AMBER Archive (2006) - Jan 2006 By Subject

202 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Sun Jan 01 2006 - 17:08:17 CST
Ending: Tue Jan 31 2006 - 23:54:56 CST

AMBER: A few problems on the parameterisation of a Glutamine residue
- Ross Walker (Wed Jan 18 2006 - 12:32:25 CST)
- Jason K (Wed Jan 18 2006 - 12:12:16 CST)
AMBER: about mmpbsa
- linfu (Mon Jan 09 2006 - 19:17:15 CST)
AMBER: About placing counter ions
- Varsha Goyal (Tue Jan 31 2006 - 12:23:03 CST)
AMBER: About preparing Zn.lib
- Ilyas Yildirim (Thu Jan 12 2006 - 01:46:03 CST)
- Varsha Goyal (Wed Jan 11 2006 - 19:21:26 CST)
AMBER: About the unit of the projection onto eigenvectors
- David A. Case (Fri Jan 27 2006 - 16:20:17 CST)
- zgleo (Tue Jan 17 2006 - 03:58:39 CST)
AMBER: About tleap
- Ross Walker (Thu Jan 12 2006 - 14:08:14 CST)
- Varsha Goyal (Thu Jan 12 2006 - 12:28:04 CST)
AMBER: ACTIVE SITE
- Claire Zerafa (Mon Jan 16 2006 - 08:06:52 CST)
AMBER: amber
- alexandratm_at_sapo.pt (Mon Jan 09 2006 - 05:31:56 CST)
AMBER: AMBER 7 and restrained bonds.
- David A. Case (Thu Jan 26 2006 - 10:26:42 CST)
- Toomas Kaevand (Thu Jan 26 2006 - 09:27:28 CST)
AMBER: Amber 8 install problem
- Andreas Svrcek-Seiler (Wed Jan 18 2006 - 05:10:38 CST)
- Andrew Box (Tue Jan 17 2006 - 22:50:21 CST)
AMBER: AMBER 8.0 : Octane Implicit Solvent?
- David A. Case (Tue Jan 24 2006 - 13:09:32 CST)
- Guillaume Bollot (Tue Jan 24 2006 - 10:25:42 CST)
AMBER: amber atom type -> length of name
- David A. Case (Thu Jan 12 2006 - 01:59:48 CST)
- Tim Meyer (Wed Jan 11 2006 - 13:22:22 CST)
AMBER: amber: problem in center command
- Vlad Cojocaru (Fri Jan 20 2006 - 03:48:42 CST)
- xiphias xie (Thu Jan 19 2006 - 20:36:27 CST)
AMBER: anal vs sander
- David A. Case (Fri Jan 27 2006 - 17:28:51 CST)
- Piotr Cieplak (Fri Jan 27 2006 - 16:59:13 CST)
- David A. Case (Fri Jan 27 2006 - 15:33:57 CST)
- Piotr Cieplak (Fri Jan 27 2006 - 14:58:39 CST)
AMBER: analysing water behavior during MD
- Fabian Boes (Fri Jan 13 2006 - 10:22:01 CST)
- Vlad Cojocaru (Fri Jan 13 2006 - 09:17:06 CST)
AMBER: antechamber
- David Case (Thu Jan 26 2006 - 17:48:55 CST)
- ping jiang (Thu Jan 26 2006 - 17:18:29 CST)
AMBER: antechamber problem
- Baker, Bo-Yang (Mon Jan 02 2006 - 18:23:40 CST)
AMBER: ATCOR.dat format
- Kateryna Miroshnychenko (Thu Jan 12 2006 - 10:43:05 CST)
AMBER: atom type "O3" not recognized by XLeap
- David A. Case (Fri Jan 27 2006 - 16:01:43 CST)
- Kenley Barrett (Fri Jan 27 2006 - 11:32:48 CST)
AMBER: base-base interaction
- Carlos Simmerling (Fri Jan 13 2006 - 12:07:57 CST)
- Douali, Latifa (Fri Jan 13 2006 - 11:54:32 CST)
AMBER: bugfix for impropers in parmchk
- David Mobley (Fri Jan 20 2006 - 12:23:39 CST)
- David Mobley (Fri Jan 20 2006 - 12:21:49 CST)
- David A. Case (Wed Jan 18 2006 - 20:04:36 CST)
- Kateryna Miroshnychenko (Wed Jan 18 2006 - 08:48:55 CST)
AMBER: Charges from NMR spin densities
- David A. Case (Fri Jan 27 2006 - 10:57:32 CST)
- David LeBard (Thu Jan 26 2006 - 17:33:50 CST)
AMBER: Charges of enantiomers for Amber8
- FyD (Thu Jan 26 2006 - 01:53:43 CST)
- lily ferreira (Thu Jan 26 2006 - 00:46:53 CST)
- FyD (Wed Jan 25 2006 - 05:41:47 CST)
- FyD (Wed Jan 25 2006 - 03:38:36 CST)
- lily ferreira (Wed Jan 25 2006 - 02:01:24 CST)
AMBER: Could you help me about mmpbsa! thank you!
