AMBER Archive (2009) - By Subject

Starting: Thu Jan 01 2009 - 21:37:45 CST
Ending: Thu Dec 31 2009 - 22:57:46 CST

• Marek Malý (Fri May 08 2009 - 14:12:39 CDT)
• (files attached) RESP with -a and witout -a flag
  • Jio M (Sat Oct 31 2009 - 00:17:55 CDT)
• =?utf-8?B?UmU6IFtBTUJFUl0gQ29tcGlsaW5nIEFtYmVyIDEwIChzZXJpYWwpIG9uIE1hYyBPUyBYIDEwLjUuNyB3LyBnY2MsCUludGVsIEZvcnRhbiAxMS4wIGFuZCBNS0wgMTAuMA==?=
  • vitor.felix (Tue Jul 21 2009 - 22:15:06 CDT)
• [AMBER]
  • Raja Pandian (Thu Jun 18 2009 - 07:35:10 CDT)
  • guntheyp_at_aston.ac.uk (Thu Jun 18 2009 - 06:48:21 CDT)
• [AMBER] "bad atom type"
  • Akansha Saxena (Fri Jan 09 2009 - 11:15:11 CST)
• [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
  • case (Wed Oct 14 2009 - 06:37:35 CDT)
  • haifeng yuan (Tue Oct 13 2009 - 02:44:55 CDT)
• [AMBER] "Could not find bond parameter"
  • Ross Walker (Fri Jan 23 2009 - 12:29:46 CST)
  • George Tzotzos (Fri Jan 23 2009 - 12:16:34 CST)
• [AMBER] "extra points" incompatibility with pmemd
  • mousumi (Thu Oct 22 2009 - 00:20:48 CDT)
  • Brent Krueger (Wed Oct 21 2009 - 07:28:58 CDT)
  • case (Wed Oct 21 2009 - 07:22:28 CDT)
  • Robert Duke (Wed Oct 21 2009 - 07:02:54 CDT)
  • mousumi (Wed Oct 21 2009 - 02:57:51 CDT)
• [AMBER] "loadoff tRNA.lib" in Leap
  • Ju Zhang (Tue Jun 23 2009 - 15:55:25 CDT)
• [AMBER] "nan" in gaussian input files generated by antechamber
  • FyD (Sat Sep 12 2009 - 09:58:52 CDT)
  • case (Sat Sep 12 2009 - 08:55:14 CDT)
  • Yikan Chen (Fri Sep 11 2009 - 15:19:04 CDT)
• [AMBER] "Parameter file not generated"
  • Remya S R (Mon May 04 2009 - 01:17:23 CDT)
• [AMBER] "rfree: End of file on unit 5"
  • mathew k varghese (Mon Mar 30 2009 - 04:57:44 CDT)
  • Remya S R (Mon Mar 30 2009 - 01:21:53 CDT)
• [AMBER] (No reply) Compatibility of ONIOM and Amber
  • vaibhav dixit (Mon Dec 21 2009 - 07:58:03 CST)
• [AMBER] (no subject)
  • Prakash Patodia (Sat Oct 17 2009 - 02:12:39 CDT)
  • gunajyoti das (Mon Sep 07 2009 - 04:21:45 CDT)
  • workalemahu berhanu (Mon Aug 31 2009 - 00:19:27 CDT)
  • workalemahu berhanu (Sat Aug 29 2009 - 10:29:34 CDT)
  • workalemahu berhanu (Fri Aug 28 2009 - 11:22:31 CDT)
  • workalemahu berhanu (Fri Aug 28 2009 - 09:06:56 CDT)
  • case (Fri Aug 07 2009 - 18:54:18 CDT)
  • Ross Walker (Fri Aug 07 2009 - 10:35:32 CDT)
  • Ashish Runthala (Fri Aug 07 2009 - 08:27:04 CDT)
  • Beale, John (Fri Aug 07 2009 - 07:16:58 CDT)
  • gunajyoti das (Sun Jul 19 2009 - 10:13:01 CDT)
  • gunajyoti das (Sun Jul 19 2009 - 10:14:20 CDT)
  • Beale, John (Mon Jul 13 2009 - 12:35:46 CDT)
  • David A. Case (Thu Jun 11 2009 - 06:54:38 CDT)
  • david.lisgarten_at_canterbury.ac.uk (Thu Jun 11 2009 - 03:28:56 CDT)
  • david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 08:56:32 CDT)
  • David A. Case (Tue Jun 09 2009 - 06:47:59 CDT)
  • david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 05:23:57 CDT)
  • FyD (Mon Jun 08 2009 - 12:14:05 CDT)
  • Karl Kirschner (Mon Jun 08 2009 - 06:38:42 CDT)
  • Vishal Maingi (Mon Jun 08 2009 - 06:14:22 CDT)
  • David A. Case (Thu Apr 30 2009 - 15:16:35 CDT)
  • Collins Nganou (Thu Apr 30 2009 - 14:34:36 CDT)
  • waleed zalloum (Wed Apr 29 2009 - 13:06:44 CDT)
  • David A. Case (Wed Apr 29 2009 - 12:56:28 CDT)
  • waleed zalloum (Wed Apr 29 2009 - 07:15:12 CDT)
  • David A. Case (Fri Apr 03 2009 - 07:17:36 CDT)
  • chenquan (Fri Apr 03 2009 - 05:12:14 CDT)
  • Carlos Simmerling (Thu Feb 26 2009 - 10:24:40 CST)
  • Lake, Thomas (Thu Feb 26 2009 - 10:19:53 CST)
  • Thomas Cheatham III (Wed Feb 25 2009 - 18:48:56 CST)
  • waleed zalloum (Wed Feb 25 2009 - 10:41:14 CST)
  • Beale, John (Tue Feb 24 2009 - 05:59:51 CST)
  • Andrew Olson (Thu Feb 19 2009 - 13:46:24 CST)
  • Carlos Simmerling (Tue Feb 17 2009 - 07:10:49 CST)
  • Beale, John (Tue Feb 17 2009 - 07:02:25 CST)
  • Ross Walker (Thu Jan 22 2009 - 09:46:56 CST)
  • Lake, Thomas (Thu Jan 22 2009 - 07:43:59 CST)
  • Jenny Iskrenova (Mon Jan 19 2009 - 12:54:39 CST)
  • Ross Walker (Sun Jan 18 2009 - 12:07:24 CST)
  • Carlos Simmerling (Sun Jan 18 2009 - 07:08:41 CST)
  • David A. Case (Sat Jan 17 2009 - 20:48:25 CST)
  • Jenny Iskrenova (Fri Jan 16 2009 - 17:20:46 CST)
  • David A. Case (Fri Jan 16 2009 - 13:10:33 CST)
  • Carlos Simmerling (Fri Jan 16 2009 - 12:46:11 CST)
  • Jenny Iskrenova (Fri Jan 16 2009 - 12:42:08 CST)
  • Carlos Simmerling (Fri Jan 16 2009 - 11:43:26 CST)
  • Lake, Thomas (Fri Jan 16 2009 - 11:38:09 CST)
• [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error
  • David A. Case (Wed Feb 18 2009 - 14:35:12 CST)
  • Majeed Shaik (Wed Feb 18 2009 - 14:09:17 CST)
• [AMBER] ***PROBLEMS WITH GROUPLRES
  • Maria Mirza (Tue Aug 18 2009 - 19:34:41 CDT)
• [AMBER] -a flag :RESP
  • Jio M (Sun Jul 19 2009 - 05:48:20 CDT)
• [AMBER] -MMTSB instalation flag ?
  • Scott Brozell (Tue Feb 03 2009 - 11:38:11 CST)
  • Marek Malý (Tue Feb 03 2009 - 11:15:04 CST)
  • Scott Brozell (Tue Feb 03 2009 - 11:06:47 CST)
  • Marek Malý (Tue Feb 03 2009 - 09:31:38 CST)
• [AMBER] -np not 2^x a problem w/ sander???
  • Ross Walker (Fri Nov 06 2009 - 19:43:04 CST)
  • Dean Cuebas (Fri Nov 06 2009 - 13:27:48 CST)
• [AMBER] -np not 2^x a problem w/ sander??? update
  • Ross Walker (Sat Nov 07 2009 - 10:31:36 CST)
  • Dean Cuebas (Fri Nov 06 2009 - 13:46:39 CST)
• [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory
  • David A. Case (Wed Feb 18 2009 - 12:11:56 CST)
  • Andrew Olson (Wed Feb 18 2009 - 11:08:57 CST)
• [AMBER] .rst file error
  • ZhaoLei (Mon Dec 28 2009 - 20:57:34 CST)
  • Jason Swails (Mon Dec 28 2009 - 20:09:04 CST)
  • ZhaoLei (Mon Dec 28 2009 - 19:37:40 CST)
  • Jason Swails (Mon Dec 28 2009 - 09:44:38 CST)
  • ZhaoLei (Mon Dec 28 2009 - 04:36:17 CST)
  • Jia Xu (Mon Dec 28 2009 - 02:00:57 CST)
  • ZhaoLei (Sun Dec 27 2009 - 21:09:24 CST)
  • ZhaoLei (Sun Dec 27 2009 - 20:37:57 CST)
  • ZhaoLei (Sun Dec 27 2009 - 08:46:37 CST)
• [AMBER] .rst file generation problem.
  • Carlos Simmerling (Tue Mar 31 2009 - 06:28:35 CDT)
  • Aravind S (Tue Mar 31 2009 - 03:49:17 CDT)
  • Carlos Simmerling (Mon Mar 30 2009 - 06:30:58 CDT)
  • Aravind S (Mon Mar 30 2009 - 01:32:12 CDT)
  • Aravind S (Mon Mar 30 2009 - 00:48:55 CDT)
• [AMBER] 1-4 vdW, GB MM difference
  • David A. Case (Thu Apr 16 2009 - 09:47:55 CDT)
  • Jimmy Heimdal (Thu Apr 16 2009 - 06:57:01 CDT)
• [AMBER] 2 atoms not in residue template
  • Workalemhu Berhanu (Sat May 23 2009 - 19:11:12 CDT)
• [AMBER] 2 restraints with different force constants
  • David A. Case (Fri Jun 19 2009 - 07:06:18 CDT)
  • David A. Case (Fri Jun 19 2009 - 06:41:01 CDT)
  • Aust, Susanne (Fri Jun 19 2009 - 02:14:50 CDT)
• [AMBER] 2-step vs 3-step TI, and softcores question
  • steinbrt_at_rci.rutgers.edu (Tue Jun 23 2009 - 17:27:46 CDT)
  • Jodi Hadden (Tue Jun 23 2009 - 17:00:02 CDT)
• [AMBER] 60 giga output file .mdcrd file
  • case (Wed Nov 04 2009 - 06:17:47 CST)
  • Ross Walker (Tue Nov 03 2009 - 17:10:17 CST)
  • Silvia Carlotto (Tue Nov 03 2009 - 10:42:43 CST)
  • Richard Owczarzy (Tue Nov 03 2009 - 09:14:44 CST)
  • Jason Swails (Tue Nov 03 2009 - 07:49:01 CST)
  • Fernando Martín García (Tue Nov 03 2009 - 04:35:41 CST)
  • Silvia Carlotto (Tue Nov 03 2009 - 04:24:03 CST)
  • Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  • Peter Schmidtke (Mon Nov 02 2009 - 12:40:48 CST)
  • Silvia Carlotto (Mon Nov 02 2009 - 11:41:32 CST)
• [AMBER] 8Mureabox
  • anna berteotti (Wed Mar 11 2009 - 03:45:03 CDT)
  • David A. Case (Tue Mar 10 2009 - 07:51:08 CDT)
  • anna berteotti (Mon Mar 09 2009 - 05:07:52 CDT)
• [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy?
  • FyD (Sun Mar 22 2009 - 15:12:17 CDT)
  • Youn Kyeung Lee (Thu Mar 19 2009 - 02:31:16 CDT)
• [AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force.
  • Organization (Wed Jul 22 2009 - 14:13:37 CDT)
• [AMBER] [amber10] atom groups used in torsion constrain
  • Han Zheng (Mon Oct 26 2009 - 13:09:07 CDT)
• [AMBER] [AmberTool] xleap problem
  • ÁÖżº (Mon Aug 17 2009 - 03:57:37 CDT)
• [AMBER] [Fwd: ligand exiting a protein cavity]
  • Jason Swails (Fri Oct 30 2009 - 11:23:29 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 08:42:57 CDT)
  • Jason Swails (Fri Oct 30 2009 - 08:07:17 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 00:43:22 CDT)
  • Jason Swails (Thu Oct 29 2009 - 10:17:40 CDT)
  • Kshatresh Dutta Dubey (Thu Oct 29 2009 - 09:44:28 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:36:13 CDT)
• [AMBER] [Fwd: problem with minimization]
  • Bill Ross (Fri Oct 23 2009 - 12:40:57 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 13:53:11 CDT)
  • Bill Ross (Thu Oct 22 2009 - 11:49:45 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 07:46:32 CDT)
• [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins
  • Ross Walker (Tue Apr 14 2009 - 14:45:06 CDT)
  • sychen (Tue Apr 14 2009 - 11:33:03 CDT)
• [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation
  • Xu Dong (Sat Feb 21 2009 - 15:40:03 CST)
  • Carlos Simmerling (Sat Feb 21 2009 - 15:33:31 CST)
  • Xu Dong (Sat Feb 21 2009 - 14:27:29 CST)
• [AMBER] A bug in LEaP ?
  • FyD (Sun Oct 11 2009 - 07:08:37 CDT)
• [AMBER] A bug in LEaP II ?
  • FyD (Sun Oct 25 2009 - 07:58:36 CDT)
• [AMBER] A confusion about tutorial B1
  • Houyang Chen (Tue May 05 2009 - 12:39:18 CDT)
  • David A. Case (Tue May 05 2009 - 10:41:54 CDT)
  • Ross Walker (Tue May 05 2009 - 10:29:23 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 05:11:43 CDT)
  • Houyang Chen (Tue May 05 2009 - 00:24:39 CDT)
  • Ross Walker (Tue May 05 2009 - 00:18:43 CDT)
  • Houyang Chen (Tue May 05 2009 - 00:01:31 CDT)
• [AMBER] A good way to use an Amber force field with NAMD?
  • Sasha Buzko (Wed Mar 04 2009 - 11:58:09 CST)
  • Robert Duke (Tue Mar 03 2009 - 22:26:59 CST)
  • Sasha Buzko (Tue Mar 03 2009 - 20:55:56 CST)
  • Ross Walker (Tue Mar 03 2009 - 19:33:58 CST)
  • Sasha Buzko (Tue Mar 03 2009 - 18:26:44 CST)
  • Adrian Roitberg (Tue Mar 03 2009 - 18:11:49 CST)
  • Gustavo Seabra (Tue Mar 03 2009 - 18:08:33 CST)
  • Sasha Buzko (Tue Mar 03 2009 - 15:37:29 CST)
• [AMBER] a layer of water
  • oguz gurbulak (Wed Apr 01 2009 - 02:26:46 CDT)
  • Nancy (Tue Mar 31 2009 - 20:37:51 CDT)
• [AMBER] a method or program to try to guess the net charge of a small molecule
  • Alan (Fri Jun 26 2009 - 05:00:48 CDT)
• [AMBER] a problem in building oligosaccharides using LEaP
  • Song Lin (Thu Dec 24 2009 - 20:12:10 CST)
• [AMBER] A problem with xleap and pdb file
  • Ross Walker (Fri Feb 27 2009 - 09:55:23 CST)
  • Peter Gannett (Fri Feb 27 2009 - 08:32:20 CST)
  • nancy4619 (Fri Feb 27 2009 - 08:20:17 CST)
  • David A. Case (Fri Feb 27 2009 - 07:56:26 CST)
  • nancy4619 (Fri Feb 27 2009 - 06:28:01 CST)
• [AMBER] a query
  • Molecular Dynamics (Sat Feb 28 2009 - 13:45:46 CST)
• [AMBER] a question about ptraj
  • qiaoyan (Fri Dec 25 2009 - 07:58:44 CST)
• [AMBER] A question about SMD force constant
  • Carlos Simmerling (Tue Apr 07 2009 - 05:32:09 CDT)
  • Jackie. J. Shen (Mon Apr 06 2009 - 20:40:13 CDT)
• [AMBER] a question about umbrella sampling (US)
  • xiaoqin huang (Wed Feb 04 2009 - 16:23:12 CST)
  • Carlos Simmerling (Wed Feb 04 2009 - 11:20:46 CST)
  • xiaoqin huang (Wed Feb 04 2009 - 11:12:02 CST)
• [AMBER] ABMD Reaction Coordinates
  • stephane acoca (Mon Aug 24 2009 - 00:04:58 CDT)
  • stephane acoca (Sun Aug 23 2009 - 22:25:43 CDT)
  • stephane acoca (Sun Aug 23 2009 - 22:24:32 CDT)
  • stephane acoca (Sun Aug 23 2009 - 22:11:09 CDT)
• [AMBER] About APBS radiopt
  • Robert Konecny (Mon Dec 28 2009 - 09:43:18 CST)
  • Youn Kyeung Lee (Mon Dec 28 2009 - 04:12:07 CST)
• [AMBER] about divcon
  • Jason Swails (Wed Nov 18 2009 - 13:09:43 CST)
  • Alan (Wed Nov 18 2009 - 11:07:44 CST)
  • case (Wed Nov 18 2009 - 10:53:16 CST)
  • Alan (Wed Nov 18 2009 - 10:24:51 CST)
• [AMBER] About error of "vertex atom mismatch"
  • å»–é�’å�Ž (Wed Mar 18 2009 - 03:30:29 CDT)
• [AMBER] about file format
  • Jia Xu (Sun Aug 30 2009 - 00:32:30 CDT)
  • Tom Joseph (Sat Aug 29 2009 - 09:50:37 CDT)
  • Jia Xu (Sat Aug 29 2009 - 02:55:49 CDT)
• [AMBER] About Free energy decomposition
  • Rajesh Raju (Wed Mar 25 2009 - 09:08:00 CDT)
• [AMBER] about MD simulation
  • Carlos Simmerling (Wed Mar 11 2009 - 05:56:43 CDT)
  • ÁÎÇ໪ (Wed Mar 11 2009 - 04:19:28 CDT)
• [AMBER] about mm-pbsa
  • å»–é�’å�Ž (Mon Mar 23 2009 - 04:10:29 CDT)
  • å»–é�’å�Ž (Thu Mar 19 2009 - 01:48:21 CDT)
  • Wei Huang (Mon Mar 16 2009 - 10:17:30 CDT)
  • å»–é�’å�Ž (Mon Mar 16 2009 - 10:02:49 CDT)
  • å»–é�’å�Ž (Mon Mar 16 2009 - 09:59:40 CDT)
• [AMBER] about saltcon
  • Carlos Simmerling (Sun Apr 19 2009 - 05:49:57 CDT)
  • zgong.hust (Sat Apr 18 2009 - 21:45:53 CDT)
• [AMBER] About the "FATAL: Atom err!"
  • Aurum Bai (Mon Jun 22 2009 - 05:12:23 CDT)
• [AMBER] About the "FATAL: Atom err"!
  • case (Mon Jun 22 2009 - 06:47:59 CDT)
  • Aurum Bai (Mon Jun 22 2009 - 05:14:20 CDT)
• [AMBER] About the Amber tutorial
  • Aurum Bai (Mon Jun 22 2009 - 05:03:49 CDT)
• [AMBER] About the croase grainded FF
  • Vlad Cojocaru (Tue Feb 24 2009 - 02:40:53 CST)
  • James W (Tue Feb 24 2009 - 01:58:12 CST)
• [AMBER] about the number of residues after MD
  • Qinghua Liao (Wed Sep 09 2009 - 02:23:03 CDT)
• [AMBER] About the PMEMD compiling for CUDA
  • Ross Walker (Wed Sep 16 2009 - 01:55:11 CDT)
  • Ross Walker (Wed Sep 16 2009 - 00:26:19 CDT)
  • wang (Wed Sep 16 2009 - 00:17:52 CDT)
• [AMBER] About zinc parameters ?
  • Sally Pias (Tue Nov 17 2009 - 11:38:29 CST)
  • Jason Swails (Tue Nov 17 2009 - 09:17:23 CST)
  • steinbrt_at_rci.rutgers.edu (Tue Nov 17 2009 - 04:35:24 CST)
  • xuemeiwang1103 (Tue Nov 17 2009 - 02:52:56 CST)
• [AMBER] ACE and NME patch: VMD ???
  • Ross Walker (Tue Sep 01 2009 - 12:54:38 CDT)
  • Siddharth Rastogi (Mon Aug 31 2009 - 19:25:47 CDT)
• [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels
  • David A. Case (Wed May 27 2009 - 06:57:07 CDT)
  • Tomasio, Susana (Wed May 27 2009 - 06:25:35 CDT)
• [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels
  • Tomasio, Susana (Wed May 27 2009 - 07:13:58 CDT)
• [AMBER] acetone lib and frcmod files?
  • FyD (Tue Aug 25 2009 - 02:50:57 CDT)
  • FyD (Tue Aug 25 2009 - 02:47:50 CDT)
  • Jose Borreguero (Mon Aug 24 2009 - 16:34:07 CDT)
  • FyD (Mon Aug 24 2009 - 15:13:33 CDT)
  • Jose Borreguero (Mon Aug 24 2009 - 07:56:51 CDT)
  • FyD (Mon Aug 24 2009 - 02:31:40 CDT)
  • Ross Walker (Mon Aug 24 2009 - 00:08:16 CDT)
  • Jose Borreguero (Sun Aug 23 2009 - 16:36:43 CDT)
• [AMBER] Acetylate and Amidate
  • Carlos Simmerling (Thu Jul 09 2009 - 06:52:28 CDT)
  • Bill Ross (Wed Jul 08 2009 - 18:13:09 CDT)
  • Alison Saunders (Wed Jul 08 2009 - 17:47:59 CDT)
  • Carlos Simmerling (Wed Jul 08 2009 - 17:22:58 CDT)
  • Alison Saunders (Wed Jul 08 2009 - 17:19:44 CDT)
• [AMBER] ACS COMP division awards- Oct 19th deadline
  • Carlos Simmerling (Mon Sep 21 2009 - 12:49:28 CDT)
• [AMBER] ACS computational chemistry awards - March 9th deadline
  • Carlos Simmerling (Fri Feb 20 2009 - 10:27:18 CST)
• [AMBER] Active site - Ion - Search engine
  • s. Bill (Wed Sep 02 2009 - 09:53:39 CDT)
• [AMBER] Actual force constant in SMD
  • Dmitri Nilov (Mon Mar 16 2009 - 13:07:09 CDT)
• [AMBER] ADD SALT
  • Simon Becker (Thu Jun 25 2009 - 04:57:37 CDT)
  • Rilei Yu (Thu Jun 25 2009 - 04:22:20 CDT)
• [AMBER] ADD SALT additional question
  • Vlad Cojocaru (Thu Jun 25 2009 - 09:55:15 CDT)
  • Vlad Cojocaru (Thu Jun 25 2009 - 09:51:54 CDT)
  • Simon Becker (Thu Jun 25 2009 - 07:34:36 CDT)
• [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
  • Carlos Simmerling (Wed Oct 14 2009 - 08:49:00 CDT)
  • FyD (Wed Oct 14 2009 - 08:40:09 CDT)
  • Andrew Purkiss-Trew (Wed Oct 14 2009 - 07:19:43 CDT)
  • xuemeiwang1103 (Wed Oct 14 2009 - 07:05:48 CDT)
• [AMBER] adding a standard amino acid as ligand
  • FyD (Fri May 15 2009 - 08:39:18 CDT)
  • sheerychen (Fri May 15 2009 - 04:37:51 CDT)
• [AMBER] adding chain id to ptraj pdb output
  • Joe Krahn (Mon Mar 23 2009 - 18:20:30 CDT)
  • Bala subramanian (Mon Mar 23 2009 - 06:37:43 CDT)
  • Paul Brandt (Sat Mar 21 2009 - 21:09:59 CDT)
• [AMBER] adding MG2 problem
  • Rausch, Felix (Wed Feb 04 2009 - 07:04:51 CST)
  • Scott Brozell (Tue Feb 03 2009 - 13:09:32 CST)
  • balaji nagarajan (Fri Jan 30 2009 - 03:45:58 CST)
• [AMBER] Adding non standard residues
  • Jorgen Simonsen (Mon May 11 2009 - 16:11:49 CDT)
  • David A. Case (Mon May 11 2009 - 12:30:56 CDT)
  • Jorgen Simonsen (Mon May 11 2009 - 03:54:25 CDT)
• [AMBER] Adding single distance restraint
  • Jason Swails (Wed Dec 23 2009 - 21:11:48 CST)
  • Adler, Marc (Wed Dec 23 2009 - 20:00:35 CST)
• [AMBER] addions
  • Shubhra Gupta (Wed Jun 03 2009 - 00:47:11 CDT)
• [AMBER] addles - neb error
  • balaji nagarajan (Wed Dec 16 2009 - 21:20:22 CST)
  • case (Wed Dec 16 2009 - 15:01:20 CST)
  • balaji nagarajan (Tue Dec 15 2009 - 21:26:51 CST)
  • Ross Walker (Tue Dec 15 2009 - 10:45:19 CST)
  • balaji nagarajan (Tue Dec 15 2009 - 08:38:53 CST)
• [AMBER] addles segmentation fault
  • xiaonan zhang (Mon Mar 09 2009 - 08:08:47 CDT)
  • Carlos Simmerling (Mon Mar 09 2009 - 06:45:24 CDT)
  • gmail (Mon Mar 09 2009 - 03:28:56 CDT)
• [AMBER] Alignment of small molecule on peptide fragment
  • Workalemhu Berhanu (Sat May 16 2009 - 04:32:38 CDT)
  • Workalemhu Berhanu (Sat May 16 2009 - 04:31:08 CDT)
• [AMBER] Alpha helix plot
  • Carlos Simmerling (Fri Jan 30 2009 - 16:11:10 CST)
  • Beale, John (Thu Jan 29 2009 - 14:10:11 CST)
• [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
  • Bill Ross (Wed Jul 15 2009 - 11:53:41 CDT)
  • Sushil Mishra (Wed Jul 15 2009 - 08:58:13 CDT)
  • Shubhra Gupta (Wed Jul 15 2009 - 07:38:34 CDT)
  • Sushil Mishra (Wed Jul 15 2009 - 05:36:26 CDT)
• [AMBER] Am I doing the right thing
  • nicholus bhattacharjee (Tue Jul 28 2009 - 23:36:31 CDT)
  • Ashish Runthala (Tue Jul 28 2009 - 22:44:59 CDT)
  • Bill Ross (Tue Jul 28 2009 - 21:39:48 CDT)
  • Ashish Runthala (Tue Jul 28 2009 - 20:35:09 CDT)
  • nicholus bhattacharjee (Tue Jul 28 2009 - 12:20:57 CDT)
• [AMBER] Amber - Leap- SolvateBox help
  • Ross Walker (Wed May 20 2009 - 00:20:50 CDT)
  • David A. Case (Tue May 19 2009 - 06:48:39 CDT)
  • Remya S R (Tue May 19 2009 - 01:22:12 CDT)
  • Shubhra Gupta (Mon May 18 2009 - 22:54:23 CDT)
  • David A. Case (Fri May 15 2009 - 18:57:00 CDT)
  • Ross Walker (Thu May 14 2009 - 07:28:36 CDT)
  • Shubhra Gupta (Thu May 14 2009 - 00:04:16 CDT)
• [AMBER] Amber 1.2 tools test suite failure?
  • Ross Walker (Sat Apr 11 2009 - 13:00:45 CDT)
  • Jim Parker (Sat Apr 11 2009 - 12:41:54 CDT)
• [AMBER] Amber 10 and core i7
  • Supat Jiranusornkul (Thu Mar 26 2009 - 04:13:10 CDT)
• [AMBER] Amber 10 install parallel problem
  • Hopkins, Robert (Sat May 16 2009 - 19:38:16 CDT)
• [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found
  • Jason Swails (Fri Dec 04 2009 - 11:42:19 CST)
  • case (Fri Dec 04 2009 - 08:18:09 CST)
  • Diego Javier Alonso de Armiño (Fri Dec 04 2009 - 06:09:04 CST)
  • Jason Swails (Thu Dec 03 2009 - 20:55:09 CST)
  • Mengjuei Hsieh (Thu Dec 03 2009 - 20:52:48 CST)
  • Diego Javier Alonso de Armiño (Thu Dec 03 2009 - 19:47:08 CST)
• [AMBER] AMBER 10 output
  • Sergey Samsonov (Tue May 19 2009 - 09:53:41 CDT)
  • steinbrt_at_rci.rutgers.edu (Tue May 19 2009 - 08:53:03 CDT)
  • Sergey Samsonov (Tue May 19 2009 - 02:33:21 CDT)
• [AMBER] amber 10 test fails with pathscale 3.2
  • Ross Walker (Mon Aug 17 2009 - 11:34:28 CDT)
  • Raj (Mon Aug 17 2009 - 07:54:45 CDT)
• [AMBER] amber 10 test failures...
  • peker milas (Tue Nov 03 2009 - 08:11:01 CST)
  • Jason Swails (Mon Nov 02 2009 - 18:19:43 CST)
  • Mark Williamson (Mon Nov 02 2009 - 18:11:40 CST)
  • Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  • peker milas (Mon Nov 02 2009 - 08:18:29 CST)
• [AMBER] AMBER 10: sleap diff errors?
  • David A. Case (Thu Jun 04 2009 - 14:19:44 CDT)
  • Catein Catherine (Thu Jun 04 2009 - 00:37:35 CDT)
• [AMBER] AMBER 11.
  • case (Thu Oct 15 2009 - 11:52:51 CDT)
  • Peter Winn (Thu Oct 15 2009 - 11:27:39 CDT)
• [AMBER] amber 9 compilation
  • Myunggi Yi (Fri Nov 06 2009 - 09:13:00 CST)
• [AMBER] Amber 9 Install - AMBERBUILDFLAGS error
  • David A. Case (Mon Feb 16 2009 - 22:29:41 CST)
  • ben rodriguez (Mon Feb 16 2009 - 21:39:14 CST)
• [AMBER] Amber 9 installation problem on Ubuntu
  • David A. Case (Mon Jan 12 2009 - 06:01:31 CST)
  • drugdesign (Mon Jan 12 2009 - 00:26:34 CST)
• [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
  • todd_at_semichem.com (Sun May 10 2009 - 16:56:24 CDT)
  • FyD (Sun May 10 2009 - 00:49:55 CDT)
  • todd_at_semichem.com (Sat May 09 2009 - 13:36:17 CDT)
  • Adrian Roitberg (Sat May 09 2009 - 13:07:08 CDT)
  • todd_at_semichem.com (Sat May 09 2009 - 11:27:52 CDT)
• [AMBER] Amber and CHARMM summer school
  • David A. Case (Thu Apr 16 2009 - 10:04:18 CDT)
• [AMBER] amber dihedral format
  • case (Sun Jul 12 2009 - 16:49:12 CDT)
  • s. Bill (Sun Jul 12 2009 - 09:05:23 CDT)
• [AMBER] AMBER efficiency: Intel vs. AMD
  • Ross Walker (Mon Jan 19 2009 - 09:39:33 CST)
  • Ye MEI (Sun Jan 18 2009 - 20:20:47 CST)
  • Swarup Gupta (Sun Jan 18 2009 - 19:43:32 CST)
• [AMBER] AMBER ERROR
  • Vikas Sharma (Sat Jun 13 2009 - 02:16:52 CDT)
• [AMBER] AMBER External keyword
  • Gustavo Seabra (Sat Jan 24 2009 - 20:32:10 CST)
  • Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 09:59:33 CST)
• [AMBER] Amber FF and Glycam
  • Carlos Simmerling (Fri May 01 2009 - 07:41:35 CDT)
  • Hannes Loeffler (Fri May 01 2009 - 03:33:34 CDT)
  • Carlos Simmerling (Thu Apr 30 2009 - 13:36:21 CDT)
  • Lachele Foley (Lists) (Thu Apr 30 2009 - 12:16:17 CDT)
  • Dong Xu (Wed Apr 29 2009 - 20:42:55 CDT)
• [AMBER] AMBER FF and NAMD
  • FyD (Fri Oct 16 2009 - 14:19:13 CDT)
  • Nicolas Sapay (Fri Oct 16 2009 - 09:59:53 CDT)
  • Hannes Loeffler (Fri Oct 16 2009 - 09:45:25 CDT)
  • stefano_elli\_at_libero\.it (Fri Oct 16 2009 - 09:26:14 CDT)
• [AMBER] AMBER for dual core processor?
  • Ross Walker (Thu May 07 2009 - 10:26:09 CDT)
  • Catein Catherine (Thu May 07 2009 - 03:05:17 CDT)
• [AMBER] AMBER installation : compilation error
  • Catein Catherine (Wed Mar 04 2009 - 20:53:54 CST)
• [AMBER] Amber Installation problem
  • ÁÖżº (Thu Apr 23 2009 - 20:35:46 CDT)
  • Ross Walker (Thu Apr 23 2009 - 08:16:18 CDT)
  • ÁÖżº (Thu Apr 23 2009 - 08:10:42 CDT)
• [AMBER] AMBER is running silently
  • Kefa Lu (Mon Aug 17 2009 - 20:25:14 CDT)
  • Ross Walker (Mon Aug 17 2009 - 18:33:09 CDT)
  • Kefa Lu (Mon Aug 17 2009 - 18:10:17 CDT)
  • Bill Ross (Mon Aug 17 2009 - 18:04:02 CDT)
  • Kefa Lu (Mon Aug 17 2009 - 17:47:34 CDT)
• [AMBER] AMBER job restart problem
  • Kefa Lu (Sun Aug 16 2009 - 00:09:22 CDT)
  • Thomas Cheatham (Sat Aug 15 2009 - 23:44:27 CDT)
  • Kefa Lu (Sat Aug 15 2009 - 23:36:59 CDT)
  • Thomas Cheatham (Sat Aug 15 2009 - 10:49:10 CDT)
  • case (Sat Aug 15 2009 - 10:40:51 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 09:39:56 CDT)
  • case (Sat Aug 15 2009 - 08:49:44 CDT)
  • Kefa Lu (Sat Aug 15 2009 - 05:12:21 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 04:57:48 CDT)
  • Kefa Lu (Sat Aug 15 2009 - 03:22:08 CDT)
• [AMBER] AMBER on a Mac Mini cluster PoC
  • Abdul Rehman Gani (Mon Aug 17 2009 - 07:31:37 CDT)
  • Alan (Mon Aug 17 2009 - 05:50:30 CDT)
  • Abdul Rehman Gani (Mon Aug 17 2009 - 03:13:38 CDT)
  • Ross Walker (Sun Aug 16 2009 - 12:08:47 CDT)
  • Abdul Rehman Gani (Sun Aug 16 2009 - 10:51:44 CDT)
• [AMBER] AMBER on a Mac Mini cluster PoC - solved
  • Abdul Rehman Gani (Mon Aug 17 2009 - 09:44:07 CDT)
• [AMBER] Amber on GPU
  • Sasha Buzko (Thu Apr 09 2009 - 19:54:29 CDT)
  • Sasha Buzko (Tue Apr 07 2009 - 01:11:24 CDT)
  • Ross Walker (Mon Apr 06 2009 - 20:14:07 CDT)
  • Sasha Buzko (Mon Apr 06 2009 - 19:56:31 CDT)
• [AMBER] amber parallel test fail
  • Nahoum Anthony (Fri Oct 23 2009 - 10:12:40 CDT)
  • Jason Swails (Fri Oct 23 2009 - 06:58:19 CDT)
  • Nahoum Anthony (Fri Oct 23 2009 - 05:20:45 CDT)
• [AMBER] amber parameter file creation and usage
  • Donald Keidel (Wed Nov 04 2009 - 11:53:23 CST)
  • Jason Swails (Tue Nov 03 2009 - 23:29:30 CST)
  • Donald Keidel (Tue Nov 03 2009 - 22:47:36 CST)
• [AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide
  • Osmar Norberto de Souza (Wed Jan 07 2009 - 12:23:06 CST)
• [AMBER] amber question
  • Vikas Sharma (Sun Apr 26 2009 - 04:56:26 CDT)
  • Vikas Sharma (Sun Apr 26 2009 - 04:51:38 CDT)
  • Barbault Florent (Sun Apr 26 2009 - 03:48:31 CDT)
  • Vikas Sharma (Sun Apr 26 2009 - 01:00:06 CDT)
• [AMBER] AMBER question: bad atom type: MN
  • Edward M (Mon Jun 22 2009 - 22:05:51 CDT)
• [AMBER] Amber Sulfate Ion Parameters
  • Gary Clark (Thu Apr 23 2009 - 14:55:24 CDT)
  • FyD (Thu Apr 23 2009 - 01:07:40 CDT)
  • FyD (Thu Apr 23 2009 - 00:18:28 CDT)
  • Gary Clark (Wed Apr 22 2009 - 17:31:00 CDT)
• [AMBER] amber test fails with ICC 11.0.081
  • Carlos Simmerling (Mon Aug 17 2009 - 10:16:26 CDT)
  • Raj (Mon Aug 17 2009 - 09:57:57 CDT)
• [AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip)
  • Myunggi Yi (Wed Jun 24 2009 - 13:57:25 CDT)
• [AMBER] amber tools installation
  • case (Mon Mar 30 2009 - 11:28:38 CDT)
  • Jayalakshmi Sridhar (Mon Mar 30 2009 - 10:44:57 CDT)
• [AMBER] amber tools reading netcdf files
  • Cojocaru,Vlad (Tue Feb 24 2009 - 12:46:27 CST)
  • Chris Moth (Tue Feb 24 2009 - 11:35:22 CST)
  • Jeremy Harris (Tue Feb 24 2009 - 09:54:09 CST)
• [AMBER] Amber top file to Charmm top file
  • sarvin moghaddam (Fri Jan 30 2009 - 08:48:44 CST)
• [AMBER] AMBER windows version ?
  • Siddharth Rastogi (Thu Jul 09 2009 - 18:17:33 CDT)
  • Ross Walker (Thu Jul 09 2009 - 17:45:49 CDT)
  • Siddharth Rastogi (Thu Jul 09 2009 - 16:14:05 CDT)
• [AMBER] Amber with AMOEBA force-field
  • Tomasio, Susana (Mon Apr 06 2009 - 08:40:49 CDT)
  • Tomasio, Susana (Mon Apr 06 2009 - 08:14:22 CDT)
  • David A. Case (Mon Apr 06 2009 - 08:00:47 CDT)
  • Wei Zhang (Mon Apr 06 2009 - 07:57:21 CDT)
  • Wei Zhang (Mon Apr 06 2009 - 07:55:59 CDT)
  • Tomasio, Susana (Mon Apr 06 2009 - 07:52:01 CDT)
  • Tomasio, Susana (Mon Apr 06 2009 - 07:49:28 CDT)
  • Wei Zhang (Mon Apr 06 2009 - 07:48:28 CDT)
  • David A. Case (Mon Apr 06 2009 - 07:47:11 CDT)
  • Tomasio, Susana (Mon Apr 06 2009 - 07:41:18 CDT)
• [AMBER] Amber/CHARMM summer school
  • CHAMI F. (Thu May 21 2009 - 06:56:23 CDT)
  • David A. Case (Wed May 20 2009 - 07:40:39 CDT)
• [AMBER] amber10 installation problem
  • Lan JIN (Fri Jul 10 2009 - 02:41:34 CDT)
  • case (Thu Jul 09 2009 - 07:38:01 CDT)
  • Lan JIN (Wed Jul 08 2009 - 21:46:22 CDT)
  • case (Wed Jul 08 2009 - 06:56:19 CDT)
  • Lan JIN (Wed Jul 08 2009 - 01:49:05 CDT)
• [AMBER] amber10 parallel compiling error
  • nam kim (Thu Jul 23 2009 - 23:32:14 CDT)
  • case (Wed Jul 22 2009 - 21:15:50 CDT)
  • nam kim (Tue Jul 21 2009 - 12:06:32 CDT)
  • Toshifumi Yui (Tue Jul 21 2009 - 00:46:11 CDT)
  • nam kim (Mon Jul 20 2009 - 17:53:24 CDT)
  • nam kim (Mon Jul 20 2009 - 13:34:41 CDT)
  • nam kim (Mon Jul 20 2009 - 13:15:16 CDT)
  • Ross Walker (Mon Jul 20 2009 - 12:33:08 CDT)
  • nam kim (Mon Jul 20 2009 - 12:24:14 CDT)
  • nam kim (Sat Jul 18 2009 - 12:19:39 CDT)
  • Ross Walker (Thu Jul 16 2009 - 22:43:15 CDT)
  • Nam Kim (Thu Jul 16 2009 - 19:50:57 CDT)
• [AMBER] Amber10 Parallel Installation
  • case (Sat Jun 20 2009 - 17:04:14 CDT)
  • Hopkins, Robert (Sat Jun 20 2009 - 14:50:16 CDT)
• [AMBER] Amber10 Parallel Installation 8%
  • Hopkins, Robert (Mon Jun 22 2009 - 14:54:17 CDT)
• [AMBER] amber10 pmemd fail
  • Ross Walker (Fri Dec 11 2009 - 21:43:53 CST)
  • Robert Duke (Fri Dec 11 2009 - 15:40:31 CST)
  • Aragorn Steiger (Fri Dec 11 2009 - 14:35:49 CST)
• [AMBER] Amber10, Serial compilation with ifort
  • Ross Walker (Sun Jul 12 2009 - 16:41:07 CDT)
  • Aldo Humberto Romero (Sun Jul 12 2009 - 15:57:40 CDT)
• [AMBER] AMBER10: error message mdfil flag.....
  • David A. Case (Wed Jun 03 2009 - 09:30:08 CDT)
  • Catein Catherine (Wed Jun 03 2009 - 09:14:50 CDT)
• [AMBER] amber8 pmemd trajectory coordinates problem
  • Robert Duke (Tue Oct 20 2009 - 20:15:56 CDT)
  • Robert Duke (Tue Oct 20 2009 - 20:03:37 CDT)
  • Sergio Wong (Tue Oct 20 2009 - 19:49:11 CDT)
  • Thomas Cheatham (Tue Oct 20 2009 - 19:39:22 CDT)
  • wong105_at_llnl.gov (Tue Oct 20 2009 - 19:32:24 CDT)
• [AMBER] amber9 compilation
  • David Watson (Fri Nov 06 2009 - 10:16:58 CST)
  • Myunggi Yi (Fri Nov 06 2009 - 09:50:25 CST)
  • David Watson (Fri Nov 06 2009 - 09:19:31 CST)
  • Myunggi Yi (Fri Nov 06 2009 - 09:10:03 CST)
• [AMBER] amber9 in fedora10
  • Bala subramanian (Thu Jul 02 2009 - 03:05:55 CDT)
  • Bala subramanian (Thu Jul 02 2009 - 02:02:54 CDT)
  • Ross Walker (Wed Jul 01 2009 - 11:36:33 CDT)
  • Bala subramanian (Wed Jul 01 2009 - 09:09:15 CDT)
  • Bala subramanian (Thu May 14 2009 - 03:18:07 CDT)
  • Ross Walker (Wed May 13 2009 - 18:22:20 CDT)
  • Bala subramanian (Wed May 13 2009 - 04:50:25 CDT)
  • Eric (Tue Jan 13 2009 - 12:28:33 CST)
  • Bala subramanian (Tue Jan 13 2009 - 12:16:19 CST)
  • Ross Walker (Tue Jan 13 2009 - 12:00:33 CST)
  • Mark Williamson (Tue Jan 13 2009 - 11:56:31 CST)
  • Bala subramanian (Tue Jan 13 2009 - 11:51:49 CST)
• [AMBER] amber9 installation problem in SMP IA64
  • Ross Walker (Thu Feb 12 2009 - 08:54:49 CST)
  • Vijay Manickam Achari (Thu Feb 12 2009 - 03:21:01 CST)
  • Vijay Manickam Achari (Thu Feb 12 2009 - 03:13:55 CST)
  • David A. Case (Wed Feb 11 2009 - 07:07:48 CST)
  • Vijay Manickam Achari (Wed Feb 11 2009 - 03:36:31 CST)
  • Ross Walker (Tue Feb 10 2009 - 11:56:22 CST)
  • David A. Case (Tue Feb 10 2009 - 06:41:29 CST)
  • Vijay Manickam Achari (Tue Feb 10 2009 - 02:30:55 CST)
  • David A. Case (Fri Feb 06 2009 - 07:25:55 CST)
  • Vijay Manickam Achari (Fri Feb 06 2009 - 01:00:16 CST)
• [AMBER] amber9 serial compilation issues
  • Francesco Pietra (Fri Apr 03 2009 - 17:04:17 CDT)
  • David A. Case (Fri Apr 03 2009 - 15:01:02 CDT)
  • Francesco Pietra (Fri Apr 03 2009 - 13:38:12 CDT)
• [AMBER] Amber99SB
  • Carlos Simmerling (Tue Aug 11 2009 - 09:42:44 CDT)
  • eric johnson (Tue Aug 11 2009 - 09:33:34 CDT)
• [AMBER] AMBER: chiral restraint on protein
  • David A. Case (Wed Feb 11 2009 - 06:56:05 CST)
  • amit jain (Tue Feb 10 2009 - 18:48:12 CST)
• [AMBER] AMBER: Problems in solvation with xleap
  • vallespardojl_at_chem.leidenuniv.nl (Wed Jan 07 2009 - 07:39:56 CST)
• [AMBER] AMBER: segmentation fault when running parmchk
  • Scott Brozell (Mon Dec 14 2009 - 12:14:15 CST)
  • Junmei Wang (Wed Nov 04 2009 - 13:22:54 CST)
  • Bill Ross (Wed Nov 04 2009 - 12:39:32 CST)
  • Mark Williamson (Wed Nov 04 2009 - 11:06:53 CST)
  • Alexander Boncheff (Wed Nov 04 2009 - 10:02:50 CST)
  • Bill Ross (Tue Nov 03 2009 - 17:15:00 CST)
  • Alexander Boncheff (Tue Nov 03 2009 - 16:29:00 CST)
  • Jason Swails (Tue Nov 03 2009 - 14:22:10 CST)
  • Alexander Boncheff (Tue Nov 03 2009 - 13:41:55 CST)
• [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory
  • Jeff Schwinefus (Wed Mar 04 2009 - 23:22:34 CST)
  • Thomas Cheatham III (Wed Mar 04 2009 - 13:59:30 CST)
  • Jeff Schwinefus (Tue Mar 03 2009 - 16:18:25 CST)
• [AMBER] amber@ambermd.org
  • shumao_at_cqut.edu.cn (Sun Dec 13 2009 - 21:01:18 CST)
• [AMBER] amber@ambermd.org open for business
  • Ross Walker (Tue Jan 06 2009 - 17:34:31 CST)
• [AMBER] AmberTools 1.2
  • David A. Case (Fri Jan 30 2009 - 06:04:41 CST)
  • James W. Caldwell (Thu Jan 29 2009 - 18:04:36 CST)
• [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala
  • Wallace Kunin (Thu Nov 12 2009 - 10:05:03 CST)
  • Ross Walker (Thu Nov 12 2009 - 04:52:44 CST)
  • Wallace Kunin (Thu Nov 12 2009 - 02:15:40 CST)
  • case (Wed Nov 11 2009 - 16:36:59 CST)
  • Jason Swails (Wed Nov 11 2009 - 16:30:35 CST)
  • Wallace Kunin (Wed Nov 11 2009 - 16:04:28 CST)
  • Bill Ross (Wed Nov 11 2009 - 11:54:01 CST)
  • David Watson (Wed Nov 11 2009 - 10:56:01 CST)
  • Giorgio Maccari (Wed Nov 11 2009 - 10:53:04 CST)
  • Wallace Kunin (Wed Nov 11 2009 - 08:17:42 CST)
  • case (Tue Nov 10 2009 - 10:28:17 CST)
  • Wallace Kunin (Tue Nov 10 2009 - 09:41:18 CST)
  • David Watson (Mon Nov 09 2009 - 18:25:12 CST)
  • David Watson (Mon Nov 09 2009 - 16:35:32 CST)
  • Wallace Kunin (Mon Nov 09 2009 - 16:05:32 CST)
  • case (Mon Nov 09 2009 - 14:41:59 CST)
  • Mark Williamson (Mon Nov 09 2009 - 14:14:03 CST)
  • case (Mon Nov 09 2009 - 14:02:42 CST)
  • David Watson (Mon Nov 09 2009 - 13:28:31 CST)
  • Wallace Kunin (Mon Nov 09 2009 - 13:14:25 CST)
• [AMBER] AmberTools 1.3 / CHAMBER
  • Mag. Thomas Taylor (Tue Sep 08 2009 - 09:29:23 CDT)
• [AMBER] AmberTools 1.3 has a likely release date?
  • case (Fri Nov 20 2009 - 08:50:23 CST)
  • Alan (Thu Nov 19 2009 - 12:15:30 CST)
• [AMBER] AmberTools and ptraj clustering on Mac OS X
  • David Watson (Sat Jan 24 2009 - 15:41:04 CST)
• [AMBER] ambertools and Snow Leopard 64 bits kernel
  • Scott Brozell (Wed Dec 09 2009 - 15:48:30 CST)
  • case (Wed Sep 23 2009 - 15:26:16 CDT)
  • Alan (Wed Sep 23 2009 - 09:21:30 CDT)
  • gilbert_at_bluemarble.net (Tue Sep 22 2009 - 21:18:12 CDT)
  • Tom Joseph (Tue Sep 22 2009 - 19:18:17 CDT)
  • Alan (Tue Sep 22 2009 - 16:41:18 CDT)
  • Tom Joseph (Tue Sep 22 2009 - 13:12:55 CDT)
  • Alan (Tue Sep 22 2009 - 08:55:25 CDT)
• [AMBER] AmberTools compilation error
  • Marius Retegan (Wed Apr 01 2009 - 15:03:59 CDT)
  • Kijeong Kwac (Wed Apr 01 2009 - 14:04:00 CDT)
• [AMBER] AmberTools compiling error
  • Farly Walsh (Wed Apr 29 2009 - 14:49:27 CDT)
  • Ross Walker (Sun Apr 26 2009 - 20:55:06 CDT)
  • Farly Walsh (Sun Apr 26 2009 - 19:40:38 CDT)
• [AMBER] ambertools failed - SMP IA64
  • David A. Case (Thu Apr 16 2009 - 09:10:20 CDT)
  • Vijay Manickam Achari (Thu Apr 16 2009 - 08:17:34 CDT)
• [AMBER] ambertools for NAMD
  • Jorgen Simonsen (Thu May 07 2009 - 13:29:41 CDT)
  • Andrew Purkiss-Trew (Thu May 07 2009 - 10:16:40 CDT)
  • Wei Huang (Thu May 07 2009 - 09:51:06 CDT)
  • Andrew Purkiss-Trew (Thu May 07 2009 - 09:30:14 CDT)
  • Carlos Simmerling (Thu May 07 2009 - 09:23:25 CDT)
  • David A. Case (Thu May 07 2009 - 09:09:55 CDT)
  • Carlos Simmerling (Thu May 07 2009 - 08:36:27 CDT)
  • Jorgen Simonsen (Thu May 07 2009 - 07:35:24 CDT)
• [AMBER] AmberTools modifications for Ubuntu 9.10
  • case (Fri Dec 04 2009 - 09:31:16 CST)
  • peker milas (Thu Dec 03 2009 - 15:58:31 CST)
• [AMBER] ambertools test faied
  • case (Tue Aug 25 2009 - 06:39:16 CDT)
  • subarna thakur (Tue Aug 25 2009 - 06:01:12 CDT)
• [AMBER] AmberTools-1.3 not compiling on MacOsX
  • Jason Swails (Wed Dec 23 2009 - 05:38:08 CST)
  • Mengjuei Hsieh (Wed Dec 23 2009 - 04:05:48 CST)
  • Mengjuei Hsieh (Wed Dec 23 2009 - 03:12:19 CST)
  • David Watson (Wed Dec 23 2009 - 00:59:09 CST)
  • Cesar Millan (Wed Dec 23 2009 - 00:37:37 CST)
• [AMBER] ambmask question
  • Ed Pate (Mon Apr 06 2009 - 23:36:40 CDT)
• [AMBER] ambmol2?
  • David A. Case (Wed Apr 01 2009 - 08:19:00 CDT)
  • Junmei Wang (Tue Mar 31 2009 - 21:41:35 CDT)
  • Taufik Al-Sarraj (Tue Mar 31 2009 - 21:15:00 CDT)
  • Junmei Wang (Tue Mar 31 2009 - 18:08:25 CDT)
  • Taufik Al-Sarraj (Tue Mar 31 2009 - 17:28:51 CDT)
• [AMBER] ambpdb is changing atom names, a feature or bug?
  • David A. Case (Sat Jan 10 2009 - 10:02:53 CST)
  • Ye Mei (Sat Jan 10 2009 - 02:03:10 CST)
  • David A. Case (Fri Jan 09 2009 - 12:58:20 CST)
  • Bill Ross (Fri Jan 09 2009 - 11:53:23 CST)
  • David A. Case (Fri Jan 09 2009 - 07:01:54 CST)
  • Markus Kaukonen (Fri Jan 09 2009 - 06:55:41 CST)
• [AMBER] ambpdb problem
  • Ashish Runthala (Fri Jul 31 2009 - 20:28:42 CDT)
  • Jordan Monnet (Fri Jul 31 2009 - 09:30:54 CDT)
  • Jio M (Fri Jul 31 2009 - 02:11:32 CDT)
  • Ashish Runthala (Thu Jul 30 2009 - 22:44:10 CDT)
  • Jordan Monnet (Thu Jul 30 2009 - 14:32:57 CDT)
  • Jio M (Thu Jul 30 2009 - 14:12:10 CDT)
• [AMBER] ambpdb water removal for rst files
  • Bill Ross (Sun Dec 06 2009 - 14:09:26 CST)
  • Bill Ross (Sun Dec 06 2009 - 14:03:00 CST)
  • Andrew Voronkov (Sun Dec 06 2009 - 13:44:28 CST)
  • Bill Ross (Sat Aug 22 2009 - 09:45:30 CDT)
  • Andrew Voronkov (Sat Aug 22 2009 - 01:53:14 CDT)
• [AMBER] ambr parameter file creation and usage
  • Donald Keidel (Tue Nov 03 2009 - 22:39:38 CST)
• [AMBER] amino acids caps for truncated proteins
  • FyD (Thu Jul 16 2009 - 11:58:32 CDT)
  • Andrew Voronkov (Thu Jul 16 2009 - 11:31:18 CDT)
• [AMBER] AMOEBA and carbon nanotubes + include parameters
  • Tomasio, Susana (Thu May 28 2009 - 05:23:00 CDT)
• [AMBER] amoeba.prm problem?
  • Ivan Gladich (Fri Sep 18 2009 - 14:57:39 CDT)
  • case (Sat Sep 12 2009 - 08:46:52 CDT)
  • Ivan Gladich (Fri Sep 11 2009 - 15:34:07 CDT)
  • case (Wed Sep 09 2009 - 14:17:39 CDT)
  • Ivan Gladich (Tue Sep 08 2009 - 09:31:43 CDT)
• [AMBER] anal output: Entalphy or Free Energy?
  • Edward M (Tue May 12 2009 - 19:14:37 CDT)
  • E.M. (Tue May 12 2009 - 17:25:41 CDT)
• [AMBER] ANAL problems
  • Edward M (Tue Apr 28 2009 - 18:01:34 CDT)
  • Bill Ross (Tue Apr 28 2009 - 15:40:59 CDT)
  • E.M. (Tue Apr 28 2009 - 15:12:04 CDT)
• [AMBER] analysing DNA trajectory
  • Bala subramanian (Fri Mar 20 2009 - 03:06:08 CDT)
  • balaji nagarajan (Fri Mar 20 2009 - 00:09:10 CDT)
• [AMBER] analysis
  • Adrien Delmont (Tue Jan 20 2009 - 11:03:16 CST)
• [AMBER] analysis of QM/MM - LCOD
  • Aust, Susanne (Fri Jul 03 2009 - 04:51:34 CDT)
• [AMBER] Analysis of the solt-bridge
  • Rilei Yu (Mon Jun 29 2009 - 17:42:23 CDT)
  • Alessandro Nascimento (Mon Jun 29 2009 - 07:58:49 CDT)
  • Rilei Yu (Sun Jun 28 2009 - 17:24:28 CDT)
• [AMBER] analysis on Amber
  • Thomas Cheatham (Sat Mar 07 2009 - 12:18:58 CST)
  • oguz gurbulak (Sat Mar 07 2009 - 12:04:19 CST)
• [AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack
  • Naser Alijabbari (Sun Nov 08 2009 - 19:43:56 CST)
• [AMBER] Analyzing per-residue decomposition data
  • manoj singh (Thu Oct 29 2009 - 15:18:45 CDT)
• [AMBER] angle between ligand ring plane and axis
  • Jia Xu (Wed Mar 04 2009 - 05:00:08 CST)
• [AMBER] angle with ptraj
  • Seetin, Matthew (Wed Aug 19 2009 - 14:42:07 CDT)
  • E.M. (Wed Aug 19 2009 - 14:27:29 CDT)
• [AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany
  • Harald Lanig (Fri Mar 20 2009 - 06:25:09 CDT)
• [AMBER] Announcing NMR validation web interface iCing
  • Alan (Mon Mar 30 2009 - 11:55:00 CDT)
• [AMBER] antechamber
  • R. A. (Thu Jul 02 2009 - 19:35:42 CDT)
  • Alan (Thu Jul 02 2009 - 05:16:55 CDT)
  • FyD (Thu Jul 02 2009 - 01:33:46 CDT)
  • R. A. (Wed Jul 01 2009 - 19:46:19 CDT)
  • FyD (Wed Jul 01 2009 - 07:26:39 CDT)
  • gilbert_at_bluemarble.net (Wed Jul 01 2009 - 07:11:17 CDT)
  • case (Wed Jul 01 2009 - 07:04:02 CDT)
  • Alan (Wed Jul 01 2009 - 06:37:40 CDT)
  • R. A. (Wed Jul 01 2009 - 04:19:54 CDT)
  • R. A. (Wed Jul 01 2009 - 04:17:51 CDT)
  • kureeckal ramesh (Thu Feb 19 2009 - 19:36:03 CST)
• [AMBER] antechamber & multiple low-energy conformations
  • Alessandro Nascimento (Fri Apr 03 2009 - 07:01:39 CDT)
• [AMBER] antechamber : missed atoms
  • David A. Case (Tue Jan 27 2009 - 09:23:27 CST)
  • Khaled Barakat (Mon Jan 26 2009 - 14:22:14 CST)
  • Sean Johnston (Mon Jan 26 2009 - 13:40:59 CST)
  • Khaled Barakat (Mon Jan 26 2009 - 13:20:52 CST)
  • Khaled Barakat (Mon Jan 26 2009 - 13:15:33 CST)
  • Khaled Barakat (Mon Jan 26 2009 - 12:54:07 CST)
• [AMBER] antechamber am1-bcc issues
  • Ross Walker (Thu Aug 20 2009 - 09:29:14 CDT)
  • Khavrutskii, Ilja (Thu Aug 20 2009 - 08:04:44 CDT)
  • gilbert_at_bluemarble.net (Thu Aug 20 2009 - 07:37:53 CDT)
  • Khavrutskii, Ilja (Thu Aug 20 2009 - 07:03:43 CDT)
  • Khavrutskii, Ilja (Thu Aug 20 2009 - 06:37:47 CDT)
  • case (Thu Aug 20 2009 - 06:18:52 CDT)
  • Alan (Thu Aug 20 2009 - 03:28:09 CDT)
  • Khavrutskii, Ilja (Tue Aug 18 2009 - 16:00:03 CDT)
  • David Mobley (Fri Aug 07 2009 - 13:19:53 CDT)
• [AMBER] Antechamber am1bcc questions
  • gilbert_at_bluemarble.net (Mon Jun 15 2009 - 08:04:19 CDT)
• [AMBER] Antechamber and Parmchk problems
  • Junmei Wang (Thu Nov 05 2009 - 15:16:51 CST)
  • cyk5056 (Thu Nov 05 2009 - 12:59:28 CST)
  • Junmei Wang (Wed Nov 04 2009 - 15:07:35 CST)
  • cyk5056 (Wed Nov 04 2009 - 14:37:55 CST)
  • cyk5056 (Wed Nov 04 2009 - 13:56:32 CST)
  • Junmei Wang (Wed Nov 04 2009 - 13:21:25 CST)
  • case (Wed Nov 04 2009 - 09:26:03 CST)
  • cyk5056 (Tue Nov 03 2009 - 20:22:38 CST)
• [AMBER] antechamber and wrong net charge with gasteiger method
  • David A. Case (Tue Apr 14 2009 - 13:42:14 CDT)
  • Alan (Tue Apr 14 2009 - 12:41:30 CDT)
• [AMBER] antechamber bond type error
  • case (Sat Dec 19 2009 - 11:33:40 CST)
  • Mark M Huntress (Fri Dec 18 2009 - 16:26:57 CST)
• [AMBER] antechamber bug report
  • case (Mon Aug 31 2009 - 12:36:33 CDT)
  • Matthew Walsh (Mon Aug 31 2009 - 11:43:08 CDT)
• [AMBER] antechamber bug: output of incorrect bond character
  • case (Thu Sep 03 2009 - 11:29:03 CDT)
  • Matthew Walsh (Thu Sep 03 2009 - 10:15:00 CDT)
  • case (Thu Sep 03 2009 - 06:26:19 CDT)
  • Matthew Walsh (Wed Sep 02 2009 - 23:30:04 CDT)
  • case (Wed Sep 02 2009 - 20:53:37 CDT)
  • Matthew Walsh (Wed Sep 02 2009 - 13:37:44 CDT)
• [AMBER] antechamber cation failure
  • Ross Walker (Wed Jan 14 2009 - 11:45:43 CST)
  • Rausch, Felix (Wed Jan 14 2009 - 07:32:04 CST)
• [AMBER] Antechamber Connectivity
  • David Watson (Mon Jan 26 2009 - 13:59:58 CST)
  • George Tzotzos (Mon Jan 26 2009 - 12:23:58 CST)
• [AMBER] antechamber error
  • case (Fri Dec 11 2009 - 06:51:44 CST)
  • David Watson (Thu Dec 10 2009 - 17:26:00 CST)
  • Mike Hanby (Thu Dec 10 2009 - 16:34:30 CST)
  • Taufik Al-Sarraj (Wed Sep 16 2009 - 14:11:26 CDT)
  • Taufik Al-Sarraj (Wed Sep 16 2009 - 13:52:26 CDT)
  • case (Wed Sep 16 2009 - 13:43:56 CDT)
  • Taufik Al-Sarraj (Wed Sep 16 2009 - 13:18:32 CDT)
• [AMBER] antechamber execution
  • FyD (Tue Aug 18 2009 - 18:59:40 CDT)
  • subarna thakur (Tue Aug 18 2009 - 01:06:52 CDT)
• [AMBER] Antechamber generate a prep file in a wrong order...
