Amber Archive Apr 2004: by subject

a new question
- Viktor Hornak (Mon Apr 12 2004 - 20:02:35 PDT)
AMBER:
- Holger Gohlke (Thu Apr 08 2004 - 07:20:51 PDT)
- Beale, John (Thu Apr 08 2004 - 06:04:04 PDT)
- riccardodesantis.fastwebnet.it (Tue Apr 06 2004 - 23:02:57 PDT)
- anshul.imtech.res.in (Tue Apr 06 2004 - 14:58:07 PDT)
AMBER: "matrix" in ptraj
- Thomas E. Cheatham, III (Sat Apr 24 2004 - 17:30:34 PDT)
- Sichun Yang (Sat Apr 24 2004 - 16:20:50 PDT)
- Holger Gohlke (Sat Apr 24 2004 - 04:47:41 PDT)
- Sichun Yang (Fri Apr 23 2004 - 18:19:28 PDT)
AMBER: "No radius found for F" error and vdw radii for F in MMPBSA
- Ming Lei (Tue Apr 20 2004 - 08:47:40 PDT)
AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms
- David A. Case (Wed Apr 28 2004 - 10:56:10 PDT)
- Jiten (Tue Apr 27 2004 - 19:29:25 PDT)
AMBER: a general question about the mmpbsa method
- a b (Wed Apr 28 2004 - 20:51:00 PDT)
AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH
- Robert Duke (Tue Apr 27 2004 - 15:36:51 PDT)
- David E. Konerding DSD Staff (Tue Apr 27 2004 - 15:11:33 PDT)
- Robert Duke (Tue Apr 27 2004 - 11:29:35 PDT)
AMBER: Alignment tensor for Sander RDCs
- David A. Case (Fri Apr 02 2004 - 09:46:24 PST)
- tim (Fri Apr 02 2004 - 06:47:47 PST)
AMBER: AMBER 7 Installation
- David A. Case (Fri Apr 02 2004 - 17:37:57 PST)
- Ilyas Yildirim (Fri Apr 02 2004 - 15:17:09 PST)
AMBER: Amber 7 on SGI: Sander MPI problem
- Rohn Wood (Wed Apr 14 2004 - 16:48:58 PDT)
- Rohn Wood (Wed Apr 14 2004 - 10:28:17 PDT)
- Tru Huynh (Wed Apr 14 2004 - 05:45:08 PDT)
- David A. Case (Tue Apr 13 2004 - 17:37:04 PDT)
- Rohn Wood (Tue Apr 13 2004 - 15:34:12 PDT)
AMBER: Amber 8 ptraj segmentation fault
- Sivakolundu, Sivashankar (Tue Apr 06 2004 - 22:49:08 PDT)
AMBER: Amber and Linux compilation
- Teletchéa Stéphane (Wed Apr 14 2004 - 08:08:29 PDT)
- Andreas Svrcek-Seiler (Wed Apr 14 2004 - 07:44:21 PDT)
- Raj Badhan (Wed Apr 14 2004 - 07:17:18 PDT)
- Ye Mei (Wed Apr 14 2004 - 06:26:40 PDT)
- Raj Badhan (Wed Apr 14 2004 - 05:54:54 PDT)
- Raj Badhan (Wed Apr 14 2004 - 04:59:34 PDT)
- Ye Mei (Wed Apr 14 2004 - 04:52:55 PDT)
- Raj Badhan (Wed Apr 14 2004 - 04:26:36 PDT)
AMBER: AMBER Gibbs Memory problem
- David A. Case (Tue Apr 27 2004 - 12:04:15 PDT)
- Jiten (Tue Apr 27 2004 - 09:01:09 PDT)
AMBER: amber/pmemd with mpiexec
- Robert Duke (Mon Apr 12 2004 - 07:41:22 PDT)
- Lubos Vrbka (Sun Apr 11 2004 - 07:00:36 PDT)
- Robert Duke (Sat Apr 10 2004 - 10:21:15 PDT)
- Lubos Vrbka (Sat Apr 10 2004 - 09:50:30 PDT)
AMBER: Amber8 compilation error
- Bill Ross (Fri Apr 30 2004 - 13:50:28 PDT)
- David A. Case (Fri Apr 30 2004 - 11:31:57 PDT)
- Arvind (Fri Apr 30 2004 - 10:04:02 PDT)
AMBER: amber8 performance on linux cluster
- Yong Duan (Tue Apr 27 2004 - 10:47:21 PDT)
- Lubos Vrbka (Tue Apr 27 2004 - 10:26:14 PDT)
- quch quch (Tue Apr 27 2004 - 10:05:45 PDT)
AMBER: amber8 tutorial
- Ross Walker (Sun Apr 04 2004 - 19:45:52 PDT)
- Viktor Hornak (Sun Apr 04 2004 - 19:03:56 PDT)
- Patil, Sachin (Sun Apr 04 2004 - 17:03:20 PDT)
AMBER: ANAL: how can i buld the anal.in file?
