Amber Archive May 2008: by subject

amber 9 compilation problem on IBM SP5
- Andrew Emerson (Mon May 05 2008 - 00:57:53 PDT)
Amber9 vs Amber10+MKL benchmark
- Francesco Pietra (Sat May 24 2008 - 07:50:45 PDT)
- Francesco Pietra (Sat May 24 2008 - 06:51:53 PDT)
AMBER: $AMBERHOME/dat/slko
- Gustavo Seabra (Thu May 22 2008 - 11:41:41 PDT)
- Francesco Pietra (Thu May 22 2008 - 10:48:49 PDT)
- Gustavo Seabra (Thu May 22 2008 - 10:00:36 PDT)
- Francesco Pietra (Thu May 22 2008 - 08:44:10 PDT)
- Ross Walker (Thu May 22 2008 - 08:24:47 PDT)
- Francesco Pietra (Thu May 22 2008 - 02:14:55 PDT)
- Gustavo Seabra (Wed May 21 2008 - 07:29:35 PDT)
- Francesco Pietra (Wed May 21 2008 - 05:47:59 PDT)
AMBER: 3rd Annual CMM Workshop on QM/MM Simulations
- Ross Walker (Mon May 19 2008 - 16:33:55 PDT)
AMBER: about addles:“forrtl: severe (71): integer divide by z
- Ross Walker (Fri May 16 2008 - 11:00:34 PDT)
- 成全 (Thu May 15 2008 - 23:56:34 PDT)
AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
- Ross Walker (Thu May 15 2008 - 10:37:22 PDT)
- 成全 (Wed May 14 2008 - 17:18:05 PDT)
- Ross Walker (Wed May 14 2008 - 09:30:51 PDT)
- 成全 (Wed May 14 2008 - 07:57:25 PDT)
AMBER: about glycam06
- WANG,YING (Mon May 05 2008 - 07:30:19 PDT)
- Bill Ross (Sun May 04 2008 - 15:46:05 PDT)
- WANG,YING (Sat May 03 2008 - 19:40:14 PDT)
- WANG,YING (Sat May 03 2008 - 19:35:05 PDT)
- Austin B. Yongye (Sat May 03 2008 - 18:59:47 PDT)
- David A. Case (Sat May 03 2008 - 17:32:10 PDT)
- WANG,YING (Sat May 03 2008 - 16:57:35 PDT)
- WANG,YING (Sat May 03 2008 - 16:55:11 PDT)
- David A. Case (Sat May 03 2008 - 16:49:27 PDT)
- WANG,YING (Sat May 03 2008 - 16:22:18 PDT)
AMBER: about hydrogen bond in amber force field
- Carlos Simmerling (Thu May 22 2008 - 00:08:08 PDT)
- Ross Walker (Wed May 21 2008 - 20:32:06 PDT)
- WANG,YING (Wed May 21 2008 - 19:24:47 PDT)
AMBER: About Hydrophobic Interactions.
- cgji (Mon May 12 2008 - 09:14:00 PDT)
AMBER: About reading in heme and CO molecule together with myoglobin
- David A. Case (Mon May 05 2008 - 16:51:44 PDT)
- Yang, Lee-Wei (Mon May 05 2008 - 11:08:53 PDT)
AMBER: Adjust Force Field parameters
- Chih-Ying Lin (Thu May 08 2008 - 16:46:21 PDT)
AMBER: Amber 10 ambpdb bug?
- Sam Danziger (Sun May 18 2008 - 20:41:43 PDT)
- David A. Case (Sat May 17 2008 - 21:37:09 PDT)
- Sam Danziger (Sat May 17 2008 - 19:17:44 PDT)
AMBER: AMBER entropy calculation
- Swarup Gupta (Wed May 14 2008 - 19:20:07 PDT)
- Dong Xu (Wed May 14 2008 - 17:37:27 PDT)
- Thomas Leonard (Wed May 14 2008 - 16:00:45 PDT)
AMBER: AMBER file preparation for protein-carbohydrate complex
- Karl Kirschner (Sun May 25 2008 - 02:25:35 PDT)
- n.gandhiau.gmail.com (Sun May 25 2008 - 00:17:55 PDT)
- Lachele Foley (Lists) (Thu May 22 2008 - 14:39:44 PDT)
- Neha Gandhi (Thu May 22 2008 - 07:31:50 PDT)
AMBER: AMBER Parallel test error
- jitrayut jitonnom (Thu May 08 2008 - 02:10:49 PDT)
- sudipta sinha (Wed May 07 2008 - 09:09:28 PDT)
- Ross Walker (Tue May 06 2008 - 08:25:46 PDT)
- jitrayut jitonnom (Tue May 06 2008 - 06:38:53 PDT)
- jitrayut jitonnom (Tue May 06 2008 - 06:09:10 PDT)
- Ross Walker (Mon May 05 2008 - 12:42:09 PDT)
- jitrayut jitonnom (Mon May 05 2008 - 11:37:39 PDT)
AMBER: Amber Parameter Schema
- Shultz, Jack (Tue May 06 2008 - 17:22:02 PDT)
AMBER: AMBER PBSA
- Thomas Leonard (Wed May 14 2008 - 02:35:54 PDT)
AMBER: amber tools installation
- vijayaraj.clri.info (Thu May 22 2008 - 01:55:00 PDT)
- David A. Case (Wed May 21 2008 - 08:30:32 PDT)
- vijayaraj.clri.info (Wed May 21 2008 - 08:22:37 PDT)
AMBER: amber10 installation
- Ross Walker (Thu May 22 2008 - 08:40:20 PDT)
- Ibrahim Moustafa (Thu May 22 2008 - 08:03:15 PDT)
- vijayaraj.clri.info (Thu May 22 2008 - 07:22:47 PDT)
AMBER: Amber10 installation error
- David A. Case (Fri May 02 2008 - 09:07:50 PDT)
- Ross Walker (Fri May 02 2008 - 08:33:43 PDT)
- juyong Lee (Thu May 01 2008 - 21:52:10 PDT)
- Ross Walker (Thu May 01 2008 - 21:01:02 PDT)
- juyong Lee (Thu May 01 2008 - 19:28:07 PDT)
AMBER: Amber10 Installation error - incorrect file suffix
- juyong Lee (Sun May 04 2008 - 19:01:02 PDT)
- David A. Case (Sun May 04 2008 - 18:20:55 PDT)
- juyong Lee (Sun May 04 2008 - 05:46:10 PDT)
AMBER: Amber10 testing problem
- Cenk $Jenk$ Andac (Wed May 14 2008 - 02:13:13 PDT)
- Ross Walker (Tue May 13 2008 - 14:20:53 PDT)
- Cenk $Jenk$ Andac (Tue May 13 2008 - 12:46:02 PDT)
AMBER: Amber10:Compiling with gcc 2.4.1
- David A. Case (Fri May 16 2008 - 13:16:56 PDT)
- yongleli (Thu May 15 2008 - 21:03:41 PDT)
- David A. Case (Thu May 15 2008 - 20:42:31 PDT)
- Gustavo Seabra (Thu May 15 2008 - 15:58:05 PDT)
- yongleli (Thu May 15 2008 - 08:36:29 PDT)
AMBER: amber9 , ptraj vector commad issue
- Vijay Singh (Sat May 31 2008 - 16:34:23 PDT)
AMBER: Amber9 vs Amber10+MKL benchmark
- Francesco Pietra (Sat May 24 2008 - 06:48:12 PDT)
AMBER: AmberTools on OS X fails tests
- David A. Case (Thu May 08 2008 - 12:30:53 PDT)
- Wei Zhang (Thu May 08 2008 - 12:15:46 PDT)
- Hans Martin Senn (Thu May 08 2008 - 11:59:12 PDT)
AMBER: ambertools: static linking of user binaries is not supported on Mac OS X
- Hans Martin Senn (Mon May 19 2008 - 03:35:24 PDT)
- Alan (Mon May 19 2008 - 02:39:32 PDT)
AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-
- David A. Case (Sun May 18 2008 - 13:09:00 PDT)
- Catein Catherine (Tue May 13 2008 - 03:17:29 PDT)