  • case (Sun Sep 06 2009 - 07:26:02 CDT)
  • Yikan Chen (Sat Sep 05 2009 - 14:37:53 CDT)
• [AMBER] Antechamber ligand prep
  • George Tzotzos (Tue Jan 27 2009 - 10:44:06 CST)
  • George Tzotzos (Tue Jan 27 2009 - 09:43:19 CST)
  • David Watson (Tue Jan 27 2009 - 09:34:25 CST)
  • David A. Case (Tue Jan 27 2009 - 09:33:57 CST)
  • George Tzotzos (Tue Jan 27 2009 - 09:24:30 CST)
  • David A. Case (Tue Jan 27 2009 - 08:59:47 CST)
  • George Tzotzos (Tue Jan 27 2009 - 08:48:11 CST)
• [AMBER] Antechamber prep question
  • FyD (Fri Jul 10 2009 - 10:24:08 CDT)
  • Andrew Olson (Fri Jul 10 2009 - 08:33:09 CDT)
  • gilbert_at_bluemarble.net (Fri Jul 10 2009 - 08:10:32 CDT)
  • FyD (Fri Jul 10 2009 - 00:52:12 CDT)
  • case (Thu Jul 09 2009 - 13:54:44 CDT)
  • Andrew Olson (Thu Jul 09 2009 - 12:00:19 CDT)
  • case (Thu Jul 09 2009 - 11:48:44 CDT)
  • Andrew Olson (Thu Jul 09 2009 - 10:22:18 CDT)
  • case (Thu Jul 09 2009 - 10:16:17 CDT)
  • Andrew Olson (Thu Jul 09 2009 - 09:39:25 CDT)
• [AMBER] Antechamber problem
  • Å·ÑôµÂ·½ (Fri Mar 27 2009 - 19:55:03 CDT)
  • Junmei Wang (Fri Mar 27 2009 - 16:21:33 CDT)
  • David A. Case (Fri Mar 27 2009 - 07:29:48 CDT)
  • Å·ÑôµÂ·½ (Thu Mar 26 2009 - 23:44:24 CDT)
• [AMBER] antechamber problems
  • Jia Xu (Fri Apr 10 2009 - 09:41:53 CDT)
  • Nicholas Musolino (Thu Apr 09 2009 - 13:03:45 CDT)
  • David A. Case (Thu Apr 09 2009 - 13:04:51 CDT)
  • Jia Xu (Thu Apr 09 2009 - 12:12:44 CDT)
• [AMBER] Antechamber: stuck at bondtype
  • Ye MEI (Wed Jun 17 2009 - 08:48:18 CDT)
  • David A. Case (Wed Jun 17 2009 - 08:28:15 CDT)
  • Jack Shultz (Wed Jun 17 2009 - 07:50:11 CDT)
• [AMBER] Any Comment, please
  • s. Bill (Tue Aug 11 2009 - 02:56:20 CDT)
• [AMBER] Any link to a major QM code?
  • Gustavo Seabra (Mon Feb 16 2009 - 10:51:03 CST)
  • Francesco Pietra (Mon Feb 16 2009 - 08:47:04 CST)
  • Adrian Roitberg (Sun Feb 15 2009 - 20:59:01 CST)
  • Gustavo Seabra (Sun Feb 15 2009 - 18:17:32 CST)
  • Francesco Pietra (Sun Feb 15 2009 - 11:58:30 CST)
• [AMBER] Any tutorial on the proper way to merge a ligand and protein?
  • Scott Brozell (Fri Oct 16 2009 - 14:40:56 CDT)
  • case (Fri Sep 11 2009 - 14:54:39 CDT)
  • cc cc (Fri Sep 11 2009 - 13:16:55 CDT)
  • Dean Cuebas (Wed Sep 09 2009 - 14:12:00 CDT)
  • case (Wed Sep 09 2009 - 13:50:13 CDT)
  • Dean Cuebas (Wed Sep 09 2009 - 13:26:02 CDT)
• [AMBER] apbs-amber
  • Rilei Yu (Tue Sep 22 2009 - 20:41:08 CDT)
  • Robert Konecny (Tue Sep 22 2009 - 18:18:28 CDT)
  • Rilei Yu (Tue Sep 22 2009 - 17:58:40 CDT)
• [AMBER] Appropriate nmode input file for gas and vacuum phase simulation
  • Scott Pendley (Fri Aug 07 2009 - 12:48:52 CDT)
• [AMBER] APS & ff03
  • Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 08:49:56 CST)
• [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations?
  • Ross Walker (Mon Jun 15 2009 - 09:49:43 CDT)
  • Catein Catherine (Mon Jun 15 2009 - 05:04:53 CDT)
• [AMBER] aromatic ring getting distorted
  • Jio M (Mon Dec 07 2009 - 01:04:55 CST)
  • case (Sun Dec 06 2009 - 14:14:45 CST)
  • Jio M (Fri Dec 04 2009 - 04:03:49 CST)
• [AMBER] array out of bound in Amber10 tests
  • Shan-ho Tsai (Mon Feb 16 2009 - 10:53:05 CST)
  • Carlos Simmerling (Fri Feb 13 2009 - 10:38:04 CST)
  • Shan-ho Tsai (Wed Feb 11 2009 - 16:24:10 CST)
  • Carlos Simmerling (Wed Feb 11 2009 - 10:14:49 CST)
  • Shan-ho Tsai (Wed Feb 11 2009 - 09:38:23 CST)
  • David A. Case (Tue Feb 10 2009 - 15:30:36 CST)
  • Shan-ho Tsai (Tue Feb 10 2009 - 15:04:43 CST)
  • David A. Case (Tue Feb 10 2009 - 10:39:43 CST)
  • Shan-ho Tsai (Tue Feb 10 2009 - 10:19:42 CST)
• [AMBER] ask for parm99MOD
  • xiaoqin huang (Mon Jun 01 2009 - 15:25:02 CDT)
  • Carlos Simmerling (Mon Jun 01 2009 - 15:12:47 CDT)
  • David A. Case (Thu May 28 2009 - 16:52:29 CDT)
  • xiaoqin huang (Thu May 28 2009 - 16:43:15 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 16:17:05 CDT)
  • xiaoqin huang (Thu May 28 2009 - 16:09:26 CDT)
  • Adrian Roitberg (Thu May 28 2009 - 15:56:14 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 15:52:56 CDT)
  • xiaoqin huang (Thu May 28 2009 - 15:32:02 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 15:22:31 CDT)
  • xiaoqin huang (Thu May 28 2009 - 15:09:28 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 14:57:24 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 14:56:26 CDT)
  • xiaoqin huang (Thu May 28 2009 - 14:51:59 CDT)
  • xiaoqin huang (Thu May 28 2009 - 14:46:23 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 14:44:41 CDT)
  • Adrian Roitberg (Thu May 28 2009 - 14:44:08 CDT)
  • xiaoqin huang (Thu May 28 2009 - 14:41:54 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 14:41:20 CDT)
  • Adrian Roitberg (Thu May 28 2009 - 14:38:23 CDT)
  • xiaoqin huang (Thu May 28 2009 - 14:31:14 CDT)
  • xiaoqin huang (Thu May 28 2009 - 13:16:35 CDT)
• [AMBER] Asking help for parallel installation of Amber9
  • David Watson (Wed Nov 18 2009 - 12:04:38 CST)
  • Bill Ross (Wed Nov 18 2009 - 11:48:51 CST)
  • David Watson (Wed Nov 18 2009 - 07:23:17 CST)
  • nicholus bhattacharjee (Wed Nov 18 2009 - 07:00:36 CST)
  • David Watson (Wed Nov 18 2009 - 06:36:03 CST)
  • nicholus bhattacharjee (Wed Nov 18 2009 - 06:27:03 CST)
• [AMBER] assigning velocities to each atom without heating the system
  • Ross Walker (Mon Mar 02 2009 - 14:23:22 CST)
  • Parimal Kar (Mon Mar 02 2009 - 11:46:25 CST)
  • Gustavo Seabra (Mon Mar 02 2009 - 11:31:09 CST)
  • Parimal Kar (Mon Mar 02 2009 - 10:44:26 CST)
• [AMBER] Atom names
  • Rose Tamil (Wed Jun 03 2009 - 15:43:56 CDT)
  • David A. Case (Wed Jun 03 2009 - 11:00:15 CDT)
  • Rose Tamil (Wed Jun 03 2009 - 09:53:51 CDT)
  • Rose Tamil (Tue Jun 02 2009 - 06:50:47 CDT)
  • David A. Case (Tue Jun 02 2009 - 06:44:39 CDT)
  • Carlos Simmerling (Tue Jun 02 2009 - 06:39:25 CDT)
  • Rose Tamil (Tue Jun 02 2009 - 05:53:50 CDT)
• [AMBER] atom number exceeds the MAXATOM when running antechamber
  • Gustavo Seabra (Tue Jun 02 2009 - 10:04:33 CDT)
  • xueqin pang (Mon Jun 01 2009 - 07:53:23 CDT)
• [AMBER] atom numbers
  • Vikas Sharma (Tue Apr 21 2009 - 13:36:35 CDT)
  • David A. Case (Tue Apr 21 2009 - 12:26:32 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 12:15:07 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 11:58:41 CDT)
  • David A. Case (Tue Apr 21 2009 - 10:52:22 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 10:33:12 CDT)
  • David A. Case (Tue Apr 21 2009 - 06:54:37 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 06:12:27 CDT)
• [AMBER] atom type
  • FyD (Wed Dec 23 2009 - 07:00:39 CST)
  • shamoon siddiqui (Tue Dec 22 2009 - 23:31:42 CST)
  • Taufik Al-Sarraj (Fri Jun 05 2009 - 11:07:14 CDT)
  • Taufik Al-Sarraj (Fri Jun 05 2009 - 08:58:50 CDT)
  • David A. Case (Fri Jun 05 2009 - 07:32:45 CDT)
  • Taufik Al-Sarraj (Thu Jun 04 2009 - 20:03:14 CDT)
• [AMBER] Atom type error
  • Vikas Sharma (Tue Apr 21 2009 - 01:55:24 CDT)
  • Vikas Sharma (Mon Apr 20 2009 - 05:46:34 CDT)
  • Ross Walker (Sun Apr 19 2009 - 16:23:38 CDT)
  • Vikas Sharma (Sun Apr 19 2009 - 13:33:36 CDT)
  • David A. Case (Sun Apr 19 2009 - 12:41:11 CDT)
  • Vikas Sharma (Sun Apr 19 2009 - 11:50:28 CDT)
  • Vikas Sharma (Sun Apr 19 2009 - 11:49:53 CDT)
  • Carlos Simmerling (Sun Apr 19 2009 - 06:06:07 CDT)
  • nicholus bhattacharjee (Sun Apr 19 2009 - 05:55:37 CDT)
  • Vikas Sharma (Sun Apr 19 2009 - 04:48:01 CDT)
• [AMBER] Atom Type List
  • Bill Ross (Mon Jun 22 2009 - 11:43:39 CDT)
  • Javier Klett (Mon Jun 22 2009 - 11:34:43 CDT)
  • case (Mon Jun 22 2009 - 06:38:24 CDT)
  • Javier Klett (Mon Jun 22 2009 - 04:54:43 CDT)
• [AMBER] atom type no recognize - xleap version 10 but fine in v 9
  • case (Sat Jun 20 2009 - 13:31:40 CDT)
  • Peter Gannett (Fri Jun 19 2009 - 14:40:47 CDT)
• [AMBER] atom types
  • David A. Case (Tue Jan 27 2009 - 09:13:30 CST)
  • deepti nayar (Tue Jan 27 2009 - 03:47:12 CST)
  • George Tzotzos (Mon Jan 19 2009 - 12:02:42 CST)
  • Ross Walker (Mon Jan 19 2009 - 09:46:10 CST)
  • George Tzotzos (Mon Jan 19 2009 - 08:04:09 CST)
• [AMBER] atom types in pdb files
  • David A. Case (Mon Apr 13 2009 - 15:25:04 CDT)
  • Dan Kaps (Mon Apr 13 2009 - 14:29:43 CDT)
  • Kristina Furse (Mon Apr 13 2009 - 11:30:05 CDT)
  • Dan Kaps (Mon Apr 13 2009 - 09:23:58 CDT)
• [AMBER] Atome Type
  • David A. Case (Thu Jan 29 2009 - 07:08:09 CST)
  • Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 04:59:42 CST)
• [AMBER] atomic charge
  • Barbault Florent (Thu Jan 29 2009 - 02:24:48 CST)
  • m m (Thu Jan 29 2009 - 02:08:47 CST)
• [AMBER] Atomic radii assignment for WAT molecules
  • Ray Luo (Sat Nov 28 2009 - 12:13:42 CST)
  • DIMAS SUAREZ RODRIGUEZ (Thu Nov 26 2009 - 10:43:33 CST)
• [AMBER] atoms fly out of the box in NVT calculations
  • iccy liu (Sun Feb 15 2009 - 17:34:37 CST)
  • Ross Walker (Thu Feb 12 2009 - 20:22:57 CST)
  • Carlos Simmerling (Thu Feb 12 2009 - 16:05:10 CST)
  • iccy liu (Thu Feb 12 2009 - 15:48:24 CST)
• [AMBER] atomtypes in gaff
  • FyD (Thu Jun 25 2009 - 06:45:16 CDT)
  • FyD (Thu Jun 25 2009 - 03:55:03 CDT)
  • Aust, Susanne (Thu Jun 25 2009 - 01:49:48 CDT)
• [AMBER] ATP and GTP parameters
  • E.M. (Thu Sep 03 2009 - 21:08:02 CDT)
  • Carlos Simmerling (Thu Sep 03 2009 - 06:54:13 CDT)
  • FyD (Thu Sep 03 2009 - 04:36:45 CDT)
  • FyD (Thu Sep 03 2009 - 03:35:11 CDT)
  • Sergey Samsonov (Thu Sep 03 2009 - 01:35:33 CDT)
  • E.M. (Thu Sep 03 2009 - 01:30:31 CDT)
  • FyD (Thu Sep 03 2009 - 01:15:54 CDT)
  • E.M. (Thu Sep 03 2009 - 00:29:47 CDT)
• [AMBER] ATP/GTP parameters
  • E.M. (Tue Dec 08 2009 - 22:36:19 CST)
  • Steve Seibold (Tue Sep 01 2009 - 11:29:59 CDT)
  • FyD (Tue Sep 01 2009 - 11:25:45 CDT)
  • Steve Seibold (Tue Sep 01 2009 - 06:42:09 CDT)
  • FyD (Tue Sep 01 2009 - 01:10:41 CDT)
  • wang (Tue Sep 01 2009 - 00:02:08 CDT)
  • E.M. (Mon Aug 31 2009 - 23:48:39 CDT)
  • E.M. (Mon Aug 31 2009 - 15:50:09 CDT)
  • FyD (Mon Aug 31 2009 - 15:20:50 CDT)
  • case (Mon Aug 31 2009 - 07:41:22 CDT)
  • Steve Seibold (Mon Aug 31 2009 - 07:33:04 CDT)
• [AMBER] Attaching a ligand to a protein residue.
  • Kipras Redeckas (Sun Sep 27 2009 - 05:23:42 CDT)
  • case (Sat Sep 26 2009 - 09:23:18 CDT)
  • Kipras Redeckas (Fri Sep 25 2009 - 16:33:58 CDT)
• [AMBER] Average structure over simulation
  • Olotu Odunayo (Mon Jul 27 2009 - 08:38:59 CDT)
• [AMBER] average torsional energy
  • Francesco Pietra (Mon Jun 08 2009 - 04:11:52 CDT)
  • Karl Kirschner (Mon Jun 08 2009 - 03:29:05 CDT)
  • Carlos Simmerling (Sun Jun 07 2009 - 11:14:17 CDT)
  • Adrian Roitberg (Sun Jun 07 2009 - 11:09:14 CDT)
  • Francesco Pietra (Sat Jun 06 2009 - 11:57:49 CDT)
• [AMBER] Averaging simulations
  • Carlos Simmerling (Thu Apr 02 2009 - 10:24:28 CDT)
  • Naser Alijabbari (Thu Apr 02 2009 - 10:21:41 CDT)
• [AMBER] B-factor
  • Cristina Sisu (Sat Oct 17 2009 - 05:58:34 CDT)
  • Thomas Cheatham III (Fri Oct 16 2009 - 17:16:35 CDT)
  • Cristina Sisu (Thu Oct 15 2009 - 12:04:25 CDT)
• [AMBER] Backbone restraint
  • Rilei Yu (Mon Apr 20 2009 - 20:21:09 CDT)
  • Jackie. J. Shen (Mon Apr 20 2009 - 20:12:13 CDT)
  • Carlos Simmerling (Sat Apr 18 2009 - 06:08:39 CDT)
  • Rilei Yu (Fri Apr 17 2009 - 22:29:12 CDT)
  • Carlos Simmerling (Fri Apr 17 2009 - 21:35:26 CDT)
  • Rilei Yu (Fri Apr 17 2009 - 21:30:38 CDT)
• [AMBER] bad atom type in mm_pbsa calculation. How to solve it? Thanks!
  • Haizhen Zhong (Wed Jun 03 2009 - 18:00:34 CDT)
• [AMBER] bad atom type: MN
  • Edward M (Mon Jun 22 2009 - 18:12:09 CDT)
  • Edward M (Mon Jun 22 2009 - 18:12:09 CDT)
  • Edward M (Mon Jun 22 2009 - 18:10:54 CDT)
• [AMBER] bad energy??!!
  • Ross Walker (Wed Jan 14 2009 - 13:40:24 CST)
  • momo momo (Wed Jan 14 2009 - 13:19:20 CST)
• [AMBER] Bad value during integer read by sander
  • Collins Nganou (Thu Apr 16 2009 - 10:09:45 CDT)
• [AMBER] basepair
  • Bala subramanian (Tue Apr 14 2009 - 06:09:21 CDT)
  • balaji nagarajan (Fri Apr 10 2009 - 00:30:57 CDT)
• [AMBER] Beginner question
  • Heath Watts (Fri Feb 13 2009 - 19:20:46 CST)
  • Heath Watts (Fri Feb 13 2009 - 19:19:44 CST)
  • Barbault Florent (Fri Feb 13 2009 - 15:25:13 CST)
  • Carlos Simmerling (Fri Feb 13 2009 - 15:24:37 CST)
  • Heath Watts (Fri Feb 13 2009 - 15:18:42 CST)
• [AMBER] Best rms fit for correlation and covariance analysis
  • Bill Ross (Tue Apr 28 2009 - 11:57:10 CDT)
  • Cihan Aydin (Tue Apr 28 2009 - 00:02:14 CDT)
• [AMBER] BINDER/xaLeap
  • taufik.alsarraj_at_utoronto.ca (Mon Mar 30 2009 - 21:16:32 CDT)
  • Ross Walker (Mon Mar 30 2009 - 20:29:46 CDT)
  • Taufik Al-Sarraj (Mon Mar 30 2009 - 20:00:10 CDT)
• [AMBER] binding energy
  • steinbrt_at_rci.rutgers.edu (Fri Oct 16 2009 - 06:27:24 CDT)
  • Simon Becker (Fri Oct 16 2009 - 04:28:39 CDT)
  • Vikas Sharma (Thu Jun 04 2009 - 06:25:01 CDT)
• [AMBER] binding energy of multiple ligand-receptor complex
  • Å·ÑôµÂ·½ (Fri Dec 04 2009 - 15:59:21 CST)
  • Jason Swails (Fri Dec 04 2009 - 14:20:58 CST)
  • steinbrt_at_rci.rutgers.edu (Fri Dec 04 2009 - 03:47:26 CST)
  • Oliver Kuhn (Fri Dec 04 2009 - 03:10:39 CST)
  • Å·ÑôµÂ·½ (Thu Dec 03 2009 - 04:51:17 CST)
• [AMBER] binding free energy
  • Ross Walker (Mon Mar 02 2009 - 14:16:55 CST)
  • Robert Duke (Mon Mar 02 2009 - 07:22:22 CST)
  • Maryam Hamzehee (Mon Mar 02 2009 - 01:33:44 CST)
  • Ross Walker (Sun Mar 01 2009 - 11:29:35 CST)
  • Don.Bashford_at_stjude.org (Sun Mar 01 2009 - 11:18:39 CST)
  • Barbault Florent (Sun Mar 01 2009 - 06:20:39 CST)
  • Maryam Hamzehee (Sun Mar 01 2009 - 05:52:43 CST)
• [AMBER] bintraj and amber 10
  • Naser Alijabbari (Sat Apr 25 2009 - 13:47:34 CDT)
  • Naser Alijabbari (Thu Apr 23 2009 - 19:37:06 CDT)
  • Chris Moth (Thu Apr 23 2009 - 12:46:44 CDT)
  • Ross Walker (Thu Apr 23 2009 - 08:31:08 CDT)
  • Naser Alijabbari (Wed Apr 22 2009 - 20:05:21 CDT)
  • Ross Walker (Wed Apr 22 2009 - 05:59:47 CDT)
  • Naser Alijabbari (Wed Apr 22 2009 - 01:31:51 CDT)
• [AMBER] bond length energy
  • Karl Kirschner (Fri Jun 19 2009 - 04:57:04 CDT)
  • Mark Williamson (Wed Jun 17 2009 - 12:29:09 CDT)
  • Thomas Lake (Wed Jun 17 2009 - 09:04:55 CDT)
• [AMBER] Boundary Condition Problem
  • case (Sat Jul 04 2009 - 08:45:45 CDT)
  • Pepe` Falahat (Sat Jul 04 2009 - 07:10:59 CDT)
• [AMBER] Box Center
  • Jagan Mohan (Fri Jun 26 2009 - 03:02:05 CDT)
• [AMBER] box problem
  • Nancy (Mon Aug 17 2009 - 22:27:59 CDT)
  • Nancy (Mon Aug 17 2009 - 22:18:02 CDT)
  • Ashish Runthala (Mon Aug 17 2009 - 22:08:28 CDT)
  • Nancy (Mon Aug 17 2009 - 22:02:21 CDT)
  • Nancy (Mon Aug 17 2009 - 21:49:20 CDT)
  • Ross Walker (Sun Aug 16 2009 - 11:59:59 CDT)
  • Ashish Runthala (Sun Aug 16 2009 - 09:00:50 CDT)
  • Nancy (Sun Aug 16 2009 - 02:31:02 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 01:12:10 CDT)
  • Nancy (Thu Aug 13 2009 - 21:43:02 CDT)
  • case (Thu Aug 13 2009 - 06:50:54 CDT)
  • Nancy (Thu Aug 13 2009 - 06:20:20 CDT)
• [AMBER] Box shape change
  • Hemant Kumar (Sun Jul 19 2009 - 12:38:43 CDT)
  • Carlos Simmerling (Sun Jul 19 2009 - 08:51:44 CDT)
  • Hemant Kumar (Sun Jul 19 2009 - 07:05:04 CDT)
  • Carlos Simmerling (Sun Jul 19 2009 - 06:40:03 CDT)
  • Hemant Kumar (Sun Jul 19 2009 - 06:00:18 CDT)
  • Carlos Simmerling (Sat Jul 18 2009 - 20:35:41 CDT)
  • Hemant Kumar (Sat Jul 18 2009 - 14:38:46 CDT)
• [AMBER] box volume not understood?
  • Bill Ross (Fri Aug 21 2009 - 11:15:51 CDT)
  • Jio M (Thu Aug 20 2009 - 23:43:31 CDT)
  • Bill Ross (Thu Aug 20 2009 - 21:53:52 CDT)
  • Ross Walker (Thu Aug 20 2009 - 18:21:00 CDT)
  • Jio M (Thu Aug 20 2009 - 13:26:41 CDT)
  • Ross Walker (Thu Aug 20 2009 - 10:43:42 CDT)
  • Jio M (Thu Aug 20 2009 - 08:54:52 CDT)
• [AMBER] branched aminoacids
  • Alessandro Contini (Thu Dec 17 2009 - 05:22:56 CST)
  • FyD (Thu Dec 17 2009 - 03:49:16 CST)
  • Alessandro Contini (Thu Dec 17 2009 - 03:14:34 CST)
• [AMBER] broken Ligand
  • David A. Case (Sun May 31 2009 - 07:50:57 CDT)
  • Shubhra Gupta (Sat May 30 2009 - 01:35:46 CDT)
  • David A. Case (Fri May 29 2009 - 09:45:20 CDT)
  • Shubhra Gupta (Fri May 29 2009 - 08:28:22 CDT)
• [AMBER] bug in antechamber
  • David Mobley (Wed Jul 08 2009 - 11:19:12 CDT)
• [AMBER] bugfix 10 failing for ambertools1.2
  • Alan (Mon Jul 20 2009 - 03:14:16 CDT)
• [AMBER] build up solvate box
  • Huikuan Chao (Sat Nov 07 2009 - 14:29:50 CST)
• [AMBER] Building atom and angle parameters
  • George Tzotzos (Tue Jan 27 2009 - 12:24:52 CST)
• [AMBER] building quadruplex with NAB
  • case (Tue Oct 27 2009 - 21:23:29 CDT)
  • Peter Varnai (Tue Oct 27 2009 - 15:00:09 CDT)
  • David A. Case (Wed May 13 2009 - 06:48:38 CDT)
  • Peter Varnai (Sun May 10 2009 - 18:27:38 CDT)
• [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5
  • Nils Jan Daniel Drechsel (Fri Dec 18 2009 - 04:37:53 CST)
  • case (Thu Dec 17 2009 - 07:03:27 CST)
  • Nils Jan Daniel Drechsel (Thu Dec 17 2009 - 03:52:59 CST)
• [AMBER] Calculaiton stop ?
  • xuemeiwang1103 (Thu Nov 05 2009 - 07:11:31 CST)
• [AMBER] calculate shear viscosity
  • oguz gurbulak (Mon Mar 02 2009 - 07:35:06 CST)
• [AMBER] calculating the hydrogen bonding energy between the two molecule
  • bharat lakhani (Wed Jun 24 2009 - 04:19:01 CDT)
• [AMBER] calculation of binding energy for lectin and fucuse..
  • Sushil Mishra (Fri Jul 10 2009 - 13:26:20 CDT)
• [AMBER] calculation of Pi-Pi interaction energy
  • Jiri Sponer (Wed Apr 01 2009 - 07:38:49 CDT)
  • Jacopo Sgrignani (Wed Apr 01 2009 - 07:24:28 CDT)
  • aneesh cna (Wed Apr 01 2009 - 07:01:51 CDT)
• [AMBER] calculation of the solvent accessibility
  • Rilei Yu (Sat Jul 04 2009 - 03:54:23 CDT)
• [AMBER] can antechamber convert a prep file from cartesian to internal coordinates?
  • Paul Ledbetter (Tue Sep 15 2009 - 18:40:09 CDT)
  • Paul Ledbetter (Tue Sep 15 2009 - 18:34:54 CDT)
  • Bill Ross (Tue Sep 15 2009 - 17:15:38 CDT)
  • case (Tue Sep 15 2009 - 17:12:25 CDT)
  • Paul Ledbetter (Tue Sep 15 2009 - 15:25:56 CDT)
• [AMBER] Can bond clevage & formation conducted by qm/mm via sander?
  • Gustavo Seabra (Tue May 05 2009 - 12:28:10 CDT)
  • Mahmoud A. A. Ibrahim (Tue May 05 2009 - 12:15:18 CDT)
  • Gustavo Seabra (Tue May 05 2009 - 12:04:37 CDT)
  • sychen (Tue May 05 2009 - 08:12:32 CDT)
• [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint?
  • liu junjun (Mon Feb 02 2009 - 10:25:41 CST)
  • David A. Case (Sun Feb 01 2009 - 12:35:03 CST)
  • Carlos Simmerling (Sun Feb 01 2009 - 11:55:54 CST)
  • liu junjun (Sun Feb 01 2009 - 01:51:39 CST)
• [AMBER] Can I do DNA bending with AMBER?
  • Catein Catherine (Mon Aug 17 2009 - 01:00:08 CDT)
  • case (Sun Aug 16 2009 - 08:13:05 CDT)
  • Catein Catherine (Sat Aug 15 2009 - 23:15:26 CDT)
• [AMBER] Can I get an average trajectory?
  • cyk5056 (Wed Nov 18 2009 - 10:02:38 CST)
  • Carlos Simmerling (Wed Nov 18 2009 - 06:08:59 CST)
  • cyk5056 (Tue Nov 17 2009 - 22:46:25 CST)
• [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP
  • FyD (Sun May 31 2009 - 07:51:50 CDT)
  • xueqin pang (Sun May 31 2009 - 07:43:09 CDT)
• [AMBER] Can I get the torsion angle between base-pairs using ptraj ?
  • Jordan Monnet (Wed Jul 15 2009 - 17:56:12 CDT)
  • Myeong Lee (Wed Jul 15 2009 - 16:51:02 CDT)
• [AMBER] can I install amber11 on a windowsPC under cygwin?
  • case (Tue Dec 29 2009 - 17:36:46 CST)
  • Jason Swails (Tue Dec 29 2009 - 17:08:38 CST)
  • Bill Ross (Tue Dec 29 2009 - 15:05:07 CST)
  • case (Tue Dec 29 2009 - 13:44:18 CST)
  • Mengjuei Hsieh (Tue Dec 29 2009 - 13:44:06 CST)
  • Jason Swails (Tue Dec 29 2009 - 13:42:34 CST)
  • Lixia Jin Day (Tue Dec 29 2009 - 12:06:30 CST)
• [AMBER] Can i link and refine the modeled domains with different proteins bound on it
  • Ashish Runthala (Tue Aug 18 2009 - 06:13:23 CDT)
• [AMBER] Can i link and refine two domains of a single protein
  • Ashish Runthala (Mon Aug 17 2009 - 10:32:33 CDT)
• [AMBER] can I run EVB in other ensemble than NVE?
  • case (Tue Oct 20 2009 - 12:08:58 CDT)
  • Jose Borreguero (Tue Oct 20 2009 - 11:57:04 CDT)
• [AMBER] Can I use only a single point calculation to derive RESP charges?
  • FyD (Sun May 10 2009 - 01:52:12 CDT)
  • Josmar R. da Rocha (Sat May 09 2009 - 10:19:07 CDT)
  • FyD (Sat May 09 2009 - 01:00:36 CDT)
  • Josmar R. da Rocha (Fri May 08 2009 - 19:08:54 CDT)
• [AMBER] Can I use other ntb options in constant pH simulation
  • Jason Swails (Wed Oct 21 2009 - 06:42:42 CDT)
  • nicholus bhattacharjee (Wed Oct 21 2009 - 04:26:43 CDT)
• [AMBER] can ptraj output the trajectory of the residue CM?
  • Jose Borreguero (Mon Feb 16 2009 - 13:47:34 CST)
• [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF?
  • David A. Case (Mon Jun 08 2009 - 11:47:54 CDT)
  • Catein Catherine (Mon Jun 08 2009 - 10:16:23 CDT)
• [AMBER] Can we use AMBER?
  • Ross Walker (Thu Jan 08 2009 - 12:47:18 CST)
  • Casey,Richard (Thu Jan 08 2009 - 11:25:57 CST)
  • Casey,Richard (Thu Jan 08 2009 - 11:16:50 CST)
• [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy
  • jacky zhao (Wed Jun 03 2009 - 08:44:12 CDT)
  • Marc Baaden (Tue Jun 02 2009 - 15:56:29 CDT)
  • Gustavo Seabra (Tue Jun 02 2009 - 09:53:19 CDT)
  • xueqin pang (Sun May 31 2009 - 07:47:57 CDT)
• [AMBER] Can't reproduce RESP charges
  • FyD (Tue Jan 13 2009 - 05:52:13 CST)
  • Sanghwa Han (Sun Jan 11 2009 - 23:57:15 CST)
• [AMBER] Carbon Nanotube Library file (CNT)
  • Christopher Stiles (Mon Sep 14 2009 - 08:59:57 CDT)
• [AMBER] carbonic anhydrase (CA) simulation
  • case (Thu Jul 16 2009 - 06:36:17 CDT)
  • vhakkim boy (Thu Jul 16 2009 - 02:03:23 CDT)
• [AMBER] catenan simulation problems
  • David A. Case (Wed Mar 18 2009 - 06:47:32 CDT)
  • David A. Case (Sat Mar 07 2009 - 17:25:07 CST)
  • Cristina S.D. Sisu (Fri Mar 06 2009 - 09:35:46 CST)
  • Cristina Sisu (Fri Mar 06 2009 - 09:28:00 CST)
  • David A. Case (Fri Mar 06 2009 - 08:59:24 CST)
  • Cristina Sisu (Fri Mar 06 2009 - 07:16:08 CST)
• [AMBER] CCL4 simulation
  • David A. Case (Wed Mar 18 2009 - 06:06:30 CDT)
  • sudipta (Wed Mar 18 2009 - 02:47:48 CDT)
  • David A. Case (Tue Mar 17 2009 - 21:14:51 CDT)
  • sudipta (Tue Mar 17 2009 - 13:18:07 CDT)
• [AMBER] center of mass
  • dhacademic (Thu Aug 20 2009 - 15:50:47 CDT)
• [AMBER] Centering and reimaging with ptraj- stop rotating.
  • Bill Ross (Tue Oct 20 2009 - 00:14:10 CDT)
  • Thomas Cheatham (Mon Oct 19 2009 - 22:47:07 CDT)
  • ben rodriguez (Mon Oct 19 2009 - 22:00:26 CDT)
• [AMBER] CH3Hg+ parameters
  • babak minoofar (Thu Sep 24 2009 - 07:08:12 CDT)
• [AMBER] chain restrain x TI
  • Josmar R. da Rocha (Sat May 02 2009 - 12:09:53 CDT)
  • David A. Case (Thu Apr 30 2009 - 13:01:13 CDT)
  • Josmar R. da Rocha (Wed Apr 29 2009 - 17:04:52 CDT)
• [AMBER] change in protein ligand order
  • Hannes Wallnoefer (Tue Mar 24 2009 - 15:45:16 CDT)
  • Bill Ross (Tue Mar 24 2009 - 13:07:42 CDT)
  • Hannes Wallnoefer (Tue Mar 24 2009 - 07:38:18 CDT)
  • Hannes Loeffler (Tue Mar 24 2009 - 06:27:24 CDT)
  • Hannes Wallnoefer (Tue Mar 24 2009 - 06:05:36 CDT)
• [AMBER] Changing bond length
  • manoj singh (Thu May 28 2009 - 12:00:14 CDT)
  • Ross Walker (Wed May 27 2009 - 23:38:59 CDT)
  • manoj singh (Wed May 27 2009 - 22:47:52 CDT)
• [AMBER] Changing Force Fields in "Midstream"
  • Hopkins, Robert (Thu Mar 12 2009 - 15:45:46 CDT)
  • David A. Case (Wed Mar 11 2009 - 17:36:56 CDT)
  • Kristina Furse (Wed Mar 11 2009 - 16:58:06 CDT)
  • Wei Zhang (Wed Mar 11 2009 - 16:42:52 CDT)
  • Hopkins, Robert (Wed Mar 11 2009 - 16:36:12 CDT)
  • Hopkins, Robert (Tue Mar 10 2009 - 18:29:44 CDT)
  • Ross Walker (Mon Mar 09 2009 - 19:21:15 CDT)
  • Hopkins, Robert (Mon Mar 09 2009 - 19:12:27 CDT)
• [AMBER] Changing pH of the system
  • nicholus bhattacharjee (Tue Sep 01 2009 - 08:43:01 CDT)
  • Adrian Roitberg (Sun Aug 30 2009 - 11:18:32 CDT)
  • nicholus bhattacharjee (Sun Aug 30 2009 - 10:40:42 CDT)
  • Adrian Roitberg (Sun Aug 30 2009 - 10:26:01 CDT)
  • nicholus bhattacharjee (Sun Aug 30 2009 - 06:13:17 CDT)
• [AMBER] charge consideration
  • case (Sat Sep 12 2009 - 08:59:56 CDT)
  • Jio M (Fri Sep 11 2009 - 15:17:34 CDT)
• [AMBER] charge derivation for ATP molecule using antechamber
  • David A. Case (Fri Jan 23 2009 - 10:51:49 CST)
  • prachi munjal (Fri Jan 23 2009 - 07:19:27 CST)
• [AMBER] charge not zero on group: RESP
  • Ben Roberts (Sat Jul 18 2009 - 07:45:10 CDT)
  • Jio M (Sat Jul 18 2009 - 00:14:58 CDT)
• [AMBER] charge of Fe-heme
  • FyD (Sat May 02 2009 - 11:02:48 CDT)
  • David A. Case (Fri May 01 2009 - 17:52:45 CDT)
  • ¶­ê» (Fri May 01 2009 - 14:08:12 CDT)
• [AMBER] Charge Problem
  • FyD (Sat Aug 15 2009 - 07:06:45 CDT)
  • Karl Kirschner (Fri Aug 14 2009 - 03:55:07 CDT)
  • s. Bill (Fri Aug 14 2009 - 03:25:05 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 07:58:31 CDT)
  • Remya S R (Tue May 05 2009 - 07:19:51 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 07:16:32 CDT)
  • Remya S R (Tue May 05 2009 - 06:43:47 CDT)
• [AMBER] charged or not
  • case (Thu Jul 09 2009 - 10:10:14 CDT)
  • s. Bill (Thu Jul 09 2009 - 07:33:05 CDT)
• [AMBER] charges for heme-cys in p450
  • FyD (Fri Oct 23 2009 - 05:57:43 CDT)
  • Jayalakshmi Sridhar (Thu Oct 22 2009 - 11:03:08 CDT)
• [AMBER] charges in topology file
  • Carlos Simmerling (Fri Jul 10 2009 - 11:36:30 CDT)
  • Jeffrey (Fri Jul 10 2009 - 11:20:01 CDT)
  • Carlos Simmerling (Wed Jan 14 2009 - 05:24:52 CST)
  • vallespardojl_at_chem.leidenuniv.nl (Wed Jan 14 2009 - 04:33:35 CST)
• [AMBER] CHARMM psf file to Amber prmtop file
  • Ross Walker (Thu Dec 24 2009 - 17:11:36 CST)
  • David A. Case (Wed Dec 23 2009 - 20:39:24 CST)
  • Jason Swails (Wed Dec 23 2009 - 14:32:11 CST)
  • xmzpzengs (Wed Dec 23 2009 - 10:40:28 CST)
  • Sarvin Moghaddam (Wed Dec 23 2009 - 10:20:30 CST)
• [AMBER] check MAXPR in locmem.f error on minimization
  • Robert Duke (Fri Nov 27 2009 - 08:44:36 CST)
  • Jason Swails (Wed Nov 25 2009 - 12:50:43 CST)
  • Jodi Hadden (Wed Nov 25 2009 - 12:29:51 CST)
  • case (Wed Nov 25 2009 - 07:29:41 CST)
  • Jodi Hadden (Tue Nov 24 2009 - 17:46:03 CST)
• [AMBER] chemical shift penalty
  • David A. Case (Thu Mar 05 2009 - 17:59:33 CST)
  • Jacopo Sgrignani (Thu Mar 05 2009 - 03:47:03 CST)
• [AMBER] chemical shifts: nter and cter
  • case (Wed Dec 16 2009 - 14:52:11 CST)
  • Eliana Asciutto (Wed Dec 16 2009 - 13:55:14 CST)
• [AMBER] Chirality error in pdb
  • case (Fri Aug 28 2009 - 06:33:41 CDT)
  • xiawei (Fri Aug 28 2009 - 01:41:45 CDT)
  • case (Wed Aug 26 2009 - 06:52:18 CDT)
  • xiawei (Wed Aug 26 2009 - 02:02:43 CDT)
• [AMBER] Chlorine containing molecule
  • Carlos Simmerling (Wed Feb 11 2009 - 07:48:27 CST)
  • CHAMI F. (Wed Feb 11 2009 - 07:39:19 CST)
• [AMBER] Choice of force feild
  • Gustavo Seabra (Tue Jun 02 2009 - 09:58:11 CDT)
  • manoj singh (Sun May 31 2009 - 12:12:23 CDT)
• [AMBER] Choice of force field
  • Carlos Simmerling (Mon Jun 01 2009 - 06:14:09 CDT)
  • manoj singh (Sun May 31 2009 - 15:39:13 CDT)
• [AMBER] chosing complex in amber
  • Vikas Sharma (Tue Apr 14 2009 - 00:18:43 CDT)
• [AMBER] Circular RNA topology file
  • Filip Lankas (Mon Oct 26 2009 - 05:13:46 CDT)
  • case (Wed Oct 21 2009 - 14:06:17 CDT)
  • Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 13:26:04 CDT)
• [AMBER] Citing AMBER Tools...
  • David A. Case (Thu Feb 05 2009 - 09:44:37 CST)
  • Aydin, Cihan (Sat Jan 31 2009 - 23:08:36 CST)
• [AMBER] clarification DNA forcefield
  • Taufik Al-Sarraj (Mon Dec 07 2009 - 18:22:33 CST)
  • Jiri Sponer (Fri Dec 04 2009 - 03:19:05 CST)
  • Taufik Al-Sarraj (Thu Dec 03 2009 - 22:01:02 CST)
• [AMBER] coarse grained
  • Francesco Pietra (Sun Dec 27 2009 - 14:36:02 CST)
• [AMBER] Coarse grained MD in AMBER ?
  • Lili Peng (Wed Jun 17 2009 - 13:57:58 CDT)
  • Siddharth Rastogi (Wed Jun 17 2009 - 13:50:13 CDT)
• [AMBER] coarse-grained MD
  • Francesco Pietra (Wed Nov 11 2009 - 02:27:27 CST)
• [AMBER] Combine and rename group of residues in xleap
  • case (Fri Oct 09 2009 - 08:32:57 CDT)
  • Lili Peng (Wed Oct 07 2009 - 16:49:23 CDT)
• [AMBER] combine many coord files into trajectory file
  • Peter Gannett (Tue Mar 31 2009 - 09:25:00 CDT)
  • Carlos Simmerling (Tue Mar 31 2009 - 08:55:58 CDT)
  • Peter Gannett (Tue Mar 31 2009 - 08:51:16 CDT)
• [AMBER] combining MD runs for post-MD analysis
  • Bill Ross (Mon Sep 21 2009 - 12:32:53 CDT)
  • case (Sun Sep 20 2009 - 20:35:08 CDT)
  • Qinghua Liao (Sun Sep 20 2009 - 20:01:22 CDT)
  • Jeff Yeo (Sun Sep 20 2009 - 19:02:12 CDT)
• [AMBER] combining parameter files of ligand and enzyme
  • FyD (Wed Nov 18 2009 - 01:49:23 CST)
  • Amire-Brahimi Benjamin (Tue Nov 17 2009 - 16:31:32 CST)
• [AMBER] command for RESP fitting
  • bharat lakhani (Mon Jul 20 2009 - 02:01:23 CDT)
  • FyD (Thu Jul 16 2009 - 09:34:28 CDT)
  • bharat lakhani (Thu Jul 16 2009 - 02:10:33 CDT)
• [AMBER] compare MMPBSA result
  • Ray Luo (Wed Apr 08 2009 - 12:02:41 CDT)
  • m m (Wed Apr 08 2009 - 01:28:06 CDT)
• [AMBER] comparing coordinates from restart file and ptraj outputs
  • Sidney Elmer (Tue Dec 15 2009 - 14:15:06 CST)
  • Daniel Roe (Tue Dec 15 2009 - 09:45:20 CST)
  • Jason Swails (Tue Dec 15 2009 - 06:00:41 CST)
  • Sidney Elmer (Tue Dec 15 2009 - 02:21:35 CST)
  • case (Mon Dec 14 2009 - 21:28:32 CST)
  • Jason Swails (Mon Dec 14 2009 - 19:53:39 CST)
  • Sidney Elmer (Mon Dec 14 2009 - 19:23:50 CST)
• [AMBER] Comparison of the CHARMM and AMBER parameters for alkane
  • FyD (Fri Dec 04 2009 - 14:02:17 CST)
  • Ross Walker (Fri Dec 04 2009 - 13:16:50 CST)
  • FyD (Fri Dec 04 2009 - 11:44:57 CST)
  • intra\\sa175950 (Fri Dec 04 2009 - 03:54:55 CST)
  • FyD (Thu Dec 03 2009 - 13:43:10 CST)
  • Ross Walker (Thu Dec 03 2009 - 11:52:58 CST)
  • intra\\sa175950 (Thu Dec 03 2009 - 10:49:28 CST)
• [AMBER] Compatibility of ONIOM and Amber
  • vaibhav dixit (Fri Dec 18 2009 - 00:30:32 CST)
• [AMBER] Compilation and qmmm_div
  • Benjamin Roberts (Wed Mar 04 2009 - 18:15:37 CST)
  • Ross Walker (Wed Mar 04 2009 - 10:36:07 CST)
  • Benjamin Roberts (Wed Mar 04 2009 - 09:48:16 CST)
• [AMBER] Compilation and usage of NAB in parallel ?
  • Marek Malý (Fri Jan 30 2009 - 10:01:06 CST)
  • David A. Case (Fri Jan 30 2009 - 09:51:31 CST)
  • Marek Malý (Fri Jan 30 2009 - 08:59:07 CST)
  • David A. Case (Thu Jan 29 2009 - 07:22:08 CST)
  • Marek Malý (Wed Jan 28 2009 - 16:25:24 CST)
• [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits
  • Nicolas SAPAY (Fri Jul 31 2009 - 07:55:18 CDT)
  • Robert Duke (Fri Jul 31 2009 - 07:33:52 CDT)
  • Nicolas SAPAY (Fri Jul 31 2009 - 04:41:21 CDT)
• [AMBER] compilation problem of amber
  • Jason Swails (Tue Nov 17 2009 - 08:51:42 CST)
  • sculiujl (Tue Nov 17 2009 - 01:33:52 CST)
• [AMBER] compilation problem of amber9
  • Jason Swails (Tue Nov 17 2009 - 08:55:46 CST)
  • sculiujl (Tue Nov 17 2009 - 01:03:22 CST)
• [AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc
  • David Watson (Thu Jul 23 2009 - 15:03:59 CDT)
• [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0
  • Scott Brozell (Wed Jul 22 2009 - 14:52:59 CDT)
  • David Watson (Tue Jul 21 2009 - 16:20:36 CDT)
• [AMBER] Compiling amber 9 with openMPI
  • Myunggi Yi (Tue Jun 23 2009 - 13:11:46 CDT)
  • case (Tue Jun 23 2009 - 09:13:18 CDT)
  • Myunggi Yi (Tue Jun 23 2009 - 08:31:58 CDT)
• [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
  • Mengjuei Hsieh (Tue Oct 06 2009 - 21:05:54 CDT)
  • Ben Roberts (Fri Oct 02 2009 - 09:20:47 CDT)
  • case (Fri Oct 02 2009 - 08:19:11 CDT)
  • Ben Roberts (Tue Sep 29 2009 - 16:37:31 CDT)
• [AMBER] Compiling Amber10
  • Williams, John (Tue Sep 22 2009 - 07:56:43 CDT)
• [AMBER] compiling amber10 with mac intel, ifort/icc and mpi
  • Alan (Sat Jun 13 2009 - 13:37:54 CDT)
  • David Watson (Thu Jun 11 2009 - 07:43:28 CDT)
  • Alan (Thu Jun 11 2009 - 06:14:42 CDT)
  • David A. Case (Wed Jun 10 2009 - 11:54:38 CDT)
  • Alan (Wed Jun 10 2009 - 11:26:13 CDT)
  • David A. Case (Wed Jun 10 2009 - 10:34:59 CDT)
  • Alan (Wed Jun 10 2009 - 09:47:00 CDT)
• [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
  • David Watson (Thu Jul 30 2009 - 14:10:39 CDT)
  • Alan (Thu Jul 30 2009 - 08:39:03 CDT)
  • David Watson (Wed Jul 29 2009 - 11:21:50 CDT)
  • Alan (Wed Jul 29 2009 - 11:00:42 CDT)
• [AMBER] Compiling and running NAB programs in parallel using MPI
  • case (Tue Jun 30 2009 - 11:02:57 CDT)
  • Kaushik Raha (Tue Jun 30 2009 - 09:48:11 CDT)
  • case (Mon Jun 29 2009 - 07:19:10 CDT)
  • Kaushik Raha (Fri Jun 26 2009 - 10:12:11 CDT)
  • case (Fri Jun 26 2009 - 08:19:04 CDT)
  • Kaushik Raha (Thu Jun 25 2009 - 16:36:35 CDT)
• [AMBER] Compiling Carnal Amber7 in Amber9
  • Bill Ross (Thu Feb 12 2009 - 14:32:29 CST)
  • Ross Walker (Thu Feb 12 2009 - 08:55:54 CST)
  • David A. Case (Thu Feb 12 2009 - 06:58:03 CST)
  • Vijay Manickam Achari (Thu Feb 12 2009 - 03:12:29 CST)
  • Bill Ross (Wed Feb 11 2009 - 13:04:53 CST)
  • Ross Walker (Wed Feb 11 2009 - 10:53:10 CST)
  • Vijay Manickam Achari (Wed Feb 11 2009 - 01:58:08 CST)
  • Bill Ross (Thu Feb 05 2009 - 11:36:00 CST)
  • Vijay Manickam Achari (Wed Feb 04 2009 - 21:21:14 CST)
• [AMBER] compiling errors
  • Ross Walker (Wed Feb 04 2009 - 18:48:14 CST)
  • Carlos Simmerling (Wed Feb 04 2009 - 18:35:28 CST)
  • Gard Nelson (Wed Feb 04 2009 - 18:30:22 CST)
• [AMBER] Completed installation of AmberTools, version 1.1
  • David A. Case (Wed Jun 10 2009 - 09:10:22 CDT)
  • Alan (Wed Jun 10 2009 - 08:13:37 CDT)
• [AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version?
  • Haizhen Zhong (Fri Jun 05 2009 - 18:17:01 CDT)
• [AMBER] Computational Resources
  • Ross Walker (Wed Aug 05 2009 - 11:08:21 CDT)
  • s. Bill (Wed Aug 05 2009 - 10:17:34 CDT)
• [AMBER] Computing an Hessian matrix using NAB
  • Brut Marie (Tue Oct 13 2009 - 14:00:53 CDT)
  • Brut Marie (Tue Oct 13 2009 - 13:56:19 CDT)
  • case (Tue Oct 13 2009 - 07:13:42 CDT)
  • Brut Marie (Mon Oct 12 2009 - 17:12:44 CDT)
• [AMBER] Conference or workshop on AMBER?
  • Dharmik Meghana shankar (Tue Aug 18 2009 - 00:25:25 CDT)
  • Ross Walker (Mon Aug 17 2009 - 23:15:52 CDT)
  • Ashish Runthala (Mon Aug 17 2009 - 22:04:12 CDT)
  • Ross Walker (Mon Aug 17 2009 - 22:00:14 CDT)
  • Catein Catherine (Mon Aug 17 2009 - 21:30:04 CDT)
  • Ross Walker (Mon Aug 17 2009 - 09:22:14 CDT)
  • Catein Catherine (Mon Aug 17 2009 - 00:56:41 CDT)
• [AMBER] Conference or workshop on AMBER? Thank you.
  • Catein Catherine (Tue Aug 18 2009 - 01:44:45 CDT)
• [AMBER] Conformation of sulfated Glucosamine
  • Matthew Tessier (Wed May 06 2009 - 10:19:22 CDT)
  • Neha Gandhi (Wed May 06 2009 - 04:54:31 CDT)
• [AMBER] Confusion regarding box size
  • parul sharma (Tue Feb 10 2009 - 07:29:38 CST)
  • Wei Zhang (Tue Feb 10 2009 - 07:07:38 CST)
  • vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:35:24 CST)
  • parul sharma (Tue Feb 10 2009 - 01:20:01 CST)
• [AMBER] connecting residues
  • Bill Ross (Tue Jun 16 2009 - 11:39:02 CDT)
  • Bill Ross (Tue Jun 16 2009 - 11:37:33 CDT)
  • KIRTANA S (Tue Jun 16 2009 - 10:59:37 CDT)
• [AMBER] Constant pH simulation
  • Tom Joseph (Wed Jun 10 2009 - 20:08:36 CDT)
  • Rukman Hertadi (Wed Jun 10 2009 - 19:56:59 CDT)
• [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation
  • David A. Case (Sat Apr 04 2009 - 08:20:28 CDT)
  • Therese Malliavin (Wed Apr 01 2009 - 04:06:19 CDT)
• [AMBER] constph tutorial help
  • Prem Prakash Pathak (Tue Feb 17 2009 - 06:53:37 CST)
• [AMBER] contacts in ptraj
  • Å·ÑôµÂ·½ (Thu May 28 2009 - 06:55:28 CDT)
• [AMBER] contant force pulling simulation with amber 10
  • Gustavo Seabra (Mon Feb 16 2009 - 12:11:40 CST)
  • li hui (Mon Feb 16 2009 - 11:01:36 CST)
• [AMBER] continuam water
  • Carlos Simmerling (Tue Mar 24 2009 - 08:36:15 CDT)
  • Mannan (Mon Mar 23 2009 - 23:11:50 CDT)
• [AMBER] Contour plot
  • Gustavo Seabra (Thu Apr 02 2009 - 14:47:14 CDT)
  • Beale, John (Thu Apr 02 2009 - 14:31:22 CDT)
• [AMBER] contradictive hydrogen bonds using ptraj
  • Binbin Liu (Mon Oct 26 2009 - 11:42:20 CDT)
• [AMBER] Conversion of Gaussian output file into mol2
  • Junmei Wang (Thu Oct 29 2009 - 10:45:27 CDT)
  • megha bajaj (Wed Oct 28 2009 - 03:00:35 CDT)
• [AMBER] Conversion of Gaussian output file to mol2
  • megha bajaj (Wed Oct 28 2009 - 02:49:51 CDT)
• [AMBER] conversion of kelvin to kcal/mol
  • aneesh cna (Mon Nov 09 2009 - 00:56:36 CST)
  • manoj singh (Sun Nov 08 2009 - 23:17:03 CST)
  • aneesh cna (Sun Nov 08 2009 - 23:08:33 CST)
• [AMBER] convert .mol2 file to .pdb with atomtype definitions
  • Pankaj R. Daga (Tue Mar 17 2009 - 11:41:20 CDT)
  • Wei Zhang (Tue Mar 17 2009 - 11:33:27 CDT)
  • Pansy Patel (Tue Mar 17 2009 - 11:09:10 CDT)
  • David A. Case (Tue Mar 17 2009 - 11:00:19 CDT)
  • Pansy Patel (Tue Mar 17 2009 - 10:50:57 CDT)
• [AMBER] converting vibrational frequency
  • aneesh cna (Mon Jun 01 2009 - 11:53:22 CDT)
  • David A. Case (Mon Jun 01 2009 - 06:39:32 CDT)
  • aneesh cna (Mon Jun 01 2009 - 06:22:01 CDT)
• [AMBER] COOH group troubling
  • Bill Ross (Sun Dec 06 2009 - 13:07:44 CST)
  • Jio M (Sun Dec 06 2009 - 12:53:22 CST)
  • Bill Ross (Sun Dec 06 2009 - 10:46:58 CST)
  • Jason Swails (Sun Dec 06 2009 - 09:05:07 CST)
  • Jio M (Sun Dec 06 2009 - 07:57:06 CST)
• [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
  • steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 04:01:15 CDT)
  • Zhongjie Liang (Thu Jul 16 2009 - 03:37:29 CDT)
• [AMBER] Copper semiempirical parameters
  • Ross Walker (Thu Jun 11 2009 - 11:09:14 CDT)
  • Jacopo Sgrignani (Thu Jun 11 2009 - 08:49:50 CDT)
• [AMBER] correlation motion at production simulation period still changing. Is it normal?
  • Catein Catherine (Mon Jun 22 2009 - 04:26:40 CDT)
• [AMBER] Could not find angle parameter
  • Marius Retegan (Fri Apr 03 2009 - 05:58:47 CDT)
  • chenquan (Fri Apr 03 2009 - 05:46:47 CDT)
• [AMBER] Could not find bond parameter for O2 - ca
  • Yogesh Aher (Fri Jul 17 2009 - 01:37:52 CDT)
  • case (Tue Jul 14 2009 - 22:28:02 CDT)
  • Yogesh Aher (Tue Jul 14 2009 - 07:53:35 CDT)
• [AMBER] Could not find type: MG Parameter file was not saved.
  • Mannan (Sat Jul 25 2009 - 22:41:24 CDT)
• [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded
  • FyD (Mon Jul 27 2009 - 00:03:00 CDT)
  • Mannan (Sun Jul 26 2009 - 22:49:54 CDT)
• [AMBER] Counter-ions
  • waleed zalloum (Thu Apr 02 2009 - 05:15:12 CDT)
• [AMBER] Counterion release and Free energy of binding ?
  • Marek Maly (Fri Jul 17 2009 - 06:10:40 CDT)
  • case (Tue Jul 14 2009 - 22:10:18 CDT)
  • Marek Maly (Tue Jul 14 2009 - 17:27:18 CDT)
• [AMBER] covalent interaction
  • å»–é�’å�Ž (Mon Jun 15 2009 - 03:06:52 CDT)
• [AMBER] cpin error
  • case (Tue Sep 01 2009 - 07:23:04 CDT)
  • Rukman Hertadi (Tue Jul 28 2009 - 00:22:18 CDT)
  • case (Fri Jul 24 2009 - 14:41:00 CDT)
  • Rukman Hertadi (Fri Jul 24 2009 - 02:18:52 CDT)
• [AMBER] create a simulation box
  • Gustavo Seabra (Tue Jun 02 2009 - 10:08:46 CDT)
  • Workalemhu Berhanu (Sat May 30 2009 - 22:06:24 CDT)
• [AMBER] create new crd files from transformed coordinates
  • case (Wed Mar 25 2009 - 07:26:29 CDT)
  • Donald Keidel (Tue Mar 24 2009 - 20:49:03 CDT)
• [AMBER] creating a restart file from md.out
  • Carlos Simmerling (Tue Feb 03 2009 - 09:34:44 CST)
  • oguz gurbulak (Tue Feb 03 2009 - 09:29:47 CST)
  • Carlos Simmerling (Tue Feb 03 2009 - 07:36:44 CST)
  • oguz gurbulak (Tue Feb 03 2009 - 07:22:45 CST)
  • Carlos Simmerling (Tue Feb 03 2009 - 05:30:44 CST)
  • oguz gurbulak (Tue Feb 03 2009 - 04:44:10 CST)
• [AMBER] creating bond
  • Bill Ross (Wed Jun 03 2009 - 16:40:09 CDT)
  • Jorgen Simonsen (Wed Jun 03 2009 - 14:56:29 CDT)
  • Bill Ross (Wed Jun 03 2009 - 13:40:52 CDT)
  • David A. Case (Wed Jun 03 2009 - 13:32:57 CDT)
  • Jorgen Simonsen (Wed Jun 03 2009 - 12:04:11 CDT)
• [AMBER] Creating conditions for biased MD
  • Francesco Pietra (Wed Apr 22 2009 - 13:01:39 CDT)
  • Bill Ross (Wed Apr 22 2009 - 11:19:20 CDT)
  • Francesco Pietra (Wed Apr 22 2009 - 05:16:11 CDT)
  • Francesco Pietra (Tue Apr 21 2009 - 16:49:14 CDT)
  • Carlos Simmerling (Tue Apr 21 2009 - 16:32:09 CDT)
  • Francesco Pietra (Tue Apr 21 2009 - 16:29:36 CDT)
  • Carlos Simmerling (Tue Apr 21 2009 - 14:44:03 CDT)
  • Francesco Pietra (Tue Apr 21 2009 - 13:40:35 CDT)
  • Carlos Simmerling (Mon Apr 20 2009 - 13:46:41 CDT)
  • Francesco Pietra (Mon Apr 20 2009 - 12:31:52 CDT)
  • Carlos Simmerling (Mon Mar 30 2009 - 06:56:36 CDT)
  • Francesco Pietra (Mon Mar 30 2009 - 05:16:54 CDT)
• [AMBER] Creating new counterions
  • case (Tue Sep 01 2009 - 15:03:48 CDT)
  • Bill Ross (Tue Sep 01 2009 - 14:58:55 CDT)
  • Timothy Robbins (trobbins) (Tue Sep 01 2009 - 14:00:37 CDT)
• [AMBER] creating new residue adds none wanted ter
  • David A. Case (Tue May 05 2009 - 07:07:53 CDT)
  • Jorgen Simonsen (Tue May 05 2009 - 04:57:29 CDT)
  • David A. Case (Mon May 04 2009 - 13:27:58 CDT)
  • Jorgen Simonsen (Mon May 04 2009 - 09:09:08 CDT)
  • David A. Case (Mon May 04 2009 - 08:35:41 CDT)
  • Jorgen Simonsen (Mon May 04 2009 - 02:49:47 CDT)
• [AMBER] Creating new residue with tleap.