- David A. Case (Wed Apr 07 2004 - 08:21:53 PDT)
- riccardodesantis.fastwebnet.it (Tue Apr 06 2004 - 23:14:49 PDT)
AMBER: Angle Restraining
- David A. Case (Fri Apr 30 2004 - 08:39:27 PDT)
- Pooja Narang (Fri Apr 30 2004 - 00:17:30 PDT)
AMBER: antechamber bcctype.c typo
- David A. Case (Wed Apr 28 2004 - 14:42:11 PDT)
- Chris Moth (Thu Apr 22 2004 - 05:07:32 PDT)
AMBER: Antechamber compilation error
- David A. Case (Mon Apr 05 2004 - 10:12:05 PDT)
- Arvind (Mon Apr 05 2004 - 09:22:21 PDT)
AMBER: Antechamber compilation: leap error
- Ye Mei (Mon Apr 12 2004 - 04:55:11 PDT)
- Arvind (Mon Apr 12 2004 - 04:05:58 PDT)
AMBER: antechamber: frcmod parameter need revision
- atchara.mercury.hec.utah.edu (Mon Apr 05 2004 - 14:11:12 PDT)
AMBER: Antechamber: problems with bcc correction
- David A. Case (Sun Apr 25 2004 - 00:26:59 PDT)
- Oliver Hucke (Fri Apr 23 2004 - 15:08:47 PDT)
AMBER: atomicfluct in ptraj
- Qiang Lu (Wed Apr 14 2004 - 15:06:32 PDT)
- Holger Gohlke (Wed Apr 14 2004 - 12:14:47 PDT)
- Qiang Lu (Wed Apr 14 2004 - 11:12:06 PDT)
AMBER: Bond type in leap
- Bill Ross (Thu Apr 22 2004 - 09:53:33 PDT)
- anshul.imtech.res.in (Thu Apr 22 2004 - 12:22:31 PDT)
AMBER: bug of leap?
- Chris Moth (Thu Apr 08 2004 - 09:10:06 PDT)
- Ye Mei (Wed Apr 07 2004 - 19:40:29 PDT)
- Ye Mei (Wed Apr 07 2004 - 19:29:07 PDT)
- Ye Mei (Wed Apr 07 2004 - 19:27:11 PDT)
AMBER: Carnal in Amber7
- Bill Ross (Thu Apr 08 2004 - 11:16:02 PDT)
- Sichun Yang (Wed Apr 07 2004 - 21:03:35 PDT)
AMBER: CHARMM PSF to PRMTOP
- Gabbar Daaku (Thu Apr 29 2004 - 14:42:33 PDT)
AMBER: compile amber8 in linux with ifort
- quch quch (Fri Apr 23 2004 - 14:50:52 PDT)
- Viktor Hornak (Fri Apr 23 2004 - 14:49:49 PDT)
- Ross Walker (Fri Apr 23 2004 - 14:42:39 PDT)
- Ross Walker (Fri Apr 23 2004 - 14:23:21 PDT)
- quch quch (Fri Apr 23 2004 - 14:08:05 PDT)
AMBER: compiling Amber 8
- Bill Ross (Fri Apr 16 2004 - 12:45:06 PDT)
- Bill Ross (Fri Apr 16 2004 - 12:36:44 PDT)
- Ross Walker (Fri Apr 16 2004 - 11:47:36 PDT)
- Beale, John (Fri Apr 16 2004 - 10:23:23 PDT)
- Bill Ross (Tue Apr 13 2004 - 09:38:58 PDT)
- Andreas Svrcek-Seiler (Tue Apr 13 2004 - 02:57:29 PDT)
- Robert Duke (Mon Apr 12 2004 - 07:22:27 PDT)
- Viktor Hornak (Mon Apr 12 2004 - 06:53:29 PDT)
- Beale, John (Mon Apr 12 2004 - 06:44:25 PDT)
AMBER: Creating Parmtop files for NAMD
- Thomas C. Bishop (Wed Apr 14 2004 - 06:49:23 PDT)
- M. L. Dodson (Tue Apr 13 2004 - 18:39:26 PDT)
- Edward Patrick Obrien (Tue Apr 13 2004 - 17:37:52 PDT)
AMBER: Dipole moment changes during MD
- Jiten (Fri Apr 09 2004 - 17:48:03 PDT)
- Ross Walker (Fri Apr 09 2004 - 14:56:48 PDT)
- Jiten (Fri Apr 09 2004 - 11:05:01 PDT)
- Ross Walker (Fri Apr 09 2004 - 09:48:29 PDT)
- Jiten (Thu Apr 08 2004 - 18:31:17 PDT)
AMBER: distance dependent dielectric
- Viktor Hornak (Wed Apr 21 2004 - 05:23:31 PDT)
- anshul.imtech.res.in (Wed Apr 21 2004 - 08:30:49 PDT)
AMBER: distance measurement in carnal and ptraj
- Bill Ross (Fri Apr 16 2004 - 11:32:07 PDT)
- David A. Case (Fri Apr 16 2004 - 08:46:04 PDT)
- anshul.imtech.res.in (Fri Apr 16 2004 - 13:56:33 PDT)
AMBER: Do we have to optimize the structure in order to do MEP Calculations?