AMBER: anal
- Marina Grabar (Tue May 20 2008 - 02:20:04 PDT)
- David A. Case (Tue May 20 2008 - 01:25:13 PDT)
- Marina Grabar (Mon May 19 2008 - 06:30:13 PDT)
AMBER: analysis REMD
- Carlos Simmerling (Wed May 21 2008 - 10:18:06 PDT)
- rebeca.mmb.pcb.ub.es (Wed May 21 2008 - 10:03:59 PDT)
- Adrian Roitberg (Tue May 20 2008 - 12:17:39 PDT)
- rebeca.mmb.pcb.ub.es (Tue May 20 2008 - 11:31:30 PDT)
- Carlos Simmerling (Tue May 20 2008 - 05:11:29 PDT)
- rebeca.mmb.pcb.ub.es (Tue May 20 2008 - 03:49:00 PDT)
- Carlos Simmerling (Mon May 19 2008 - 23:51:22 PDT)
- rebeca (Mon May 19 2008 - 11:41:15 PDT)
AMBER: atom type in glycam06
- Lachele Foley (Lists) (Wed May 21 2008 - 06:37:51 PDT)
- tinni sona (Mon May 19 2008 - 10:06:57 PDT)
AMBER: Azobenzene: AMBER+Gromos Force Field parameters
- Chih-Ying Lin (Wed May 07 2008 - 14:43:17 PDT)
AMBER: B-factor calculation from data with different write frequencies
- Adrian Roitberg (Wed May 28 2008 - 11:58:53 PDT)
- Bill Ross (Wed May 28 2008 - 11:18:06 PDT)
- Bill Ross (Wed May 28 2008 - 11:11:30 PDT)
- Adrian Roitberg (Wed May 28 2008 - 10:54:09 PDT)
- Bill Ross (Wed May 28 2008 - 10:47:28 PDT)
- Sally Pias (Tue May 27 2008 - 20:42:13 PDT)
- Bill Ross (Tue May 27 2008 - 09:44:23 PDT)
- Sally Pias (Mon May 26 2008 - 21:19:42 PDT)
AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system
- Ross Walker (Thu May 22 2008 - 08:54:51 PDT)
- Pavan G (Thu May 22 2008 - 08:37:56 PDT)
AMBER: bugfix (imin=5) in amber9
- David A. Case (Tue May 27 2008 - 22:16:40 PDT)
- Xioling Chuang (Tue May 27 2008 - 21:23:09 PDT)
AMBER: build proline
- Qiuting Hong (Fri May 16 2008 - 14:32:47 PDT)
AMBER: building quadruplex with nab
- David A. Case (Tue May 20 2008 - 22:08:10 PDT)
- Rabin (Tue May 20 2008 - 15:30:17 PDT)
- Rabin (Tue May 13 2008 - 06:38:15 PDT)
AMBER: bye
- Sara Alexandra Moura (Tue May 20 2008 - 07:14:51 PDT)
- frustrated modeller (Mon May 19 2008 - 11:29:40 PDT)
AMBER: caculating nonpolar solvation energies
- ke dong (Sat May 24 2008 - 07:53:17 PDT)
AMBER: Calculate number of ions
- Ruchi Sachdeva (Wed May 14 2008 - 00:24:08 PDT)
- Mathy Froeyen (Tue May 13 2008 - 00:50:29 PDT)
- Dong Xu (Sat May 10 2008 - 11:32:01 PDT)
AMBER: Calculate the RESP charge Fe3+ of heme (p450)
- David A. Case (Thu May 22 2008 - 22:35:29 PDT)
- chen bents (Thu May 22 2008 - 19:16:12 PDT)
AMBER: calculating the energy from the restart file
- priya priya (Sat May 24 2008 - 07:03:46 PDT)
AMBER: calibration of constant pH simulations
- Pradipta Bandyopadhyay (Wed Apr 30 2008 - 21:02:55 PDT)
AMBER: can amber read .xyz files?
- Ross Walker (Thu May 08 2008 - 10:23:16 PDT)
- WANG,YING (Thu May 08 2008 - 08:29:57 PDT)
AMBER: cannot read big .pdb files
- WANG,YING (Tue May 13 2008 - 06:40:34 PDT)
- David Watson (Mon May 12 2008 - 16:32:49 PDT)
- WANG,YING (Mon May 12 2008 - 12:42:27 PDT)
- WANG,YING (Mon May 12 2008 - 07:37:24 PDT)
- Wei Zhang (Mon May 12 2008 - 07:34:40 PDT)
- WANG,YING (Sun May 11 2008 - 06:36:48 PDT)
- WANG,YING (Sun May 11 2008 - 06:38:41 PDT)
- Lynn F. Ten Eyck (Sat May 10 2008 - 09:37:02 PDT)
- David A. Case (Sat May 10 2008 - 08:24:41 PDT)
- WANG,YING (Fri May 09 2008 - 19:00:29 PDT)
AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
- ke dong (Sat May 24 2008 - 07:46:19 PDT)
- Ray Luo (Thu May 22 2008 - 13:37:04 PDT)
- Marcin Krol (Tue May 13 2008 - 06:44:48 PDT)
AMBER: cfortran.h error with xlf90 compiler
- David A. Case (Fri May 02 2008 - 10:10:54 PDT)
- Ross Walker (Fri May 02 2008 - 09:58:27 PDT)
- juyong Lee (Fri May 02 2008 - 09:35:32 PDT)
AMBER: COM RESTRAINT
- David A. Case (Thu May 22 2008 - 22:19:24 PDT)
- fatima.chami.durham.ac.uk (Thu May 22 2008 - 05:17:09 PDT)
AMBER: Compilation of PMEMD
- Robert Duke (Thu May 08 2008 - 05:17:43 PDT)
- sudipta sinha (Thu May 08 2008 - 04:07:28 PDT)
AMBER: compilation problem with AMBER10
- Atro Tossavainen (Wed May 28 2008 - 01:04:09 PDT)
- bhargav patel (Tue May 27 2008 - 22:56:15 PDT)
AMBER: Compiling amber10 with xlf90 fortran compiler
- juyong Lee (Fri May 02 2008 - 11:27:10 PDT)
AMBER: Cysteine sulphonic acid parameters
- Rima Chaudhuri (Thu May 01 2008 - 08:43:48 PDT)
- FyD (Thu May 01 2008 - 05:03:19 PDT)
AMBER: DCCM correlation analysis
- Ibrahim Moustafa (Mon May 05 2008 - 13:21:37 PDT)
AMBER: Deriving Force Field Parameters
- FyD (Mon May 05 2008 - 07:14:22 PDT)
- Shultz, Jack (Sun May 04 2008 - 14:32:03 PDT)
AMBER: DFTB parameters for O-P
- Gustavo Seabra (Wed May 07 2008 - 12:19:50 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Tue May 06 2008 - 13:01:55 PDT)
AMBER: Discontinuous Constant pH Restarts
- David A. Case (Thu May 08 2008 - 10:21:57 PDT)
- Smriti Sharma (Thu May 08 2008 - 04:05:31 PDT)
- David A. Case (Wed May 07 2008 - 14:34:23 PDT)
- Neil Bruce (Wed May 07 2008 - 13:21:28 PDT)
- David A. Case (Fri May 02 2008 - 12:44:31 PDT)
- Neil Bruce (Thu May 01 2008 - 06:41:21 PDT)
AMBER: distance
- Ibrahim Moustafa (Fri May 09 2008 - 07:49:37 PDT)
- E.M. (Fri May 09 2008 - 07:43:12 PDT)
- Urszula Uciechowska (Fri May 09 2008 - 07:36:18 PDT)
AMBER: divcon
- Gustavo Seabra (Tue May 13 2008 - 10:43:35 PDT)
- E.M. (Tue May 13 2008 - 09:58:49 PDT)
AMBER: drawing repeated units
- Taufik Al-Sarraj (Fri May 09 2008 - 11:10:56 PDT)
- Ross Walker (Fri May 09 2008 - 09:03:28 PDT)