- linfu (Sun Jan 08 2006 - 03:28:13 CST)
AMBER: creating a RST file from specific set of binpos/crd file
- Ross Walker (Fri Jan 06 2006 - 12:01:39 CST)
- Thomas E. Cheatham, III (Fri Jan 06 2006 - 11:53:51 CST)
- Baird, Jamie \(bairdje\) (Fri Jan 06 2006 - 11:33:00 CST)
AMBER: Decomposed GB energy in idecomp=3 option
- Sukjoon Yoon (Mon Jan 30 2006 - 20:13:27 CST)
AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS
- Carlos Simmerling (Thu Jan 12 2006 - 16:10:58 CST)
- Ilyas Yildirim (Thu Jan 12 2006 - 16:00:24 CST)
- Carlos Simmerling (Thu Jan 12 2006 - 07:04:46 CST)
- Ilyas Yildirim (Thu Jan 12 2006 - 01:43:06 CST)
AMBER: Gibbs pmf calculation
- Atsutoshi Okabe (Wed Jan 11 2006 - 04:14:30 CST)
AMBER: GLUTATHIONE
- Tim Meyer (Wed Jan 11 2006 - 13:13:11 CST)
- Ilyas Yildirim (Wed Jan 11 2006 - 09:38:56 CST)
- Joachim Reichelt (Wed Jan 11 2006 - 08:40:30 CST)
AMBER: h-bond
- Gustavo Pierdominici Sottile (Fri Jan 27 2006 - 08:59:07 CST)
AMBER: heme improper torsions
- David A. Case (Mon Jan 16 2006 - 10:46:47 CST)
- Vlad Cojocaru (Mon Jan 16 2006 - 03:50:50 CST)
- nkyx_at_sohu.com (Mon Jan 16 2006 - 02:55:38 CST)
AMBER: How to run mm_pbsa_statistics.pl?
- Peng Tao (Tue Jan 10 2006 - 09:49:00 CST)
- Peng Tao (Thu Jan 05 2006 - 17:11:42 CST)
- Peng Tao (Thu Jan 05 2006 - 07:39:19 CST)
- Holger Gohlke (Wed Jan 04 2006 - 11:27:05 CST)
- Peng Tao (Wed Jan 04 2006 - 07:51:55 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: IGB=10
- Ahammadunny Pathiaseril (Wed Jan 18 2006 - 09:53:25 CST)
AMBER: Installation of AMBER8 on a PC with a Pentium EE type
- Amber admin (Fri Jan 06 2006 - 15:36:19 CST)
AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU
- David Mathews (Sun Jan 01 2006 - 17:29:40 CST)
- David Mathews (Sun Jan 01 2006 - 17:08:17 CST)
AMBER: is there any relationship between RMSD and B-factor?