- Ilyas Yildirim (Tue Apr 20 2004 - 16:42:34 PDT)
- David A. Case (Tue Apr 20 2004 - 14:50:42 PDT)
- Ilyas Yildirim (Tue Apr 20 2004 - 13:51:55 PDT)
- David A. Case (Tue Apr 20 2004 - 13:29:47 PDT)
- Ilyas Yildirim (Tue Apr 20 2004 - 13:28:13 PDT)
- Ilyas Yildirim (Tue Apr 20 2004 - 13:13:09 PDT)
- David A. Case (Mon Apr 19 2004 - 14:45:34 PDT)
- Ilyas Yildirim (Mon Apr 19 2004 - 13:35:45 PDT)
AMBER: energy criteria.
- Chris Moth (Fri Apr 30 2004 - 11:03:39 PDT)
- David A. Case (Fri Apr 30 2004 - 08:36:13 PDT)
- anshul.imtech.res.in (Fri Apr 30 2004 - 13:51:04 PDT)
AMBER: equilibration does not start with SHAKE
- David A. Case (Fri Apr 09 2004 - 16:16:09 PDT)
- Oliver Hucke (Fri Apr 09 2004 - 15:30:55 PDT)
AMBER: error in antechamber
- David A. Case (Thu Apr 08 2004 - 07:58:42 PDT)
- anshul.imtech.res.in (Thu Apr 08 2004 - 10:36:57 PDT)
- David A. Case (Wed Apr 07 2004 - 08:27:43 PDT)
- Ilyas Yildirim (Wed Apr 07 2004 - 06:30:55 PDT)
- anshul.imtech.res.in (Wed Apr 07 2004 - 15:49:47 PDT)
AMBER: Error in building a molecule
- anshul.imtech.res.in (Mon Apr 05 2004 - 15:01:54 PDT)
AMBER: Error message while testing
- Scott Brozell (Mon Apr 12 2004 - 18:10:30 PDT)
- Alessio Comisso (Wed Apr 07 2004 - 04:53:24 PDT)
AMBER: esp or resp for all_amino94.lib
- Mikyung Seo (Fri Apr 30 2004 - 16:06:54 PDT)
AMBER: Euclidean distances
- Bill Ross (Thu Apr 22 2004 - 09:34:37 PDT)
- Wen Li (Thu Apr 22 2004 - 07:49:45 PDT)
AMBER: free energy perturbation
- David A. Case (Tue Apr 06 2004 - 18:26:37 PDT)
- Herbert Georg (Tue Apr 06 2004 - 10:03:51 PDT)
- Kristina Furse (Tue Apr 06 2004 - 09:53:39 PDT)
- David Smith (Tue Apr 06 2004 - 08:45:06 PDT)
- Herbert Georg (Tue Apr 06 2004 - 08:21:55 PDT)
AMBER: free energy perturbation questions
- hj zou (Sat Apr 17 2004 - 07:38:28 PDT)
AMBER: gaff "ha" atom type
- Oliver Hucke (Wed Apr 21 2004 - 13:38:20 PDT)
AMBER: Gaussian 98 Installation
- Ilyas Yildirim (Thu Apr 08 2004 - 13:52:05 PDT)
AMBER: gibbs calculation
- Carsten Detering (Tue Apr 06 2004 - 11:11:55 PDT)
AMBER: gibbs termination
- David A. Case (Wed Apr 14 2004 - 18:24:10 PDT)
- Bill Ross (Wed Apr 14 2004 - 13:16:50 PDT)
- Carsten Detering (Wed Apr 14 2004 - 12:17:29 PDT)
AMBER: Group in sander
- Chris Moth (Mon Apr 12 2004 - 12:20:37 PDT)
- Thomas E. Cheatham, III (Mon Apr 12 2004 - 12:30:46 PDT)
- Viktor Hornak (Mon Apr 12 2004 - 12:13:15 PDT)
- xiaowei li (Mon Apr 12 2004 - 12:05:29 PDT)
AMBER: how to check metal ion bonding ?
- Bill Ross (Tue Apr 13 2004 - 14:34:52 PDT)
- Oliver Hucke (Tue Apr 13 2004 - 13:28:09 PDT)
- Venkata S Koppuravuri (Tue Apr 13 2004 - 12:13:52 PDT)
AMBER: How to solve these warnings?
