Ilyas Yildirim (Tue Aug 01 2006 - 14:23:30 CDT)
AMBER: any work-around for 80 character mask string limit? Tanya Johannsen (Tue Aug 01 2006 - 15:12:22 CDT)
Re: AMBER: any work-around for 80 character mask string limit? David A. Case (Tue Aug 01 2006 - 16:37:36 CDT)
AMBER: brookhaven to amber pdb format AYTUG TUNCEL (Wed Aug 02 2006 - 04:08:50 CDT)
AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 07:07:22 CDT)
Re: AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 08:58:48 CDT)
AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru (Wed Aug 02 2006 - 09:21:31 CDT)
Re: AMBER: brookhaven to amber pdb format David A. Case (Wed Aug 02 2006 - 09:48:23 CDT)
AMBER: Bugfixes available for pmemd iwrap problem Robert Duke (Wed Aug 02 2006 - 12:05:32 CDT)
Re: AMBER: brookhaven to amber pdb format Ilyas Yildirim (Wed Aug 02 2006 - 13:55:38 CDT)
AMBER: where can I find the force field paramete r for Silica yxiong99 (Wed Aug 02 2006 - 14:53:33 CDT)
AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta (Wed Aug 02 2006 - 21:03:11 CDT)
AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher (Thu Aug 03 2006 - 00:26:22 CDT)
Re: AMBER: TI-FEP for ILE--->VAL. Ilyas Yildirim (Thu Aug 03 2006 - 01:15:10 CDT)
Re: AMBER: Maximum system size in simulated annealing Andreas Svrcek-Seiler (Thu Aug 03 2006 - 04:23:13 CDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03 Vlad Cojocaru (Thu Aug 03 2006 - 05:07:48 CDT)
Re: AMBER: Maximum system size in simulated annealing Carlos Simmerling (Thu Aug 03 2006 - 05:26:58 CDT)
AMBER: ff03 and ff99SB force fields Carlos Simmerling (Thu Aug 03 2006 - 05:59:11 CDT)
AMBER: problems with ptraj anna.schrey_at_gmx.de (Thu Aug 03 2006 - 09:49:39 CDT)
AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Lwin, ThuZar (Thu Aug 03 2006 - 10:14:28 CDT)
AMBER: about Silica's polarizability yxiong99 (Thu Aug 03 2006 - 10:20:19 CDT)
Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Carlos Simmerling (Thu Aug 03 2006 - 10:33:34 CDT)
Re: AMBER: about Silica's polarizability David A. Case (Thu Aug 03 2006 - 11:16:40 CDT)
Re: AMBER: TI-FEP for ILE--->VAL. David A. Case (Thu Aug 03 2006 - 11:43:44 CDT)
Re: AMBER: problems with ptraj David A. Case (Thu Aug 03 2006 - 11:46:19 CDT)
AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar (Thu Aug 03 2006 - 12:08:07 CDT)
AMBER: restraint=0.0000 during minimization? Evan Kelly (Thu Aug 03 2006 - 12:48:17 CDT)
AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly (Thu Aug 03 2006 - 12:57:46 CDT)
AMBER: SURFTEN in GB (mm_pbsa calculations) Shuting Wei (Thu Aug 03 2006 - 14:18:10 CDT)
RE: AMBER: ff03 and ff99SB force fields Yong Duan (Thu Aug 03 2006 - 14:29:51 CDT)
Re: AMBER: SURFTEN in GB (mm_pbsa calculations) Carlos Simmerling (Thu Aug 03 2006 - 14:38:59 CDT)
Re: AMBER: ff03 and ff99SB force fields Ray Luo (Thu Aug 03 2006 - 07:21:03 CDT)
Re: AMBER: ff03 and ff99SB force fields Vlad Cojocaru (Fri Aug 04 2006 - 03:17:59 CDT)
RE: AMBER: ff03 and ff99SB force fields Yong Duan (Fri Aug 04 2006 - 06:58:51 CDT)
AMBER: HBOND ANALYSIS Claire Zerafa (Fri Aug 04 2006 - 09:35:50 CDT)
AMBER: H-bonds of peptide with water sangeeta (Fri Aug 04 2006 - 08:20:13 CDT)
AMBER: Residue connection points on prep.in Gloria T. Anderle (Fri Aug 04 2006 - 11:10:53 CDT)
Re: AMBER: question on chargning free energy in solvent vs vacuum David A. Case (Fri Aug 04 2006 - 11:18:53 CDT)
AMBER: parameter for Cd2+? JunJun Liu (Fri Aug 04 2006 - 10:50:46 CDT)
AMBER: to do tutorial 4 using tleap Come On (Fri Aug 04 2006 - 11:50:53 CDT)
AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 13:27:39 CDT)
AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 13:31:53 CDT)
RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar (Fri Aug 04 2006 - 14:02:10 CDT)
Re: AMBER: neutral N-terminal amino-acid parameters for ff03 FyD (Sat Aug 05 2006 - 03:16:23 CDT)
Fw: AMBER: HBOND ANALYSIS Claire Zerafa (Sat Aug 05 2006 - 14:45:10 CDT)
AMBER: Amber Installation Help Kirk Hevener (Mon Aug 07 2006 - 07:43:25 CDT)
AMBER: Info regarding reduced cysteines Rafi Ahmad (Mon Aug 07 2006 - 09:06:40 CDT)
Re: AMBER: Info regarding reduced cysteines David A. Case (Mon Aug 07 2006 - 10:02:57 CDT)
AMBER: transition state John Chuang²øÂ`»·¦Ñ®v (Mon Aug 07 2006 - 11:06:50 CDT)
Re: AMBER: H-bonds of peptide with water Scott Pendley (Mon Aug 07 2006 - 14:56:04 CDT)
AMBER: Glass, Kevin A (Mon Aug 07 2006 - 15:09:02 CDT)
AMBER: antechamber bond typing questions David Mobley (Mon Aug 07 2006 - 15:14:42 CDT)
Re: AMBER: Scott Brozell (Mon Aug 07 2006 - 19:37:19 CDT)
AMBER: RE: antechamber bond typing questions Junmei Wang (Mon Aug 07 2006 - 20:43:05 CDT)
AMBER: Problem with restarting MD simulation Gobind Bisht (Tue Aug 08 2006 - 00:02:56 CDT)
Re: AMBER: Problem with restarting MD simulation Carlos Simmerling (Tue Aug 08 2006 - 06:08:27 CDT)
AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 07:12:37 CDT)
Re: AMBER: cutting the box after "solvatebox" Carlos Simmerling (Tue Aug 08 2006 - 07:43:47 CDT)
Re: AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 07:52:39 CDT)
AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 09:17:31 CDT)
Re: AMBER: cutting the box after "solvatebox" Guanglei Cui (Tue Aug 08 2006 - 09:38:06 CDT)
Re: AMBER: PCA: can't complete projection Vlad Cojocaru (Tue Aug 08 2006 - 09:56:49 CDT)
AMBER: ptraj: nofit option for rmsd Joseph Nachman (Tue Aug 08 2006 - 10:27:41 CDT)
Re: AMBER: Amber Installation Help David A. Case (Tue Aug 08 2006 - 10:25:49 CDT)
Re: AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 11:42:04 CDT)
Re: AMBER: Amber Installation Help; link woes Scott Brozell (Tue Aug 08 2006 - 14:36:32 CDT)
AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Tue Aug 08 2006 - 14:53:49 CDT)
Re: AMBER: GAFF parameters: DPPC Bilayer Nitin Bhardwaj (Tue Aug 08 2006 - 14:58:59 CDT)
RE: AMBER: GAFF parameters: DPPC Bilayer Yong Duan (Tue Aug 08 2006 - 15:42:50 CDT)
AMBER: Format of mdcrd files Gobind Bisht (Wed Aug 09 2006 - 08:56:18 CDT)
Re: AMBER: Format of mdcrd files Carlos Simmerling (Wed Aug 09 2006 - 09:24:35 CDT)
Re: AMBER: Format of mdcrd files Mark Williamson (Wed Aug 09 2006 - 09:32:06 CDT)
AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 09:46:56 CDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Wed Aug 09 2006 - 10:01:27 CDT)
AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 13:06:30 CDT)
AMBER: how to reassign charges Lwin, ThuZar (Wed Aug 09 2006 - 13:16:01 CDT)
Re: AMBER: transition state Eric Hu (Wed Aug 09 2006 - 14:05:14 CDT)
Re: AMBER: how to reassign charges David Mobley (Wed Aug 09 2006 - 15:03:10 CDT)
Re: AMBER: how to reassign charges David A. Case (Wed Aug 09 2006 - 15:43:07 CDT)
Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition David A. Case (Wed Aug 09 2006 - 15:45:42 CDT)
RE: AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Wed Aug 09 2006 - 16:08:00 CDT)
Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 16:30:04 CDT)
RE: AMBER: how to reassign charges Yong Duan (Wed Aug 09 2006 - 16:26:10 CDT)
AMBER: Heme parameters Marcelo Puiatti (Wed Aug 09 2006 - 17:58:35 CDT)
Re: AMBER: Heme parameters Weihua Li (Wed Aug 09 2006 - 21:44:15 CDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0 backy (Thu Aug 10 2006 - 01:47:37 CDT)
AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 04:22:27 CDT)
AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 04:26:01 CDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Thu Aug 10 2006 - 05:09:23 CDT)
AMBER: Re: Simulated annealing Carlos Simmerling (Thu Aug 10 2006 - 06:40:24 CDT)
Re: AMBER: Phosphated Tyrosine, not a type (xleap)? David A. Case (Thu Aug 10 2006 - 11:07:09 CDT)
AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Thu Aug 10 2006 - 14:23:55 CDT)
Re: AMBER: problems with ptraj Thomas Cheatham (Thu Aug 10 2006 - 14:25:18 CDT)
Re: AMBER: Leap adds hydrogens but cannot resolve their type. David A. Case (Thu Aug 10 2006 - 15:15:16 CDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? Thomas Cheatham (Thu Aug 10 2006 - 17:18:00 CDT)
Re: AMBER: HBOND ANALYSIS Thomas Cheatham (Thu Aug 10 2006 - 18:57:34 CDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 21:39:54 CDT)
Re: AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 21:38:47 CDT)
AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang (Fri Aug 11 2006 - 08:35:12 CDT)
Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Guanglei Cui (Fri Aug 11 2006 - 08:57:46 CDT)
AMBER: ptraj quasiharmonic analysis question Shawn yy (Fri Aug 11 2006 - 09:45:21 CDT)
AMBER: Could mm_pbsa decompose energy only for the receptor ? backy (Fri Aug 11 2006 - 09:10:52 CDT)
AMBER: how to do a molecular dynamic study on a trimer Abhilash (Fri Aug 11 2006 - 10:05:44 CDT)
Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Fri Aug 11 2006 - 11:05:12 CDT)
AMBER: AMBER8 - RDF bug Petr Kulhanek (Fri Aug 11 2006 - 11:00:57 CDT)
AMBER: Nature of QM scanning protocol for parameter development Isherwood, James (Fri Aug 11 2006 - 11:17:01 CDT)
AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S (Fri Aug 11 2006 - 11:55:19 CDT)
Re: AMBER: Middlebury College Cluster and Amber 8 Robert Duke (Fri Aug 11 2006 - 12:33:13 CDT)
Re: AMBER: Middlebury College Cluster and Amber 8 David A. Case (Fri Aug 11 2006 - 13:30:46 CDT)
AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui (Fri Aug 11 2006 - 13:50:54 CDT)
AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D. (Fri Aug 11 2006 - 15:41:32 CDT)
Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Adrian Roitberg (Fri Aug 11 2006 - 15:23:10 CDT)
AMBER: impose command in leap problem Piotr Cieplak (Fri Aug 11 2006 - 19:56:40 CDT)
Re: AMBER: impose command in leap problem Scott Brozell (Fri Aug 11 2006 - 20:57:21 CDT)
AMBER: DIELC? backy (Sat Aug 12 2006 - 07:16:47 CDT)
AMBER: parallel pmemd with intel 9 fc bala (Sat Aug 12 2006 - 10:56:15 CDT)
Re: AMBER: how to do a molecular dynamic study on a trimer Gobind Bisht (Sat Aug 12 2006 - 12:05:29 CDT)
Re: AMBER: parallel pmemd with intel 9 fc Robert Duke (Sat Aug 12 2006 - 13:58:59 CDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? FyD (Sat Aug 12 2006 - 14:09:29 CDT)
Re: AMBER: DIELC? David A. Case (Sun Aug 13 2006 - 11:43:58 CDT)
Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file David A. Case (Sun Aug 13 2006 - 11:49:27 CDT)
Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Sun Aug 13 2006 - 11:37:03 CDT)
Re: AMBER: antechamber error -> metals Scott Brozell (Sun Aug 13 2006 - 16:58:14 CDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? a a (Sun Aug 13 2006 - 23:29:59 CDT)
AMBER: Problem with sander in Linux Wimal (Mon Aug 14 2006 - 03:14:00 CDT)
AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 06:25:31 CDT)
AMBER: klambda Vitor Manuel Sousa F?x (Mon Aug 14 2006 - 05:45:10 CDT)
AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko (Mon Aug 14 2006 - 08:19:46 CDT)
AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 11:27:24 CDT)
Re: AMBER: problem imposing arbitrary peptide bonds through leap David A. Case (Mon Aug 14 2006 - 11:45:48 CDT)
Re: AMBER: klambda David A. Case (Mon Aug 14 2006 - 11:48:30 CDT)
Re: AMBER: Problem with sander in Linux David A. Case (Mon Aug 14 2006 - 11:49:53 CDT)
Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 11:56:31 CDT)
Re: AMBER: klambda Ilyas Yildirim (Mon Aug 14 2006 - 12:31:24 CDT)
AMBER: source code Yannick Bomble (Mon Aug 14 2006 - 13:09:31 CDT)
AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 13:25:19 CDT)
Re: AMBER: source code Thomas Cheatham (Mon Aug 14 2006 - 13:31:08 CDT)
AMBER: Advice on linux cluster sought Feng X Zhou (Mon Aug 14 2006 - 13:34:16 CDT)
Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Thomas Cheatham (Mon Aug 14 2006 - 13:42:52 CDT)
Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 14:06:56 CDT)
Re: AMBER: impose command in leap problem Piotr Cieplak (Mon Aug 14 2006 - 15:44:02 CDT)
Re: AMBER: transition state John Chuang²øÂ`»·¦Ñ®v (Mon Aug 14 2006 - 17:20:20 CDT)
RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Tue Aug 15 2006 - 00:48:49 CDT)
AMBER: (no subject) a a (Tue Aug 15 2006 - 05:13:49 CDT)
AMBER: amber9 Test Failer kawamura_hiro_at_riken.jp (Tue Aug 15 2006 - 07:21:49 CDT)
Re: AMBER: (no subject) Navnit Kumar Mishra (Tue Aug 15 2006 - 07:51:49 CDT)
AMBER: amber 9 intel 9.1 ia64 Tim Robinson (Tue Aug 15 2006 - 08:45:16 CDT)
Re: AMBER: amber 9 intel 9.1 ia64 Fabian Boes (Tue Aug 15 2006 - 08:59:39 CDT)
Re: AMBER: amber9 Test Failer David A. Case (Tue Aug 15 2006 - 10:05:54 CDT)
AMBER: Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 10:58:40 CDT)
AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 12:51:16 CDT)
AMBER: DOTA-Lanthanide complexes in Amber opitz_at_che.udel.edu (Tue Aug 15 2006 - 12:48:23 CDT)
AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 13:04:42 CDT)
Re: AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 13:16:47 CDT)
Re: AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Tue Aug 15 2006 - 10:39:08 CDT)
Re: AMBER: Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 16:15:26 CDT)
AMBER: TI tutorial Mingfeng Yang (Tue Aug 15 2006 - 17:22:10 CDT)
AMBER: input conversion error mm_pbsa AYTUG TUNCEL (Tue Aug 15 2006 - 17:23:28 CDT)
Re: AMBER: input conversion error mm_pbsa David A. Case (Tue Aug 15 2006 - 17:47:19 CDT)
Re: AMBER: (Another) Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 18:09:56 CDT)
Re: AMBER: antechamber failure on FMN David A. Case (Tue Aug 15 2006 - 18:14:41 CDT)
Re: AMBER: TI tutorial David A. Case (Tue Aug 15 2006 - 18:34:58 CDT)
AMBER: MM_PBSA : Question about Stability? Guillaume Bollot (Wed Aug 16 2006 - 02:00:15 CDT)
Re: AMBER: Question about using antechamber with G03 Gustavo Seabra (Wed Aug 16 2006 - 08:49:42 CDT)
AMBER: MMPBSA: positive energies during nmode Zu Thur Yew (Wed Aug 16 2006 - 09:15:11 CDT)
Re: AMBER: MMPBSA: positive energies during nmode David A. Case (Wed Aug 16 2006 - 11:10:29 CDT)
Re: AMBER: MM_PBSA : Question about Stability? David A. Case (Wed Aug 16 2006 - 11:24:48 CDT)
AMBER: reading ff file into XLeap Petr Jerabek (Wed Aug 16 2006 - 11:21:00 CDT)
Re: AMBER: DOTA-Lanthanide complexes in Amber David A. Case (Wed Aug 16 2006 - 11:59:22 CDT)
AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 12:05:16 CDT)
Re: AMBER: reading ff file into XLeap David A. Case (Wed Aug 16 2006 - 12:21:47 CDT)
Re: AMBER: Ptraj selecting specific atoms in specific residues Scott Pendley (Wed Aug 16 2006 - 12:19:31 CDT)
Re: AMBER: DOTA-Lanthanide complexes in Amber opitz_at_che.udel.edu (Wed Aug 16 2006 - 12:27:23 CDT)
Re: AMBER: Ptraj selecting specific atoms in specific residues Thomas Cheatham (Wed Aug 16 2006 - 12:32:24 CDT)
RE: AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 12:50:16 CDT)
AMBER: checkmask Steve Seibold (Wed Aug 16 2006 - 13:14:29 CDT)
AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Wed Aug 16 2006 - 13:23:44 CDT)
AMBER: pmf input files Lauren O'Neil (Wed Aug 16 2006 - 12:20:45 CDT)
AMBER: generate "template" frcmod from standard residues? mernst_at_tricity.wsu.edu (Wed Aug 16 2006 - 13:41:02 CDT)
Re: AMBER: DOTA-Lanthanide complexes in Amber Brent Krueger (Wed Aug 16 2006 - 15:08:57 CDT)
Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Wed Aug 16 2006 - 16:51:47 CDT)
AMBER: help with leap sethl_at_gatech.edu (Wed Aug 16 2006 - 18:24:42 CDT)
Re: AMBER: help with leap Bill Ross (Wed Aug 16 2006 - 19:51:56 CDT)
RE: AMBER: antechamber error -> metals Junmei Wang (Wed Aug 16 2006 - 21:29:46 CDT)
Re: AMBER: help with leap Franck_Vendeix_at_ncsu.edu (Thu Aug 17 2006 - 09:46:07 CDT)
Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 11:04:22 CDT)
AMBER: ´ð¸´: AMBER: pmf input files Chunhu Tan (Thu Aug 17 2006 - 11:36:30 CDT)
Re: AMBER: generate "template" frcmod from standard residues? mernst_at_tricity.wsu.edu (Thu Aug 17 2006 - 12:06:07 CDT)
Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 13:01:45 CDT)
Re: AMBER: cutting the box after "solvatebox" Ilyas Yildirim (Thu Aug 17 2006 - 14:28:55 CDT)
AMBER: RE: antechamber failure on FMN Junmei Wang (Thu Aug 17 2006 - 18:14:47 CDT)
AMBER: Execution time discrepancies Glass, Kevin A (Thu Aug 17 2006 - 19:18:20 CDT)
Re: AMBER: Execution time discrepancies Bill Ross (Thu Aug 17 2006 - 20:24:13 CDT)
AMBER: identical high energies Tanya Johannsen (Thu Aug 17 2006 - 21:22:40 CDT)
AMBER: GBSA EGB = NaN William Lianhu Wei (Thu Aug 17 2006 - 21:30:50 CDT)
RE: AMBER: identical high energies Ross Walker (Thu Aug 17 2006 - 21:52:38 CDT)
RE: AMBER: GBSA EGB = NaN Ross Walker (Thu Aug 17 2006 - 21:57:29 CDT)
Re: AMBER: identical high energies Thomas Cheatham (Thu Aug 17 2006 - 21:57:23 CDT)
RE: AMBER: Execution time discrepancies Ross Walker (Thu Aug 17 2006 - 22:00:29 CDT)
Re: AMBER: GBSA EGB = NaN William Wei (Fri Aug 18 2006 - 10:12:10 CDT)
Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Fri Aug 18 2006 - 11:13:08 CDT)
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 12:50:32 CDT)
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Fri Aug 18 2006 - 13:23:17 CDT)
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 13:35:04 CDT)
AMBER: Re: antechamber failure on FMN David Mobley (Fri Aug 18 2006 - 13:46:58 CDT)
AMBER: amidine group/ gaff parameters Prashanth Athri (Fri Aug 18 2006 - 14:00:17 CDT)
AMBER: ptraj script Jardas sucuriba (Fri Aug 18 2006 - 15:08:31 CDT)
RE: AMBER: GBSA EGB = NaN Ross Walker (Fri Aug 18 2006 - 17:11:52 CDT)
Re: AMBER: DIELC? backy (Sat Aug 19 2006 - 03:04:14 CDT)
AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sun Aug 20 2006 - 09:07:57 CDT)
AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Mon Aug 21 2006 - 01:37:24 CDT)
AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Mon Aug 21 2006 - 02:46:29 CDT)
Re: AMBER: Details about Gaussian basis set for Cobalt complex FyD (Mon Aug 21 2006 - 07:28:49 CDT)
AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL (Mon Aug 21 2006 - 08:15:31 CDT)
Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Mon Aug 21 2006 - 09:19:10 CDT)
Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Mon Aug 21 2006 - 09:20:42 CDT)
RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Ross Walker (Mon Aug 21 2006 - 10:48:00 CDT)
Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 11:04:26 CDT)
Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 11:04:36 CDT)
Re: AMBER: GBSA EGB = NaN Ilyas Yildirim (Mon Aug 21 2006 - 11:14:54 CDT)
Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 11:37:47 CDT)
Re: AMBER: mm_pbsa calculation allocation error Ray Luo (Mon Aug 21 2006 - 11:37:14 CDT)
Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 12:10:24 CDT)
Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 13:00:21 CDT)
Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 13:21:10 CDT)
Re: AMBER: transition state Eric Hu (Mon Aug 21 2006 - 19:06:22 CDT)