- Taufik Al-Sarraj (Fri May 09 2008 - 08:10:19 PDT)
AMBER: energy pairwise decomposition in GB/SA simulation
- wfli.biophy.nju.edu.cn (Wed May 28 2008 - 03:29:42 PDT)
AMBER: error in compilation elsize.cc
- Scott Brozell (Mon May 05 2008 - 11:55:49 PDT)
AMBER: error when read inpcrd
- WANG,YING (Tue May 27 2008 - 14:14:02 PDT)
- Ross Walker (Tue May 27 2008 - 13:50:23 PDT)
- WANG,YING (Tue May 27 2008 - 13:32:02 PDT)
AMBER: Ewald error estimate
- Thomas Cheatham III (Thu May 08 2008 - 10:21:38 PDT)
- David A. Case (Thu May 08 2008 - 10:16:43 PDT)
- Ross Walker (Thu May 08 2008 - 08:27:15 PDT)
- 欧阳德方 (Wed May 07 2008 - 22:04:05 PDT)
- Thomas Cheatham (Wed May 07 2008 - 20:51:55 PDT)
- 欧阳德方 (Wed May 07 2008 - 20:38:18 PDT)
- David A. Case (Wed May 07 2008 - 08:57:03 PDT)
- 欧阳德方 (Wed May 07 2008 - 01:25:22 PDT)
AMBER: Ewald PARAMETER RANGE WRONG
- WANG,YING (Mon May 12 2008 - 10:06:03 PDT)
- David A. Case (Mon May 12 2008 - 09:00:44 PDT)
- WANG,YING (Sun May 11 2008 - 11:01:09 PDT)
AMBER: Example .prepi file for nonstandard amino acids
- finke.oakland.edu (Fri May 02 2008 - 18:06:30 PDT)
- David A. Case (Fri May 02 2008 - 15:54:03 PDT)
- finke.oakland.edu (Fri May 02 2008 - 15:00:45 PDT)
AMBER: ff94 vs. ff03
- Ross Walker (Fri May 23 2008 - 19:58:45 PDT)
- Swarup Gupta (Fri May 23 2008 - 17:26:46 PDT)
AMBER: ff99 and ff03 forcefield parameters
- Peter Kiss (Fri May 23 2008 - 11:42:48 PDT)
- Vlad Cojocaru (Fri May 23 2008 - 08:52:03 PDT)
- Peter Kiss (Fri May 23 2008 - 07:27:15 PDT)
- Vlad Cojocaru (Fri May 23 2008 - 02:43:38 PDT)
- Vlad Cojocaru (Fri May 23 2008 - 02:31:47 PDT)
- Peter Kiss (Wed May 21 2008 - 14:01:47 PDT)
AMBER: Force field in water and in vacuum ??
- Ross Walker (Thu May 22 2008 - 09:06:36 PDT)
- Chih-Ying Lin (Thu May 22 2008 - 08:46:15 PDT)
AMBER: Free Energy Calculations - parameters for MM
- Seth Lilavivat (Tue May 13 2008 - 09:29:23 PDT)
AMBER: from Gromax to AMBER
- Cristina Sisu (Tue May 13 2008 - 06:49:12 PDT)
- jacopo.sgrignani.unifi.it (Tue May 13 2008 - 06:19:19 PDT)
- Cristina Sisu (Tue May 13 2008 - 03:00:24 PDT)
AMBER: GAFF Schema
- David A. Case (Sun May 04 2008 - 18:21:59 PDT)
- Shultz, Jack (Sun May 04 2008 - 15:11:37 PDT)
AMBER: gasteiger is not working with ambertools 1.0
- Alan (Mon May 19 2008 - 07:51:05 PDT)
AMBER: GBSA SA calculation
- Carlos Simmerling (Tue May 13 2008 - 10:46:30 PDT)
- Carlos Simmerling (Wed May 07 2008 - 15:05:26 PDT)
- David A. Case (Wed May 07 2008 - 14:17:07 PDT)
- Carlos Simmerling (Wed May 07 2008 - 12:05:44 PDT)
- Titus, Jamie $bairdje$ (Wed May 07 2008 - 11:32:43 PDT)
AMBER: Harmonic Force Constant
- Shultz, Jack (Thu May 08 2008 - 13:21:00 PDT)
- Shultz, Jack (Wed May 07 2008 - 12:32:18 PDT)
AMBER: help MD running error
- Ross Walker (Fri May 23 2008 - 08:30:03 PDT)
- Qiuting Hong (Fri May 23 2008 - 01:40:12 PDT)
AMBER: help to install AMBER9
- Jeffrey (Mon May 12 2008 - 17:51:46 PDT)
- Gustavo Seabra (Mon May 12 2008 - 07:56:41 PDT)
- Jeffrey (Sun May 11 2008 - 02:12:18 PDT)
- Ross Walker (Fri May 09 2008 - 09:12:53 PDT)
- Gustavo Seabra (Fri May 09 2008 - 08:01:04 PDT)
- Ye Mei (Fri May 09 2008 - 07:55:56 PDT)
- Jeffrey (Fri May 09 2008 - 07:47:16 PDT)
AMBER: Help with NMODE
- Seth Lilavivat (Mon May 05 2008 - 12:39:06 PDT)
- David A. Case (Sun May 04 2008 - 18:26:07 PDT)
- Seth Lilavivat (Sun May 04 2008 - 15:15:53 PDT)
- David A. Case (Fri May 02 2008 - 12:28:51 PDT)
- Seth Lilavivat (Fri May 02 2008 - 11:05:19 PDT)
- David A. Case (Fri May 02 2008 - 10:06:33 PDT)
- Seth Lilavivat (Fri May 02 2008 - 09:50:35 PDT)
- David A. Case (Fri May 02 2008 - 09:23:34 PDT)
- Seth Lilavivat (Fri May 02 2008 - 08:24:25 PDT)
AMBER: how generate the final output file using mmpbsa
- Miguel Ortiz-Lombardía (Fri May 23 2008 - 23:40:40 PDT)
- luzhenw1.msu.edu (Fri May 23 2008 - 13:49:33 PDT)
AMBER: how to calculate delta G from IC50
- Chris Moth (Tue May 20 2008 - 05:30:29 PDT)
- Thomas Leonard (Mon May 19 2008 - 22:12:04 PDT)
AMBER: how to extract energy
- WANG,YING (Sun May 25 2008 - 06:57:20 PDT)
- David A. Case (Sat May 24 2008 - 13:21:22 PDT)
- Francesco Pietra (Sat May 24 2008 - 00:24:13 PDT)
- Ross Walker (Fri May 23 2008 - 20:07:41 PDT)
- WANG,YING (Fri May 23 2008 - 18:08:13 PDT)
AMBER: how to overcome theunusual bonds formation
- Swarup Gupta (Thu May 29 2008 - 05:27:36 PDT)
- Adrian Roitberg (Thu May 29 2008 - 05:07:14 PDT)
- Thomas Leonard (Thu May 29 2008 - 05:01:43 PDT)
- Florian Haberl (Thu May 29 2008 - 04:54:20 PDT)
- Thomas Leonard (Thu May 29 2008 - 04:03:29 PDT)
AMBER: How to set a ZN atom radius for PB calculations
- Ray Luo (Thu May 22 2008 - 13:41:36 PDT)
- Sam Danziger (Tue May 20 2008 - 17:23:30 PDT)
AMBER: How to transfer unformatted coordinates into formatted ones
- David A. Case (Thu May 08 2008 - 10:13:59 PDT)
- Qi Yan (Wed May 07 2008 - 19:55:18 PDT)
- David A. Case (Wed May 07 2008 - 18:14:04 PDT)
- Qi Yan (Wed May 07 2008 - 12:44:10 PDT)
AMBER: Hybrid REMD amber10
- Geoff Wood (Tue May 20 2008 - 07:24:11 PDT)
- Carlos Simmerling (Mon May 19 2008 - 23:55:06 PDT)
- Ross Walker (Mon May 19 2008 - 08:51:13 PDT)
- Geoff Wood (Mon May 19 2008 - 05:41:54 PDT)
AMBER: Hydration free energies of charged ions using PME
- David A. Case (Wed May 28 2008 - 09:51:26 PDT)
- Markus Kaukonen (Tue May 27 2008 - 23:51:26 PDT)
AMBER: Hydroxyprolines!!!