  • case (Wed Nov 11 2009 - 06:37:47 CST)
  • rrd (Wed Nov 11 2009 - 05:02:23 CST)
• [AMBER] cross correlation analysis with ptraj
  • Junmei Wang (Thu Oct 15 2009 - 11:49:29 CDT)
• [AMBER] crystal waters
  • steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:37:34 CST)
  • Carmen Domene (Mon Jan 12 2009 - 14:32:28 CST)
  • steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:16:25 CST)
  • Carmen Domene (Mon Jan 12 2009 - 14:04:24 CST)
• [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB
  • Hector A. Baldoni (Wed Aug 12 2009 - 15:43:28 CDT)
  • case (Wed Aug 12 2009 - 14:57:33 CDT)
  • Manish Kumar (Wed Aug 12 2009 - 14:44:37 CDT)
• [AMBER] Current Amber10 bugfix.all doesn't apply cleanly
  • Mark Dixon (Fri Feb 27 2009 - 10:44:28 CST)
  • Mark Dixon (Thu Feb 26 2009 - 05:54:03 CST)
• [AMBER] Custom RNA modeling
  • Jiri Sponer (Mon Dec 14 2009 - 16:08:07 CST)
  • Carlos Simmerling (Mon Dec 14 2009 - 15:55:20 CST)
  • Wallace Kunin (Mon Dec 14 2009 - 15:49:29 CST)
  • Thomas Cheatham (Mon Dec 14 2009 - 12:35:44 CST)
  • case (Mon Dec 14 2009 - 12:32:11 CST)
  • Wallace Kunin (Mon Dec 14 2009 - 11:50:25 CST)
  • Wallace Kunin (Wed Dec 09 2009 - 10:10:44 CST)
  • Ilyas Yildirim (Tue Dec 08 2009 - 16:01:42 CST)
  • Wallace Kunin (Tue Dec 08 2009 - 14:27:55 CST)
• [AMBER] CY3 dye parameters
  • Brent Krueger (Sat Apr 25 2009 - 14:33:40 CDT)
  • FyD (Sat Apr 25 2009 - 01:04:22 CDT)
  • jcmoore_at_student.umass.edu (Thu Apr 23 2009 - 16:42:59 CDT)
• [AMBER] Cyclodextrin forcefield
  • Rajesh Raju (Fri May 01 2009 - 12:21:21 CDT)
  • Lachele Foley (Lists) (Fri May 01 2009 - 10:23:37 CDT)
  • Rajesh Raju (Fri May 01 2009 - 09:51:17 CDT)
• [AMBER] Cygwin Home Directory
  • Bill Ross (Mon Sep 21 2009 - 12:45:02 CDT)
  • case (Mon Sep 21 2009 - 12:14:59 CDT)
  • Wallace Kunin (Mon Sep 21 2009 - 11:29:11 CDT)
  • Ashish Runthala (Sat Sep 19 2009 - 21:51:11 CDT)
  • case (Sat Sep 19 2009 - 17:11:57 CDT)
  • Bill Ross (Sat Sep 19 2009 - 12:29:59 CDT)
  • Wallace Kunin (Sat Sep 19 2009 - 11:13:20 CDT)
  • Bill Ross (Fri Sep 18 2009 - 15:56:17 CDT)
  • manoj singh (Fri Sep 18 2009 - 14:30:28 CDT)
  • Wallace Kunin (Fri Sep 18 2009 - 14:12:22 CDT)
  • Bill Ross (Fri Sep 18 2009 - 13:19:44 CDT)
  • Wallace Kunin (Fri Sep 18 2009 - 12:51:17 CDT)
• [AMBER] database
  • case (Fri Sep 18 2009 - 21:46:39 CDT)
  • FyD (Fri Sep 18 2009 - 19:49:17 CDT)
  • Steve Seibold (Fri Sep 18 2009 - 14:10:19 CDT)
  • case (Fri Sep 18 2009 - 12:23:08 CDT)
  • Steve Seibold (Fri Sep 18 2009 - 10:03:44 CDT)
  • FyD (Fri Sep 18 2009 - 02:28:53 CDT)
  • case (Thu Sep 17 2009 - 17:23:30 CDT)
  • FyD (Thu Sep 17 2009 - 16:54:29 CDT)
  • Jeff Yeo (Thu Sep 17 2009 - 16:01:48 CDT)
  • Steve Seibold (Thu Sep 17 2009 - 14:46:20 CDT)
  • FyD (Thu Sep 17 2009 - 11:00:22 CDT)
  • Steve Seibold (Thu Sep 17 2009 - 08:43:25 CDT)
  • FyD (Wed Sep 16 2009 - 13:58:38 CDT)
  • FyD (Wed Sep 16 2009 - 13:56:16 CDT)
  • Bill Ross (Wed Sep 16 2009 - 12:54:47 CDT)
  • Steve Seibold (Wed Sep 16 2009 - 12:14:46 CDT)
  • FyD (Wed Sep 16 2009 - 11:59:30 CDT)
  • case (Wed Sep 16 2009 - 11:53:56 CDT)
  • Steve Seibold (Wed Sep 16 2009 - 11:11:47 CDT)
  • case (Wed Sep 16 2009 - 10:26:24 CDT)
  • Steve Seibold (Wed Sep 16 2009 - 09:59:14 CDT)
• [AMBER] DCCM
  • Duggan, Brendan M. (Wed Jul 15 2009 - 11:06:57 CDT)
  • Raja Pandian (Tue Jul 07 2009 - 06:05:20 CDT)
• [AMBER] decomposing energies
  • Beroza, Paul (Thu Oct 01 2009 - 11:15:07 CDT)
• [AMBER] decomposition and alanine scanning
  • å»–é�’å�Ž (Fri May 22 2009 - 09:13:49 CDT)
• [AMBER] decomposition and calculation of entropy
  • Qinghua Liao (Sat Oct 10 2009 - 01:13:49 CDT)
• [AMBER] deduce correlation from covariance matrix
  • Yi Mao (Sun Jan 25 2009 - 15:01:05 CST)
• [AMBER] default integration scheme in 7 vs. 10
  • case (Thu Jul 02 2009 - 06:37:17 CDT)
  • Ross Walker (Wed Jul 01 2009 - 16:29:12 CDT)
  • Paul Brandt (Wed Jul 01 2009 - 15:48:46 CDT)
• [AMBER] deffision
  • Nancy (Sat Apr 04 2009 - 09:30:50 CDT)
• [AMBER] deffision coefficient
  • David A. Case (Mon Apr 06 2009 - 21:16:39 CDT)
  • Nancy (Mon Apr 06 2009 - 20:18:32 CDT)
• [AMBER] density and volume in NVT ensamble
  • Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:45:25 CST)
  • oguz gurbulak (Mon Feb 16 2009 - 08:32:07 CST)
  • Adrian Roitberg (Fri Feb 06 2009 - 08:31:24 CST)
  • Carlos Simmerling (Mon Feb 16 2009 - 08:30:02 CST)
  • oguz gurbulak (Mon Feb 16 2009 - 08:27:01 CST)
  • oguz gurbulak (Mon Feb 16 2009 - 08:25:52 CST)
  • Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:14:40 CST)
  • Carlos Simmerling (Mon Feb 16 2009 - 08:04:22 CST)
  • oguz gurbulak (Mon Feb 16 2009 - 07:58:13 CST)
• [AMBER] Density in MD simulation
  • Ibrahim Moustafa (Fri Apr 17 2009 - 18:26:46 CDT)
  • Carlos Simmerling (Fri Apr 17 2009 - 11:10:51 CDT)
  • Ibrahim Moustafa (Fri Apr 17 2009 - 11:09:16 CDT)
• [AMBER] DFT SK parameter for P atom
  • Qizhi Cui (Mon Feb 02 2009 - 15:37:41 CST)
  • Adrian Roitberg (Mon Feb 02 2009 - 14:24:00 CST)
  • Qizhi Cui (Mon Feb 02 2009 - 13:59:19 CST)
• [AMBER] dftb_disper problem
  • Fernando Martín García (Mon May 11 2009 - 07:34:01 CDT)
  • Gustavo Seabra (Fri May 08 2009 - 11:34:39 CDT)
  • fmgarcia_at_cbm.uam.es (Fri May 08 2009 - 11:27:30 CDT)
  • Ross Walker (Fri May 08 2009 - 10:47:39 CDT)
  • Fernando Martín García (Fri May 08 2009 - 07:43:19 CDT)
  • Fernando Martín García (Thu May 07 2009 - 08:32:06 CDT)
  • Gustavo Seabra (Thu May 07 2009 - 08:01:42 CDT)
  • Fernando Martín García (Thu May 07 2009 - 07:30:25 CDT)
• [AMBER] DG improper torsion problem, two missing parameters
  • Bill Ross (Fri Oct 09 2009 - 12:25:30 CDT)
  • case (Fri Oct 09 2009 - 06:46:34 CDT)
  • Youn Kyeung Lee (Fri Oct 09 2009 - 02:02:03 CDT)
• [AMBER] difference between two inputs
  • case (Fri Nov 27 2009 - 08:59:01 CST)
  • Jio M (Thu Nov 26 2009 - 00:32:12 CST)
• [AMBER] difference in temperature
  • Naser Alijabbari (Wed May 06 2009 - 07:29:48 CDT)
  • David A. Case (Wed May 06 2009 - 07:08:01 CDT)
  • Naser Alijabbari (Tue May 05 2009 - 19:02:28 CDT)
• [AMBER] different comformations to choose for RESP
  • FyD (Mon Jun 01 2009 - 09:32:21 CDT)
  • xueqin pang (Mon Jun 01 2009 - 08:47:30 CDT)
• [AMBER] Different machines
  • Ross Walker (Sun Jul 19 2009 - 11:28:52 CDT)
  • s. Bill (Sun Jul 19 2009 - 04:55:48 CDT)
• [AMBER] Different optimized structures with HF and B3LYP
  • Karl Kirschner (Fri Oct 02 2009 - 03:07:08 CDT)
  • Sanghwa Han (Fri Oct 02 2009 - 02:50:10 CDT)
• [AMBER] different results for antechamber/mopac for the same input
  • case (Thu Jul 16 2009 - 06:30:08 CDT)
  • Alan (Wed Jul 15 2009 - 17:05:07 CDT)
• [AMBER] Different results for different computers
  • Robert Duke (Sat Oct 31 2009 - 17:56:28 CDT)
  • Jason Swails (Sat Oct 31 2009 - 14:57:34 CDT)
  • manoj singh (Sat Oct 31 2009 - 14:47:36 CDT)
  • cyk5056 (Sat Oct 31 2009 - 14:39:59 CDT)
• [AMBER] Different simulation times for similar systems
  • Carlos Simmerling (Mon Dec 14 2009 - 12:11:56 CST)
  • Oliver Kuhn (Mon Dec 14 2009 - 06:31:50 CST)
• [AMBER] diffusion coeficients
  • felix (Fri Jul 17 2009 - 08:41:43 CDT)
  • case (Fri Jul 17 2009 - 06:59:41 CDT)
  • felix (Fri Jul 17 2009 - 03:15:35 CDT)
• [AMBER] Dihedral energy profile in a single molecule
  • Jason Swails (Fri Oct 16 2009 - 10:02:35 CDT)
  • Frank X. Vázquez (Fri Oct 16 2009 - 09:55:53 CDT)
• [AMBER] dihedral force calculation
  • case (Sat Sep 12 2009 - 09:04:34 CDT)
  • Germain Vallverdu (Fri Sep 11 2009 - 09:35:08 CDT)
• [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates?
  • Bill Ross (Tue Aug 18 2009 - 17:59:12 CDT)
  • Jose Borreguero (Tue Aug 18 2009 - 17:33:32 CDT)
  • FyD (Tue Aug 18 2009 - 19:05:19 CDT)
  • Jose Borreguero (Tue Aug 18 2009 - 09:37:39 CDT)
• [AMBER] dipole autocorrelation functions
  • aneesh cna (Tue Apr 28 2009 - 01:23:05 CDT)
• [AMBER] Dipole command in ptraj
  • musa özboyacý (Wed Jan 14 2009 - 17:15:26 CST)
  • musa özboyacý (Wed Jan 14 2009 - 09:41:07 CST)
• [AMBER] dipole correlation function
  • Jeffrey (Thu Feb 19 2009 - 19:31:08 CST)
  • Carlos Simmerling (Thu Feb 19 2009 - 11:23:03 CST)
  • Jeffrey (Thu Feb 19 2009 - 10:39:15 CST)
  • Carlos Simmerling (Thu Feb 19 2009 - 08:39:16 CST)
  • Jeffrey (Thu Feb 19 2009 - 08:18:20 CST)
• [AMBER] Dipole moment visualization.
  • K.R. (Thu Oct 01 2009 - 16:37:29 CDT)
• [AMBER] dipole printing
  • Hemant Kumar (Fri Jun 12 2009 - 14:03:17 CDT)
  • Ross Walker (Fri Jun 12 2009 - 11:13:30 CDT)
  • Hemant Kumar (Fri Jun 12 2009 - 10:58:29 CDT)
• [AMBER] Directory - GAFF Parameter File?
  • Patrick Gedeon (Mon Jul 06 2009 - 18:31:49 CDT)
• [AMBER] Disappearing common atoms in Amber 10 with TI
  • steinbrt_at_rci.rutgers.edu (Mon Jul 20 2009 - 07:05:24 CDT)
  • Khavrutskii, Ilja (Mon Jul 20 2009 - 06:46:38 CDT)
  • case (Fri Jul 17 2009 - 06:41:39 CDT)
  • steinbrt_at_rci.rutgers.edu (Fri Jul 17 2009 - 03:53:19 CDT)
  • Khavrutskii, Ilja (Thu Jul 16 2009 - 16:02:10 CDT)
  • steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 09:09:39 CDT)
  • Khavrutskii, Ilja (Thu Jul 16 2009 - 08:38:43 CDT)
• [AMBER] Discrepancy between AMBER and VMD calculation
  • Sunita Patel (Thu Sep 17 2009 - 14:11:07 CDT)
• [AMBER] distance calculation by reading in the restraint file
  • xiaoqin huang (Fri Feb 06 2009 - 17:28:59 CST)
  • David A. Case (Fri Feb 06 2009 - 16:35:55 CST)
  • David A. Case (Fri Feb 06 2009 - 16:03:08 CST)
  • xiaoqin huang (Fri Feb 06 2009 - 12:34:34 CST)
  • xiaoqin huang (Fri Feb 06 2009 - 11:52:56 CST)
• [AMBER] distance matrix plot and secondary structure analysis
  • Carlos Simmerling (Thu Feb 19 2009 - 06:48:57 CST)
  • Siddharth Rastogi (Thu Feb 19 2009 - 00:17:47 CST)
• [AMBER] Distance Replica Exchange
  • Steve Seibold (Fri Oct 09 2009 - 09:21:13 CDT)
  • Carlos Simmerling (Fri Oct 09 2009 - 08:40:17 CDT)
  • Steve Seibold (Fri Oct 09 2009 - 08:18:44 CDT)
• [AMBER] Distance restraint and periodic boundary conditions
  • Robert Duke (Sun Aug 23 2009 - 09:50:56 CDT)
  • Peter Varnai (Thu Aug 20 2009 - 10:23:48 CDT)
  • case (Wed Aug 19 2009 - 19:53:15 CDT)
  • Keith Van Nostrand (Wed Aug 19 2009 - 11:44:49 CDT)
  • Peter Varnai (Wed Aug 19 2009 - 11:16:01 CDT)
  • Peter Varnai (Wed Aug 19 2009 - 10:13:04 CDT)
  • case (Tue Aug 18 2009 - 21:02:45 CDT)
  • Thomas Cheatham (Tue Aug 18 2009 - 20:23:56 CDT)
  • Cyril Falvo (Tue Aug 18 2009 - 19:58:29 CDT)
• [AMBER] distance restraint and SHAKE
  • Thomas Cheatham III (Tue Jan 27 2009 - 12:16:30 CST)
  • Michael J Yonkunas (Tue Jan 27 2009 - 11:39:56 CST)
• [AMBER] Distance restraints between groups of atoms
  • David A. Case (Tue Jun 09 2009 - 06:45:14 CDT)
  • Germain Vallverdu (Tue Jun 09 2009 - 03:39:45 CDT)
  • David A. Case (Wed Jun 03 2009 - 11:32:33 CDT)
  • Germain Vallverdu (Wed Jun 03 2009 - 09:43:37 CDT)
  • David A. Case (Wed Jun 03 2009 - 07:27:04 CDT)
  • Germain Vallverdu (Wed Jun 03 2009 - 01:58:57 CDT)
• [AMBER] Distance-covariance and PCA questions...
  • Hannes Loeffler (Wed Jun 17 2009 - 02:41:42 CDT)
  • Bill Ross (Tue Jun 16 2009 - 11:18:40 CDT)
  • Cihan Aydin (Mon Jun 15 2009 - 23:18:58 CDT)
• [AMBER] distance-dependent dielectric constant minimization
  • Rilei Yu (Sun Dec 06 2009 - 01:37:13 CST)
  • case (Sat Dec 05 2009 - 21:03:47 CST)
  • Bill Ross (Sat Dec 05 2009 - 11:30:09 CST)
  • Rilei Yu (Sat Dec 05 2009 - 02:21:58 CST)
  • Robert Duke (Tue Dec 01 2009 - 07:06:40 CST)
  • case (Tue Dec 01 2009 - 06:48:32 CST)
  • Rilei Yu (Mon Nov 30 2009 - 23:31:58 CST)
  • case (Mon Nov 30 2009 - 07:02:11 CST)
  • Rilei Yu (Mon Nov 30 2009 - 01:02:32 CST)
• [AMBER] Disulfide bond
  • Wei Zhang (Wed Apr 22 2009 - 10:00:02 CDT)
  • quantum_mania_at_yahoo.com (Wed Apr 22 2009 - 00:25:45 CDT)
  • Wei Zhang (Tue Apr 21 2009 - 22:30:36 CDT)
  • Dong Xu (Tue Apr 21 2009 - 21:41:02 CDT)
  • Wei Zhang (Tue Apr 21 2009 - 20:46:19 CDT)
  • Dong Xu (Tue Apr 21 2009 - 20:37:46 CDT)
• [AMBER] DivCon - QM/MM
  • s. Bill (Tue Aug 11 2009 - 02:54:38 CDT)
  • s. Bill (Mon Aug 10 2009 - 09:11:39 CDT)
• [AMBER] divcon error during antechamber run, convergence problem
  • Andrew Voronkov (Sat Mar 07 2009 - 09:58:19 CST)
  • David A. Case (Fri Mar 06 2009 - 12:33:24 CST)
  • Andrew Voronkov (Fri Mar 06 2009 - 12:04:55 CST)
  • Martin Peters (Thu Mar 05 2009 - 08:21:19 CST)
  • drugdesign (Thu Mar 05 2009 - 07:53:59 CST)
• [AMBER] Divcon or Mopac
  • Martin Peters (Wed Jan 14 2009 - 03:01:12 CST)
  • Cen Gao (Tue Jan 13 2009 - 17:54:33 CST)
• [AMBER] divcon question
  • case (Mon Aug 31 2009 - 07:34:14 CDT)
  • Andrei Neamtu (Mon Aug 31 2009 - 06:31:35 CDT)
• [AMBER] DM complexation
  • Carlos Simmerling (Tue Feb 17 2009 - 09:59:15 CST)
  • . .. (Tue Feb 17 2009 - 09:36:01 CST)
  • Carlos Simmerling (Tue Feb 17 2009 - 09:28:34 CST)
  • . .. (Tue Feb 17 2009 - 09:10:49 CST)
• [AMBER] DMF solvent box
  • FyD (Thu Oct 08 2009 - 23:08:59 CDT)
  • Abhishek Banerjee (Thu Oct 08 2009 - 22:41:02 CDT)
  • FyD (Wed Oct 07 2009 - 15:34:35 CDT)
  • Abhishek Banerjee (Tue Oct 06 2009 - 23:10:22 CDT)
  • FyD (Sat Sep 19 2009 - 01:36:20 CDT)
  • Abhishek Banerjee (Sat Sep 19 2009 - 00:24:08 CDT)
  • FyD (Thu Sep 17 2009 - 02:00:06 CDT)
  • Abhishek Banerjee (Thu Sep 17 2009 - 01:15:53 CDT)
  • FyD (Wed Sep 16 2009 - 00:09:42 CDT)
  • Abhishek Banerjee (Tue Sep 15 2009 - 23:33:23 CDT)
  • FyD (Mon Sep 14 2009 - 10:04:58 CDT)
  • Abhishek Banerjee (Mon Sep 14 2009 - 08:18:30 CDT)
  • FyD (Sun Sep 13 2009 - 12:01:13 CDT)
  • Abhishek Banerjee (Sun Sep 13 2009 - 09:24:04 CDT)
  • FyD (Sun Sep 13 2009 - 04:25:33 CDT)
  • Abhishek Banerjee (Sun Sep 13 2009 - 03:56:18 CDT)
  • Abhishek Banerjee (Sun Sep 13 2009 - 00:33:39 CDT)
  • FyD (Sat Sep 12 2009 - 09:07:30 CDT)
  • Jio M (Fri Sep 11 2009 - 10:00:40 CDT)
  • Abhishek Banerjee (Thu Sep 10 2009 - 21:40:21 CDT)
• [AMBER] DNA + intercalator
  • Ashish Runthala (Fri Jul 24 2009 - 22:12:27 CDT)
  • Bill Ross (Fri Jul 24 2009 - 18:03:06 CDT)
  • Rodrigo Galindo (Fri Jul 24 2009 - 17:22:35 CDT)
• [AMBER] DNA as well as protein distorted during MD run in sander
  • Jayalakshmi Sridhar (Tue Jun 09 2009 - 11:02:56 CDT)
  • Carlos Simmerling (Tue Jun 09 2009 - 10:48:30 CDT)
  • Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 10:47:34 CDT)
  • Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:44:39 CDT)
  • Carlos Simmerling (Tue Jun 09 2009 - 10:36:50 CDT)
  • Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:33:51 CDT)
  • Carlos Simmerling (Tue Jun 09 2009 - 09:38:14 CDT)
  • Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:30:39 CDT)
• [AMBER] DNA simulation: Problem with RMSD
  • BERGY (Fri Mar 06 2009 - 00:20:00 CST)
  • Thomas Cheatham (Wed Mar 04 2009 - 22:04:53 CST)
  • BERGY (Wed Mar 04 2009 - 21:44:26 CST)
• [AMBER] Do I need to modify the cap residues
  • Ross Walker (Mon Apr 06 2009 - 23:59:37 CDT)
  • nicholus bhattacharjee (Mon Apr 06 2009 - 23:51:22 CDT)
  • David A. Case (Mon Apr 06 2009 - 13:57:02 CDT)
  • nicholus bhattacharjee (Mon Apr 06 2009 - 12:19:41 CDT)
  • Ross Walker (Mon Apr 06 2009 - 12:00:05 CDT)
  • nicholus bhattacharjee (Mon Apr 06 2009 - 11:45:20 CDT)
• [AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues?
  • Catein Catherine (Sun Aug 02 2009 - 22:45:19 CDT)
• [AMBER] Docking with Amber
  • case (Mon Aug 31 2009 - 19:58:49 CDT)
  • Jordan, Brad (Mon Aug 31 2009 - 15:01:15 CDT)
• [AMBER] doubt-reg_ Targeted molecular dynamics
  • balaji nagarajan (Fri Mar 13 2009 - 11:20:41 CDT)
• [AMBER] Dr. Ramesh here
  • kureeckal ramesh (Mon Feb 02 2009 - 08:22:51 CST)
  • David A. Case (Fri Jan 30 2009 - 10:08:43 CST)
  • kureeckal ramesh (Thu Jan 29 2009 - 21:18:33 CST)
  • kureeckal ramesh (Thu Jan 29 2009 - 19:41:17 CST)
  • rpaduri_at_chem.wayne.edu (Thu Jan 29 2009 - 11:22:20 CST)
  • kureeckal ramesh (Thu Jan 29 2009 - 04:41:10 CST)
• [AMBER] drying of solvent possible ?
  • Jio M (Sat Aug 15 2009 - 00:59:08 CDT)
  • Bill Ross (Thu Aug 13 2009 - 11:21:35 CDT)
  • Jio M (Thu Aug 13 2009 - 08:49:00 CDT)
• [AMBER] Dummy atoms and MM-PBSA
  • Ray Luo (Fri Sep 04 2009 - 13:25:33 CDT)
  • Alireza Shaneh (Fri Sep 04 2009 - 11:48:16 CDT)
• [AMBER] Duplicate residues
  • Bill Ross (Mon Jan 19 2009 - 13:20:01 CST)
  • David A. Case (Mon Jan 19 2009 - 07:16:28 CST)
  • George Tzotzos (Mon Jan 19 2009 - 06:54:37 CST)
• [AMBER] Dyndom
  • Loeffler, Hannes (STFC,DL,CSE) (Sat Aug 29 2009 - 10:18:18 CDT)
  • Carlos Simmerling (Sat Aug 29 2009 - 09:59:23 CDT)
  • Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
  • Chunliyan (Thu Jun 18 2009 - 10:12:44 CDT)
• [AMBER] eigenvalues add up to more than trace of matrix
  • Hannes Loeffler (Fri Oct 16 2009 - 08:50:50 CDT)
  • Jason Swails (Fri Oct 16 2009 - 08:29:13 CDT)
  • Yaw Sing TAN (Thu Oct 15 2009 - 22:14:59 CDT)
• [AMBER] Energy minimisation and NaN
  • David A. Case (Mon Apr 13 2009 - 14:28:10 CDT)
  • vivek.viv.sharma_at_gmail.com (Mon Apr 13 2009 - 06:55:55 CDT)
• [AMBER] Energy-from-MM/PBSA-VS-experiment
  • Rilei Yu (Sun Oct 11 2009 - 17:51:26 CDT)
  • Jason Swails (Sun Oct 11 2009 - 09:54:08 CDT)
  • Rilei Yu (Sun Oct 11 2009 - 07:53:00 CDT)
• [AMBER] Enquiry about MM/GBSA output file.
  • Catein Catherine (Tue Sep 08 2009 - 02:14:19 CDT)
• [AMBER] enquiry regarding parameter file to be used
  • Carlos Simmerling (Fri Nov 20 2009 - 05:20:05 CST)
  • bharat lakhani (Thu Nov 19 2009 - 23:35:14 CST)
  • Carlos Simmerling (Mon Nov 16 2009 - 05:40:49 CST)
  • bharat lakhani (Fri Nov 13 2009 - 23:52:58 CST)
  • Carlos Simmerling (Fri Nov 13 2009 - 07:41:50 CST)
  • bharat lakhani (Fri Nov 13 2009 - 07:35:30 CST)
• [AMBER] entangle-less building
  • Bill Ross (Wed Jun 10 2009 - 17:38:31 CDT)
  • Vishal Maingi (Wed Jun 10 2009 - 12:52:51 CDT)
• [AMBER] Environment Variables in Cygwin Don't Remain
  • Bill Ross (Thu Oct 01 2009 - 13:57:43 CDT)
  • Jack Shultz (Thu Oct 01 2009 - 12:12:19 CDT)
  • Wallace Kunin (Thu Oct 01 2009 - 11:54:29 CDT)
• [AMBER] Epsilon value for Iron
  • bharat lakhani (Tue Aug 25 2009 - 07:24:10 CDT)
• [AMBER] EPtot for Alpha-L- methyl fucose
  • Sushil Mishra (Fri Jul 10 2009 - 09:12:28 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 08:57:34 CDT)
  • Sushil Mishra (Fri Jul 10 2009 - 08:47:26 CDT)
• [AMBER] Equilibration Scaling to System Size
  • Carlos Simmerling (Tue Feb 24 2009 - 16:49:10 CST)
  • Hopkins, Robert (Tue Feb 24 2009 - 16:31:37 CST)
• [AMBER] Equilibration step
  • Olotu Odunayo (Thu Jul 23 2009 - 01:52:50 CDT)
  • Tom Joseph (Wed Jul 22 2009 - 14:05:58 CDT)
  • Olotu Odunayo (Wed Jul 22 2009 - 11:46:12 CDT)
  • Olotu Odunayo (Wed Jul 22 2009 - 11:41:13 CDT)
  • Tom Joseph (Wed Jul 22 2009 - 07:35:15 CDT)
  • Olotu Odunayo (Wed Jul 22 2009 - 04:47:37 CDT)
• [AMBER] equilibration stops for dimer simulation with REMD
  • Sunita Patel (Thu May 07 2009 - 13:35:59 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 12:32:42 CDT)
  • Sunita Patel (Tue May 05 2009 - 12:26:09 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 11:39:52 CDT)
  • Sunita Patel (Tue May 05 2009 - 11:33:40 CDT)
  • Sunita Patel (Sun May 03 2009 - 20:30:05 CDT)
  • Carlos Simmerling (Sun May 03 2009 - 06:11:07 CDT)
  • Sunita Patel (Sat May 02 2009 - 15:11:48 CDT)
• [AMBER] Equilibrium bond lengths and angle values
  • Dmitri Nilov (Tue Apr 28 2009 - 05:56:38 CDT)
  • FyD (Fri Apr 24 2009 - 16:05:42 CDT)
  • Dmitri Nilov (Fri Apr 24 2009 - 08:19:56 CDT)
• [AMBER] Equilibrium water density
  • case (Wed Jul 15 2009 - 14:53:54 CDT)
  • Myeong Lee (Wed Jul 15 2009 - 03:58:52 CDT)
• [AMBER] equivalent atoms
  • Ye MEI (Mon Jul 20 2009 - 23:56:52 CDT)
• [AMBER] error for nmode
  • David A. Case (Thu Mar 19 2009 - 06:31:24 CDT)
  • Dechang Li (Thu Mar 19 2009 - 06:00:09 CDT)
• [AMBER] Error in AMBER ( Vertex atom mismatch in Amber)
  • Vikas Sharma (Wed Jun 10 2009 - 08:14:28 CDT)
• [AMBER] error in AMBer distance constraint
  • Carlos Simmerling (Tue Oct 27 2009 - 06:28:22 CDT)
  • xuemeiwang1103 (Mon Oct 26 2009 - 02:35:08 CDT)
  • Bill Ross (Sun Oct 25 2009 - 22:03:19 CDT)
  • Carlos Simmerling (Sun Oct 25 2009 - 21:38:23 CDT)
  • xuemeiwang1103 (Sun Oct 25 2009 - 21:24:09 CDT)
• [AMBER] error in antechamber
  • Qinghua Liao (Tue Jul 28 2009 - 00:13:49 CDT)
  • case (Mon Jul 27 2009 - 23:23:54 CDT)
  • Qinghua Liao (Mon Jul 27 2009 - 20:02:26 CDT)
  • Mengjuei Hsieh (Mon Jul 27 2009 - 17:29:06 CDT)
  • Qinghua Liao (Mon Jul 27 2009 - 06:57:50 CDT)
• [AMBER] Error in binding energy (MM PBSA)
  • Vikas Sharma (Tue May 12 2009 - 00:05:08 CDT)
  • Ray Luo (Mon May 11 2009 - 13:14:20 CDT)
  • Vikas Sharma (Mon May 11 2009 - 03:08:28 CDT)
  • Vikas Sharma (Sun May 10 2009 - 04:03:07 CDT)
  • Ray Luo (Sat May 09 2009 - 20:39:05 CDT)
  • Vikas Sharma (Sat May 09 2009 - 02:20:09 CDT)
  • Vikas Sharma (Sat May 09 2009 - 02:19:20 CDT)
  • Ray Luo (Fri May 08 2009 - 11:42:58 CDT)
  • Vikas Sharma (Fri May 08 2009 - 01:50:40 CDT)
  • Vikas Sharma (Fri May 08 2009 - 01:44:33 CDT)
  • Vikas Sharma (Fri May 08 2009 - 01:42:32 CDT)
  • Ray Luo (Thu May 07 2009 - 13:12:18 CDT)
  • Vikas Sharma (Thu May 07 2009 - 08:29:22 CDT)
  • David A. Case (Thu May 07 2009 - 06:33:20 CDT)
  • Vikas Sharma (Thu May 07 2009 - 00:47:33 CDT)
• [AMBER] error in constructing DNA from nucgen
  • Bill Ross (Tue Mar 17 2009 - 17:47:07 CDT)
  • Ross Walker (Tue Mar 17 2009 - 14:31:16 CDT)
  • Pansy Patel (Tue Mar 17 2009 - 14:24:58 CDT)
  • Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  • Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  • Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  • Pansy Patel (Tue Mar 17 2009 - 13:43:49 CDT)
• [AMBER] error in distance restraint
  • Carlos Simmerling (Thu Oct 29 2009 - 05:20:13 CDT)
  • xuemeiwang1103 (Wed Oct 28 2009 - 22:43:55 CDT)
  • Carlos Simmerling (Wed Oct 28 2009 - 15:48:13 CDT)
  • Adrian Roitberg (Wed Oct 28 2009 - 09:01:07 CDT)
  • xuemeiwang1103 (Wed Oct 28 2009 - 08:56:48 CDT)
• [AMBER] Error in equilibration: file _ew_box.f
  • case (Fri Aug 07 2009 - 17:34:29 CDT)
  • Biswaranjan Meher (Fri Aug 07 2009 - 15:39:00 CDT)
• [AMBER] error in executing sander.MPI in amber9
  • Atro Tossavainen (Thu Feb 05 2009 - 05:08:59 CST)
  • Vijay Manickam Achari (Thu Feb 05 2009 - 02:37:09 CST)
• [AMBER] error in kclust of MMTB_tool set
  • kureeckal ramesh (Tue Nov 10 2009 - 06:41:31 CST)
  • kureeckal ramesh (Sun Nov 08 2009 - 18:10:58 CST)
  • kureeckal ramesh (Fri Nov 06 2009 - 01:33:01 CST)
• [AMBER] Error in minimal
  • case (Tue Sep 15 2009 - 17:15:06 CDT)
  • xuemeiwang1103 (Tue Sep 15 2009 - 08:54:58 CDT)
  • case (Tue Sep 15 2009 - 06:56:02 CDT)
  • xuemeiwang1103 (Tue Sep 15 2009 - 02:27:18 CDT)
• [AMBER] Error in MM PBSA
  • Ray Luo (Mon Jun 08 2009 - 13:12:22 CDT)
  • Vikas Sharma (Mon Jun 08 2009 - 12:44:06 CDT)
  • Ray Luo (Sun Jun 07 2009 - 14:17:30 CDT)
  • Vikas Sharma (Sun Jun 07 2009 - 12:02:03 CDT)
  • Ray Luo (Sat Jun 06 2009 - 09:37:43 CDT)
  • Vikas Sharma (Sat Jun 06 2009 - 04:03:22 CDT)
  • Ray Luo (Thu Jun 04 2009 - 16:00:51 CDT)
  • Vikas Sharma (Thu Jun 04 2009 - 09:58:43 CDT)
  • Vikas Sharma (Wed Jun 03 2009 - 09:24:14 CDT)
  • David A. Case (Wed Jun 03 2009 - 06:43:54 CDT)
  • Vikas Sharma (Wed Jun 03 2009 - 01:46:06 CDT)
  • Vikas Sharma (Wed Jun 03 2009 - 01:46:03 CDT)
  • Vikas Sharma (Wed Jun 03 2009 - 01:45:35 CDT)
  • David A. Case (Tue Jun 02 2009 - 09:05:09 CDT)
  • Vikas Sharma (Tue Jun 02 2009 - 08:42:16 CDT)
  • Vikas Sharma (Wed May 06 2009 - 03:35:57 CDT)
  • Vikas Sharma (Sun Apr 05 2009 - 23:27:21 CDT)
  • Vikas Sharma (Sun Apr 05 2009 - 01:09:35 CDT)
  • David A. Case (Sat Apr 04 2009 - 16:16:42 CDT)
  • Hemant Gangwar (Sat Apr 04 2009 - 12:08:08 CDT)
  • Vikas Sharma (Sat Apr 04 2009 - 12:06:57 CDT)
• [AMBER] Error in MM PBSA (vertex atom mismatch)
  • Vikas Sharma (Tue Jun 09 2009 - 01:33:38 CDT)
• [AMBER] error in output file
  • Vikas Sharma (Thu Apr 23 2009 - 08:55:20 CDT)
  • Vikas Sharma (Thu Apr 23 2009 - 08:33:49 CDT)
  • Ross Walker (Thu Apr 23 2009 - 08:28:18 CDT)
  • Hemant Kumar (Thu Apr 23 2009 - 07:20:25 CDT)
  • Vikas Sharma (Thu Apr 23 2009 - 06:58:24 CDT)
  • Carlos Simmerling (Thu Apr 23 2009 - 06:42:02 CDT)
  • Vikas Sharma (Thu Apr 23 2009 - 06:39:42 CDT)
• [AMBER] Error in parallel run
  • Catein Catherine (Wed May 06 2009 - 21:46:02 CDT)
• [AMBER] Error in PMEMD run
  • Marek Malý (Fri May 08 2009 - 20:36:49 CDT)
  • Robert Duke (Fri May 08 2009 - 20:26:37 CDT)
  • Marek Malý (Fri May 08 2009 - 20:05:40 CDT)
  • Robert Duke (Fri May 08 2009 - 19:01:23 CDT)
  • Marek Malý (Fri May 08 2009 - 18:37:28 CDT)
  • Robert Duke (Fri May 08 2009 - 14:44:08 CDT)
  • Marek Malý (Fri May 08 2009 - 14:10:41 CDT)
  • Marek Malý (Fri May 08 2009 - 13:27:20 CDT)
  • Robert Duke (Fri May 08 2009 - 13:24:35 CDT)
  • Robert Duke (Fri May 08 2009 - 13:14:12 CDT)
  • Ross Walker (Fri May 08 2009 - 13:11:19 CDT)
  • Robert Duke (Fri May 08 2009 - 13:06:17 CDT)
  • Marek Malý (Fri May 08 2009 - 13:02:53 CDT)
  • Marek Malý (Fri May 08 2009 - 12:57:36 CDT)
  • Gustavo Seabra (Fri May 08 2009 - 12:28:35 CDT)
  • Marek Malý (Fri May 08 2009 - 11:38:27 CDT)
  • Robert Duke (Fri May 08 2009 - 08:29:48 CDT)
  • Marek Malý (Fri May 08 2009 - 07:54:57 CDT)
  • Robert Duke (Thu May 07 2009 - 19:11:25 CDT)
  • Marek Malý (Thu May 07 2009 - 18:59:23 CDT)
  • Robert Duke (Wed May 06 2009 - 18:04:10 CDT)
  • Ross Walker (Wed May 06 2009 - 16:53:07 CDT)
  • Marek Malý (Wed May 06 2009 - 16:27:17 CDT)
  • Marek Malý (Wed May 06 2009 - 16:25:02 CDT)
  • Robert Duke (Wed May 06 2009 - 15:40:29 CDT)
  • Ross Walker (Wed May 06 2009 - 15:36:36 CDT)
  • Marek Malý (Wed May 06 2009 - 15:26:58 CDT)
  • Robert Duke (Wed May 06 2009 - 15:08:56 CDT)
  • Marek Malý (Wed May 06 2009 - 15:02:11 CDT)
  • Robert Duke (Wed May 06 2009 - 14:58:29 CDT)
  • Robert Duke (Wed May 06 2009 - 14:55:49 CDT)
  • Marek Malý (Wed May 06 2009 - 14:48:26 CDT)
  • Ross Walker (Wed May 06 2009 - 14:41:10 CDT)
  • Robert Duke (Wed May 06 2009 - 14:29:41 CDT)
  • Robert Duke (Wed May 06 2009 - 14:20:37 CDT)
  • Marek Malý (Wed May 06 2009 - 13:51:03 CDT)
  • Marek Malý (Wed May 06 2009 - 13:42:36 CDT)
  • Marek Malý (Wed May 06 2009 - 13:30:43 CDT)
  • Robert Duke (Wed May 06 2009 - 12:30:43 CDT)
  • Ross Walker (Wed May 06 2009 - 12:07:01 CDT)
  • Marek Malý (Wed May 06 2009 - 10:58:33 CDT)
  • Robert Duke (Mon May 04 2009 - 23:08:37 CDT)
  • Marek Malý (Mon May 04 2009 - 21:19:20 CDT)
  • Robert Duke (Mon May 04 2009 - 20:35:54 CDT)
  • Marek Malý (Mon May 04 2009 - 20:23:33 CDT)
• [AMBER] ERROR in ptrajInitializeState(): Attempting ....
  • Siavoush Dastmalchi (Sat May 30 2009 - 11:06:51 CDT)
• [AMBER] error in reading namelist cntrl
  • Ross Walker (Tue Nov 03 2009 - 16:57:58 CST)
  • Giuseppe De Marco (Tue Nov 03 2009 - 13:44:01 CST)
• [AMBER] ERROR In Restraint file.
  • David A. Case (Tue Apr 28 2009 - 19:05:23 CDT)
  • Catein Catherine (Tue Apr 28 2009 - 18:32:26 CDT)
  • David A. Case (Tue Apr 28 2009 - 11:17:36 CDT)
  • Catein Catherine (Tue Apr 28 2009 - 10:27:18 CDT)
  • Catein Catherine (Tue Apr 28 2009 - 10:12:34 CDT)
• [AMBER] error in sander (Amber10)
  • archana sonawani (Tue Jan 13 2009 - 02:21:09 CST)
• [AMBER] Error in Sander Output File
  • Alison Saunders (Tue Jul 28 2009 - 12:00:12 CDT)
• [AMBER] error in tleap of AMBER 10
  • case (Fri Jun 26 2009 - 07:09:58 CDT)
  • kureeckal ramesh (Fri Jun 26 2009 - 02:10:56 CDT)
  • case (Thu Jun 25 2009 - 06:54:47 CDT)
  • kureeckal ramesh (Wed Jun 24 2009 - 00:03:55 CDT)
• [AMBER] Error in trajin and rms
  • Pansy Patel (Thu Apr 02 2009 - 14:25:58 CDT)
  • iccy liu (Thu Apr 02 2009 - 14:19:16 CDT)
  • Carlos Simmerling (Thu Apr 02 2009 - 14:19:39 CDT)
  • Pansy Patel (Thu Apr 02 2009 - 13:58:47 CDT)
• [AMBER] Error in using Amber
  • sri noraima othman (Thu Feb 26 2009 - 00:27:14 CST)
  • Ross Walker (Thu Feb 26 2009 - 00:03:12 CST)
  • sri noraima othman (Wed Feb 25 2009 - 21:27:29 CST)
• [AMBER] Error in xleap
  • Ross Walker (Thu Jan 15 2009 - 10:01:20 CST)
  • archana sonawani (Thu Jan 15 2009 - 01:39:16 CST)
• [AMBER] error in xleap: ligand binding using MMand QMMM tech
  • Gustavo Seabra (Thu Feb 12 2009 - 08:32:17 CST)
  • kureeckal ramesh (Thu Feb 12 2009 - 04:27:41 CST)
• [AMBER] Error installing Amber
  • David Patiño (Tue Feb 17 2009 - 08:58:05 CST)
  • David A. Case (Mon Feb 16 2009 - 08:21:41 CST)
  • David Patiño (Mon Feb 16 2009 - 06:02:31 CST)
• [AMBER] Error message for tutorial 1 (run in parallel)
  • Catein Catherine (Mon May 04 2009 - 08:31:05 CDT)
  • David A. Case (Mon May 04 2009 - 07:40:36 CDT)
  • Catein Catherine (Mon May 04 2009 - 04:05:17 CDT)
• [AMBER] error message from iAPBS
  • Oliver Kuhn (Mon Oct 19 2009 - 06:47:32 CDT)
• [AMBER] Error message in "make test.sander"
  • Catein Catherine (Wed May 06 2009 - 01:58:04 CDT)
  • Ross Walker (Wed May 06 2009 - 01:28:01 CDT)
  • Catein Catherine (Wed May 06 2009 - 00:40:54 CDT)
  • Ross Walker (Tue May 05 2009 - 22:37:28 CDT)
  • Catein Catherine (Tue May 05 2009 - 21:52:26 CDT)
• [AMBER] Error message in "make test.sander" Is amber compatible with dual processors?
  • Catein Catherine (Wed May 06 2009 - 08:08:49 CDT)
• [AMBER] Error message? INFO: Old style inpcrd file read
  • Catein Catherine (Sun Jun 07 2009 - 22:55:28 CDT)
  • Robert Duke (Sun Jun 07 2009 - 22:19:38 CDT)
  • Catein Catherine (Sun Jun 07 2009 - 22:11:27 CDT)
• [AMBER] Error on equilibriation of Amber10
  • Masakazu SEKIJIMA (Mon Jun 22 2009 - 05:59:55 CDT)
• [AMBER] error on open distatance restraint
  • xiaonan zhang (Sat Jan 24 2009 - 21:56:02 CST)
  • David A. Case (Fri Jan 23 2009 - 21:18:17 CST)
  • gmail (Fri Jan 23 2009 - 20:58:27 CST)
• [AMBER] error reading namelist cntrl
  • Jason Swails (Wed Nov 11 2009 - 08:01:42 CST)
  • Shaikh Abdul R S Ramaju (Wed Nov 11 2009 - 00:51:45 CST)
• [AMBER] Error running MM _PBSA.pl script
  • Vikas Sharma (Wed May 20 2009 - 03:29:42 CDT)
  • liuhui (Tue May 19 2009 - 21:20:26 CDT)
  • Vikas Sharma (Tue May 19 2009 - 13:21:47 CDT)
  • liuhui (Tue May 19 2009 - 11:15:24 CDT)
  • Vikas Sharma (Tue May 19 2009 - 10:02:21 CDT)
  • liuhui (Tue May 19 2009 - 09:29:23 CDT)
  • Vikas Sharma (Mon May 18 2009 - 23:34:18 CDT)
  • Ray Luo (Mon May 18 2009 - 12:43:30 CDT)
  • Vikas Sharma (Mon May 18 2009 - 07:00:13 CDT)
• [AMBER] Error running sander.MPI
  • Anselm Horn (Tue Feb 17 2009 - 04:28:47 CST)
  • Rausch, Felix (Tue Feb 17 2009 - 02:15:19 CST)
  • Carlos Simmerling (Mon Feb 16 2009 - 05:51:08 CST)
  • Vijay Manickam Achari (Mon Feb 16 2009 - 02:23:05 CST)
• [AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA
  • Vikas Sharma (Mon Apr 13 2009 - 15:11:07 CDT)
• [AMBER] Error when installing amber11 on OpenSuse
  • steinbrt_at_rci.rutgers.edu (Thu Jun 25 2009 - 07:19:59 CDT)
• [AMBER] Error with calculation of the potential energy
  • Robert Duke (Mon Apr 27 2009 - 14:26:06 CDT)
  • Per Jr. Greisen (Mon Apr 27 2009 - 13:57:58 CDT)
  • Robert Duke (Mon Apr 27 2009 - 13:46:43 CDT)
  • Robert Duke (Mon Apr 27 2009 - 13:25:14 CDT)
  • Per Jr. Greisen (Mon Apr 27 2009 - 12:11:32 CDT)
  • Carlos Simmerling (Mon Apr 27 2009 - 06:08:47 CDT)
  • Per Jr. Greisen (Mon Apr 27 2009 - 06:03:44 CDT)
• [AMBER] error xleap: XaLeap_wcl is empty
  • case (Mon Sep 14 2009 - 07:02:12 CDT)
  • Mari Carmen Pérez (Mon Sep 14 2009 - 04:59:09 CDT)
• [AMBER] Error: cannot run prepgen
  • Rose Tamil (Tue May 05 2009 - 10:20:52 CDT)
• [AMBER] ERROR: Could not read coords from {filename}
  • Paul Brandt (Tue Dec 29 2009 - 03:46:55 CST)
  • ZhaoLei (Mon Dec 28 2009 - 20:58:53 CST)
  • Carlos Simmerling (Mon Dec 28 2009 - 20:04:27 CST)
  • ZhaoLei (Mon Dec 28 2009 - 19:34:29 CST)
  • case (Mon Dec 28 2009 - 08:57:11 CST)
  • ZhaoLei (Mon Dec 28 2009 - 08:12:54 CST)
  • case (Mon Dec 28 2009 - 07:00:34 CST)
  • Paul Brandt (Sun Dec 27 2009 - 22:14:50 CST)
• [AMBER] Error: unable to find mopac charges in mopac.out
  • case (Tue Oct 20 2009 - 06:45:59 CDT)
  • Rilei Yu (Tue Oct 20 2009 - 02:12:19 CDT)
  • Ross Walker (Tue Oct 20 2009 - 00:50:17 CDT)
  • Rilei Yu (Tue Oct 20 2009 - 00:34:34 CDT)
• [AMBER] errorin sander---Amber10
  • David A. Case (Tue Jan 13 2009 - 07:22:36 CST)
  • archana sonawani (Tue Jan 13 2009 - 03:27:43 CST)
• [AMBER] errors about install amber9 on MAC OS
  • David A. Case (Wed Mar 18 2009 - 06:08:44 CDT)
  • zgong.hust (Wed Mar 18 2009 - 03:41:19 CDT)
• [AMBER] errors of PMEMD installation
  • Mengjuei Hsieh (Sat Jul 25 2009 - 22:10:11 CDT)
  • Mengjuei Hsieh (Thu Jul 23 2009 - 14:25:27 CDT)
  • å»–é�’å�Ž (Wed Jul 22 2009 - 09:28:45 CDT)
• [AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure
  • Yunjie Zhao (Thu Nov 19 2009 - 22:37:34 CST)
• [AMBER] errors on leap for a RNA+Adenine pdb structure
  • FyD (Wed Nov 04 2009 - 07:39:02 CST)
  • zgong.hust (Wed Nov 04 2009 - 06:59:20 CST)
  • case (Wed Nov 04 2009 - 06:17:53 CST)
  • zgong.hust (Wed Nov 04 2009 - 00:18:41 CST)
• [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber
  • FyD (Wed Nov 04 2009 - 09:28:04 CST)
  • zgong.hust (Wed Nov 04 2009 - 09:07:23 CST)
• [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber
  • FyD (Wed Nov 04 2009 - 23:42:43 CST)
  • zgong.hust (Wed Nov 04 2009 - 20:18:52 CST)
• [AMBER] errors on reading time series file in WHAM calculation
  • Jenny Iskrenova (Tue Mar 24 2009 - 09:35:51 CDT)
  • gmail (Mon Mar 23 2009 - 19:35:02 CDT)
• [AMBER] errors on REMD
  • Carlos Simmerling (Mon Jan 26 2009 - 11:38:39 CST)
  • z g (Thu Jan 22 2009 - 19:02:08 CST)
  • Carlos Simmerling (Tue Jan 20 2009 - 08:29:07 CST)
  • z g (Tue Jan 20 2009 - 07:39:12 CST)
  • Carlos Simmerling (Tue Jan 20 2009 - 05:02:06 CST)
  • z g (Mon Jan 19 2009 - 20:41:35 CST)
• [AMBER] errors when add ions
  • David A. Case (Thu May 21 2009 - 07:23:08 CDT)
  • zgong.hust (Wed May 20 2009 - 21:51:48 CDT)
• [AMBER] errors while testing
  • Per Jr. Greisen (Wed Apr 08 2009 - 06:06:40 CDT)
  • Atro Tossavainen (Tue Apr 07 2009 - 05:18:08 CDT)
  • Per Jr. Greisen (Tue Apr 07 2009 - 05:00:19 CDT)
• [AMBER] ESP charges of Fe4S4
  • subarna thakur (Wed Jul 22 2009 - 00:19:48 CDT)
• [AMBER] essential dynamics
  • David A. Case (Wed May 13 2009 - 12:15:50 CDT)
  • Chunliyan (Wed May 13 2009 - 11:23:23 CDT)
• [AMBER] Etot positive
  • Ross Walker (Mon Nov 16 2009 - 20:50:02 CST)
  • Carlos Simmerling (Mon Nov 16 2009 - 05:13:55 CST)
  • Jio M (Sun Nov 15 2009 - 23:06:22 CST)
• [AMBER] Ewald error estimated
  • Robert Duke (Fri Sep 25 2009 - 10:50:18 CDT)
  • case (Fri Sep 25 2009 - 10:15:31 CDT)
  • Qinghua Liao (Fri Sep 25 2009 - 02:48:14 CDT)
  • xuemeiwang1103 (Thu Sep 24 2009 - 22:01:05 CDT)
  • xuemeiwang1103 (Thu Sep 24 2009 - 22:01:02 CDT)
• [AMBER] exchange attempt in REMD
  • Carlos Simmerling (Thu Dec 31 2009 - 09:50:24 CST)
  • zgong.hust (Wed Dec 30 2009 - 22:22:54 CST)
  • Carlos Simmerling (Wed Dec 30 2009 - 21:09:02 CST)
  • zgong.hust (Wed Dec 30 2009 - 20:34:21 CST)
• [AMBER] Exclamation marks in trajectory
  • Ross Walker (Mon Jul 13 2009 - 14:20:37 CDT)
  • Hugh Heldenbrand (Mon Jul 13 2009 - 13:52:37 CDT)
  • Ross Walker (Mon Jul 13 2009 - 13:13:17 CDT)
  • Hugh Heldenbrand (Mon Jul 13 2009 - 10:16:26 CDT)
• [AMBER] explicit ion with igb=1
  • Carlos Simmerling (Thu Apr 02 2009 - 08:53:54 CDT)
  • Bala subramanian (Thu Apr 02 2009 - 08:39:10 CDT)
• [AMBER] explicit solvent NMR refinement
  • case (Sun Jun 28 2009 - 08:19:11 CDT)
  • Carlos Simmerling (Sun Jun 28 2009 - 07:36:42 CDT)
  • Sally Pias (Sun Jun 28 2009 - 03:46:56 CDT)
• [AMBER] extra torsion terms in tleap.top-file
  • Astrid Maaß (Thu Feb 26 2009 - 08:32:30 CST)
• [AMBER] extract frames from a .mdcrd
  • Carlos Simmerling (Tue Feb 10 2009 - 04:58:12 CST)
  • vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:52:19 CST)
  • Bill Ross (Fri Feb 06 2009 - 13:13:27 CST)
  • Carlos Simmerling (Fri Feb 06 2009 - 05:12:00 CST)
  • vallespardojl_at_chem.leidenuniv.nl (Fri Feb 06 2009 - 04:48:23 CST)
• [AMBER] Extreme optimization problems
  • case (Thu Aug 06 2009 - 10:51:23 CDT)
  • ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 06 2009 - 07:04:09 CDT)
• [AMBER] Fail to allocate ff
  • Gustavo Seabra (Tue Mar 03 2009 - 14:36:53 CST)
  • Madhurima Jana (Tue Mar 03 2009 - 08:27:41 CST)
  • Nicholas Musolino (Tue Mar 03 2009 - 07:10:21 CST)
  • Madhurima Jana (Tue Mar 03 2009 - 05:17:57 CST)
• [AMBER] Failure to compile amber9 serial ifort gcc
  • Francesco Pietra (Thu Apr 02 2009 - 11:00:46 CDT)
  • Ross Walker (Thu Apr 02 2009 - 10:45:19 CDT)
  • Francesco Pietra (Thu Apr 02 2009 - 06:16:36 CDT)
  • Alessandro Nascimento (Wed Apr 01 2009 - 06:09:42 CDT)
  • Francesco Pietra (Wed Apr 01 2009 - 06:04:18 CDT)
• [AMBER] failure to run antechamber with amber 10
  • Francesco Pietra (Fri Jan 30 2009 - 02:04:33 CST)
  • George Tzotzos (Thu Jan 29 2009 - 16:48:50 CST)
  • David A. Case (Thu Jan 29 2009 - 16:45:53 CST)
  • Francesco Pietra (Thu Jan 29 2009 - 16:29:18 CST)
• [AMBER] Failures of tests
  • Per Jr. Greisen (Thu Apr 09 2009 - 07:52:32 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 17:43:08 CDT)
  • Per Jr. Greisen (Wed Apr 08 2009 - 11:17:16 CDT)
  • Seetin, Matthew (Wed Apr 08 2009 - 10:57:27 CDT)
  • Per Jr. Greisen (Wed Apr 08 2009 - 10:41:34 CDT)
• [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex
  • case (Thu Sep 24 2009 - 17:13:39 CDT)
  • Jeff Yeo (Wed Sep 23 2009 - 18:24:51 CDT)
• [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber
  • Rubben Torella (Tue May 26 2009 - 17:33:18 CDT)
  • Workalemhu Berhanu (Tue May 26 2009 - 16:45:55 CDT)
• [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule.
  • Soni Mufaddal Saifee (Tue Apr 07 2009 - 23:19:25 CDT)
  • Carlos Simmerling (Mon Apr 06 2009 - 05:07:09 CDT)
  • Soni Mufaddal Saifee (Mon Apr 06 2009 - 04:07:51 CDT)
• [AMBER] Fe and Mn simulations
  • Alessandro Nascimento (Tue Jun 30 2009 - 15:22:14 CDT)
• [AMBER] Fe-S topology
  • case (Tue Jun 30 2009 - 12:45:27 CDT)
  • Markus Kaukonen (Tue Jun 30 2009 - 02:28:51 CDT)
  • subarna thakur (Tue Jun 30 2009 - 01:29:16 CDT)
• [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'
  • David A. Case (Fri May 15 2009 - 18:56:34 CDT)
  • ben rodriguez (Fri May 15 2009 - 17:09:44 CDT)
• [AMBER] ff fitting ?
  • Marek Maly (Mon Nov 09 2009 - 06:38:35 CST)
  • case (Sun Nov 08 2009 - 11:42:42 CST)
  • Marek Maly (Thu Nov 05 2009 - 15:38:38 CST)
• [AMBER] ff parameters
  • case (Thu Jul 09 2009 - 08:23:31 CDT)
  • oguz gurbulak (Wed Jul 08 2009 - 09:35:40 CDT)
• [AMBER] FF Parameters Transformations ...?
  • Marek Malý (Mon Apr 06 2009 - 15:03:58 CDT)
  • Karl Kirschner (Mon Apr 06 2009 - 02:39:31 CDT)
  • Marek Malý (Wed Apr 01 2009 - 12:29:26 CDT)
• [AMBER] ff03 parameter for GDP and GTP
  • FyD (Sun Oct 11 2009 - 06:42:25 CDT)
  • Carlos Simmerling (Sat Oct 10 2009 - 06:36:35 CDT)
  • FyD (Sat Oct 10 2009 - 00:52:27 CDT)
  • FyD (Fri Oct 09 2009 - 15:38:08 CDT)
  • mmg8_at_ualberta.ca (Fri Oct 09 2009 - 09:30:46 CDT)
  • Carlos Simmerling (Fri Oct 09 2009 - 08:09:32 CDT)
  • case (Fri Oct 09 2009 - 08:03:02 CDT)
  • Carlos Simmerling (Fri Oct 09 2009 - 07:45:04 CDT)
  • FyD (Fri Oct 09 2009 - 05:37:40 CDT)
  • mmg8_at_ualberta.ca (Thu Oct 08 2009 - 20:05:18 CDT)
• [AMBER] file contains 2 atoms not in residue templates
  • David A. Case (Sun May 24 2009 - 08:12:14 CDT)
  • Workalemhu Berhanu (Sat May 23 2009 - 19:17:09 CDT)
• [AMBER] File conversion for from Amber to Charmm
  • case (Fri Jul 17 2009 - 06:53:06 CDT)
  • Yogesh Aher (Fri Jul 17 2009 - 01:45:11 CDT)
• [AMBER] File format for reading in charges in antechamber
  • Dean Cuebas (Sun Oct 04 2009 - 15:20:42 CDT)
• [AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA
  • Sushil Mishra (Mon Jul 20 2009 - 07:26:27 CDT)
• [AMBER] fillratio
  • Qinghua Liao (Mon Nov 30 2009 - 23:59:05 CST)
  • Ray Luo (Mon Nov 30 2009 - 21:30:50 CST)
  • Qinghua Liao (Mon Nov 30 2009 - 20:38:34 CST)
• [AMBER] fillratio error in mmpbsa
  • Ray Luo (Wed Apr 01 2009 - 14:24:20 CDT)
  • Han Ming (Wed Apr 01 2009 - 10:06:08 CDT)
  • m m (Wed Apr 01 2009 - 06:42:45 CDT)
• [AMBER] Fix Residue continued...
