Amber Archive Jan 2006: by author

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- AMBER: Workshops (Wed Jan 11 2006 - 06:27:59 PST)
Adrian Roitberg
- Re: AMBER: minimalization prior to nmode analysis, is it necessary? (Thu Jan 05 2006 - 18:38:51 PST)
Ahammadunny Pathiaseril
- AMBER: IGB=10 (Wed Jan 18 2006 - 07:53:25 PST)
alexandra.marques.fc.up.pt
- AMBER: NAD parameters (Mon Jan 30 2006 - 08:04:43 PST)
- AMBER: parameters for C=S (Mon Jan 09 2006 - 06:53:30 PST)
alexandratm.sapo.pt
- AMBER: amber (Mon Jan 09 2006 - 03:31:56 PST)
Amber admin
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type (Fri Jan 06 2006 - 13:36:19 PST)
Andreas Svrcek-Seiler
- Re: AMBER: Amber 8 install problem (Wed Jan 18 2006 - 03:10:38 PST)
Andrew Box
- AMBER: Amber 8 install problem (Tue Jan 17 2006 - 20:50:21 PST)
Andy Purkiss
- Re: AMBER: is there any relationship between RMSD and B-factor? (Thu Jan 19 2006 - 05:19:06 PST)
- Re: AMBER: Trimming ptraj output (Fri Jan 13 2006 - 10:03:54 PST)
- AMBER: Trimming ptraj output (Fri Jan 13 2006 - 09:29:00 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 07:01:09 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 06:52:14 PST)
Atsutoshi Okabe
- AMBER: Gibbs pmf calculation (Wed Jan 11 2006 - 02:14:30 PST)
Baird, Jamie \(bairdje\)
- AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 09:33:00 PST)
Baker, Bo-Yang
- RE: AMBER: antechamber problem (Mon Jan 02 2006 - 16:23:40 PST)
Bill Ross
- Re: AMBER: problem in center command (Fri Jan 20 2006 - 17:40:51 PST)
- Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 16:39:12 PST)
- Re: AMBER: Ligand charge (Thu Jan 05 2006 - 10:24:18 PST)
- Re: AMBER: Leap (Wed Jan 04 2006 - 14:02:20 PST)
brmeher.iitg.ernet.in
- AMBER: problem with the output file for free energy perturbation calculation (Mon Jan 09 2006 - 21:15:30 PST)
bybaker.itsa.ucsf.edu
- AMBER: Ligand charge (Wed Jan 04 2006 - 10:51:57 PST)
Carlos Simmerling
- Re: AMBER: is there any relationship between RMSD and B-factor? (Thu Jan 19 2006 - 04:59:39 PST)
- Re: AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 19:53:26 PST)
- AMBER: Re: RE：AMBER: the problem of mdcrd (Tue Jan 17 2006 - 04:56:58 PST)
- Re: AMBER: base-base interaction (Fri Jan 13 2006 - 10:07:57 PST)
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 14:10:58 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 07:04:45 PST)
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 05:04:46 PST)
Claire Zerafa
- AMBER: ACTIVE SITE (Mon Jan 16 2006 - 06:06:52 PST)
David A. Case
- Re: AMBER: anal vs sander (Fri Jan 27 2006 - 15:28:51 PST)
- Re: AMBER: About the unit of the projection onto eigenvectors (Fri Jan 27 2006 - 14:20:17 PST)
- Re: AMBER: atom type "O3" not recognized by XLeap (Fri Jan 27 2006 - 14:01:43 PST)
- Re: AMBER: anal vs sander (Fri Jan 27 2006 - 13:33:57 PST)
- Re: AMBER: Charges from NMR spin densities (Fri Jan 27 2006 - 08:57:32 PST)
- Re: AMBER: AMBER 7 and restrained bonds. (Thu Jan 26 2006 - 08:26:42 PST)
- Re: AMBER: AMBER 8.0 : Octane Implicit Solvent? (Tue Jan 24 2006 - 11:09:32 PST)
- Re: AMBER: bugfix for impropers in parmchk (Wed Jan 18 2006 - 18:04:36 PST)
- Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 10:52:51 PST)
- Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 08:30:51 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue (Mon Jan 16 2006 - 11:44:22 PST)
- Re: AMBER: heme improper torsions (Mon Jan 16 2006 - 08:46:47 PST)
- Re: AMBER: Problem in Antechamber (Thu Jan 12 2006 - 17:40:50 PST)
- Re: AMBER: Na+ with GB/SA? (Thu Jan 12 2006 - 14:24:17 PST)
- Re: AMBER: amber atom type -> length of name (Wed Jan 11 2006 - 23:59:48 PST)
- Re: AMBER: regarding Hydrogen bond analysis (Tue Jan 10 2006 - 00:45:50 PST)
- Re: AMBER: parameters for C=S (Mon Jan 09 2006 - 15:04:52 PST)
- Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 14:59:46 PST)
- Re: AMBER: SHAKE - ntc = 3 (Fri Jan 06 2006 - 17:26:55 PST)
- Re: AMBER: minimalization prior to nmode analysis, is it necessary? (Thu Jan 05 2006 - 17:56:26 PST)
- Re: AMBER: requirement of delphi for mm_pbsa (Wed Jan 04 2006 - 08:22:53 PST)
David Case
- Re: AMBER: antechamber (Thu Jan 26 2006 - 15:48:55 PST)
David LeBard
- Re: AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 15:23:16 PST)
- AMBER: Charges from NMR spin densities (Thu Jan 26 2006 - 15:33:50 PST)
David Mathews
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU (Sun Jan 01 2006 - 15:29:40 PST)
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU (Sun Jan 01 2006 - 15:08:17 PST)
David Mobley
- Re: AMBER: bugfix for impropers in parmchk (Fri Jan 20 2006 - 10:21:49 PST)
- Re: AMBER: bugfix for impropers in parmchk (Fri Jan 20 2006 - 10:23:39 PST)
- Re: AMBER: Ligand charge (Wed Jan 04 2006 - 11:43:54 PST)
Douali, Latifa
- AMBER: MM-PBSA (Wed Jan 25 2006 - 15:03:06 PST)
- AMBER: base-base interaction (Fri Jan 13 2006 - 09:54:32 PST)
Fabian Boes
- Re: AMBER: analysing water behavior during MD (Fri Jan 13 2006 - 08:22:01 PST)
Fren T
- AMBER: monosaccharide residues (Tue Jan 24 2006 - 14:20:03 PST)
FyD
- Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 23:53:43 PST)
- Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 03:41:47 PST)
- Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 01:38:36 PST)
- RE: AMBER: partial charge glycam (Wed Jan 25 2006 - 01:23:06 PST)
- Re: AMBER: partial charge glycam (Fri Jan 20 2006 - 23:30:37 PST)
- AMBER: Release of RESP ESP charge DDatabase (Mon Jan 16 2006 - 08:04:47 PST)
Guillaume Bollot
- AMBER: AMBER 8.0 : Octane Implicit Solvent? (Tue Jan 24 2006 - 08:25:42 PST)
Gustavo Pierdominici Sottile
- AMBER: lifetimes (Mon Jan 30 2006 - 07:15:55 PST)
- AMBER: h-bond (Fri Jan 27 2006 - 06:59:07 PST)
haixiao jin
- Re: AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 20:58:28 PST)
- AMBER: is there any relationship between RMSD and B-factor? (Wed Jan 18 2006 - 19:30:33 PST)
hayden
- AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 10:55:34 PST)
- AMBER: PTRAJ generating wrong dihedral angles (Tue Jan 10 2006 - 03:40:05 PST)
Holger Gohlke
- Re: AMBER: ptraj distance matrix (Wed Jan 11 2006 - 00:09:33 PST)
- Re: AMBER: How to run mm_pbsa_statistics.pl? (Wed Jan 04 2006 - 09:27:05 PST)
- Re: AMBER: requirement of delphi for mm_pbsa (Wed Jan 04 2006 - 09:09:46 PST)
Holly Freedman