- Kristina Furse (Wed Apr 21 2004 - 13:35:57 PDT)
- Bill Ross (Wed Apr 21 2004 - 11:21:30 PDT)
- Jiten (Wed Apr 21 2004 - 05:06:41 PDT)
- Xiao He (Wed Apr 21 2004 - 01:37:40 PDT)
AMBER: how to use mm_pbsa_statistics.pl independently
- Holger Gohlke (Tue Apr 13 2004 - 10:06:43 PDT)
- Chris Moth (Tue Apr 13 2004 - 08:34:26 PDT)
- Jufang Shan (Mon Apr 12 2004 - 19:23:36 PDT)
AMBER: instalation of amber7 on SUN
- David A. Case (Sat Apr 24 2004 - 11:00:40 PDT)
- anshul.imtech.res.in (Thu Apr 22 2004 - 09:35:37 PDT)
- David A. Case (Tue Apr 20 2004 - 11:14:58 PDT)
- anshul.imtech.res.in (Tue Apr 20 2004 - 19:53:20 PDT)
AMBER: installing amber8 on a dual processor single box
- David A. Case (Fri Apr 02 2004 - 11:39:24 PST)
- Robert Duke (Fri Apr 02 2004 - 10:58:35 PST)
- Carsten Detering (Fri Apr 02 2004 - 10:37:46 PST)
AMBER: Intel fortran compiler and -static switch in older pmemd releases
- Robert Duke (Fri Apr 02 2004 - 13:35:45 PST)
- David E. Konerding DSD Staff (Fri Apr 02 2004 - 13:21:11 PST)
- Robert Duke (Fri Apr 02 2004 - 13:10:49 PST)
AMBER: Intel Fortran Compiler, 7.1 status
- Robert Duke (Mon Apr 19 2004 - 08:32:49 PDT)
AMBER: just sander not run
- David A. Case (Fri Apr 30 2004 - 08:34:47 PDT)
- Helios Chen (Fri Apr 30 2004 - 02:27:45 PDT)
AMBER: loading PDB problem in leap
- Jiten (Sun Apr 18 2004 - 20:57:16 PDT)
- Suwipa saen-oon (Sun Apr 18 2004 - 02:35:35 PDT)
AMBER: Mac OSX xleap compilation
- Mengjuei Hsieh (Fri Apr 02 2004 - 11:46:14 PST)
- Yusuf Abdulghani (Fri Apr 02 2004 - 11:16:14 PST)
- Mengjuei Hsieh (Thu Apr 01 2004 - 23:19:30 PST)
- Sergio Pantano (Thu Apr 01 2004 - 22:32:07 PST)
AMBER: MD for protein-carbohydrate complex
- Bill Ross (Thu Apr 22 2004 - 13:03:54 PDT)
- Mikyung Seo (Thu Apr 22 2004 - 13:03:33 PDT)
AMBER: memory problem in NMODE
- David A. Case (Mon Apr 19 2004 - 17:56:44 PDT)
- xhu1.memphis.edu (Mon Apr 19 2004 - 16:43:47 PDT)
- David A. Case (Mon Apr 19 2004 - 14:54:34 PDT)
- xhu1.memphis.edu (Mon Apr 19 2004 - 13:06:46 PDT)
AMBER: minimization of GLH
- David A. Case (Mon Apr 05 2004 - 10:06:39 PDT)
- Hailong Lin (Mon Apr 05 2004 - 08:51:47 PDT)
- David A. Case (Mon Apr 05 2004 - 08:26:27 PDT)
- Hailong Lin (Mon Apr 05 2004 - 04:57:31 PDT)
AMBER: mm_pbsa examples; delphi in mm_pbsa
- Holger Gohlke (Mon Apr 26 2004 - 06:11:28 PDT)
- Kazuo Koyano (Thu Apr 22 2004 - 01:34:03 PDT)
AMBER: mm_pbsa question: MAXAT=10000 exceeded
- Holger Gohlke (Wed Apr 28 2004 - 23:42:27 PDT)
- Fang, Jianwen (Wed Apr 28 2004 - 21:48:09 PDT)
AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly?
- David A. Case (Wed Apr 07 2004 - 08:19:27 PDT)
- Ilyas Yildirim (Tue Apr 06 2004 - 18:25:46 PDT)
- Ilyas Yildirim (Tue Apr 06 2004 - 17:27:31 PDT)
AMBER: more vlimit exceeded problems...
