Amber Archive Jan 2007: by subject

a request
- Ross Walker (Wed Jan 24 2007 - 09:57:32 PST)
AMBER:
- Ross Walker (Fri Jan 19 2007 - 12:47:24 PST)
- Steve Seibold (Fri Jan 19 2007 - 11:53:47 PST)
- Steve Seibold (Wed Jan 10 2007 - 11:03:30 PST)
- Ross Walker (Wed Jan 10 2007 - 09:17:11 PST)
- Vladimir Tchoupakhine (Wed Jan 10 2007 - 08:51:46 PST)
- Steve Seibold (Wed Jan 10 2007 - 08:46:28 PST)
AMBER: (no subject)
- Sophie Barbe (Wed Jan 24 2007 - 09:26:20 PST)
- Yusheng Dou (Fri Jan 19 2007 - 06:51:51 PST)
- mahdi fathi (Thu Jan 18 2007 - 02:10:24 PST)
- Yusheng Dou (Wed Jan 17 2007 - 09:29:10 PST)
AMBER: 22 improper torsions in old prep form
- Bill Ross (Fri Jan 05 2007 - 10:39:23 PST)
- saurabh agrawal (Thu Jan 04 2007 - 22:29:21 PST)
AMBER: a question about analysis of DNA duplex after MD simulation with curves
- wendy chen (Sat Jan 20 2007 - 19:28:19 PST)
AMBER: about coordinates ****** and diffusion
- Thomas Cheatham (Sun Jan 28 2007 - 13:09:00 PST)
- Ross Walker (Sun Jan 28 2007 - 09:28:30 PST)
- kepa koldo burusco (Sun Jan 28 2007 - 09:15:57 PST)
AMBER: About the problem of the PMEMD and cutoff
- Robert Duke (Mon Jan 15 2007 - 05:19:26 PST)
- 方磊 (Mon Jan 15 2007 - 04:45:29 PST)
- Robert Duke (Sun Jan 14 2007 - 20:20:22 PST)
- 方磊 (Sun Jan 14 2007 - 19:56:17 PST)
AMBER: ADDIONS do not neutralize to ZERO
- Chris Moth (Mon Jan 29 2007 - 13:30:20 PST)
- Akshay Patny (Mon Jan 29 2007 - 09:04:58 PST)
- Ross Walker (Sun Jan 28 2007 - 20:38:25 PST)
- saurabh agrawal (Sun Jan 28 2007 - 20:07:37 PST)
- Bill Ross (Sun Jan 28 2007 - 12:41:43 PST)
- Akshay Patny (Fri Jan 26 2007 - 15:38:48 PST)
- Bill Ross (Tue Jan 23 2007 - 09:30:06 PST)
- Akshay Patny (Mon Jan 22 2007 - 18:10:47 PST)
- Bill Ross (Mon Jan 22 2007 - 17:58:11 PST)
- Akshay Patny (Mon Jan 22 2007 - 17:19:20 PST)
AMBER: Amber 8.0 : how to represent EPS with VMD?
- Guillaume Bollot (Fri Jan 12 2007 - 06:49:28 PST)
AMBER: amber 9
- Chris Moth (Thu Jan 11 2007 - 11:43:27 PST)
- David A. Case (Thu Jan 11 2007 - 11:21:09 PST)
- Sophie Barbe (Wed Jan 10 2007 - 10:28:51 PST)
- Ross Walker (Wed Jan 10 2007 - 10:11:44 PST)
- Sophie Barbe (Wed Jan 10 2007 - 09:54:36 PST)
- Ross Walker (Tue Jan 09 2007 - 08:31:36 PST)
- Sophie Barbe (Tue Jan 09 2007 - 07:29:04 PST)
AMBER: AMBER citation questions
- Carlos Simmerling (Thu Jan 04 2007 - 03:36:28 PST)
- caoch.cherry.bio.titech.ac.jp (Thu Jan 04 2007 - 00:59:08 PST)
AMBER: AMBER complile problem
- Chengwen Chen (Mon Jan 01 2007 - 19:19:08 PST)
AMBER: amber parallel compile error with g95
- Seaclear Theory (Fri Jan 26 2007 - 11:00:52 PST)
AMBER: amber9 installation error
- Seaclear Theory (Thu Jan 04 2007 - 13:27:14 PST)
- Seaclear Theory (Wed Jan 03 2007 - 20:34:49 PST)
- David A. Case (Wed Jan 03 2007 - 18:05:35 PST)
- Seaclear Theory (Wed Jan 03 2007 - 10:04:27 PST)
- Seaclear Theory (Wed Jan 03 2007 - 07:55:51 PST)
- David A. Case (Tue Jan 02 2007 - 23:00:50 PST)
- Seaclear Theory (Tue Jan 02 2007 - 18:10:12 PST)
AMBER: amber9 parralel compiling
- Seaclear Theory (Sat Jan 27 2007 - 15:16:19 PST)
- David A. Case (Sat Jan 27 2007 - 11:28:27 PST)
- Seaclear Theory (Sat Jan 27 2007 - 10:59:23 PST)
- David A. Case (Fri Jan 26 2007 - 15:45:25 PST)
- Seaclear Theory (Fri Jan 26 2007 - 10:55:43 PST)
- Seaclear Theory (Thu Jan 25 2007 - 18:15:05 PST)
AMBER: another sander bug?