- AMBER: ptraj distance matrix (Tue Jan 10 2006 - 14:03:36 PST)
Ilyas Yildirim
- Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 03:10:52 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 02:40:56 PST)
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Thu Jan 12 2006 - 14:00:24 PST)
- Re: AMBER: About preparing Zn.lib (Wed Jan 11 2006 - 23:46:03 PST)
- AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS (Wed Jan 11 2006 - 23:43:06 PST)
- Re: AMBER: GLUTATHIONE (Wed Jan 11 2006 - 07:38:56 PST)
- Re: AMBER: Ligand charge (Wed Jan 04 2006 - 22:02:42 PST)
- Re: AMBER: water molecules with in 3 angstroms to the solute (Tue Jan 03 2006 - 16:40:07 PST)
- Re: AMBER: water molecules with in 3 angstroms to the solute (Tue Jan 03 2006 - 01:05:24 PST)
ivan.mmb.pcb.ub.es
- Re: AMBER: NAD parameters (Mon Jan 30 2006 - 08:20:19 PST)
Jan Dohnalek
- AMBER: MPICH on OpenMosix (Mon Jan 16 2006 - 05:21:04 PST)
- Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 02:32:18 PST)
- AMBER: mpich Amber7 problem (Tue Jan 10 2006 - 06:31:38 PST)
Jason K
- AMBER: A few problems on the parameterisation of a Glutamine residue (Wed Jan 18 2006 - 10:12:16 PST)
Jennie Thomas
- Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 17:54:09 PST)
- Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 16:07:47 PST)
- Re: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 14:38:24 PST)
- AMBER: SHAKE - ntc = 3 (Fri Jan 06 2006 - 17:05:09 PST)
Jianyin Shao
- Re: AMBER: MM-PBSA (Tue Jan 31 2006 - 09:08:09 PST)
Jiten
- AMBER: nmode calculations error (Tue Jan 17 2006 - 05:58:53 PST)
- Re: AMBER: Leap compilation issues (Tue Jan 10 2006 - 19:19:14 PST)
Joachim Reichelt
- AMBER: GLUTATHIONE (Wed Jan 11 2006 - 06:40:30 PST)
Joseph Fernandez
- AMBER: Leap (Wed Jan 04 2006 - 13:36:13 PST)
Junmei Wang
- RE: AMBER: Problem in Antechamber (Thu Jan 19 2006 - 15:02:39 PST)
Kateryna Miroshnychenko
- AMBER: bugfix for impropers in parmchk (Wed Jan 18 2006 - 06:48:55 PST)
- AMBER: ATCOR.dat format (Thu Jan 12 2006 - 08:43:05 PST)
Kenley Barrett
- AMBER: atom type "O3" not recognized by XLeap (Fri Jan 27 2006 - 09:32:48 PST)
Kevin Murphy
- RE: AMBER: partial charge glycam (Tue Jan 24 2006 - 04:18:05 PST)
- AMBER: partial charge glycam (Fri Jan 20 2006 - 03:28:27 PST)
kkirschn.hamilton.edu
- Re: AMBER: partial charge glycam (Thu Jan 26 2006 - 06:49:35 PST)
- Re: AMBER: partial charge glycam (Fri Jan 20 2006 - 07:39:14 PST)
lily ferreira
- Re: AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 22:46:53 PST)
- AMBER: Charges of enantiomers for Amber8 (Wed Jan 25 2006 - 00:01:24 PST)
linfu
- Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 01:27:57 PST)
- AMBER: about mmpbsa (Mon Jan 09 2006 - 17:17:15 PST)
- AMBER: Could you help me about mmpbsa! thank you! (Sun Jan 08 2006 - 01:28:13 PST)
luckyang.gmail.com
- Re: AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 15:51:06 PST)
- AMBER: Problem in compiling AMBER8 parallel version (Tue Jan 31 2006 - 15:09:09 PST)
- Re: AMBER: Problem in compiling sander with MMTSB (Mon Jan 30 2006 - 22:10:15 PST)
- AMBER: Problem in compiling sander with MMTSB (Mon Jan 30 2006 - 18:06:32 PST)
Lydia