- David A. Case (Wed Apr 07 2004 - 08:06:31 PDT)
- Linda Prengaman (Tue Apr 06 2004 - 19:22:44 PDT)
AMBER: neutral residues
- Yong Duan (Mon Apr 26 2004 - 10:25:46 PDT)
- tim (Mon Apr 26 2004 - 07:26:09 PDT)
- Mikyung Seo (Mon Apr 26 2004 - 09:33:04 PDT)
AMBER: new atom and increase the number of bonds
- Tomas Hrobarik (Fri Apr 16 2004 - 07:01:56 PDT)
AMBER: new leap with old gibbs
- David A. Case (Tue Apr 06 2004 - 17:13:57 PDT)
- Carsten Detering (Tue Apr 06 2004 - 14:48:26 PDT)
- David A. Case (Tue Apr 06 2004 - 14:31:10 PDT)
- Carsten Detering (Tue Apr 06 2004 - 12:16:01 PDT)
AMBER: NMODE
- David A. Case (Fri Apr 09 2004 - 15:46:35 PDT)
- xiaowei li (Fri Apr 09 2004 - 13:20:23 PDT)
AMBER: non-isotropic pressure scaling
- Robert Duke (Sun Apr 18 2004 - 06:44:09 PDT)
- Lubos Vrbka (Wed Apr 14 2004 - 12:21:54 PDT)
- David A. Case (Wed Apr 14 2004 - 09:56:52 PDT)
- Lubos Vrbka (Wed Apr 14 2004 - 09:18:22 PDT)
- David A. Case (Wed Apr 14 2004 - 08:36:52 PDT)
- Lubos Vrbka (Wed Apr 14 2004 - 05:48:59 PDT)
AMBER: non-periodic simulation and box information !!
- Michael Crowley (Wed Apr 21 2004 - 10:32:58 PDT)
- Robert Duke (Wed Apr 21 2004 - 09:04:54 PDT)
- Pradipta Bandyopadhyay (Wed Apr 21 2004 - 08:56:31 PDT)
AMBER: NSNB parameter
- Robert Duke (Sat Apr 24 2004 - 20:05:51 PDT)
- David A. Case (Sat Apr 24 2004 - 13:13:11 PDT)
- Robert Duke (Sat Apr 24 2004 - 07:05:05 PDT)
- Chris Moth (Sat Apr 24 2004 - 05:31:55 PDT)
- Helios Chen (Fri Apr 23 2004 - 20:45:42 PDT)
AMBER: nucgen generated RNA duplex: leap problems
- Bill Ross (Wed Apr 21 2004 - 13:34:40 PDT)
- Arvind (Wed Apr 21 2004 - 13:23:28 PDT)
- Bill Ross (Wed Apr 21 2004 - 11:33:00 PDT)
- David A. Case (Tue Apr 20 2004 - 11:26:17 PDT)
- Skauge Tormod (Tue Apr 20 2004 - 08:03:09 PDT)
- Arvind (Tue Apr 20 2004 - 04:44:37 PDT)
AMBER: Optimizing a structure and the interpretation of it
- Kazuo Koyano (Sun Apr 25 2004 - 22:14:25 PDT)
- Ilyas Yildirim (Sat Apr 24 2004 - 16:08:14 PDT)
AMBER: overlap between HE and OE in GLH
- Hailong Lin (Tue Apr 27 2004 - 07:32:47 PDT)
- Yong Duan (Mon Apr 26 2004 - 10:24:32 PDT)
- Yong Duan (Mon Apr 26 2004 - 10:17:00 PDT)
- tim (Mon Apr 26 2004 - 07:11:08 PDT)
- Hailong Lin (Mon Apr 26 2004 - 08:49:36 PDT)
AMBER: Parameters for ions?
- nie beining (Fri Apr 02 2004 - 10:15:51 PST)
AMBER: parameters for neutral Arg
- Adrian E. Roitberg (Fri Apr 23 2004 - 14:05:03 PDT)
- Mikyung Seo (Fri Apr 23 2004 - 13:51:14 PDT)
AMBER: Parameters for nonpolar contribution to solvation
- Holger Gohlke (Sat Apr 24 2004 - 05:06:34 PDT)
- Thomas Steinbrecher (Fri Apr 23 2004 - 10:48:42 PDT)
AMBER: PARMSCAN
- Sergio Emanuel Galembeck (Mon Apr 26 2004 - 11:29:05 PDT)
AMBER: partition error in shake
- Scott Brozell (Tue Apr 27 2004 - 15:26:44 PDT)
- Guanglei Cui (Fri Apr 23 2004 - 08:18:19 PDT)
AMBER: pbsa
- rluo.uci.edu (Thu Apr 15 2004 - 11:14:34 PDT)
- Chenglong Li (Thu Apr 15 2004 - 10:26:51 PDT)
AMBER: PERT.charge problem in xleap
- Helios Chen (Fri Apr 02 2004 - 04:10:54 PST)
AMBER: PMEMD and ifort 8 update
- David A. Case (Tue Apr 27 2004 - 11:52:02 PDT)
- Robert Duke (Tue Apr 27 2004 - 11:08:05 PDT)
AMBER: pmemd and mpich - myrinet
- Lubos Vrbka (Tue Apr 27 2004 - 07:58:25 PDT)
- Lubos Vrbka (Sat Apr 24 2004 - 14:18:11 PDT)
- Robert Duke (Sat Apr 24 2004 - 05:31:59 PDT)
- Lubos Vrbka (Sat Apr 24 2004 - 03:50:02 PDT)
- Lubos Vrbka (Fri Apr 23 2004 - 11:18:36 PDT)
- Robert Duke (Fri Apr 23 2004 - 10:57:48 PDT)
- Lubos Vrbka (Fri Apr 23 2004 - 10:33:32 PDT)
- Robert Duke (Fri Apr 23 2004 - 09:23:37 PDT)
- Lubos Vrbka (Fri Apr 23 2004 - 08:59:31 PDT)
AMBER: PMEMD Problems...