- Ross Walker (Thu Jan 25 2007 - 23:50:39 PST)
- Nursultan Bogatov (Thu Jan 25 2007 - 22:43:13 PST)
AMBER: Antechamber Charge Calculation Method
- Junmei Wang (Mon Jan 29 2007 - 18:48:17 PST)
- A Box (Mon Jan 29 2007 - 16:46:42 PST)
AMBER: Antechamber esp calculation
- FyD (Mon Jan 22 2007 - 22:05:46 PST)
- Ilyas Yildirim (Mon Jan 22 2007 - 22:07:31 PST)
- mathew k varghese (Mon Jan 22 2007 - 20:44:42 PST)
AMBER: assign atom hybrid
- xiaoqin huang (Tue Jan 02 2007 - 17:54:52 PST)
AMBER: calcium parameter for GB
- Qing Zhang (Wed Jan 24 2007 - 09:33:24 PST)
- Ji-Lai Li (Tue Jan 23 2007 - 18:07:21 PST)
- Qing Zhang (Tue Jan 23 2007 - 10:49:54 PST)
- Bill Ross (Thu Jan 18 2007 - 10:36:01 PST)
- Wei Chen (Thu Jan 18 2007 - 08:15:45 PST)
- Ji-Lai Li (Wed Jan 17 2007 - 17:25:20 PST)
- Qing Zhang (Wed Jan 17 2007 - 09:06:36 PST)
- Wei Chen (Wed Jan 17 2007 - 08:25:47 PST)
- Ji-Lai Li (Wed Jan 17 2007 - 00:19:09 PST)
- David A. Case (Tue Jan 16 2007 - 15:33:43 PST)
- Wei Chen (Tue Jan 16 2007 - 15:21:08 PST)
AMBER: Can't run decompose energy in MM-PBSA
- vanessa wai (Mon Jan 22 2007 - 17:37:02 PST)
- Ray Luo (Mon Jan 22 2007 - 09:27:03 PST)
- jitrayut jitonnom (Mon Jan 22 2007 - 06:20:51 PST)
AMBER: Can't run Normal Mode Analysis !!!
- Scott Pendley (Mon Jan 22 2007 - 09:05:26 PST)
- jitrayut jitonnom (Sun Jan 21 2007 - 21:09:48 PST)
AMBER: Charges in TI calculations and leap
- David A. Case (Tue Jan 30 2007 - 13:24:33 PST)
- Austin B. Yongye (Tue Jan 30 2007 - 12:10:54 PST)
- Ilyas Yildirim (Tue Jan 30 2007 - 11:48:00 PST)
- Austin B. Yongye (Tue Jan 30 2007 - 11:35:50 PST)
AMBER: convert pdb files to restart files
- Ross Walker (Tue Jan 16 2007 - 07:19:54 PST)
- Stefano Pieraccini (Tue Jan 16 2007 - 04:57:41 PST)
- khn _ (Tue Jan 16 2007 - 02:50:47 PST)
AMBER: coordinates ******
- David A. Case (Thu Jan 25 2007 - 12:08:52 PST)
- Bill Ross (Tue Jan 23 2007 - 13:20:10 PST)
- kepa koldo burusco (Tue Jan 23 2007 - 08:19:54 PST)
AMBER: CYX residue missing from Amber 9 ff03ua (?)
- Ray Luo (Thu Jan 11 2007 - 14:59:29 PST)
- Chris Moth (Thu Jan 11 2007 - 11:32:04 PST)
AMBER: Deep energetics problem
- sai vikram (Wed Jan 03 2007 - 00:26:42 PST)
- Ross Walker (Tue Jan 02 2007 - 11:12:53 PST)
- sai vikram (Tue Jan 02 2007 - 09:10:19 PST)
AMBER: Defining BOX INFO during TLEAP
- Ross Walker (Wed Jan 24 2007 - 12:09:30 PST)
- Akshay Patny (Wed Jan 24 2007 - 11:54:37 PST)
- David A. Case (Wed Jan 24 2007 - 07:04:24 PST)
- Akshay Patny (Mon Jan 22 2007 - 19:02:15 PST)
AMBER: deformation of DNA duplex after MD simulation (AMBER9)
- Chengwen Chen (Sat Jan 20 2007 - 20:28:59 PST)
AMBER: dihedral angle by Ptraj
- Esther Brugger (Wed Jan 24 2007 - 09:08:15 PST)
- Esther Brugger (Wed Jan 24 2007 - 08:02:38 PST)
- Thomas Cheatham (Tue Jan 23 2007 - 19:57:47 PST)
- Esther Brugger (Tue Jan 23 2007 - 15:02:00 PST)
- Thomas Cheatham III (Tue Jan 23 2007 - 10:41:22 PST)
- Esther Brugger (Tue Jan 23 2007 - 10:24:42 PST)
AMBER: Dihedral FF parameters
- Ye Mei (Fri Jan 19 2007 - 07:44:14 PST)
- FyD (Fri Jan 19 2007 - 07:40:10 PST)
AMBER: Distance Restraints
- Esther Brugger (Fri Jan 05 2007 - 07:17:38 PST)
- Esther Brugger (Wed Jan 03 2007 - 14:04:03 PST)
- Esther Brugger (Wed Jan 03 2007 - 12:29:26 PST)