- David A. Case (Wed May 07 2008 - 18:26:16 PDT)
- Titus, Jamie $bairdje$ (Wed May 07 2008 - 11:54:03 PDT)
AMBER: igb and ibelly
- Holly Freedman (Fri May 30 2008 - 15:36:03 PDT)
- Holly Freedman (Fri May 30 2008 - 13:21:06 PDT)
- David A. Case (Fri May 30 2008 - 13:20:52 PDT)
- Ross Walker (Fri May 30 2008 - 13:16:11 PDT)
- Holly Freedman (Fri May 30 2008 - 12:23:21 PDT)
AMBER: Improper dihedral parameters
- Da-Wei Li (Tue May 06 2008 - 12:30:29 PDT)
- Bill Ross (Tue May 06 2008 - 12:23:55 PDT)
- Chih-Ying Lin (Tue May 06 2008 - 12:00:36 PDT)
AMBER: initial velocities of MD
- Ross Walker (Tue May 13 2008 - 10:05:05 PDT)
- Carlos Simmerling (Tue May 13 2008 - 09:59:26 PDT)
- Jena M (Tue May 13 2008 - 09:37:31 PDT)
AMBER: Inquiry on B-factor of NMR
- James Thomas (Fri May 02 2008 - 12:31:09 PDT)
AMBER: install amber tools
- David A. Case (Wed May 28 2008 - 09:56:30 PDT)
- Alejandro Valbuena (Wed May 28 2008 - 03:14:35 PDT)
AMBER: Installation error on IBM cluster
- Ross Walker (Mon May 05 2008 - 08:06:11 PDT)
- juyong Lee (Mon May 05 2008 - 01:40:59 PDT)
AMBER: Installation problem of AMBER on cluster
- Bertrand P. S. Russell (Mon May 05 2008 - 05:40:56 PDT)
- sudipta sinha (Mon May 05 2008 - 04:24:29 PDT)
- sudipta sinha (Mon May 05 2008 - 02:47:38 PDT)
- Bertrand P. S. Russell (Mon May 05 2008 - 00:09:20 PDT)
- Bertrand P. S. Russell (Mon May 05 2008 - 00:03:39 PDT)
- sudipta sinha (Sun May 04 2008 - 23:52:58 PDT)
- Bertrand P. S. Russell (Sun May 04 2008 - 18:50:13 PDT)
- David A. Case (Sun May 04 2008 - 18:32:02 PDT)
- sudipta sinha (Sun May 04 2008 - 05:31:22 PDT)
- David A. Case (Sat May 03 2008 - 16:56:32 PDT)
- sudipta sinha (Fri May 02 2008 - 22:59:23 PDT)
- Ross Walker (Fri May 02 2008 - 14:33:48 PDT)
- Ross Walker (Fri May 02 2008 - 14:18:48 PDT)
- Gustavo Seabra (Fri May 02 2008 - 14:16:22 PDT)
- sudipta sinha (Fri May 02 2008 - 13:29:38 PDT)
- Ross Walker (Fri May 02 2008 - 12:07:10 PDT)
- sudipta sinha (Fri May 02 2008 - 11:29:37 PDT)
- Ross Walker (Fri May 02 2008 - 08:41:48 PDT)
- Bertrand P. S. Russell (Fri May 02 2008 - 03:11:15 PDT)
- sudipta sinha (Fri May 02 2008 - 00:39:09 PDT)
- David A. Case (Thu May 01 2008 - 11:55:17 PDT)
- sudipta sinha (Thu May 01 2008 - 11:16:44 PDT)
AMBER: Installing PMEMD with Amber10
- Justin A. Lemkul (Sat May 31 2008 - 05:24:30 PDT)
- Atro Tossavainen (Sat May 31 2008 - 04:23:31 PDT)
- Justin A. Lemkul (Fri May 30 2008 - 03:42:53 PDT)
- Atro Tossavainen (Thu May 29 2008 - 23:42:02 PDT)
- Justin A. Lemkul (Thu May 29 2008 - 13:41:30 PDT)
- Robert Duke (Thu May 29 2008 - 13:16:39 PDT)
- Justin A. Lemkul (Thu May 29 2008 - 12:12:26 PDT)
- Robert Duke (Thu May 29 2008 - 07:44:38 PDT)
- Justin A. Lemkul (Thu May 29 2008 - 06:23:05 PDT)
AMBER: Iron-Sulfur Cluster
- FyD (Sat May 31 2008 - 05:35:31 PDT)
- Justine Condo (Fri May 30 2008 - 10:52:24 PDT)
- Joachim Reichelt (Fri May 30 2008 - 02:46:30 PDT)
AMBER: is in vacuo simulation neccessary?