- Robert Duke (Mon Apr 05 2004 - 21:38:58 PDT)
- Jon Gray (Mon Apr 05 2004 - 20:56:47 PDT)
- Robert Duke (Mon Apr 05 2004 - 14:13:24 PDT)
- Jon Gray (Mon Apr 05 2004 - 13:38:23 PDT)
AMBER: PMEMD scaling
- Robert Duke (Sun Apr 25 2004 - 08:24:11 PDT)
- Lubos Vrbka (Sun Apr 25 2004 - 07:07:43 PDT)
AMBER: Problem in loading a PDB file in Leap - Please help me
- Bill Ross (Sat Apr 17 2004 - 12:40:06 PDT)
- Mike (Sat Apr 17 2004 - 10:35:22 PDT)
- Bill Ross (Fri Apr 16 2004 - 22:55:43 PDT)
- Mike (Fri Apr 16 2004 - 22:19:02 PDT)
- tim (Wed Apr 14 2004 - 22:53:41 PDT)
- Mike (Wed Apr 14 2004 - 23:25:07 PDT)
AMBER: protein-carbohydrate complex
- Bill Ross (Thu Apr 22 2004 - 15:39:16 PDT)
- Mikyung Seo (Thu Apr 22 2004 - 15:27:31 PDT)
AMBER: ptraj
- ayongye.sunchem.chem.uga.edu (Tue Apr 13 2004 - 08:48:54 PDT)
- pengyo.UMDNJ.EDU (Mon Apr 12 2004 - 14:22:26 PDT)
- Thomas E. Cheatham, III (Mon Apr 12 2004 - 13:23:12 PDT)
- pengyo.UMDNJ.EDU (Mon Apr 12 2004 - 13:09:22 PDT)
AMBER: ptraj parser
- Viktor Hornak (Wed Apr 07 2004 - 09:20:40 PDT)
- Thomas C. Bishop (Wed Apr 07 2004 - 08:01:15 PDT)
AMBER: ptraj projections help
- Thomas C. Bishop (Mon Apr 19 2004 - 10:41:08 PDT)
AMBER: ptraj-6.5
- cailliez (Thu Apr 15 2004 - 02:42:36 PDT)
AMBER: Question about compiling PMEMD
- Robert Duke (Thu Apr 22 2004 - 05:10:47 PDT)
- Robert Duke (Thu Apr 22 2004 - 04:35:45 PDT)
- Tod Pascal (Wed Apr 21 2004 - 23:29:55 PDT)
- Robert Duke (Wed Apr 21 2004 - 05:27:02 PDT)
- Tod Pascal (Wed Apr 21 2004 - 00:21:40 PDT)
AMBER: question about image
- Thomas E. Cheatham, III (Mon Apr 05 2004 - 09:37:00 PDT)
- pengyo.UMDNJ.EDU (Fri Apr 02 2004 - 19:35:06 PST)
- Thomas E. Cheatham, III (Fri Apr 02 2004 - 15:51:01 PST)
- Youyi Peng (Fri Apr 02 2004 - 14:41:36 PST)
AMBER: question about image - truncated octahedron
- Thomas E. Cheatham, III (Mon Apr 05 2004 - 14:21:36 PDT)
- Chris Moth (Sat Apr 03 2004 - 07:22:14 PST)
AMBER: Question on Amber7...