AMBER: Distance Restraints Problem
- David A. Case (Tue Jan 02 2007 - 15:37:18 PST)
- Esther Brugger (Tue Jan 02 2007 - 14:00:16 PST)
AMBER: DNA structure analysis
- Catein Catherine (Wed Jan 17 2007 - 08:24:16 PST)
- Catein Catherine (Wed Jan 17 2007 - 08:23:08 PST)
- Fenghui Fan (Wed Jan 17 2007 - 07:31:00 PST)
- Jiri Sponer (Wed Jan 17 2007 - 02:39:36 PST)
- Catein Catherine (Tue Jan 16 2007 - 19:12:42 PST)
AMBER: Does amber use water density around 1 at room temperature
- Thomas Steinbrecher (Wed Jan 24 2007 - 15:26:50 PST)
- Li Su (Wed Jan 24 2007 - 14:44:40 PST)
- Ross Walker (Tue Jan 23 2007 - 15:11:41 PST)
- Li Su (Tue Jan 23 2007 - 14:07:20 PST)
AMBER: Drug bound to the protein
- Bill Ross (Wed Jan 17 2007 - 11:28:15 PST)
- David A. Case (Wed Jan 17 2007 - 08:57:02 PST)
- Guillermo Mulliert Carlín (Wed Jan 17 2007 - 07:27:45 PST)
- Sophie Barbe (Wed Jan 17 2007 - 00:56:21 PST)
AMBER: Drug Leads interaction with ds and Triplex DNA
- puneet kacker (Wed Jan 24 2007 - 21:28:41 PST)
AMBER: entropy units
- Giulio Rastelli (Mon Jan 08 2007 - 02:33:19 PST)
AMBER: enzyme kinetics in silico
- Fenghui Fan (Thu Jan 04 2007 - 13:34:41 PST)
- Suxin Zheng (Thu Jan 04 2007 - 09:54:47 PST)
- Sean Rathlef (Thu Jan 04 2007 - 09:24:46 PST)
AMBER: equilibration with amber5, production of MD with amber7
- David A. Case (Sun Jan 21 2007 - 21:28:46 PST)
- Carlos Javier Nuñez Aguero (Fri Jan 19 2007 - 12:47:05 PST)
AMBER: error when compiling Moilview
- Carlos Simmerling (Thu Jan 25 2007 - 09:34:26 PST)
- Kailee (Thu Jan 25 2007 - 08:12:09 PST)
- Gustavo Seabra (Thu Jan 25 2007 - 07:50:57 PST)
- Kailee (Thu Jan 25 2007 - 05:03:07 PST)
- Carlos Simmerling (Thu Jan 25 2007 - 04:24:53 PST)
- Kailee (Thu Jan 25 2007 - 03:31:24 PST)
AMBER: error when using sander.LES: exceeded MAXLES
- David A. Case (Thu Jan 18 2007 - 09:12:23 PST)
- Carlos Simmerling (Thu Jan 18 2007 - 09:03:08 PST)
- Kailee (Thu Jan 18 2007 - 08:33:18 PST)
AMBER: evaluate expression
- Ji-Lai Li (Wed Jan 24 2007 - 20:14:11 PST)
AMBER: experimental phi-values as restraints
- Vladimir Tchoupakhine (Wed Jan 10 2007 - 08:23:58 PST)
- rebeca.mmb.pcb.ub.es (Wed Jan 10 2007 - 08:06:11 PST)
AMBER: explicit implicit solvent
- Carlos Simmerling (Wed Jan 10 2007 - 06:53:53 PST)
- Ji-Lai Li (Wed Jan 10 2007 - 06:24:20 PST)
AMBER: Fatal error: Command failed for target `test.sander.no_lmod'
- Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 17:26:45 PST)
- Gustavo Seabra (Tue Jan 23 2007 - 08:54:09 PST)
- Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 01:50:58 PST)
AMBER: fluctuations
- Jardas sucuriba (Tue Jan 02 2007 - 07:21:22 PST)
AMBER: format of .xyz files and pdb
- Steven Winfield (Wed Jan 31 2007 - 14:20:43 PST)
AMBER: Fwd: a request
- Gustavo Seabra (Tue Jan 30 2007 - 07:53:33 PST)
- santanu roy (Tue Jan 30 2007 - 02:04:46 PST)
- Gustavo Seabra (Mon Jan 29 2007 - 09:24:12 PST)
- santanu roy (Sun Jan 28 2007 - 22:43:53 PST)
- Gustavo Seabra (Sat Jan 27 2007 - 20:52:08 PST)
- santanu roy (Fri Jan 26 2007 - 22:34:15 PST)
- Gustavo Seabra (Thu Jan 25 2007 - 07:49:49 PST)
- santanu roy (Thu Jan 25 2007 - 05:15:08 PST)
- Gustavo Seabra (Thu Jan 25 2007 - 04:44:58 PST)
- santanu roy (Thu Jan 25 2007 - 00:55:32 PST)