- Andy Purkiss (Thu Jan 19 2006 - 07:19:06 CST)
- Carlos Simmerling (Thu Jan 19 2006 - 06:59:39 CST)
- haixiao jin (Wed Jan 18 2006 - 22:58:28 CST)
- Carlos Simmerling (Wed Jan 18 2006 - 21:53:26 CST)
- haixiao jin (Wed Jan 18 2006 - 21:30:33 CST)
AMBER: Leap
- Bill Ross (Wed Jan 04 2006 - 16:02:20 CST)
- Joseph Fernandez (Wed Jan 04 2006 - 15:36:13 CST)
AMBER: Leap compilation issues
- Jiten (Tue Jan 10 2006 - 21:19:14 CST)
AMBER: lifetimes
- Gustavo Pierdominici Sottile (Mon Jan 30 2006 - 09:15:55 CST)
AMBER: Ligand charge
- Bill Ross (Thu Jan 05 2006 - 12:24:18 CST)
- Ilyas Yildirim (Thu Jan 05 2006 - 00:02:42 CST)
- David Mobley (Wed Jan 04 2006 - 13:43:54 CST)
- bybaker_at_itsa.ucsf.edu (Wed Jan 04 2006 - 12:51:57 CST)
AMBER: minimalization prior to nmode analysis, is it necessary?
- Adrian Roitberg (Thu Jan 05 2006 - 20:38:51 CST)
- David A. Case (Thu Jan 05 2006 - 19:56:26 CST)
- Magne Olufsen (Wed Jan 04 2006 - 11:42:21 CST)
AMBER: MM-PBSA
- Jianyin Shao (Tue Jan 31 2006 - 11:08:09 CST)
- Douali, Latifa (Wed Jan 25 2006 - 17:03:06 CST)
AMBER: monosaccharide residues
- Fren T (Tue Jan 24 2006 - 16:20:03 CST)
AMBER: mpich Amber7 problem
- Jan Dohnalek (Wed Jan 11 2006 - 04:32:18 CST)
- Petr Kulhanek (Wed Jan 11 2006 - 03:27:01 CST)
- linfu (Wed Jan 11 2006 - 03:27:57 CST)
- Jan Dohnalek (Tue Jan 10 2006 - 08:31:38 CST)
AMBER: MPICH on OpenMosix
- Jan Dohnalek (Mon Jan 16 2006 - 07:21:04 CST)
AMBER: Na+ with GB/SA?
- David A. Case (Thu Jan 12 2006 - 16:24:17 CST)
- Steve Gwaltney (Thu Jan 12 2006 - 11:59:22 CST)
AMBER: NAD parameters
- Ross Walker (Mon Jan 30 2006 - 10:34:20 CST)
- ivan_at_mmb.pcb.ub.es (Mon Jan 30 2006 - 10:20:19 CST)
- alexandra.marques_at_fc.up.pt (Mon Jan 30 2006 - 10:04:43 CST)
AMBER: nmode calculations error
- Jiten (Tue Jan 17 2006 - 07:58:53 CST)
AMBER: parallel compile problems on amber8
- Ross Walker (Tue Jan 31 2006 - 16:03:31 CST)
- Ross Walker (Tue Jan 31 2006 - 16:04:52 CST)
- hayden (Tue Jan 31 2006 - 12:55:34 CST)
AMBER: parameters for C=S
- David A. Case (Mon Jan 09 2006 - 17:04:52 CST)
- alexandra.marques_at_fc.up.pt (Mon Jan 09 2006 - 08:53:30 CST)
AMBER: partial charge glycam
- kkirschn_at_hamilton.edu (Thu Jan 26 2006 - 08:49:35 CST)
- FyD (Wed Jan 25 2006 - 03:23:06 CST)
- Kevin Murphy (Tue Jan 24 2006 - 06:18:05 CST)
- FyD (Sat Jan 21 2006 - 01:30:37 CST)
- kkirschn_at_hamilton.edu (Fri Jan 20 2006 - 09:39:14 CST)