  • Carlos Simmerling (Thu Jun 18 2009 - 13:56:54 CDT)
  • Vishal Maingi (Thu Jun 18 2009 - 13:48:03 CDT)
• [AMBER] Fix the local structure as a rigid body
  • David A. Case (Tue Jun 16 2009 - 10:41:04 CDT)
  • Carlos Simmerling (Tue Jun 16 2009 - 09:13:45 CDT)
  • Yunjie Zhao (Tue Jun 16 2009 - 08:57:10 CDT)
  • Carlos Simmerling (Tue Jun 16 2009 - 08:15:12 CDT)
  • Yunjie Zhao (Tue Jun 16 2009 - 08:11:43 CDT)
• [AMBER] Flexible ring simulation
  • Dong Xu (Tue Apr 21 2009 - 18:04:55 CDT)
• [AMBER] follow-up to previous discussion: nmr refinement of dimer
  • David A. Case (Tue Feb 24 2009 - 07:15:27 CST)
  • Sally Pias (Tue Feb 24 2009 - 01:50:41 CST)
• [AMBER] force field choice
  • ahmed said (Fri Jun 26 2009 - 03:21:16 CDT)
• [AMBER] Force Field Fitting
  • manoj singh (Thu Sep 17 2009 - 14:32:33 CDT)
  • s. Bill (Thu Sep 17 2009 - 14:27:46 CDT)
  • manoj singh (Thu Sep 17 2009 - 12:20:50 CDT)
  • s. Bill (Thu Sep 17 2009 - 06:36:33 CDT)
• [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5
  • FyD (Fri Jun 19 2009 - 03:47:39 CDT)
  • Madhurima Jana (Fri Jun 19 2009 - 01:40:43 CDT)
• [AMBER] force field parameters
  • Piotr Cieplak (Mon Dec 07 2009 - 01:25:03 CST)
• [AMBER] force fields
  • Gustavo Seabra (Wed Apr 15 2009 - 07:43:49 CDT)
  • Ross Walker (Wed Apr 08 2009 - 19:36:05 CDT)
  • Mark M Huntress (Wed Apr 08 2009 - 19:23:38 CDT)
• [AMBER] force units
  • Brad Dickson (Thu Jun 18 2009 - 02:14:31 CDT)
• [AMBER] force-field for cyclic oligosaccharide using leap
  • Madhurima Jana (Sun Jan 11 2009 - 22:21:23 CST)
  • Madhurima Jana (Thu Jan 08 2009 - 22:50:18 CST)
• [AMBER] force.f routine
  • David A. Case (Wed Jun 10 2009 - 09:09:47 CDT)
  • Brad Dickson (Wed Jun 10 2009 - 07:56:39 CDT)
• [AMBER] formate parameters
  • Dmitri Nilov (Tue Feb 10 2009 - 08:47:31 CST)
• [AMBER] Fortran error in standard simulation
  • Ross Walker (Tue Nov 24 2009 - 10:21:33 CST)
  • Oliver Kuhn (Mon Nov 23 2009 - 03:26:30 CST)
• [AMBER] Fortran error in standard simulation 2
  • Oliver Kuhn (Mon Nov 23 2009 - 03:34:21 CST)
• [AMBER] Fortran error in standard simulation 3
  • Oliver Kuhn (Mon Nov 23 2009 - 03:47:44 CST)
• [AMBER] four prepin/frcmod files be read simultaneously by leap
  • David A. Case (Wed Jan 07 2009 - 12:39:56 CST)
  • Yi Mao (Wed Jan 07 2009 - 10:38:52 CST)
  • rpaduri_at_chem.wayne.edu (Wed Jan 07 2009 - 10:05:09 CST)
  • Yi Mao (Wed Jan 07 2009 - 08:46:05 CST)
• [AMBER] Free Energy Decomposition Problem
  • ozlem ulucan (Mon Mar 09 2009 - 08:55:45 CDT)
• [AMBER] free enrgy error in MM PBSA
  • Vikas Sharma (Thu May 07 2009 - 05:11:44 CDT)
• [AMBER] From DLG to Antechamber
  • FyD (Fri Jun 19 2009 - 10:54:05 CDT)
  • Jack Shultz (Fri Jun 19 2009 - 09:34:33 CDT)
  • Jack Shultz (Fri Jun 19 2009 - 09:21:37 CDT)
  • gilbert_at_bluemarble.net (Fri Jun 19 2009 - 09:17:09 CDT)
  • Jack Shultz (Fri Jun 19 2009 - 08:09:06 CDT)
  • gilbert_at_bluemarble.net (Fri Jun 19 2009 - 07:57:04 CDT)
  • Jack Shultz (Fri Jun 19 2009 - 07:27:20 CDT)
  • FyD (Fri Jun 19 2009 - 04:26:46 CDT)
  • Jack Shultz (Thu Jun 18 2009 - 19:04:15 CDT)
• [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10
  • Ray Luo (Thu Mar 26 2009 - 18:54:17 CDT)
  • Daniel Oehme (Thu Mar 26 2009 - 18:44:59 CDT)
• [AMBER] Fwd: average torsional energy
  • Francesco Pietra (Sun Jun 07 2009 - 11:09:37 CDT)
• [AMBER] Fwd: Group specification
  • Bill Ross (Thu Oct 08 2009 - 15:22:54 CDT)
  • Bill Ross (Thu Oct 08 2009 - 15:15:44 CDT)
  • Carlos Simmerling (Thu Oct 08 2009 - 13:35:43 CDT)
  • Pavan G (Thu Oct 08 2009 - 13:30:09 CDT)
• [AMBER] Fwd: please help me out
  • bharat lakhani (Wed Mar 04 2009 - 22:42:06 CST)
• [AMBER] Fwd: yacc parser
  • Francesco Pietra (Wed Apr 01 2009 - 15:53:01 CDT)
• [AMBER] g(r) extrapolation
  • Lorenzo Gontrani (Thu Feb 19 2009 - 03:23:19 CST)
  • Thomas Cheatham III (Wed Feb 18 2009 - 11:15:36 CST)
  • Lorenzo Gontrani (Wed Feb 18 2009 - 09:16:26 CST)
• [AMBER] gaff and aromatic compounds
  • Junmei Wang (Tue May 26 2009 - 11:03:53 CDT)
  • rebeca (Fri May 22 2009 - 04:04:45 CDT)
  • Junmei Wang (Thu May 21 2009 - 20:24:52 CDT)
  • David A. Case (Wed May 20 2009 - 07:04:05 CDT)
  • rebeca (Wed May 20 2009 - 03:54:43 CDT)
  • David A. Case (Tue May 19 2009 - 11:07:29 CDT)
  • rebeca (Tue May 19 2009 - 10:50:02 CDT)
• [AMBER] GAFF and NME, ACE terminal res
  • FyD (Thu Jul 16 2009 - 01:25:03 CDT)
  • Jio M (Wed Jul 15 2009 - 23:29:08 CDT)
  • FyD (Tue Jul 14 2009 - 02:40:00 CDT)
  • Jio M (Mon Jul 13 2009 - 15:51:06 CDT)
• [AMBER] GAFF and solvents.lib error
  • David A. Case (Wed Jun 10 2009 - 10:54:05 CDT)
  • Vishal Maingi (Wed Jun 10 2009 - 05:25:38 CDT)
• [AMBER] GAFF atom type question
  • Cen Gao (Sun Jun 14 2009 - 23:12:19 CDT)
  • Cen Gao (Thu Jun 11 2009 - 19:31:25 CDT)
  • Ross Walker (Thu Jun 11 2009 - 10:43:50 CDT)
  • Cen Gao (Thu Jun 11 2009 - 08:36:52 CDT)
  • Cen Gao (Wed Jun 10 2009 - 10:49:00 CDT)
• [AMBER] Gaff compatible with ff899.SB
  • Carlos Simmerling (Mon Dec 21 2009 - 09:32:40 CST)
  • Pol Boudard (Mon Dec 21 2009 - 09:03:25 CST)
• [AMBER] GAFF conjugated ring system dihedrals
  • David A. Case (Thu Jan 29 2009 - 12:37:24 CST)
  • Floris Buelens (Wed Jan 28 2009 - 06:04:55 CST)
• [AMBER] GAFF parameter
  • Ross Walker (Tue Oct 20 2009 - 13:50:18 CDT)
  • Jason Swails (Tue Oct 20 2009 - 09:57:09 CDT)
  • stefano_elli\_at_libero\.it (Tue Oct 20 2009 - 08:26:26 CDT)
• [AMBER] gaff.dat questions
  • case (Wed Sep 09 2009 - 09:16:23 CDT)
  • gilbert_at_bluemarble.net (Wed Sep 09 2009 - 09:02:28 CDT)
• [AMBER] Gap in rst file
  • Katrina Lexa (Mon Sep 28 2009 - 09:47:43 CDT)
• [AMBER] gaussain output
  • FyD (Mon Aug 17 2009 - 17:59:39 CDT)
  • FyD (Mon Aug 17 2009 - 04:50:53 CDT)
  • subarna thakur (Mon Aug 17 2009 - 02:11:00 CDT)
• [AMBER] gaussian 98 input/output for antechamber/resp
  • Karl Kirschner (Thu Aug 13 2009 - 02:26:12 CDT)
  • Karl Kirschner (Thu Aug 13 2009 - 01:57:41 CDT)
  • wong105_at_llnl.gov (Wed Aug 12 2009 - 13:41:45 CDT)
• [AMBER] Gaussian log file error
  • Junmei Wang (Mon Nov 02 2009 - 09:58:10 CST)
  • Ben Roberts (Mon Nov 02 2009 - 09:16:23 CST)
  • megha bajaj (Sat Oct 31 2009 - 08:10:22 CDT)
• [AMBER] Gaussian network model (GNM)
  • Adrian Roitberg (Fri Aug 21 2009 - 19:49:04 CDT)
  • Chih-Ying Lin (Fri Aug 21 2009 - 19:39:07 CDT)
• [AMBER] GB and Atom Type
  • Sally Pias (Wed Nov 18 2009 - 23:11:27 CST)
  • Alexander Seifert (Wed Nov 18 2009 - 02:58:32 CST)
• [AMBER] GBSA: dielectric symmetry
  • David A. Case (Thu Mar 05 2009 - 18:05:51 CST)
  • Giacomo Bastianelli (Thu Mar 05 2009 - 17:29:50 CST)
• [AMBER] general query: implicit solvation
  • Carlos Simmerling (Tue Sep 08 2009 - 05:11:24 CDT)
  • Jio M (Tue Sep 08 2009 - 04:28:49 CDT)
• [AMBER] generalized distance restraint
  • Rausch, Felix (Wed Mar 11 2009 - 02:39:05 CDT)
  • M. L. Dodson (Mon Mar 09 2009 - 11:51:19 CDT)
  • Carlos Simmerling (Mon Mar 09 2009 - 11:39:43 CDT)
  • Rausch, Felix (Mon Mar 09 2009 - 11:15:11 CDT)
  • Carlos Simmerling (Mon Mar 09 2009 - 10:13:50 CDT)
  • Rausch, Felix (Mon Mar 09 2009 - 08:48:01 CDT)
• [AMBER] Generate AM1-CM2 charges using antechamber
  • Sishi Tang (Fri Apr 03 2009 - 17:36:46 CDT)
• [AMBER] generate prmtop file from CHARMM psf file
  • Jeffrey (Mon Sep 21 2009 - 09:34:59 CDT)
• [AMBER] Generating LeAP file for helix containing non-standard amino acid
  • Brothers, Michael Charles (Fri Jun 19 2009 - 12:46:25 CDT)
  • FyD (Fri Jun 19 2009 - 00:41:54 CDT)
  • Brothers, Michael Charles (Thu Jun 18 2009 - 16:01:52 CDT)
  • FyD (Thu Jun 18 2009 - 14:55:34 CDT)
  • Brothers, Michael Charles (Thu Jun 18 2009 - 12:38:53 CDT)
  • FyD (Thu Jun 11 2009 - 01:48:27 CDT)
  • Brothers, Michael Charles (Wed Jun 10 2009 - 14:40:21 CDT)
  • David A. Case (Wed Jun 10 2009 - 14:23:36 CDT)
  • David A. Case (Wed Jun 10 2009 - 14:14:49 CDT)
  • Brothers, Michael Charles (Wed Jun 10 2009 - 13:26:32 CDT)
• [AMBER] generating top file using antechmaber
  • Wei Zhang (Thu Jan 29 2009 - 10:26:22 CST)
  • sarvin moghaddam (Thu Jan 29 2009 - 09:24:50 CST)
  • David A. Case (Thu Jan 29 2009 - 06:51:56 CST)
  • sarvin moghaddam (Wed Jan 28 2009 - 14:33:00 CST)
  • Wei Zhang (Wed Jan 28 2009 - 14:23:21 CST)
  • Wei Zhang (Wed Jan 28 2009 - 14:12:20 CST)
  • sarvin moghaddam (Wed Jan 28 2009 - 13:49:20 CST)
• [AMBER] get typeid of -1, sleap - AMBER with amoeba ff
  • Tomasio, Susana (Tue May 26 2009 - 10:51:18 CDT)
• [AMBER] Getting minimized .pdb file without non-polar hydrogens
  • Francesco Pietra (Mon Nov 09 2009 - 13:31:40 CST)
• [AMBER] Gly -> Ala mutation
  • manoj singh (Mon Nov 09 2009 - 10:26:00 CST)
  • Adrian Roitberg (Mon Nov 09 2009 - 10:13:11 CST)
  • manoj singh (Mon Nov 09 2009 - 10:10:40 CST)
  • Carlos Simmerling (Mon Nov 09 2009 - 09:13:08 CST)
  • manoj singh (Sun Nov 08 2009 - 15:18:37 CST)
  • Jason Swails (Sun Nov 08 2009 - 14:16:42 CST)
  • manoj singh (Sun Nov 08 2009 - 13:14:23 CST)
  • Jason Swails (Sun Nov 08 2009 - 11:53:29 CST)
  • manoj singh (Sun Nov 08 2009 - 11:25:46 CST)
• [AMBER] glycam and solvateoct command
  • Lachele Foley (Lists) (Wed Feb 18 2009 - 09:00:34 CST)
  • Heath Watts (Tue Feb 17 2009 - 16:31:35 CST)
  • Barbault Florent (Tue Feb 17 2009 - 14:13:58 CST)
  • Heath Watts (Tue Feb 17 2009 - 13:51:13 CST)
• [AMBER] GLYCAM: warnings by writing topology
  • Sergey Samsonov (Thu Jun 18 2009 - 07:49:31 CDT)
  • Bill Ross (Wed Jun 17 2009 - 12:32:43 CDT)
  • FyD (Wed Jun 17 2009 - 10:40:06 CDT)
  • Shubhra Gupta (Wed Jun 17 2009 - 05:33:50 CDT)
  • Sergey Samsonov (Wed Jun 17 2009 - 04:09:23 CDT)
  • Karl Kirschner (Wed Jun 17 2009 - 03:33:55 CDT)
  • Sergey Samsonov (Wed Jun 17 2009 - 03:18:33 CDT)
  • Sergey Samsonov (Wed Jun 17 2009 - 03:10:33 CDT)
  • Bill Ross (Wed Jun 17 2009 - 03:01:28 CDT)
  • Sergey Samsonov (Wed Jun 17 2009 - 02:50:46 CDT)
  • FyD (Wed Jun 17 2009 - 02:30:26 CDT)
  • Sergey Samsonov (Wed Jun 17 2009 - 01:38:56 CDT)
• [AMBER] glycopeptide Parametrization
  • FyD (Sat Jun 13 2009 - 02:40:00 CDT)
  • Ross Walker (Fri Jun 12 2009 - 11:09:37 CDT)
  • Karl Kirschner (Fri Jun 12 2009 - 10:06:17 CDT)
  • guardiani_at_fi.infn.it (Fri Jun 12 2009 - 09:06:24 CDT)
  • FyD (Fri Jun 12 2009 - 02:05:51 CDT)
  • Ahammadunny Pathiaseril (Wed Jun 10 2009 - 15:25:21 CDT)
  • guardiani_at_fi.infn.it (Wed Jun 10 2009 - 10:41:14 CDT)
• [AMBER] group distance restraint
  • XIAOHUICANG (Tue Sep 22 2009 - 14:36:03 CDT)
• [AMBER] GTP/ATP parameters
  • Steve Seibold (Mon Aug 31 2009 - 07:44:56 CDT)
• [AMBER] guessing the charge of a small molecule
  • Alan (Tue Jun 23 2009 - 03:06:51 CDT)
• [AMBER] H-bond information
  • Beale, John (Thu Feb 12 2009 - 09:32:30 CST)
• [AMBER] H-bond vs. VdW
  • case (Mon Jul 06 2009 - 12:29:49 CDT)
  • Cihan Aydin (Mon Jul 06 2009 - 10:13:39 CDT)
  • FyD (Sat Jul 04 2009 - 00:01:58 CDT)
  • Taufik Al-Sarraj (Fri Jul 03 2009 - 13:48:12 CDT)
• [AMBER] H-Bonds
  • Thomas Cheatham III (Wed Mar 04 2009 - 15:00:30 CST)
  • Beale, John (Thu Feb 26 2009 - 08:38:04 CST)
• [AMBER] Half charge reported during NN ?
  • Marek Maly (Wed Jun 24 2009 - 12:43:26 CDT)
  • case (Wed Jun 24 2009 - 12:31:45 CDT)
  • Marek Maly (Wed Jun 24 2009 - 11:33:54 CDT)
• [AMBER] Hard limit in Amber10?
  • Ross Walker (Wed Jun 24 2009 - 11:02:17 CDT)
  • Yang, Ping (Mon Jun 22 2009 - 20:52:39 CDT)
  • Yang, Ping (Sat Jun 20 2009 - 18:44:11 CDT)
  • Ross Walker (Sat Jun 20 2009 - 12:40:46 CDT)
  • Yang, Ping (Fri Jun 19 2009 - 19:21:14 CDT)
• [AMBER] have a question
  • Bill Ross (Tue Nov 17 2009 - 20:02:45 CST)
  • jacky zhao (Tue Nov 17 2009 - 19:54:36 CST)
• [AMBER] HB for each snapshot
  • Nicolas Sapay (Thu Nov 05 2009 - 02:30:51 CST)
  • Jason Swails (Wed Nov 04 2009 - 13:35:07 CST)
  • Marcin Krol (Wed Nov 04 2009 - 13:14:41 CST)
• [AMBER] hbond analysis
  • qiaoyan (Thu Dec 31 2009 - 02:40:22 CST)
  • Marcin Krol (Tue Oct 20 2009 - 10:42:35 CDT)
  • Carlos Simmerling (Mon Feb 09 2009 - 12:52:14 CST)
  • Bala subramanian (Mon Feb 09 2009 - 12:33:39 CST)
  • aneesh cna (Mon Feb 09 2009 - 11:55:25 CST)
• [AMBER] hbond analysis by ptraj- segmentation fault
  • Jayalakshmi Sridhar (Mon Nov 23 2009 - 12:36:25 CST)
  • Daniel Roe (Mon Nov 23 2009 - 11:49:23 CST)
  • Daniel Roe (Mon Nov 23 2009 - 11:42:49 CST)
  • Jayalakshmi Sridhar (Mon Nov 23 2009 - 09:51:00 CST)
• [AMBER] Hbond analysis output giving no hbonds
  • Jayalakshmi Sridhar (Tue Nov 24 2009 - 11:52:47 CST)
  • Thomas Cheatham (Tue Nov 24 2009 - 10:58:27 CST)
  • Jayalakshmi Sridhar (Tue Nov 24 2009 - 10:32:41 CST)
• [AMBER] Hbond analysis: Direction of the hydrogen
  • Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 16:56:50 CDT)
  • Shulin Zhuang (Tue Sep 08 2009 - 14:54:22 CDT)
  • Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 14:45:19 CDT)
• [AMBER] hbond-error in amber9
  • Alessandro S. Nascimento (Thu Apr 30 2009 - 05:46:02 CDT)
  • balaji nagarajan (Wed Apr 29 2009 - 21:09:17 CDT)
• [AMBER] hbond_DNAtraj
  • Jianyin Shao (Wed Jun 03 2009 - 11:52:41 CDT)
  • balaji nagarajan (Mon Jun 01 2009 - 12:08:15 CDT)
• [AMBER] hbond_ptraj
  • Thomas Cheatham (Wed May 27 2009 - 19:39:15 CDT)
  • balaji nagarajan (Mon May 25 2009 - 15:05:12 CDT)
• [AMBER] hbond_ptraj_eror
  • balaji nagarajan (Wed Apr 15 2009 - 01:53:29 CDT)
• [AMBER] Heat and Equilibrate Hybrid GB solvent?
  • Carlos Simmerling (Fri Jan 16 2009 - 15:21:27 CST)
  • Jason A. Ford-Green (Fri Jan 16 2009 - 15:14:41 CST)
• [AMBER] heating advice
  • Mark M Huntress (Wed May 27 2009 - 15:44:26 CDT)
• [AMBER] heating system in NEB
  • balaji nagarajan (Sat Dec 26 2009 - 05:29:35 CST)
• [AMBER] helical parameters
  • Bala subramanian (Mon Mar 23 2009 - 13:14:29 CDT)
  • balaji nagarajan (Mon Mar 23 2009 - 11:21:04 CDT)
• [AMBER] help
  • Ross Walker (Fri Jun 12 2009 - 11:02:06 CDT)
  • KIRTANA S (Fri Jun 12 2009 - 08:42:04 CDT)
  • Ross Walker (Fri Jan 30 2009 - 07:42:33 CST)
  • momo momo (Fri Jan 30 2009 - 06:35:22 CST)
• [AMBER] help needed for HID
  • FyD (Mon Jul 13 2009 - 15:27:13 CDT)
  • Marius Retegan (Sun Jul 12 2009 - 13:24:40 CDT)
  • s. Bill (Sun Jul 12 2009 - 13:16:08 CDT)
• [AMBER] Help needed in amber parallel installation
  • Ross Walker (Fri Mar 20 2009 - 10:40:30 CDT)
  • Carlos Simmerling (Fri Mar 20 2009 - 06:34:31 CDT)
  • sushobhan_at_iiar.res.in (Fri Mar 20 2009 - 01:39:36 CDT)
• [AMBER] help regarding force fields
  • Vikas Sharma (Fri Apr 17 2009 - 01:06:32 CDT)
• [AMBER] help regarding step size
  • Vikas Sharma (Wed Apr 22 2009 - 23:40:33 CDT)
  • Carlos Simmerling (Wed Apr 22 2009 - 06:03:28 CDT)
  • Vikas Sharma (Wed Apr 22 2009 - 05:50:27 CDT)
  • Carlos Simmerling (Wed Apr 22 2009 - 05:13:54 CDT)
  • Vikas Sharma (Wed Apr 22 2009 - 03:57:31 CDT)
• [AMBER] help with parameters for ions
  • rebeca (Tue Jun 02 2009 - 13:33:41 CDT)
  • InSuk Joung (Tue Jun 02 2009 - 13:14:46 CDT)
  • rebeca (Tue Jun 02 2009 - 12:38:00 CDT)
  • InSuk Joung (Tue Jun 02 2009 - 10:28:55 CDT)
  • rebeca (Tue Jun 02 2009 - 10:10:17 CDT)
  • David A. Case (Tue Jun 02 2009 - 08:46:40 CDT)
  • rebeca (Tue Jun 02 2009 - 07:46:14 CDT)
• [AMBER] help with RESP tutorial using antechamber and gaussian
  • Josmar R. da Rocha (Sun May 03 2009 - 12:59:23 CDT)
• [AMBER] help with TIP4P and mpi pmemd
  • Lizzard Man (Fri Dec 04 2009 - 16:47:08 CST)
  • Hashem Taha (Fri Dec 04 2009 - 15:44:44 CST)
  • Robert Duke (Fri Dec 04 2009 - 15:26:41 CST)
  • case (Fri Dec 04 2009 - 15:16:22 CST)
  • Hashem Taha (Fri Dec 04 2009 - 15:01:50 CST)
  • Robert Duke (Thu Dec 03 2009 - 23:58:58 CST)
  • Hashem Taha (Thu Dec 03 2009 - 23:29:38 CST)
  • Hashem Taha (Thu Dec 03 2009 - 20:26:57 CST)
  • Robert Duke (Thu Dec 03 2009 - 16:37:14 CST)
  • Hashem Taha (Thu Dec 03 2009 - 16:16:22 CST)
• [AMBER] Help with torsions in parm99.dat file
  • Wei Zhang (Mon Mar 09 2009 - 09:38:56 CDT)
  • Astrid Maaß (Mon Mar 09 2009 - 08:27:30 CDT)
  • Ross Walker (Sat Mar 07 2009 - 00:32:23 CST)
  • Gregersen, Brent (Fri Mar 06 2009 - 20:15:11 CST)
  • Ross Walker (Fri Mar 06 2009 - 18:52:05 CST)
  • Gregersen, Brent (Fri Mar 06 2009 - 16:44:17 CST)
• [AMBER] help- regarding - TMD
  • Carlos Simmerling (Tue Apr 21 2009 - 18:35:42 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 21 2009 - 17:40:36 CDT)
  • Carlos Simmerling (Tue Apr 21 2009 - 16:23:23 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 21 2009 - 15:25:15 CDT)
  • Carlos Simmerling (Tue Apr 21 2009 - 14:46:41 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 11:21:06 CDT)
  • Carlos Simmerling (Mon Apr 20 2009 - 10:30:52 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 10:28:30 CDT)
  • Carlos Simmerling (Mon Apr 20 2009 - 10:12:40 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 10:05:38 CDT)
  • balaji nagarajan (Thu Apr 16 2009 - 12:01:39 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Thu Apr 16 2009 - 08:30:22 CDT)
  • balaji nagarajan (Thu Apr 16 2009 - 00:21:26 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 15 2009 - 12:56:07 CDT)
  • balaji nagarajan (Wed Apr 15 2009 - 11:19:59 CDT)
• [AMBER] Help: An error happened when I calculate mm/pbsa
  • thirsty (Fri Apr 03 2009 - 02:11:19 CDT)
  • Carlos Simmerling (Thu Apr 02 2009 - 06:19:04 CDT)
  • thirsty (Thu Apr 02 2009 - 03:12:25 CDT)
• [AMBER] help_me to know the reason
  • Carlos Simmerling (Sat Apr 18 2009 - 05:53:50 CDT)
  • balaji nagarajan (Fri Apr 17 2009 - 23:30:07 CDT)
• [AMBER] heme (united-atom)
  • case (Mon Nov 30 2009 - 07:28:05 CST)
  • Simon Becker (Thu Nov 26 2009 - 08:34:59 CST)
  • case (Wed Nov 25 2009 - 10:39:10 CST)
  • Simon Becker (Wed Nov 25 2009 - 10:30:51 CST)
• [AMBER] Heme + Fe(II) + O2 + histidine parameter
  • FyD (Fri Sep 04 2009 - 02:43:00 CDT)
  • Haining Liu (Thu Sep 03 2009 - 16:13:09 CDT)
  • FyD (Thu Sep 03 2009 - 02:03:45 CDT)
  • Haining Liu (Wed Sep 02 2009 - 22:36:31 CDT)
• [AMBER] hi
  • David Watson (Mon Dec 21 2009 - 03:09:53 CST)
  • ashish pandey (Mon Dec 21 2009 - 00:45:40 CST)
• [AMBER] High energy during minimization
  • Ross Walker (Wed May 06 2009 - 01:24:30 CDT)
  • aneesh cna (Wed May 06 2009 - 00:58:00 CDT)
  • Bill Ross (Sun May 03 2009 - 13:00:32 CDT)
  • David A. Case (Sun May 03 2009 - 08:40:22 CDT)
  • aneesh cna (Sat May 02 2009 - 23:26:16 CDT)
• [AMBER] High RMSD for DNA: A to B transition study
  • David A. Case (Fri Mar 13 2009 - 07:00:40 CDT)
  • SENTHIL KUMAR (Fri Mar 13 2009 - 01:36:43 CDT)
  • David A. Case (Fri Mar 06 2009 - 08:57:02 CST)
  • BERGY (Fri Mar 06 2009 - 01:26:57 CST)
• [AMBER] High-temperature simulation ?
  • Carlos Simmerling (Wed Nov 11 2009 - 11:26:15 CST)
  • Chih-Ying Lin (Wed Nov 11 2009 - 09:36:16 CST)
• [AMBER] Histidine, which form?
  • M. L. Dodson (Mon Jun 15 2009 - 11:45:25 CDT)
  • Ross Walker (Mon Jun 15 2009 - 11:39:04 CDT)
  • s. Bill (Mon Jun 15 2009 - 11:28:27 CDT)
  • Ross Walker (Mon Jun 15 2009 - 10:06:49 CDT)
  • Carlos Simmerling (Mon Jun 15 2009 - 09:57:40 CDT)
  • s_bill36_at_yahoo.co.uk (Mon Jun 15 2009 - 09:54:05 CDT)
• [AMBER] Holding ligand rigid for minimization
  • Andrew Olson (Tue Jul 14 2009 - 13:23:31 CDT)
  • Andrew Olson (Tue Jul 14 2009 - 10:23:01 CDT)
  • Andrew Olson (Tue Jul 14 2009 - 10:14:38 CDT)
• [AMBER] how can i deal with large number atoms
  • Wang,Ying (Wed Feb 04 2009 - 23:04:23 CST)
• [AMBER] how can i include ANP residue
  • David Watson (Mon Dec 14 2009 - 16:44:30 CST)
  • Bradley Dickson (Mon Dec 14 2009 - 16:00:32 CST)
  • FyD (Mon Dec 14 2009 - 14:29:42 CST)
  • Bradley Dickson (Mon Dec 14 2009 - 09:07:50 CST)
• [AMBER] How can I use the charge I calculated (using mol2 file) ?
  • FyD (Tue Mar 03 2009 - 08:12:18 CST)
  • David A. Case (Tue Mar 03 2009 - 07:39:26 CST)
  • ÀÌÀ±°æ (Mon Mar 02 2009 - 19:39:37 CST)
  • David A. Case (Mon Mar 02 2009 - 08:56:54 CST)
  • ÀÌÀ±°æ (Mon Mar 02 2009 - 07:27:39 CST)
• [AMBER] How create PRMTOP and INCPRD for surface?
  • rrd (Sat Oct 17 2009 - 21:40:02 CDT)
• [AMBER] how many processors for parallel test
  • michael bane (Thu Jan 08 2009 - 07:56:59 CST)
  • David A. Case (Thu Jan 08 2009 - 07:44:52 CST)
  • michael bane (Thu Jan 08 2009 - 07:31:31 CST)
  • David A. Case (Thu Jan 08 2009 - 06:08:06 CST)
  • michael (Thu Jan 08 2009 - 05:01:41 CST)
• [AMBER] how much % of the total protein motion are described by the first eigenvector?
  • jackie (Thu Aug 27 2009 - 10:52:19 CDT)
  • Catein Catherine (Thu Aug 27 2009 - 05:02:37 CDT)
  • Hannes Loeffler (Thu Aug 27 2009 - 02:21:28 CDT)
  • Catein Catherine (Thu Aug 27 2009 - 00:58:27 CDT)
  • Hannes Loeffler (Wed Aug 26 2009 - 04:41:31 CDT)
  • Catein Catherine (Wed Aug 26 2009 - 04:05:17 CDT)
• [AMBER] How to add a hydrogen to the residue?
  • case (Wed Oct 14 2009 - 06:51:08 CDT)
  • xuemeiwang1103 (Tue Oct 13 2009 - 22:57:53 CDT)
• [AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis
  • TaoPaul (Mon Aug 24 2009 - 09:03:51 CDT)
• [AMBER] how to add charge in metal ion
  • bharat lakhani (Tue Apr 14 2009 - 07:49:44 CDT)
  • Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  • bharat lakhani (Tue Apr 07 2009 - 04:11:23 CDT)
• [AMBER] how to add charge on metal ions
  • bharat lakhani (Thu Apr 30 2009 - 01:44:46 CDT)
• [AMBER] how to add desired number of water
  • Ross Walker (Fri Dec 11 2009 - 21:47:19 CST)
  • Bill Ross (Fri Dec 11 2009 - 16:19:57 CST)
  • Hopkins, Robert (Fri Dec 11 2009 - 16:05:51 CST)
  • Bill Ross (Wed Dec 09 2009 - 11:46:59 CST)
  • Simon Becker (Wed Dec 09 2009 - 10:09:51 CST)
  • balaji nagarajan (Tue Dec 08 2009 - 21:18:49 CST)
• [AMBER] how to add desired numberof water
  • Dean Cuebas (Mon Dec 14 2009 - 20:40:25 CST)
  • Bill Ross (Fri Dec 11 2009 - 18:57:41 CST)
  • Richard Owczarzy (Fri Dec 11 2009 - 18:19:31 CST)
  • Hopkins, Robert (Fri Dec 11 2009 - 16:24:02 CST)
• [AMBER] how to add desirednumberof water
  • Hopkins, Robert (Sat Dec 12 2009 - 18:29:04 CST)
• [AMBER] how to add ions
  • bharat lakhani (Tue Jun 02 2009 - 02:25:46 CDT)
• [AMBER] how to add water for membrane, in Z direction only or xyz
  • xueqin pang (Thu Jun 04 2009 - 03:13:07 CDT)
• [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber
  • FyD (Sat May 02 2009 - 11:06:28 CDT)
  • Ye MEI (Sat May 02 2009 - 07:01:20 CDT)
  • Ye MEI (Sat May 02 2009 - 07:00:06 CDT)
• [AMBER] How to build amide bond etween two protein chains
  • FyD (Wed Jun 24 2009 - 01:18:25 CDT)
  • journal.update (Tue Jun 23 2009 - 23:36:07 CDT)
• [AMBER] How to build reference coordinate file for targeted MD
  • Ross Walker (Fri Feb 06 2009 - 02:14:14 CST)
  • gmail (Thu Feb 05 2009 - 23:20:59 CST)
  • xiaonan zhang (Thu Feb 05 2009 - 06:00:38 CST)
  • Carlos Simmerling (Thu Feb 05 2009 - 05:19:12 CST)
  • gmail (Thu Feb 05 2009 - 00:44:22 CST)
• [AMBER] How to calculate cavity volume from MD structures?
  • Jason A. Ford-Green (Wed Jan 21 2009 - 09:39:57 CST)
  • ben rodriguez (Tue Jan 20 2009 - 16:21:43 CST)
• [AMBER] how to calculate correct RMSF?
  • Catein Catherine (Mon Sep 14 2009 - 19:57:20 CDT)
  • case (Mon Sep 14 2009 - 07:33:29 CDT)
  • Catein Catherine (Mon Sep 14 2009 - 06:21:52 CDT)
• [AMBER] How to calculate SASA in vmd
  • Mannan (Wed Jun 17 2009 - 01:40:05 CDT)
• [AMBER] How to calculate the distance of CA of all residues in the trajectory
  • Thomas Leonard (Sun Jun 07 2009 - 20:45:54 CDT)
• [AMBER] How to change the input matrix for "analyze matrix" instruction?
  • ³ÂÒ»Ù© (Wed Nov 18 2009 - 10:18:51 CST)
  • cyk5056 (Tue Nov 17 2009 - 22:37:43 CST)
• [AMBER] how to choose different comformations for RESP
  • cgji (Tue Jun 02 2009 - 00:14:02 CDT)
  • xueqin pang (Mon Jun 01 2009 - 19:32:51 CDT)
• [AMBER] how to choose exclusion policy for GPCR
  • xueqin pang (Tue Jul 28 2009 - 21:12:33 CDT)
• [AMBER] How to choose the counter ions for proteins?
  • Chih-Ying Lin (Sat May 23 2009 - 13:16:49 CDT)
  • Ross Walker (Sat May 23 2009 - 13:09:27 CDT)
  • Chih-Ying Lin (Sat May 23 2009 - 00:42:40 CDT)
• [AMBER] How to compile and recompile ptraj?
  • cyk5056 (Sun Nov 29 2009 - 16:06:55 CST)
• [AMBER] How to consider the off centre charges
  • case (Wed Sep 02 2009 - 10:50:12 CDT)
  • Ashish Runthala (Wed Sep 02 2009 - 10:28:40 CDT)
• [AMBER] How to constrain the hydrogen bonding distances...
  • David A. Case (Wed Feb 18 2009 - 08:28:56 CST)
  • Carlos Simmerling (Wed Feb 18 2009 - 08:25:47 CST)
  • Majeed Shaik (Wed Feb 18 2009 - 08:11:37 CST)
• [AMBER] how to convert secstruct output file into plot or pictorial representation
  • Siddharth Rastogi (Tue Mar 31 2009 - 05:56:37 CDT)
• [AMBER] how to creat an mixture sovlent of hexane and water
  • TaoPaul (Sun Jun 28 2009 - 10:58:19 CDT)
• [AMBER] How to create FF for diamond.
  • rrd (Tue Oct 20 2009 - 01:16:07 CDT)
• [AMBER] How to create parameter file for unknown residue
  • Marius Retegan (Fri Apr 03 2009 - 05:50:30 CDT)
  • nicholus bhattacharjee (Fri Apr 03 2009 - 05:33:03 CDT)
• [AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine
  • Madhurima Jana (Thu Jun 18 2009 - 07:39:03 CDT)
• [AMBER] how to deal with aromatic nitro group with antechamber
  • case (Wed Sep 02 2009 - 21:15:14 CDT)
  • Lin Xu (Wed Sep 02 2009 - 17:04:13 CDT)
• [AMBER] How to delete the frames at specific intervals
  • Bala subramanian (Fri Apr 03 2009 - 04:55:35 CDT)
  • Mannan (Thu Apr 02 2009 - 20:16:49 CDT)
• [AMBER] How to denature DNA
  • balaji nagarajan (Wed Sep 09 2009 - 12:14:37 CDT)
  • Bill Ross (Wed Sep 09 2009 - 11:38:04 CDT)
  • balaji nagarajan (Tue Sep 08 2009 - 23:01:55 CDT)
  • Bill Ross (Tue Sep 08 2009 - 12:33:09 CDT)
  • Adrian Roitberg (Tue Sep 08 2009 - 12:12:00 CDT)
  • balaji nagarajan (Tue Sep 08 2009 - 11:58:36 CDT)
  • Adrian Roitberg (Tue Sep 08 2009 - 11:46:51 CDT)
  • balaji nagarajan (Tue Sep 08 2009 - 11:29:57 CDT)
  • Adrian Roitberg (Tue Sep 08 2009 - 09:04:30 CDT)
  • balaji nagarajan (Tue Sep 08 2009 - 09:00:43 CDT)
• [AMBER] How to derive charges from the output
  • bharat lakhani (Tue Sep 01 2009 - 03:46:12 CDT)
  • FyD (Mon Aug 31 2009 - 15:35:46 CDT)
  • bharat lakhani (Mon Aug 31 2009 - 08:43:15 CDT)
  • Barbault Florent (Mon Aug 31 2009 - 02:38:09 CDT)
  • bharat lakhani (Mon Aug 31 2009 - 00:33:21 CDT)
• [AMBER] How to find a protein's energy
  • Ashish Runthala (Sun Sep 06 2009 - 07:30:26 CDT)
  • Carlos Simmerling (Sun Sep 06 2009 - 06:49:53 CDT)
  • Ashish Runthala (Sat Sep 05 2009 - 22:48:01 CDT)
• [AMBER] How to find out residence time of water molecules
  • Hannes Loeffler (Fri Apr 03 2009 - 02:31:32 CDT)
  • Bala subramanian (Fri Apr 03 2009 - 01:12:18 CDT)
  • Mannan (Thu Apr 02 2009 - 20:52:36 CDT)
• [AMBER] How to find water-mediated hydrogen bond?
  • Hannes Loeffler (Thu Sep 03 2009 - 02:53:51 CDT)
  • Catein Catherine (Wed Sep 02 2009 - 09:10:37 CDT)
• [AMBER] How to fix specific atoms? (not residue)
  • Tom Joseph (Sat Jul 11 2009 - 17:01:04 CDT)
  • Myeong Lee (Sat Jul 11 2009 - 06:46:06 CDT)
• [AMBER] how to get amber 10
  • Ross Walker (Tue Feb 10 2009 - 21:20:33 CST)
  • Prem Prakash Pathak (Tue Feb 10 2009 - 20:42:37 CST)
• [AMBER] how to get hold of older versions of MKL ?
  • Ross Walker (Mon Oct 19 2009 - 11:58:54 CDT)
  • Jason Swails (Mon Oct 19 2009 - 05:54:45 CDT)
  • Nahoum Anthony (Mon Oct 19 2009 - 03:59:57 CDT)
• [AMBER] How to get the energy of a molecule in a whole system
  • Wang,Ying (Tue Feb 17 2009 - 10:28:39 CST)
• [AMBER] How to get total energy of a system from QM/MM
  • steinbrt_at_rci.rutgers.edu (Wed Dec 02 2009 - 03:53:03 CST)
  • gunajyoti das (Wed Dec 02 2009 - 02:56:06 CST)
• [AMBER] How to get total energy of asystem
  • case (Tue Nov 24 2009 - 06:36:30 CST)
  • steinbrt_at_rci.rutgers.edu (Tue Nov 24 2009 - 03:43:06 CST)
  • gunajyoti das (Tue Nov 24 2009 - 03:14:06 CST)
• [AMBER] how to give force values in TMD
  • balaji nagarajan (Wed Sep 02 2009 - 05:03:41 CDT)
• [AMBER] How to introduce the second protein molecule into simulation box?
  • Jason Swails (Fri Oct 16 2009 - 08:15:57 CDT)
  • Siddharth Rastogi (Fri Oct 16 2009 - 02:00:03 CDT)
• [AMBER] How to jude whether the trajectory is stable or not
  • Jeffrey (Thu Feb 12 2009 - 20:33:53 CST)
• [AMBER] How to keep the closest solvent mols to each atoms by PTRAJ?
  • u8613020_at_msg.ndhu.edu.tw (Thu Aug 06 2009 - 20:40:17 CDT)
• [AMBER] how to know that adequate equilibration from rmsd curve of equilibration
  • Cihan Aydin (Sun Jun 28 2009 - 11:19:07 CDT)
  • Naser Alijabbari (Sat Jun 27 2009 - 13:19:23 CDT)
  • Cihan Aydin (Sat Jun 27 2009 - 09:29:21 CDT)
  • Carlos Simmerling (Thu May 28 2009 - 13:15:09 CDT)
  • nicholus bhattacharjee (Thu May 28 2009 - 13:08:52 CDT)
  • Bill Ross (Thu May 28 2009 - 10:42:13 CDT)
  • nicholus bhattacharjee (Thu May 28 2009 - 08:37:29 CDT)
• [AMBER] How to know that the md is stable in equilibration run
  • nicholus bhattacharjee (Mon May 25 2009 - 06:54:25 CDT)
• [AMBER] how to launch XLEaP from SSH Secure Shell?
  • Thomas Patko (Wed Jul 22 2009 - 19:47:51 CDT)
  • David Watson (Wed Jul 22 2009 - 19:30:12 CDT)
  • Tom Joseph (Wed Jul 22 2009 - 18:24:56 CDT)
  • Robert Duke (Wed Jul 22 2009 - 18:07:24 CDT)
  • Yana Berezovskaya (Wed Jul 22 2009 - 17:44:45 CDT)
• [AMBER] how to make 50% aqueous TFE box?
  • FyD (Fri Sep 18 2009 - 19:22:35 CDT)
  • parul sharma (Fri Sep 18 2009 - 08:47:01 CDT)
• [AMBER] how to make the different/specific displacement of ligand around protein?
  • Chih-Ying Lin (Fri May 15 2009 - 18:55:49 CDT)
• [AMBER] How to obtain amber top and crd from pdb file with POPE lipids?
  • Hannes Loeffler (Mon Sep 28 2009 - 02:34:12 CDT)
  • decastro_at_physics.usyd.edu.au (Sun Sep 27 2009 - 23:52:20 CDT)
• [AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ?
  • Marek Maly (Tue Dec 22 2009 - 12:49:42 CST)
• [AMBER] how to ouput the electrostatic potential at a single atomic position?
  • Jose Borreguero (Thu Sep 17 2009 - 14:06:54 CDT)
• [AMBER] how to plot this kind of map?
  • Dechang Li (Thu Apr 09 2009 - 03:46:16 CDT)
  • lnin_1431_at_sina.com (Thu Apr 09 2009 - 03:36:45 CDT)
• [AMBER] How to prepare the acetate ion file in leap?
  • Balazs Jojart (Tue Oct 13 2009 - 02:36:03 CDT)
  • xuemeiwang1103 (Tue Oct 13 2009 - 02:05:57 CDT)
• [AMBER] How to prepare the coordinate and toplogy files in leap ?
  • case (Mon Sep 14 2009 - 06:56:08 CDT)
  • xuemeiwang1103 (Mon Sep 14 2009 - 04:03:59 CDT)
• [AMBER] how to pull a dna
  • balaji nagarajan (Tue Sep 01 2009 - 09:24:29 CDT)
  • Sam Danziger (Tue Sep 01 2009 - 06:17:09 CDT)
  • balaji nagarajan (Mon Aug 31 2009 - 21:39:10 CDT)
• [AMBER] How to put another 10 ligands into the simulation system?
  • David A. Case (Thu Dec 24 2009 - 11:17:11 CST)
  • Chih-Ying Lin (Wed Dec 23 2009 - 22:00:02 CST)
  • Chih-Ying Lin (Wed Dec 23 2009 - 10:51:23 CST)
  • Chih-Ying Lin (Wed Dec 23 2009 - 10:18:47 CST)
• [AMBER] How to read md trajectory for each time slice as an input coordinate
  • Myeong Lee (Mon Jul 27 2009 - 03:16:47 CDT)
• [AMBER] How to remove Hydrogen using ptraj
  • Thomas Cheatham III (Tue Sep 01 2009 - 12:25:10 CDT)
  • case (Tue Sep 01 2009 - 12:19:51 CDT)
  • Thomas Cheatham III (Tue Sep 01 2009 - 10:55:43 CDT)
  • Mannan (Tue Sep 01 2009 - 05:50:44 CDT)
• [AMBER] How to reproduce a parallel PMEMD run?
  • Robert Duke (Wed Mar 25 2009 - 18:45:49 CDT)
  • Siang Yip (Wed Mar 25 2009 - 17:33:56 CDT)
• [AMBER] how to restart the stopped MM-GBSA job
  • Zhongjie Liang (Sun Dec 06 2009 - 19:36:56 CST)
• [AMBER] How to restart the umbrella sampling jobs?
  • Gustavo Seabra (Tue Mar 03 2009 - 14:41:25 CST)
  • Ross Walker (Tue Mar 03 2009 - 10:00:04 CST)
  • Catein Catherine (Mon Mar 02 2009 - 23:52:16 CST)
• [AMBER] How to run LEaP in a shell file?
  • SongLin (Mon Dec 14 2009 - 07:45:03 CST)
  • case (Mon Dec 14 2009 - 06:44:29 CST)
  • SongLin (Mon Dec 14 2009 - 01:10:00 CST)
• [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent"
  • Carlos Simmerling (Tue Jan 20 2009 - 08:33:55 CST)
  • Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 03:03:39 CST)
• [AMBER] How to setup the pH value?
  • David A. Case (Tue May 19 2009 - 14:08:53 CDT)
  • Chih-Ying Lin (Sat May 16 2009 - 12:29:21 CDT)
• [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
  • Jianping Lin (Fri Aug 07 2009 - 15:32:47 CDT)
  • Ross Walker (Mon Aug 03 2009 - 14:38:23 CDT)
  • Jianping Lin (Mon Aug 03 2009 - 09:57:28 CDT)
• [AMBER] How to split mdcrd files
  • Thomas Cheatham (Sun Nov 15 2009 - 15:06:34 CST)
  • Carlos Simmerling (Sun Nov 15 2009 - 11:56:48 CST)
  • Jason Swails (Sun Nov 15 2009 - 11:35:24 CST)
  • Carlos Simmerling (Sun Nov 15 2009 - 11:28:06 CST)
  • shamoon siddiqui (Sun Nov 15 2009 - 11:22:52 CST)
• [AMBER] How to strip water for MM/GBSA calculations?
  • Carlos Simmerling (Fri Aug 21 2009 - 05:53:59 CDT)
  • Catein Catherine (Fri Aug 21 2009 - 05:38:27 CDT)
• [AMBER] How to take into account the charge in GAFF parameterization
  • cgji (Fri May 29 2009 - 01:49:44 CDT)
  • Workalemhu Berhanu (Thu May 28 2009 - 18:22:07 CDT)
• [AMBER] How to use AMBER 10 for PCA analysis.
  • Catein Catherine (Tue Sep 01 2009 - 10:30:56 CDT)
• [AMBER] how to use amber to verify the reason for difference in affinity
  • case (Sun Nov 29 2009 - 20:55:38 CST)
  • Josmar R. da Rocha (Tue Nov 24 2009 - 16:01:34 CST)
• [AMBER] how to use GLYCAM04 for carbonhydrate in amber9?
  • Karl Kirschner (Mon Nov 30 2009 - 02:53:27 CST)
  • sculiujl (Sun Nov 29 2009 - 21:39:08 CST)
• [AMBER] how to use those water models off the list in amber?
  • GZ Zhang (Thu Jan 22 2009 - 14:47:02 CST)
  • David A. Case (Thu Jan 22 2009 - 07:29:41 CST)
  • Lauren Wickstrom (Wed Jan 21 2009 - 17:58:22 CST)
  • GZ Zhang (Wed Jan 21 2009 - 15:39:50 CST)
• [AMBER] how to use two dimensions periodic boundary ?
  • Nancy (Wed May 20 2009 - 20:32:50 CDT)
• [AMBER] How to visualize PCA results without IED?
  • Shozeb Haider (Tue Jul 28 2009 - 06:02:22 CDT)
  • Vlad Cojocaru (Tue Jul 28 2009 - 05:42:05 CDT)
  • Hannes Loeffler (Tue Jul 28 2009 - 05:12:04 CDT)
  • Vlad Cojocaru (Tue Jul 28 2009 - 04:58:50 CDT)
  • Catein Catherine (Tue Jul 28 2009 - 04:30:22 CDT)
• [AMBER] hpux sander.serial failure info
  • David A. Case (Wed Apr 15 2009 - 07:07:45 CDT)
  • Yiannis Georgiadis (Wed Apr 15 2009 - 16:41:06 CDT)
  • David A. Case (Thu Apr 09 2009 - 06:56:51 CDT)
  • Yiannis Georgiadis (Thu Apr 09 2009 - 17:28:28 CDT)
• [AMBER] hydrogen bond
  • Ross Walker (Wed Mar 04 2009 - 10:39:49 CST)
  • Carlos Simmerling (Wed Mar 04 2009 - 05:20:53 CST)
  • . .. (Wed Mar 04 2009 - 05:12:33 CST)
• [AMBER] Hydrogen bond analysis for protein dna complex using ptraj
  • Thomas Cheatham (Sat Nov 14 2009 - 11:06:15 CST)
  • shamoon siddiqui (Sat Nov 14 2009 - 10:19:04 CST)
  • Carlos Simmerling (Sat Nov 14 2009 - 10:00:39 CST)
  • shamoon siddiqui (Sat Nov 14 2009 - 09:56:04 CST)
• [AMBER] hydrogen bond?
  • Jio M (Sun Aug 09 2009 - 06:29:23 CDT)
• [AMBER] I need a professional help about xleap and pdb file
  • Peter Gannett (Fri Feb 27 2009 - 08:17:31 CST)
  • nancy4619 (Fri Feb 27 2009 - 07:56:14 CST)
• [AMBER] i-APBS and apbs
  • Rilei Yu (Wed Nov 25 2009 - 05:14:15 CST)
  • Jason Swails (Tue Nov 24 2009 - 23:33:31 CST)
  • Robert Konecny (Tue Nov 24 2009 - 23:33:37 CST)
  • Rilei Yu (Tue Nov 24 2009 - 23:14:18 CST)
• [AMBER] iAPBS - how to set the right grid dimensions
  • Robert Konecny (Wed Oct 14 2009 - 08:21:07 CDT)
  • Oliver Kuhn (Wed Oct 14 2009 - 08:16:28 CDT)
  • Robert Konecny (Tue Oct 13 2009 - 12:12:04 CDT)
  • Oliver Kuhn (Tue Oct 13 2009 - 10:17:06 CDT)
  • Robert Konecny (Tue Oct 13 2009 - 09:42:12 CDT)
  • Oliver Kuhn (Tue Oct 13 2009 - 03:36:27 CDT)
• [AMBER] IDIVF and PN
  • Ross Walker (Thu Jul 16 2009 - 22:40:11 CDT)
  • s. Bill (Thu Jul 16 2009 - 07:11:27 CDT)
• [AMBER] IG not change at each restart of NPT simulation
  • Robert Duke (Fri Mar 20 2009 - 08:58:18 CDT)
  • Rajesh Raju (Fri Mar 20 2009 - 08:20:09 CDT)
  • Robert Duke (Thu Mar 19 2009 - 09:05:35 CDT)
  • Adrian Roitberg (Thu Mar 19 2009 - 08:30:10 CDT)
  • Robert Duke (Thu Mar 19 2009 - 08:24:02 CDT)
  • Rajesh Raju (Thu Mar 19 2009 - 07:54:26 CDT)
  • Hopkins, Robert (Wed Mar 18 2009 - 18:15:54 CDT)
  • Ross Walker (Wed Mar 18 2009 - 18:07:07 CDT)
  • Hopkins, Robert (Wed Mar 18 2009 - 17:55:33 CDT)
  • Adrian Roitberg (Wed Feb 18 2009 - 08:46:36 CST)
  • Robert Duke (Wed Feb 18 2009 - 08:15:00 CST)
  • Carlos Simmerling (Wed Feb 18 2009 - 08:04:47 CST)
  • Robert Duke (Wed Feb 18 2009 - 07:57:35 CST)
  • Jeffrey (Wed Feb 18 2009 - 06:49:47 CST)
• [AMBER] igb=0 vs. igb=6 give different answers
  • David A. Case (Thu Apr 09 2009 - 21:48:31 CDT)
  • Hugh Heldenbrand (Thu Apr 09 2009 - 15:51:02 CDT)
• [AMBER] IGB=7 vs IGB=5
  • Carlos Simmerling (Tue Jul 21 2009 - 08:51:22 CDT)
  • guardiani_at_fi.infn.it (Thu Jun 25 2009 - 06:20:15 CDT)
• [AMBER] implicit and explicit simulation: salt effect
  • David A. Case (Sat Jan 10 2009 - 10:26:45 CST)
  • David A. Case (Sat Jan 10 2009 - 10:23:08 CST)
  • David LeBard (Fri Jan 09 2009 - 22:23:24 CST)
  • David Watson (Fri Jan 09 2009 - 21:49:48 CST)
  • Catein Catherine (Fri Jan 09 2009 - 21:03:35 CST)
• [AMBER] implicit solvent (GB version2) MD simulation
  • Carlos Simmerling (Fri Jul 10 2009 - 10:57:57 CDT)
  • workalemahu berhanu (Fri Jul 10 2009 - 10:53:47 CDT)
• [AMBER] implicit solvent MD with fixed residues
  • David A. Case (Fri Dec 25 2009 - 14:22:31 CST)
  • Hakan Gunaydin (Thu Dec 24 2009 - 17:43:13 CST)
• [AMBER] implicit solvent simulation
  • Manish Kumar (Thu Aug 06 2009 - 01:53:54 CDT)
  • Ross Walker (Thu Aug 06 2009 - 01:32:24 CDT)
  • Manish Kumar (Thu Aug 06 2009 - 00:19:11 CDT)
  • Ashish Runthala (Thu Aug 06 2009 - 00:00:50 CDT)
  • Manish Kumar (Wed Aug 05 2009 - 23:49:30 CDT)
• [AMBER] implicit solvent simulation with new ligand
  • Manish Kumar (Thu Aug 06 2009 - 22:29:37 CDT)
• [AMBER] implicit_run_error
  • case (Fri Nov 20 2009 - 08:53:31 CST)
  • balaji nagarajan (Thu Nov 19 2009 - 12:37:21 CST)
• [AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list.
  • Ross Walker (Sat Feb 28 2009 - 16:19:16 CST)
• [AMBER] Improper dihedrals between residues?
  • Bill Ross (Tue Jun 09 2009 - 16:17:03 CDT)
  • Ben Roberts (Tue Jun 09 2009 - 14:12:07 CDT)
  • Bill Ross (Tue Jun 09 2009 - 14:04:02 CDT)
  • Carlos Simmerling (Tue Jun 09 2009 - 12:51:40 CDT)
  • David A. Case (Tue Jun 09 2009 - 12:14:57 CDT)
  • Carlos Simmerling (Tue Jun 09 2009 - 11:28:04 CDT)
  • Ben Roberts (Tue Jun 09 2009 - 11:11:15 CDT)
• [AMBER] Improper dihedrals from .off and .lib files
  • David A. Case (Thu Jun 18 2009 - 06:28:40 CDT)
  • Johan Sund (Thu Jun 18 2009 - 05:15:37 CDT)
• [AMBER] improper torsion problem
  • Bill Ross (Wed Jun 17 2009 - 02:47:12 CDT)
  • Youn Kyeung Lee (Tue Jun 16 2009 - 21:36:14 CDT)
• [AMBER] Increase Temperature to 550 K
  • Carlos Simmerling (Fri Nov 13 2009 - 07:35:28 CST)
  • FyD (Fri Nov 13 2009 - 05:43:48 CST)
  • Chih-Ying Lin (Thu Nov 12 2009 - 22:36:07 CST)
  • Carlos Simmerling (Thu Nov 12 2009 - 16:29:13 CST)
  • Chih-Ying Lin (Thu Nov 12 2009 - 15:59:11 CST)
  • Carlos Simmerling (Thu Nov 12 2009 - 08:22:08 CST)
  • case (Thu Nov 12 2009 - 06:55:18 CST)
  • FyD (Thu Nov 12 2009 - 01:51:24 CST)
  • Carlos Simmerling (Wed Nov 11 2009 - 15:14:24 CST)
  • Chih-Ying Lin (Wed Nov 11 2009 - 15:08:12 CST)
  • Carlos Simmerling (Wed Nov 11 2009 - 11:52:55 CST)
  • Chih-Ying Lin (Wed Nov 11 2009 - 09:27:41 CST)
• [AMBER] Influence about HIS-HIE-HIS-HIP
  • Rilei Yu (Thu Apr 30 2009 - 19:37:17 CDT)
  • David A. Case (Thu Apr 30 2009 - 09:27:02 CDT)
  • Rilei Yu (Wed Apr 29 2009 - 22:25:48 CDT)
• [AMBER] inhibitor prepin not recognized in xleap
  • Bill Ross (Fri Oct 23 2009 - 13:32:03 CDT)
  • Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:05:46 CDT)
  • Jayalakshmi Sridhar (Fri Oct 23 2009 - 10:56:40 CDT)
• [AMBER] Inorganic Phosphate Parameters
  • Cihan Aydin (Fri Dec 18 2009 - 14:19:21 CST)
• [AMBER] Inorganic Phosphate Parameters. .
  • case (Sat Dec 19 2009 - 11:39:28 CST)
  • Jason Swails (Fri Dec 18 2009 - 16:54:39 CST)
  • Don.Bashford_at_stjude.org (Fri Dec 18 2009 - 16:12:58 CST)
• [AMBER] inpcrd and prmtop
  • Gustavo Seabra (Tue Mar 03 2009 - 14:20:38 CST)
  • FyD (Tue Mar 03 2009 - 04:19:43 CST)
  • m m (Tue Mar 03 2009 - 04:08:51 CST)
  • Hannes Loeffler (Tue Mar 03 2009 - 03:37:16 CST)
  • m m (Tue Mar 03 2009 - 03:27:06 CST)
• [AMBER] input coordinates for vdW transition step in Amber 10 TI
  • steinbrt_at_rci.rutgers.edu (Thu Jun 11 2009 - 05:42:51 CDT)
  • Ye MEI (Thu Jun 11 2009 - 03:22:34 CDT)
  • Tom Joseph (Wed Jun 10 2009 - 20:02:51 CDT)
  • Jodi Hadden (Wed Jun 10 2009 - 15:27:16 CDT)
• [AMBER] input error in TI calculation
  • David A. Case (Wed Apr 29 2009 - 13:48:04 CDT)
  • Hannes Wallnoefer (Wed Apr 29 2009 - 10:40:58 CDT)
• [AMBER] input file
  • Bill Ross (Thu Sep 10 2009 - 11:51:10 CDT)
  • Ashish Runthala (Thu Sep 10 2009 - 09:05:32 CDT)
  • Jenny Iskrenova (Thu Sep 10 2009 - 08:05:03 CDT)
  • Carlos Simmerling (Thu Sep 10 2009 - 06:03:17 CDT)
  • Mag. Thomas Taylor (Thu Sep 10 2009 - 05:48:06 CDT)
• [AMBER] input file / skinnb
  • Mag. Thomas Taylor (Thu Sep 17 2009 - 00:50:16 CDT)
  • Robert Duke (Wed Sep 16 2009 - 09:23:06 CDT)
  • case (Wed Sep 16 2009 - 06:56:01 CDT)
  • Mag. Thomas Taylor (Wed Sep 16 2009 - 02:49:32 CDT)
• [AMBER] Input file of the second stage RESP fitting
  • Cen Gao (Tue Mar 17 2009 - 16:24:24 CDT)
  • FyD (Tue Mar 17 2009 - 08:32:58 CDT)
  • Cen Gao (Mon Mar 16 2009 - 23:29:17 CDT)
• [AMBER] Inquiries about antechamber
  • jackie (Thu Aug 27 2009 - 10:48:24 CDT)
  • FyD (Thu Aug 27 2009 - 01:15:55 CDT)
  • Yikan Chen (Wed Aug 26 2009 - 21:05:40 CDT)
  • Nicholas Musolino (Wed Aug 26 2009 - 16:02:21 CDT)
  • Yikan Chen (Wed Aug 26 2009 - 12:07:20 CDT)
• [AMBER] Install
  • ÁÖżº (Sun Apr 26 2009 - 08:45:45 CDT)
• [AMBER] install Amber 10 to Macbook
  • David Watson (Sun Feb 15 2009 - 13:52:36 CST)
  • Tyler Luchko (Sun Feb 15 2009 - 13:27:53 CST)
  • David A. Case (Sat Feb 14 2009 - 17:17:53 CST)
  • Adrien Delmont (Sat Feb 14 2009 - 05:06:50 CST)
• [AMBER] install ambertools
  • case (Thu Sep 17 2009 - 08:40:28 CDT)
  • Karl Kirschner (Thu Sep 17 2009 - 07:55:22 CDT)
• [AMBER] install and test Amber 10 parallel on Ubuntu 8.10
  • Jim Parker (Sat Apr 11 2009 - 19:20:25 CDT)
• [AMBER] Installation directory
  • Atro Tossavainen (Mon May 25 2009 - 03:10:34 CDT)
  • Thomas Spraggins (Thu May 21 2009 - 14:18:13 CDT)
  • David A. Case (Thu May 21 2009 - 13:19:28 CDT)
  • Thomas Spraggins (Thu May 21 2009 - 13:02:59 CDT)
• [AMBER] Installation error - Amber10
  • David A. Case (Thu Jan 29 2009 - 12:33:33 CST)
  • Andreas Svrcek-Seiler (Thu Jan 29 2009 - 05:52:44 CST)
  • Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 05:47:44 CST)
• [AMBER] Installation issue
  • Bill Ross (Wed Sep 23 2009 - 11:36:59 CDT)
  • Bill Ross (Wed Sep 23 2009 - 11:29:28 CDT)
  • Tom Joseph (Wed Sep 23 2009 - 11:08:33 CDT)
  • Ashveen Seenauth (Wed Sep 23 2009 - 10:54:27 CDT)
  • Tom Joseph (Wed Sep 23 2009 - 10:43:42 CDT)
  • Ashveen Seenauth (Wed Sep 23 2009 - 10:41:53 CDT)
  • Tom Joseph (Wed Sep 23 2009 - 10:35:44 CDT)
  • Ashveen Seenauth (Wed Sep 23 2009 - 10:28:55 CDT)
  • Bill Ross (Tue Sep 22 2009 - 13:28:43 CDT)
  • Tom Joseph (Tue Sep 22 2009 - 13:16:01 CDT)
  • Ashveen Seenauth (Tue Sep 22 2009 - 12:59:46 CDT)
  • Bill Ross (Tue Sep 22 2009 - 12:59:22 CDT)
  • Bill Ross (Tue Sep 22 2009 - 12:55:34 CDT)
  • Bill Ross (Tue Sep 22 2009 - 12:50:28 CDT)
  • Tom Joseph (Tue Sep 22 2009 - 12:41:51 CDT)
  • Ashveen Seenauth (Tue Sep 22 2009 - 12:25:12 CDT)
  • Tom Joseph (Tue Sep 22 2009 - 11:55:20 CDT)
  • Ashveen Seenauth (Tue Sep 22 2009 - 11:45:13 CDT)
  • Bill Ross (Tue Sep 22 2009 - 11:31:47 CDT)
  • Ashveen Seenauth (Tue Sep 22 2009 - 11:17:49 CDT)
• [AMBER] installation of Amber on OSX
  • Jason Swails (Wed Oct 14 2009 - 17:41:31 CDT)
  • case (Wed Oct 14 2009 - 17:10:04 CDT)
  • David Watson (Wed Oct 14 2009 - 17:03:51 CDT)
  • Ramgopal Mettu (Wed Oct 14 2009 - 16:46:59 CDT)
• [AMBER] installation of RESP programm
  • FyD (Fri Jun 26 2009 - 04:15:39 CDT)
  • subarna thakur (Fri Jun 26 2009 - 03:52:57 CDT)
• [AMBER] Installation on MacOSX
  • Alan (Tue Dec 15 2009 - 10:11:20 CST)
  • David Watson (Tue Dec 15 2009 - 06:54:06 CST)
  • Jason Swails (Tue Dec 15 2009 - 05:43:47 CST)
  • Alan (Tue Dec 15 2009 - 04:26:48 CST)
  • David Watson (Mon Dec 14 2009 - 14:01:52 CST)
  • Freedman, Tanya (Mon Dec 14 2009 - 12:59:06 CST)
• [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala
  • Jason Swails (Wed Nov 18 2009 - 13:00:09 CST)
  • Wallace Kunin (Wed Nov 18 2009 - 08:21:57 CST)
  • case (Tue Nov 17 2009 - 11:29:42 CST)
  • Wallace Kunin (Tue Nov 17 2009 - 09:20:13 CST)
  • Mark Williamson (Mon Nov 16 2009 - 13:49:58 CST)
  • Wallace Kunin (Mon Nov 16 2009 - 13:07:20 CST)
  • Mark Williamson (Mon Nov 16 2009 - 11:37:18 CST)
  • Wallace Kunin (Mon Nov 16 2009 - 10:43:18 CST)
• [AMBER] Installing Amber10 on Ubuntu
  • Rodrigo Galindo (Wed Jul 29 2009 - 14:49:33 CDT)
  • David Dubins (Wed Jul 29 2009 - 13:50:12 CDT)
• [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.
  • oguz gurbulak (Tue Sep 22 2009 - 01:46:27 CDT)
  • David Dubins (Mon Sep 21 2009 - 18:02:47 CDT)
• [AMBER] installing AmberTools on Windows machines
  • David A. Case (Wed Mar 11 2009 - 15:27:07 CDT)
• [AMBER] Installing of amber10
  • case (Wed Jul 08 2009 - 06:42:02 CDT)
  • Rilei Yu (Wed Jul 08 2009 - 03:34:24 CDT)
• [AMBER] installing of amber10 problem
  • Rilei Yu (Wed Jul 08 2009 - 03:47:13 CDT)
• [AMBER] installing resp on linux 64bit
  • aditya chhikara (Thu Mar 26 2009 - 16:36:50 CDT)
  • FyD (Thu Mar 26 2009 - 14:37:22 CDT)
  • aditya chhikara (Thu Mar 26 2009 - 12:24:27 CDT)
• [AMBER] Iron 2+ parameters
  • FyD (Mon Feb 16 2009 - 12:25:45 CST)
  • Syed Tarique Moin (Mon Feb 16 2009 - 10:25:34 CST)
  • Hrvoje Brkiæ (Mon Feb 16 2009 - 07:53:57 CST)
• [AMBER] iron in prepi file generation for heme
  • David A. Case (Thu Dec 24 2009 - 11:27:07 CST)
  • Donald Keidel (Wed Dec 23 2009 - 16:27:10 CST)
• [AMBER] Irregularity in box during md
  • Bill Ross (Tue Feb 10 2009 - 11:24:12 CST)
  • Carlos Simmerling (Tue Feb 10 2009 - 04:57:02 CST)
  • parul sharma (Tue Feb 10 2009 - 04:35:18 CST)
• [AMBER] Is it possible to simulate transmembrane protein with GB model ?
  • cgji (Mon Nov 02 2009 - 14:52:44 CST)
• [AMBER] Is it taking too much time
  • Nicolas Sapay (Tue Nov 03 2009 - 02:57:55 CST)
  • nicholus bhattacharjee (Mon Nov 02 2009 - 23:35:04 CST)
  • nicholus bhattacharjee (Mon Nov 02 2009 - 23:14:26 CST)
  • Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  • Nicolas SAPAY (Mon Nov 02 2009 - 09:00:58 CST)
  • nicholus bhattacharjee (Mon Nov 02 2009 - 08:40:25 CST)
  • Nicolas SAPAY (Mon Nov 02 2009 - 08:19:17 CST)
  • manoj singh (Mon Nov 02 2009 - 07:50:21 CST)
  • nicholus bhattacharjee (Mon Nov 02 2009 - 02:37:28 CST)
  • manoj singh (Mon Nov 02 2009 - 01:31:07 CST)
  • nicholus bhattacharjee (Mon Nov 02 2009 - 00:08:46 CST)
• [AMBER] Is it the correct procedures to strip water for MM/GBSA calculations?