AMBER: G5 OSX serial compile error
- Mengjuei Hsieh (Mon Jan 08 2007 - 16:26:26 PST)
- Kevin Kelliher (Fri Jan 05 2007 - 10:58:56 PST)
- Mengjuei Hsieh (Mon Jan 01 2007 - 02:16:12 PST)
AMBER: Gas-phase energies (and more)
- Yong Duan (Tue Jan 30 2007 - 12:32:39 PST)
- Yong Duan (Sun Jan 28 2007 - 19:43:56 PST)
- David A. Case (Sun Jan 28 2007 - 18:23:29 PST)
- Carlos Simmerling (Sun Jan 28 2007 - 10:48:13 PST)
- Jason K (Fri Jan 26 2007 - 13:36:25 PST)
- Yong Duan (Thu Jan 25 2007 - 15:58:48 PST)
- Jason K (Thu Jan 25 2007 - 15:04:16 PST)
AMBER: gaussian output to prepin problem
- Junmei Wang (Mon Jan 29 2007 - 18:43:56 PST)
- Rima Chaudhuri (Mon Jan 29 2007 - 09:14:31 PST)
AMBER: H-acceptors problem in ptraj
- nag raj (Wed Jan 03 2007 - 21:20:09 PST)
AMBER: H-bond in each fram
- nag raj (Sun Jan 07 2007 - 21:49:57 PST)
AMBER: H-bond in ptraj
- nag raj (Fri Jan 05 2007 - 23:22:10 PST)
- Barbault Florent (Fri Jan 05 2007 - 00:20:22 PST)
- nag raj (Thu Jan 04 2007 - 20:34:59 PST)
- Jianyin Shao (Thu Jan 04 2007 - 11:49:38 PST)
- nag raj (Wed Jan 03 2007 - 04:17:51 PST)
AMBER: HF/6-31G* ESP Charges do not match with ff02 charges
- Pavan G (Sun Jan 28 2007 - 07:45:32 PST)
- FyD (Fri Jan 19 2007 - 12:30:43 PST)
- mernst.tricity.wsu.edu (Fri Jan 19 2007 - 10:59:52 PST)
- FyD (Fri Jan 19 2007 - 00:31:46 PST)
- mernst.tricity.wsu.edu (Thu Jan 18 2007 - 23:02:10 PST)
- Pavan G (Thu Jan 18 2007 - 22:19:19 PST)
AMBER: How are water molecules at cutoff being treated?
- David A. Case (Tue Jan 16 2007 - 15:36:07 PST)
- Li Su (Tue Jan 16 2007 - 14:48:47 PST)
AMBER: How many steps should be used for a MD calculation?
- Michel Becker (Tue Jan 09 2007 - 01:12:55 PST)
AMBER: how much restraint ?
- AYTUG TUNCEL (Mon Jan 22 2007 - 14:09:12 PST)
AMBER: How to change the force field equation in amber by programming...
- David A. Case (Mon Jan 08 2007 - 15:00:10 PST)
- Gobind Singh Bisht (Sun Jan 07 2007 - 06:06:06 PST)
- David A. Case (Fri Jan 05 2007 - 13:34:41 PST)
- Gobind Singh Bisht (Fri Jan 05 2007 - 11:55:22 PST)
AMBER: How to do minimization..
- Ross Walker (Mon Jan 08 2007 - 08:32:09 PST)
- sai vikram (Mon Jan 08 2007 - 07:30:59 PST)
AMBER: How to get a periodic box of modified water molecules
- David A. Case (Wed Jan 03 2007 - 22:04:10 PST)
- Li Su (Wed Jan 03 2007 - 09:25:11 PST)
AMBER: Hydrogen in a phosphate ion
- David A. Case (Tue Jan 09 2007 - 11:46:43 PST)
- Nitin Bhardwaj (Fri Jan 05 2007 - 14:00:09 PST)
AMBER: I need some constant pressure MD help
- Ross Walker (Tue Jan 30 2007 - 21:47:38 PST)
- David Cerutti (Tue Jan 30 2007 - 20:39:06 PST)
AMBER: image command
- Petr Kulhanek (Wed Jan 10 2007 - 00:45:45 PST)
- Thomas Cheatham (Tue Jan 09 2007 - 22:25:48 PST)
- venditti2.unisi.it (Tue Jan 09 2007 - 06:09:07 PST)
AMBER: Improper angle by Antechamber
- David A. Case (Sun Jan 28 2007 - 18:20:26 PST)
- Pavan G (Sun Jan 28 2007 - 09:28:29 PST)
AMBER: improper dihedral
- David A. Case (Fri Jan 26 2007 - 08:09:55 PST)
- lishan yao (Fri Jan 26 2007 - 06:42:15 PST)
AMBER: improper torsions
- Bill Ross (Mon Jan 08 2007 - 12:00:06 PST)
- Fenghui Fan (Mon Jan 08 2007 - 11:45:09 PST)
- Ed Pate (Mon Jan 08 2007 - 11:08:36 PST)
AMBER: Including Relevant Subject Lines