- Re: AMBER: rms in principal component analysis (Wed Jan 18 2006 - 09:43:03 PST)
- AMBER: rms in principal component analysis (Tue Jan 17 2006 - 12:54:32 PST)
Magne Olufsen
- AMBER: minimalization prior to nmode analysis, is it necessary? (Wed Jan 04 2006 - 09:42:21 PST)
Manish Datt
- AMBER: requirement of delphi for mm_pbsa (Tue Jan 03 2006 - 10:46:53 PST)
Marcela Madrid
- AMBER: ptraj PCA (Thu Jan 19 2006 - 17:04:46 PST)
nag raj
- AMBER: water molecules with in 3 angstroms to the solute (Mon Jan 02 2006 - 20:47:06 PST)
nkyx.sohu.com
- AMBER: heme improper torsions (Mon Jan 16 2006 - 00:55:38 PST)
Peng Tao
- Re: AMBER: How to run mm_pbsa_statistics.pl? (Tue Jan 10 2006 - 07:49:00 PST)
- Re: AMBER: How to run mm_pbsa_statistics.pl? (Thu Jan 05 2006 - 15:11:42 PST)
- Re: AMBER: How to run mm_pbsa_statistics.pl? (Thu Jan 05 2006 - 05:39:19 PST)
- AMBER: How to run mm_pbsa_statistics.pl? (Wed Jan 04 2006 - 05:51:55 PST)
Peter Gannett
- Re: AMBER: problem with ssh and xleap (Mon Jan 02 2006 - 08:26:18 PST)
Petr Kulhanek
- Re: AMBER: mpich Amber7 problem (Wed Jan 11 2006 - 01:27:01 PST)
ping jiang
- AMBER: antechamber (Thu Jan 26 2006 - 15:18:29 PST)
Piotr Cieplak
- Re: AMBER: anal vs sander (Fri Jan 27 2006 - 14:59:13 PST)
- AMBER: anal vs sander (Fri Jan 27 2006 - 12:58:39 PST)
Priti Hansia
- RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 20:29:03 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 03:50:36 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 02:51:13 PST)
- AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 01:58:04 PST)
Ray Luo
- Re: AMBER: Q: results from PB solver in example no.3 (Wed Jan 04 2006 - 18:45:28 PST)
Robyn Ayscue
- Re: AMBER: problem with ssh and xleap (Mon Jan 02 2006 - 18:33:13 PST)
Ross Walker
- RE: AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 14:03:31 PST)
- RE: AMBER: parallel compile problems on amber8 (Tue Jan 31 2006 - 14:04:52 PST)
- RE: AMBER: NAD parameters (Mon Jan 30 2006 - 08:34:20 PST)
- RE: AMBER: A few problems on the parameterisation of a Glutamine residue (Wed Jan 18 2006 - 10:32:25 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue (Mon Jan 16 2006 - 08:44:11 PST)
- RE: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 08:44:11 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 08:49:17 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue (Fri Jan 13 2006 - 08:44:12 PST)
- RE: AMBER: About tleap (Thu Jan 12 2006 - 12:08:14 PST)
- RE: AMBER: SHAKE - ntc = 3 (Mon Jan 09 2006 - 14:51:01 PST)
- RE: AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 10:01:39 PST)
- RE: AMBER: Where to modify the atom type in sander? (Thu Jan 05 2006 - 08:12:34 PST)
S.Sundar Raman
- AMBER: regarding Hydrogen bond analysis (Mon Jan 09 2006 - 19:19:15 PST)
Sai Kumar Ramadugu
- Re: AMBER: Problem in Antechamber (Thu Jan 26 2006 - 20:46:42 PST)
- Re: AMBER: Problem in Antechamber (Thu Jan 12 2006 - 22:01:46 PST)
- AMBER: Problem in Antechamber (Tue Jan 10 2006 - 03:17:53 PST)
Scott Brozell
- Re: AMBER: Problem in compiling sander with MMTSB (Tue Jan 31 2006 - 21:54:56 PST)
- Re: AMBER: Problem in compiling sander with MMTSB (Mon Jan 30 2006 - 19:44:06 PST)
snowyowls