- Mark Abraham (Sun May 25 2008 - 22:44:20 PDT)
- Anamika Awasthi (Sun May 25 2008 - 22:18:58 PDT)
AMBER: Jarzinsky relationship
- David Mobley (Thu May 08 2008 - 14:29:29 PDT)
- E.M. (Thu May 08 2008 - 03:58:10 PDT)
- Adrian Roitberg (Mon May 05 2008 - 08:13:51 PDT)
- E.M. (Mon May 05 2008 - 08:02:49 PDT)
- Adrian Roitberg (Mon May 05 2008 - 07:46:53 PDT)
- E.M. (Sun May 04 2008 - 19:39:51 PDT)
AMBER: Jarzynski
- fatima.chami.durham.ac.uk (Sat May 31 2008 - 04:50:24 PDT)
- David Mobley (Fri May 30 2008 - 09:02:28 PDT)
- fatima.chami.durham.ac.uk (Fri May 30 2008 - 04:44:41 PDT)
AMBER: Ligand energy minimization
- Ross Walker (Tue May 13 2008 - 08:14:53 PDT)
- Dong Xu (Mon May 12 2008 - 15:07:31 PDT)
AMBER: ligand unit charge is not zero
- Swarup Gupta (Thu May 29 2008 - 05:48:13 PDT)
- amor san juan (Thu May 29 2008 - 05:32:57 PDT)
- mori.cerm.unifi.it (Thu May 29 2008 - 02:17:55 PDT)
- amor san juan (Thu May 29 2008 - 01:44:58 PDT)
AMBER: mass weighted rms fit
- Adrian Roitberg (Sun May 25 2008 - 09:26:11 PDT)
- Dong Xu (Sun May 25 2008 - 09:11:43 PDT)
AMBER: massively parallel computation
- Atro Tossavainen (Wed May 21 2008 - 10:49:03 PDT)
- Robert Duke (Wed May 21 2008 - 10:37:34 PDT)
- Atro Tossavainen (Wed May 21 2008 - 00:17:10 PDT)
- Mingfeng Yang (Tue May 20 2008 - 09:58:56 PDT)
- Robert Duke (Tue May 20 2008 - 07:46:34 PDT)
- Robert Duke (Tue May 20 2008 - 07:32:22 PDT)
- Lars Skjærven (Tue May 20 2008 - 07:28:24 PDT)
- Robert Duke (Tue May 20 2008 - 07:22:56 PDT)
- Adrian Roitberg (Tue May 20 2008 - 07:11:46 PDT)
- Mingfeng Yang (Tue May 20 2008 - 00:03:51 PDT)
AMBER: mbondi radii for gaff atom types
- David A. Case (Wed May 28 2008 - 10:31:30 PDT)
- Sara J (Wed May 28 2008 - 08:03:52 PDT)
AMBER: Minimization in Octahedric Box
- Ross Walker (Tue May 06 2008 - 10:22:39 PDT)
- David A. Case (Tue May 06 2008 - 10:28:20 PDT)
- guardiani.fi.infn.it (Tue May 06 2008 - 04:31:50 PDT)
AMBER: misplacement of TER by leap
- David A. Case (Mon May 05 2008 - 11:55:29 PDT)
- Tim Meyer (Mon May 05 2008 - 06:03:54 PDT)
- Jena M (Mon May 05 2008 - 04:00:55 PDT)
AMBER: MKL libraries/Amber10
- Francesco Pietra (Sat May 31 2008 - 07:22:35 PDT)
- Francesco Pietra (Fri May 30 2008 - 23:44:24 PDT)
- Ross Walker (Fri May 30 2008 - 15:41:51 PDT)
- Francesco Pietra (Fri May 30 2008 - 02:40:41 PDT)
- Ross Walker (Thu May 29 2008 - 21:50:30 PDT)
- Cenk $Jenk$ Andac (Thu May 29 2008 - 17:24:38 PDT)
- Cenk $Jenk$ Andac (Sat May 24 2008 - 05:26:37 PDT)
- Cenk $Jenk$ Andac (Sat May 24 2008 - 05:02:34 PDT)
- Cenk $Jenk$ Andac (Fri May 23 2008 - 09:35:36 PDT)
- Cenk $Jenk$ Andac (Fri May 23 2008 - 07:57:48 PDT)
- Ross Walker (Thu May 22 2008 - 15:40:54 PDT)
- Cenk $Jenk$ Andac (Thu May 22 2008 - 15:29:55 PDT)
- Cenk $Jenk$ Andac (Thu May 22 2008 - 15:28:34 PDT)
- Cenk $Jenk$ Andac (Thu May 22 2008 - 15:24:33 PDT)
- Francesco Pietra (Thu May 22 2008 - 03:06:48 PDT)
- Francesco Pietra (Wed May 21 2008 - 12:09:10 PDT)
- Ross Walker (Wed May 21 2008 - 11:05:20 PDT)
- Cenk $Jenk$ Andac (Wed May 21 2008 - 06:33:35 PDT)
- Ross Walker (Mon May 19 2008 - 14:25:45 PDT)
- Cenk $Jenk$ Andac (Mon May 19 2008 - 14:18:11 PDT)
- Francesco Pietra (Mon May 19 2008 - 14:17:25 PDT)
- Cenk $Jenk$ Andac (Mon May 19 2008 - 13:40:37 PDT)
- Ross Walker (Mon May 19 2008 - 10:19:37 PDT)
- Cenk $Jenk$ Andac (Mon May 19 2008 - 09:48:21 PDT)
- Ross Walker (Mon May 19 2008 - 08:41:59 PDT)
- Francesco Pietra (Mon May 19 2008 - 08:24:43 PDT)
- Gustavo Seabra (Mon May 19 2008 - 07:18:07 PDT)
- Francesco Pietra (Sun May 18 2008 - 10:33:54 PDT)
- Francesco Pietra (Sat May 17 2008 - 14:14:18 PDT)
- Francesco Pietra (Sat May 17 2008 - 10:33:10 PDT)
- Francesco Pietra (Sat May 17 2008 - 10:12:06 PDT)
- Thomas Patko (Fri May 16 2008 - 14:26:33 PDT)
- David A. Case (Fri May 16 2008 - 13:27:40 PDT)
- Ross Walker (Fri May 16 2008 - 11:25:36 PDT)
- Francesco Pietra (Fri May 16 2008 - 09:31:17 PDT)
- Ross Walker (Thu May 15 2008 - 19:59:16 PDT)
- yongleli (Thu May 15 2008 - 19:03:57 PDT)
- Gustavo Seabra (Thu May 15 2008 - 16:02:42 PDT)
- Francesco Pietra (Thu May 15 2008 - 11:01:34 PDT)
AMBER: MM-PBSA for carbohydrates
- Navnit Kumar Mishra (Tue May 20 2008 - 04:25:20 PDT)
- Neha Gandhi (Mon May 19 2008 - 19:07:24 PDT)
AMBER: MM_PBSA output file
- Alessandro Nascimento (Fri May 09 2008 - 09:22:35 PDT)
- Navnit Kumar Mishra (Fri May 09 2008 - 09:21:17 PDT)
- Qi Yan (Fri May 09 2008 - 09:03:38 PDT)
AMBER: MM_PBSA problem in binding_energy
- jacopo sgrignani (Wed May 14 2008 - 11:43:55 PDT)
- mori.cerm.unifi.it (Wed May 14 2008 - 07:17:40 PDT)
AMBER: mm_pbsa problem: bad atom type: IP
- David A. Case (Thu May 08 2008 - 10:27:22 PDT)
- mori.cerm.unifi.it (Thu May 08 2008 - 04:59:12 PDT)
AMBER: mm_pbsa.pl not reading parameters for nmode
- David A. Case (Tue May 06 2008 - 11:13:54 PDT)
- Seth Lilavivat (Tue May 06 2008 - 10:50:18 PDT)
AMBER: MMPBSA error
- Cristina Sisu (Sat May 31 2008 - 07:53:32 PDT)
- Peter Gannett (Sat May 31 2008 - 07:15:40 PDT)
- Cristina Sisu (Sat May 31 2008 - 07:00:08 PDT)
AMBER: Mn2+ parameters in AMBER
- jitrayut jitonnom (Fri May 23 2008 - 01:58:10 PDT)
- Guillermo Mulliert Carlín (Thu May 22 2008 - 23:26:51 PDT)
- jitrayut jitonnom (Fri May 02 2008 - 11:46:25 PDT)