- Ross Walker (Tue Jan 30 2007 - 08:43:59 PST)
AMBER: Installation help - SGI Altix 350
- Gustavo Seabra (Wed Jan 10 2007 - 08:07:26 PST)
- Ross Walker (Tue Jan 09 2007 - 08:18:55 PST)
- bertrand russell (Mon Jan 08 2007 - 23:17:54 PST)
AMBER: installing amber 8 on 5 nodes cluster PC
- Syed Tarique Moin (Wed Jan 03 2007 - 10:25:45 PST)
- David A. Case (Wed Jan 03 2007 - 09:26:17 PST)
- Syed Tarique Moin (Wed Jan 03 2007 - 08:44:54 PST)
AMBER: intra-molecular h-bonds in ptraj
- Jianyin Shao (Thu Jan 04 2007 - 12:11:36 PST)
- lily ferreira (Thu Jan 04 2007 - 07:17:37 PST)
AMBER: Is there a pmemd machine file for OSX Intel
- Kevin Kelliher (Fri Jan 26 2007 - 13:50:29 PST)
AMBER: issues with restrt file
- Carlos Simmerling (Thu Jan 18 2007 - 10:02:48 PST)
- Carlos Simmerling (Thu Jan 18 2007 - 10:30:01 PST)
- Amit Kumar (Thu Jan 18 2007 - 10:27:12 PST)
- Amit Kumar (Thu Jan 18 2007 - 09:59:40 PST)
- Carlos Simmerling (Thu Jan 18 2007 - 09:07:35 PST)
- Amit Kumar (Thu Jan 18 2007 - 08:15:52 PST)
AMBER: Leap adding 3 extra atoms
- Bill Ross (Thu Jan 11 2007 - 11:33:14 PST)
- Akshay Patny (Thu Jan 11 2007 - 09:35:00 PST)
AMBER: Leap adding extra atoms
- Scott Brozell (Mon Jan 15 2007 - 13:30:00 PST)
- Scott Brozell (Mon Jan 15 2007 - 12:39:49 PST)
- Akshay Patny (Thu Jan 11 2007 - 13:38:37 PST)
AMBER: Ligand-Protein Distance Restraints during MD Simulation
- David Mobley (Tue Jan 30 2007 - 09:16:19 PST)
- Akshay Patny (Fri Jan 26 2007 - 16:06:26 PST)
AMBER: LJ potential
- David A. Case (Sat Jan 27 2007 - 10:03:15 PST)
- Steve Seibold (Wed Jan 24 2007 - 11:44:58 PST)
AMBER: minimization using fcap
- David A. Case (Wed Jan 24 2007 - 07:05:20 PST)
- Syed Tarique Moin (Wed Jan 24 2007 - 01:08:40 PST)
AMBER: MM-PBSA doubt
- Ray Luo (Mon Jan 29 2007 - 21:29:01 PST)
- mathew k varghese (Mon Jan 29 2007 - 20:22:50 PST)
- Ray Luo (Mon Jan 29 2007 - 20:04:52 PST)
- mathew k varghese (Mon Jan 29 2007 - 18:12:44 PST)
AMBER: MM-PBSA problem: Why
- vanessa wai (Mon Jan 22 2007 - 02:47:30 PST)
- jitrayut jitonnom (Sun Jan 21 2007 - 21:20:38 PST)
AMBER: mm-pbsa, long distance free energy calculation problem
- Bing Liu (Thu Jan 18 2007 - 13:09:38 PST)
- Wei Chen (Thu Jan 18 2007 - 12:24:26 PST)
- Bing Liu (Thu Jan 18 2007 - 09:06:53 PST)
AMBER: MM-PSBA decoupling
- Sergey Samsonov (Wed Jan 24 2007 - 05:03:24 PST)
AMBER: mm_pbsa Array reference error
- Syed Tarique Moin (Wed Jan 31 2007 - 21:19:48 PST)
- Scott Pendley (Wed Jan 31 2007 - 09:48:36 PST)
- Syed Tarique Moin (Sat Jan 27 2007 - 00:02:16 PST)
- Syed Tarique Moin (Thu Jan 25 2007 - 22:21:07 PST)
AMBER: mm_pbsa error
- Syed Tarique Moin (Wed Jan 31 2007 - 01:19:02 PST)
- Syed Tarique Moin (Wed Jan 31 2007 - 01:19:46 PST)
- vanessa wai (Sat Jan 27 2007 - 07:02:33 PST)
- Syed Tarique Moin (Thu Jan 25 2007 - 22:04:22 PST)
- vanessa wai (Thu Jan 25 2007 - 18:13:19 PST)
- Varsha Goyal (Thu Jan 25 2007 - 08:16:31 PST)
- Syed Tarique Moin (Thu Jan 25 2007 - 02:04:36 PST)
- vanessa wai (Wed Jan 24 2007 - 23:24:43 PST)
- Syed Tarique Moin (Wed Jan 24 2007 - 23:15:29 PST)
AMBER: mm_pbsa problems
- Jardas sucuriba (Tue Jan 30 2007 - 07:55:00 PST)
AMBER: mm_pbsa vertex atom mismatch
- AYTUG TUNCEL (Tue Jan 16 2007 - 15:10:35 PST)