Re: AMBER: Calculate interaction energy between small organic molecules David A. Case (Tue Aug 22 2006 - 01:14:15 CDT)
AMBER: amber naming conventions for structure files sethl_at_gatech.edu (Tue Aug 22 2006 - 16:36:56 CDT)
Re: AMBER: amber naming conventions for structure files Bill Ross (Tue Aug 22 2006 - 17:00:10 CDT)
AMBER: holding a pair of residues fixed during minimization Seth Lilavivat (Tue Aug 22 2006 - 22:22:06 CDT)
RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Tue Aug 22 2006 - 23:16:42 CDT)
Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Wed Aug 23 2006 - 07:18:03 CDT)
AMBER: compiling parallel amber 9 in linux Amber admin (Wed Aug 23 2006 - 14:00:08 CDT)
RE: AMBER: compiling parallel amber 9 in linux Ross Walker (Wed Aug 23 2006 - 14:54:39 CDT)
Re: AMBER: compiling parallel amber 9 in linux David A. Case (Wed Aug 23 2006 - 15:01:35 CDT)
Re: AMBER: holding a pair of residues fixed during minimization David A. Case (Wed Aug 23 2006 - 15:05:25 CDT)
Re: AMBER: holding a pair of residues fixed during minimization Bill Ross (Wed Aug 23 2006 - 15:45:13 CDT)
AMBER: Carnal: Internal error: stream file name 2 out of range Shuting Wei (Wed Aug 23 2006 - 15:43:31 CDT)
AMBER: 0 steps the same as 1 step? S. Jamal Rahi (Wed Aug 23 2006 - 16:25:44 CDT)
Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross (Wed Aug 23 2006 - 16:16:16 CDT)
Re: AMBER: 0 steps the same as 1 step? David A. Case (Wed Aug 23 2006 - 20:14:53 CDT)
AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert (Wed Aug 23 2006 - 20:59:08 CDT)
AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Thu Aug 24 2006 - 01:17:56 CDT)
AMBER: ptraj dumpq feature/bug Markus Kaukonen (Thu Aug 24 2006 - 03:31:51 CDT)
AMBER: Can I run RED/RESP for Platinum Complexes? a a (Thu Aug 24 2006 - 04:50:42 CDT)
AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 08:13:14 CDT)
AMBER: TI vlimit exceeded Andrea Bortolato (Thu Aug 24 2006 - 08:42:21 CDT)
AMBER: increase force constants Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 08:45:28 CDT)
Re: AMBER: Backbone & Sidechain atoms: Definition David A. Case (Thu Aug 24 2006 - 10:15:44 CDT)
AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 10:29:13 CDT)
AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 11:05:50 CDT)
AMBER: missing values in md.out Jardas sucuriba (Thu Aug 24 2006 - 11:15:40 CDT)
Re: AMBER: nmode memory problem Knut Langsestmo (Thu Aug 24 2006 - 11:17:04 CDT)
Re: AMBER: missing values in md.out Carlos Simmerling (Thu Aug 24 2006 - 11:24:28 CDT)
Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 12:04:59 CDT)
RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 12:23:02 CDT)
Re: AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 12:32:14 CDT)
RE: AMBER: nmode memory problem Ross Walker (Thu Aug 24 2006 - 12:57:12 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 14:00:04 CDT)
AMBER: how to use AddPdbAtomMap sethl_at_gatech.edu (Thu Aug 24 2006 - 15:03:59 CDT)
Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Thu Aug 24 2006 - 15:07:57 CDT)
Re: AMBER: ptraj dumpq feature/bug Thomas Cheatham (Thu Aug 24 2006 - 15:16:23 CDT)
Re: AMBER: how to use AddPdbAtomMap Ilyas Yildirim (Thu Aug 24 2006 - 15:27:41 CDT)
Re: AMBER: Calculate interaction energy between small organic molecules David LeBard (Thu Aug 24 2006 - 16:01:16 CDT)
Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 16:05:55 CDT)
RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 17:08:03 CDT)
Re: AMBER: how to use AddPdbAtomMap David A. Case (Thu Aug 24 2006 - 17:47:50 CDT)
Re: AMBER: increase force constants David A. Case (Thu Aug 24 2006 - 17:56:33 CDT)
RE: AMBER: compiling parallel amber 9 in linux Amber admin (Thu Aug 24 2006 - 19:10:57 CDT)
Re: AMBER: increase force constants Amber admin (Thu Aug 24 2006 - 19:15:24 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 20:29:58 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 20:50:31 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 21:39:43 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 21:48:07 CDT)
AMBER: building AMBER9 with gfortran/cygwin Jyh-Shyong Ho (Thu Aug 24 2006 - 21:30:02 CDT)
Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 Scott Brozell (Thu Aug 24 2006 - 21:57:03 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 21:58:20 CDT)
RE: AMBER: antechamber charge calculation very sensitive to conformations ? Junmei Wang (Thu Aug 24 2006 - 21:51:07 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 21:59:09 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 22:09:29 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 22:20:12 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Fri Aug 25 2006 - 01:28:35 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Fri Aug 25 2006 - 01:45:09 CDT)
Re: AMBER: nmode memory problem Atro Tossavainen (Fri Aug 25 2006 - 05:10:50 CDT)
Re: AMBER: building AMBER9 with gfortran/cygwin Andreas Svrcek-Seiler (Fri Aug 25 2006 - 05:39:08 CDT)
AMBER: atomifluct Miguel Ferreira (Fri Aug 25 2006 - 06:09:03 CDT)
Re: AMBER: missing values in md.out Jardas sucuriba (Fri Aug 25 2006 - 07:36:45 CDT)
Re: AMBER: missing values in md.out Carlos Simmerling (Fri Aug 25 2006 - 07:53:26 CDT)
Re: AMBER: antechamber charge calculation very sensitive to conformations ? David Mobley (Fri Aug 25 2006 - 10:08:44 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 David A. Case (Fri Aug 25 2006 - 10:03:10 CDT)
Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 10:41:49 CDT)
RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Fri Aug 25 2006 - 11:16:13 CDT)
Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 11:39:40 CDT)
Re: AMBER: Details about Gaussian basis set for Cobalt complex Thomas Cheatham (Fri Aug 25 2006 - 13:21:07 CDT)
AMBER: How to create a modified NA in leap sethl_at_gatech.edu (Fri Aug 25 2006 - 15:20:35 CDT)
Re: AMBER: How to create a modified NA in leap Bill Ross (Fri Aug 25 2006 - 16:52:40 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 20:20:47 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Jyh-Shyong Ho (Fri Aug 25 2006 - 21:11:21 CDT)
Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 21:41:46 CDT)
Re: AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sat Aug 26 2006 - 05:51:04 CDT)