  • Catein Catherine (Tue Aug 18 2009 - 00:06:18 CDT)
• [AMBER] Is it the way to do simulation in vacuum
  • Ross Walker (Fri Oct 30 2009 - 14:15:01 CDT)
  • Carlos Simmerling (Fri Oct 30 2009 - 11:10:22 CDT)
  • Jason Swails (Fri Oct 30 2009 - 11:06:14 CDT)
  • Carlos Simmerling (Fri Oct 30 2009 - 08:26:20 CDT)
  • case (Fri Oct 30 2009 - 07:49:46 CDT)
  • nicholus bhattacharjee (Fri Oct 30 2009 - 06:11:03 CDT)
  • Carlos Simmerling (Fri Oct 30 2009 - 05:21:49 CDT)
  • nicholus bhattacharjee (Fri Oct 30 2009 - 05:18:45 CDT)
• [AMBER] Is iwrap mapping water molecules to my protein cavity?
  • Carlos Simmerling (Mon Oct 12 2009 - 14:28:12 CDT)
  • Bill Ross (Mon Oct 12 2009 - 14:12:19 CDT)
  • ben rodriguez (Mon Oct 12 2009 - 13:55:23 CDT)
• [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation?
  • Catein Catherine (Wed Jul 08 2009 - 04:45:41 CDT)
• [AMBER] is rst file the last structure?
  • case (Sun Nov 15 2009 - 08:33:16 CST)
  • Jason Swails (Sat Nov 14 2009 - 11:18:22 CST)
  • qiaoyan (Fri Nov 13 2009 - 22:52:40 CST)
• [AMBER] Is the integral value from RDF the same as average number of atoms?
  • Gustaf Olsson (go22bi_at_student.hik.se) (Wed Nov 18 2009 - 15:56:31 CST)
• [AMBER] Is the result of sander same as that of pmemd?
  • Ross Walker (Sat Jun 13 2009 - 11:12:51 CDT)
  • Catein Catherine (Fri Jun 12 2009 - 21:55:10 CDT)
  • Robert Duke (Fri Jun 12 2009 - 09:09:45 CDT)
  • Catein Catherine (Fri Jun 12 2009 - 09:04:38 CDT)
• [AMBER] Issue related to saving the vector in ptraj
  • S.Sundar Raman (Sat May 16 2009 - 07:41:10 CDT)
• [AMBER] Issue related to vector saving
  • S.Sundar Raman (Fri May 15 2009 - 08:35:01 CDT)
• [AMBER] J coupling constant calculation
  • Gustavo Seabra (Tue Jun 02 2009 - 09:18:08 CDT)
  • Dechang Li (Fri May 29 2009 - 00:31:06 CDT)
  • Neha Gandhi (Fri May 29 2009 - 00:24:37 CDT)
• [AMBER] Ki and G
  • Marek Maly (Tue Sep 15 2009 - 06:58:07 CDT)
  • case (Mon Sep 14 2009 - 15:24:05 CDT)
  • steinbrt_at_rci.rutgers.edu (Mon Sep 14 2009 - 15:09:55 CDT)
  • Marek Maly (Mon Sep 14 2009 - 13:41:33 CDT)
  • case (Mon Sep 14 2009 - 12:23:49 CDT)
  • Marek Maly (Mon Sep 14 2009 - 12:02:36 CDT)
  • Adrian Roitberg (Mon Sep 14 2009 - 09:28:57 CDT)
  • steinbrt_at_rci.rutgers.edu (Mon Sep 14 2009 - 06:59:40 CDT)
  • s. Bill (Mon Sep 14 2009 - 06:39:20 CDT)
• [AMBER] Kinetics
  • Soumya Lipsa Rath (Tue Sep 08 2009 - 01:36:18 CDT)
  • case (Fri Sep 04 2009 - 14:29:24 CDT)
  • Soumya Lipsa Rath (Fri Sep 04 2009 - 01:39:54 CDT)
• [AMBER] Langevin dynamics
  • David A. Case (Mon Feb 02 2009 - 13:24:59 CST)
  • Antonios Samiotakis (Mon Feb 02 2009 - 11:54:31 CST)
• [AMBER] Langevin Dynamics in AMBER10
  • Carlos Simmerling (Fri Jul 24 2009 - 07:01:28 CDT)
  • Biswaranjan Meher (Thu Jul 23 2009 - 18:12:59 CDT)
  • Carlos Simmerling (Thu Jul 23 2009 - 16:57:44 CDT)
  • Biswaranjan Meher (Thu Jul 23 2009 - 16:54:58 CDT)
• [AMBER] Large File Support
  • Ross Walker (Thu Oct 15 2009 - 13:14:01 CDT)
  • Beale, John (Thu Oct 15 2009 - 07:40:27 CDT)
• [AMBER] large resp charges for non-natural amino acid
  • Arturas Ziemys (Sat Jan 31 2009 - 11:03:44 CST)
  • Arturas Ziemys (Sat Jan 31 2009 - 11:03:09 CST)
  • FyD (Thu Jan 29 2009 - 15:58:34 CST)
  • Arturas Ziemys (Thu Jan 29 2009 - 15:38:12 CST)
  • FyD (Thu Jan 29 2009 - 14:57:51 CST)
  • Arturas Ziemys (Thu Jan 29 2009 - 09:10:50 CST)
  • FyD (Wed Jan 28 2009 - 22:04:11 CST)
  • Arturas Ziemys (Tue Jan 27 2009 - 16:40:49 CST)
• [AMBER] LCPO or Molsurf?
  • Dong Xu (Sat May 02 2009 - 22:14:55 CDT)
• [AMBER] leap and chirality
  • Wei Zhang (Tue Mar 24 2009 - 07:55:47 CDT)
  • Karl Kirschner (Tue Mar 24 2009 - 03:11:38 CDT)
  • Wei Zhang (Mon Mar 23 2009 - 13:36:54 CDT)
  • Karl Kirschner (Mon Mar 23 2009 - 09:05:56 CDT)
  • David A. Case (Mon Mar 23 2009 - 08:16:14 CDT)
  • Karl Kirschner (Mon Mar 23 2009 - 04:54:29 CDT)
• [AMBER] Leap Questions...
  • Ross Walker (Sun Jul 05 2009 - 23:01:34 CDT)
  • Cihan Aydin (Sat Jul 04 2009 - 20:41:39 CDT)
• [AMBER] Leap warning
  • Bill Ross (Wed Sep 09 2009 - 11:49:05 CDT)
  • case (Wed Sep 09 2009 - 06:31:36 CDT)
  • Ashish Runthala (Wed Sep 09 2009 - 02:21:03 CDT)
  • manoj singh (Wed Sep 09 2009 - 00:38:33 CDT)
• [AMBER] Lennard Jones potential
  • Ross Walker (Mon Aug 03 2009 - 14:28:06 CDT)
  • Rizwan Tai (Mon Aug 03 2009 - 12:13:16 CDT)
• [AMBER] Lennard Jones Potential A and B coefficients in Topology file
  • Crowley, Michael (Sat Oct 31 2009 - 12:32:12 CDT)
  • Peter Schmidtke (Sat Oct 31 2009 - 10:10:12 CDT)
  • Tom Joseph (Sat Oct 31 2009 - 09:59:14 CDT)
  • Tom Joseph (Sat Oct 31 2009 - 00:23:03 CDT)
  • Peter Schmidtke (Fri Oct 30 2009 - 19:09:46 CDT)
  • Tom Joseph (Fri Oct 30 2009 - 17:04:43 CDT)
  • Peter Schmidtke (Fri Oct 30 2009 - 13:32:32 CDT)
• [AMBER] LES and NEB problem
  • Carlos Simmerling (Thu Oct 15 2009 - 13:09:34 CDT)
  • Jason Swails (Thu Oct 15 2009 - 13:09:14 CDT)
  • Rima Chaudhuri (Thu Oct 15 2009 - 12:53:41 CDT)
  • Carlos Simmerling (Thu Oct 15 2009 - 11:54:18 CDT)
  • Rima Chaudhuri (Thu Oct 15 2009 - 11:50:08 CDT)
  • Carlos Simmerling (Wed Oct 14 2009 - 09:14:04 CDT)
  • Rima Chaudhuri (Tue Oct 13 2009 - 14:35:37 CDT)
• [AMBER] Ligand covalent bonds appear to be broken
  • Thomas Cheatham (Fri Oct 30 2009 - 10:48:07 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 08:43:25 CDT)
  • Jason Swails (Fri Oct 30 2009 - 08:11:03 CDT)
  • Tom Joseph (Fri Oct 30 2009 - 06:53:44 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 01:32:39 CDT)
• [AMBER] Ligand Diffusion Studies?
  • Jason A. Ford-Green (Thu Jan 15 2009 - 11:42:03 CST)
• [AMBER] ligand exiting a protein cavity
  • moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:27:58 CDT)
• [AMBER] ligand parameterization
  • Ilyas Yildirim (Thu Nov 26 2009 - 18:13:09 CST)
  • Jason Swails (Thu Nov 26 2009 - 16:12:34 CST)
  • Nahoum Anthony (Thu Nov 26 2009 - 11:19:47 CST)
  • Jason Swails (Thu Nov 26 2009 - 09:47:58 CST)
  • case (Thu Nov 26 2009 - 09:09:05 CST)
  • Nahoum Anthony (Thu Nov 26 2009 - 04:49:51 CST)
• [AMBER] ligand QM/semi-empirical coords optmisation
  • Francesco Pietra (Fri Jun 05 2009 - 13:17:45 CDT)
  • Junmei Wang (Fri Jun 05 2009 - 10:01:32 CDT)
  • Alan (Thu Jun 04 2009 - 13:05:27 CDT)
  • David A. Case (Thu Jun 04 2009 - 10:06:28 CDT)
  • Alan (Thu Jun 04 2009 - 09:19:28 CDT)
  • David A. Case (Tue May 26 2009 - 06:41:25 CDT)
  • Alan (Tue May 26 2009 - 05:55:09 CDT)
• [AMBER] ligand/protein minimization
  • Andrew Olson (Mon Jul 13 2009 - 12:10:18 CDT)
  • case (Mon Jul 13 2009 - 11:29:06 CDT)
  • Andrew Olson (Mon Jul 13 2009 - 10:53:11 CDT)
  • case (Sun Jul 12 2009 - 21:32:29 CDT)
  • Andrew Olson (Fri Jul 10 2009 - 16:00:26 CDT)
• [AMBER] LINMIN failure notice
  • Ross Walker (Fri Sep 18 2009 - 18:41:33 CDT)
  • Bill Ross (Fri Sep 18 2009 - 11:18:41 CDT)
  • case (Fri Sep 18 2009 - 06:38:33 CDT)
  • Ashish Runthala (Fri Sep 18 2009 - 05:46:09 CDT)
  • Jio M (Fri Sep 18 2009 - 05:20:18 CDT)
• [AMBER] linux install problem
  • Gustavo Seabra (Thu Feb 19 2009 - 14:47:18 CST)
  • Andrew Olson (Thu Feb 19 2009 - 12:44:14 CST)
• [AMBER] linux version for Amber10
  • liangchen88_at_ucla.edu (Sat Nov 07 2009 - 21:59:53 CST)
  • Jason Swails (Sat Nov 07 2009 - 21:38:41 CST)
  • Sudeep Narayan Banerjee (Sat Nov 07 2009 - 20:56:19 CST)
  • Peter Schmidtke (Sat Nov 07 2009 - 09:58:18 CST)
  • liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
  • liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
• [AMBER] lipid bliayers
  • Hannes Loeffler (Wed Mar 18 2009 - 08:17:04 CDT)
  • Urszula Uciechowska (Wed Mar 18 2009 - 08:00:32 CDT)
• [AMBER] lipid membrane(dppc) in amber
  • Myunggi Yi (Fri May 22 2009 - 08:45:20 CDT)
  • xueqin pang (Fri May 22 2009 - 04:01:26 CDT)
  • xueqin pang (Fri May 22 2009 - 03:42:54 CDT)
• [AMBER] Lisp library for amber analysis?
  • Eric Shamay (Wed Nov 11 2009 - 15:54:12 CST)
• [AMBER] LJ parameters for HO and HW
  • Bill Ross (Mon Nov 09 2009 - 11:29:40 CST)
  • steinbrt_at_rci.rutgers.edu (Mon Nov 09 2009 - 02:23:20 CST)
  • Jason Swails (Sun Nov 08 2009 - 09:14:45 CST)
  • manoj singh (Sun Nov 08 2009 - 00:09:13 CST)
  • Jason Swails (Sat Nov 07 2009 - 23:50:03 CST)
  • manoj singh (Sat Nov 07 2009 - 23:21:22 CST)
• [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol
  • FyD (Mon Sep 28 2009 - 13:23:20 CDT)
  • Ganesh Kamath (Mon Sep 28 2009 - 12:03:13 CDT)
• [AMBER] lmod calculation for complexe
  • . .. (Wed Feb 11 2009 - 03:09:04 CST)
• [AMBER] load .crd & .top in xleap
  • oguz gurbulak (Sun Sep 13 2009 - 14:20:26 CDT)
  • vallespardojl_at_chem.leidenuniv.nl (Sun Sep 13 2009 - 09:21:15 CDT)
• [AMBER] Load protein complex to Xleap (Combine)
  • David A. Case (Sun Mar 29 2009 - 13:41:13 CDT)
  • Rilei Yu (Sat Mar 28 2009 - 23:00:00 CDT)
  • Rilei Yu (Sat Mar 28 2009 - 22:07:47 CDT)
  • David A. Case (Sat Mar 28 2009 - 21:26:58 CDT)
  • Rilei Yu (Sat Mar 28 2009 - 20:17:21 CDT)
  • David A. Case (Sat Mar 28 2009 - 16:39:35 CDT)
  • Rilei Yu (Fri Mar 27 2009 - 21:30:04 CDT)
• [AMBER] loading a following attached protein in amber 10
  • albert albert (Tue Sep 08 2009 - 12:43:55 CDT)
  • case (Tue Sep 08 2009 - 12:27:47 CDT)
  • David Watson (Tue Sep 08 2009 - 12:26:19 CDT)
  • albert albert (Tue Sep 08 2009 - 12:09:09 CDT)
• [AMBER] loading a mol2 file in xleap
  • FyD (Mon Jul 27 2009 - 08:44:50 CDT)
  • vallespardojl_at_chem.leidenuniv.nl (Mon Jul 27 2009 - 07:40:13 CDT)
  • FyD (Fri Jul 24 2009 - 15:00:41 CDT)
  • vallespardojl_at_chem.leidenuniv.nl (Fri Jul 24 2009 - 12:40:13 CDT)
• [AMBER] loading PDB of a RNA sequence
  • case (Tue Sep 08 2009 - 06:38:34 CDT)
  • Carlos Simmerling (Tue Sep 08 2009 - 05:33:57 CDT)
  • gunajyoti das (Tue Sep 08 2009 - 05:31:47 CDT)
• [AMBER] Loading PDB of complex
  • Vikas Sharma (Fri May 22 2009 - 00:56:36 CDT)
  • Carlos Simmerling (Thu May 21 2009 - 08:48:06 CDT)
  • Vikas Sharma (Thu May 21 2009 - 08:13:36 CDT)
• [AMBER] loading RNA sequence in xleap
  • case (Thu Sep 17 2009 - 07:13:38 CDT)
  • FyD (Thu Sep 17 2009 - 04:39:09 CDT)
  • gunajyoti das (Thu Sep 17 2009 - 03:27:49 CDT)
• [AMBER] loadpdb
  • Carlos Simmerling (Wed Sep 09 2009 - 06:35:04 CDT)
  • Bill Ross (Tue Sep 08 2009 - 21:53:32 CDT)
  • Jagdeesh C (Tue Sep 08 2009 - 20:55:36 CDT)
  • Bill Ross (Tue Sep 08 2009 - 11:58:12 CDT)
  • Bill Ross (Tue Sep 08 2009 - 11:53:03 CDT)
  • Carlos Simmerling (Tue Sep 08 2009 - 08:39:12 CDT)
  • Tom Joseph (Tue Sep 08 2009 - 07:31:56 CDT)
  • Ashish Runthala (Mon Sep 07 2009 - 22:00:47 CDT)
  • Jagdeesh C (Mon Sep 07 2009 - 13:31:42 CDT)
  • Carlos Simmerling (Mon Sep 07 2009 - 13:01:10 CDT)
  • Jagdeesh C (Mon Sep 07 2009 - 12:36:58 CDT)
• [AMBER] loadpdb atom type
  • David A. Case (Tue May 19 2009 - 13:19:44 CDT)
  • Mark M Huntress (Tue May 19 2009 - 13:15:02 CDT)
  • Carlos Simmerling (Tue May 19 2009 - 12:09:29 CDT)
  • Mark M Huntress (Tue May 19 2009 - 11:20:20 CDT)
• [AMBER] logdvdl does not work
  • steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:37:31 CDT)
  • helde010_at_umn.edu (Tue Sep 08 2009 - 11:53:14 CDT)
• [AMBER] lone pairs on CYX and MET
  • Ross Walker (Thu Jan 08 2009 - 12:17:52 CST)
  • Beale, John (Thu Jan 08 2009 - 12:08:42 CST)
• [AMBER] long polymer chain and image command in ptraj
  • Karl Kirschner (Mon Apr 06 2009 - 03:15:00 CDT)
  • iccy liu (Thu Apr 02 2009 - 14:11:26 CDT)
• [AMBER] look at Amber's slides, email
  • Sally Pias (Wed Dec 02 2009 - 23:08:47 CST)
• [AMBER] looking for parameters for DHFR substrates and inhibitors...
  • Sidney Elmer (Sat Nov 21 2009 - 22:47:50 CST)
• [AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try]
  • FyD (Wed Dec 02 2009 - 02:19:00 CST)
• [AMBER] Lost mail
  • Robert Duke (Mon Jun 08 2009 - 06:58:02 CDT)
• [AMBER] Low frequency Raman spectra
  • case (Sat Nov 07 2009 - 09:02:02 CST)
  • babak minoofar (Sat Nov 07 2009 - 06:53:37 CST)
• [AMBER] LYN again
  • FyD (Mon Apr 06 2009 - 09:26:14 CDT)
  • Marius Retegan (Mon Apr 06 2009 - 08:55:24 CDT)
  • FyD (Sun Apr 05 2009 - 14:24:27 CDT)
  • Marius Retegan (Sat Apr 04 2009 - 08:12:09 CDT)
• [AMBER] LYS-ASP
  • case (Fri Nov 27 2009 - 21:08:58 CST)
  • Jason Swails (Fri Nov 27 2009 - 19:25:33 CST)
  • s. Bill (Fri Nov 27 2009 - 15:47:28 CST)
• [AMBER] mailing list
  • Qinghua Liao (Thu Jul 23 2009 - 20:45:50 CDT)
• [AMBER] mairun
  • wl2290_at_columbia.edu (Thu Jan 08 2009 - 17:11:56 CST)
  • Ross Walker (Thu Jan 08 2009 - 16:51:49 CST)
  • wl2290_at_columbia.edu (Thu Jan 08 2009 - 16:33:52 CST)
  • Ross Walker (Thu Jan 08 2009 - 12:25:26 CST)
  • wl2290_at_columbia.edu (Thu Jan 08 2009 - 11:30:05 CST)
• [AMBER] Make parallel test faillure
  • Ross Walker (Thu Apr 30 2009 - 14:48:06 CDT)
  • Collins Nganou (Thu Apr 30 2009 - 14:36:55 CDT)
• [AMBER] make test.parallel.MM error
  • Collins Nganou (Sun May 03 2009 - 16:20:51 CDT)
• [AMBER] make test.serial.QMMM
  • Seth Hayik (Wed Apr 01 2009 - 12:26:21 CDT)
  • michael bane (Wed Apr 01 2009 - 10:44:51 CDT)
• [AMBER] makeDIST_RST: no map function
  • Workalemahu Berhanu (Tue Sep 15 2009 - 10:24:56 CDT)
  • Workalemahu Berhanu (Tue Sep 15 2009 - 10:11:27 CDT)
  • case (Tue Sep 15 2009 - 09:38:23 CDT)
  • Duggan, Brendan M. (Tue Sep 15 2009 - 08:40:00 CDT)
  • Workalemahu Berhanu (Mon Sep 14 2009 - 14:30:15 CDT)
• [AMBER] makeDIST_RST: no map function for ambiguous restraint
  • Peter Varnai (Mon Jun 01 2009 - 14:49:36 CDT)
  • David A. Case (Tue May 19 2009 - 07:35:31 CDT)
  • Peter Varnai (Sun May 17 2009 - 13:41:24 CDT)
• [AMBER] making leap to recognize 5' phosphate
  • FyD (Wed Jun 24 2009 - 01:02:42 CDT)
  • FyD (Tue Jun 23 2009 - 04:48:34 CDT)
  • Bala subramanian (Tue Jun 23 2009 - 03:49:05 CDT)
  • FyD (Tue Jun 23 2009 - 02:45:31 CDT)
  • Bala subramanian (Mon Jun 22 2009 - 08:45:43 CDT)
• [AMBER] man pages?
  • Jason Swails (Tue Oct 20 2009 - 16:28:56 CDT)
  • Louis-Frédéric Feuillette (Tue Oct 20 2009 - 15:17:52 CDT)
  • Ben Roberts (Tue Oct 20 2009 - 12:33:16 CDT)
  • Louis-Frédéric Feuillette (Tue Oct 20 2009 - 12:09:09 CDT)
• [AMBER] Manganese
  • Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
• [AMBER] Manganese bondi radii
  • Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
• [AMBER] Manganese bondi radii for mm/pbsa calculation
  • Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
• [AMBER] manganese bondi radii for mm_pbsa calculation
  • Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
• [AMBER] Mass of LP
  • David A. Case (Thu Mar 19 2009 - 06:27:48 CDT)
  • PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 22:27:24 CDT)
• [AMBER] matrixInfoStack
  • Naser Alijabbari (Mon Nov 23 2009 - 08:42:43 CST)
  • Naser Alijabbari (Fri Nov 13 2009 - 08:52:52 CST)
  • Naser Alijabbari (Tue Nov 10 2009 - 08:45:12 CST)
• [AMBER] max atoms for antechamber
  • Alan (Mon Jun 22 2009 - 08:00:48 CDT)
  • case (Mon Jun 22 2009 - 07:48:43 CDT)
  • Alan (Mon Jun 22 2009 - 07:37:39 CDT)
• [AMBER] Max filename length in Sander?
  • Robert Duke (Tue Jun 09 2009 - 10:01:39 CDT)
  • Paul Mortenson (Tue Jun 09 2009 - 09:47:57 CDT)
  • Robert Duke (Mon Jun 08 2009 - 12:30:47 CDT)
  • David A. Case (Mon Jun 08 2009 - 07:36:32 CDT)
  • David A. Case (Mon Jun 08 2009 - 07:28:41 CDT)
  • Paul Mortenson (Mon Jun 08 2009 - 05:59:52 CDT)
• [AMBER] MaxRad ?
  • Marek Maly (Sat Jun 06 2009 - 15:56:44 CDT)
• [AMBER] Maxwell-Boltzmann distribution and ig=-1
  • Carlos Simmerling (Wed Apr 01 2009 - 06:01:51 CDT)
  • Ross Walker (Tue Mar 31 2009 - 22:52:42 CDT)
  • Naser Alijabbari (Tue Mar 31 2009 - 21:43:28 CDT)
  • Carlos Simmerling (Tue Mar 31 2009 - 21:24:34 CDT)
  • Naser Alijabbari (Tue Mar 31 2009 - 21:15:13 CDT)
  • Carlos Simmerling (Tue Mar 31 2009 - 20:41:49 CDT)
  • Naser Alijabbari (Tue Mar 31 2009 - 20:35:43 CDT)
• [AMBER] MD
  • Ross Walker (Wed Jan 07 2009 - 18:33:46 CST)
  • Beale, John (Wed Jan 07 2009 - 08:40:07 CST)
• [AMBER] MD analysis
  • oguz gurbulak (Sat Feb 07 2009 - 08:56:10 CST)
• [AMBER] MD on GPU: an existing commercial implementation
  • Sasha Buzko (Sat Apr 11 2009 - 19:47:46 CDT)
• [AMBER] MD simulation at constant pH
  • Francesco Pietra (Thu Feb 26 2009 - 04:52:47 CST)
• [AMBER] md simulation on parallel PMEMD
  • Robert Duke (Mon Feb 02 2009 - 08:03:59 CST)
  • Carlos Simmerling (Mon Feb 02 2009 - 07:55:44 CST)
  • David A. Case (Mon Feb 02 2009 - 07:54:58 CST)
  • oguz gurbulak (Mon Feb 02 2009 - 07:32:31 CST)
• [AMBER] MD simulation with a partially flexible system
  • Carlos Simmerling (Wed Feb 18 2009 - 06:35:40 CST)
  • Jeffrey (Tue Feb 17 2009 - 20:19:47 CST)
  • Carlos Simmerling (Tue Feb 17 2009 - 08:45:33 CST)
  • Jeffrey (Tue Feb 17 2009 - 08:38:10 CST)
• [AMBER] MD simulations on a protein with FAD and NADH
  • FyD (Fri Feb 27 2009 - 02:24:37 CST)
  • Ross Walker (Thu Feb 26 2009 - 22:32:05 CST)
  • Mannan (Thu Feb 26 2009 - 19:11:54 CST)
• [AMBER] MD snapshots of most probable protein conformations in Amber
  • Andrew Voronkov (Mon Nov 30 2009 - 06:56:42 CST)
  • Carlos Simmerling (Wed Nov 18 2009 - 11:14:50 CST)
  • Andrew Voronkov (Wed Nov 18 2009 - 09:33:54 CST)
  • Andrew Voronkov (Wed Nov 18 2009 - 09:32:11 CST)
  • Carlos Simmerling (Wed Nov 18 2009 - 07:53:14 CST)
  • Renata KWIECIEN (Wed Nov 18 2009 - 07:39:52 CST)
  • Andrew Voronkov (Wed Nov 18 2009 - 07:09:52 CST)
  • Adrian Roitberg (Thu Nov 12 2009 - 07:30:53 CST)
  • Andrew Voronkov (Thu Nov 12 2009 - 07:23:22 CST)
• [AMBER] MD vs scattering
  • Chih-Ying Lin (Tue Jan 20 2009 - 15:26:49 CST)
  • Ross Walker (Tue Jan 20 2009 - 15:18:26 CST)
  • Chih-Ying Lin (Tue Jan 20 2009 - 15:10:47 CST)
• [AMBER] mdfil: Error unknown flag during sander minimization
  • Shubhra Gupta (Tue May 26 2009 - 23:07:25 CDT)
  • David A. Case (Tue May 26 2009 - 09:05:37 CDT)
  • Workalemhu Berhanu (Tue May 26 2009 - 08:57:29 CDT)
• [AMBER] mean of character in frcmod.ff03
  • chenquan (Wed Apr 15 2009 - 18:36:32 CDT)
  • Ross Walker (Wed Apr 15 2009 - 09:58:31 CDT)
  • chenquan (Wed Apr 15 2009 - 07:26:38 CDT)
• [AMBER] mean square displacment
  • Bill Ross (Tue Oct 13 2009 - 19:09:49 CDT)
  • Nancy (Tue Oct 13 2009 - 18:59:15 CDT)
• [AMBER] Meaning of GMAX
  • Ashish Runthala (Mon Aug 24 2009 - 10:38:46 CDT)
  • Adrian Roitberg (Mon Aug 24 2009 - 10:05:36 CDT)
  • Ashish Runthala (Mon Aug 24 2009 - 09:59:53 CDT)
  • case (Mon Aug 24 2009 - 06:44:34 CDT)
  • E.M. (Mon Aug 24 2009 - 04:05:10 CDT)
• [AMBER] Measuring volume of the binding pocket
  • Mannan (Tue Aug 11 2009 - 21:31:18 CDT)
  • Mannan (Tue Aug 11 2009 - 21:03:49 CDT)
• [AMBER] Metal in MD simulation
  • priya priya (Fri Mar 20 2009 - 01:15:06 CDT)
  • Bill Ross (Thu Mar 19 2009 - 16:22:12 CDT)
  • Ross Walker (Thu Mar 19 2009 - 10:12:24 CDT)
  • Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 09:48:28 CDT)
  • priya priya (Thu Mar 19 2009 - 01:25:09 CDT)
• [AMBER] Metalloproteins - Ligand Protonation
  • s. Bill (Fri Jul 31 2009 - 13:01:42 CDT)
• [AMBER] method used to determine partial charges?
  • FyD (Thu Oct 01 2009 - 23:27:13 CDT)
  • Jihang Wang (Thu Oct 01 2009 - 17:42:38 CDT)
  • Carlos Simmerling (Thu Oct 01 2009 - 17:30:21 CDT)
  • Jihang Wang (Thu Oct 01 2009 - 17:26:24 CDT)
  • Bill Ross (Thu Oct 01 2009 - 17:18:01 CDT)
  • Jihang Wang (Thu Oct 01 2009 - 16:28:45 CDT)
  • Bill Ross (Thu Oct 01 2009 - 16:19:29 CDT)
  • Jihang Wang (Thu Oct 01 2009 - 15:36:31 CDT)
  • Paul Brandt (Thu Oct 01 2009 - 15:25:54 CDT)
• [AMBER] methyl group at the N-terminal
  • FyD (Fri Jun 19 2009 - 07:12:36 CDT)
  • Francesca Poletti (Fri Jun 19 2009 - 07:03:56 CDT)
• [AMBER] Micelles set-up??
  • Alexander Schierholt (Tue Feb 03 2009 - 04:09:52 CST)
• [AMBER] minimisation with igb=10
  • Ray Luo (Mon Mar 16 2009 - 11:34:21 CDT)
  • Carlos Simmerling (Mon Mar 16 2009 - 11:04:37 CDT)
  • Bala subramanian (Mon Mar 16 2009 - 10:56:48 CDT)
  • Carlos Simmerling (Mon Mar 16 2009 - 10:45:47 CDT)
  • Bala subramanian (Mon Mar 16 2009 - 10:43:10 CDT)
• [AMBER] minimization error
  • case (Fri Oct 02 2009 - 07:00:52 CDT)
  • balaji nagarajan (Fri Oct 02 2009 - 06:42:54 CDT)
• [AMBER] Minimization error on protonated system? Please help. Thanks!
  • David A. Case (Thu May 28 2009 - 10:17:59 CDT)
  • Haizhen Zhong (Thu May 28 2009 - 09:58:49 CDT)
• [AMBER] Minimization on MM-PBSA
  • Rubben Torella (Thu May 28 2009 - 10:23:07 CDT)
• [AMBER] minimization to reduce covalent deviation
  • David A. Case (Tue Jun 02 2009 - 08:38:58 CDT)
  • Peter Varnai (Mon Jun 01 2009 - 15:25:07 CDT)
• [AMBER] missing amber force field parameters
  • FyD (Thu Apr 16 2009 - 04:41:44 CDT)
  • Neha Gandhi (Thu Apr 16 2009 - 04:19:57 CDT)
• [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
  • suhaib sh (Thu Jul 02 2009 - 08:18:05 CDT)
• [AMBER] missing violations of the covalent geometry
  • Helena P M Tossavainen (Tue Apr 07 2009 - 07:10:16 CDT)
  • David A. Case (Tue Apr 07 2009 - 06:10:42 CDT)
  • Helena P M Tossavainen (Tue Apr 07 2009 - 04:36:44 CDT)
• [AMBER] Missing X11 Libraries
  • Bill Ross (Fri Oct 09 2009 - 19:24:47 CDT)
  • FyD (Fri Oct 09 2009 - 16:06:20 CDT)
  • Thomas Patko (Fri Oct 09 2009 - 15:53:14 CDT)
  • FyD (Fri Oct 09 2009 - 15:35:59 CDT)
  • case (Fri Oct 09 2009 - 15:02:06 CDT)
  • Wallace Kunin (Fri Oct 09 2009 - 14:20:00 CDT)
  • Bill Ross (Fri Oct 09 2009 - 12:52:01 CDT)
  • Thomas Patko (Fri Oct 09 2009 - 12:13:22 CDT)
  • Wallace Kunin (Fri Oct 09 2009 - 12:03:51 CDT)
  • Wallace Kunin (Fri Oct 09 2009 - 11:59:06 CDT)
  • Thomas Patko (Thu Oct 08 2009 - 12:26:26 CDT)
  • Bill Ross (Thu Oct 08 2009 - 12:25:32 CDT)
  • Wallace Kunin (Thu Oct 08 2009 - 12:09:55 CDT)
  • Bill Ross (Wed Oct 07 2009 - 17:28:34 CDT)
  • Thomas Patko (Wed Oct 07 2009 - 16:14:15 CDT)
  • Wallace Kunin (Wed Oct 07 2009 - 16:10:34 CDT)
  • FyD (Wed Oct 07 2009 - 15:45:34 CDT)
  • Mengjuei Hsieh (Wed Oct 07 2009 - 15:19:20 CDT)
  • Wallace Kunin (Wed Oct 07 2009 - 13:04:39 CDT)
  • Wallace Kunin (Sat Oct 03 2009 - 12:02:05 CDT)
  • Wallace Kunin (Fri Oct 02 2009 - 14:57:49 CDT)
  • case (Fri Oct 02 2009 - 13:56:34 CDT)
  • Wallace Kunin (Fri Oct 02 2009 - 11:43:59 CDT)
• [AMBER] Mixing of forcefields in case of covaletly bonded systems
  • Marek Malý (Mon Apr 27 2009 - 07:06:38 CDT)
• [AMBER] MKL error ?
  • Marek Malý (Thu Feb 05 2009 - 14:00:10 CST)
  • Ross Walker (Thu Feb 05 2009 - 12:29:45 CST)
  • Marek Malý (Thu Feb 05 2009 - 06:26:05 CST)
  • Ross Walker (Tue Feb 03 2009 - 23:22:48 CST)
  • Marek Malý (Tue Feb 03 2009 - 17:00:03 CST)
• [AMBER] MM - PBSA problem
  • musa özboyacý (Mon Jan 26 2009 - 10:32:40 CST)
  • Cenk \(Jenk\) Andac (Mon Jan 26 2009 - 10:20:25 CST)
  • musa özboyacý (Mon Jan 26 2009 - 06:43:33 CST)
  • Cenk \(Jenk\) Andac (Mon Jan 26 2009 - 06:14:52 CST)
  • musa özboyacý (Mon Jan 26 2009 - 05:15:13 CST)
  • Cenk \(Jenk\) Andac (Sun Jan 25 2009 - 14:38:16 CST)
  • David A. Case (Sun Jan 25 2009 - 08:26:07 CST)
  • David A. Case (Sun Jan 25 2009 - 08:21:33 CST)
  • musa özboyacý (Sun Jan 25 2009 - 07:12:05 CST)
  • Cenk \(Jenk\) Andac (Fri Jan 23 2009 - 08:34:46 CST)
  • musa özboyacý (Fri Jan 23 2009 - 07:14:05 CST)
  • Niel Henriksen (Thu Jan 22 2009 - 18:52:09 CST)
  • Cenk \(Jenk\) Andac (Thu Jan 22 2009 - 16:00:13 CST)
  • musa özboyacý (Thu Jan 22 2009 - 13:52:10 CST)
  • Ray Luo (Thu Jan 22 2009 - 11:31:53 CST)
  • musa özboyacý (Thu Jan 22 2009 - 11:06:54 CST)
• [AMBER] MM decomp energy - zero values for Eele, Evdw
  • Thomas Lake (Tue Jun 16 2009 - 10:36:50 CDT)
• [AMBER] MM PBSA ( Vertex atom mismatch in Amber)
  • Vikas Sharma (Tue Jun 09 2009 - 22:28:22 CDT)
• [AMBER] MM PBSA ERROR
  • Vikas Sharma (Fri Jun 12 2009 - 09:04:25 CDT)
• [AMBER] MM PBSA output
  • Vikas Sharma (Wed May 20 2009 - 06:53:57 CDT)
• [AMBER] MM PBSA stats
  • Peter Jones (Mon Dec 21 2009 - 23:57:51 CST)
• [AMBER] MM-GBAS decomp error
  • Catein Catherine (Fri Sep 04 2009 - 05:29:35 CDT)
• [AMBER] MM-GBSA energy decomposition and pairwise decomposition question
  • Dong Xu (Fri May 15 2009 - 17:05:52 CDT)
• [AMBER] MM-GBSA Free enegy decomposition
  • Rajesh Raju (Mon Apr 27 2009 - 07:27:23 CDT)
• [AMBER] mm-GBSA from implicit
  • Carlos Simmerling (Sat Jan 10 2009 - 07:25:10 CST)
  • Catein Catherine (Fri Jan 09 2009 - 21:13:28 CST)
• [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
  • Ashish Runthala (Mon Aug 17 2009 - 22:02:43 CDT)
  • case (Mon Aug 17 2009 - 21:56:17 CDT)
  • Ashish Runthala (Mon Aug 17 2009 - 01:21:45 CDT)
  • Catein Catherine (Mon Aug 17 2009 - 00:58:49 CDT)
  • Ross Walker (Sat Aug 15 2009 - 23:40:26 CDT)
  • Catein Catherine (Sat Aug 15 2009 - 23:12:42 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 22:59:11 CDT)
  • Catein Catherine (Sat Aug 15 2009 - 21:45:34 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 01:05:53 CDT)
  • Catein Catherine (Thu Aug 13 2009 - 22:38:02 CDT)
  • case (Thu Aug 13 2009 - 06:46:02 CDT)
  • Catein Catherine (Wed Aug 12 2009 - 21:23:40 CDT)
  • case (Tue Aug 11 2009 - 06:54:43 CDT)
  • Catein Catherine (Tue Aug 11 2009 - 06:10:09 CDT)
• [AMBER] MM-PB/GBSA NMODE
  • Zhongjie Liang (Wed Nov 25 2009 - 00:50:50 CST)
• [AMBER] MM-PBSA and NetCDF
  • Bradshaw, Richard (Wed May 27 2009 - 10:38:13 CDT)
• [AMBER] MM-PBSA cannot finish without error message.
  • Catein Catherine (Thu Jul 23 2009 - 04:57:00 CDT)
• [AMBER] MM-PBSA decomp by residue and snapshot?
  • Bradshaw, Richard (Thu Mar 05 2009 - 11:55:05 CST)
• [AMBER] MM-PBSA delphi.crg and delphi.siz
  • Manish Kumar (Wed Jul 08 2009 - 16:29:40 CDT)
• [AMBER] MM-PBSA energy decomposition
  • Hannes Kopitz (Thu Apr 30 2009 - 05:37:35 CDT)
  • Dong Xu (Wed Apr 29 2009 - 21:03:34 CDT)
• [AMBER] MM-PBSA error while running heat.in
  • Vikas Sharma (Mon Apr 06 2009 - 04:32:55 CDT)
• [AMBER] MM-PBSA NMODE
  • case (Wed Nov 25 2009 - 07:31:28 CST)
  • Zhongjie Liang (Tue Nov 24 2009 - 21:12:38 CST)
• [AMBER] MM-PBSA nmode statistics
  • Ray Luo (Mon Jun 01 2009 - 14:05:48 CDT)
  • Dmitry Osolodkin (Mon Jun 01 2009 - 08:12:15 CDT)
  • Ray Luo (Sun May 31 2009 - 12:32:49 CDT)
  • Dmitry Osolodkin (Sat May 30 2009 - 12:25:46 CDT)
  • Ray Luo (Fri May 29 2009 - 13:01:36 CDT)
  • Dmitry Osolodkin (Fri May 29 2009 - 05:53:27 CDT)
  • Kshatresh Dutta Dubey (Fri May 29 2009 - 00:13:34 CDT)
  • Dmitry Osolodkin (Thu May 28 2009 - 06:54:18 CDT)
• [AMBER] MM-PBSA problem
  • Giorgos Lamprinidis (Mon Jul 06 2009 - 03:07:14 CDT)
  • Rubben Torella (Fri Jul 03 2009 - 08:57:09 CDT)
  • Giorgos Lamprinidis (Fri Jul 03 2009 - 08:50:36 CDT)
• [AMBER] MM-PBSA results
  • Dmitry Osolodkin (Fri Aug 07 2009 - 09:31:48 CDT)
• [AMBER] MM-PBSA statistics
  • Musa Ozboyaci (Sun May 10 2009 - 05:00:19 CDT)
• [AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex
  • Sushil Mishra (Mon Jul 20 2009 - 03:32:32 CDT)
• [AMBER] MM-PBSA tutorial
  • Cihan Aydin (Thu May 14 2009 - 20:19:04 CDT)
  • Workalemhu Berhanu (Thu May 14 2009 - 13:53:25 CDT)
  • steinbrt_at_rci.rutgers.edu (Thu May 14 2009 - 12:26:50 CDT)
  • Workalemhu Berhanu (Thu May 14 2009 - 12:16:55 CDT)
• [AMBER] MM-PBSA with explicit water
  • mathew k varghese (Fri May 15 2009 - 01:45:23 CDT)
• [AMBER] MM-PBSA: decompose energy error
  • Maria Mirza (Sun Aug 16 2009 - 14:49:06 CDT)
  • Lucilla Angeli (Mon Apr 06 2009 - 09:35:58 CDT)
• [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis
  • Ray Luo (Wed Jul 29 2009 - 19:25:14 CDT)
  • Matthias Negri (Wed Jul 29 2009 - 05:55:46 CDT)
• [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
  • Rubben Torella (Tue Oct 06 2009 - 02:56:18 CDT)
  • Jeff Yeo (Mon Oct 05 2009 - 18:22:53 CDT)
• [AMBER] MM_PBSA
  • Zhongjie Liang (Tue Sep 29 2009 - 20:30:40 CDT)
• [AMBER] MM_PBSA decomp problem
  • B. Nandy (Tue Sep 22 2009 - 07:29:23 CDT)
• [AMBER] MM_PBSA decomposition pair question
  • Rubben Torella (Fri Oct 02 2009 - 06:09:38 CDT)
• [AMBER] MM_PBSA energy per residue
  • Hemant Kumar (Thu Nov 12 2009 - 08:27:22 CST)
• [AMBER] MM_PBSA enquiries
  • manoj singh (Sun Nov 08 2009 - 09:21:12 CST)
  • s. Bill (Sun Nov 08 2009 - 08:53:04 CST)
• [AMBER] MM_PBSA error
  • Jagdeesh C (Thu Nov 26 2009 - 22:28:44 CST)
• [AMBER] MM_PBSA not successful
  • Ross Walker (Sun Aug 16 2009 - 13:15:42 CDT)
  • workalemahu berhanu (Sun Aug 16 2009 - 12:22:01 CDT)
  • monnet.jordan_at_free.fr (Sat Aug 15 2009 - 17:10:08 CDT)
  • Qinghua Liao (Sat Aug 15 2009 - 01:55:40 CDT)
  • workalemahu berhanu (Fri Aug 14 2009 - 23:22:57 CDT)
  • Qinghua Liao (Fri Aug 14 2009 - 21:43:23 CDT)
  • workalemahu berhanu (Fri Aug 14 2009 - 21:36:39 CDT)
  • workalemahu berhanu (Fri Aug 14 2009 - 21:21:32 CDT)
  • Qinghua Liao (Fri Aug 14 2009 - 20:20:55 CDT)
  • Jordan Monnet (Fri Aug 14 2009 - 19:05:00 CDT)
  • workalemahu berhanu (Fri Aug 14 2009 - 16:45:41 CDT)
• [AMBER] mm_pbsa problem
  • Giorgos Lamprinidis (Wed Apr 01 2009 - 02:36:53 CDT)
  • Ray Luo (Mon Mar 30 2009 - 12:27:59 CDT)
  • Giorgos Lamprinidis (Mon Mar 30 2009 - 08:59:55 CDT)
  • case (Mon Mar 30 2009 - 07:48:05 CDT)
  • Giorgos Lamprinidis (Mon Mar 30 2009 - 05:02:07 CDT)
• [AMBER] MM_PBSA Problem (no radius for ion)
  • s. Bill (Fri Dec 18 2009 - 09:33:57 CST)
  • Scott Brozell (Thu Dec 17 2009 - 21:07:21 CST)
  • s. Bill (Thu Dec 17 2009 - 13:39:49 CST)
• [AMBER] MM_PBSA problem in Amber 9
  • Sean Zhao (Mon May 04 2009 - 04:09:14 CDT)
• [AMBER] mm_pbsa- Decomposition: bad atom type
  • Antonija Tomić (Fri Dec 04 2009 - 04:57:59 CST)
  • Hannes Kopitz (Fri Dec 04 2009 - 04:45:10 CST)
  • Antonija Tomić (Fri Dec 04 2009 - 03:27:31 CST)
  • Antonija Tomić (Tue Oct 06 2009 - 08:53:25 CDT)
• [AMBER] mm_pbsa-Binding and Stability tests?
  • Antonija Tomić (Wed Aug 26 2009 - 04:15:54 CDT)
  • Niel Henriksen (Mon Aug 24 2009 - 12:24:09 CDT)
  • Antonija Tomić (Mon Aug 24 2009 - 04:51:28 CDT)
  • Ray Luo (Fri Aug 21 2009 - 16:29:58 CDT)
  • Niel Henriksen (Fri Aug 21 2009 - 09:52:49 CDT)
  • Antonija Tomić (Fri Aug 21 2009 - 05:04:35 CDT)
• [AMBER] MM_PBSA: abnormal VDW interaction energy
  • LIU Huanxiang (Tue Oct 06 2009 - 21:54:49 CDT)
  • steinbrt_at_rci.rutgers.edu (Tue Oct 06 2009 - 03:09:27 CDT)
  • LIU Huanxiang (Mon Oct 05 2009 - 21:43:21 CDT)
• [AMBER] mm_pbsa_statistics-CALC DELTA parameter ?
  • Marek Maly (Mon Jun 08 2009 - 14:16:19 CDT)
• [AMBER] MMGBSA
  • Zhongjie Liang (Wed Dec 02 2009 - 19:17:44 CST)
• [AMBER] MMGBSA error
  • David A. Case (Fri Dec 25 2009 - 16:17:26 CST)
  • Jason Swails (Fri Dec 25 2009 - 07:28:15 CST)
  • Zhongjie Liang (Fri Dec 25 2009 - 00:59:16 CST)
  • Carlos Simmerling (Tue Dec 22 2009 - 07:05:41 CST)
  • Zhongjie Liang (Tue Dec 22 2009 - 07:04:09 CST)
• [AMBER] MMGBSA IG Value
  • Carlos Simmerling (Fri Mar 20 2009 - 12:42:14 CDT)
  • Rajesh Raju (Fri Mar 20 2009 - 12:36:37 CDT)
  • Carlos Simmerling (Fri Mar 20 2009 - 12:25:38 CDT)
  • Rajesh Raju (Fri Mar 20 2009 - 12:20:52 CDT)
• [AMBER] MMPB(GB)SA on trimer
  • quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 20:01:39 CDT)
• [AMBER] MMPBSA and mm_pbsa_statistics.pl error
  • Ray Luo (Tue Jun 02 2009 - 23:49:34 CDT)
  • john smith (Tue Jun 02 2009 - 00:38:54 CDT)
• [AMBER] MMPBSA extract coordinate
  • vijayaraj_at_clri.res.in (Fri May 22 2009 - 13:00:57 CDT)
• [AMBER] MMPBSA on a selected region
  • Jason Swails (Thu Dec 10 2009 - 13:15:58 CST)
  • ERIK.LAURINI_at_phd.units.it (Thu Dec 10 2009 - 12:20:19 CST)
• [AMBER] MMPBSA- interaction energy for every frame
  • Jack Colis (Tue May 05 2009 - 03:22:35 CDT)
  • Wei Huang (Mon May 04 2009 - 09:58:26 CDT)
  • Jack Colis (Mon May 04 2009 - 09:38:38 CDT)
• [AMBER] MMPBSA: No radius found for F
  • Jeff Yeo (Sun Oct 04 2009 - 19:10:12 CDT)
• [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
  • Cenk \(Jenk\) Andac (Mon Oct 19 2009 - 16:44:42 CDT)
  • Jianyin Shao (Mon Oct 19 2009 - 13:16:47 CDT)
  • Cenk \(Jenk\) Andac (Sat Oct 17 2009 - 02:02:20 CDT)
  • Thomas Cheatham III (Fri Oct 16 2009 - 10:33:22 CDT)
  • Cenk \(Jenk\) Andac (Fri Oct 16 2009 - 07:19:24 CDT)
• [AMBER] MMTSB tool set PDF
  • kureeckal ramesh (Tue Nov 10 2009 - 08:02:39 CST)
• [AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st
  • Harald Lanig (Thu Aug 06 2009 - 03:39:07 CDT)
• [AMBER] Modification of His
  • Bill Ross (Mon May 18 2009 - 15:06:16 CDT)
  • David A. Case (Mon May 18 2009 - 07:31:33 CDT)
  • Jorgen Simonsen (Mon May 18 2009 - 07:16:10 CDT)
  • David A. Case (Mon May 18 2009 - 06:58:34 CDT)
  • Jorgen Simonsen (Mon May 18 2009 - 05:51:50 CDT)
• [AMBER] Modifying a water molecule
  • Jorgen Simonsen (Sat May 09 2009 - 08:16:54 CDT)
• [AMBER] modifying LYN
  • Marius Retegan (Tue Mar 31 2009 - 11:58:06 CDT)
  • FyD (Tue Mar 31 2009 - 10:41:56 CDT)
  • Marius Retegan (Tue Mar 31 2009 - 08:36:21 CDT)
• [AMBER] mol2 - pdb conversion
  • David A. Case (Wed Mar 18 2009 - 16:53:06 CDT)
  • Taufik Al-Sarraj (Wed Mar 18 2009 - 14:20:54 CDT)
  • David A. Case (Tue Mar 17 2009 - 10:47:53 CDT)
  • Taufik Al-Sarraj (Mon Mar 16 2009 - 16:38:09 CDT)
• [AMBER] mol2 file to amber pdb file format
  • David A. Case (Thu Jun 04 2009 - 11:55:39 CDT)
  • balaji nagarajan (Thu Jun 04 2009 - 11:32:06 CDT)
• [AMBER] molecular crystal simulation
  • David A. Case (Wed May 13 2009 - 17:28:37 CDT)
  • Simona Irrera (Tue May 12 2009 - 06:04:26 CDT)
• [AMBER] molecular mechanic minimisation with amber
  • Ross Walker (Wed Jan 14 2009 - 11:56:23 CST)
  • momo momo (Wed Jan 14 2009 - 08:58:47 CST)
• [AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany
  • Harald Lanig (Tue Jul 14 2009 - 09:02:16 CDT)
• [AMBER] Molecular simulation of a protein using special H2O cluster
  • Carlos Simmerling (Tue May 26 2009 - 19:25:03 CDT)
  • Rilei Yu (Tue May 26 2009 - 19:21:15 CDT)
  • Carlos Simmerling (Tue May 26 2009 - 06:45:50 CDT)
  • Rilei Yu (Tue May 26 2009 - 03:20:56 CDT)
• [AMBER] molsurf and probe radius
  • David A. Case (Mon May 11 2009 - 10:03:10 CDT)
  • David Watson (Sat May 09 2009 - 12:32:43 CDT)
• [AMBER] momentum in MD simulation
  • dhacademic (Wed Sep 02 2009 - 12:37:50 CDT)
  • case (Tue Sep 01 2009 - 06:48:52 CDT)
  • dhacademic (Mon Aug 31 2009 - 09:37:42 CDT)
• [AMBER] MPI error
  • Robert Duke (Wed Jul 29 2009 - 07:05:57 CDT)
  • vhakkim boy (Wed Jul 29 2009 - 04:44:35 CDT)
• [AMBER] MPI process terminated unexpectedly after cluster upgrade
  • Ross Walker (Thu Nov 05 2009 - 10:22:19 CST)
  • Dmitri Nilov (Thu Nov 05 2009 - 08:55:16 CST)
  • Dmitri Nilov (Thu Nov 05 2009 - 08:38:32 CST)
  • Jason Swails (Thu Nov 05 2009 - 08:12:39 CST)
  • Dmitri Nilov (Thu Nov 05 2009 - 07:39:59 CST)
  • Ross Walker (Tue Nov 03 2009 - 17:13:45 CST)
  • Jason Swails (Tue Nov 03 2009 - 08:11:48 CST)
  • Dmitri Nilov (Tue Nov 03 2009 - 08:06:11 CST)
  • Dmitri Nilov (Tue Nov 03 2009 - 07:20:17 CST)
  • Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
  • Jason Swails (Mon Nov 02 2009 - 11:04:14 CST)
  • Dmitri Nilov (Mon Nov 02 2009 - 07:11:15 CST)
  • Jason Swails (Mon Nov 02 2009 - 06:15:19 CST)
  • Dmitri Nilov (Mon Nov 02 2009 - 03:17:19 CST)
• [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT)
  • Ross Walker (Wed Jul 08 2009 - 10:01:24 CDT)
  • Andrew Voronkov (Wed Jul 08 2009 - 05:05:52 CDT)
  • Andrew Voronkov (Wed Jul 08 2009 - 04:39:03 CDT)
• [AMBER] mpirun
  • Ross Walker (Thu Jan 08 2009 - 17:28:12 CST)
• [AMBER] mpirun error
  • Vijay Manickam Achari (Mon Dec 28 2009 - 21:00:11 CST)
• [AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup).
  • Naser Alijabbari (Tue Jul 14 2009 - 05:41:39 CDT)
• [AMBER] mpirun problem in HPC
  • Ross Walker (Fri Feb 06 2009 - 02:05:37 CST)
  • Vijay Manickam Achari (Fri Feb 06 2009 - 01:01:29 CST)
• [AMBER] MSD and stress tensors
  • oguz gurbulak (Fri Feb 06 2009 - 05:09:12 CST)
• [AMBER] MSD of ligand??
  • Chih-Ying Lin (Tue Nov 17 2009 - 13:07:12 CST)
• [AMBER] multiple chain specification in Sander
  • Siddharth Rastogi (Thu May 07 2009 - 15:29:28 CDT)
  • Carlos Simmerling (Thu May 07 2009 - 05:19:09 CDT)
  • Siddharth Rastogi (Wed May 06 2009 - 22:17:57 CDT)
• [AMBER] multisander error
  • Justine Condo (Mon Jan 12 2009 - 17:01:41 CST)
  • Ross Walker (Mon Jan 12 2009 - 16:51:48 CST)
  • Justine Condo (Mon Jan 12 2009 - 16:39:44 CST)
  • Justine Condo (Mon Jan 12 2009 - 16:32:31 CST)
  • Ross Walker (Mon Jan 12 2009 - 16:20:06 CST)
  • David Watson (Mon Jan 12 2009 - 16:15:26 CST)
  • Justine Condo (Mon Jan 12 2009 - 16:03:37 CST)
• [AMBER] my FF
  • David A. Case (Wed Apr 15 2009 - 07:28:16 CDT)
  • m m (Tue Apr 14 2009 - 17:21:38 CDT)
• [AMBER] My step size
  • Vikas Sharma (Tue Apr 21 2009 - 23:49:47 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 10:01:25 CDT)
  • Ross Walker (Tue Apr 21 2009 - 06:27:07 CDT)
  • Vikas Sharma (Tue Apr 21 2009 - 01:50:16 CDT)
• [AMBER] myristate to palmitate transformation
  • Anthony Pemberton (Tue Dec 08 2009 - 10:24:59 CST)
• [AMBER] NAB bug with parmbsc0
  • David A. Case (Thu Apr 23 2009 - 11:25:27 CDT)
• [AMBER] nab compile error with -scalapack
  • chaitanya koppisetty (Tue Feb 03 2009 - 12:52:54 CST)
  • David A. Case (Tue Feb 03 2009 - 08:27:24 CST)
  • chaitanya koppisetty (Tue Feb 03 2009 - 07:23:46 CST)
• [AMBER] nab conjgrad min problem
  • Jeremy Harris (Mon Jan 19 2009 - 09:00:30 CST)
  • David A. Case (Fri Jan 16 2009 - 09:33:01 CST)
  • Jeremy Harris (Fri Jan 16 2009 - 09:11:12 CST)
• [AMBER] NAB entropy calcualtion
  • David A. Case (Fri Jan 09 2009 - 07:13:32 CST)
  • Andreas Svrcek-Seiler (Fri Jan 09 2009 - 03:28:48 CST)
  • chaitanya koppisetty (Fri Jan 09 2009 - 03:01:13 CST)
• [AMBER] NAB example scripts in AmberTools (Amber 10)
  • case (Thu Dec 03 2009 - 07:12:27 CST)
  • Christopher Wassman (Thu Dec 03 2009 - 03:08:37 CST)
• [AMBER] nab installation
  • case (Tue Dec 29 2009 - 13:26:35 CST)
  • Lixia Jin Day (Tue Dec 29 2009 - 11:32:37 CST)
• [AMBER] NAB md function prints strange output
  • Scott Brozell (Thu Mar 12 2009 - 16:04:15 CDT)
  • David A. Case (Tue Feb 10 2009 - 06:46:40 CST)
  • Jochen Heil (Tue Feb 10 2009 - 06:19:56 CST)
  • David A. Case (Mon Feb 09 2009 - 06:58:43 CST)
  • Jochen Heil (Mon Feb 09 2009 - 05:30:21 CST)
• [AMBER] NAB memory
  • case (Fri Jun 26 2009 - 13:42:03 CDT)
  • E.M. (Fri Jun 26 2009 - 13:06:41 CDT)
• [AMBER] NAB memory increase
  • Bill Ross (Thu Jun 25 2009 - 11:34:58 CDT)
  • case (Thu Jun 25 2009 - 06:33:03 CDT)
  • E.M. (Wed Jun 24 2009 - 15:12:09 CDT)
• [AMBER] nab normal mode analysis has imaginary frequencies
  • case (Wed Oct 14 2009 - 13:34:05 CDT)
  • Junmei Wang (Wed Oct 14 2009 - 11:05:06 CDT)
• [AMBER] NAB optimization
  • case (Thu Aug 13 2009 - 08:56:28 CDT)
  • ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 13 2009 - 08:45:26 CDT)
• [AMBER] NAB syntax
  • case (Thu Sep 17 2009 - 10:22:29 CDT)
  • Andreas Svrcek-Seiler (Thu Sep 17 2009 - 10:21:51 CDT)
  • Michael Durney (Thu Sep 17 2009 - 09:58:58 CDT)
• [AMBER] Nab units ?
  • Marek Maly (Fri May 22 2009 - 20:43:41 CDT)
  • David A. Case (Fri May 22 2009 - 20:33:34 CDT)
  • Marek Maly (Fri May 22 2009 - 19:20:14 CDT)
• [AMBER] NAD - mmpbsa
  • Urszula Uciechowska (Sun Nov 22 2009 - 05:02:22 CST)
• [AMBER] NALA-ALA-CALA peptide with antechamber
  • David A. Case (Sat Apr 04 2009 - 08:04:32 CDT)
  • Alan (Fri Apr 03 2009 - 11:33:17 CDT)
• [AMBER] NAMD dcd files in ptraj
  • Ganesh Kamath (Wed Dec 16 2009 - 15:04:25 CST)
• [AMBER] nanoseconds of simulation with nscm=0
  • Thomas Cheatham (Sun May 24 2009 - 15:37:23 CDT)
  • Naser Alijabbari (Sun May 24 2009 - 14:56:28 CDT)
  • Thomas Cheatham (Sun May 24 2009 - 13:27:33 CDT)
  • Naser Alijabbari (Sun May 24 2009 - 12:20:18 CDT)
• [AMBER] nasty memory bug in calculatePrincipalAxis
  • Scott Brozell (Mon Oct 12 2009 - 16:38:06 CDT)
  • Hannes Loeffler (Mon Jul 20 2009 - 03:30:38 CDT)
• [AMBER] NATOM in prmtop and inpcrd files does not agree with the input
  • Ross Walker (Tue Aug 25 2009 - 12:55:39 CDT)
  • Ashish Runthala (Tue Aug 25 2009 - 00:45:33 CDT)
  • Ross Walker (Mon Aug 24 2009 - 23:55:52 CDT)
  • Maria Mirza (Mon Aug 24 2009 - 23:41:39 CDT)
• [AMBER] neb error while heating
  • Carlos Simmerling (Mon Dec 28 2009 - 11:34:56 CST)
  • balaji nagarajan (Sat Dec 26 2009 - 21:09:00 CST)
• [AMBER] NEB-error
  • Carlos Simmerling (Wed Dec 23 2009 - 10:46:59 CST)
  • xmzpzengs (Wed Dec 23 2009 - 10:44:36 CST)
  • Carlos Simmerling (Wed Dec 23 2009 - 10:12:01 CST)
  • balaji nagarajan (Wed Dec 23 2009 - 10:04:46 CST)
• [AMBER] NEB-NAN error
  • balaji nagarajan (Mon Dec 28 2009 - 09:16:43 CST)
• [AMBER] need charges of FE-S cluster
  • Markus Kaukonen (Tue Jul 21 2009 - 13:50:39 CDT)
  • case (Mon Jul 06 2009 - 07:35:19 CDT)
  • subarna thakur (Mon Jul 06 2009 - 05:44:05 CDT)
• [AMBER] Need help for PMEMD 10 installation
  • Robert Duke (Tue Jul 14 2009 - 06:50:26 CDT)
  • Giorgos Lamprinidis (Tue Jul 14 2009 - 02:29:09 CDT)
  • Ross Walker (Mon Jul 13 2009 - 14:18:26 CDT)
  • Jun Dong (Mon Jul 13 2009 - 13:10:34 CDT)
  • Ross Walker (Fri Jul 10 2009 - 13:52:13 CDT)
  • Jun Dong (Fri Jul 10 2009 - 12:25:03 CDT)
  • Ross Walker (Fri Jul 10 2009 - 11:26:29 CDT)
  • Jun Dong (Fri Jul 10 2009 - 11:05:49 CDT)
• [AMBER] Need help with nab code to access the m_prm struct in a molecule
  • M. L. Dodson (Mon Jun 15 2009 - 14:49:02 CDT)
• [AMBER] Need help with point to plane distance calculation in nab
  • M. L. Dodson (Thu Jan 08 2009 - 13:54:15 CST)
  • IN SUK JOUNG (Thu Jan 08 2009 - 13:41:09 CST)
  • M. L. Dodson (Thu Jan 08 2009 - 13:16:51 CST)
  • IN SUK JOUNG (Thu Jan 08 2009 - 13:00:20 CST)
  • M. L. Dodson (Thu Jan 08 2009 - 12:39:16 CST)
• [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation
  • Adrian Roitberg (Tue Feb 17 2009 - 12:57:56 CST)
  • Xu Dong (Tue Feb 17 2009 - 12:54:58 CST)
• [AMBER] Need you help
  • Carlos Simmerling (Wed Aug 26 2009 - 08:48:20 CDT)
  • bharat lakhani (Wed Aug 26 2009 - 08:41:17 CDT)
• [AMBER] need- help-for TMD
  • balaji nagarajan (Tue Mar 17 2009 - 00:16:34 CDT)
• [AMBER] Negative "number of measurements" in PTRAJ
  • Thomas Cheatham (Tue Apr 07 2009 - 11:57:28 CDT)
  • Jenny Iskrenova (Mon Apr 06 2009 - 12:28:59 CDT)
• [AMBER] net charge
  • case (Tue Jun 23 2009 - 09:34:07 CDT)
  • Vishal Maingi (Tue Jun 23 2009 - 09:19:51 CDT)
• [AMBER] New atom type with 7 bonds
  • David A. Case (Mon Feb 16 2009 - 08:28:25 CST)
  • Akansha Saxena (Fri Feb 13 2009 - 17:56:47 CST)
• [AMBER] new process_mdout.pl script????