AMBER: mm_pbsa_statistics.pl
- Antonio Morreale (Tue Jan 16 2007 - 04:28:52 PST)
AMBER: Molecular dynamic issues
- Sophie Barbe (Wed Jan 24 2007 - 06:41:19 PST)
- Carlos Simmerling (Tue Jan 23 2007 - 06:54:24 PST)
- Chupakhin Vladimir (Tue Jan 23 2007 - 06:50:56 PST)
- Sophie Barbe (Tue Jan 23 2007 - 06:34:50 PST)
AMBER: MPI is slower than single processor with water
- Yu Chen (Tue Jan 16 2007 - 12:23:23 PST)
- Mike Summers (Tue Jan 16 2007 - 09:32:53 PST)
- Ross Walker (Tue Jan 16 2007 - 08:50:36 PST)
- Mike Summers (Tue Jan 16 2007 - 08:30:18 PST)
AMBER: NH3 potential
- Jennie Thomas (Wed Jan 03 2007 - 13:00:28 PST)
AMBER: nonpolar solvation energy
- Carlos Simmerling (Wed Jan 31 2007 - 11:54:14 PST)
- Ray Luo (Wed Jan 31 2007 - 11:37:34 PST)
- khn _ (Wed Jan 31 2007 - 08:33:55 PST)
AMBER: nuc.in file
- David A. Case (Thu Jan 25 2007 - 11:59:12 PST)
- Bill Ross (Tue Jan 23 2007 - 09:42:44 PST)
- deepti nayar (Tue Jan 23 2007 - 00:21:27 PST)
AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation
- David A. Case (Fri Jan 26 2007 - 17:45:51 PST)
- Akshay Patny (Fri Jan 26 2007 - 15:27:56 PST)
- Ross Walker (Fri Jan 26 2007 - 15:11:06 PST)
- Akshay Patny (Fri Jan 26 2007 - 14:23:46 PST)
AMBER: organic solvent : hexan octan
- FyD (Wed Jan 24 2007 - 20:50:33 PST)
- Cenk Andac (Wed Jan 24 2007 - 11:37:12 PST)
- Gustavo Seabra (Wed Jan 24 2007 - 11:12:40 PST)
- Sophie Barbe (Wed Jan 24 2007 - 10:28:38 PST)
- Cenk Andac (Wed Jan 24 2007 - 10:18:19 PST)
- Sophie Barbe (Wed Jan 24 2007 - 09:38:50 PST)
AMBER: output
- Thaison Tran (Sat Jan 13 2007 - 23:59:56 PST)
- David A. Case (Sat Jan 13 2007 - 21:38:24 PST)
- khn _ (Sat Jan 13 2007 - 20:24:11 PST)
AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f
- David A. Case (Wed Jan 24 2007 - 07:14:24 PST)
- Ray Luo (Tue Jan 23 2007 - 10:43:23 PST)
- emilia wu (Mon Jan 22 2007 - 18:45:46 PST)
- Ray Luo (Mon Jan 22 2007 - 18:35:06 PST)
- emilia wu (Mon Jan 22 2007 - 16:22:39 PST)
- emilia wu (Sun Jan 21 2007 - 17:42:18 PST)
- Ray Luo (Sat Jan 20 2007 - 10:45:36 PST)
- emilia wu (Fri Jan 19 2007 - 17:54:27 PST)
- Ray Luo (Fri Jan 19 2007 - 09:50:19 PST)
- emilia wu (Fri Jan 19 2007 - 05:15:56 PST)
AMBER: perturbed atoms are not bonded on using TIP5P wate
- David A. Case (Thu Jan 18 2007 - 09:40:37 PST)
- sugino tatsuro (Tue Jan 16 2007 - 21:47:51 PST)
AMBER: perturbed atoms are not bonded on using TIP5P water
- sugino tatsuro (Tue Jan 16 2007 - 09:35:22 PST)
- sugino tatsuro (Mon Jan 15 2007 - 19:33:18 PST)
- sugino tatsuro (Mon Jan 15 2007 - 19:19:59 PST)
- David A. Case (Mon Jan 15 2007 - 18:23:17 PST)
- sugino tatsuro (Mon Jan 15 2007 - 17:40:32 PST)
- David A. Case (Sun Jan 14 2007 - 09:39:13 PST)
- Steven Winfield (Fri Jan 12 2007 - 06:07:38 PST)
- sugino tatsuro (Fri Jan 12 2007 - 05:58:40 PST)
- David A. Case (Thu Jan 11 2007 - 14:12:23 PST)
- sugino tatsuro (Thu Jan 11 2007 - 06:12:09 PST)
AMBER: pmemd install error
- Robert Duke (Tue Jan 30 2007 - 12:24:19 PST)
- Ji-Lai Li (Sun Jan 28 2007 - 19:18:05 PST)
- David A. Case (Fri Jan 26 2007 - 15:45:14 PST)
- Robert Duke (Tue Jan 23 2007 - 05:01:46 PST)
- Ji-Lai Li (Mon Jan 22 2007 - 22:59:27 PST)
AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..."