- David A. Case (Tue Apr 06 2004 - 17:25:37 PDT)
- Pmartin (Tue Apr 06 2004 - 14:44:34 PDT)
- David A. Case (Thu Apr 01 2004 - 17:33:30 PST)
- Pmartin (Thu Apr 01 2004 - 15:31:49 PST)
AMBER: question on simulated annealing
- David A. Case (Wed Apr 28 2004 - 09:24:59 PDT)
- Venkata S Koppuravuri (Wed Apr 28 2004 - 09:00:39 PDT)
AMBER: questions about NMODE
- xhu1.memphis.edu (Thu Apr 29 2004 - 16:34:08 PDT)
- David A. Case (Thu Apr 29 2004 - 12:03:54 PDT)
- xhu1.memphis.edu (Thu Apr 29 2004 - 11:11:41 PDT)
- David A. Case (Wed Apr 28 2004 - 17:21:41 PDT)
- xhu1.memphis.edu (Wed Apr 28 2004 - 16:04:04 PDT)
- David A. Case (Wed Apr 28 2004 - 15:24:34 PDT)
- xhu1.memphis.edu (Wed Apr 28 2004 - 14:47:18 PDT)
- David A. Case (Wed Apr 28 2004 - 12:06:01 PDT)
- xhu1.memphis.edu (Wed Apr 28 2004 - 10:43:34 PDT)
AMBER: rdparm: a parameter array overflowed
- David A. Case (Wed Apr 21 2004 - 10:15:16 PDT)
- Wen Li (Wed Apr 21 2004 - 09:04:17 PDT)
AMBER: Redhat install
- Mengjuei Hsieh (Thu Apr 29 2004 - 21:44:12 PDT)
- scopio (Thu Apr 29 2004 - 17:32:26 PDT)
- David A. Case (Thu Apr 29 2004 - 10:32:33 PDT)
- Helios Chen (Thu Apr 29 2004 - 07:24:17 PDT)
AMBER: respgen
- David A. Case (Wed Apr 07 2004 - 18:20:36 PDT)
- Ilyas Yildirim (Wed Apr 07 2004 - 15:45:33 PDT)
AMBER: restraintmask and ambmask
- Viktor Hornak (Thu Apr 22 2004 - 05:27:38 PDT)
- Oliver Hucke (Wed Apr 21 2004 - 17:17:24 PDT)
AMBER: salt concentration
- tim (Wed Apr 14 2004 - 04:56:52 PDT)
- cailliez (Wed Apr 14 2004 - 07:45:44 PDT)
AMBER: sander + ew_legal.h
- David A. Case (Fri Apr 02 2004 - 17:34:32 PST)
- Carsten Detering (Fri Apr 02 2004 - 17:08:07 PST)
AMBER: scali amber8
- Scott Brozell (Mon Apr 12 2004 - 15:54:42 PDT)
- Guanglei Cui (Mon Apr 12 2004 - 13:02:11 PDT)
AMBER: script on tutorial page
- Thomas E. Cheatham, III (Sat Apr 10 2004 - 13:31:51 PDT)
- Ioana Cozmuta (Fri Apr 09 2004 - 15:03:57 PDT)
- Ross Walker (Thu Apr 08 2004 - 21:21:44 PDT)
- Ioana Cozmuta (Thu Apr 08 2004 - 19:25:50 PDT)
AMBER: Simulation of lipid bilayers
- Greg Jezierski (Tue Apr 20 2004 - 07:41:50 PDT)
AMBER: solvateCap warning
- Chenglong Li (Fri Apr 23 2004 - 10:44:14 PDT)
- Guanglei Cui (Fri Apr 23 2004 - 06:47:49 PDT)
- Helios Chen (Fri Apr 23 2004 - 02:47:25 PDT)
AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD
- David E. Konerding DSD Staff (Fri Apr 09 2004 - 15:41:57 PDT)
- Ross Walker (Fri Apr 09 2004 - 14:38:18 PDT)
- Robert Duke (Fri Apr 09 2004 - 14:13:59 PDT)
AMBER: Ti of CH3 -> NH2
- David A. Case (Wed Apr 07 2004 - 18:17:30 PDT)
- Carsten Detering (Wed Apr 07 2004 - 15:14:11 PDT)
AMBER: Time to minimize the energy by NMODE
- David A. Case (Wed Apr 14 2004 - 15:54:10 PDT)
- Holger Gohlke (Wed Apr 14 2004 - 12:40:28 PDT)
- xiaowei li (Wed Apr 14 2004 - 11:23:02 PDT)
AMBER: Titratable amino acid termini
- John Mongan (Tue Apr 27 2004 - 16:28:15 PDT)
- Sarah Harris (Tue Apr 27 2004 - 02:43:16 PDT)
AMBER: Turning off non-bond interactions
- Bill Ross (Wed Apr 21 2004 - 11:09:44 PDT)
- Robert Duke (Wed Apr 21 2004 - 09:12:11 PDT)
- david.evans.ulsop.ac.uk (Wed Apr 21 2004 - 09:09:26 PDT)
- David A. Case (Wed Apr 21 2004 - 08:54:54 PDT)
- Chris Moth (Wed Apr 21 2004 - 08:58:07 PDT)
- Chris Moth (Wed Apr 21 2004 - 08:00:14 PDT)
- david.evans.ulsop.ac.uk (Wed Apr 21 2004 - 01:22:21 PDT)
AMBER: tutorial of Biotin/Streptavidin
- David A. Case (Sat Apr 24 2004 - 13:08:00 PDT)
- Helios Chen (Sat Apr 24 2004 - 06:37:43 PDT)
AMBER: unique atom names
- Chris Moth (Wed Apr 07 2004 - 07:20:11 PDT)
- Chris Moth (Wed Apr 07 2004 - 07:21:50 PDT)
- anshul.imtech.res.in (Wed Apr 07 2004 - 16:00:31 PDT)
AMBER: universal recognition of chemicals
- Ross Walker (Mon Apr 26 2004 - 15:35:41 PDT)
- Ioana Cozmuta (Mon Apr 26 2004 - 15:15:55 PDT)
AMBER: Using pbsa
- David A. Case (Tue Apr 20 2004 - 18:26:08 PDT)
- Chenglong Li (Tue Apr 20 2004 - 16:47:34 PDT)
- Thomas Steinbrecher (Tue Apr 20 2004 - 16:16:37 PDT)
AMBER: VS: mmpbsa question
- Holger Gohlke (Fri Apr 30 2004 - 00:47:32 PDT)
- Olayiwola Adekoya (Thu Apr 29 2004 - 02:32:32 PDT)
AMBER: warning about improper dihedral in leap!!