  • Ross Walker (Mon Oct 05 2009 - 13:38:17 CDT)
  • Dean Cuebas (Mon Oct 05 2009 - 13:11:49 CDT)
• [AMBER] nmod no run proprely in mmbsa
  • David A. Case (Thu Apr 23 2009 - 07:47:44 CDT)
  • mohamed mohamed (Thu Apr 23 2009 - 07:20:36 CDT)
• [AMBER] Nmode "not running properly" problem in MM_PBSA
  • case (Sun Dec 13 2009 - 09:06:36 CST)
  • Du Yun (Tue Dec 08 2009 - 19:56:48 CST)
• [AMBER] nmode output
  • Vahdati N. (Wed Aug 05 2009 - 17:26:11 CDT)
• [AMBER] nmoldyn2 with Amber
  • Thomas Cheatham (Sun Mar 08 2009 - 15:10:17 CDT)
  • David Watson (Sun Mar 08 2009 - 15:00:39 CDT)
  • M. L. Dodson (Sun Mar 08 2009 - 13:34:03 CDT)
  • M. L. Dodson (Sun Mar 08 2009 - 13:32:22 CDT)
  • David Watson (Sun Mar 08 2009 - 10:02:55 CDT)
  • David Watson (Sun Mar 08 2009 - 09:54:57 CDT)
  • Adrien Delmont (Sun Mar 08 2009 - 09:37:40 CDT)
• [AMBER] nmr refinement of dimer
  • David A. Case (Thu Feb 12 2009 - 07:08:08 CST)
  • Sally Pias (Thu Feb 12 2009 - 03:17:44 CST)
  • David A. Case (Wed Feb 11 2009 - 07:02:37 CST)
  • Therese Malliavin (Wed Feb 11 2009 - 04:57:06 CST)
  • Sally Pias (Wed Feb 11 2009 - 03:05:56 CST)
• [AMBER] NMR restraint
  • Sally Pias (Tue Oct 27 2009 - 23:32:33 CDT)
  • xuemeiwang1103 (Tue Oct 27 2009 - 21:31:39 CDT)
• [AMBER] nmr restraint for angle between vectors
  • Peter Varnai (Fri Aug 28 2009 - 20:10:20 CDT)
• [AMBER] nmropt option
  • Carlos Simmerling (Sat Sep 05 2009 - 05:59:04 CDT)
  • Jio M (Sat Sep 05 2009 - 00:23:09 CDT)
  • Carlos Simmerling (Fri Sep 04 2009 - 13:15:13 CDT)
  • Jio M (Fri Sep 04 2009 - 13:05:25 CDT)
• [AMBER] no equilibrium
  • steinbrt_at_rci.rutgers.edu (Mon May 18 2009 - 22:00:40 CDT)
  • Nancy (Mon May 18 2009 - 21:44:03 CDT)
  • Nancy (Mon May 18 2009 - 21:32:01 CDT)
• [AMBER] no output when running Antechamber(espgen)
  • xueqin pang (Thu Jun 04 2009 - 01:02:32 CDT)
• [AMBER] NO output when running espgen?
  • xueqin pang (Wed Jun 03 2009 - 08:13:06 CDT)
• [AMBER] No restrt file
  • case (Wed Sep 30 2009 - 07:06:47 CDT)
  • null (Wed Sep 30 2009 - 06:39:24 CDT)
  • case (Wed Sep 30 2009 - 05:29:32 CDT)
  • xuemeiwang1103 (Wed Sep 30 2009 - 04:32:38 CDT)
• [AMBER] No sp2 improper torsion term for NB-CA-CB-CB
  • case (Tue Sep 08 2009 - 07:58:33 CDT)
  • qiaoyan (Tue Sep 08 2009 - 07:29:17 CDT)
• [AMBER] NOE
  • David A. Case (Thu Jun 11 2009 - 12:29:06 CDT)
  • Beale, John (Thu Jun 11 2009 - 07:30:36 CDT)
• [AMBER] non bonded parameteters index
  • Adrian Roitberg (Thu Feb 12 2009 - 18:15:33 CST)
  • Alessandro Nascimento (Thu Feb 12 2009 - 18:14:44 CST)
  • Swarup Gupta (Thu Feb 12 2009 - 18:07:46 CST)
• [AMBER] non standard residue
  • FyD (Tue Jul 14 2009 - 15:01:32 CDT)
  • FyD (Tue Jul 14 2009 - 01:47:00 CDT)
  • FyD (Tue Jul 07 2009 - 02:50:09 CDT)
  • Neha Gandhi (Mon Jul 06 2009 - 03:07:35 CDT)
• [AMBER] non standard residue and bond command
  • Bill Ross (Wed Dec 16 2009 - 15:20:08 CST)
  • case (Wed Dec 16 2009 - 15:06:34 CST)
  • Neha Bharat Gajaria (Wed Dec 16 2009 - 03:50:02 CST)
• [AMBER] non standart residue library creation with tleap (Zn atom)
  • Bill Ross (Tue Nov 24 2009 - 12:09:45 CST)
  • Ross Walker (Tue Nov 24 2009 - 10:29:42 CST)
  • Ross Walker (Tue Nov 24 2009 - 10:28:21 CST)
  • Andrew Voronkov (Tue Nov 24 2009 - 08:57:30 CST)
  • FyD (Tue Nov 24 2009 - 08:16:54 CST)
  • Andrew Voronkov (Tue Nov 24 2009 - 04:12:53 CST)
  • FyD (Tue Nov 24 2009 - 03:26:37 CST)
  • Andrew Voronkov (Tue Nov 24 2009 - 02:40:42 CST)
  • FyD (Mon Nov 23 2009 - 13:50:42 CST)
  • FyD (Mon Nov 23 2009 - 11:49:05 CST)
  • Andrew Voronkov (Mon Nov 23 2009 - 11:38:28 CST)
  • FyD (Mon Nov 23 2009 - 11:31:31 CST)
  • FyD (Mon Nov 23 2009 - 11:22:23 CST)
  • Andrew Voronkov (Mon Nov 23 2009 - 10:35:51 CST)
  • FyD (Mon Nov 23 2009 - 10:06:01 CST)
  • Andrew Voronkov (Mon Nov 23 2009 - 09:44:45 CST)
  • FyD (Mon Nov 23 2009 - 07:25:15 CST)
  • Andrew Voronkov (Mon Nov 23 2009 - 06:35:55 CST)
  • FyD (Fri Nov 20 2009 - 11:47:00 CST)
  • Andrew Voronkov (Fri Nov 20 2009 - 10:02:57 CST)
  • FyD (Fri Nov 20 2009 - 09:40:50 CST)
  • Andrew Voronkov (Fri Nov 20 2009 - 09:25:30 CST)
  • Andrew Voronkov (Fri Nov 20 2009 - 09:07:26 CST)
  • FyD (Fri Nov 20 2009 - 07:42:58 CST)
  • case (Fri Nov 20 2009 - 07:30:54 CST)
  • Andrew Voronkov (Fri Nov 20 2009 - 05:35:31 CST)
  • FyD (Wed Nov 18 2009 - 08:29:14 CST)
  • Andrew Voronkov (Wed Nov 18 2009 - 07:19:58 CST)
  • FyD (Tue Nov 17 2009 - 14:10:03 CST)
  • Jason Swails (Tue Nov 17 2009 - 12:05:05 CST)
  • Andrew Voronkov (Tue Nov 17 2009 - 10:34:33 CST)
  • intra\\sa175950 (Tue Nov 17 2009 - 10:18:38 CST)
  • Jason Swails (Tue Nov 17 2009 - 09:57:41 CST)
  • Andrew Voronkov (Tue Nov 17 2009 - 09:47:12 CST)
• [AMBER] non-natural amino acids
  • FyD (Thu Jan 22 2009 - 17:25:31 CST)
  • Arturas Ziemys (Thu Jan 22 2009 - 11:32:11 CST)
• [AMBER] Non-planarity of amide atoms after optimization
  • Sanghwa Han (Wed Jan 07 2009 - 21:17:18 CST)
• [AMBER] Non-Standard Amino Acid Residue LEAP ERROR
  • Ashish Runthala (Fri Jul 31 2009 - 20:39:54 CDT)
  • Brothers, Michael Charles (Fri Jul 31 2009 - 12:36:10 CDT)
  • Ashish Runthala (Thu Jul 30 2009 - 22:40:45 CDT)
  • Brothers, Michael Charles (Thu Jul 30 2009 - 17:28:43 CDT)
• [AMBER] Non-Standard Atoms
  • Jack Shultz (Sun Dec 20 2009 - 18:40:26 CST)
  • case (Sun Dec 20 2009 - 13:02:46 CST)
  • Jason Swails (Sat Dec 19 2009 - 20:54:20 CST)
  • Jack Shultz (Sat Dec 19 2009 - 19:56:28 CST)
• [AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations
  • Dmitry Osolodkin (Mon May 04 2009 - 04:24:59 CDT)
• [AMBER] nonbon.f question
  • Ross Walker (Mon Aug 03 2009 - 13:32:18 CDT)
  • Rizwan Tai (Mon Aug 03 2009 - 11:13:21 CDT)
  • Carlos Simmerling (Mon Jul 27 2009 - 14:34:20 CDT)
  • Rizwan Tai (Mon Jul 27 2009 - 14:30:12 CDT)
  • Rizwan Tai (Mon Jul 20 2009 - 14:31:17 CDT)
• [AMBER] Nonstandard molecules simulated with parm99EP ?
  • Marek Maly (Wed Jul 01 2009 - 11:02:29 CDT)
  • Marek Maly (Wed Jul 01 2009 - 10:47:04 CDT)
  • case (Tue Jun 30 2009 - 11:19:00 CDT)
  • FyD (Tue Jun 30 2009 - 02:31:53 CDT)
  • Marek Maly (Mon Jun 29 2009 - 15:48:52 CDT)
  • FyD (Mon Jun 29 2009 - 13:28:19 CDT)
  • Marek Maly (Mon Jun 29 2009 - 12:06:27 CDT)
• [AMBER] Nonterminal, was not found in name map
  • Bill Ross (Wed Apr 29 2009 - 00:05:12 CDT)
  • Ross Walker (Tue Apr 28 2009 - 21:49:50 CDT)
  • Sunita Patel (Tue Apr 28 2009 - 19:50:08 CDT)
• [AMBER] Normal errors on job kill?
  • David A. Case (Mon Feb 16 2009 - 22:25:54 CST)
  • ben rodriguez (Mon Feb 16 2009 - 20:35:43 CST)
• [AMBER] normal mode analysis
  • David A. Case (Mon May 04 2009 - 13:06:32 CDT)
  • Hannes Wallnoefer (Mon May 04 2009 - 10:56:11 CDT)
  • David A. Case (Mon May 04 2009 - 08:37:02 CDT)
  • Hannes Wallnoefer (Mon May 04 2009 - 04:39:16 CDT)
• [AMBER] Normal mode analysis of water
  • case (Thu Jul 30 2009 - 09:11:23 CDT)
  • bharat lakhani (Thu Jul 30 2009 - 04:27:19 CDT)
• [AMBER] normal modes calculation
  • chaitanya koppisetty (Thu May 14 2009 - 03:51:28 CDT)
  • Neha Gandhi (Wed May 13 2009 - 22:12:13 CDT)
• [AMBER] Not able to compile pmemd with openmpi in Amber9
  • Robert Duke (Wed Nov 25 2009 - 16:48:21 CST)
  • case (Wed Nov 25 2009 - 15:06:53 CST)
  • Ross Walker (Wed Nov 25 2009 - 14:24:23 CST)
  • Jason Swails (Wed Nov 25 2009 - 10:50:41 CST)
  • Kito (Wed Nov 25 2009 - 02:12:51 CST)
  • Kito (Wed Nov 25 2009 - 01:50:25 CST)
  • Kito (Wed Nov 25 2009 - 01:11:00 CST)
  • Jason Swails (Wed Nov 25 2009 - 01:06:14 CST)
  • Kito (Wed Nov 25 2009 - 00:39:42 CST)
• [AMBER] note on Antechamber error
  • Mark M Huntress (Fri Dec 18 2009 - 16:27:50 CST)
• [AMBER] Note regarding posting of the same message multiple times
  • Ross Walker (Mon Aug 24 2009 - 00:19:36 CDT)
• [AMBER] NOTICE: File size limits on AMBER reflector
  • Ross Walker (Tue Jan 27 2009 - 10:35:50 CST)
• [AMBER] NPT md with PME method for a water box
  • Ross Walker (Wed Jan 14 2009 - 12:07:13 CST)
  • Jeffrey (Wed Jan 14 2009 - 08:41:24 CST)
• [AMBER] ntf, ntc with softcore potentials and TI in amber10
  • steinbrt_at_rci.rutgers.edu (Tue May 05 2009 - 22:39:02 CDT)
  • Matthew Wilce (Tue May 05 2009 - 20:33:28 CDT)
• [AMBER] ntt=3 and ibelly=1
  • Kristina Furse (Fri Jul 17 2009 - 11:41:29 CDT)
  • Ross Walker (Thu Jul 16 2009 - 22:44:47 CDT)
  • Kristina Furse (Thu Jul 16 2009 - 11:07:23 CDT)
• [AMBER] ntwr
  • Carlos Simmerling (Wed Apr 08 2009 - 17:45:57 CDT)
  • taufik.alsarraj_at_utoronto.ca (Wed Apr 08 2009 - 17:35:57 CDT)
  • Carlos Simmerling (Wed Apr 08 2009 - 16:47:04 CDT)
  • taufik.alsarraj_at_utoronto.ca (Wed Apr 08 2009 - 16:45:01 CDT)
• [AMBER] Number of Cycles
  • Ross Walker (Tue Dec 15 2009 - 13:01:40 CST)
  • Robert Duke (Tue Dec 15 2009 - 13:00:19 CST)
  • Jason Swails (Tue Dec 15 2009 - 12:32:40 CST)
  • Niel Henriksen (Tue Dec 15 2009 - 12:11:08 CST)
  • Robert Duke (Tue Dec 15 2009 - 11:54:28 CST)
  • Bill Ross (Tue Dec 15 2009 - 11:53:24 CST)
  • Niel Henriksen (Tue Dec 15 2009 - 11:41:55 CST)
  • Robert Duke (Tue Dec 15 2009 - 11:29:22 CST)
  • Jason Swails (Tue Dec 15 2009 - 11:18:37 CST)
  • Carlos Simmerling (Tue Dec 15 2009 - 11:13:17 CST)
  • Jason Swails (Tue Dec 15 2009 - 11:10:31 CST)
  • Robert Duke (Tue Dec 15 2009 - 11:09:42 CST)
  • Carlos Simmerling (Tue Dec 15 2009 - 10:53:06 CST)
  • Robert Duke (Tue Dec 15 2009 - 08:55:31 CST)
  • Jason Swails (Tue Dec 15 2009 - 07:34:29 CST)
  • Jason Swails (Tue Dec 15 2009 - 07:32:31 CST)
  • Carlos Simmerling (Tue Dec 15 2009 - 07:31:09 CST)
  • Robert Duke (Tue Dec 15 2009 - 07:23:04 CST)
  • Robert Duke (Tue Dec 15 2009 - 07:16:51 CST)
  • Jason Swails (Tue Dec 15 2009 - 06:10:02 CST)
  • s. Bill (Tue Dec 15 2009 - 02:31:21 CST)
• [AMBER] Number of LES copies in ptraj
  • Thomas Exner (Tue Apr 21 2009 - 10:28:41 CDT)
• [AMBER] Number of processor in pmemd
  • Robert Duke (Mon May 04 2009 - 12:28:11 CDT)
  • Carlos Simmerling (Mon May 04 2009 - 12:27:06 CDT)
  • Hemant Kumar (Mon May 04 2009 - 12:17:13 CDT)
• [AMBER] number of waters in first and second solvation shell
  • Siddharth Rastogi (Thu Apr 02 2009 - 06:40:21 CDT)
• [AMBER] number-of-EPS-exceeds-MAXESP
  • Karol Kaszuba (Sat Jan 17 2009 - 04:41:22 CST)
  • Karol Kaszuba (Mon Jan 12 2009 - 01:57:50 CST)
  • FyD (Mon Jan 12 2009 - 01:43:48 CST)
  • Karol Kaszuba (Sun Jan 11 2009 - 02:01:07 CST)
  • FyD (Sun Jan 11 2009 - 01:00:40 CST)
  • Karol Kaszuba (Sat Jan 10 2009 - 09:27:08 CST)
  • FyD (Sat Jan 10 2009 - 02:26:13 CST)
  • Karol Kaszuba (Fri Jan 09 2009 - 15:07:13 CST)
• [AMBER] number_rec_numbers in mm_pbsa
  • Zhu, Yong-Liang (Mon Apr 06 2009 - 18:52:06 CDT)
• [AMBER] NVT vs NPT
  • Carlos Simmerling (Wed Feb 18 2009 - 06:18:49 CST)
  • Chih-Ying Lin (Tue Feb 17 2009 - 21:23:05 CST)
• [AMBER] OE and CG types
  • Jio M (Tue Dec 29 2009 - 22:18:51 CST)
  • Carlos Simmerling (Mon Dec 28 2009 - 11:42:41 CST)
  • Dean Cuebas (Sat Dec 26 2009 - 19:10:06 CST)
  • Jason Swails (Fri Dec 25 2009 - 06:32:03 CST)
  • Jio M (Fri Dec 25 2009 - 01:29:19 CST)
  • Carlos Simmerling (Thu Dec 24 2009 - 09:38:24 CST)
  • Jio M (Thu Dec 24 2009 - 09:18:31 CST)
  • Jason Swails (Thu Dec 24 2009 - 06:46:35 CST)
  • Jio M (Thu Dec 24 2009 - 03:26:43 CST)
• [AMBER] Off topic. Hardware problem
  • Francesco Pietra (Sat Jan 10 2009 - 02:26:55 CST)
• [AMBER] ongoing issues using sander with AMOEBA
  • Tomasio, Susana (Wed May 13 2009 - 05:00:00 CDT)
• [AMBER] only ff94 and ff99 for GBSA?
  • FyD (Tue Jul 28 2009 - 02:32:52 CDT)
  • Andrew Voronkov (Tue Jul 28 2009 - 01:12:15 CDT)
  • case (Mon Jul 27 2009 - 12:05:48 CDT)
  • Andrew Voronkov (Mon Jul 27 2009 - 11:41:27 CDT)
  • David A. Case (Wed Jun 03 2009 - 07:24:56 CDT)
  • Andrew Voronkov (Wed Jun 03 2009 - 06:52:13 CDT)
  • Carlos Simmerling (Wed Jun 03 2009 - 05:51:09 CDT)
  • Andrew Voronkov (Wed Jun 03 2009 - 05:28:15 CDT)
• [AMBER] OpenMP
  • michael (Tue Oct 13 2009 - 09:43:09 CDT)
  • Ross Walker (Mon Oct 12 2009 - 13:29:45 CDT)
  • Ben Roberts (Mon Oct 12 2009 - 12:35:35 CDT)
• [AMBER] Optimization problem
  • Gustavo Seabra (Thu Feb 12 2009 - 08:48:23 CST)
  • David A. Case (Thu Feb 12 2009 - 08:35:52 CST)
  • Carlos Simmerling (Thu Feb 12 2009 - 08:21:28 CST)
  • Daniel Emery (Thu Feb 12 2009 - 08:11:14 CST)
  • David A. Case (Thu Feb 12 2009 - 06:58:17 CST)
  • Daniel Emery (Thu Feb 12 2009 - 04:01:49 CST)
• [AMBER] optimization step length
  • Ashish Runthala (Mon Aug 03 2009 - 09:26:28 CDT)
  • ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 05:40:15 CDT)
• [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs
  • David A. Case (Sat Feb 21 2009 - 17:51:38 CST)
  • Piotr Cieplak (Fri Feb 20 2009 - 15:40:14 CST)
• [AMBER] ouput trajectory of only CA atom
  • Jordan Monnet (Wed Jul 08 2009 - 11:03:32 CDT)
  • Vlad Cojocaru (Wed Jul 08 2009 - 10:07:30 CDT)
  • Bala subramanian (Wed Jul 08 2009 - 10:01:27 CDT)
  • Carlos Simmerling (Wed Jul 08 2009 - 09:41:25 CDT)
  • Bala subramanian (Wed Jul 08 2009 - 08:24:56 CDT)
• [AMBER] out error
  • Carlos Simmerling (Tue Feb 03 2009 - 13:18:39 CST)
  • . .. (Tue Feb 03 2009 - 12:58:46 CST)
• [AMBER] Output Does Not Match in Tutorial B1
  • Wallace Kunin (Tue Dec 01 2009 - 12:41:08 CST)
  • Wallace Kunin (Tue Dec 01 2009 - 12:00:48 CST)
  • case (Mon Nov 30 2009 - 13:50:34 CST)
  • Wallace Kunin (Mon Nov 30 2009 - 13:11:02 CST)
  • Bill Ross (Mon Nov 30 2009 - 13:03:19 CST)
  • case (Mon Nov 30 2009 - 13:01:20 CST)
  • Wallace Kunin (Mon Nov 30 2009 - 12:38:07 CST)
• [AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA
  • Sushil Mishra (Mon Jul 20 2009 - 05:40:51 CDT)
• [AMBER] Output forces in Sander
  • case (Mon Jul 27 2009 - 10:11:30 CDT)
  • Frank X. Vázquez (Tue Jul 21 2009 - 16:58:36 CDT)
• [AMBER] pairwise per-residue decomposition
  • manoj singh (Sat Oct 31 2009 - 23:59:38 CDT)
  • manoj singh (Fri Oct 30 2009 - 13:26:14 CDT)
  • Tom Joseph (Fri Oct 30 2009 - 13:18:52 CDT)
  • manoj singh (Fri Oct 30 2009 - 00:46:22 CDT)
  • Tom Joseph (Fri Oct 30 2009 - 00:15:40 CDT)
  • Tom Joseph (Thu Oct 29 2009 - 19:30:51 CDT)
  • manoj singh (Thu Oct 29 2009 - 12:32:38 CDT)
  • Carlos Simmerling (Thu Oct 29 2009 - 05:20:55 CDT)
  • manoj singh (Wed Oct 28 2009 - 23:34:32 CDT)
• [AMBER] paper of interest for FF development/solvent models
  • David Mobley (Thu Feb 19 2009 - 09:15:04 CST)
• [AMBER] Papers on Amber package usage
  • David A. Case (Sun Apr 26 2009 - 07:48:31 CDT)
  • Andrew Voronkov (Sun Apr 26 2009 - 00:07:42 CDT)
• [AMBER] parallel amber on cluster
  • David A. Case (Mon May 18 2009 - 06:54:18 CDT)
  • Siavoush Dastmalchi (Mon May 18 2009 - 01:04:58 CDT)
• [AMBER] parallel error
  • Tom Joseph (Mon Jun 15 2009 - 06:54:19 CDT)
  • å»–é�’å�Ž (Mon Jun 15 2009 - 02:31:27 CDT)
• [AMBER] parallel installation of amber on sun
  • Atro Tossavainen (Fri Apr 03 2009 - 17:33:52 CDT)
  • Atro Tossavainen (Fri Apr 03 2009 - 16:40:42 CDT)
  • Per Jr. Greisen (Fri Apr 03 2009 - 05:22:45 CDT)
  • Atro Tossavainen (Fri Apr 03 2009 - 04:39:25 CDT)
  • Per Jr. Greisen (Thu Apr 02 2009 - 15:38:54 CDT)
  • Atro Tossavainen (Thu Apr 02 2009 - 15:23:05 CDT)
  • Per Jr. Greisen (Thu Apr 02 2009 - 14:02:47 CDT)
• [AMBER] parallel problem of QM/MM calculation for AMBER 9
  • liu junjun (Tue Apr 28 2009 - 21:18:31 CDT)
  • Ross Walker (Tue Apr 28 2009 - 17:24:12 CDT)
  • liu junjun (Tue Apr 28 2009 - 16:53:06 CDT)
• [AMBER] parallel run error
  • Carlos Simmerling (Tue Feb 17 2009 - 06:40:03 CST)
  • balaji nagarajan (Tue Feb 17 2009 - 02:19:23 CST)
• [AMBER] Parallel sander & polarisability
  • case (Thu Oct 29 2009 - 12:02:28 CDT)
  • Ross Walker (Thu Oct 29 2009 - 12:00:13 CDT)
  • Thomas Taylor (Thu Oct 29 2009 - 11:19:14 CDT)
• [AMBER] Parallelepiped periodic box
  • David A. Case (Fri Jan 16 2009 - 13:50:32 CST)
  • Ian Streeter (Mon Jan 12 2009 - 09:57:55 CST)
• [AMBER] Parameter file content
  • Tom Joseph (Sat May 30 2009 - 21:23:48 CDT)
  • manoj singh (Sat May 30 2009 - 20:53:37 CDT)
• [AMBER] parameter file for the sulphate ion
  • Fenghui Fan (Thu Dec 03 2009 - 18:02:30 CST)
• [AMBER] Parameter file not saved
  • Carlos Simmerling (Mon May 04 2009 - 07:19:14 CDT)
  • Remya S R (Mon May 04 2009 - 07:03:08 CDT)
  • Remya S R (Mon May 04 2009 - 01:30:19 CDT)
• [AMBER] parameter files for D-amino acid
  • Carlos Simmerling (Thu Feb 05 2009 - 09:10:18 CST)
  • Andrew Purkiss-Trew (Thu Feb 05 2009 - 09:02:25 CST)
  • Carlos Simmerling (Thu Feb 05 2009 - 09:06:09 CST)
  • FyD (Thu Feb 05 2009 - 09:00:55 CST)
  • vijayaraj_at_clri.res.in (Thu Feb 05 2009 - 08:49:56 CST)
  • Carlos Simmerling (Thu Feb 05 2009 - 07:37:32 CST)
  • Vsatheesh Patil (Thu Feb 05 2009 - 07:04:12 CST)
• [AMBER] parameter for amoeba
  • Hemant Kumar (Sat Apr 04 2009 - 06:46:01 CDT)
• [AMBER] parameter for dihedral angle
  • Catein Catherine (Sun Jun 07 2009 - 22:08:17 CDT)
  • David A. Case (Sat Jun 06 2009 - 07:47:35 CDT)
  • raja pandian (Sat Jun 06 2009 - 00:13:52 CDT)
  • David A. Case (Fri Jun 05 2009 - 14:50:03 CDT)
  • Jorgen Simonsen (Fri Jun 05 2009 - 10:16:56 CDT)
• [AMBER] parameter for manganese
  • Mahmoud A. A. Ibrahim (Thu Sep 24 2009 - 07:17:29 CDT)
  • Yuqin Cai (Tue Sep 22 2009 - 17:48:41 CDT)
• [AMBER] Parameter Problem
  • Manish Kumar (Wed Sep 23 2009 - 08:28:11 CDT)
  • FyD (Wed Sep 23 2009 - 03:28:49 CDT)
  • manoj singh (Tue Sep 22 2009 - 14:46:59 CDT)
  • manoj singh (Tue Sep 22 2009 - 14:35:53 CDT)
• [AMBER] parameterization of protein-ligand complex
  • Jeff Yeo (Mon Sep 14 2009 - 10:03:25 CDT)
  • cc cc (Wed Sep 09 2009 - 12:44:17 CDT)
  • cc cc (Wed Sep 09 2009 - 12:41:52 CDT)
  • Bill Ross (Wed Sep 09 2009 - 12:12:28 CDT)
  • case (Wed Sep 09 2009 - 11:39:05 CDT)
  • cc cc (Wed Sep 09 2009 - 11:29:07 CDT)
• [AMBER] parameters Fe4S4 cluster
  • KIRTANA S (Sun Jun 21 2009 - 21:30:08 CDT)
• [AMBER] Parameters for haloacetates
  • Joseph Nachman (Mon Aug 10 2009 - 09:54:13 CDT)
  • Lili Peng (Fri Aug 07 2009 - 23:43:50 CDT)
  • Joseph Nachman (Fri Aug 07 2009 - 13:22:34 CDT)
• [AMBER] parameters for HIV protease inhibitors
  • FyD (Wed Aug 12 2009 - 07:56:18 CDT)
  • Oliver Kuhn (Tue Aug 11 2009 - 09:57:24 CDT)
  • Carlos Simmerling (Thu Aug 06 2009 - 10:29:39 CDT)
  • Oliver Kuhn (Thu Aug 06 2009 - 09:51:03 CDT)
• [AMBER] Parameters for HYP and CGU
  • Alessandro Contini (Thu Dec 17 2009 - 03:11:44 CST)
  • FyD (Thu Dec 17 2009 - 02:46:55 CST)
  • Rilei Yu (Wed Dec 16 2009 - 23:58:26 CST)
  • Rilei Yu (Wed Dec 16 2009 - 23:57:13 CST)
  • Jason Swails (Wed Dec 16 2009 - 21:58:02 CST)
  • Adrian Roitberg (Wed Dec 16 2009 - 21:27:25 CST)
  • Rilei Yu (Wed Dec 16 2009 - 21:17:40 CST)
• [AMBER] parameters for O2 molecule
  • Jeffrey (Thu Oct 29 2009 - 08:01:44 CDT)
  • Jason Swails (Thu Oct 22 2009 - 09:19:51 CDT)
  • Jeffrey (Thu Oct 22 2009 - 08:32:07 CDT)
• [AMBER] Parametrisation of Silicon based molecules for Amber simulations ?
  • Marek Malý (Thu Mar 19 2009 - 18:49:21 CDT)
• [AMBER] Parametrizing charges for modified DNA bases
  • FyD (Mon Dec 07 2009 - 13:31:02 CST)
  • Bob Johnson (Mon Dec 07 2009 - 12:05:09 CST)
• [AMBER] PARMCAL calculation ?
  • Marek Maly (Wed May 27 2009 - 09:19:48 CDT)
• [AMBER] parmchk
  • Ross Walker (Mon Feb 09 2009 - 10:28:20 CST)
  • s. Bill (Mon Feb 09 2009 - 09:55:20 CST)
• [AMBER] parmchk problem
  • case (Tue Aug 11 2009 - 08:51:57 CDT)
  • isaac sugden (Wed Aug 05 2009 - 12:21:53 CDT)
  • case (Wed Aug 05 2009 - 11:36:27 CDT)
  • isaac sugden (Tue Aug 04 2009 - 09:12:29 CDT)
• [AMBER] Parmchk wrongly calculates missing parameters (fwd)
  • Gijs Schaftenaar (Fri Feb 20 2009 - 07:16:17 CST)
• [AMBER] PARMSCAN
  • alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:41:54 CDT)
  • alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:26:42 CDT)
• [AMBER] part of the protein escaped from the water box
  • Jason Swails (Thu Oct 15 2009 - 06:43:00 CDT)
  • case (Thu Oct 15 2009 - 06:40:53 CDT)
  • Carlos Simmerling (Thu Oct 15 2009 - 06:39:40 CDT)
  • qiaoyan (Thu Oct 15 2009 - 06:33:00 CDT)
• [AMBER] partial charge and topology of intrastrand cross-link DNA
  • FyD (Wed May 27 2009 - 00:27:40 CDT)
  • Shuang Ding (Mon May 25 2009 - 21:27:43 CDT)
• [AMBER] partial charges from AM1-BCC and RESP differ a lot
  • FyD (Wed Jun 17 2009 - 01:32:11 CDT)
  • xueqin pang (Tue Jun 16 2009 - 02:57:25 CDT)
  • FyD (Thu Jun 11 2009 - 13:59:27 CDT)
  • xueqin pang (Wed Jun 10 2009 - 07:39:31 CDT)
• [AMBER] partial charges in Amber force field
  • FyD (Mon Sep 28 2009 - 13:32:42 CDT)
  • Jihang Wang (Mon Sep 28 2009 - 12:52:28 CDT)
• [AMBER] Partial charges of heme
  • Justine Shaw Condo (Tue Jun 30 2009 - 13:28:11 CDT)
• [AMBER] partial charges of lipid membrane for GPCR system
  • xueqin pang (Tue May 26 2009 - 08:34:34 CDT)
• [AMBER] Partial entropy calculations ?
  • Piotr Cieplak (Fri Feb 27 2009 - 12:44:21 CST)
  • Marek Malý (Fri Feb 27 2009 - 12:21:29 CST)
• [AMBER] Partial interactions
  • steinbrt_at_rci.rutgers.edu (Fri Apr 24 2009 - 12:48:58 CDT)
  • Ignacio J. General (Fri Apr 24 2009 - 12:11:31 CDT)
  • steinbrt_at_rci.rutgers.edu (Fri Apr 24 2009 - 11:20:21 CDT)
  • Ignacio J. General (Fri Apr 24 2009 - 09:49:07 CDT)
  • steinbrt_at_rci.rutgers.edu (Wed Apr 22 2009 - 21:55:52 CDT)
  • Ignacio J. General (Wed Apr 22 2009 - 14:02:00 CDT)
  • steinbrt_at_rci.rutgers.edu (Tue Apr 21 2009 - 10:17:55 CDT)
  • Ignacio J. General (Tue Apr 21 2009 - 09:31:26 CDT)
  • steinbrt_at_rci.rutgers.edu (Mon Apr 20 2009 - 16:47:35 CDT)
  • Ignacio J. General (Mon Apr 20 2009 - 16:07:24 CDT)
• [AMBER] Particle-mesh Ewald method
  • Ross Walker (Mon Mar 09 2009 - 14:53:52 CDT)
  • Yunjie Zhao (Mon Mar 09 2009 - 04:46:15 CDT)
• [AMBER] Patching terminal
  • Manish Kumar (Tue Jul 21 2009 - 18:53:54 CDT)
• [AMBER] PB Bomb from MM-PBSA of Amber 10
  • Ray Luo (Tue Mar 10 2009 - 11:28:15 CDT)
  • Wei Huang (Tue Mar 10 2009 - 11:20:29 CDT)
  • Zhu, Yong-Liang (Tue Mar 10 2009 - 11:06:43 CDT)
  • Wei Huang (Tue Mar 10 2009 - 05:30:50 CDT)
  • Zhu, Yong-Liang (Mon Mar 09 2009 - 23:30:33 CDT)
• [AMBER] PBSA for gp41 binding free energy
  • Ray Luo (Fri Sep 11 2009 - 20:59:07 CDT)
  • shuqing wang (Fri Sep 11 2009 - 01:42:59 CDT)
• [AMBER] PBSA Radii option
  • quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 14:31:18 CDT)
• [AMBER] PBSA: PB bomb in pb_setgrd()
  • Ray Luo (Wed Jan 07 2009 - 12:24:15 CST)
  • Larry Layne (Wed Jan 07 2009 - 09:33:57 CST)
• [AMBER] PCA analysis with ptraj
  • Alessandro Contini (Tue Nov 10 2009 - 06:03:48 CST)
  • hannes.loeffler_at_stfc.ac.uk (Tue Nov 10 2009 - 02:13:29 CST)
  • Alessandro Contini (Mon Nov 09 2009 - 11:00:19 CST)
• [AMBER] PCA analysis: the first vector is the movement of whole molecule.
  • Catein Catherine (Sun Aug 02 2009 - 22:47:07 CDT)
  • Hannes Loeffler (Fri Jul 31 2009 - 02:27:54 CDT)
  • Catein Catherine (Thu Jul 30 2009 - 22:46:49 CDT)
  • Hannes Loeffler (Thu Jul 30 2009 - 05:52:48 CDT)
  • Catein Catherine (Thu Jul 30 2009 - 05:37:49 CDT)
• [AMBER] PCA for CA of specific resiudes
  • case (Thu Jun 25 2009 - 07:27:01 CDT)
  • Patrick Gedeon (Thu Jun 25 2009 - 06:43:20 CDT)
• [AMBER] PCL
  • Ross Walker (Sat Feb 28 2009 - 11:23:30 CST)
  • waleed zalloum (Sat Feb 28 2009 - 11:17:51 CST)
• [AMBER] pdb file no bond and charges
  • Jio M (Wed Jul 29 2009 - 01:28:48 CDT)
• [AMBER] PDB of a specific frame
  • Carlos Simmerling (Wed Feb 04 2009 - 13:52:49 CST)
  • Jason A. Ford-Green (Wed Feb 04 2009 - 13:46:52 CST)
• [AMBER] PDMED
  • Ross Walker (Tue Jun 09 2009 - 01:35:25 CDT)
  • Catein Catherine (Tue Jun 09 2009 - 01:18:59 CDT)
  • Ross Walker (Tue Jun 09 2009 - 00:19:36 CDT)
  • Catein Catherine (Mon Jun 08 2009 - 23:28:58 CDT)
• [AMBER] PEMD
  • Tom Joseph (Mon Oct 26 2009 - 18:03:26 CDT)
  • Cristina Sisu (Mon Oct 26 2009 - 16:44:42 CDT)
• [AMBER] Pentane UA model
  • FyD (Tue Sep 22 2009 - 02:02:50 CDT)
  • aneesh cna (Tue Sep 22 2009 - 01:23:35 CDT)
• [AMBER] Pentavalent Phosphorous and Antechamber
  • FyD (Thu Jun 04 2009 - 01:29:59 CDT)
  • Shubhra Gupta (Wed Jun 03 2009 - 23:37:08 CDT)
  • David A. Case (Wed Jun 03 2009 - 11:35:26 CDT)
  • Peterson, Matthew W. (Wed Jun 03 2009 - 09:12:44 CDT)
• [AMBER] Peptide bond broken
  • Syed Tarique Moin (Mon Jul 13 2009 - 08:20:02 CDT)
  • Shubhra Gupta (Sun Jul 12 2009 - 23:17:31 CDT)
  • case (Sun Jul 12 2009 - 21:35:35 CDT)
  • FyD (Sat Jul 11 2009 - 01:58:06 CDT)
  • Syed Tarique Moin (Fri Jul 10 2009 - 13:19:02 CDT)
• [AMBER] per atom energies in sander/pmemd
  • Tamara Rogers (Tue Apr 21 2009 - 18:41:27 CDT)
• [AMBER] perform an analysis using ptraj
  • oguz gurbulak (Tue Feb 24 2009 - 10:19:11 CST)
• [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command
  • case (Thu Sep 10 2009 - 21:04:53 CDT)
  • Workalemahu Berhanu (Thu Sep 10 2009 - 17:37:32 CDT)
• [AMBER] PES QM and MM
  • Bill Ross (Thu Sep 17 2009 - 11:08:35 CDT)
  • s. Bill (Thu Sep 17 2009 - 05:53:46 CDT)
• [AMBER] pH calculations
  • Michael Durney (Thu Sep 17 2009 - 10:01:08 CDT)
• [AMBER] PhD position in Computational Structural Biology at Cambridge, UK
  • Swanand Gore (Wed Jan 28 2009 - 04:31:16 CST)
• [AMBER] phosphorus to carbon on minimization
  • FyD (Mon Dec 07 2009 - 12:56:28 CST)
  • Jason Swails (Mon Dec 07 2009 - 12:43:05 CST)
  • Alexander Boncheff (Mon Dec 07 2009 - 09:48:45 CST)
• [AMBER] Phosphorylated Threonine
  • FyD (Tue Nov 03 2009 - 13:41:49 CST)
  • Beale, John (Tue Nov 03 2009 - 10:31:09 CST)
• [AMBER] Phosphothreonine
  • Anselm Horn (Thu Nov 05 2009 - 07:17:59 CST)
  • Beale, John (Thu Nov 05 2009 - 07:03:58 CST)
  • David A. Case (Wed Jan 07 2009 - 13:29:35 CST)
  • Khaled Barakat (Wed Jan 07 2009 - 13:11:43 CST)
• [AMBER] PIMD test stalling
  • peker milas (Tue Dec 08 2009 - 20:23:45 CST)
• [AMBER] PK zero for specific dihedral and parmchk
  • case (Wed Sep 09 2009 - 06:32:51 CDT)
  • Carlos Simmerling (Wed Sep 09 2009 - 05:23:31 CDT)
  • Loeffler, Hannes (STFC,DL,CSE) (Wed Sep 09 2009 - 03:00:20 CDT)
• [AMBER] pKa data base....
  • s. Bill (Mon Jun 15 2009 - 11:01:14 CDT)
• [AMBER] PLEASE HELP - PDB Modification
  • Tom Joseph (Sun Jun 14 2009 - 18:36:16 CDT)
  • s_bill36_at_yahoo.co.uk (Sun Jun 14 2009 - 12:29:31 CDT)
• [AMBER] Please help me out
  • case (Wed Jul 15 2009 - 14:55:21 CDT)
  • bharat lakhani (Wed Jul 15 2009 - 05:43:21 CDT)
  • Wei Zhang (Sun May 10 2009 - 08:21:06 CDT)
  • Nancy (Sun May 10 2009 - 02:56:33 CDT)
  • bharat lakhani (Thu Apr 16 2009 - 01:41:08 CDT)
  • David A. Case (Thu Apr 09 2009 - 06:46:12 CDT)
  • bharat lakhani (Thu Apr 09 2009 - 00:10:22 CDT)
  • David A. Case (Wed Apr 08 2009 - 13:10:04 CDT)
  • Hugh Heldenbrand (Wed Apr 08 2009 - 10:44:54 CDT)
  • Ross Walker (Wed Apr 08 2009 - 10:34:51 CDT)
  • bharat lakhani (Wed Apr 08 2009 - 04:18:41 CDT)
  • David A. Case (Thu Apr 02 2009 - 12:48:10 CDT)
  • bharat lakhani (Thu Apr 02 2009 - 05:13:48 CDT)
  • bharat lakhani (Tue Mar 24 2009 - 08:57:18 CDT)
  • bharat lakhani (Mon Mar 23 2009 - 02:58:52 CDT)
  • Ross Walker (Sat Mar 14 2009 - 11:54:22 CDT)
  • David A. Case (Sat Mar 14 2009 - 08:06:34 CDT)
  • bharat lakhani (Sat Mar 14 2009 - 06:04:37 CDT)
  • rpaduri_at_chem.wayne.edu (Thu Mar 12 2009 - 11:37:09 CDT)
  • bharat lakhani (Thu Mar 12 2009 - 01:04:00 CDT)
  • FyD (Mon Mar 09 2009 - 05:05:06 CDT)
  • bharat lakhani (Mon Mar 09 2009 - 03:43:08 CDT)
  • FyD (Mon Mar 09 2009 - 03:10:08 CDT)
  • bharat lakhani (Mon Mar 09 2009 - 00:04:45 CDT)
  • bharat lakhani (Thu Mar 05 2009 - 05:16:45 CST)
  • FyD (Thu Mar 05 2009 - 03:22:20 CST)
  • bharat lakhani (Thu Mar 05 2009 - 02:35:44 CST)
• [AMBER] please read this mail
  • David A. Case (Sat Apr 18 2009 - 08:01:08 CDT)
  • bharat lakhani (Sat Apr 18 2009 - 02:38:12 CDT)
• [AMBER] PLUMED release 1.0.0 available
  • Massimiliano Bonomi (Thu Feb 26 2009 - 07:11:54 CST)
• [AMBER] PLUMED release 1.1.0 available
  • Massimiliano Bonomi (Tue Jul 28 2009 - 03:10:39 CDT)
• [AMBER] PME doesn't work
  • Robert Duke (Mon Feb 23 2009 - 07:48:04 CST)
  • Carlos Simmerling (Mon Feb 23 2009 - 06:08:07 CST)
  • parul sharma (Mon Feb 23 2009 - 06:03:54 CST)
  • Carlos Simmerling (Mon Feb 23 2009 - 05:19:27 CST)
  • parul sharma (Mon Feb 23 2009 - 03:43:40 CST)
• [AMBER] pmemd
  • Robert Duke (Mon Aug 24 2009 - 08:42:05 CDT)
  • michael (Sat Aug 15 2009 - 06:30:28 CDT)
  • Ross Walker (Mon Aug 10 2009 - 19:00:12 CDT)
  • michael (Mon Aug 10 2009 - 14:51:59 CDT)
  • case (Fri Aug 07 2009 - 10:18:52 CDT)
  • michael (Fri Aug 07 2009 - 04:50:29 CDT)
• [AMBER] PMEMD 10 overflow issues
  • Ross Walker (Sat Aug 22 2009 - 12:25:31 CDT)
  • Ross Walker (Sat Aug 22 2009 - 12:21:30 CDT)
  • Ashish Runthala (Fri Aug 21 2009 - 21:52:55 CDT)
  • ben rodriguez (Fri Aug 21 2009 - 16:17:36 CDT)
  • Ross Walker (Fri Aug 21 2009 - 15:57:12 CDT)
  • ben rodriguez (Fri Aug 21 2009 - 15:38:05 CDT)
• [AMBER] PMEMD 9 on MVAPICH / Infiniband problem
  • Robert Duke (Tue Mar 31 2009 - 07:21:22 CDT)
  • fohm fohm (Tue Mar 31 2009 - 06:04:10 CDT)
  • Ross Walker (Fri Mar 27 2009 - 20:04:04 CDT)
  • Nick Holway (Fri Mar 27 2009 - 10:55:38 CDT)
• [AMBER] pmemd and internal dielectric
  • Robert Duke (Fri Sep 25 2009 - 17:19:10 CDT)
  • case (Fri Sep 25 2009 - 16:59:56 CDT)
  • Robert Duke (Fri Sep 25 2009 - 15:10:57 CDT)
  • Serguei Vassiliev (Fri Sep 25 2009 - 14:47:46 CDT)
  • Adrian Roitberg (Fri Sep 25 2009 - 11:44:56 CDT)
  • Robert Duke (Fri Sep 25 2009 - 11:07:06 CDT)
  • Serguei Vassiliev (Fri Sep 25 2009 - 10:47:50 CDT)
• [AMBER] PMEMD compilation
  • Ross Walker (Sat Jun 20 2009 - 23:32:18 CDT)
  • manoj singh (Sat Jun 20 2009 - 23:30:17 CDT)
  • manoj singh (Sat Jun 20 2009 - 23:22:01 CDT)
  • Ross Walker (Sat Jun 20 2009 - 23:15:23 CDT)
  • manoj singh (Sat Jun 20 2009 - 23:05:44 CDT)
  • Ross Walker (Sat Jun 20 2009 - 12:36:14 CDT)
  • manoj singh (Fri Jun 19 2009 - 17:49:31 CDT)
• [AMBER] pmemd compilation error
  • john smith (Tue May 05 2009 - 06:20:08 CDT)
  • Robert Duke (Mon Apr 27 2009 - 23:09:15 CDT)
  • john smith (Mon Apr 27 2009 - 22:30:21 CDT)
• [AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o
  • Vijay Manickam Achari (Mon Apr 06 2009 - 02:27:24 CDT)
• [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o
  • Vijay Manickam Achari (Mon Apr 06 2009 - 23:25:36 CDT)
  • Robert Duke (Mon Apr 06 2009 - 09:25:14 CDT)
• [AMBER] pmemd compilation/make failed-mkl_vml_service_threader_z_1i_c_1o
  • Robert Duke (Tue Apr 07 2009 - 07:43:36 CDT)
• [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
  • Vijay Manickam Achari (Wed Apr 08 2009 - 01:27:46 CDT)
  • Robert Duke (Tue Apr 07 2009 - 07:55:00 CDT)
• [AMBER] pmemd compile error
  • Robert Duke (Mon Mar 23 2009 - 16:03:45 CDT)
  • Giorgos Lamprinidis (Mon Mar 23 2009 - 15:54:37 CDT)
• [AMBER] pmemd compile error....
  • Robert Duke (Tue Mar 24 2009 - 07:19:45 CDT)
  • case (Tue Mar 24 2009 - 07:12:46 CDT)
  • Yiannis Georgiadis (Tue Mar 24 2009 - 15:10:27 CDT)
  • Robert Duke (Thu Mar 19 2009 - 10:25:04 CDT)
  • Robert Duke (Thu Mar 19 2009 - 10:24:29 CDT)
  • Giorgos Lamprinidis (Thu Mar 19 2009 - 10:06:04 CDT)
• [AMBER] PMEMD error message
  • Robert Duke (Tue Mar 10 2009 - 10:39:38 CDT)
  • neville forlemu (Tue Mar 10 2009 - 09:55:31 CDT)
  • Ross Walker (Sun Mar 08 2009 - 16:52:01 CDT)
  • Robert Duke (Sun Mar 08 2009 - 15:47:16 CDT)
  • neville forlemu (Sun Mar 08 2009 - 15:37:09 CDT)
• [AMBER] pmemd failure
  • Francesco Pietra (Sun Nov 08 2009 - 13:08:53 CST)
  • Robert Duke (Sun Nov 08 2009 - 11:00:52 CST)
  • Francesco Pietra (Sun Nov 08 2009 - 10:52:28 CST)
• [AMBER] pmemd ifort problem
  • Robert Duke (Fri Oct 23 2009 - 10:33:27 CDT)
  • Sel Ercan (Fri Oct 23 2009 - 09:57:59 CDT)
• [AMBER] PMEMD in a Cygwin Environment
  • Robert Duke (Tue Jul 14 2009 - 15:16:46 CDT)
  • Hopkins, Robert (Tue Jul 14 2009 - 14:48:41 CDT)
• [AMBER] PMEMD in a Cygwin Environment 8%
  • Hopkins, Robert (Thu Jul 23 2009 - 15:37:12 CDT)
• [AMBER] pmemd in amber10 - compile failed in HPC
  • Robert Duke (Thu Apr 16 2009 - 07:24:45 CDT)
  • Vijay Manickam Achari (Thu Apr 16 2009 - 05:13:49 CDT)
• [AMBER] pmemd installation in intelmpi
  • Vijay Manickam Achari (Thu Feb 05 2009 - 02:38:38 CST)
  • Robert Duke (Wed Feb 04 2009 - 22:34:37 CST)
  • Vijay Manickam Achari (Wed Feb 04 2009 - 21:16:06 CST)
• [AMBER] pmemd on BlueGene/P?
  • Hannes Loeffler (Fri Feb 06 2009 - 03:01:37 CST)
  • Carlos P Sosa (Thu Feb 05 2009 - 14:48:57 CST)
  • Robert Duke (Thu Feb 05 2009 - 07:42:32 CST)
  • Hannes Loeffler (Thu Feb 05 2009 - 07:09:45 CST)
• [AMBER] pmemd running very slow in amber10
  • Robert Duke (Thu May 14 2009 - 08:38:29 CDT)
  • Ross Walker (Thu May 14 2009 - 07:57:43 CDT)
  • Carlos Simmerling (Thu May 14 2009 - 05:09:11 CDT)
  • Vijay Manickam Achari (Thu May 14 2009 - 00:41:40 CDT)
• [AMBER] PMEMD vs GROMACS?
  • Sasha Buzko (Tue Feb 24 2009 - 11:15:59 CST)
  • Vlad Cojocaru (Tue Feb 24 2009 - 02:46:36 CST)
  • Hannes Loeffler (Tue Feb 24 2009 - 02:39:29 CST)
  • Vlad Cojocaru (Tue Feb 24 2009 - 02:24:16 CST)
  • Sasha Buzko (Mon Feb 23 2009 - 13:55:27 CST)
• [AMBER] pmemd vs sander.MPI
  • Marek Maly (Thu Nov 05 2009 - 17:58:50 CST)
  • Ross Walker (Thu Nov 05 2009 - 16:58:37 CST)
  • Marek Maly (Thu Nov 05 2009 - 12:47:06 CST)
  • Marek Maly (Thu Nov 05 2009 - 12:34:31 CST)
  • Ross Walker (Thu Nov 05 2009 - 12:27:19 CST)
  • Robert Duke (Thu Nov 05 2009 - 12:06:24 CST)
  • Marek Maly (Thu Nov 05 2009 - 12:03:08 CST)
  • Robert Duke (Thu Nov 05 2009 - 07:35:41 CST)
  • Marek Maly (Thu Nov 05 2009 - 07:36:39 CST)
  • Ross Walker (Wed Nov 04 2009 - 12:33:23 CST)
  • Taufik Al-Sarraj (Wed Nov 04 2009 - 11:32:05 CST)
• [AMBER] pmemd | Compilation problem with ifort and mvapich environment
  • Ross Walker (Wed Jan 14 2009 - 11:53:20 CST)
  • fohm fohm (Wed Jan 14 2009 - 11:23:50 CST)
• [AMBER] pmemd/bintraj and ifort 10.1.0.21
  • Robert Duke (Wed Jul 01 2009 - 13:54:52 CDT)
  • Peter Varnai (Wed Jul 01 2009 - 13:28:30 CDT)
• [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o
  • Vijay Manickam Achari (Thu Apr 09 2009 - 04:55:53 CDT)
  • Ross Walker (Wed Apr 08 2009 - 09:53:31 CDT)
• [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
  • Robert Duke (Wed Apr 08 2009 - 08:35:49 CDT)
  • Robert Duke (Wed Apr 08 2009 - 07:13:23 CDT)
• [AMBER] PMF calculation
  • David A. Case (Tue Feb 17 2009 - 20:23:20 CST)
  • Arnaud (Tue Feb 17 2009 - 12:10:18 CST)
• [AMBER] POL3
  • Hemant Kumar (Sun Jun 07 2009 - 13:27:29 CDT)
• [AMBER] POL3 & SHAKE
  • David A. Case (Wed Jun 10 2009 - 14:11:40 CDT)
  • Hemant Gangwar (Tue Jun 09 2009 - 15:53:27 CDT)
• [AMBER] polarizable force field and solvent
  • zeinab bagheri (Thu Mar 12 2009 - 00:40:33 CDT)
  • zeinab bagheri (Wed Mar 11 2009 - 17:02:06 CDT)
• [AMBER] polarizable force field for 18-crown-6
  • Piotr Cieplak (Fri Apr 17 2009 - 02:48:03 CDT)
  • Gert von Helden (Thu Apr 16 2009 - 12:33:15 CDT)
• [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing
  • Piotr Cieplak (Mon Apr 27 2009 - 14:07:38 CDT)
  • David A. Case (Mon Apr 27 2009 - 12:30:55 CDT)
  • Tommaso Cupido (Mon Apr 27 2009 - 09:10:12 CDT)
• [AMBER] Polarizable simulation of the slab
  • Robert Duke (Fri Nov 27 2009 - 10:48:07 CST)
  • Jan Heyda (Fri Nov 27 2009 - 10:27:13 CST)
  • case (Fri Nov 27 2009 - 10:10:38 CST)
  • Jan Heyda (Fri Nov 27 2009 - 08:53:57 CST)
  • case (Fri Nov 27 2009 - 08:24:41 CST)
  • Jan Heyda (Thu Nov 26 2009 - 12:20:52 CST)
  • Jan Heyda (Sun Nov 22 2009 - 07:13:16 CST)
• [AMBER] POLARIZABLE WATER MODEL
  • CHAMI F. (Tue Mar 24 2009 - 13:03:25 CDT)
• [AMBER] position v time graph
  • Shozeb Haider (Wed Jul 15 2009 - 13:21:35 CDT)
• [AMBER] positive value of binding enrgy after MM PBSA
  • Vikas Sharma (Wed May 06 2009 - 10:07:03 CDT)
• [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
  • Lachele Foley (Lists) (Fri Apr 17 2009 - 13:13:49 CDT)
  • quantum_mania_at_yahoo.com (Fri Apr 17 2009 - 12:52:28 CDT)
  • Marek Malý (Thu Apr 16 2009 - 16:25:12 CDT)
  • Carlos Simmerling (Wed Apr 15 2009 - 08:33:00 CDT)
  • Karl Kirschner (Wed Apr 15 2009 - 02:07:00 CDT)
  • Marek Malý (Tue Apr 14 2009 - 19:40:22 CDT)
  • Ross Walker (Tue Apr 14 2009 - 18:27:37 CDT)
  • Marek Malý (Tue Apr 14 2009 - 18:18:18 CDT)
  • Ross Walker (Mon Apr 13 2009 - 23:10:38 CDT)
  • Marek Malý (Mon Apr 13 2009 - 22:29:17 CDT)
• [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
  • Marek Malý (Thu Apr 23 2009 - 09:30:07 CDT)
  • Karl Kirschner (Thu Apr 23 2009 - 08:54:14 CDT)
  • Marek Malý (Thu Apr 23 2009 - 08:41:03 CDT)
  • Karl Kirschner (Thu Apr 23 2009 - 06:43:31 CDT)
  • Marek Malý (Tue Apr 21 2009 - 21:31:34 CDT)
  • Karl Kirschner (Tue Apr 21 2009 - 02:24:18 CDT)
  • Marek Malý (Mon Apr 20 2009 - 22:52:46 CDT)
  • FyD (Mon Apr 20 2009 - 09:50:12 CDT)
  • Karl Kirschner (Mon Apr 20 2009 - 07:27:45 CDT)
  • Marek Malý (Mon Apr 20 2009 - 06:52:36 CDT)
• [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
  • Carlos Simmerling (Tue Oct 27 2009 - 18:22:43 CDT)
  • Han Zheng (Tue Oct 27 2009 - 17:47:20 CDT)
  • Seetin, Matthew (Tue Oct 27 2009 - 16:17:41 CDT)
  • Han Zheng (Tue Oct 27 2009 - 12:28:16 CDT)
• [AMBER] Postdoc Position Available at SDSC/UCSD
  • Ross Walker (Wed Jan 14 2009 - 14:35:52 CST)
• [AMBER] Postdoc position in biomolecular simulation
  • Ivaylo, Ivanov (Thu Jun 18 2009 - 18:26:05 CDT)
• [AMBER] PQR file - HELP PLEASE
  • s. Bill (Tue Dec 22 2009 - 15:27:48 CST)
  • Jason Swails (Tue Dec 22 2009 - 11:21:41 CST)
  • s. Bill (Tue Dec 22 2009 - 06:57:48 CST)
• [AMBER] PQR files
  • s. Bill (Fri Dec 25 2009 - 12:27:22 CST)
  • Jason Swails (Fri Dec 25 2009 - 10:57:51 CST)
  • s. Bill (Fri Dec 25 2009 - 08:38:36 CST)
• [AMBER] precision in the trajectory files
  • Jenny Iskrenova (Tue Feb 03 2009 - 11:07:58 CST)
  • David A. Case (Mon Feb 02 2009 - 08:55:40 CST)
  • Adrian Roitberg (Mon Feb 02 2009 - 08:46:49 CST)
  • Jenny Iskrenova (Mon Feb 02 2009 - 08:43:38 CST)
• [AMBER] prep file
  • case (Fri Sep 04 2009 - 09:09:06 CDT)
  • Jio M (Fri Sep 04 2009 - 04:24:04 CDT)
• [AMBER] preparation of small molecule libraries with most probable conformations using Amber
  • Andrew Voronkov (Sat Dec 26 2009 - 05:38:09 CST)
• [AMBER] preparation of two solutes of organic molecules in a simulation box
  • Workalemhu Berhanu (Tue Jun 02 2009 - 18:09:04 CDT)
• [AMBER] Preparing distance restraints
  • case (Mon Oct 26 2009 - 16:26:26 CDT)
  • Yunjie Zhao (Mon Oct 26 2009 - 03:44:58 CDT)
• [AMBER] pressure tensor components
  • case (Sun Dec 13 2009 - 09:10:02 CST)
  • Silvia Carlotto (Thu Dec 10 2009 - 07:12:51 CST)
• [AMBER] principal component vector onto C-alpha
  • S.Sundar Raman (Tue Jan 13 2009 - 16:46:20 CST)
  • Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 14:52:31 CST)
• [AMBER] PRINCIPAL QUESTION
  • Marek Maly (Thu Jun 11 2009 - 10:41:42 CDT)
• [AMBER] Principle Questions
  • Ross Walker (Tue Jul 07 2009 - 18:42:42 CDT)
  • s_bill36_at_yahoo.co.uk (Tue Jul 07 2009 - 02:50:53 CDT)
• [AMBER] prmtop
  • Ross Walker (Sun May 03 2009 - 21:18:04 CDT)
  • Mark M Huntress (Sun May 03 2009 - 18:20:39 CDT)
• [AMBER] prmtop residue format
  • David A. Case (Tue Apr 07 2009 - 15:35:40 CDT)
  • taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 15:04:25 CDT)
• [AMBER] probelm-APBS
  • Rilei Yu (Sun Oct 04 2009 - 19:51:10 CDT)
  • Robert Konecny (Sun Oct 04 2009 - 19:20:18 CDT)
  • Rilei Yu (Sat Oct 03 2009 - 00:41:07 CDT)
• [AMBER] Problem about adding a small residue to DNA
  • FyD (Mon Sep 07 2009 - 04:53:14 CDT)
  • case (Fri Sep 04 2009 - 14:32:53 CDT)
  • Yikan Chen (Thu Sep 03 2009 - 23:33:52 CDT)
• [AMBER] problem about trajectory analysis
  • Thomas Cheatham III (Wed Feb 25 2009 - 18:57:49 CST)
  • Adrien Delmont (Wed Feb 25 2009 - 08:24:41 CST)
• [AMBER] Problem build pmemd
  • Robert Duke (Wed Mar 18 2009 - 08:53:17 CDT)
  • Giorgos Lamprinidis (Wed Mar 18 2009 - 08:28:06 CDT)
  • Yiannis Georgiadis (Wed Mar 18 2009 - 19:57:44 CDT)
  • Atro Tossavainen (Sat Mar 14 2009 - 14:10:53 CDT)
  • Robert Duke (Fri Mar 13 2009 - 07:40:09 CDT)
  • Yiannis Georgiadis (Fri Mar 13 2009 - 19:14:49 CDT)
• [AMBER] problem building AmberTools/sleap on AIX
  • Shan-ho Tsai (Wed Jan 21 2009 - 15:53:00 CST)
  • Wei Zhang (Fri Jan 16 2009 - 15:19:42 CST)
  • Shan-ho Tsai (Fri Jan 16 2009 - 14:58:53 CST)
  • Shan-ho Tsai (Mon Jan 12 2009 - 09:31:51 CST)
  • Wei Zhang (Fri Jan 09 2009 - 16:28:08 CST)
  • Shan-ho Tsai (Fri Jan 09 2009 - 15:49:17 CST)
  • Bill Ross (Fri Jan 09 2009 - 11:45:55 CST)
  • Shan-ho Tsai (Fri Jan 09 2009 - 10:46:59 CST)
  • Wei Zhang (Fri Jan 09 2009 - 10:37:43 CST)
  • Shan-ho Tsai (Fri Jan 09 2009 - 10:27:56 CST)
• [AMBER] problem building sander.apbs
  • Robert Konecny (Tue Sep 22 2009 - 14:55:40 CDT)
  • case (Tue Sep 22 2009 - 14:12:50 CDT)
  • Oliver Kuhn (Tue Sep 22 2009 - 03:10:10 CDT)
  • case (Mon Sep 21 2009 - 09:38:20 CDT)
  • Oliver Kuhn (Mon Sep 21 2009 - 09:03:34 CDT)
  • case (Mon Sep 21 2009 - 06:39:41 CDT)
  • Oliver Kuhn (Mon Sep 21 2009 - 05:49:48 CDT)
• [AMBER] problem compiling amber tools with gcc-4.4.1
  • case (Tue Aug 25 2009 - 07:52:35 CDT)
  • gilbert_at_bluemarble.net (Mon Aug 24 2009 - 22:07:44 CDT)
• [AMBER] problem compiling nmode.c
  • Shan-ho Tsai (Thu Feb 19 2009 - 08:49:39 CST)
  • David A. Case (Tue Feb 17 2009 - 20:45:03 CST)
  • Shan-ho Tsai (Tue Feb 17 2009 - 14:38:00 CST)
• [AMBER] problem from xleap
  • Tom Joseph (Sat Aug 01 2009 - 06:19:22 CDT)
  • Ashish Runthala (Fri Jul 31 2009 - 22:33:10 CDT)
  • Qinghua Liao (Fri Jul 31 2009 - 20:38:19 CDT)
  • Tom Joseph (Fri Jul 31 2009 - 11:41:49 CDT)
  • Qinghua Liao (Fri Jul 31 2009 - 09:38:18 CDT)
• [AMBER] problem in calculation of binding energy in final step (MM-PBSA)
  • Maryam Hamzehee (Tue Apr 07 2009 - 08:59:03 CDT)
• [AMBER] Problem in compiling AMBER9 in parallel !