- Ross Walker (Wed Jan 03 2007 - 15:34:23 PST)
- Mike Hanby (Wed Jan 03 2007 - 14:53:43 PST)
AMBER: problem compiling Amber 7
- David A. Case (Mon Jan 15 2007 - 09:38:26 PST)
- Scott Brozell (Mon Jan 15 2007 - 09:29:10 PST)
- Kevin Cahill (Sun Jan 14 2007 - 18:35:00 PST)
AMBER: problem with distance restraints
- David A. Case (Mon Jan 22 2007 - 15:41:50 PST)
- Ed Pate (Mon Jan 22 2007 - 14:29:15 PST)
- David A. Case (Mon Jan 22 2007 - 12:10:12 PST)
- Ed Pate (Mon Jan 22 2007 - 11:43:58 PST)
AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2
- Ross Walker (Wed Jan 24 2007 - 09:49:20 PST)
- David A. Case (Wed Jan 24 2007 - 07:09:36 PST)
- Steven Winfield (Tue Jan 23 2007 - 04:11:12 PST)
- Cenk Andac (Tue Jan 23 2007 - 04:03:37 PST)
AMBER: problems in energy minimization using TIP5P water model
- sugino tatsuro (Sun Jan 14 2007 - 08:35:11 PST)
AMBER: problems trying to modify Amber8
- David A. Case (Tue Jan 02 2007 - 15:53:36 PST)
AMBER: ptraj
- Thomas Cheatham III (Wed Jan 31 2007 - 16:03:00 PST)
- khn _ (Wed Jan 31 2007 - 08:26:00 PST)
AMBER: Ptraj: watershell and distance
- Pavan G (Tue Jan 30 2007 - 14:01:07 PST)
- Esther Brugger (Tue Jan 30 2007 - 13:26:17 PST)
AMBER: question about the testing of AMBER9
- Shaoqing.Zhang.mail.uh.edu (Mon Jan 08 2007 - 13:56:44 PST)
- Mark Williamson (Mon Jan 08 2007 - 13:10:53 PST)
- Bill Ross (Mon Jan 08 2007 - 12:05:19 PST)
- Ross Walker (Mon Jan 08 2007 - 11:52:55 PST)
- Shaoqing.Zhang.mail.uh.edu (Mon Jan 08 2007 - 09:06:18 PST)
- Andreas Svrcek-Seiler (Mon Jan 08 2007 - 03:15:58 PST)
- Mark Williamson (Mon Jan 08 2007 - 01:36:55 PST)
- Shaoqing.Zhang.mail.uh.edu (Sun Jan 07 2007 - 17:18:05 PST)
- Mark Williamson (Sun Jan 07 2007 - 15:36:28 PST)
- Shaoqing.Zhang.mail.uh.edu (Sun Jan 07 2007 - 13:25:39 PST)
- Ross Walker (Sat Jan 06 2007 - 15:37:06 PST)
- Shaoqing.Zhang.mail.uh.edu (Sat Jan 06 2007 - 15:07:04 PST)
- David A. Case (Fri Jan 05 2007 - 20:54:53 PST)
- Shaoqing.Zhang.mail.uh.edu (Fri Jan 05 2007 - 18:25:16 PST)
AMBER: questions about analysing LES results
- Kailee (Tue Jan 30 2007 - 09:00:40 PST)
AMBER: Radii for water hydrogens are different
- David A. Case (Fri Jan 19 2007 - 10:13:41 PST)
- Steve Spronk (Tue Jan 16 2007 - 12:29:45 PST)
AMBER: radius of gyration
- Esther Brugger (Mon Jan 29 2007 - 14:27:34 PST)
- Thomas Cheatham III (Mon Jan 29 2007 - 13:21:20 PST)
- Esther Brugger (Mon Jan 29 2007 - 13:06:00 PST)
- Bill Ross (Mon Jan 29 2007 - 11:51:39 PST)
- Esther Brugger (Mon Jan 29 2007 - 07:51:26 PST)
- Bill Ross (Sun Jan 28 2007 - 12:01:05 PST)
- Esther Brugger (Fri Jan 26 2007 - 12:17:37 PST)
AMBER: Regarding energy of decomposition tutorials
- zachary hartman (Fri Jan 26 2007 - 07:29:50 PST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
- Akshay Patny (Mon Jan 29 2007 - 08:57:45 PST)
- FyD (Fri Jan 19 2007 - 05:19:17 PST)
- Akshay Patny (Fri Jan 19 2007 - 00:34:58 PST)
AMBER: RESP charges for charged species
- FyD (Tue Jan 16 2007 - 21:13:51 PST)
- Michel Becker (Tue Jan 16 2007 - 13:44:26 PST)
AMBER: sander bug?
- Ross Walker (Thu Jan 25 2007 - 23:26:55 PST)
- Nursultan Bogatov (Thu Jan 25 2007 - 18:28:53 PST)
AMBER: sander crashes during minimization
- Ross Walker (Wed Jan 10 2007 - 11:40:05 PST)
- Seth Lilavivat (Wed Jan 10 2007 - 11:29:15 PST)
AMBER: sanger
- David A. Case (Thu Jan 18 2007 - 09:05:34 PST)
- Carlos Simmerling (Thu Jan 18 2007 - 06:09:31 PST)
- Chupakhin Vladimir (Thu Jan 18 2007 - 06:05:01 PST)
- deepti nayar (Thu Jan 18 2007 - 03:29:19 PST)
AMBER: Section missing from AMBER 9 manual?