- David A. Case (Thu Apr 08 2004 - 08:09:11 PDT)
- Pradipta Bandyopadhyay (Thu Apr 08 2004 - 04:50:18 PDT)
AMBER: water hole
- Bill Ross (Thu Apr 15 2004 - 11:49:02 PDT)
- Holly Freedman (Wed Apr 14 2004 - 17:32:06 PDT)
- Amber Administration (Wed Apr 14 2004 - 16:59:31 PDT)
- Andreas Svrcek-Seiler (Tue Apr 13 2004 - 03:02:12 PDT)
- Bill Ross (Mon Apr 12 2004 - 18:58:47 PDT)
- Holly Freedman (Mon Apr 12 2004 - 17:39:19 PDT)
- David A. Case (Mon Apr 12 2004 - 17:13:37 PDT)
- Carlos Simmerling (Mon Apr 12 2004 - 15:40:13 PDT)
- Holly Freedman (Mon Apr 12 2004 - 14:43:32 PDT)
AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber?
- Chris Moth (Thu Apr 22 2004 - 05:02:30 PDT)
- Ilyas Yildirim (Wed Apr 21 2004 - 21:51:40 PDT)
AMBER: which atoms are H's for SHAKE?
- Bill Ross (Tue Apr 06 2004 - 13:11:41 PDT)
- Oliver Hucke (Tue Apr 06 2004 - 10:32:12 PDT)
AMBER: WHICH LINUX
- Andreas Svrcek-Seiler (Tue Apr 13 2004 - 08:30:20 PDT)
- Marc Baaden (Tue Apr 13 2004 - 08:20:35 PDT)
- Raj Badhan (Tue Apr 13 2004 - 07:50:52 PDT)
AMBER: which parameters for Ca2+ ?
- cailliez (Tue Apr 06 2004 - 00:50:03 PDT)
AMBER: Why are there LENNARD_JONES_COEF A,B zero
- David A. Case (Wed Apr 21 2004 - 08:57:26 PDT)
- Dr. Yong Duan (Wed Apr 21 2004 - 08:59:58 PDT)
- Dr. Yong Duan (Wed Apr 21 2004 - 07:41:59 PDT)
- Xiao He (Wed Apr 21 2004 - 06:48:06 PDT)
- Jiten (Wed Apr 21 2004 - 06:28:26 PDT)
- Xiao He (Wed Apr 21 2004 - 06:05:49 PDT)
- Dr. Yong Duan (Wed Apr 21 2004 - 05:56:19 PDT)
- Xiao He (Wed Apr 21 2004 - 01:46:29 PDT)
AMBER: xleap bug?
- Ross Walker (Wed Apr 14 2004 - 15:48:18 PDT)
- Carsten Detering (Wed Apr 14 2004 - 15:28:07 PDT)
AMBER: xleap console message
- Bill Ross (Mon Apr 19 2004 - 13:58:05 PDT)
- Guanglei Cui (Mon Apr 19 2004 - 13:48:28 PDT)
- Bill Ross (Mon Apr 19 2004 - 10:28:17 PDT)
- Guanglei Cui (Mon Apr 19 2004 - 10:11:11 PDT)
- David A. Case (Mon Apr 19 2004 - 09:40:46 PDT)
- Guanglei Cui (Mon Apr 19 2004 - 08:06:05 PDT)
AMBER: xleap don't recognize formaldehyde?
- David A. Case (Tue Apr 27 2004 - 11:56:30 PDT)
- scopio (Tue Apr 27 2004 - 07:53:00 PDT)
AMBER: XLeap: head/tail and frcmod
- David A. Case (Mon Apr 12 2004 - 08:15:29 PDT)
- L Jin (Mon Apr 12 2004 - 04:35:47 PDT)
Out of Office AutoReply: Boost your sex life
- Bernor, Sandie L (Tue Apr 13 2004 - 17:34:52 PDT)
Ready and (0nline) amber preview.jpg
- Date Chatters (Tue Apr 27 2004 - 07:14:28 PDT)
- Date Chatters (Tue Apr 27 2004 - 07:14:24 PDT)
Returned mail: see transcript for details
- Mail Delivery Subsystem (Sat Apr 10 2004 - 13:42:30 PDT)

Amber Archive Apr 2004 by subject