AMBER: waters closest to specific residues Jardas sucuriba (Sat Aug 26 2006 - 10:39:35 CDT)
Re: AMBER: TI vlimit exceeded David A. Case (Sat Aug 26 2006 - 12:38:58 CDT)
Re: AMBER: How to create a modified NA in leap sethl_at_gatech.edu (Sat Aug 26 2006 - 15:13:10 CDT)
Re: AMBER: How to create a modified NA in leap Bill Ross (Sat Aug 26 2006 - 19:21:41 CDT)
AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht (Sun Aug 27 2006 - 00:24:12 CDT)
Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine David A. Case (Sun Aug 27 2006 - 11:03:54 CDT)
AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht (Sun Aug 27 2006 - 14:06:49 CDT)
Re: AMBER: Temperature fluctuation with Langevin Temperature control Adrian Roitberg (Sun Aug 27 2006 - 16:07:07 CDT)
AMBER: TI, mutation eric.henon_at_univ-reims.fr (Mon Aug 28 2006 - 07:39:48 CDT)
Re: AMBER: TI, mutation Carlos Simmerling (Mon Aug 28 2006 - 07:18:56 CDT)
Re: AMBER: TI, mutation Pradipta Bandyopadhyay (Mon Aug 28 2006 - 07:46:43 CDT)
Re: AMBER: Temperature fluctuation with Langevin Temperature control David A. Case (Mon Aug 28 2006 - 12:32:08 CDT)
AMBER: preparing ligand/rna structure for MD sethl_at_gatech.edu (Mon Aug 28 2006 - 13:45:17 CDT)
AMBER: Periodic boundary condition (PBC) Rahaman, Asif (Mon Aug 28 2006 - 15:24:19 CDT)
Re: AMBER: Periodic boundary condition (PBC) Carlos Simmerling (Mon Aug 28 2006 - 15:40:05 CDT)
AMBER: nmode: number of atoms limitation AYTUG TUNCEL (Mon Aug 28 2006 - 18:15:04 CDT)
Re: AMBER: Periodic boundary condition (PBC) Bill Ross (Mon Aug 28 2006 - 18:21:57 CDT)
Re: AMBER: preparing ligand/rna structure for MD David A. Case (Mon Aug 28 2006 - 19:11:34 CDT)
Re: AMBER: Periodic boundary condition (PBC) David A. Case (Mon Aug 28 2006 - 19:17:42 CDT)
AMBER: how to limit the simulation space Eric Hu (Mon Aug 28 2006 - 19:55:11 CDT)
Re: AMBER: how to limit the simulation space Bill Ross (Mon Aug 28 2006 - 20:04:39 CDT)
Re: AMBER: nmode: number of atoms limitation David A. Case (Tue Aug 29 2006 - 00:55:53 CDT)
Re: Re: AMBER: nmode: number of atoms limitation Changge Ji (Tue Aug 29 2006 - 01:33:27 CDT)
Re: AMBER: TI, mutation eric.henon_at_univ-reims.fr (Tue Aug 29 2006 - 03:43:04 CDT)
AMBER: counterions and particle-mesh-ewald cristian obiol (Tue Aug 29 2006 - 03:06:20 CDT)
AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp a a (Tue Aug 29 2006 - 05:15:07 CDT)
AMBER: Qingning Shu (Tue Aug 29 2006 - 08:01:58 CDT)
AMBER: RDF output Jardas sucuriba (Tue Aug 29 2006 - 09:48:29 CDT)
Re: AMBER: David A. Case (Tue Aug 29 2006 - 10:09:23 CDT)
Re: Re: AMBER: Qingning Shu (Tue Aug 29 2006 - 11:26:34 CDT)
AMBER: Missing LES reference in Amber 9 manual Chris Moth (Tue Aug 29 2006 - 13:43:12 CDT)
AMBER: mm_pbsa_statistical.pl William Wei (Tue Aug 29 2006 - 16:02:32 CDT)
Re: AMBER: nmode: number of atoms limitation Cenk Andac (Wed Aug 30 2006 - 08:01:58 CDT)
AMBER: REMD: Hybrid topology file Austin B. Yongye (Wed Aug 30 2006 - 09:30:34 CDT)
Re: AMBER: REMD: Hybrid topology file Carlos Simmerling (Wed Aug 30 2006 - 09:48:20 CDT)
Re: AMBER: Missing LES reference in Amber 9 manual David A. Case (Wed Aug 30 2006 - 11:03:34 CDT)
Re: AMBER: mm_pbsa_statistical.pl Jianyin Shao (Wed Aug 30 2006 - 12:52:56 CDT)
AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 14:08:09 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 14:22:13 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 14:48:28 CDT)
Re: AMBER: counterions and particle-mesh-ewald David A. Case (Wed Aug 30 2006 - 15:14:40 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 16:05:27 CDT)
Re: AMBER: mm_pbsa_statistical.pl William Wei (Wed Aug 30 2006 - 16:11:51 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 16:15:23 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 16:17:10 CDT)
Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 16:23:26 CDT)
RE: AMBER: RDF output Jardas sucuriba (Wed Aug 30 2006 - 16:31:08 CDT)
Re: AMBER: RDF output Thomas Cheatham (Wed Aug 30 2006 - 17:18:29 CDT)
Re: AMBER: counterions and particle-mesh-ewald darden (Wed Aug 30 2006 - 17:59:32 CDT)
RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp Ross Walker (Wed Aug 30 2006 - 21:04:36 CDT)
AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 10:59:51 CDT)
Re: AMBER: reference of ff99 Carlos Simmerling (Thu Aug 31 2006 - 11:18:09 CDT)
Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 11:21:59 CDT)
Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 11:26:09 CDT)
Re: AMBER: reference of ff99 David A. Case (Thu Aug 31 2006 - 11:43:50 CDT)
AMBER: Question about free energy with mm_pbsa William Wei (Thu Aug 31 2006 - 13:50:11 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 15:24:43 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 15:49:42 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 16:34:50 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 16:50:33 CDT)
AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 17:01:24 CDT)
Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 17:12:24 CDT)
Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 17:22:08 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 17:29:25 CDT)
Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 17:50:26 CDT)
Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 18:13:29 CDT)
Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 18:47:54 CDT)
Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 20:16:49 CDT)
Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 22:37:18 CDT)
Re: AMBER: minimization with my own charges Thomas Cheatham (Thu Aug 31 2006 - 23:07:40 CDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 23:38:02 CDT)
Re: AMBER: Question about free energy with mm_pbsa David A. Case (Fri Sep 01 2006 - 00:32:54 CDT)
Re: AMBER: Question about free energy with mm_pbsa Thomas Cheatham (Fri Sep 01 2006 - 01:23:59 CDT)
AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c Jiten (Fri Sep 01 2006 - 01:55:21 CDT)
Re: AMBER: Question about free energy with mm_pbsa William Wei (Fri Sep 01 2006 - 08:32:29 CDT)
Re: AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c David A. Case (Fri Sep 01 2006 - 09:34:10 CDT)
AMBER: force fields for proflavine molecule sethl_at_gatech.edu (Fri Sep 01 2006 - 12:49:00 CDT)
AMBER: output file not generated bala (Fri Sep 01 2006 - 10:35:40 CDT)