- David A. Case (Wed Jan 10 2007 - 13:02:12 PST)
- Steven Winfield (Wed Jan 10 2007 - 08:57:36 PST)
AMBER: Simulation of a charged system
- Carlos Simmerling (Fri Jan 05 2007 - 15:41:02 PST)
- Kijeong Kwac (Fri Jan 05 2007 - 15:08:42 PST)
AMBER: Simulations with GB models
- Carlos Simmerling (Thu Jan 11 2007 - 10:28:16 PST)
- Wei Chen (Thu Jan 11 2007 - 08:23:15 PST)
AMBER: solaris 10 and compilers on X86_64 hardware
- Knut Langsetmo (Wed Jan 17 2007 - 08:03:33 PST)
- M. L. Dodson (Wed Jan 17 2007 - 07:45:27 PST)
AMBER: solvation of protein using TIP3PBOX in amber 8
- Syed Tarique Moin (Mon Jan 15 2007 - 21:14:12 PST)
- Syed Tarique Moin (Sun Jan 14 2007 - 01:59:32 PST)
- David A. Case (Sat Jan 13 2007 - 21:40:46 PST)
- Syed Tarique Moin (Sat Jan 13 2007 - 10:25:46 PST)
AMBER: some questions about minimization and MD of DNA duplex with sander
- Ross Walker (Wed Jan 31 2007 - 08:36:27 PST)
- Chengwen Chen (Tue Jan 30 2007 - 23:44:13 PST)
AMBER: test submission through PBS queue
- Ross Walker (Wed Jan 10 2007 - 11:35:27 PST)
- Scott Brozell (Wed Jan 10 2007 - 11:33:09 PST)
- Evan Kelly (Wed Jan 10 2007 - 11:20:45 PST)
AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux)
- Chengwen Chen (Sat Jan 20 2007 - 19:55:46 PST)
- David A. Case (Fri Jan 19 2007 - 08:36:34 PST)
- Chengwen Chen (Fri Jan 19 2007 - 01:37:53 PST)
AMBER: The unperturbed charge of the unit: -20.999999 is not zero.
- Carlos Simmerling (Thu Jan 04 2007 - 11:31:29 PST)
- Nitin Bhardwaj (Thu Jan 04 2007 - 07:54:39 PST)
- saurabh agrawal (Wed Jan 03 2007 - 23:03:49 PST)
AMBER: torsion angle penalty calculation
- David A. Case (Wed Jan 03 2007 - 08:54:33 PST)
- Mike Summers (Wed Jan 03 2007 - 07:18:34 PST)
AMBER: torsion angle penalty calculationy
- Mike Summers (Wed Jan 03 2007 - 10:13:24 PST)
AMBER: Unable to compile amber9
- Ross Walker (Wed Jan 24 2007 - 07:48:41 PST)
- Vinh To (Wed Jan 24 2007 - 06:41:06 PST)
AMBER: united atom parameters for -NH2 and -OH groups
- emine cebe (Mon Jan 22 2007 - 11:47:12 PST)
AMBER: unsubscribe
- Perdita Barran (Sun Jan 07 2007 - 10:13:40 PST)
AMBER: vdW parameters for chlorine atom
- David A. Case (Wed Jan 17 2007 - 17:55:15 PST)
- Austin B. Yongye (Wed Jan 17 2007 - 09:19:34 PST)
AMBER: vertex atom mismatch
- saurabh agrawal (Wed Jan 17 2007 - 23:49:25 PST)
AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0
- saurabh agrawal (Thu Jan 18 2007 - 09:15:40 PST)
AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1
- Jiapu.Zhang.csiro.au (Mon Jan 29 2007 - 14:08:26 PST)
- Ross Walker (Sun Jan 28 2007 - 22:16:32 PST)
- Jiapu.Zhang.csiro.au (Sun Jan 28 2007 - 22:04:34 PST)
AMBER: xleap
- Gustavo Seabra (Tue Jan 30 2007 - 07:57:11 PST)
- Navnit Kumar Mishra (Tue Jan 30 2007 - 03:53:11 PST)
- Chupakhin Vladimir (Tue Jan 30 2007 - 02:55:40 PST)
- deepti nayar (Tue Jan 30 2007 - 02:40:10 PST)
AMBER: yet another SANDER bug?
- Ross Walker (Sat Jan 27 2007 - 20:18:24 PST)
- Miyeegombo Enkhbold (Sat Jan 27 2007 - 19:11:22 PST)
Fwd: AMBER: Atoms overlapping
- Nitin Bhardwaj (Thu Jan 04 2007 - 16:58:26 PST)
Fwd: AMBER: Can't run Normal Mode Analysis !!!
- jitrayut jitonnom (Mon Jan 22 2007 - 04:58:24 PST)
Fwd: AMBER: Improper angle by Antechamber
- Pavan G (Tue Jan 30 2007 - 10:46:34 PST)
Fwd: AMBER: mm_pbsa Array reference error
- Syed Tarique Moin (Fri Jan 26 2007 - 10:54:56 PST)
help
- Ross Walker (Tue Jan 16 2007 - 08:23:44 PST)
pmemd install error
- Ji-Lai Li (Mon Jan 22 2007 - 23:03:33 PST)
Re : AMBER: intra-molecular h-bonds in ptraj
- Thomas Cheatham (Sun Jan 07 2007 - 20:51:29 PST)
- Esther Brugger (Fri Jan 05 2007 - 07:11:43 PST)
- lily ferreira (Fri Jan 05 2007 - 05:37:52 PST)
tree name generated by tleap is different from the input PREP parameter file
- xiaoqin huang (Wed Jan 03 2007 - 07:05:18 PST)
- Bill Ross (Tue Jan 02 2007 - 20:26:14 PST)
- xiaoqin huang (Tue Jan 02 2007 - 18:41:13 PST)

Amber Archive Jan 2007 by subject