- Kevin Murphy (Fri Jan 20 2006 - 05:28:27 CST)
AMBER: Problem in Antechamber
- Sai Kumar Ramadugu (Thu Jan 26 2006 - 22:46:42 CST)
- Junmei Wang (Thu Jan 19 2006 - 17:02:39 CST)
- Sai Kumar Ramadugu (Fri Jan 13 2006 - 00:01:46 CST)
- David A. Case (Thu Jan 12 2006 - 19:40:50 CST)
- Sai Kumar Ramadugu (Tue Jan 10 2006 - 05:17:53 CST)
AMBER: problem in center command
- Thomas Cheatham (Fri Jan 20 2006 - 21:37:49 CST)
- Bill Ross (Fri Jan 20 2006 - 19:40:51 CST)
- xiphias xie (Fri Jan 20 2006 - 19:30:44 CST)
AMBER: Problem in compiling AMBER8 parallel version
- luckyang_at_gmail.com (Tue Jan 31 2006 - 17:51:06 CST)
- David LeBard (Tue Jan 31 2006 - 17:23:16 CST)
- luckyang_at_gmail.com (Tue Jan 31 2006 - 17:09:09 CST)
AMBER: Problem in compiling sander with MMTSB
- Scott Brozell (Tue Jan 31 2006 - 23:54:56 CST)
- luckyang_at_gmail.com (Tue Jan 31 2006 - 00:10:15 CST)
- Scott Brozell (Mon Jan 30 2006 - 21:44:06 CST)
- luckyang_at_gmail.com (Mon Jan 30 2006 - 20:06:32 CST)
AMBER: problem in saving parameter file for non-standard residue
- David A. Case (Mon Jan 16 2006 - 13:44:22 CST)
- Ross Walker (Mon Jan 16 2006 - 10:44:11 CST)
- Priti Hansia (Fri Jan 13 2006 - 22:29:03 CST)
- Ross Walker (Fri Jan 13 2006 - 10:49:17 CST)
- Ross Walker (Fri Jan 13 2006 - 10:44:12 CST)
- Priti Hansia (Fri Jan 13 2006 - 05:50:36 CST)
- Ilyas Yildirim (Fri Jan 13 2006 - 05:10:52 CST)
- Priti Hansia (Fri Jan 13 2006 - 04:51:13 CST)
- Ilyas Yildirim (Fri Jan 13 2006 - 04:40:56 CST)
- Priti Hansia (Fri Jan 13 2006 - 03:58:04 CST)
AMBER: problem with ssh and xleap
- Robyn Ayscue (Mon Jan 02 2006 - 20:33:13 CST)
- Peter Gannett (Mon Jan 02 2006 - 10:26:18 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: ptraj distance matrix
- Holger Gohlke (Wed Jan 11 2006 - 02:09:33 CST)
- Holly Freedman (Tue Jan 10 2006 - 16:03:36 CST)
AMBER: PTRAJ generating wrong dihedral angles
- Thomas E. Cheatham, III (Tue Jan 10 2006 - 13:42:42 CST)
- hayden (Tue Jan 10 2006 - 05:40:05 CST)
AMBER: ptraj grid output
- Thomas E. Cheatham, III (Thu Jan 19 2006 - 12:47:05 CST)
- Vlad Cojocaru (Thu Jan 19 2006 - 12:25:49 CST)
AMBER: ptraj mask question
- Vlad Cojocaru (Thu Jan 12 2006 - 04:50:37 CST)
AMBER: ptraj PCA
- Vlad Cojocaru (Tue Jan 24 2006 - 10:02:20 CST)
- Marcela Madrid (Thu Jan 19 2006 - 19:04:46 CST)
AMBER: ptraj PCA: projection mask bug??