  • case (Tue Sep 29 2009 - 13:08:41 CDT)
  • Abhishek Banerjee (Tue Sep 29 2009 - 12:25:36 CDT)
  • Pradipta Bandyopadhyay (Tue Sep 29 2009 - 08:04:47 CDT)
• [AMBER] problem in input
  • Rausch, Felix (Fri Apr 03 2009 - 03:04:36 CDT)
  • balaji nagarajan (Thu Apr 02 2009 - 15:23:18 CDT)
  • Rausch, Felix (Thu Apr 02 2009 - 06:08:27 CDT)
  • balaji nagarajan (Thu Apr 02 2009 - 05:29:39 CDT)
• [AMBER] problem in installing amber tools on Mac OSX 10.6
  • case (Mon Dec 28 2009 - 07:07:48 CST)
  • David Watson (Mon Dec 28 2009 - 07:06:30 CST)
  • Chun-Wei Pao (Mon Dec 28 2009 - 01:54:26 CST)
• [AMBER] problem in installing AMBER10
  • Dr. Debaprasad Giri (Sat Apr 04 2009 - 07:13:46 CDT)
  • David A. Case (Fri Mar 27 2009 - 07:05:31 CDT)
  • Dr. Debaprasad Giri (Fri Mar 27 2009 - 05:16:47 CDT)
  • David A. Case (Mon Mar 23 2009 - 06:07:17 CDT)
  • Dr. Debaprasad Giri (Mon Mar 23 2009 - 05:31:26 CDT)
• [AMBER] Problem in Nmode
  • Kshatresh Dutta Dubey (Mon May 18 2009 - 01:07:52 CDT)
• [AMBER] Problem in pb simulation, PB_Bomb
  • Waqas Nasir (Thu Jan 29 2009 - 03:08:22 CST)
• [AMBER] problem in pressure equillibration
  • David A. Case (Tue Jun 16 2009 - 06:56:34 CDT)
  • wong105_at_llnl.gov (Tue Jun 16 2009 - 01:18:22 CDT)
• [AMBER] Problem in production run
  • Carlos Simmerling (Tue May 05 2009 - 05:07:11 CDT)
  • nicholus bhattacharjee (Tue May 05 2009 - 00:50:07 CDT)
• [AMBER] problem in QM/MM input file
  • Tom Joseph (Tue Sep 08 2009 - 07:37:56 CDT)
  • gaurav panwar (Mon Sep 07 2009 - 12:33:20 CDT)
• [AMBER] problem in rmsd
  • Carlos Simmerling (Tue Mar 10 2009 - 05:29:20 CDT)
  • Hannes Loeffler (Tue Mar 10 2009 - 03:30:16 CDT)
  • Thomas Cheatham (Mon Mar 09 2009 - 22:48:53 CDT)
  • Parimal Kar (Mon Mar 09 2009 - 22:36:13 CDT)
  • Thomas Cheatham (Mon Mar 09 2009 - 22:25:18 CDT)
  • Parimal Kar (Mon Mar 09 2009 - 22:18:48 CDT)
• [AMBER] problem in running sander
  • David A. Case (Thu Mar 19 2009 - 07:13:11 CDT)
  • Kshatresh Dutta Dubey (Thu Mar 19 2009 - 02:17:21 CDT)
  • Carlos Simmerling (Wed Mar 18 2009 - 10:51:07 CDT)
  • kshatresh (Mon Jun 30 2008 - 15:27:42 CDT)
  • Carlos Simmerling (Wed Mar 18 2009 - 09:58:04 CDT)
  • kshatresh (Mon Jun 30 2008 - 14:33:24 CDT)
• [AMBER] Problem in test run
  • case (Tue Sep 29 2009 - 11:50:19 CDT)
  • Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:23:29 CDT)
  • Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:14:35 CDT)
  • Carlos Simmerling (Tue Sep 29 2009 - 10:06:55 CDT)
  • Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:05:13 CDT)
  • Carlos Simmerling (Tue Sep 29 2009 - 09:26:38 CDT)
  • Kshatresh Dutta Dubey (Tue Sep 29 2009 - 09:21:56 CDT)
• [AMBER] Problem in watercap simulation, PB_Bomb
  • Ray Luo (Thu Jan 29 2009 - 11:45:33 CST)
  • Waqas Nasir (Thu Jan 29 2009 - 08:21:20 CST)
• [AMBER] Problem of MM-PBSA
  • Ray Luo (Mon Dec 07 2009 - 16:44:53 CST)
  • Å·ÑôµÂ·½ (Mon Dec 07 2009 - 16:30:41 CST)
  • Ray Luo (Mon Dec 07 2009 - 12:19:02 CST)
  • Å·ÑôµÂ·½ (Sun Dec 06 2009 - 23:09:47 CST)
• [AMBER] problem of mm_pbsa
  • Jordan Monnet (Thu Aug 13 2009 - 15:04:37 CDT)
  • Qinghua Liao (Thu Aug 13 2009 - 08:58:24 CDT)
  • Jordan Monnet (Mon Aug 10 2009 - 14:37:55 CDT)
  • Qinghua Liao (Fri Aug 07 2009 - 20:11:43 CDT)
  • Jordan Monnet (Fri Aug 07 2009 - 18:13:57 CDT)
  • Qinghua Liao (Thu Aug 06 2009 - 18:58:55 CDT)
  • Rubben Torella (Thu Aug 06 2009 - 10:53:47 CDT)
  • Qinghua Liao (Wed Aug 05 2009 - 19:22:13 CDT)
  • case (Wed Aug 05 2009 - 10:42:56 CDT)
  • Qinghua Liao (Wed Aug 05 2009 - 00:46:51 CDT)
• [AMBER] problem of PBCAL/GB
  • Qinghua Liao (Tue Sep 08 2009 - 04:40:42 CDT)
  • Ray Luo (Tue Sep 08 2009 - 00:58:44 CDT)
  • Qinghua Liao (Tue Sep 08 2009 - 00:05:37 CDT)
• [AMBER] Problem on PMEMD
  • Robert Duke (Mon Sep 14 2009 - 20:46:16 CDT)
  • zyxism (Mon Sep 14 2009 - 20:41:50 CDT)
  • Adrian Roitberg (Mon Sep 14 2009 - 20:40:35 CDT)
  • Tom Joseph (Mon Sep 14 2009 - 20:34:11 CDT)
  • zyxism (Mon Sep 14 2009 - 20:11:57 CDT)
• [AMBER] Problem reading PDB file into XLEAP
  • David A. Case (Sat Mar 28 2009 - 08:28:53 CDT)
  • Hopkins, Robert (Fri Mar 27 2009 - 17:09:11 CDT)
  • David A. Case (Fri Mar 27 2009 - 07:39:26 CDT)
  • Hopkins, Robert (Thu Mar 26 2009 - 19:01:26 CDT)
• [AMBER] Problem reading PDB file into XLEAP - SLEAP
  • Hopkins, Robert (Wed Apr 01 2009 - 18:10:44 CDT)
  • David A. Case (Sun Mar 29 2009 - 13:37:35 CDT)
  • Hopkins, Robert (Sun Mar 29 2009 - 13:27:09 CDT)
  • Wei Zhang (Sat Mar 28 2009 - 18:29:20 CDT)
  • Hopkins, Robert (Sat Mar 28 2009 - 18:12:06 CDT)
• [AMBER] Problem regarding Hbond analysis
  • Bill Ross (Tue Sep 22 2009 - 15:00:55 CDT)
  • Abhishek Singh (Tue Sep 22 2009 - 14:43:50 CDT)
• [AMBER] problem running pmemd gbrna tests
  • wong105_at_llnl.gov (Tue Sep 15 2009 - 13:07:14 CDT)
• [AMBER] Problem running test.pmemd.AMOEBA
  • Robert Duke (Fri Mar 13 2009 - 09:33:55 CDT)
  • mloureiro_at_cesga.es (Fri Mar 13 2009 - 06:45:30 CDT)
• [AMBER] problem using amoeba
  • Robert Duke (Fri Mar 27 2009 - 07:22:31 CDT)
  • Hemant Gangwar (Fri Mar 27 2009 - 05:41:26 CDT)
• [AMBER] problem when doing mm/pbsa: bad atom type Br
  • Baifan Wang (Mon Sep 28 2009 - 02:26:06 CDT)
  • Ray Luo (Sun Sep 27 2009 - 22:10:25 CDT)
  • Baifan Wang (Sun Sep 27 2009 - 21:50:46 CDT)
• [AMBER] Problem with "Atom does not have a type"
  • case (Mon Mar 30 2009 - 07:46:59 CDT)
  • Richard Tseng (Sun Mar 29 2009 - 14:20:37 CDT)
  • David A. Case (Sat Mar 28 2009 - 08:25:33 CDT)
  • Richard Tseng (Fri Mar 27 2009 - 17:08:34 CDT)
  • Richard Tseng (Fri Mar 27 2009 - 16:51:32 CDT)
  • David A. Case (Fri Mar 27 2009 - 06:44:22 CDT)
  • Richard Tseng (Thu Mar 26 2009 - 18:17:19 CDT)
• [AMBER] problem with 4-Hydroxyl-Proline tutorial
  • Jia Xu (Tue Sep 01 2009 - 00:10:50 CDT)
  • FyD (Mon Aug 31 2009 - 15:10:52 CDT)
  • Jia Xu (Sun Aug 30 2009 - 02:46:18 CDT)
• [AMBER] problem with amber installation
  • nicholus bhattacharjee (Tue Mar 24 2009 - 12:14:10 CDT)
  • Ross Walker (Wed Feb 25 2009 - 09:05:26 CST)
  • David A. Case (Wed Feb 25 2009 - 06:45:01 CST)
  • Carlos Simmerling (Wed Feb 25 2009 - 05:25:34 CST)
  • nicholus bhattacharjee (Tue Feb 24 2009 - 22:29:11 CST)
  • Carlos Simmerling (Tue Feb 24 2009 - 05:47:20 CST)
  • nicholus bhattacharjee (Tue Feb 24 2009 - 00:50:12 CST)
• [AMBER] Problem with Amber8
  • Sebastian Petruczynik (Wed Aug 05 2009 - 06:33:05 CDT)
  • Ross Walker (Mon Aug 03 2009 - 14:41:28 CDT)
  • ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 08:37:01 CDT)
  • Sebastian Petruczynik (Mon Aug 03 2009 - 08:28:56 CDT)
• [AMBER] Problem with amber9 installation
  • moitrayee_at_mbu.iisc.ernet.in (Tue Jul 14 2009 - 02:02:39 CDT)
  • Ross Walker (Mon Jul 13 2009 - 22:34:54 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Mon Jul 13 2009 - 15:31:18 CDT)
• [AMBER] problem with antechamber
  • Junmei Wang (Wed Dec 09 2009 - 17:24:11 CST)
  • sculiujl (Fri Dec 04 2009 - 06:18:24 CST)
  • sculiujl (Fri Dec 04 2009 - 05:38:04 CST)
  • aneesh cna (Wed Apr 08 2009 - 01:32:32 CDT)
• [AMBER] Problem with CAP residues
  • FyD (Tue Apr 07 2009 - 06:01:35 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 05:17:27 CDT)
• [AMBER] PROBLEM WITH CHCL3BOX pdb
  • case (Fri Sep 18 2009 - 17:01:23 CDT)
  • Hannes Loeffler (Fri Sep 18 2009 - 10:16:06 CDT)
  • case (Fri Sep 18 2009 - 08:26:40 CDT)
  • Silvia Carlotto (Fri Sep 18 2009 - 07:49:12 CDT)
• [AMBER] problem with creation of prmtop and prmcrd files
  • Tom Joseph (Wed Jun 10 2009 - 20:30:19 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 08:00:18 CDT)
• [AMBER] problem with cutoff
  • Ross Walker (Mon May 04 2009 - 10:35:40 CDT)
  • Yunjie Zhao (Mon May 04 2009 - 07:58:00 CDT)
  • Ross Walker (Mon May 04 2009 - 00:02:04 CDT)
  • Yunjie Zhao (Sun May 03 2009 - 22:53:00 CDT)
• [AMBER] problem with energy calculations
  • Carlos Simmerling (Sun Jul 12 2009 - 09:15:39 CDT)
  • Thomas Lake (Sun Jul 12 2009 - 09:10:58 CDT)
  • Carlos Simmerling (Sun Jul 12 2009 - 08:42:35 CDT)
  • Lake, Thomas (Sun Jul 12 2009 - 08:35:33 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 12:25:56 CDT)
  • Thomas Lake (Fri Jul 10 2009 - 11:13:55 CDT)
• [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB.
  • David A. Case (Sat Jan 24 2009 - 08:37:31 CST)
  • Marek Malý (Wed Jan 21 2009 - 16:48:58 CST)
  • David A. Case (Wed Jan 21 2009 - 08:52:33 CST)
  • Marek Malý (Tue Jan 20 2009 - 20:48:03 CST)
  • David A. Case (Tue Jan 20 2009 - 14:53:48 CST)
  • Niel Henriksen (Tue Jan 20 2009 - 14:49:38 CST)
  • Marek Malý (Tue Jan 20 2009 - 12:24:55 CST)
• [AMBER] problem with explicit solvent in TMD
  • Ross Walker (Mon Apr 13 2009 - 10:29:11 CDT)
  • Carlos Simmerling (Mon Apr 13 2009 - 06:41:41 CDT)
  • balaji nagarajan (Mon Apr 13 2009 - 06:37:21 CDT)
• [AMBER] problem with FAD in tleap
  • M. Shahid (Tue Dec 01 2009 - 05:54:04 CST)
  • FyD (Mon Nov 30 2009 - 13:25:15 CST)
  • FyD (Mon Nov 30 2009 - 13:15:56 CST)
  • M. Shahid (Mon Nov 30 2009 - 12:33:35 CST)
  • case (Mon Nov 30 2009 - 11:15:19 CST)
  • M. Shahid (Mon Nov 30 2009 - 09:54:26 CST)
  • case (Mon Nov 30 2009 - 07:26:37 CST)
  • FyD (Mon Nov 30 2009 - 07:02:59 CST)
  • M. Shahid (Mon Nov 30 2009 - 06:17:09 CST)
• [AMBER] Problem with GROUP input
  • Jordan, Brad (Wed Sep 09 2009 - 18:58:36 CDT)
• [AMBER] Problem with loading PDB into tleap
  • Ashish Runthala (Tue Sep 08 2009 - 10:14:46 CDT)
  • Kamali Sripathi (Tue Sep 08 2009 - 08:49:20 CDT)
  • Ashish Runthala (Wed Aug 19 2009 - 21:53:04 CDT)
  • case (Wed Aug 19 2009 - 18:55:52 CDT)
  • ksripath_at_umich.edu (Wed Aug 19 2009 - 14:00:22 CDT)
  • Ashish Runthala (Wed Aug 19 2009 - 10:03:19 CDT)
  • Kamali Sripathi (Wed Aug 19 2009 - 09:06:15 CDT)
  • Ashish Runthala (Wed Aug 19 2009 - 08:56:59 CDT)
  • Kamali Sripathi (Wed Aug 19 2009 - 08:21:30 CDT)
• [AMBER] Problem with memory in nmode analysis
  • Alireza Shaneh (Tue Oct 06 2009 - 10:23:55 CDT)
• [AMBER] problem with minimization
  • moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 06:01:14 CDT)
• [AMBER] problem with MM-PBSA
  • Bill Ross (Wed May 27 2009 - 19:52:19 CDT)
  • Thomas Cheatham (Wed May 27 2009 - 19:35:30 CDT)
  • Ray Luo (Tue May 26 2009 - 11:44:14 CDT)
  • David A. Case (Tue May 26 2009 - 06:37:31 CDT)
  • Maryam Hamzehee (Mon May 25 2009 - 23:52:29 CDT)
  • Maryam Hamzehee (Sat May 23 2009 - 23:48:05 CDT)
• [AMBER] Problem with MM-PBSA energy calculation
  • Rubben Torella (Tue May 26 2009 - 06:24:56 CDT)
  • Barbault Florent (Mon May 25 2009 - 13:57:19 CDT)
  • Rubben Torella (Mon May 25 2009 - 10:58:41 CDT)
• [AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]
  • moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:28:14 CDT)
• [AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]]
  • moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:30:21 CDT)
• [AMBER] Problem with Nmode
  • David A. Case (Thu May 21 2009 - 07:29:06 CDT)
  • Kshatresh Dutta Dubey (Thu May 21 2009 - 00:14:50 CDT)
  • David A. Case (Wed May 20 2009 - 13:02:44 CDT)
  • Kshatresh Dutta Dubey (Mon May 18 2009 - 23:25:05 CDT)
• [AMBER] Problem with nonstandard residues
  • moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 11:47:38 CDT)
  • David A. Case (Tue May 19 2009 - 10:22:15 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 08:10:00 CDT)
  • David A. Case (Tue May 19 2009 - 07:54:14 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 06:48:33 CDT)
• [AMBER] Problem with NVT and NPT
  • Carlos Simmerling (Fri Feb 20 2009 - 07:30:26 CST)
  • parul sharma (Fri Feb 20 2009 - 07:27:51 CST)
  • Adrian Roitberg (Fri Feb 20 2009 - 07:14:23 CST)
  • parul sharma (Fri Feb 20 2009 - 07:07:36 CST)
• [AMBER] problem with parametrization
  • janzso_at_brc.hu (Mon Jun 29 2009 - 04:30:50 CDT)
  • FyD (Thu Jun 25 2009 - 08:47:31 CDT)
  • janzso_at_brc.hu (Thu Jun 25 2009 - 07:04:27 CDT)
  • FyD (Thu Jun 25 2009 - 06:52:45 CDT)
  • janzso_at_brc.hu (Thu Jun 25 2009 - 06:40:35 CDT)
  • FyD (Thu Jun 25 2009 - 05:04:27 CDT)
  • janzso_at_brc.hu (Thu Jun 25 2009 - 04:49:50 CDT)
  • FyD (Thu Jun 25 2009 - 00:15:23 CDT)
  • Brothers, Michael Charles (Wed Jun 24 2009 - 13:34:16 CDT)
  • janzso_at_brc.hu (Wed Jun 24 2009 - 13:24:45 CDT)
• [AMBER] problem with parmchk
  • David A. Case (Mon May 18 2009 - 15:00:07 CDT)
  • rebeca (Mon May 18 2009 - 09:34:31 CDT)
  • David A. Case (Mon May 18 2009 - 09:19:54 CDT)
  • rebeca (Mon May 18 2009 - 08:59:51 CDT)
• [AMBER] Problem with particle-mesh Ewald method
  • Ross Walker (Sat Mar 07 2009 - 00:10:34 CST)
  • steinbrt_at_rci.rutgers.edu (Fri Mar 06 2009 - 21:42:26 CST)
  • Yunjie Zhao (Fri Mar 06 2009 - 21:29:02 CST)
• [AMBER] problem with program anal within Amber10
  • David A. Case (Tue May 26 2009 - 07:03:01 CDT)
  • Marina Grabar (Tue May 26 2009 - 06:48:38 CDT)
• [AMBER] Problem with radial distribution function
  • aneesh cna (Fri Jun 26 2009 - 03:56:09 CDT)
• [AMBER] Problem with REMD
  • Carlos Simmerling (Thu Mar 12 2009 - 06:00:07 CDT)
  • parul sharma (Thu Mar 12 2009 - 02:45:09 CDT)
• [AMBER] Problem with RNA hairpin unwinding in explicit water
  • Sasha Buzko (Fri Apr 24 2009 - 12:20:13 CDT)
  • Sasha Buzko (Thu Apr 23 2009 - 12:55:58 CDT)
  • Bill Ross (Thu Apr 23 2009 - 12:53:40 CDT)
  • Sasha Buzko (Wed Apr 22 2009 - 18:59:14 CDT)
  • matthew_seetin_at_urmc.rochester.edu (Wed Apr 22 2009 - 18:59:02 CDT)
  • Sasha Buzko (Wed Apr 22 2009 - 18:10:55 CDT)
  • Thomas Cheatham III (Wed Apr 22 2009 - 17:56:25 CDT)
  • Carlos Simmerling (Wed Apr 22 2009 - 17:53:33 CDT)
  • Sasha Buzko (Wed Apr 22 2009 - 17:34:35 CDT)
  • Carlos Simmerling (Wed Apr 22 2009 - 17:25:47 CDT)
  • Seetin, Matthew (Wed Apr 22 2009 - 17:22:29 CDT)
  • Sasha Buzko (Wed Apr 22 2009 - 16:55:58 CDT)
• [AMBER] Problem with running anal module in amber
  • moitrayee_at_mbu.iisc.ernet.in (Wed Oct 21 2009 - 01:47:17 CDT)
• [AMBER] problem with secstruct action command in ptraj
  • nicholus bhattacharjee (Mon Apr 06 2009 - 06:49:44 CDT)
• [AMBER] problem with the energetics of the system
  • Mahmoud A. A. Ibrahim (Sun Jul 12 2009 - 05:37:37 CDT)
  • Ross Walker (Sat Jul 11 2009 - 18:52:42 CDT)
  • Mahmoud A. A. Ibrahim (Sat Jul 11 2009 - 18:23:13 CDT)
• [AMBER] problem with the results in the .out file!
  • Aravind S (Thu Apr 02 2009 - 00:49:19 CDT)
  • Gustavo Seabra (Tue Mar 31 2009 - 08:01:41 CDT)
  • Aravind S (Tue Mar 31 2009 - 00:30:57 CDT)
• [AMBER] problems compiling ambertool
  • Per Jr. Greisen (Wed Mar 18 2009 - 07:45:53 CDT)
  • David A. Case (Wed Mar 18 2009 - 07:39:38 CDT)
  • Per Jr. Greisen (Wed Mar 18 2009 - 06:49:57 CDT)
  • Bill Ross (Tue Mar 17 2009 - 12:24:48 CDT)
  • Bill Ross (Tue Mar 17 2009 - 12:10:01 CDT)
  • David A. Case (Tue Mar 17 2009 - 11:13:30 CDT)
  • Per Jr. Greisen (Tue Mar 17 2009 - 11:06:00 CDT)
  • David A. Case (Tue Mar 17 2009 - 07:49:20 CDT)
  • Per Jr. Greisen (Tue Mar 17 2009 - 03:10:20 CDT)
  • Bill Ross (Mon Mar 16 2009 - 17:50:44 CDT)
  • Per Jr. Greisen (Mon Mar 16 2009 - 17:35:38 CDT)
  • David A. Case (Mon Mar 16 2009 - 10:12:40 CDT)
  • Per Jr. Greisen (Mon Mar 16 2009 - 09:41:26 CDT)
  • David A. Case (Mon Mar 16 2009 - 09:27:26 CDT)
  • Per Jr. Greisen (Mon Mar 16 2009 - 09:00:14 CDT)
  • David A. Case (Mon Mar 16 2009 - 08:50:24 CDT)
  • Per Jr. Greisen (Mon Mar 16 2009 - 08:29:37 CDT)
  • David A. Case (Mon Mar 16 2009 - 07:13:23 CDT)
  • Atro Tossavainen (Mon Mar 16 2009 - 05:18:58 CDT)
  • Atro Tossavainen (Sat Mar 14 2009 - 14:09:36 CDT)
  • Per Jr. Greisen (Fri Mar 13 2009 - 17:01:35 CDT)
  • David A. Case (Fri Mar 13 2009 - 14:54:56 CDT)
  • Per Jr. Greisen (Fri Mar 13 2009 - 14:08:36 CDT)
• [AMBER] Problems in the result of MM_PBSA
  • Ray Luo (Mon May 11 2009 - 12:55:12 CDT)
  • Sean Zhao (Sun May 10 2009 - 03:23:19 CDT)
  • Ray Luo (Sat May 09 2009 - 20:36:04 CDT)
  • Sean Zhao (Fri May 08 2009 - 22:44:29 CDT)
  • David A. Case (Fri May 08 2009 - 07:45:19 CDT)
  • Ray Luo (Thu May 07 2009 - 21:02:58 CDT)
  • Sean Zhao (Thu May 07 2009 - 20:30:24 CDT)
• [AMBER] Problems using nmode in NAB
  • Andreas Svrcek-Seiler (Thu Jun 25 2009 - 08:03:15 CDT)
  • E.M. (Wed Jun 24 2009 - 23:15:38 CDT)
  • E.M. (Wed Jun 24 2009 - 04:09:44 CDT)
  • Andreas Svrcek-Seiler (Wed Jun 24 2009 - 03:52:30 CDT)
  • E.M. (Wed Jun 24 2009 - 01:05:50 CDT)
• [AMBER] problems with EP of TIP4PEW
  • rebeca (Wed Jun 03 2009 - 13:40:12 CDT)
  • David A. Case (Wed Jun 03 2009 - 11:29:43 CDT)
  • rebeca (Wed Jun 03 2009 - 10:43:58 CDT)
• [AMBER] Problems with MM-PBSA Calculation after MD
  • Hannes Kopitz (Thu Mar 12 2009 - 06:06:54 CDT)
  • German Erlenkamp (Thu Mar 12 2009 - 04:28:23 CDT)
• [AMBER] Problems with PMEMD installation for AMBER10
  • German Erlenkamp (Thu May 07 2009 - 02:18:36 CDT)
  • Robert Duke (Tue May 05 2009 - 08:48:06 CDT)
  • German Erlenkamp (Tue May 05 2009 - 08:07:13 CDT)
  • Robert Duke (Tue May 05 2009 - 08:00:54 CDT)
  • German Erlenkamp (Tue May 05 2009 - 07:40:56 CDT)
• [AMBER] problems with ptraj option IMAGE
  • Antonija Tomić (Mon Jun 29 2009 - 10:27:54 CDT)
  • Carlos Simmerling (Mon Jun 29 2009 - 10:00:59 CDT)
  • Antonija Tomić (Mon Jun 29 2009 - 09:48:54 CDT)
• [AMBER] Problems with running two separate jobs in the same time
  • Antonija Tomić (Thu Apr 09 2009 - 05:33:03 CDT)
  • Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  • Antonija Tomić (Tue Apr 07 2009 - 03:08:53 CDT)
• [AMBER] production phase
  • Ross Walker (Thu Jul 16 2009 - 22:56:13 CDT)
  • s. Bill (Thu Jul 16 2009 - 07:18:25 CDT)
• [AMBER] production run terminates due to (*) symbols in xxx.rst
  • Vijay Manickam Achari (Thu Feb 05 2009 - 20:50:20 CST)
  • Ross Walker (Thu Feb 05 2009 - 12:58:41 CST)
  • Bill Ross (Thu Feb 05 2009 - 11:42:55 CST)
  • Vijay Manickam Achari (Thu Feb 05 2009 - 04:58:26 CST)
  • vallespardojl_at_chem.leidenuniv.nl (Thu Feb 05 2009 - 04:28:33 CST)
  • Vijay Manickam Achari (Wed Feb 04 2009 - 22:17:38 CST)
• [AMBER] projections of trajectories onto the first 2 principal eigenvectors
  • Hannes Loeffler (Fri Feb 13 2009 - 03:33:19 CST)
  • Hannes Loeffler (Fri Feb 13 2009 - 02:32:20 CST)
  • Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 12:22:20 CST)
• [AMBER] Proper ISTRNG value ?
  • Marek Maly (Fri Jun 05 2009 - 11:24:58 CDT)
• [AMBER] prot-DNA simulation
  • Thomas Cheatham III (Wed Jan 21 2009 - 15:55:52 CST)
  • deepti nayar (Wed Jan 21 2009 - 05:16:09 CST)
• [AMBER] Protein Activity
  • Ashish Runthala (Tue Aug 04 2009 - 22:42:11 CDT)
  • Bill Ross (Tue Aug 04 2009 - 14:59:40 CDT)
  • Chih-Ying Lin (Tue Aug 04 2009 - 14:42:42 CDT)
  • Bill Ross (Tue Aug 04 2009 - 14:19:32 CDT)
  • Chih-Ying Lin (Tue Aug 04 2009 - 12:57:54 CDT)
• [AMBER] Protein and charged surface
  • rrd (Thu Oct 01 2009 - 22:49:18 CDT)
• [AMBER] Protein Docking
  • Chih-Ying Lin (Thu May 14 2009 - 23:28:43 CDT)
  • Simon Becker (Tue May 12 2009 - 10:23:02 CDT)
  • steinbrt_at_rci.rutgers.edu (Mon May 11 2009 - 15:33:15 CDT)
  • Chih-Ying Lin (Mon May 11 2009 - 15:21:45 CDT)
• [AMBER] Protein Domain Motion
  • Carlos Simmerling (Fri Aug 14 2009 - 07:17:28 CDT)
  • Chih-Ying Lin (Thu Aug 13 2009 - 20:51:14 CDT)
  • Carlos Simmerling (Thu Aug 13 2009 - 14:39:39 CDT)
  • Chih-Ying Lin (Thu Aug 13 2009 - 14:20:09 CDT)
• [AMBER] protein molecular weight?
  • Tom Joseph (Fri May 29 2009 - 18:40:58 CDT)
  • Chih-Ying Lin (Fri May 29 2009 - 17:44:24 CDT)
• [AMBER] protein monomerizartion times and simulation with implicit solvent
  • Carlos Simmerling (Wed Feb 18 2009 - 06:16:00 CST)
  • drugdesign (Wed Feb 18 2009 - 04:27:17 CST)
• [AMBER] Protein motions comparison
  • Hannes Loeffler (Thu Feb 19 2009 - 06:07:47 CST)
  • Dmitry Osolodkin (Thu Feb 19 2009 - 05:58:24 CST)
• [AMBER] protein PDB
  • Chih-Ying Lin (Thu Mar 19 2009 - 15:43:15 CDT)
• [AMBER] protein protrudes from unit cell
  • Carlos Simmerling (Wed Mar 18 2009 - 10:49:43 CDT)
  • Ross Walker (Wed Mar 18 2009 - 10:39:23 CDT)
  • Hannes Loeffler (Wed Mar 18 2009 - 04:08:41 CDT)
  • Jeffrey (Wed Mar 18 2009 - 03:59:06 CDT)
• [AMBER] Protein with HETATM, am I doing the
  • amit (Mon May 25 2009 - 10:26:15 CDT)
  • nicholus bhattacharjee (Thu May 21 2009 - 01:43:37 CDT)
  • Amit Bajaj (Thu May 21 2009 - 00:26:49 CDT)
  • nicholus bhattacharjee (Wed May 20 2009 - 23:48:42 CDT)
• [AMBER] Protein with HETATM, am I doing the right thing
  • David A. Case (Sat May 23 2009 - 07:13:01 CDT)
  • nicholus bhattacharjee (Thu May 21 2009 - 11:28:52 CDT)
  • David A. Case (Thu May 21 2009 - 07:39:14 CDT)
  • nicholus bhattacharjee (Thu May 21 2009 - 06:21:15 CDT)
• [AMBER] protein-ligand binding simulation times
  • Andrew Voronkov (Sat Aug 22 2009 - 05:32:42 CDT)
  • steinbrt_at_rci.rutgers.edu (Sat Aug 22 2009 - 04:50:35 CDT)
  • Andrew Voronkov (Sat Aug 22 2009 - 00:09:54 CDT)
• [AMBER] Protonated or not
  • Adrian Roitberg (Fri Jul 31 2009 - 12:32:50 CDT)
  • s. Bill (Fri Jul 31 2009 - 12:15:32 CDT)
• [AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs
  • Ross Walker (Fri Sep 04 2009 - 13:51:44 CDT)
• [AMBER] Pseudoatoms
  • David A. Case (Mon Mar 02 2009 - 17:25:29 CST)
  • waleed zalloum (Mon Mar 02 2009 - 06:12:33 CST)
• [AMBER] ptraj "image" "center" commands
  • Ross Walker (Thu Jun 11 2009 - 10:30:08 CDT)
  • Catein Catherine (Thu Jun 11 2009 - 04:13:38 CDT)
• [AMBER] ptraj (vector and corrplane)
  • taufik.alsarraj_at_utoronto.ca (Fri Apr 10 2009 - 19:45:46 CDT)
• [AMBER] ptraj - cluster
  • Cihan Aydin (Fri Jul 17 2009 - 09:22:37 CDT)
  • Wei Huang (Fri Jul 17 2009 - 07:34:00 CDT)
  • Cihan Aydin (Thu Jul 16 2009 - 00:55:07 CDT)
• [AMBER] ptraj amber 10 file.
  • Catein Catherine (Wed Jun 10 2009 - 11:02:32 CDT)
• [AMBER] ptraj analyze
  • Thomas Cheatham III (Wed Feb 25 2009 - 18:45:17 CST)
  • Beale, John (Wed Feb 25 2009 - 10:56:59 CST)
• [AMBER] ptraj and namd charmm dcd
  • Thomas Cheatham III (Wed Apr 01 2009 - 11:08:51 CDT)
  • Sandro L. Fornili (Wed Apr 01 2009 - 10:59:37 CDT)
• [AMBER] ptraj and prmtop
  • Carlos Simmerling (Wed Oct 14 2009 - 08:41:04 CDT)
  • Beale, John (Wed Oct 14 2009 - 07:46:11 CDT)
• [AMBER] ptraj cluster - snapshot number of a representative structure
  • Jianyin Shao (Thu Aug 20 2009 - 10:50:22 CDT)
  • Marcin Krol (Thu Aug 20 2009 - 03:26:09 CDT)
• [AMBER] ptraj clustering with sieve- unexpected Bus Error
  • Rachel Rice (Tue Jun 30 2009 - 10:06:03 CDT)
  • David Watson (Fri Jun 26 2009 - 06:31:26 CDT)
  • Rachel Rice (Thu Jun 25 2009 - 22:24:18 CDT)
  • David Watson (Thu Jun 25 2009 - 21:51:11 CDT)
  • Rachel Rice (Thu Jun 25 2009 - 21:36:06 CDT)
  • David Watson (Thu Jun 25 2009 - 21:28:22 CDT)
  • Rachel Rice (Thu Jun 25 2009 - 19:54:31 CDT)
  • David Watson (Thu Jun 25 2009 - 13:53:16 CDT)
  • Rachel Rice (Thu Jun 25 2009 - 10:24:25 CDT)
• [AMBER] ptraj correlation
  • Catein Catherine (Thu Jun 18 2009 - 08:47:01 CDT)
• [AMBER] ptraj fails to recognize binary REMD output
  • Kevin Wiehe (Fri Feb 06 2009 - 11:44:21 CST)
• [AMBER] ptraj failure to parse psf input
  • Sasha Buzko (Thu Aug 13 2009 - 18:34:07 CDT)
  • Sasha Buzko (Thu Aug 13 2009 - 11:25:32 CDT)
  • Thomas Cheatham (Wed Aug 12 2009 - 23:27:34 CDT)
  • Sasha Buzko (Wed Aug 12 2009 - 16:16:07 CDT)
  • Sasha Buzko (Wed Aug 05 2009 - 14:33:54 CDT)
  • case (Wed Aug 05 2009 - 12:32:00 CDT)
  • Sasha Buzko (Wed Aug 05 2009 - 11:39:57 CDT)
• [AMBER] ptraj grid option
  • Youn Kyeung Lee (Tue Jul 21 2009 - 02:15:11 CDT)
• [AMBER] ptraj image
  • Daniel Roe (Wed Dec 09 2009 - 10:21:18 CST)
  • Thomas Cheatham (Wed Dec 09 2009 - 07:41:54 CST)
  • Neha Bharat Gajaria (Wed Dec 09 2009 - 00:13:36 CST)
  • Bill Ross (Tue Dec 08 2009 - 18:29:03 CST)
  • Taufik Al-Sarraj (Tue Dec 08 2009 - 17:54:46 CST)
  • Bill Ross (Tue Dec 08 2009 - 16:08:42 CST)
  • Thomas Cheatham (Tue Dec 08 2009 - 15:50:09 CST)
  • Taufik Al-Sarraj (Tue Dec 08 2009 - 15:37:55 CST)
• [AMBER] ptraj image in non-orthorhombic cell
  • Joanna Panecka (Wed Jun 03 2009 - 15:19:52 CDT)
• [AMBER] ptraj imaging of namd generated trajectories
  • Vlad Cojocaru (Thu Aug 13 2009 - 04:35:49 CDT)
• [AMBER] ptraj limit on trajectory size
  • Sasha Buzko (Mon Aug 24 2009 - 17:31:14 CDT)
  • Ross Walker (Mon Aug 24 2009 - 17:07:00 CDT)
  • Sasha Buzko (Mon Aug 24 2009 - 11:59:30 CDT)
• [AMBER] ptraj mask selection
  • Patrick Gedeon (Mon Jul 13 2009 - 14:58:18 CDT)
  • Jianyin Shao (Mon Jul 13 2009 - 14:02:03 CDT)
  • case (Mon Jul 13 2009 - 13:10:46 CDT)
  • Jianyin Shao (Mon Jul 13 2009 - 12:57:23 CDT)
  • Patrick Gedeon (Sun Jul 12 2009 - 22:45:56 CDT)
• [AMBER] ptraj netcdf
  • Chris Moth (Tue May 12 2009 - 10:46:31 CDT)
  • Bala subramanian (Tue May 12 2009 - 07:04:00 CDT)
• [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated?
  • Hannes Loeffler (Thu May 07 2009 - 02:47:23 CDT)
  • Patrick Gedeon (Wed May 06 2009 - 23:12:39 CDT)
• [AMBER] ptraj problem
  • Thomas Cheatham III (Fri Apr 03 2009 - 15:23:21 CDT)
  • Ed Pate (Fri Apr 03 2009 - 15:13:37 CDT)
• [AMBER] ptraj quasiharmonic analysis
  • Hannes Loeffler (Tue Jun 09 2009 - 02:19:23 CDT)
  • Neha Gandhi (Tue Jun 09 2009 - 01:38:01 CDT)
• [AMBER] ptraj questions
  • Jia Xu (Sun May 24 2009 - 00:06:10 CDT)
  • Myunggi Yi (Fri May 22 2009 - 08:57:08 CDT)
  • Jia Xu (Wed May 20 2009 - 09:39:13 CDT)
• [AMBER] ptraj randomizeions
  • taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 18:32:23 CDT)
• [AMBER] ptraj script for H bond for protein (explicit )
  • kureeckal ramesh (Sat Nov 07 2009 - 01:38:29 CST)
• [AMBER] Ptraj Segmentation Fault
  • Katrina Hill (Wed Oct 21 2009 - 21:15:31 CDT)
• [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial
  • Carlos Simmerling (Tue Dec 08 2009 - 08:59:48 CST)
  • Andrew Voronkov (Tue Dec 08 2009 - 08:48:56 CST)
  • Thomas Cheatham (Sun Dec 06 2009 - 11:23:48 CST)
  • Andrew Voronkov (Sun Dec 06 2009 - 07:39:39 CST)
  • Andrew Voronkov (Sun Dec 06 2009 - 05:58:41 CST)
  • Thomas Cheatham III (Fri Dec 04 2009 - 13:20:21 CST)
  • Andrew Voronkov (Fri Dec 04 2009 - 13:09:58 CST)
  • Thomas Cheatham III (Fri Dec 04 2009 - 11:01:35 CST)
  • Andrew Voronkov (Fri Dec 04 2009 - 03:55:05 CST)
• [AMBER] ptraj utility
  • Neha Bharat Gajaria (Tue Dec 01 2009 - 20:13:41 CST)
  • case (Tue Dec 01 2009 - 06:56:52 CST)
  • Carlos Simmerling (Tue Dec 01 2009 - 06:48:27 CST)
  • Daniel Roe (Tue Dec 01 2009 - 06:45:19 CST)
  • Neha Bharat Gajaria (Tue Dec 01 2009 - 02:30:07 CST)
• [AMBER] ptraj, CHARMM PSF and CMAP
  • Ross Walker (Wed Jan 14 2009 - 10:46:17 CST)
  • Hannes Loeffler (Wed Jan 14 2009 - 03:45:07 CST)
• [AMBER] PTRAJ, rms for separated residues.
  • Germain Vallverdu (Mon Jun 22 2009 - 04:27:43 CDT)
  • Catein Catherine (Mon Jun 22 2009 - 04:20:36 CDT)
• [AMBER] ptraj-image
  • Nancy (Thu Aug 13 2009 - 05:35:01 CDT)
• [AMBER] ptraj-radial distribution function
  • Christof Jaeger (Thu Jul 16 2009 - 03:22:02 CDT)
  • Nancy (Thu Jul 16 2009 - 01:34:12 CDT)
• [AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift
  • Andrew Voronkov (Sun Aug 23 2009 - 06:55:01 CDT)
• [AMBER] PTRAJ: solvent accessible surface area
  • Carlos Simmerling (Wed Jan 14 2009 - 09:00:59 CST)
  • steinbrt_at_rci.rutgers.edu (Wed Jan 14 2009 - 08:59:19 CST)
  • Catein Catherine (Wed Jan 14 2009 - 01:32:15 CST)
• [AMBER] ptraj_hbond_problem
  • Thomas Cheatham (Fri Jun 05 2009 - 00:28:11 CDT)
  • balaji nagarajan (Thu Jun 04 2009 - 17:08:24 CDT)
• [AMBER] pucker calculation for six member rings
  • Ganesh Kamath (Mon Oct 05 2009 - 13:03:15 CDT)
• [AMBER] pulling two atoms in SMD
  • Santosh Mogurampelly (Tue Jul 28 2009 - 07:10:12 CDT)
• [AMBER] pupil and amber
  • Ben Roberts (Tue Dec 22 2009 - 20:59:04 CST)
  • davide branduardi (Tue Dec 22 2009 - 14:29:37 CST)
• [AMBER] QM/MM
  • steinbrt_at_rci.rutgers.edu (Tue Jul 28 2009 - 02:19:32 CDT)
  • s. Bill (Tue Jul 28 2009 - 01:44:15 CDT)
  • Syed Tarique Moin (Wed May 06 2009 - 02:12:17 CDT)
  • Syed Tarique Moin (Wed May 06 2009 - 02:11:54 CDT)
  • Catein Catherine (Tue May 05 2009 - 21:48:44 CDT)
  • Ross Walker (Tue May 05 2009 - 17:16:26 CDT)
  • Syed Tarique Moin (Mon May 04 2009 - 17:13:22 CDT)
  • Ross Walker (Mon May 04 2009 - 12:47:21 CDT)
  • Syed Tarique Moin (Mon May 04 2009 - 10:32:29 CDT)
• [AMBER] QM/MM assigns Cd to C, Se to S
  • Ross Walker (Fri May 08 2009 - 02:16:09 CDT)
  • Ross Walker (Sat May 02 2009 - 23:45:41 CDT)
  • C Liu (Sat May 02 2009 - 21:09:27 CDT)
• [AMBER] QM/MM charges
  • Ross Walker (Fri Mar 20 2009 - 10:37:34 CDT)
  • Jacopo Sgrignani (Fri Mar 20 2009 - 04:38:30 CDT)
• [AMBER] QM/MM input file error
  • Ross Walker (Thu Dec 03 2009 - 11:36:47 CST)
  • mahesh kumar (Thu Dec 03 2009 - 08:05:25 CST)
• [AMBER] QM/MM minimization
  • Ross Walker (Fri Dec 11 2009 - 21:39:55 CST)
  • Hashem Taha (Fri Dec 11 2009 - 12:24:25 CST)
  • Pansy Patel (Thu Sep 10 2009 - 09:09:48 CDT)
  • gaurav panwar (Thu Sep 10 2009 - 09:05:37 CDT)
• [AMBER] QM/MM simulation
  • Ross Walker (Thu Sep 03 2009 - 15:43:45 CDT)
  • gaurav panwar (Thu Sep 03 2009 - 15:11:42 CDT)
• [AMBER] QM/MM types.
  • Ross Walker (Thu Aug 13 2009 - 11:11:57 CDT)
  • ros_at_servidor.unam.mx (Thu Aug 13 2009 - 10:49:02 CDT)
• [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320
  • case (Sat Sep 12 2009 - 09:17:16 CDT)
  • Keith Van Nostrand (Tue Sep 08 2009 - 14:26:14 CDT)
• [AMBER] QMMM outupts
  • Gustavo Seabra (Thu Jul 09 2009 - 11:58:30 CDT)
  • Myeong Lee (Tue Jul 07 2009 - 12:13:27 CDT)
• [AMBER] QQD psuedoatom restraints
  • David A. Case (Mon Jun 15 2009 - 07:00:23 CDT)
  • Titus, Jamie (bairdje) (Fri Jun 12 2009 - 13:51:25 CDT)
  • Titus, Jamie (bairdje) (Mon Jun 01 2009 - 06:21:19 CDT)
  • David A. Case (Fri May 29 2009 - 14:26:27 CDT)
  • Titus, Jamie (bairdje) (Fri May 29 2009 - 14:01:34 CDT)
  • David A. Case (Fri May 29 2009 - 10:18:29 CDT)
  • Titus, Jamie (bairdje) (Fri May 29 2009 - 09:02:31 CDT)
• [AMBER] Quality/size of HDD for Amber
  • Gustavo Seabra (Mon Mar 09 2009 - 12:44:54 CDT)
  • M. L. Dodson (Fri Mar 06 2009 - 09:44:45 CST)
  • Francesco Pietra (Fri Mar 06 2009 - 03:26:03 CST)
• [AMBER] query
  • bharat lakhani (Fri Aug 07 2009 - 04:11:42 CDT)
  • Ashish Runthala (Fri Jul 31 2009 - 20:23:07 CDT)
  • Pansy Patel (Fri Jul 31 2009 - 09:41:05 CDT)
  • bharat lakhani (Fri Jul 31 2009 - 02:42:04 CDT)
• [AMBER] query about the charge fitting procedure about C- and N-terminal residues
  • FyD (Fri Jun 26 2009 - 04:41:52 CDT)
  • Ye MEI (Fri Jun 26 2009 - 04:19:47 CDT)
• [AMBER] query regarding FE4S4
  • case (Thu Jul 16 2009 - 06:45:06 CDT)
  • subarna thakur (Thu Jul 16 2009 - 02:14:27 CDT)
• [AMBER] query regarding fes cluster
  • FyD (Wed Aug 12 2009 - 08:00:37 CDT)
  • subarna thakur (Wed Aug 12 2009 - 00:39:55 CDT)
• [AMBER] query regarding resp
  • Oliver Kuhn (Tue Aug 11 2009 - 09:24:19 CDT)
  • subarna thakur (Fri Aug 07 2009 - 07:14:35 CDT)
• [AMBER] Query regarding watershell command
  • Mannan (Mon Aug 31 2009 - 05:38:08 CDT)
• [AMBER] question
  • Ross Walker (Wed Jun 10 2009 - 22:19:01 CDT)
  • lev kantorovich (Wed Jun 10 2009 - 09:20:08 CDT)
  • Tatyana Fedotova (Fri Apr 24 2009 - 14:55:40 CDT)
  • David A. Case (Sat Mar 28 2009 - 08:38:49 CDT)
  • Kshatresh Dutta Dubey (Sat Mar 28 2009 - 04:16:03 CDT)
  • Rausch, Felix (Fri Mar 27 2009 - 08:37:29 CDT)
  • Kshatresh Dutta Dubey (Fri Mar 27 2009 - 08:06:09 CDT)
• [AMBER] Question about &dipoles printing in AMBER 8
  • Karen Callahan (Mon May 25 2009 - 18:46:00 CDT)
• [AMBER] Question about distance restraint ?
  • Carlos Simmerling (Fri Oct 23 2009 - 05:56:24 CDT)
  • xuemeiwang1103 (Fri Oct 23 2009 - 05:07:47 CDT)
• [AMBER] question about failures
  • peker milas (Tue Dec 08 2009 - 00:25:10 CST)
  • Jason Swails (Tue Dec 08 2009 - 00:00:00 CST)
  • peker milas (Mon Dec 07 2009 - 23:31:06 CST)
  • Jason Swails (Mon Dec 07 2009 - 22:51:28 CST)
  • peker milas (Mon Dec 07 2009 - 21:37:40 CST)
• [AMBER] Question about improper torsions...
  • David A. Case (Sat Feb 14 2009 - 07:32:21 CST)
  • Antonios Samiotakis (Fri Feb 13 2009 - 16:57:03 CST)
• [AMBER] Question about NAB module
  • Andreas Svrcek-Seiler (Mon Mar 02 2009 - 03:23:52 CST)
  • Wei Huang (Sun Mar 01 2009 - 08:57:50 CST)
  • David A. Case (Sun Mar 01 2009 - 07:52:19 CST)
  • Wei Huang (Sat Feb 28 2009 - 18:23:49 CST)
• [AMBER] question about pair wise per-residue energy decomposition; idecomp=3
  • case (Wed Mar 25 2009 - 13:58:02 CDT)
  • wfli_at_biophy.nju.edu.cn (Wed Mar 25 2009 - 04:48:29 CDT)
• [AMBER] question about ptraj
  • Niel Henriksen (Wed Sep 02 2009 - 09:37:39 CDT)
  • Jeffrey (Wed Sep 02 2009 - 03:20:12 CDT)
• [AMBER] question about ptraj hydrogen bond analysis
  • Thomas Cheatham III (Wed Feb 18 2009 - 14:21:27 CST)
  • monica bhattacharee (Wed Feb 18 2009 - 13:45:17 CST)
• [AMBER] Question about the debug forces
  • Faezeh Salehi (Wed Sep 02 2009 - 16:30:47 CDT)
• [AMBER] Question about Thermal Integration with Softcore
  • steinbrt_at_rci.rutgers.edu (Wed May 13 2009 - 10:11:16 CDT)
  • Elodie Laine (Wed May 13 2009 - 04:13:22 CDT)
• [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script
  • David A. Case (Tue Jun 09 2009 - 08:20:22 CDT)
  • Samuel Genheden (Tue Jun 09 2009 - 07:43:19 CDT)
• [AMBER] question of ibelly used in pmemd
  • Kristina Furse (Tue Jul 21 2009 - 11:27:29 CDT)
  • Robert Duke (Tue Jul 21 2009 - 09:16:21 CDT)
  • Kristina Furse (Tue Jul 21 2009 - 08:53:21 CDT)
  • Robert Duke (Tue Jul 21 2009 - 08:15:20 CDT)
  • Robert Duke (Mon Jul 20 2009 - 12:55:23 CDT)
  • xiaoqin huang (Mon Jul 20 2009 - 12:39:16 CDT)
  • Ross Walker (Mon Jul 20 2009 - 12:32:08 CDT)
  • xiaoqin huang (Mon Jul 20 2009 - 12:20:36 CDT)
  • Robert Duke (Mon Jul 20 2009 - 12:10:03 CDT)
  • Kristina Furse (Mon Jul 20 2009 - 11:56:26 CDT)
  • Robert Duke (Mon Jul 20 2009 - 11:42:08 CDT)
  • xiaoqin huang (Mon Jul 20 2009 - 11:28:42 CDT)
  • Robert Duke (Mon Jul 20 2009 - 10:53:50 CDT)
  • xiaoqin huang (Mon Jul 20 2009 - 10:20:32 CDT)
  • Robert Duke (Mon Jul 20 2009 - 09:42:15 CDT)
  • xiaoqin huang (Mon Jul 20 2009 - 09:21:20 CDT)
  • Robert Duke (Fri Jul 17 2009 - 10:48:41 CDT)
  • xiaoqin huang (Fri Jul 17 2009 - 09:54:55 CDT)
  • xiaoqin huang (Fri Jul 17 2009 - 09:36:06 CDT)
  • Ross Walker (Wed Jul 15 2009 - 20:32:07 CDT)
  • Robert Duke (Wed Jul 15 2009 - 16:56:00 CDT)
  • xiaoqin huang (Wed Jul 15 2009 - 16:28:52 CDT)
  • Robert Duke (Wed Jul 15 2009 - 13:22:23 CDT)
  • xiaoqin huang (Wed Jul 15 2009 - 12:34:20 CDT)
• [AMBER] question of mm_pbsa
  • Ray Luo (Fri Jul 10 2009 - 11:47:12 CDT)
  • Hannes Kopitz (Fri Jul 10 2009 - 04:36:44 CDT)
  • å»–é�’å�Ž (Thu Jul 09 2009 - 20:49:40 CDT)
• [AMBER] Question on ECAVITY term of MM_PBSA
  • Ray Luo (Mon Sep 21 2009 - 20:28:32 CDT)
  • Ray Luo (Mon Sep 21 2009 - 12:30:57 CDT)
  • Gianluca Degliesposti (Mon Sep 21 2009 - 06:18:27 CDT)
  • Gianluca Degliesposti (Mon Sep 14 2009 - 10:28:12 CDT)
• [AMBER] Question on heating for homology based model.
  • Carlos Simmerling (Sun Feb 01 2009 - 11:47:02 CST)
  • drugdesign (Sat Jan 31 2009 - 12:43:06 CST)
• [AMBER] Question on REST and VALUE1 keywords
  • Ashish Runthala (Tue Jul 28 2009 - 20:26:19 CDT)
  • Carlos Simmerling (Tue Jul 28 2009 - 16:14:20 CDT)
  • hwu_at_clarku.edu (Tue Jul 28 2009 - 16:06:34 CDT)
• [AMBER] Question regarding PCA analysis.
  • Catein Catherine (Thu Sep 03 2009 - 21:55:42 CDT)
  • Chris Moth (Thu Sep 03 2009 - 09:17:42 CDT)
  • Catein Catherine (Tue Sep 01 2009 - 22:53:10 CDT)
• [AMBER] question with hbond
  • Ganesh Kamath (Wed Sep 16 2009 - 16:36:18 CDT)
• [AMBER] question with hbond in carnal
  • Bill Ross (Tue Oct 20 2009 - 11:32:56 CDT)
  • Ganesh Kamath (Tue Oct 20 2009 - 08:58:36 CDT)
• [AMBER] question with pucker in six member ring
  • Bill Ross (Mon Oct 19 2009 - 12:54:03 CDT)
  • Ganesh Kamath (Mon Oct 19 2009 - 12:42:17 CDT)
  • Bill Ross (Fri Oct 16 2009 - 14:48:04 CDT)
  • Ganesh Kamath (Fri Oct 16 2009 - 14:31:31 CDT)
  • Bill Ross (Fri Oct 16 2009 - 13:43:56 CDT)
  • Ganesh Kamath (Fri Oct 16 2009 - 13:36:41 CDT)
  • Thomas Cheatham III (Fri Oct 16 2009 - 13:23:05 CDT)
  • Nicolas Sapay (Fri Oct 16 2009 - 10:04:24 CDT)
  • Ganesh Kamath (Thu Oct 15 2009 - 14:55:45 CDT)
• [AMBER] question with radial distribution function
  • Ganesh Kamath (Thu Sep 10 2009 - 17:08:34 CDT)
• [AMBER] questions about RESP
  • FyD (Thu Jul 23 2009 - 12:49:23 CDT)
  • Jeffrey (Thu Jul 23 2009 - 07:51:34 CDT)
  • FyD (Mon Jul 20 2009 - 15:46:04 CDT)
  • Jeffrey (Mon Jul 20 2009 - 02:42:29 CDT)
  • FyD (Thu Jul 16 2009 - 09:27:44 CDT)
  • Jeffrey (Thu Jul 16 2009 - 01:57:28 CDT)
• [AMBER] Questions on targeted MD with explicit solvent
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 14 2009 - 08:51:40 CDT)
• [AMBER] R.E.D intra-mcc and reorientation
  • Ganesh Krishnan (Sat Jul 11 2009 - 17:56:18 CDT)
  • FyD (Sat Jul 11 2009 - 03:05:56 CDT)
  • Ganesh Krishnan (Fri Jul 10 2009 - 17:00:35 CDT)
• [AMBER] R.E.D. : Gaussian Error
  • manoj singh (Mon Sep 07 2009 - 00:46:54 CDT)
  • FyD (Mon Sep 07 2009 - 00:07:34 CDT)
  • manoj singh (Sun Sep 06 2009 - 23:22:44 CDT)
  • FyD (Sun Sep 06 2009 - 14:41:41 CDT)
  • manoj singh (Sun Sep 06 2009 - 13:40:48 CDT)
• [AMBER] R.E.D. help please
  • FyD (Wed Jul 15 2009 - 11:35:57 CDT)
  • s. Bill (Wed Jul 15 2009 - 09:11:46 CDT)
• [AMBER] R.E.D. resp error
  • FyD (Thu Nov 12 2009 - 23:36:44 CST)
  • s. Bill (Thu Nov 12 2009 - 14:23:31 CST)
• [AMBER] R.E.D. too small charges
  • FyD (Fri Nov 13 2009 - 07:06:51 CST)
  • Andrei Neamtu (Fri Nov 13 2009 - 02:57:04 CST)
• [AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
  • FyD (Sun Oct 04 2009 - 09:37:06 CDT)
• [AMBER] radial distribution function
  • Dharmik Meghana shankar (Sat Aug 01 2009 - 00:33:58 CDT)
• [AMBER] radial distribution function in amber
  • Ganesh Kamath (Mon Sep 14 2009 - 09:58:56 CDT)
• [AMBER] radial distribution function mask
  • iccy liu (Wed Mar 04 2009 - 12:57:08 CST)
• [AMBER] radial distribution without normalization
  • Thomas Cheatham (Wed Jun 10 2009 - 17:11:40 CDT)
  • CHAMI F. (Wed Jun 10 2009 - 10:48:12 CDT)
• [AMBER] radical simulation
  • Jeffrey (Sun Jul 26 2009 - 07:28:39 CDT)
  • FyD (Fri Jul 24 2009 - 05:27:34 CDT)
  • Manish Kumar (Fri Jul 24 2009 - 02:48:01 CDT)
  • Jeffrey (Fri Jul 24 2009 - 02:34:53 CDT)
• [AMBER] Radius for Bromine in MMPBSA calculation
  • Ray Luo (Tue May 26 2009 - 14:02:27 CDT)
  • john smith (Tue May 26 2009 - 00:00:52 CDT)
  • Ray Luo (Mon May 25 2009 - 16:10:41 CDT)
  • john smith (Sun May 24 2009 - 23:52:48 CDT)
  • Ray Luo (Thu May 21 2009 - 11:32:41 CDT)
  • john smith (Thu May 21 2009 - 00:24:05 CDT)
• [AMBER] radius for Manganese ion
  • E.M. (Sun Aug 30 2009 - 18:38:38 CDT)
  • Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
  • Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
• [AMBER] radius of gyration
  • Beale, John (Fri Apr 17 2009 - 06:39:31 CDT)
  • priya priya (Tue Feb 03 2009 - 23:30:07 CST)
  • Beale, John (Mon Feb 02 2009 - 11:34:35 CST)
• [AMBER] Ramesh here
  • kureeckal ramesh (Sat Feb 28 2009 - 09:36:43 CST)
  • FyD (Sat Feb 28 2009 - 07:45:39 CST)
  • kureeckal ramesh (Fri Feb 27 2009 - 21:20:49 CST)
• [AMBER] RDC analysis: "No restraint defined"
  • case (Wed Sep 16 2009 - 11:47:41 CDT)
  • Michael Durney (Wed Sep 16 2009 - 11:10:34 CDT)
• [AMBER] RDC and alignment tensor
  • Eliana Asciutto (Fri Oct 23 2009 - 14:19:00 CDT)
  • case (Tue Oct 20 2009 - 07:24:45 CDT)
  • Eliana Asciutto (Mon Oct 19 2009 - 14:03:43 CDT)
  • case (Mon Oct 19 2009 - 12:36:16 CDT)
  • Eliana Asciutto (Mon Oct 19 2009 - 11:50:31 CDT)
  • Thomas Cheatham III (Fri Oct 16 2009 - 15:45:25 CDT)
  • Eliana Asciutto (Fri Oct 16 2009 - 15:21:34 CDT)
• [AMBER] RDC import from PALES
  • case (Fri Aug 28 2009 - 07:01:30 CDT)
  • Thomas Pochapsky (Tue Aug 18 2009 - 09:33:42 CDT)
• [AMBER] rdparm bug?
  • Paul Mortenson (Tue Jul 07 2009 - 11:29:44 CDT)
• [AMBER] reaction coordinates
  • Catein Catherine (Wed Jan 14 2009 - 23:25:31 CST)
  • David A. Case (Wed Jan 14 2009 - 07:00:59 CST)
  • Rausch, Felix (Wed Jan 14 2009 - 05:54:57 CST)
• [AMBER] read substrate into leap
  • Bill Ross (Wed Nov 18 2009 - 19:59:33 CST)
  • Jason Swails (Wed Nov 18 2009 - 19:35:37 CST)
  • sculiujl (Wed Nov 18 2009 - 19:12:13 CST)
  • Jason Swails (Wed Nov 18 2009 - 12:53:30 CST)
  • sculiujl (Wed Nov 18 2009 - 07:37:19 CST)
• [AMBER] reagarding Dihedral PCA
  • jani sahil (Mon Nov 30 2009 - 00:24:28 CST)
• [AMBER] reclaiming space from amber10 installation
  • Ross Walker (Mon Jun 22 2009 - 20:26:36 CDT)
  • Alan (Sun Jun 21 2009 - 17:04:53 CDT)
• [AMBER] rectangular box with PME problem
  • Ivan Gladich (Mon Nov 09 2009 - 16:18:16 CST)
• [AMBER] RED Geometry Calculation Error
  • FyD (Sat Jun 20 2009 - 01:41:46 CDT)
  • Brothers, Michael Charles (Fri Jun 19 2009 - 16:10:12 CDT)
  • FyD (Fri Jun 19 2009 - 14:19:00 CDT)
  • Brothers, Michael Charles (Fri Jun 19 2009 - 13:52:37 CDT)
• [AMBER] red problem
  • FyD (Thu Oct 01 2009 - 23:48:57 CDT)
  • James Moore (Thu Oct 01 2009 - 20:52:46 CDT)
• [AMBER] REd program!