- AMBER: strange result of mm/pbsa (Mon Jan 09 2006 - 20:43:11 PST)
Steve Gwaltney
- AMBER: Na+ with GB/SA? (Thu Jan 12 2006 - 09:59:22 PST)
Sukjoon Yoon
- AMBER: Decomposed GB energy in idecomp=3 option (Mon Jan 30 2006 - 18:13:27 PST)
Thomas Cheatham
- Re: AMBER: problem in center command (Fri Jan 20 2006 - 19:37:49 PST)
Thomas E. Cheatham, III
- Re: AMBER: ptraj grid output (Thu Jan 19 2006 - 10:47:05 PST)
- Re: AMBER: Trimming ptraj output (Fri Jan 13 2006 - 09:37:45 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 08:59:35 PST)
- Re: AMBER: PTRAJ generating wrong dihedral angles (Tue Jan 10 2006 - 11:42:42 PST)
- Re: AMBER: creating a RST file from specific set of binpos/crd file (Fri Jan 06 2006 - 09:53:51 PST)
Tim Meyer
- AMBER: amber atom type -> length of name (Wed Jan 11 2006 - 11:22:22 PST)
- Re: AMBER: GLUTATHIONE (Wed Jan 11 2006 - 11:13:11 PST)
Tomimoto_Masaki.takeda.co.jp
- AMBER: Q: results from PB solver in example no.3 (Wed Jan 04 2006 - 15:09:42 PST)
tonglei
- AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number? (Sun Jan 08 2006 - 18:36:30 PST)
Toomas Kaevand
- AMBER: AMBER 7 and restrained bonds. (Thu Jan 26 2006 - 07:27:28 PST)
Varsha Goyal
- AMBER: About placing counter ions (Tue Jan 31 2006 - 10:23:03 PST)
- AMBER: About tleap (Thu Jan 12 2006 - 10:28:04 PST)
- AMBER: About preparing Zn.lib (Wed Jan 11 2006 - 17:21:26 PST)
Vlad Cojocaru
- AMBER: ptraj PCA: projection mask bug?? (Wed Jan 25 2006 - 05:28:42 PST)
- AMBER: ptraj PCA (Tue Jan 24 2006 - 08:02:20 PST)
- Re: AMBER: amber: problem in center command (Fri Jan 20 2006 - 01:48:42 PST)
- AMBER: ptraj grid output (Thu Jan 19 2006 - 10:25:49 PST)
- AMBER: Re: RE：AMBER: the problem of mdcrd (Wed Jan 18 2006 - 01:48:36 PST)
- AMBER: Re: RE：AMBER: the problem of mdcrd (Tue Jan 17 2006 - 04:40:41 PST)
- Re: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 01:55:45 PST)
- Re: AMBER: heme improper torsions (Mon Jan 16 2006 - 01:50:50 PST)
- AMBER: analysing water behavior during MD (Fri Jan 13 2006 - 07:17:06 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:25:56 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 09:13:58 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 07:51:57 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 07:42:41 PST)
- AMBER: stripping trajectories: ptraj versus Carnal (Thu Jan 12 2006 - 06:19:17 PST)
- AMBER: ptraj mask question (Thu Jan 12 2006 - 02:50:37 PST)
xiphias xie
- Re: AMBER: problem in center command (Fri Jan 20 2006 - 17:30:44 PST)
- AMBER: amber: problem in center command (Thu Jan 19 2006 - 18:36:27 PST)
- RE：AMBER: the problem of mdcrd (Wed Jan 18 2006 - 00:54:18 PST)
- RE：AMBER: the problem of mdcrd (Mon Jan 16 2006 - 23:52:03 PST)
- 回复： Re: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 18:23:00 PST)
- 回复： RE: AMBER: the problem of mdcrd (Mon Jan 16 2006 - 18:13:53 PST)
- AMBER: the problem of mdcrd (Mon Jan 16 2006 - 01:16:09 PST)
zgleo
- AMBER: About the unit of the projection onto eigenvectors (Tue Jan 17 2006 - 01:58:39 PST)
zhli_2000.126.com
- AMBER: Where to modify the atom type in sander? (Thu Jan 05 2006 - 01:21:20 PST)

Amber Archive Jan 2006 by author