- Vlad Cojocaru (Wed Jan 25 2006 - 07:28:42 CST)
AMBER: Q: results from PB solver in example no.3
- Ray Luo (Wed Jan 04 2006 - 20:45:28 CST)
- Tomimoto_Masaki_at_takeda.co.jp (Wed Jan 04 2006 - 17:09:42 CST)
AMBER: regarding Hydrogen bond analysis
- David A. Case (Tue Jan 10 2006 - 02:45:50 CST)
- S.Sundar Raman (Mon Jan 09 2006 - 21:19:15 CST)
AMBER: Release of RESP ESP charge DDatabase
- FyD (Mon Jan 16 2006 - 10:04:47 CST)
AMBER: requirement of delphi for mm_pbsa
- Holger Gohlke (Wed Jan 04 2006 - 11:09:46 CST)
- David A. Case (Wed Jan 04 2006 - 10:22:53 CST)
- Manish Datt (Tue Jan 03 2006 - 12:46:53 CST)
AMBER: rms in principal component analysis
- David A. Case (Wed Jan 18 2006 - 12:52:51 CST)
- Lydia (Wed Jan 18 2006 - 11:43:03 CST)
- David A. Case (Wed Jan 18 2006 - 10:30:51 CST)
- Lydia (Tue Jan 17 2006 - 14:54:32 CST)
AMBER: SHAKE - ntc = 3
- Jennie Thomas (Mon Jan 09 2006 - 19:54:09 CST)
- Bill Ross (Mon Jan 09 2006 - 18:39:12 CST)
- Jennie Thomas (Mon Jan 09 2006 - 18:07:47 CST)
- David A. Case (Mon Jan 09 2006 - 16:59:46 CST)
- Ross Walker (Mon Jan 09 2006 - 16:51:01 CST)
- Jennie Thomas (Mon Jan 09 2006 - 16:38:24 CST)
- David A. Case (Fri Jan 06 2006 - 19:26:55 CST)
- Jennie Thomas (Fri Jan 06 2006 - 19:05:09 CST)
AMBER: strange result of mm/pbsa
- snowyowls (Mon Jan 09 2006 - 22:43:11 CST)
AMBER: stripping trajectories: ptraj versus Carnal
- Vlad Cojocaru (Thu Jan 12 2006 - 11:25:56 CST)
- Vlad Cojocaru (Thu Jan 12 2006 - 11:13:58 CST)
- Thomas E. Cheatham, III (Thu Jan 12 2006 - 10:59:35 CST)
- Vlad Cojocaru (Thu Jan 12 2006 - 09:51:57 CST)
- Vlad Cojocaru (Thu Jan 12 2006 - 09:42:41 CST)
- Carlos Simmerling (Thu Jan 12 2006 - 09:04:45 CST)
- Andy Purkiss (Thu Jan 12 2006 - 09:01:09 CST)
- Andy Purkiss (Thu Jan 12 2006 - 08:52:14 CST)
- Vlad Cojocaru (Thu Jan 12 2006 - 08:19:17 CST)
AMBER: the problem of mdcrd
- xiphias xie (Mon Jan 16 2006 - 20:23:00 CST)
- xiphias xie (Mon Jan 16 2006 - 20:13:53 CST)
- Ross Walker (Mon Jan 16 2006 - 10:44:11 CST)
- Vlad Cojocaru (Mon Jan 16 2006 - 03:55:45 CST)
- xiphias xie (Mon Jan 16 2006 - 03:16:09 CST)
AMBER: Trimming ptraj output
- Andy Purkiss (Fri Jan 13 2006 - 12:03:54 CST)
- Thomas E. Cheatham, III (Fri Jan 13 2006 - 11:37:45 CST)
- Andy Purkiss (Fri Jan 13 2006 - 11:29:00 CST)
AMBER: water molecules with in 3 angstroms to the solute
- Ilyas Yildirim (Tue Jan 03 2006 - 18:40:07 CST)
- Ilyas Yildirim (Tue Jan 03 2006 - 03:05:24 CST)
- nag raj (Mon Jan 02 2006 - 22:47:06 CST)
AMBER: Where to modify the atom type in sander?
- Ross Walker (Thu Jan 05 2006 - 10:12:34 CST)
- zhli_2000_at_126.com (Thu Jan 05 2006 - 03:21:20 CST)
AMBER: Workshops
- a a (Wed Jan 11 2006 - 08:27:59 CST)
RE£ºAMBER: the problem of mdcrd
- Vlad Cojocaru (Wed Jan 18 2006 - 03:48:36 CST)
- xiphias xie (Wed Jan 18 2006 - 02:54:18 CST)
- Carlos Simmerling (Tue Jan 17 2006 - 06:56:58 CST)
- Vlad Cojocaru (Tue Jan 17 2006 - 06:40:41 CST)
- xiphias xie (Tue Jan 17 2006 - 01:52:03 CST)

Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:15 CST

202 messages sorted by: [ author ] [ date ] [ thread ]
About this archive