AMBER: molsurf
- jacopo.sgrignani.unifi.it (Wed May 07 2008 - 04:11:34 PDT)
AMBER: nab
- David A. Case (Fri May 30 2008 - 07:55:10 PDT)
- Joachim Reichelt (Fri May 30 2008 - 02:48:56 PDT)
- Rabin (Tue May 13 2008 - 06:17:51 PDT)
- Andreas Svrcek-Seiler (Tue May 13 2008 - 02:39:19 PDT)
- Alessandro Nascimento (Mon May 12 2008 - 17:59:27 PDT)
- Rabin (Mon May 12 2008 - 17:40:54 PDT)
AMBER: neutral C-terminus and N-terminus parameters for amber
- FyD (Sat May 10 2008 - 00:52:10 PDT)
- Lisa Perez (Fri May 09 2008 - 10:32:13 PDT)
AMBER: nfft1-3 too large
- WANG,YING (Mon May 19 2008 - 07:46:51 PDT)
AMBER: nmode "Atom out of bounds" for min of multiple ligands
- David A. Case (Thu May 08 2008 - 13:49:31 PDT)
- Seth Lilavivat (Thu May 08 2008 - 13:01:45 PDT)
- Ross Walker (Thu May 08 2008 - 10:19:34 PDT)
- Seth Lilavivat (Thu May 08 2008 - 07:30:24 PDT)
AMBER: nmode: number of atoms limitation
- Qi Yan (Wed May 07 2008 - 11:10:48 PDT)
- Ross Walker (Wed May 07 2008 - 14:39:44 PDT)
- Qi Yan (Wed May 07 2008 - 11:25:58 PDT)
AMBER: NON-BONDED parameters
- David A. Case (Mon May 05 2008 - 16:54:32 PDT)
- Chih-Ying Lin (Mon May 05 2008 - 15:10:05 PDT)
- Thomas Steinbrecher (Mon May 05 2008 - 11:14:59 PDT)
- Chih-Ying Lin (Mon May 05 2008 - 10:32:23 PDT)
AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
- Kateryna Miroshnychenko (Thu May 29 2008 - 00:22:17 PDT)
- David A. Case (Wed May 28 2008 - 10:27:31 PDT)
- Kateryna Miroshnychenko (Wed May 28 2008 - 08:08:19 PDT)
AMBER: NTC and NTF
- dpandit.brandeis.edu (Thu May 29 2008 - 12:39:33 PDT)
- Ross Walker (Thu May 29 2008 - 12:30:28 PDT)
- dpandit.brandeis.edu (Thu May 29 2008 - 12:18:14 PDT)
AMBER: Parallel Self-guided Langevin simulation
- Dirar Homouz (Wed May 28 2008 - 22:18:34 PDT)
- David A. Case (Wed May 28 2008 - 09:46:55 PDT)
- Dirar Homouz (Tue May 27 2008 - 23:31:03 PDT)
- David A. Case (Sun May 25 2008 - 23:06:03 PDT)
- Dirar Homouz (Thu May 22 2008 - 08:58:27 PDT)
- David A. Case (Thu May 22 2008 - 03:16:23 PDT)
- Dirar Homouz (Wed May 21 2008 - 15:23:27 PDT)
AMBER: parallel test / libmpi_f90.so.0
- Arturas Ziemys (Wed May 28 2008 - 08:24:14 PDT)
- Arturas Ziemys (Wed May 28 2008 - 08:10:36 PDT)
AMBER: parameters in ff03 and ff99
- Peter Kiss (Mon May 19 2008 - 04:21:21 PDT)
AMBER: parmbsc0 parameters for RNA.DNA systems
- David A. Case (Sat May 10 2008 - 08:27:36 PDT)
- Cenk $Jenk$ Andac (Sat May 10 2008 - 06:47:50 PDT)
AMBER: PBC in 2D
- fatima.chami.durham.ac.uk (Fri May 23 2008 - 06:13:39 PDT)
AMBER: peptide at the box center during NVT-MD
- David A. Case (Mon May 26 2008 - 09:09:51 PDT)
- Darek Czapiewski (Mon May 26 2008 - 03:01:45 PDT)
AMBER: periodic bondary condition
- WANG,YING (Fri May 23 2008 - 18:16:34 PDT)
AMBER: periodic boundary condition
- WANG,YING (Sun May 25 2008 - 06:58:20 PDT)
- Ross Walker (Fri May 23 2008 - 20:09:39 PDT)
- David A. Case (Wed May 14 2008 - 06:50:40 PDT)
- WANG,YING (Tue May 13 2008 - 06:55:00 PDT)
AMBER: PGI amber9 problems
- Ross Walker (Fri May 16 2008 - 11:06:14 PDT)
- Lorenzo Gontrani (Fri May 16 2008 - 05:02:53 PDT)
- David A. Case (Fri May 16 2008 - 04:29:06 PDT)
- Lorenzo Gontrani (Fri May 16 2008 - 02:52:21 PDT)
AMBER: point charges
- David A. Case (Sat May 03 2008 - 17:36:08 PDT)
- Chih-Ying Lin (Sat May 03 2008 - 14:47:23 PDT)
- Ross Walker (Fri May 02 2008 - 16:03:08 PDT)
- Chih-Ying Lin (Fri May 02 2008 - 15:42:18 PDT)
- Ross Walker (Fri May 02 2008 - 14:32:43 PDT)
- Chih-Ying Lin (Fri May 02 2008 - 13:53:50 PDT)
AMBER: Points on a Sphere
- Justine Condo (Thu May 15 2008 - 09:27:06 PDT)
AMBER: potassium ion
- Bill Ross (Thu May 22 2008 - 11:27:21 PDT)
- Lars Skjærven (Thu May 22 2008 - 06:09:59 PDT)
AMBER: Prepgen
- yongleli (Thu May 15 2008 - 09:18:31 PDT)
- Junmei Wang (Thu May 15 2008 - 08:46:34 PDT)
- Rajendra P. OJHA (Wed May 14 2008 - 02:45:47 PDT)
AMBER: Prepgen does not give correct result?
- Rajendra P. OJHA (Fri May 09 2008 - 09:13:58 PDT)
AMBER: pressure regulation methods
- Vlad Cojocaru (Wed May 21 2008 - 09:25:08 PDT)
AMBER: printing dipoles in Amber10 (and earlier)
- Ross Walker (Fri May 02 2008 - 14:16:08 PDT)
- Piotr Cieplak (Fri May 02 2008 - 13:29:49 PDT)
AMBER: Problems installing Amber Tools for Amber 10
- Scott Brozell (Tue May 27 2008 - 10:17:19 PDT)
- David A. Case (Fri May 16 2008 - 13:24:08 PDT)
- Sam Danziger (Fri May 16 2008 - 11:29:32 PDT)
- Sam Danziger (Fri May 16 2008 - 10:41:31 PDT)
- Sam Danziger (Fri May 16 2008 - 10:06:05 PDT)
- Lynn F. Ten Eyck (Fri May 16 2008 - 08:12:49 PDT)
- David A. Case (Thu May 15 2008 - 21:47:19 PDT)
- Sam Danziger (Mon May 12 2008 - 11:20:23 PDT)
AMBER: protonate in Amber10
- David A. Case (Thu May 29 2008 - 14:10:34 PDT)
- Benjamin Juhl (Wed May 28 2008 - 07:55:06 PDT)
AMBER: ptraj analyze matrix
- Seth Lilavivat (Wed May 21 2008 - 07:53:28 PDT)
AMBER: ptraj analyze modes from nmode
- Miguel Ortiz-Lombardía (Sat May 31 2008 - 08:40:50 PDT)
AMBER: ptraj has trouble with x-plor psf file from VMD
- Dong Xu (Thu May 29 2008 - 13:23:56 PDT)
AMBER: ptraj mask not working with psf file
- Dong Xu (Fri May 23 2008 - 19:53:27 PDT)
AMBER: ptraj rmsd calculation
- Pavan G (Thu May 29 2008 - 11:08:36 PDT)
AMBER: Ptraj | Multiple trajout commands?