AMBER: Gaussian, antechamber, RESP Ed Pate (Sat Sep 02 2006 - 16:42:11 CDT)
AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sat Sep 02 2006 - 20:52:45 CDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sun Sep 03 2006 - 00:06:04 CDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sun Sep 03 2006 - 01:20:27 CDT)
Re: AMBER: Gaussian, antechamber, RESP Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Sun Sep 03 2006 - 07:57:57 CDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sun Sep 03 2006 - 10:55:16 CDT)
AMBER: Amber9: Free Energy Franck_Vendeix_at_ncsu.edu (Sun Sep 03 2006 - 18:11:44 CDT)
Re: AMBER: Amber9: Free Energy David A. Case (Sun Sep 03 2006 - 20:57:50 CDT)
Re: AMBER: Amber9: Free Energy Franck_Vendeix_at_ncsu.edu (Sun Sep 03 2006 - 21:27:13 CDT)
AMBER: ligand file Fenghui Fan (Mon Sep 04 2006 - 13:20:27 CDT)
Re: AMBER: ligand file David A. Case (Mon Sep 04 2006 - 14:02:34 CDT)
AMBER: cAMP ligand file Fenghui Fan (Mon Sep 04 2006 - 15:00:47 CDT)
AMBER: Implicit Water - Force field parameters Ramdas Pophale (Tue Sep 05 2006 - 14:22:49 CDT)
Re: AMBER: Implicit Water - Force field parameters Fenghui Fan (Tue Sep 05 2006 - 15:16:37 CDT)
AMBER: a ligand file Fenghui Fan (Tue Sep 05 2006 - 15:18:51 CDT)
Re: AMBER: a ligand file David A. Case (Tue Sep 05 2006 - 15:55:26 CDT)
AMBER: help with antechamber - creating ligand sethl_at_gatech.edu (Tue Sep 05 2006 - 16:10:08 CDT)
Re: AMBER: help with antechamber - creating ligand Ilyas Yildirim (Tue Sep 05 2006 - 16:26:11 CDT)
Re: AMBER: Implicit Water - Force field parameters Ilyas Yildirim (Tue Sep 05 2006 - 15:22:13 CDT)
Re: AMBER: help with antechamber - creating ligand David A. Case (Tue Sep 05 2006 - 21:11:52 CDT)
AMBER: Amber parallel version Franck_Vendeix_at_ncsu.edu (Wed Sep 06 2006 - 01:05:20 CDT)
Re: AMBER: Amber parallel version Jyh-Shyong Ho (Wed Sep 06 2006 - 01:43:08 CDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Wed Sep 06 2006 - 03:46:57 CDT)
AMBER: PARAMETERISATION PROBLEM Claire Zerafa (Wed Sep 06 2006 - 09:12:04 CDT)
Re: AMBER: PARAMETERISATION PROBLEM David A. Case (Wed Sep 06 2006 - 10:20:43 CDT)
Re: AMBER: Implicit Water - Force field parameters David A. Case (Wed Sep 06 2006 - 10:54:15 CDT)
AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 12:41:12 CDT)
Re: AMBER: Question about using PMEMD and GB David A. Case (Wed Sep 06 2006 - 12:58:59 CDT)
Re: AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 13:31:20 CDT)
Re: AMBER: a ligand file Fenghui Fan (Wed Sep 06 2006 - 16:16:58 CDT)
Re: AMBER: a ligand file David A. Case (Wed Sep 06 2006 - 16:40:30 CDT)
AMBER: improper torsion angle problem Fabian Alejandro Rodriguez (Wed Sep 06 2006 - 16:52:40 CDT)
AMBER: trajout Weihua Li (Wed Sep 06 2006 - 22:22:28 CDT)
AMBER: Ca2+ polarizability Martin LEPSIK (Thu Sep 07 2006 - 04:02:38 CDT)
Re: AMBER: trajout Carlos Simmerling (Thu Sep 07 2006 - 06:04:02 CDT)
AMBER: mdcrd file Jianhui (Thu Sep 07 2006 - 09:15:45 CDT)
Re: AMBER: mdcrd file Mark Williamson (Thu Sep 07 2006 - 12:39:12 CDT)
AMBER: Re: FF problem: RG residue minimizes to non-planar structure David A. Case (Thu Sep 07 2006 - 13:53:33 CDT)
Re: AMBER: Amber parallel version Franck_Vendeix_at_ncsu.edu (Thu Sep 07 2006 - 13:45:47 CDT)
AMBER: leap - how to recognize my structure sethl_at_gatech.edu (Thu Sep 07 2006 - 17:16:06 CDT)
Re: AMBER: leap - how to recognize my structure Carlos Simmerling (Thu Sep 07 2006 - 17:34:09 CDT)
RE: AMBER: mdcrd file Ross Walker (Thu Sep 07 2006 - 17:52:28 CDT)
Re: AMBER: mdcrd file Brent Krueger (Thu Sep 07 2006 - 21:55:27 CDT)
Re: AMBER: mdcrd file David A. Case (Fri Sep 08 2006 - 00:27:54 CDT)
AMBER: nmode memory allocation error AYTUG TUNCEL (Fri Sep 08 2006 - 03:41:35 CDT)
Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 09:31:33 CDT)
AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 09:15:32 CDT)
Re: AMBER: hydronium ion parameters Jiten (Fri Sep 08 2006 - 10:12:03 CDT)
Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 11:09:55 CDT)
Re: AMBER: mdcrd file Joseph Nachman (Fri Sep 08 2006 - 12:36:42 CDT)
Re: AMBER: hydronium ion parameters Ilyas Yildirim (Fri Sep 08 2006 - 15:41:17 CDT)
AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 16:00:19 CDT)
AMBER: LEAP - "could not find type: NH" sethl_at_gatech.edu (Fri Sep 08 2006 - 16:08:11 CDT)
Re: AMBER: LEAP - "could not find type: NH" Ilyas Yildirim (Fri Sep 08 2006 - 17:42:46 CDT)
Re: AMBER: mdcrd file Carlos Simmerling (Fri Sep 08 2006 - 15:54:34 CDT)
AMBER: seg fault during test.serial Lachele Foley (Lists) (Fri Sep 08 2006 - 15:45:05 CDT)
Re: AMBER: seg fault during test.serial David A. Case (Fri Sep 08 2006 - 20:19:16 CDT)
AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 20:31:59 CDT)
Re: AMBER: a ligand file David A. Case (Fri Sep 08 2006 - 20:53:18 CDT)
AMBER: pmf with respect to a surface Rahaman, Asif (Fri Sep 08 2006 - 17:35:22 CDT)
Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 21:23:48 CDT)
Re: AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 22:06:49 CDT)
Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 23:05:11 CDT)
Re: AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 23:35:28 CDT)
AMBER: post nmanal $B?y?9_at_5F;(B (Sat Sep 09 2006 - 01:03:47 CDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 04:00:08 CDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 04:01:34 CDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 03:57:43 CDT)
AMBER: protein-ligand interaction Fenghui Fan (Sat Sep 09 2006 - 11:59:51 CDT)
Re: AMBER: post nmanal David A. Case (Sat Sep 09 2006 - 11:54:34 CDT)
Re: AMBER: protein-ligand interaction Ilyas Yildirim (Sat Sep 09 2006 - 16:58:10 CDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 20:07:48 CDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 20:03:06 CDT)
Re: AMBER: pmf with respect to a surface David A. Case (Sat Sep 09 2006 - 23:14:30 CDT)
Re: AMBER: nmode memory allocation error David A. Case (Sat Sep 09 2006 - 23:17:54 CDT)
Re: AMBER: resp FyD (Sun Sep 10 2006 - 02:46:11 CDT)
AMBER: (no subject) Prashanth Athri (Sun Sep 10 2006 - 19:23:05 CDT)
AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Sun Sep 10 2006 - 19:23:25 CDT)
Re: AMBER: post nmanal $B?y?9_at_5F;(B (Mon Sep 11 2006 - 01:09:28 CDT)