- Jianyin Shao (Sat May 31 2008 - 17:02:17 PDT)
- Ian (Fri May 30 2008 - 01:39:23 PDT)
AMBER: QM/MM
- Gustavo Seabra (Fri May 09 2008 - 07:18:21 PDT)
- Syed Tarique Moin (Fri May 09 2008 - 01:28:06 PDT)
AMBER: reading PDB trajectory
- Mark Abraham (Thu May 15 2008 - 20:49:55 PDT)
AMBER: Regarding binding free energy calculation using MM_PBSA method
- nag raj (Thu May 22 2008 - 05:18:59 PDT)
- nag raj (Wed May 21 2008 - 00:01:14 PDT)
AMBER: regarding segfault during energy minimization
- Anamika Awasthi (Wed Apr 30 2008 - 22:57:35 PDT)
AMBER: reset time and comments
- Ross Walker (Thu May 08 2008 - 08:24:50 PDT)
- Benjamin Juhl (Thu May 08 2008 - 02:12:11 PDT)
- E.M. (Wed May 07 2008 - 21:13:02 PDT)
AMBER: RESP and Jaguar
- Seth Lilavivat (Thu May 15 2008 - 13:52:35 PDT)
AMBER: RESP charges of an unusual substrate
- FyD (Sun May 18 2008 - 23:46:40 PDT)
- Jiayun Pang (Fri May 16 2008 - 03:45:54 PDT)
AMBER: Restart MD Simulation
- dpandit.brandeis.edu (Sat May 24 2008 - 06:40:40 PDT)
- Ross Walker (Fri May 23 2008 - 15:28:16 PDT)
- dpandit.brandeis.edu (Fri May 23 2008 - 14:56:23 PDT)
AMBER: restarting molecular dynamics
- Adrian Roitberg (Wed May 28 2008 - 08:48:45 PDT)
- Germain Vallverdu (Wed May 28 2008 - 07:25:23 PDT)
- Adrian Roitberg (Wed May 28 2008 - 06:34:17 PDT)
- Germain Vallverdu (Wed May 28 2008 - 06:18:16 PDT)
AMBER: rms
- Vlad Cojocaru (Wed May 14 2008 - 07:01:17 PDT)
- Cenk $Jenk$ Andac (Mon May 12 2008 - 06:51:56 PDT)
- Urszula Uciechowska (Mon May 12 2008 - 06:41:06 PDT)
- Vlad Cojocaru (Mon May 12 2008 - 05:40:46 PDT)
- Urszula Uciechowska (Mon May 12 2008 - 04:19:41 PDT)
AMBER: rmsd per residue
- Furia Gargano (Tue May 06 2008 - 07:28:59 PDT)
AMBER: rmsd vs frame
- Francesco Pietra (Wed May 28 2008 - 15:56:24 PDT)
AMBER: SANDER and PMEMD with openmpi
- Ross Walker (Fri May 30 2008 - 15:18:04 PDT)
AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
- Ross Walker (Sat May 31 2008 - 13:57:48 PDT)
- Francesco Pietra (Sat May 31 2008 - 11:31:04 PDT)
AMBER: Sander instead of PMEMD
- Francesco Pietra (Fri May 30 2008 - 10:59:35 PDT)
- Francesco Pietra (Fri May 30 2008 - 10:47:57 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Fri May 30 2008 - 09:24:39 PDT)
- Florian Haberl (Fri May 30 2008 - 08:31:18 PDT)
- Robert Duke (Fri May 30 2008 - 08:28:24 PDT)
- Cristina Sisu (Fri May 30 2008 - 08:22:10 PDT)
- Francesco Pietra (Fri May 30 2008 - 08:17:15 PDT)
- Florian Haberl (Fri May 30 2008 - 08:06:42 PDT)
- Robert Duke (Fri May 30 2008 - 07:50:36 PDT)
- Cristina Sisu (Fri May 30 2008 - 07:32:27 PDT)
- Robert Duke (Fri May 30 2008 - 07:13:20 PDT)
- Cristina Sisu (Fri May 30 2008 - 06:47:13 PDT)
AMBER: Segmentation faults trying to run sander mpi
- David A. Case (Thu May 29 2008 - 08:20:08 PDT)
- Idan Gabdank (Thu May 29 2008 - 07:57:07 PDT)
- David A. Case (Wed May 28 2008 - 10:00:34 PDT)
- Idan Gabdank (Wed May 28 2008 - 03:59:09 PDT)
AMBER: self-diffusion coefficient and Berendsen
- David A. Case (Sun May 25 2008 - 21:09:32 PDT)
- Jennifer.Thomas.cbt.uhp-nancy.fr (Sun May 25 2008 - 03:47:22 PDT)
- David A. Case (Sat May 24 2008 - 13:20:27 PDT)
- Andreas Svrcek-Seiler (Fri May 23 2008 - 02:22:57 PDT)
- Jennifer.Thomas.cbt.uhp-nancy.fr (Fri May 23 2008 - 01:03:49 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- Jianyin Shao (Fri May 30 2008 - 10:11:24 PDT)
- Jianyin Shao (Thu May 29 2008 - 14:47:43 PDT)
- Dong Xu (Thu May 29 2008 - 12:19:53 PDT)
- Jianyin Shao (Thu May 29 2008 - 11:15:15 PDT)
- Dong Xu (Wed May 28 2008 - 22:56:48 PDT)
- Jianyin Shao (Wed May 28 2008 - 21:07:18 PDT)
- Jianyin Shao (Wed May 28 2008 - 08:51:12 PDT)
- Jianyin Shao (Tue May 27 2008 - 12:29:43 PDT)
- Dong Xu (Tue May 27 2008 - 11:20:09 PDT)
- Jianyin Shao (Tue May 27 2008 - 09:03:54 PDT)
- Jianyin Shao (Tue May 27 2008 - 08:37:57 PDT)
- Ross Walker (Tue May 13 2008 - 08:08:08 PDT)
- Dong Xu (Mon May 12 2008 - 21:09:11 PDT)
- Jianyin Shao (Fri May 09 2008 - 13:05:39 PDT)
- sychen (Fri May 02 2008 - 07:22:50 PDT)
AMBER: simulate dipole moment
- Ross Walker (Wed May 14 2008 - 14:25:33 PDT)
- Neelanjana Sengupta (Wed May 14 2008 - 14:14:54 PDT)
- Qiuting Hong (Wed May 14 2008 - 13:52:33 PDT)
AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER
- yuan li (Tue May 13 2008 - 19:53:10 PDT)
AMBER: single stranded DNA
- Taufik Al-Sarraj (Tue May 06 2008 - 17:11:07 PDT)
- David A. Case (Tue May 06 2008 - 15:41:29 PDT)
- Taufik Al-Sarraj (Tue May 06 2008 - 15:37:41 PDT)
AMBER: solvatebox
- Ross Walker (Thu May 29 2008 - 08:22:53 PDT)