AMBER: Oon Modeling the metalloprotein with GB model. wenfei Li (Mon Sep 11 2006 - 02:41:16 CDT)
Re: AMBER: nmode memory allocation error Cenk Andac (Mon Sep 11 2006 - 04:48:30 CDT)
AMBER: Error in Running Sander Jianhui Tian (Mon Sep 11 2006 - 08:52:39 CDT)
AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Mon Sep 11 2006 - 09:24:44 CDT)
AMBER: How to get the ligand. ac file Fenghui Fan (Mon Sep 11 2006 - 09:46:54 CDT)
Re: AMBER: seg fault during test.serial Lachele Foley (Lists) (Mon Sep 11 2006 - 09:50:57 CDT)
AMBER: cAMP ligand charge Fenghui Fan (Mon Sep 11 2006 - 10:06:40 CDT)
AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 10:38:00 CDT)
Re: AMBER: cAMP ligand charge David A. Case (Mon Sep 11 2006 - 10:35:53 CDT)
Re: AMBER: seg fault during test.serial David A. Case (Mon Sep 11 2006 - 10:54:43 CDT)
Re: AMBER: set a trucated octahedron box in Leap David A. Case (Mon Sep 11 2006 - 10:56:59 CDT)
Re: AMBER: Error in Running Sander David A. Case (Mon Sep 11 2006 - 10:59:45 CDT)
AMBER: System in polarizable waters Martin LEPSIK (Mon Sep 11 2006 - 11:14:24 CDT)
Re: AMBER: Error in Running Sander Jianhui (Mon Sep 11 2006 - 12:10:55 CDT)
Re: AMBER: mdcrd file Joseph Nachman (Mon Sep 11 2006 - 13:00:21 CDT)
Re: AMBER: System in polarizable waters David A. Case (Mon Sep 11 2006 - 13:12:04 CDT)
Re: AMBER: Parallel compile: ld: cannot find -lfmpi David A. Case (Mon Sep 11 2006 - 13:19:12 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Mon Sep 11 2006 - 15:48:51 CDT)
Re: AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 15:39:55 CDT)
AMBER: angle between helices ÕÅÓÂ (Mon Sep 11 2006 - 21:05:51 CDT)
Re: AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Tue Sep 12 2006 - 03:30:06 CDT)
Re: AMBER: set a trucated octahedron box in Leap Ilyas Yildirim (Tue Sep 12 2006 - 03:48:56 CDT)
AMBER: Installing AMBER9 on cygwin (WinXP) HARADA Makoto (Tue Sep 12 2006 - 04:38:19 CDT)
Re: AMBER: Installing AMBER9 on cygwin (WinXP) Gobind Singh Bisht (Tue Sep 12 2006 - 06:57:06 CDT)
Re: AMBER: set a trucated octahedron box in Leap David A. Case (Tue Sep 12 2006 - 10:03:24 CDT)
Re: AMBER: Installing AMBER9 on cygwin (WinXP) David A. Case (Tue Sep 12 2006 - 10:01:41 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 10:54:08 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 12:10:55 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 13:41:21 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 14:30:02 CDT)
RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 15:44:30 CDT)
AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 16:09:34 CDT)
RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ross Walker (Tue Sep 12 2006 - 16:35:47 CDT)
RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 17:49:33 CDT)
Re: AMBER: Problem with ptraj Thomas Cheatham (Tue Sep 12 2006 - 21:47:46 CDT)
AMBER: about ligand charge Fenghui Fan (Tue Sep 12 2006 - 22:16:27 CDT)
AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 priya priya (Wed Sep 13 2006 - 04:02:33 CDT)
AMBER: 'lastrst' error for amber8 Arvind Marathe (Wed Sep 13 2006 - 07:52:07 CDT)
AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 07:57:44 CDT)
AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Hannes Barsch (Wed Sep 13 2006 - 08:54:54 CDT)
AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Fenghui Fan (Wed Sep 13 2006 - 09:23:33 CDT)
AMBER: RDC refinement Young-Tae Lee (Wed Sep 13 2006 - 10:13:30 CDT)
Re: AMBER: 'lastrst' error for amber8 michael crowley (Wed Sep 13 2006 - 10:14:08 CDT)
Re: AMBER: 'lastrst' error for amber8 Robert Duke (Wed Sep 13 2006 - 10:28:16 CDT)
Re: AMBER: RDC refinement David A. Case (Wed Sep 13 2006 - 10:35:07 CDT)
Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Thomas Cheatham (Wed Sep 13 2006 - 10:48:54 CDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Wed Sep 13 2006 - 11:32:39 CDT)
AMBER: energy data for limited part of system Tanya Johannsen (Wed Sep 13 2006 - 12:57:15 CDT)
Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Ilyas Yildirim (Wed Sep 13 2006 - 12:59:10 CDT)
AMBER: residence time of water molecules venditti2_at_unisi.it (Wed Sep 13 2006 - 09:56:34 CDT)
AMBER: the time length of the restricted MD Fenghui Fan (Wed Sep 13 2006 - 14:38:59 CDT)
AMBER: Mixed solvent? Mingfeng Yang (Wed Sep 13 2006 - 14:44:32 CDT)
AMBER: Error in reading RDC data Lee, Young-Tae (Wed Sep 13 2006 - 15:09:42 CDT)
AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 15:24:14 CDT)
AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Wed Sep 13 2006 - 15:42:02 CDT)
Re: AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 16:07:52 CDT)
Re: AMBER: MAXM in nmode David A. Case (Wed Sep 13 2006 - 16:17:29 CDT)
AMBER: pqr from constant pH MD harianto (Wed Sep 13 2006 - 16:43:13 CDT)
Re: AMBER: Error in reading RDC data David A. Case (Wed Sep 13 2006 - 16:44:14 CDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 22:21:07 CDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Thu Sep 14 2006 - 00:53:50 CDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Thu Sep 14 2006 - 01:47:07 CDT)
Re: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Thu Sep 14 2006 - 03:15:43 CDT)
Re: AMBER: residence time of water molecules Angelo (Thu Sep 14 2006 - 03:57:38 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Thu Sep 14 2006 - 08:08:08 CDT)
AMBER: MD on protein-ligand interaction Fenghui Fan (Thu Sep 14 2006 - 09:04:20 CDT)
AMBER: potential energy in the MD result Fenghui Fan (Thu Sep 14 2006 - 09:39:12 CDT)
Re: AMBER: 'lastrst' error for amber8 David A. Case (Thu Sep 14 2006 - 10:05:25 CDT)
AMBER: addions default settings. asli ertekin (Thu Sep 14 2006 - 10:37:47 CDT)
AMBER: pmemd error bala (Thu Sep 14 2006 - 10:34:12 CDT)
Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 11:46:30 CDT)
Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 11:46:40 CDT)
Re: AMBER: addions default settings. Bill Ross (Thu Sep 14 2006 - 12:14:18 CDT)
AMBER: acidifying a water box Eric Shamay (Thu Sep 14 2006 - 13:36:11 CDT)
AMBER: DPPC Bilayer size Akshay Patny (Thu Sep 14 2006 - 13:47:45 CDT)
Re: AMBER: MD on protein-ligand interaction Ilyas Yildirim (Thu Sep 14 2006 - 14:09:14 CDT)
Re: AMBER: acidifying a water box David A. Case (Thu Sep 14 2006 - 17:21:01 CDT)
AMBER: Denaturing MD Fenghui Fan (Thu Sep 14 2006 - 17:58:35 CDT)
Re: AMBER: acidifying a water box Thomas Cheatham (Thu Sep 14 2006 - 17:56:32 CDT)
AMBER: mm_pbsa snapshots for "three-trajectory" In Hee Park (Thu Sep 14 2006 - 18:42:13 CDT)
Re: AMBER: Denaturing MD Thomas Cheatham (Thu Sep 14 2006 - 18:55:59 CDT)
AMBER: Temperature not rising enough during simulated annealing Adam Pelzer (Thu Sep 14 2006 - 22:30:12 CDT)
AMBER: on the rst file of the current ruuning Fenghui Fan (Thu Sep 14 2006 - 22:33:50 CDT)
AMBER: cyclic AMP off and frcmod files? Daniel Lee (Thu Sep 14 2006 - 22:52:33 CDT)
Re: [UCE]AMBER: Temperature not rising enough during simulated annealing Thomas Cheatham (Thu Sep 14 2006 - 23:33:42 CDT)
AMBER: restraints and constant pressure Joshua (Fri Sep 15 2006 - 00:44:09 CDT)
Re: AMBER: restraints and constant pressure Thomas Cheatham (Fri Sep 15 2006 - 01:22:02 CDT)
Re: AMBER: acidifying a water box Eric Shamay (Fri Sep 15 2006 - 03:49:15 CDT)
Re: AMBER: restraints and constant pressure Joshua (Fri Sep 15 2006 - 04:09:44 CDT)
Re: AMBER: cyclic AMP off and frcmod files? Fenghui Fan (Fri Sep 15 2006 - 08:44:49 CDT)
Re: AMBER: restraints and constant pressure Myunggi Yi (Fri Sep 15 2006 - 14:52:21 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Fri Sep 15 2006 - 15:01:43 CDT)
AMBER: About Lennard-Jones Parameters Jianhui (Fri Sep 15 2006 - 16:08:13 CDT)
AMBER: distance between two atoms Fenghui Fan (Fri Sep 15 2006 - 15:49:11 CDT)
AMBER: Problems with a restrained minimization approach Abhilash (Fri Sep 15 2006 - 14:35:34 CDT)
Re: AMBER: About Lennard-Jones Parameters David A. Case (Fri Sep 15 2006 - 19:07:35 CDT)
AMBER: new article on Amber force fields Carlos Simmerling (Fri Sep 15 2006 - 14:47:34 CDT)
Re: AMBER: Problems with a restrained minimization approach David A. Case (Fri Sep 15 2006 - 19:41:04 CDT)
AMBER: have problems with restrained minimization Abhilash (Fri Sep 15 2006 - 13:10:50 CDT)
Re: AMBER: 'lastrst' error for amber8 David A. Case (Sat Sep 16 2006 - 11:50:31 CDT)
Re: AMBER: restraints and constant pressure Thomas Cheatham (Sat Sep 16 2006 - 23:38:06 CDT)
AMBER: change mdcrd file to pdb file Fenghui Fan (Sun Sep 17 2006 - 00:02:54 CDT)
Re: AMBER: change mdcrd file to pdb file Ilyas Yildirim (Sun Sep 17 2006 - 00:17:21 CDT)
Re: AMBER: restraints and constant pressure Myunggi Yi (Sun Sep 17 2006 - 01:29:38 CDT)
AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 02:36:26 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Sun Sep 17 2006 - 07:02:09 CDT)
Re: AMBER: lib-4324 : UNRECOVERABLE library error Robert Duke (Sun Sep 17 2006 - 07:30:08 CDT)
Re: AMBER: restraints and constant pressure Carlos Simmerling (Sun Sep 17 2006 - 09:01:54 CDT)
Re: AMBER: change mdcrd file to pdb file Jianhui (Sun Sep 17 2006 - 09:16:29 CDT)
Re: AMBER: restraints and constant pressure Myunggi Yi (Sun Sep 17 2006 - 09:23:33 CDT)
Re: AMBER: change mdcrd file to pdb file Fenghui Fan (Sun Sep 17 2006 - 10:30:02 CDT)
Re: AMBER: change mdcrd file to pdb file Fabian Alejandro Rodriguez (Sun Sep 17 2006 - 11:04:22 CDT)
Re: AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 12:23:24 CDT)
Re: AMBER: energy data for limited part of system David A. Case (Sun Sep 17 2006 - 18:56:23 CDT)
Re: AMBER: improper torsion angle problem David A. Case (Sun Sep 17 2006 - 18:52:38 CDT)
AMBER: potential energy Fenghui Fan (Sun Sep 17 2006 - 19:38:44 CDT)
Re: AMBER: cyclic AMP off and frcmod files? Daniel Lee (Sun Sep 17 2006 - 21:10:28 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 01:50:41 CDT)
AMBER: parameters for Nickel and iron Rachel (Mon Sep 18 2006 - 08:02:39 CDT)
Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 10:44:49 CDT)
RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 10:52:23 CDT)
RE: AMBER: on the rst file of the current ruuning Ross Walker (Mon Sep 18 2006 - 10:58:01 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 11:25:33 CDT)
Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 11:41:56 CDT)
AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 12:46:35 CDT)
Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 12:44:11 CDT)
Re: AMBER: Restart problem on PMEMD with position restraint. Robert Duke (Mon Sep 18 2006 - 13:20:27 CDT)
RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 13:32:05 CDT)
AMBER: Questions Joseph Fernandez (Mon Sep 18 2006 - 13:48:25 CDT)
Re: AMBER: Restart problem on PMEMD with position restraint. David A. Case (Mon Sep 18 2006 - 14:09:46 CDT)
AMBER: ptraj RMSD vs. RMSF Steve Seibold (Mon Sep 18 2006 - 14:54:02 CDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 15:40:21 CDT)
AMBER: Question about Streptavidin/Biotin Tutorial. Qingning Shu (Mon Sep 18 2006 - 15:39:38 CDT)
Re: AMBER: A question about Dynamics. David A. Case (Mon Sep 18 2006 - 15:55:47 CDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 15:57:17 CDT)
RE: AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 16:10:44 CDT)
Re: AMBER: A question about Dynamics. Chunhu Tan (Mon Sep 18 2006 - 16:24:22 CDT)
RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 16:57:58 CDT)
RE: AMBER: Question about Streptavidin/Biotin Tutorial. Ross Walker (Mon Sep 18 2006 - 17:10:39 CDT)
Re: RE: AMBER: potential energy linfu (Mon Sep 18 2006 - 20:44:18 CDT)
Re: [UCE]Re: RE: AMBER: potential energy Thomas Cheatham (Mon Sep 18 2006 - 21:16:20 CDT)
Re: [UCE]Re: RE: AMBER: potential energy Fenghui Fan (Mon Sep 18 2006 - 21:41:09 CDT)
Re: AMBER: parameters for Nickel and iron Fenghui Fan (Mon Sep 18 2006 - 21:45:24 CDT)
RE: [UCE]Re: RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 23:01:04 CDT)
AMBER: Can salt effect be determined in GB medel? Xioling Chuang (Mon Sep 18 2006 - 23:04:03 CDT)
Re: AMBER: Can salt effect be determined in GB medel? linfu (Tue Sep 19 2006 - 01:32:16 CDT)
AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? linfu (Tue Sep 19 2006 - 01:40:52 CDT)
AMBER: resolving a bad initial model wang_at_cbs.cnrs.fr (Tue Sep 19 2006 - 09:42:11 CDT)
Re: AMBER: resolving a bad initial model Andy Purkiss-Trew (Tue Sep 19 2006 - 09:51:01 CDT)
Re: AMBER: resolving a bad initial model Carlos Simmerling (Tue Sep 19 2006 - 09:53:47 CDT)
Re: AMBER: resolving a bad initial model Stefano Pieraccini (Tue Sep 19 2006 - 10:25:46 CDT)
Re: AMBER: parameters for Nickel and iron Rachel (