- fatima.chami.durham.ac.uk (Thu May 29 2008 - 04:46:42 PDT)
AMBER: solvatebox error
- WANG,YING (Thu May 15 2008 - 15:16:17 PDT)
- Ross Walker (Thu May 15 2008 - 14:54:08 PDT)
- WANG,YING (Thu May 15 2008 - 14:47:06 PDT)
AMBER: Solvent mixture box
- Francesco Pietra (Sun May 11 2008 - 10:04:52 PDT)
AMBER: STEERED MD
- Robert Duke (Sat May 17 2008 - 06:21:10 PDT)
- fatima.chami.durham.ac.uk (Sat May 17 2008 - 03:26:28 PDT)
- Robert Duke (Fri May 16 2008 - 10:29:29 PDT)
- Robert Duke (Fri May 16 2008 - 10:15:40 PDT)
- fatima.chami.durham.ac.uk (Fri May 16 2008 - 09:25:55 PDT)
AMBER: steered MD initial state
- M. L. Dodson (Tue May 06 2008 - 10:39:04 PDT)
- M. L. Dodson (Tue May 06 2008 - 10:27:03 PDT)
- Adrian Roitberg (Tue May 06 2008 - 10:16:52 PDT)
- Gustavo Seabra (Tue May 06 2008 - 09:37:54 PDT)
- M. L. Dodson (Tue May 06 2008 - 09:04:09 PDT)
AMBER: subscribe amber
- wangluohuaxue (Wed May 14 2008 - 07:40:04 PDT)
AMBER: test.parallel.QMMM problem
- Ross Walker (Fri May 02 2008 - 08:50:31 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Fri May 02 2008 - 06:37:28 PDT)
AMBER: tleap error message
- Wang,Ying (Fri May 30 2008 - 09:08:14 PDT)
AMBER: to unsubscribe email
- Rabin (Mon May 12 2008 - 14:29:56 PDT)
- Bill Ross (Mon May 12 2008 - 10:46:24 PDT)
- Rabin (Mon May 12 2008 - 08:47:43 PDT)
AMBER: Torsion angle restrains and Jarzinsky
- E.M. (Mon May 05 2008 - 00:06:56 PDT)
AMBER: trajectories into trajectory
- Florian Haberl (Sun May 25 2008 - 05:10:41 PDT)
- Hakkim Boy (Sun May 25 2008 - 04:30:22 PDT)
AMBER: Umbrella Sampling for proteins
- German Erlenkamp (Mon May 26 2008 - 02:23:56 PDT)
AMBER: unable to compile AmberTools 1.0
- Yu Chen (Mon May 05 2008 - 12:06:26 PDT)
- David A. Case (Mon May 05 2008 - 11:14:44 PDT)
- Rabin (Mon May 05 2008 - 10:07:00 PDT)
AMBER: uninstall of AMBER
- Ross Walker (Wed May 07 2008 - 10:05:20 PDT)
- David A. Case (Wed May 07 2008 - 09:07:25 PDT)
- sudipta sinha (Wed May 07 2008 - 08:50:37 PDT)
AMBER: Units, units units
- David A. Case (Mon May 05 2008 - 16:02:57 PDT)
- E.M. (Mon May 05 2008 - 15:18:37 PDT)
AMBER: using amber ports in Gromacs
- Carlos Simmerling (Sun May 25 2008 - 12:32:05 PDT)
- Cristina Sisu (Sun May 25 2008 - 11:28:26 PDT)
- Cristina Sisu (Sun May 25 2008 - 11:22:58 PDT)
AMBER: velocity autocorrelation function for SPC felxible water model
- David A. Case (Thu May 08 2008 - 15:54:57 PDT)
- Rahaman, Asif (Thu May 08 2008 - 13:42:22 PDT)
- David A. Case (Thu May 08 2008 - 11:00:28 PDT)
- Rahaman, Asif (Thu May 08 2008 - 10:07:41 PDT)
AMBER: Versions of mopac
- David A. Case (Fri May 16 2008 - 19:04:10 PDT)
AMBER: VMD Movie
- Carlos Simmerling (Wed May 28 2008 - 17:10:03 PDT)
- Campbell, Patrick (Wed May 28 2008 - 16:33:39 PDT)
AMBER: VMD Movie 2
- Carlos Simmerling (Thu May 29 2008 - 10:48:10 PDT)
- Campbell, Patrick (Thu May 29 2008 - 10:39:20 PDT)
AMBER: VMD Movie 3
- Campbell, Patrick (Fri May 30 2008 - 07:56:41 PDT)
- Ibrahim Moustafa (Thu May 29 2008 - 14:03:16 PDT)
- Ross Walker (Thu May 29 2008 - 11:47:52 PDT)
- Campbell, Patrick (Thu May 29 2008 - 11:12:20 PDT)
AMBER: VMD Movie 4
- Campbell, Patrick (Thu May 29 2008 - 12:37:43 PDT)
AMBER: Water residue tracking
- Steve Seibold (Thu May 01 2008 - 09:19:42 PDT)
AMBER: Water tracking
- Steve Seibold (Fri May 02 2008 - 08:09:35 PDT)
- Thomas Cheatham III (Fri May 02 2008 - 09:14:21 PDT)
AMBER: Weighting factors in RESP charge fitting
- Piotr Cieplak (Fri May 16 2008 - 11:46:51 PDT)
- Anselm Horn (Fri May 16 2008 - 05:32:22 PDT)
AMBER: Which is best temperature controlling method
- David A. Case (Thu May 29 2008 - 07:35:36 PDT)
- Robert Duke (Thu May 29 2008 - 05:19:22 PDT)
- Germain Vallverdu (Wed May 28 2008 - 13:24:55 PDT)
- sudipta sinha (Wed May 28 2008 - 11:02:53 PDT)
- Adrian Roitberg (Wed May 28 2008 - 10:43:09 PDT)
- David A. Case (Wed May 28 2008 - 10:32:33 PDT)
- Mark Abraham (Wed May 28 2008 - 00:02:14 PDT)
- sudipta sinha (Tue May 27 2008 - 23:43:32 PDT)
- Reena ..... (Tue May 27 2008 - 22:34:39 PDT)
- David A. Case (Tue May 27 2008 - 21:59:23 PDT)
- sudipta sinha (Tue May 27 2008 - 03:25:02 PDT)
AMBER: xleap (draw using edit)
- Taufik Al-Sarraj (Thu May 08 2008 - 13:58:24 PDT)
- David A. Case (Thu May 08 2008 - 11:02:58 PDT)
- Taufik Al-Sarraj (Wed May 07 2008 - 19:31:14 PDT)
AMBER: xLeap compilation issues
- Sasha Buzko (Wed May 21 2008 - 08:52:00 PDT)
- David A. Case (Tue May 20 2008 - 22:27:53 PDT)
- Sasha Buzko (Tue May 20 2008 - 16:41:49 PDT)
rmsd vs frame
- Francesco Pietra (Wed May 28 2008 - 16:19:11 PDT)

Amber Archive May 2008 by subject