  • FyD (Wed Apr 29 2009 - 08:53:12 CDT)
  • R. A. (Tue Apr 28 2009 - 23:37:38 CDT)
• [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND]
  • FyD (Tue Feb 10 2009 - 09:05:56 CST)
  • Patrick Schopf (Tue Feb 10 2009 - 08:15:42 CST)
• [AMBER] RED.III: Invalid Optimization OUTPUT
  • s. Bill (Wed Jul 29 2009 - 03:37:27 CDT)
• [AMBER] RED: Charge derivation of transtion state analogue
  • FyD (Mon Jul 06 2009 - 01:45:13 CDT)
  • FyD (Mon Jul 06 2009 - 01:29:11 CDT)
  • manoj singh (Mon Jul 06 2009 - 00:03:27 CDT)
  • FyD (Sun Jul 05 2009 - 04:39:13 CDT)
  • manoj singh (Sun Jul 05 2009 - 01:10:57 CDT)
• [AMBER] Reference Correction
  • Mahmoud A. A. Ibrahim (Sun Jun 21 2009 - 15:11:34 CDT)
• [AMBER] reference re. determining size of timestep
  • Gustavo Seabra (Fri Jul 17 2009 - 11:53:46 CDT)
  • Paul Brandt (Thu Jul 09 2009 - 13:07:50 CDT)
• [AMBER] reg . parallel run
  • Ross Walker (Thu Jan 22 2009 - 09:52:55 CST)
  • balaji nagarajan (Wed Jan 21 2009 - 23:34:03 CST)
• [AMBER] reg . run TMD
  • Carlos Simmerling (Tue Feb 10 2009 - 11:48:22 CST)
  • balaji nagarajan (Tue Feb 10 2009 - 11:36:28 CST)
• [AMBER] reg-TMD
  • balaji nagarajan (Wed Apr 29 2009 - 20:44:32 CDT)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 29 2009 - 15:56:07 CDT)
  • balaji nagarajan (Wed Apr 29 2009 - 06:54:59 CDT)
  • Carlos Simmerling (Wed Apr 29 2009 - 06:33:40 CDT)
  • balaji nagarajan (Wed Apr 29 2009 - 06:25:50 CDT)
  • Carlos Simmerling (Wed Apr 29 2009 - 05:28:35 CDT)
  • balaji nagarajan (Tue Apr 28 2009 - 23:16:17 CDT)
  • Carlos Simmerling (Tue Apr 28 2009 - 12:48:18 CDT)
  • balaji nagarajan (Tue Apr 28 2009 - 10:23:34 CDT)
• [AMBER] reg. GBA
  • case (Thu Nov 12 2009 - 07:02:43 CST)
  • balaji nagarajan (Thu Nov 12 2009 - 06:06:30 CST)
• [AMBER] Reg. snapshot_statistics.out.snap
  • Rose Tamil (Tue Sep 01 2009 - 12:04:08 CDT)
• [AMBER] reg.changing velocity
  • David A. Case (Sat Dec 26 2009 - 21:01:18 CST)
  • balaji nagarajan (Sat Dec 26 2009 - 12:47:10 CST)
• [AMBER] reg.error in parallel run
  • Ross Walker (Fri Jan 23 2009 - 09:52:20 CST)
  • balaji nagarajan (Fri Jan 23 2009 - 04:05:21 CST)
• [AMBER] reg.parallel run error
  • Ross Walker (Thu Jan 22 2009 - 14:06:33 CST)
  • balaji nagarajan (Thu Jan 22 2009 - 12:41:25 CST)
• [AMBER] reg.parallel.run error
  • Ross Walker (Sat Jan 24 2009 - 00:05:50 CST)
  • balaji nagarajan (Fri Jan 23 2009 - 19:59:21 CST)
• [AMBER] reg.parallel.run.error
  • balaji nagarajan (Sat Jan 24 2009 - 09:09:49 CST)
• [AMBER] reg.targeted molecular dynamics
  • Ross Walker (Fri Feb 27 2009 - 09:11:44 CST)
  • balaji nagarajan (Fri Feb 27 2009 - 04:28:02 CST)
  • Ross Walker (Wed Feb 25 2009 - 09:12:29 CST)
  • Carlos Simmerling (Wed Feb 25 2009 - 05:21:39 CST)
  • balaji nagarajan (Wed Feb 25 2009 - 03:34:57 CST)
  • balaji nagarajan (Wed Feb 25 2009 - 03:18:10 CST)
  • Carlos Simmerling (Mon Feb 23 2009 - 05:16:00 CST)
  • balaji nagarajan (Mon Feb 23 2009 - 00:45:18 CST)
  • Carlos Simmerling (Sun Feb 22 2009 - 09:06:32 CST)
  • balaji nagarajan (Sun Feb 22 2009 - 08:45:29 CST)
  • Carlos Simmerling (Sat Feb 21 2009 - 06:35:05 CST)
  • balaji nagarajan (Fri Feb 20 2009 - 23:10:50 CST)
  • balaji nagarajan (Wed Feb 18 2009 - 08:07:09 CST)
  • Simon Becker (Wed Feb 18 2009 - 05:38:54 CST)
  • balaji nagarajan (Tue Feb 17 2009 - 23:26:49 CST)
  • Carlos Simmerling (Wed Jan 28 2009 - 12:01:43 CST)
  • balaji nagarajan (Tue Jan 27 2009 - 07:57:01 CST)
  • balaji nagarajan (Tue Jan 27 2009 - 07:56:54 CST)
• [AMBER] reg: targeted molecular dynamics
  • Carlos Simmerling (Tue Jan 27 2009 - 07:04:57 CST)
  • balaji nagarajan (Tue Jan 27 2009 - 07:02:03 CST)
• [AMBER] regarding Dihedral PCA
  • jani sahil (Mon Nov 30 2009 - 00:25:08 CST)
• [AMBER] Regarding Hbond interactions
  • Thomas Cheatham (Thu Jul 23 2009 - 17:57:57 CDT)
  • aneesh cna (Wed Jul 22 2009 - 01:30:10 CDT)
• [AMBER] Regarding leap
  • Gustavo Seabra (Thu Mar 05 2009 - 09:32:56 CST)
  • aneesh cna (Wed Mar 04 2009 - 22:29:17 CST)
  • Gustavo Seabra (Wed Mar 04 2009 - 16:05:25 CST)
  • Carlos Simmerling (Wed Mar 04 2009 - 05:48:30 CST)
  • aneesh cna (Wed Mar 04 2009 - 05:43:52 CST)
• [AMBER] Regarding Minimization maxcyc
  • case (Mon Aug 10 2009 - 09:43:00 CDT)
  • Ashish Runthala (Sun Aug 09 2009 - 09:09:58 CDT)
• [AMBER] Regarding principal component analysis using ptraj
  • Arvind Marathe (Fri Aug 28 2009 - 06:56:53 CDT)
  • Hannes Loeffler (Fri Aug 28 2009 - 06:45:05 CDT)
  • Arvind Marathe (Fri Aug 28 2009 - 06:04:22 CDT)
  • Hannes Loeffler (Fri Aug 28 2009 - 02:28:29 CDT)
  • Arvind Marathe (Fri Aug 28 2009 - 01:54:40 CDT)
• [AMBER] Regarding rigid bond
  • Bill Ross (Wed Dec 02 2009 - 11:20:52 CST)
  • aneesh cna (Tue Dec 01 2009 - 23:17:46 CST)
  • Bill Ross (Tue Dec 01 2009 - 11:41:44 CST)
  • Adrian Roitberg (Tue Dec 01 2009 - 11:40:30 CST)
  • Bill Ross (Tue Dec 01 2009 - 11:37:27 CST)
  • Carlos Simmerling (Tue Dec 01 2009 - 06:55:17 CST)
  • case (Tue Dec 01 2009 - 06:50:15 CST)
  • Carlos Simmerling (Tue Dec 01 2009 - 05:28:58 CST)
  • aneesh cna (Mon Nov 30 2009 - 23:35:03 CST)
  • Carlos Simmerling (Fri Nov 27 2009 - 12:24:35 CST)
  • aneesh cna (Fri Nov 27 2009 - 11:29:15 CST)
• [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
  • Keith Van Nostrand (Wed Jul 22 2009 - 10:58:08 CDT)
  • Ross Walker (Thu Jul 16 2009 - 22:34:13 CDT)
  • Keith Van Nostrand (Thu Jul 16 2009 - 16:08:04 CDT)
  • Ross Walker (Fri Jul 10 2009 - 11:21:11 CDT)
  • Keith Van Nostrand (Fri Jul 10 2009 - 10:27:12 CDT)
• [AMBER] Regarding syntax for freezing different atoms
  • Ross Walker (Thu Apr 23 2009 - 08:24:55 CDT)
  • Jorgen Simonsen (Thu Apr 23 2009 - 07:50:43 CDT)
• [AMBER] regarding tutorial on united atom force field
  • Ray Luo (Tue Mar 17 2009 - 11:22:01 CDT)
  • jani sahil (Mon Mar 16 2009 - 23:51:16 CDT)
• [AMBER] Regarding united atom force field
  • FyD (Tue Sep 22 2009 - 01:13:03 CDT)
  • Ray Luo (Mon Sep 21 2009 - 12:32:34 CDT)
  • aneesh cna (Mon Sep 21 2009 - 05:17:20 CDT)
• [AMBER] Regarding Urey-Bradley term in amber calculation
  • Ross Walker (Tue Nov 24 2009 - 10:36:49 CST)
  • Jason Swails (Tue Nov 24 2009 - 06:48:31 CST)
  • aneesh cna (Tue Nov 24 2009 - 00:48:04 CST)
• [AMBER] Regarding use of PME along with Implict solvation
  • jani sahil (Mon Mar 23 2009 - 08:04:15 CDT)
  • parul sharma (Mon Mar 23 2009 - 05:55:24 CDT)
  • jani sahil (Mon Mar 23 2009 - 05:38:39 CDT)
• [AMBER] Regd : gaff force field
  • Ashish Runthala (Sat Aug 08 2009 - 07:17:37 CDT)
  • Ross Walker (Fri Aug 07 2009 - 10:52:07 CDT)
  • Ashish Runthala (Fri Aug 07 2009 - 04:08:43 CDT)
  • KIRTANA S (Thu Aug 06 2009 - 17:12:15 CDT)
  • Ross Walker (Thu Aug 06 2009 - 15:42:14 CDT)
  • Nicholas Musolino (Thu Aug 06 2009 - 15:22:37 CDT)
  • KIRTANA S (Thu Aug 06 2009 - 15:09:14 CDT)
• [AMBER] Regd: parameter Fe4S4
  • FyD (Mon Jun 29 2009 - 14:03:22 CDT)
  • KIRTANA S (Mon Jun 29 2009 - 11:11:49 CDT)
• [AMBER] Release of AmberTools, version 1.3
  • David A. Case (Mon Dec 21 2009 - 08:33:20 CST)
• [AMBER] Release of R.E.D. Server
  • FyD (Thu Apr 09 2009 - 03:31:30 CDT)
• [AMBER] Release of the R.E.D.-III.1 tools
  • FyD (Mon Jan 12 2009 - 05:59:14 CST)
• [AMBER] REM_hybrid test fails on AIX
  • Shan-ho Tsai (Thu Feb 05 2009 - 10:44:43 CST)
  • Shan-ho Tsai (Thu Jan 22 2009 - 14:28:04 CST)
• [AMBER] REMD
  • Carlos Simmerling (Tue Jun 23 2009 - 05:07:39 CDT)
  • Shaikh Abdul R S Ramaju (Tue Jun 23 2009 - 00:32:34 CDT)
• [AMBER] REMD fixed atoms
  • Carlos Simmerling (Sun Feb 01 2009 - 12:00:33 CST)
  • Maxime Louet (Fri Jan 30 2009 - 11:26:08 CST)
• [AMBER] REMD using hybrid solvent model
  • Morad Mustafa (Wed Aug 12 2009 - 14:05:40 CDT)
• [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
  • albert albert (Fri Jul 31 2009 - 14:27:02 CDT)
  • Ashish Runthala (Tue Jul 28 2009 - 08:08:48 CDT)
  • FyD (Tue Jul 28 2009 - 06:59:51 CDT)
  • Ashish Runthala (Tue Jul 28 2009 - 05:28:40 CDT)
  • Bill Ross (Mon Jul 27 2009 - 11:17:29 CDT)
  • Ashish Runthala (Mon Jul 27 2009 - 04:09:23 CDT)
  • albert albert (Mon Jul 27 2009 - 01:57:20 CDT)
• [AMBER] removing center of mass
  • Bala subramanian (Tue Mar 17 2009 - 10:21:28 CDT)
• [AMBER] Replacing DNA base with analog
  • Kristina Furse (Thu Jul 23 2009 - 09:36:26 CDT)
  • amoreno_at_wesleyan.edu (Thu Jul 23 2009 - 09:20:08 CDT)
• [AMBER] request
  • sculiujl (Fri Nov 13 2009 - 20:59:22 CST)
• [AMBER] Request an error
  • Collins Nganou (Thu Apr 30 2009 - 12:41:48 CDT)
• [AMBER] rescaling velocities
  • Carlos Simmerling (Thu Jun 04 2009 - 11:43:20 CDT)
  • abi ghanem (Thu Jun 04 2009 - 11:39:02 CDT)
• [AMBER] reset velocity
  • Tom Joseph (Thu Aug 13 2009 - 01:26:48 CDT)
  • Parimal Kar (Wed Aug 12 2009 - 20:01:33 CDT)
• [AMBER] residue
  • KIRTANA S (Thu Jun 18 2009 - 14:59:50 CDT)
• [AMBER] Residues
  • Roman Osman (Thu Jun 18 2009 - 16:58:53 CDT)
  • Bill Ross (Thu Jun 18 2009 - 16:13:53 CDT)
  • FyD (Thu Jun 18 2009 - 15:24:16 CDT)
  • KIRTANA S (Thu Jun 18 2009 - 14:57:11 CDT)
  • FyD (Mon Jun 15 2009 - 01:51:56 CDT)
  • KIRTANA S (Sat Jun 13 2009 - 19:14:31 CDT)
  • Bill Ross (Fri Jun 12 2009 - 14:49:09 CDT)
  • KIRTANA S (Fri Jun 12 2009 - 14:41:02 CDT)
  • FyD (Fri Jun 12 2009 - 10:36:10 CDT)
  • KIRTANA S (Fri Jun 12 2009 - 10:07:50 CDT)
  • FyD (Fri Jun 12 2009 - 09:24:35 CDT)
  • KIRTANA S (Fri Jun 12 2009 - 09:10:39 CDT)
• [AMBER] residues lacking connect0/connect1
  • Bill Ross (Mon Jul 27 2009 - 11:40:31 CDT)
  • Jio M (Mon Jul 27 2009 - 11:10:06 CDT)
• [AMBER] RESP
  • case (Mon Jun 29 2009 - 06:52:19 CDT)
  • Syed Tarique Moin (Mon Jun 29 2009 - 02:42:51 CDT)
• [AMBER] resp calculation for rubredoxin
  • vhakkim boy (Wed Aug 19 2009 - 05:11:22 CDT)
• [AMBER] resp charge
  • Ross Walker (Wed May 20 2009 - 10:05:20 CDT)
  • FyD (Wed May 20 2009 - 02:42:07 CDT)
  • R. A. (Tue May 19 2009 - 21:35:25 CDT)
  • Jason A. Ford-Green (Fri Feb 06 2009 - 14:38:29 CST)
  • . .. (Fri Feb 06 2009 - 11:34:12 CST)
• [AMBER] RESP charges for Fe in heme
  • Carina Backtorp (Mon Jan 19 2009 - 07:48:11 CST)
• [AMBER] RESP charges of Fe4S4 cluster
  • case (Fri Aug 21 2009 - 09:13:23 CDT)
  • vhakkim boy (Wed Aug 19 2009 - 03:40:59 CDT)
  • subarna thakur (Wed Aug 19 2009 - 02:53:20 CDT)
• [AMBER] RESP charges with -a and without -a flag
  • Jio M (Sat Oct 31 2009 - 00:13:03 CDT)
  • Junmei Wang (Fri Oct 30 2009 - 11:49:00 CDT)
  • Jio M (Fri Oct 30 2009 - 08:36:43 CDT)
• [AMBER] RESP fit
  • FyD (Sat Jul 18 2009 - 01:29:56 CDT)
  • E.M. (Fri Jul 17 2009 - 18:00:08 CDT)
• [AMBER] RESP RED
  • FyD (Sat Sep 12 2009 - 09:35:16 CDT)
  • s. Bill (Fri Sep 11 2009 - 13:40:24 CDT)
• [AMBER] RESP using antechamber with Se atom
  • Eric Pettersen (Fri Nov 06 2009 - 10:49:16 CST)
  • subarna thakur (Thu Nov 05 2009 - 23:21:46 CST)
  • Junmei Wang (Thu Nov 05 2009 - 15:39:46 CST)
  • Donald Keidel (Thu Nov 05 2009 - 13:21:37 CST)
• [AMBER] resp_problem
  • FyD (Sun Oct 25 2009 - 01:12:31 CDT)
  • Ross Walker (Sat Oct 24 2009 - 17:39:01 CDT)
  • vhakkim boy (Sat Oct 24 2009 - 05:16:22 CDT)
• [AMBER] Restarting an MD Simulation
  • Ross Walker (Wed Feb 04 2009 - 21:24:56 CST)
  • Ross Walker (Wed Feb 04 2009 - 21:03:36 CST)
  • Hopkins, Robert (Wed Feb 04 2009 - 18:34:16 CST)
• [AMBER] Restrained backbone conformation MD simulation"
  • Carlos Simmerling (Fri Jul 10 2009 - 06:47:20 CDT)
  • Prem Prakash Pathak (Fri Jul 10 2009 - 06:27:38 CDT)
• [AMBER] restrained minimization
  • David A. Case (Mon Apr 13 2009 - 21:03:11 CDT)
  • quantum_mania_at_yahoo.com (Mon Apr 13 2009 - 19:12:35 CDT)
• [AMBER] restraining atoms
  • Carlos Simmerling (Thu Jan 22 2009 - 08:55:35 CST)
  • neville forlemu (Thu Jan 22 2009 - 08:53:48 CST)
• [AMBER] Restraining counterions?
  • Bill Ross (Tue Apr 28 2009 - 13:59:52 CDT)
  • Francesco Pietra (Tue Apr 28 2009 - 12:32:18 CDT)
• [AMBER] restraint angle
  • David A. Case (Tue Feb 17 2009 - 11:52:49 CST)
  • m m (Tue Feb 17 2009 - 11:17:00 CST)
• [AMBER] restraint constant
  • Dong Xu (Sat Apr 25 2009 - 17:15:22 CDT)
• [AMBER] Restraint Mask length restriction !!
  • Ross Walker (Mon Mar 09 2009 - 14:50:08 CDT)
  • Sampath Koppole (Mon Mar 09 2009 - 09:39:38 CDT)
  • David A. Case (Mon Mar 09 2009 - 09:30:16 CDT)
  • Sampath Koppole (Mon Mar 09 2009 - 09:06:23 CDT)
  • David A. Case (Mon Mar 09 2009 - 08:43:34 CDT)
  • Sampath Koppole (Mon Mar 09 2009 - 08:32:35 CDT)
• [AMBER] restraint of REMD
  • Carlos Simmerling (Fri Jan 16 2009 - 05:57:29 CST)
  • z g (Thu Jan 15 2009 - 20:51:46 CST)
• [AMBER] retinal lib file, params?
  • Simon Becker (Mon Nov 02 2009 - 02:34:14 CST)
  • Mark M Huntress (Sun Nov 01 2009 - 11:59:34 CST)
• [AMBER] Right force fields
  • Patrick Schopf (Fri Apr 17 2009 - 08:34:04 CDT)
  • Vikas Sharma (Fri Apr 17 2009 - 08:14:04 CDT)
  • Patrick Schopf (Fri Apr 17 2009 - 07:48:14 CDT)
  • Vikas Sharma (Fri Apr 17 2009 - 01:22:16 CDT)
• [AMBER] rings getting planar
  • case (Thu Nov 26 2009 - 09:07:43 CST)
  • Jio M (Thu Nov 26 2009 - 08:40:34 CST)
  • Jio M (Thu Nov 26 2009 - 03:33:09 CST)
• [AMBER] rms fit of mutant with respect to wild type structure
  • Carlos Simmerling (Thu Oct 29 2009 - 09:03:35 CDT)
  • Siddharth Rastogi (Thu Oct 29 2009 - 08:55:12 CDT)
• [AMBER] rmsd
  • Taufik Al-Sarraj (Mon Nov 23 2009 - 13:24:49 CST)
  • Thomas Cheatham (Sat Nov 21 2009 - 15:44:41 CST)
  • Taufik Al-Sarraj (Fri Nov 20 2009 - 10:32:24 CST)
• [AMBER] RMSD vs time and RMSD vs residues
  • Sally Pias (Fri Oct 02 2009 - 14:16:33 CDT)
  • case (Fri Oct 02 2009 - 14:12:23 CDT)
  • Luis Gracia (Fri Oct 02 2009 - 13:07:10 CDT)
  • Olotu Odunayo (Fri Oct 02 2009 - 12:40:40 CDT)
• [AMBER] rmsd_dna
  • balaji nagarajan (Wed Jul 08 2009 - 20:55:53 CDT)
  • Carlos Simmerling (Wed Jul 08 2009 - 13:21:29 CDT)
  • balaji nagarajan (Wed Jul 08 2009 - 11:15:02 CDT)
• [AMBER] rmsd_ptraj
  • Thomas Cheatham (Thu Jul 09 2009 - 02:08:53 CDT)
  • balaji nagarajan (Thu Jul 09 2009 - 00:50:10 CDT)
  • Ross Walker (Wed Jul 08 2009 - 23:35:59 CDT)
  • balaji nagarajan (Wed Jul 08 2009 - 23:19:56 CDT)
• [AMBER] RMSDf of heavy atoms
  • Syed Tarique Moin (Tue Sep 22 2009 - 06:45:26 CDT)
• [AMBER] RNA and polarizable force field
  • Abhishek Singh (Wed Jun 10 2009 - 10:30:29 CDT)
• [AMBER] Rosetta Academic Training Webinar
  • Nir London (Wed Mar 25 2009 - 11:14:21 CDT)
• [AMBER] Rosetta Academic Training Workshop
  • Nir London (Tue Jan 27 2009 - 07:07:24 CST)
• [AMBER] RST file
  • David A. Case (Fri Apr 10 2009 - 07:21:19 CDT)
  • waleed zalloum (Thu Apr 09 2009 - 09:06:37 CDT)
• [AMBER] run protein with structural Ca+
  • sarah genare (Wed Apr 01 2009 - 06:01:24 CDT)
• [AMBER] Running PTRAJ command line scripts in background
  • Hopkins, Robert (Mon May 18 2009 - 17:50:06 CDT)
  • Ross Walker (Sun May 17 2009 - 22:35:09 CDT)
  • Hopkins, Robert (Sun May 17 2009 - 11:55:48 CDT)
  • Jia Xu (Sun May 17 2009 - 02:16:49 CDT)
  • Hopkins, Robert (Sat May 16 2009 - 19:47:38 CDT)
• [AMBER] S-S problem-in protein
  • Rilei Yu (Mon Oct 12 2009 - 17:14:02 CDT)
  • Jason Swails (Mon Oct 12 2009 - 06:23:25 CDT)
  • Rilei Yu (Mon Oct 12 2009 - 04:16:15 CDT)
  • Rilei Yu (Mon Oct 12 2009 - 01:28:14 CDT)
  • Jason Swails (Sun Oct 11 2009 - 23:24:51 CDT)
  • Jason Swails (Sun Oct 11 2009 - 21:15:10 CDT)
  • Rilei Yu (Sun Oct 11 2009 - 20:53:24 CDT)
• [AMBER] Saccharides chains termini
  • FyD (Tue Jun 30 2009 - 10:47:04 CDT)
  • Karl Kirschner (Tue Jun 30 2009 - 09:57:46 CDT)
  • Lachele Foley (Lists) (Tue Jun 30 2009 - 09:46:09 CDT)
  • Sergey Samsonov (Tue Jun 30 2009 - 09:32:53 CDT)
• [AMBER] Salt bridge time scale
  • Mannan (Sun Oct 25 2009 - 20:57:20 CDT)
• [AMBER] Sander
  • waleed_zalloum_at_yahoo.com (Mon Apr 06 2009 - 08:17:34 CDT)
• [AMBER] Sander and multiple residues
  • Bill Ross (Fri Apr 10 2009 - 15:42:14 CDT)
  • Dan Kaps (Fri Apr 10 2009 - 12:46:49 CDT)
  • Bill Ross (Fri Apr 10 2009 - 11:42:36 CDT)
  • Dan Kaps (Fri Apr 10 2009 - 10:01:08 CDT)
  • David A. Case (Fri Apr 10 2009 - 09:03:57 CDT)
  • Dan Kaps (Fri Apr 10 2009 - 07:57:54 CDT)
  • Dan Kaps (Fri Apr 10 2009 - 07:56:53 CDT)
  • Bill Ross (Thu Apr 09 2009 - 15:12:10 CDT)
  • Carlos Simmerling (Thu Apr 09 2009 - 15:05:23 CDT)
  • Dan Kaps (Thu Apr 09 2009 - 15:02:46 CDT)
  • Carlos Simmerling (Thu Apr 09 2009 - 14:21:56 CDT)
  • Dan Kaps (Thu Apr 09 2009 - 13:48:55 CDT)
• [AMBER] SANDER BOMB
  • David A. Case (Thu May 28 2009 - 09:29:50 CDT)
  • PRADEEP VENKATARAMAN (Wed May 27 2009 - 21:39:56 CDT)
• [AMBER] SANDER BOMB in subroutine nonbond_list
  • Bill Ross (Tue Jun 23 2009 - 11:54:30 CDT)
  • Siddharth Rastogi (Tue Jun 23 2009 - 11:39:58 CDT)
• [AMBER] Sander crash, corrupt rst file...
  • Waqas Nasir (Mon Dec 21 2009 - 05:44:42 CST)
• [AMBER] sander does not print out all residues in range.
  • Maria Mirza (Tue Aug 25 2009 - 00:17:59 CDT)
  • Ross Walker (Tue Aug 25 2009 - 00:00:03 CDT)
  • Maria Mirza (Mon Aug 24 2009 - 23:32:31 CDT)
• [AMBER] sander error
  • Robert Duke (Mon Jun 08 2009 - 22:27:52 CDT)
  • Ross Walker (Mon Jun 08 2009 - 20:41:06 CDT)
  • Beale, John (Mon Jun 08 2009 - 09:43:24 CDT)
• [AMBER] Sander imin=5 option
  • Paul Mortenson (Tue Jun 16 2009 - 10:09:54 CDT)
  • Carlos Simmerling (Tue Jun 16 2009 - 09:50:43 CDT)
  • Paul Mortenson (Tue Jun 16 2009 - 09:46:37 CDT)
• [AMBER] sander not working
  • Carlos Simmerling (Fri Jan 16 2009 - 09:01:34 CST)
  • David A. Case (Fri Jan 16 2009 - 08:58:50 CST)
  • archana sonawani (Thu Jan 15 2009 - 23:52:48 CST)
• [AMBER] Sander Stalling
  • Ross Walker (Mon Apr 06 2009 - 11:58:58 CDT)
  • Robert Duke (Mon Apr 06 2009 - 11:57:18 CDT)
  • Steve Seibold (Mon Apr 06 2009 - 11:21:51 CDT)
• [AMBER] sander.APBS install problem
  • Robert Konecny (Mon Nov 02 2009 - 22:52:09 CST)
  • Rilei Yu (Mon Nov 02 2009 - 19:58:30 CST)
• [AMBER] sander.MPI and pmemd.MPI in Fedora 8
  • John Bennett (Sun Mar 15 2009 - 16:23:16 CDT)
• [AMBER] sander.MPI parallel run problem
  • Dechang Li (Mon Apr 06 2009 - 06:09:04 CDT)
  • Carlos Simmerling (Mon Apr 06 2009 - 06:02:13 CDT)
  • Dechang Li (Mon Apr 06 2009 - 05:56:53 CDT)
  • Carlos Simmerling (Mon Apr 06 2009 - 05:09:11 CDT)
  • Dechang Li (Mon Apr 06 2009 - 02:44:12 CDT)
• [AMBER] sander.mpi. mdfil: Error unknown flag: sander
  • case (Mon Nov 09 2009 - 07:17:23 CST)
  • Andrew Voronkov (Mon Nov 09 2009 - 06:24:17 CST)
• [AMBER] saquinavir parameterization with antechamber
  • Oliver Kuhn (Thu Jul 23 2009 - 03:06:00 CDT)
  • FyD (Thu Jul 23 2009 - 02:29:57 CDT)
  • Oliver Kuhn (Thu Jul 23 2009 - 02:02:49 CDT)
  • FyD (Wed Jul 22 2009 - 13:41:21 CDT)
  • Oliver Kuhn (Wed Jul 22 2009 - 10:42:49 CDT)
• [AMBER] Scaling of dipole interactions
  • Diddo Diddens (Tue Feb 10 2009 - 08:33:18 CST)
• [AMBER] SCC-DFTB MD for mercury ions in proteins
  • Adrian Roitberg (Thu Aug 27 2009 - 11:51:21 CDT)
  • Vaida Arciðauskaitë (Thu Aug 27 2009 - 11:41:17 CDT)
• [AMBER] scee term
  • Ross Walker (Fri May 15 2009 - 10:02:09 CDT)
  • Neha Gandhi (Fri May 15 2009 - 04:03:48 CDT)
• [AMBER] Scientific Linux 5.2
  • Catein Catherine (Wed Feb 18 2009 - 01:13:23 CST)
• [AMBER] Script for parallel runs
  • Gustavo Seabra (Tue May 05 2009 - 11:31:38 CDT)
  • Catein Catherine (Mon May 04 2009 - 04:17:42 CDT)
• [AMBER] Script for parallel runs 2
  • Ross Walker (Mon May 04 2009 - 10:39:27 CDT)
  • Catein Catherine (Mon May 04 2009 - 04:41:58 CDT)
• [AMBER] script to convert GLYCAM ff in CHARMM format
  • Lachele Foley (Lists) (Fri Feb 06 2009 - 08:57:17 CST)
  • ABEL Stephane 175950 (Fri Feb 06 2009 - 08:39:04 CST)
• [AMBER] Scripting tleap
  • Jio M (Mon Dec 07 2009 - 00:56:59 CST)
  • case (Sun Dec 06 2009 - 14:11:02 CST)
  • Jio M (Fri Dec 04 2009 - 00:04:01 CST)
  • Jack Shultz (Sat Nov 28 2009 - 21:54:25 CST)
  • Tom Joseph (Sat Nov 28 2009 - 21:45:40 CST)
  • Jack Shultz (Sat Nov 28 2009 - 21:42:00 CST)
• [AMBER] second derivative matrix
  • David A. Case (Mon Feb 09 2009 - 09:05:18 CST)
  • Adrian Roitberg (Mon Feb 09 2009 - 08:29:51 CST)
  • Marie Brut (Mon Feb 09 2009 - 02:53:01 CST)
• [AMBER] second derivative matrix calculation
  • David A. Case (Fri Feb 06 2009 - 07:19:52 CST)
  • Marie Brut (Fri Feb 06 2009 - 04:47:18 CST)
• [AMBER] secstruct
  • Carlos Simmerling (Thu Mar 05 2009 - 08:27:18 CST)
  • Beale, John (Thu Mar 05 2009 - 07:54:20 CST)
  • Carlos Simmerling (Thu Feb 19 2009 - 08:45:47 CST)
  • Maxime Louet (Thu Feb 19 2009 - 08:17:17 CST)
  • Carlos Simmerling (Thu Feb 19 2009 - 07:30:16 CST)
  • Beale, John (Thu Feb 19 2009 - 07:22:20 CST)
• [AMBER] secstruct with ptraj
  • Bala subramanian (Fri May 15 2009 - 05:19:54 CDT)
• [AMBER] Seeking for suggestion related to plot the cluster out file
  • S.Sundar Raman (Wed Mar 11 2009 - 11:07:25 CDT)
  • Ross Walker (Wed Mar 11 2009 - 10:55:38 CDT)
  • S.Sundar Raman (Wed Mar 11 2009 - 09:57:40 CDT)
  • Ross Walker (Wed Mar 11 2009 - 09:33:38 CDT)
  • S.Sundar Raman (Wed Mar 11 2009 - 07:44:17 CDT)
• [AMBER] Seg-fault when creating residue
  • Bill Ross (Wed Jun 17 2009 - 02:51:02 CDT)
  • Valla Fatemi (Tue Jun 16 2009 - 20:28:43 CDT)
• [AMBER] Segmentation error in Ptraj
  • Kshatresh Dutta Dubey (Fri May 22 2009 - 02:17:27 CDT)
• [AMBER] Segmentation fault
  • gurunath katagi (Thu Dec 03 2009 - 00:45:20 CST)
  • Ross Walker (Thu Nov 05 2009 - 12:29:20 CST)
  • Beale, John (Thu Nov 05 2009 - 12:04:52 CST)
• [AMBER] Segmentation fault in antechamber
  • Scott Brozell (Mon Dec 14 2009 - 23:34:39 CST)
  • albert albert (Mon Nov 23 2009 - 09:23:00 CST)
  • case (Tue Nov 17 2009 - 22:28:14 CST)
  • albert albert (Tue Nov 17 2009 - 11:04:46 CST)
  • Mark Williamson (Mon Nov 16 2009 - 11:48:32 CST)
  • albert albert (Mon Nov 16 2009 - 10:23:02 CST)
  • case (Mon Nov 16 2009 - 09:53:30 CST)
  • albert albert (Mon Nov 16 2009 - 09:28:20 CST)
• [AMBER] Segmentation faults
  • Benjamin Roberts (Wed Mar 04 2009 - 18:17:50 CST)
• [AMBER] semiempirical copper
  • Ross Walker (Thu Dec 03 2009 - 11:28:45 CST)
  • Jacopo Sgrignani (Thu Dec 03 2009 - 08:09:57 CST)
• [AMBER] sequence function
  • taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:06:50 CDT)
  • taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:03:20 CDT)
• [AMBER] Set start timestep for mdcrd traj output
  • Dong Xu (Tue Apr 21 2009 - 18:44:50 CDT)
  • Carlos Simmerling (Tue Apr 21 2009 - 18:26:02 CDT)
  • quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:31:45 CDT)
  • quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:38:53 CDT)
• [AMBER] setBox truncated octahedron
  • Myunggi Yi (Thu Jun 11 2009 - 12:27:26 CDT)
• [AMBER] Setting a constrain in one direction
  • matthew_seetin_at_urmc.rochester.edu (Fri Aug 28 2009 - 09:35:57 CDT)
  • Nicholas Musolino (Thu Aug 27 2009 - 22:40:54 CDT)
  • Darren Yang (Thu Aug 27 2009 - 22:15:30 CDT)
• [AMBER] setting AMBERHOME
  • case (Wed Jul 22 2009 - 21:15:34 CDT)
• [AMBER] setting atomic radii for GB version 7
  • case (Thu Jun 25 2009 - 07:20:36 CDT)
  • Workalemhu Berhanu (Wed Jun 24 2009 - 22:12:55 CDT)
• [AMBER] SGLD in pmemd??
  • Robert Duke (Tue Dec 01 2009 - 14:04:14 CST)
  • Dean Cuebas (Tue Dec 01 2009 - 13:31:21 CST)
• [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues
  • case (Sun Aug 16 2009 - 08:14:14 CDT)
  • Catein Catherine (Sat Aug 15 2009 - 23:18:28 CDT)
• [AMBER] Showing error
  • bharat lakhani (Sat Aug 01 2009 - 08:12:00 CDT)
• [AMBER] Showing error in energy minimization
  • Ashish Runthala (Sun Aug 02 2009 - 22:05:06 CDT)
  • case (Sun Aug 02 2009 - 09:25:04 CDT)
  • bharat lakhani (Sun Aug 02 2009 - 01:22:30 CDT)
• [AMBER] showing error when creating topology and coordinate file
  • bharat lakhani (Mon Aug 03 2009 - 02:19:59 CDT)
• [AMBER] Simulated annealing
  • Carlos Simmerling (Wed Oct 28 2009 - 05:51:41 CDT)
  • Shaikh Abdul R S Ramaju (Wed Oct 28 2009 - 00:44:33 CDT)
  • Carlos Simmerling (Thu Oct 15 2009 - 06:43:56 CDT)
  • waleed zalloum (Thu Oct 15 2009 - 05:59:29 CDT)
  • Carlos Simmerling (Fri Apr 24 2009 - 10:44:02 CDT)
  • waleed zalloum (Fri Apr 24 2009 - 10:04:47 CDT)
  • Carlos Simmerling (Fri Apr 24 2009 - 09:49:40 CDT)
  • waleed zalloum (Fri Apr 24 2009 - 09:31:36 CDT)
  • Ibrahim Moustafa (Thu Feb 26 2009 - 10:32:32 CST)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 10:30:47 CST)
  • Carlos Simmerling (Thu Feb 26 2009 - 10:27:04 CST)
  • Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 10:22:59 CST)
  • Carlos Simmerling (Thu Feb 26 2009 - 09:55:41 CST)
  • David A. Case (Thu Feb 26 2009 - 09:52:18 CST)
  • Ibrahim Moustafa (Thu Feb 26 2009 - 09:28:44 CST)
  • Carlos Simmerling (Wed Feb 25 2009 - 19:31:30 CST)
  • Ibrahim Moustafa (Wed Feb 25 2009 - 18:26:37 CST)
• [AMBER] Simulating transmembrane protein.
  • Bill Ross (Mon Oct 12 2009 - 17:37:50 CDT)
  • case (Mon Oct 12 2009 - 16:55:42 CDT)
  • Jayalakshmi Sridhar (Mon Oct 12 2009 - 14:57:02 CDT)
  • Bill Ross (Mon Oct 12 2009 - 14:04:36 CDT)
  • Jayalakshmi Sridhar (Mon Oct 12 2009 - 13:42:11 CDT)
• [AMBER] simulation blown up
  • Robert Duke (Tue Oct 20 2009 - 22:55:39 CDT)
  • Jason Swails (Tue Oct 20 2009 - 21:58:47 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Tue Oct 20 2009 - 12:41:29 CDT)
• [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box
  • ranga nath (Sat Mar 21 2009 - 21:04:13 CDT)
  • David A. Case (Thu Mar 19 2009 - 12:38:52 CDT)
  • ranga nath (Wed Mar 18 2009 - 23:27:54 CDT)
• [AMBER] Simulation short peptide and protein interaction
  • Carlos Simmerling (Thu Sep 03 2009 - 08:34:27 CDT)
  • Rilei Yu (Thu Sep 03 2009 - 07:22:10 CDT)
  • case (Wed Sep 02 2009 - 07:15:06 CDT)
  • Rilei Yu (Tue Sep 01 2009 - 19:50:29 CDT)
• [AMBER] Simulation with United atom force field in Implicit solvent.
  • Manish Kumar (Sun Jul 26 2009 - 13:22:40 CDT)
  • Ray Luo (Sun Jul 26 2009 - 02:09:07 CDT)
  • Manish Kumar (Sat Jul 25 2009 - 22:55:42 CDT)
• [AMBER] Simulations including RNA-protein complexes...
  • Cihan Aydin (Sun Jun 28 2009 - 17:29:10 CDT)
• [AMBER] Single Adenine
  • FyD (Thu Aug 27 2009 - 16:20:48 CDT)
  • ros (Thu Aug 27 2009 - 11:27:06 CDT)
  • FyD (Thu Aug 27 2009 - 02:05:54 CDT)
  • Bill Ross (Wed Aug 26 2009 - 14:28:31 CDT)
  • ros (Wed Aug 26 2009 - 12:50:54 CDT)
  • case (Wed Aug 26 2009 - 06:48:36 CDT)
  • case (Wed Aug 26 2009 - 06:36:09 CDT)
  • ros (Wed Aug 26 2009 - 01:09:23 CDT)
• [AMBER] six member pucker calculation
  • Ganesh Kamath (Wed Oct 14 2009 - 09:27:24 CDT)
• [AMBER] skip parallel test
  • Ross Walker (Tue May 05 2009 - 10:43:34 CDT)
  • David A. Case (Tue May 05 2009 - 10:34:14 CDT)
  • Collins Nganou (Tue May 05 2009 - 08:09:00 CDT)
• [AMBER] sleap and check
  • Alan (Wed Mar 18 2009 - 16:23:51 CDT)
  • Wei Zhang (Wed Mar 18 2009 - 09:40:57 CDT)
  • Alan (Wed Mar 18 2009 - 06:18:27 CDT)
• [AMBER] sleap and delete
  • FyD (Mon Jun 01 2009 - 02:35:32 CDT)
• [AMBER] sleap fastbld error
  • Oliver Kuhn (Sat Nov 07 2009 - 14:39:29 CST)
• [AMBER] sleap fastbld error is not an error
  • Oliver Kuhn (Sat Nov 07 2009 - 15:07:35 CST)
• [AMBER] sleap in AmberTools 1.3 is not working anymore for me
  • case (Tue Dec 29 2009 - 21:40:26 CST)
  • Alan (Tue Dec 29 2009 - 15:47:52 CST)
  • David Watson (Tue Dec 29 2009 - 15:02:05 CST)
  • Alan (Tue Dec 29 2009 - 14:27:57 CST)
• [AMBER] slope
  • Carlos Simmerling (Tue Nov 17 2009 - 05:10:35 CST)
  • Jio M (Mon Nov 16 2009 - 22:07:07 CST)
  • Carlos Simmerling (Mon Nov 16 2009 - 05:11:46 CST)
  • Jio M (Sun Nov 15 2009 - 22:42:52 CST)
  • Jio M (Thu Nov 12 2009 - 13:28:02 CST)
• [AMBER] slope {no reply}
  • Sally Pias (Sun Nov 22 2009 - 00:53:39 CST)
  • Jio M (Thu Nov 19 2009 - 11:15:25 CST)
  • Sally Pias (Wed Nov 18 2009 - 23:39:53 CST)
  • Jio M (Tue Nov 17 2009 - 23:09:34 CST)
  • Bill Ross (Tue Nov 17 2009 - 19:04:48 CST)
  • Carlos Simmerling (Tue Nov 17 2009 - 17:49:39 CST)
  • Jio M (Tue Nov 17 2009 - 13:13:06 CST)
  • Bill Ross (Tue Nov 17 2009 - 11:51:08 CST)
  • Carlos Simmerling (Tue Nov 17 2009 - 05:11:23 CST)
  • Jio M (Mon Nov 16 2009 - 23:13:44 CST)
  • Bill Ross (Mon Nov 16 2009 - 11:48:22 CST)
  • Carlos Simmerling (Sun Nov 15 2009 - 13:07:02 CST)
  • Jio M (Sun Nov 15 2009 - 13:03:17 CST)
• [AMBER] SMD in Amber10
  • Dmitri Nilov (Fri Mar 13 2009 - 10:17:44 CDT)
  • Adrian Roitberg (Fri Mar 13 2009 - 10:01:31 CDT)
  • Dmitri Nilov (Fri Mar 13 2009 - 09:54:07 CDT)
  • Adrian Roitberg (Fri Mar 13 2009 - 08:45:39 CDT)
  • Dmitri Nilov (Fri Mar 13 2009 - 03:52:26 CDT)
  • Adrian Roitberg (Thu Mar 12 2009 - 13:46:14 CDT)
  • Dmitri Nilov (Thu Mar 12 2009 - 13:12:13 CDT)
• [AMBER] sodium ions before or after solvation makes a difference
  • Bill Ross (Fri Dec 04 2009 - 12:23:44 CST)
  • Thomas Cheatham III (Fri Dec 04 2009 - 11:09:17 CST)
  • Naser Alijabbari (Thu Dec 03 2009 - 23:01:13 CST)
• [AMBER] software to hydrate protein pockets
  • Hannes Kopitz (Fri Oct 23 2009 - 08:11:26 CDT)
  • Alessandro Nascimento (Fri Oct 23 2009 - 07:50:05 CDT)
  • Vlad Cojocaru (Fri Oct 23 2009 - 07:23:54 CDT)
• [AMBER] solutes in a simulation box
  • Workalemhu Berhanu (Sun May 31 2009 - 11:59:39 CDT)
• [AMBER] Solvate Box od amoeba water
  • Hemant Kumar (Sun Mar 22 2009 - 11:06:01 CDT)
  • Wei Zhang (Fri Mar 06 2009 - 08:20:09 CST)
  • Hemant Gangwar (Fri Mar 06 2009 - 03:50:01 CST)
• [AMBER] Solvate in an alkaline solution
  • case (Thu Sep 10 2009 - 07:05:44 CDT)
  • vallespardojl_at_chem.leidenuniv.nl (Thu Sep 10 2009 - 03:07:07 CDT)
• [AMBER] Solvating inside of a channel
  • Daniel Smith (Mon Feb 09 2009 - 15:03:16 CST)
• [AMBER] Solvating the interior of a channel
  • Daniel Smith (Sun Feb 15 2009 - 16:40:23 CST)
  • Daniel Smith (Fri Feb 13 2009 - 15:02:24 CST)
  • Jason A. Ford-Green (Wed Feb 11 2009 - 10:04:24 CST)
  • Shozeb Haider (Wed Feb 11 2009 - 07:15:07 CST)
  • Daniel Smith (Tue Feb 10 2009 - 14:42:09 CST)
• [AMBER] Solvation potential and free energies
  • David A. Case (Fri Feb 06 2009 - 07:34:25 CST)
  • Lorenzo Gontrani (Thu Feb 05 2009 - 06:34:47 CST)
  • Carlos Simmerling (Thu Feb 05 2009 - 06:33:08 CST)
  • guardiani_at_fi.infn.it (Thu Feb 05 2009 - 06:27:21 CST)
• [AMBER] Solved-Amber 1.2 tools test suite failure
  • Ross Walker (Sat Apr 11 2009 - 14:51:13 CDT)
  • Jim Parker (Sat Apr 11 2009 - 14:29:55 CDT)
• [AMBER] solvent
  • Jio M (Sun Nov 08 2009 - 08:12:34 CST)
• [AMBER] solvent accessible surface area
  • Ray Luo (Thu Oct 08 2009 - 13:17:09 CDT)
  • Siddharth Rastogi (Thu Oct 08 2009 - 05:02:20 CDT)
  • Siddharth Rastogi (Thu Oct 08 2009 - 04:54:01 CDT)
  • Carlos Simmerling (Wed Sep 23 2009 - 14:29:57 CDT)
  • Ganesh Kamath (Wed Sep 23 2009 - 14:26:33 CDT)
  • Carlos Simmerling (Wed Sep 23 2009 - 14:20:24 CDT)
  • Ganesh Kamath (Wed Sep 23 2009 - 14:07:23 CDT)
• [AMBER] solvent and counter ions
  • Bill Ross (Thu Mar 05 2009 - 17:29:50 CST)
  • Taufik Al-Sarraj (Thu Mar 05 2009 - 17:16:24 CST)
  • Bill Ross (Wed Mar 04 2009 - 18:20:45 CST)
  • Thomas Cheatham III (Wed Mar 04 2009 - 15:49:35 CST)
  • Taufik Al-Sarraj (Wed Mar 04 2009 - 15:36:36 CST)
• [AMBER] solvent mixture
  • Gustavo Seabra (Sat Jan 24 2009 - 20:44:31 CST)
  • iccy liu (Tue Jan 20 2009 - 16:08:34 CST)
• [AMBER] Some queries about pH simulation
  • case (Tue Nov 03 2009 - 05:30:07 CST)
  • nicholus bhattacharjee (Tue Nov 03 2009 - 01:34:02 CST)
  • nicholus bhattacharjee (Sat Oct 10 2009 - 00:07:21 CDT)
  • Carlos Simmerling (Fri Oct 09 2009 - 13:59:17 CDT)
  • Jason Swails (Fri Oct 09 2009 - 13:48:44 CDT)
  • nicholus bhattacharjee (Thu Oct 08 2009 - 23:36:56 CDT)
• [AMBER] some queries on -states flag in constant pH simulation
  • Jason Swails (Sat Oct 31 2009 - 07:28:22 CDT)
  • nicholus bhattacharjee (Sat Oct 31 2009 - 01:31:31 CDT)
  • Jason Swails (Fri Oct 30 2009 - 08:00:37 CDT)
  • nicholus bhattacharjee (Thu Oct 29 2009 - 23:21:27 CDT)
• [AMBER] SOS - too high binding energy
  • Marek Maly (Wed Jun 10 2009 - 14:47:58 CDT)
  • Marek Maly (Tue Jun 09 2009 - 05:49:43 CDT)
• [AMBER] Source of new CYX residue parameters in ff03ua
  • Ross Walker (Tue Apr 14 2009 - 23:08:14 CDT)
  • Chris Moth (Tue Apr 14 2009 - 19:42:33 CDT)
  • Chris Moth (Tue Apr 07 2009 - 14:48:46 CDT)
• [AMBER] sourcing leap commands in log file
  • Ashish Runthala (Sat Aug 15 2009 - 01:50:31 CDT)
  • Bill Ross (Wed Aug 12 2009 - 19:47:57 CDT)
  • Donald Keidel (Wed Aug 12 2009 - 19:32:31 CDT)
• [AMBER] spc.itp for the Amber force field
  • Alan (Wed Jun 03 2009 - 10:38:56 CDT)
  • rebeca (Wed Jun 03 2009 - 09:46:46 CDT)
• [AMBER] SPC/E HOH angle
  • Carlos Simmerling (Fri Oct 30 2009 - 08:47:18 CDT)
  • case (Fri Oct 30 2009 - 07:51:41 CDT)
  • Hemant Kumar (Fri Oct 30 2009 - 05:36:55 CDT)
• [AMBER] specification of antechamber AC file format?
  • Nicholas Musolino (Thu Apr 16 2009 - 08:18:32 CDT)
  • David A. Case (Thu Apr 16 2009 - 07:29:46 CDT)
  • Nicholas Musolino (Wed Apr 15 2009 - 17:07:32 CDT)
  • Nicholas Musolino (Tue Apr 07 2009 - 14:43:57 CDT)
  • David A. Case (Wed Mar 04 2009 - 16:39:44 CST)
  • Nicholas Musolino (Tue Mar 03 2009 - 01:53:23 CST)
• [AMBER] Specifying improper dihedrals
  • Bill Ross (Wed Jun 17 2009 - 14:25:55 CDT)
  • Ben Roberts (Wed Jun 17 2009 - 14:18:41 CDT)
  • Ben Roberts (Wed Jun 17 2009 - 14:17:12 CDT)
  • David A. Case (Wed Jun 17 2009 - 12:56:20 CDT)
  • Bill Ross (Wed Jun 17 2009 - 12:56:26 CDT)
  • Mark Williamson (Wed Jun 17 2009 - 12:12:08 CDT)
  • Ben Roberts (Wed Jun 17 2009 - 10:24:14 CDT)
• [AMBER] SQM and AMBER
  • Jio M (Sat Dec 19 2009 - 00:36:05 CST)
• [AMBER] SQM and AMBER :again
  • Jio M (Wed Dec 23 2009 - 23:18:37 CST)
• [AMBER] sqm x mopac in AmberTools 1.3
  • Alan (Tue Dec 29 2009 - 13:52:44 CST)
  • case (Tue Dec 29 2009 - 13:49:26 CST)
  • Alan (Tue Dec 29 2009 - 12:49:26 CST)
  • David A. Case (Tue Dec 22 2009 - 21:53:20 CST)
  • David A. Case (Tue Dec 22 2009 - 21:50:35 CST)
  • David Watson (Tue Dec 22 2009 - 09:58:56 CST)
  • David Watson (Tue Dec 22 2009 - 09:20:37 CST)
  • Alan (Tue Dec 22 2009 - 09:02:22 CST)
• [AMBER] ssh and make test.parallel
  • Francesco Pietra (Wed Apr 08 2009 - 02:19:36 CDT)
  • Atro Tossavainen (Mon Apr 06 2009 - 15:21:07 CDT)
  • Francesco Pietra (Mon Apr 06 2009 - 09:29:19 CDT)
  • Atro Tossavainen (Mon Apr 06 2009 - 05:33:21 CDT)
  • Francesco Pietra (Mon Apr 06 2009 - 04:58:39 CDT)
• [AMBER] Stability of a long NPT md trajectory?
  • Robert Duke (Tue Feb 10 2009 - 14:29:15 CST)
  • Bill K (Tue Feb 10 2009 - 13:39:22 CST)
  • Robert Duke (Tue Feb 10 2009 - 07:40:55 CST)
  • Bill K (Tue Feb 10 2009 - 01:37:31 CST)
  • Robert Duke (Mon Feb 09 2009 - 22:20:57 CST)
  • Carlos Simmerling (Mon Feb 09 2009 - 21:10:55 CST)
  • Robert Duke (Mon Feb 09 2009 - 20:21:31 CST)
  • Adrian Roitberg (Mon Feb 09 2009 - 19:03:45 CST)
  • Carlos Simmerling (Mon Feb 09 2009 - 18:56:50 CST)
  • Bill K (Mon Feb 09 2009 - 14:56:53 CST)
  • Robert Duke (Mon Feb 09 2009 - 07:25:10 CST)
  • Carlos Simmerling (Mon Feb 09 2009 - 06:08:29 CST)
  • Bill K (Mon Feb 09 2009 - 01:07:24 CST)
• [AMBER] stacking clusters
  • Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 21:44:59 CDT)
• [AMBER] standard way to upload a lipid bilayer
  • David Watson (Sat Nov 21 2009 - 07:06:29 CST)
  • Syed Kashif Zafar (Sat Nov 21 2009 - 05:40:08 CST)
• [AMBER] Steered MD---more than one pair of atoms
  • Hlengisizwe Ndlovu (Tue Jul 07 2009 - 08:27:59 CDT)
• [AMBER] Steered MD.....SHAKE error!!
  • case (Fri Jul 17 2009 - 07:01:03 CDT)
  • Hlengisizwe Ndlovu (Fri Jul 17 2009 - 03:50:11 CDT)
• [AMBER] Steps for NMR structure minimization
  • case (Wed Jul 01 2009 - 07:48:13 CDT)
  • Prem Prakash Pathak (Mon Jun 29 2009 - 09:09:34 CDT)
• [AMBER] steps for NMR structure minimization of protein
  • Prem Prakash Pathak (Mon Jun 29 2009 - 09:13:33 CDT)
  • Prem Prakash Pathak (Mon Jun 29 2009 - 09:12:40 CDT)
• [AMBER] Strange contacts with water molecules
  • Jordan MONNET (Wed Jun 17 2009 - 12:00:46 CDT)
  • Jordan MONNET (Tue Jun 09 2009 - 11:01:53 CDT)
  • Ross Walker (Mon Jun 08 2009 - 22:16:41 CDT)
  • Jordan MONNET (Mon Jun 08 2009 - 16:39:26 CDT)
• [AMBER] Strange high temperature in softcore TI
  • steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 23:13:38 CDT)
  • Tom Joseph (Sun May 24 2009 - 22:20:20 CDT)
  • steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 21:26:28 CDT)
  • Tom Joseph (Sun May 24 2009 - 20:54:43 CDT)
• [AMBER] Strange QM/MM Divcon - help me out
  • Ross Walker (Sun Aug 16 2009 - 11:55:01 CDT)
  • Ashish Runthala (Sat Aug 15 2009 - 01:42:38 CDT)
  • case (Thu Aug 13 2009 - 10:52:34 CDT)
  • s. Bill (Thu Aug 13 2009 - 10:37:54 CDT)
• [AMBER] strip frames from crd file
  • Carlos Simmerling (Mon Feb 02 2009 - 06:12:27 CST)
  • aneesh cna (Mon Feb 02 2009 - 03:35:11 CST)
  • aneesh cna (Mon Feb 02 2009 - 03:33:16 CST)
• [AMBER] Suggestion for restraining chain of a protein
  • Carlos Simmerling (Tue May 05 2009 - 07:27:05 CDT)
  • nicholus bhattacharjee (Tue May 05 2009 - 07:20:44 CDT)
  • Carlos Simmerling (Tue May 05 2009 - 05:05:16 CDT)
  • nicholus bhattacharjee (Tue May 05 2009 - 01:29:54 CDT)
• [AMBER] suggestions for PB simulation
  • Bala subramanian (Sat Mar 14 2009 - 11:41:19 CDT)
• [AMBER] suggestions pls
  • Jio M (Wed Aug 12 2009 - 08:04:16 CDT)
  • Ashish Runthala (Tue Aug 11 2009 - 21:40:40 CDT)
  • Jio M (Tue Aug 11 2009 - 12:44:19 CDT)
• [AMBER] suitable force field
  • Jio M (Wed Jul 08 2009 - 02:14:12 CDT)
  • Jio M (Wed Jul 08 2009 - 05:06:35 CDT)
• [AMBER] Sulfates parameterization for GAGs in GLYCAM_06
  • Sergey Samsonov (Thu Jun 18 2009 - 08:07:17 CDT)
• [AMBER] sulfonamide parameters
  • valeria.lapietra_at_unina.it (Thu Apr 16 2009 - 10:16:49 CDT)
• [AMBER] sulfotyrosine parameters
  • Ryan Pavlovicz (Tue Mar 10 2009 - 10:05:59 CDT)
• [AMBER] surface binding protein
  • Jason Swails (Sat Oct 31 2009 - 07:35:44 CDT)
  • sadaf iqbal (Sat Oct 31 2009 - 00:28:22 CDT)
• [AMBER] symbol lookup error
  • Ross Walker (Tue Sep 01 2009 - 14:42:49 CDT)
  • Bala subramanian (Tue Sep 01 2009 - 03:43:51 CDT)
• [AMBER] Syntax Bellymask
  • Brothers, Michael Charles (Fri Jul 10 2009 - 18:59:01 CDT)
• [AMBER] Targeted MD and QM/MM
  • Gabriel Urquiza (Tue Jun 02 2009 - 17:08:11 CDT)
  • Gustavo Seabra (Tue Jun 02 2009 - 09:43:35 CDT)
  • Gabriel Urquiza (Fri May 29 2009 - 15:09:31 CDT)
• [AMBER] Task is running on supercomputer without any output
  • Andrew Voronkov (Thu Nov 12 2009 - 07:24:56 CST)
  • michael bane (Mon Nov 09 2009 - 06:51:17 CST)
  • Andrew Voronkov (Mon Nov 09 2009 - 06:39:36 CST)
• [AMBER] temperature rises with igb=1
  • David A. Case (Thu Mar 19 2009 - 07:04:54 CDT)
  • Bala subramanian (Thu Mar 19 2009 - 06:24:45 CDT)
  • Carlos Simmerling (Tue Mar 17 2009 - 11:58:05 CDT)
  • Ross Walker (Tue Mar 17 2009 - 11:53:04 CDT)
  • Carlos Simmerling (Tue Mar 17 2009 - 11:44:32 CDT)
  • Bala subramanian (Tue Mar 17 2009 - 11:35:41 CDT)
• [AMBER] Teragrid
  • Carlos Simmerling (Thu Sep 24 2009 - 07:11:41 CDT)
  • Beale, John (Thu Sep 24 2009 - 07:08:56 CDT)
• [AMBER] test charge
  • Jenny Iskrenova (Fri Feb 20 2009 - 14:32:14 CST)
  • Dan Kaps (Fri Feb 20 2009 - 10:58:17 CST)
  • David A. Case (Thu Feb 19 2009 - 22:48:29 CST)
  • Dan Kaps (Thu Feb 19 2009 - 20:22:31 CST)
  • David A. Case (Wed Feb 18 2009 - 22:24:04 CST)
  • Dan Kaps (Wed Feb 18 2009 - 20:27:32 CST)
• [AMBER] TEST Message - please ignore.
  • Ross Walker (Tue Jan 06 2009 - 19:00:39 CST)
• [AMBER] Test run on Solaris 10 X 86
  • Manikandan Chandrasekaran (Fri Feb 06 2009 - 11:39:54 CST)
  • Atro Tossavainen (Thu Feb 05 2009 - 01:50:12 CST)
  • Manikandan Chandrasekaran (Wed Feb 04 2009 - 12:37:21 CST)
  • Atro Tossavainen (Wed Feb 04 2009 - 06:33:25 CST)
  • Manikandan Chandrasekaran (Tue Feb 03 2009 - 14:28:37 CST)
  • Atro Tossavainen (Mon Feb 02 2009 - 17:06:49 CST)
  • Manikandan Chandrasekaran (Mon Feb 02 2009 - 13:16:32 CST)
  • Atro Tossavainen (Sun Feb 01 2009 - 01:10:30 CST)
  • David A. Case (Sat Jan 31 2009 - 20:49:22 CST)
  • Manikandan Chandrasekaran (Sat Jan 31 2009 - 12:39:14 CST)
• [AMBER] test/amoeba - forrtl: severe (64): input conversion error
  • Tomasio, Susana (Wed Apr 08 2009 - 11:02:48 CDT)
  • Wei Zhang (Wed Apr 08 2009 - 10:38:50 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 17:45:57 CDT)
  • David A. Case (Tue Apr 07 2009 - 15:41:21 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 15:12:19 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 14:34:26 CDT)
  • Wei Zhang (Tue Apr 07 2009 - 13:34:11 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 11:34:57 CDT)
  • David A. Case (Tue Apr 07 2009 - 11:29:18 CDT)
  • Tomasio, Susana (Tue Apr 07 2009 - 10:16:08 CDT)
• [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM)
  • Tomasio, Susana (Wed Apr 29 2009 - 15:15:02 CDT)
  • Wei Zhang (Wed Apr 29 2009 - 13:00:28 CDT)
  • Tomasio, Susana (Wed Apr 29 2009 - 12:45:36 CDT)
• [AMBER] Testing parallel amber10: no libmkl_lapack.so
  • Francesco Pietra (Sun Apr 19 2009 - 09:36:02 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 18:39:30 CDT)
  • Francesco Pietra (Wed Apr 08 2009 - 18:17:38 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 17:24:52 CDT)
  • M. L. Dodson (Wed Apr 08 2009 - 11:06:09 CDT)
  • Francesco Pietra (Wed Apr 08 2009 - 10:14:43 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 06:20:27 CDT)
  • Francesco Pietra (Wed Apr 08 2009 - 05:03:09 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 04:35:17 CDT)
  • Francesco Pietra (Tue Apr 07 2009 - 13:56:25 CDT)
• [AMBER] testing RRR with antechamber
  • Alan (Mon Apr 06 2009 - 07:10:27 CDT)
• [AMBER] Tests to check for proper MMPBSA.py installation
  • case (Wed Dec 30 2009 - 08:23:57 CST)
  • RANAJIT SHINDE (Wed Dec 30 2009 - 06:15:48 CST)
• [AMBER] Thanks Simon and Vlad!
  • Rilei Yu (Thu Jun 25 2009 - 18:32:35 CDT)
• [AMBER] The -c option in Sander
  • case (Fri Oct 09 2009 - 20:54:05 CDT)
  • phani ghanakota (Fri Oct 09 2009 - 19:47:18 CDT)
• [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically
  • David A. Case (Sat May 30 2009 - 08:11:59 CDT)
  • Workalemhu Berhanu (Sat May 30 2009 - 06:20:03 CDT)
• [AMBER] the criterion of equilibrium
  • Adrian Roitberg (Sat Oct 24 2009 - 13:22:25 CDT)
  • Bill Ross (Sat Oct 24 2009 - 12:19:09 CDT)
  • qiaoyan (Fri Oct 23 2009 - 21:19:58 CDT)
• [AMBER] The decreasing MSD of ligand??
  • Chih-Ying Lin (Wed Nov 18 2009 - 15:19:35 CST)
• [AMBER] the different RMSD?
  • qiaoyan (Tue Nov 17 2009 - 20:47:42 CST)
  • qiaoyan (Sat Nov 14 2009 - 20:02:53 CST)
  • Thomas Cheatham (Sat Nov 14 2009 - 10:25:43 CST)
  • qiaoyan (Fri Nov 13 2009 - 22:16:27 CST)
  • Thomas Cheatham (Fri Nov 13 2009 - 21:40:56 CST)
  • qiaoyan (Fri Nov 13 2009 - 21:37:36 CST)
• [AMBER] The hydrophobic contribution
  • case (Thu Oct 08 2009 - 07:41:28 CDT)
  • Rilei Yu (Thu Oct 08 2009 - 00:48:32 CDT)
• [AMBER] The largest AMBER calculation(s)?
  • Vlad (Mon May 18 2009 - 21:58:27 CDT)
• [AMBER] The MSD and periodic boundary condition
  • Jason Swails (Thu Nov 19 2009 - 18:00:30 CST)
  • Chih-Ying Lin (Thu Nov 19 2009 - 17:30:46 CST)
• [AMBER] the output files
  • Ross Walker (Tue Feb 10 2009 - 11:45:37 CST)
  • Carlos Simmerling (Tue Feb 10 2009 - 08:18:34 CST)
  • oguz gurbulak (Tue Feb 10 2009 - 08:11:44 CST)
  • Carlos Simmerling (Tue Feb 10 2009 - 05:22:04 CST)
  • oguz gurbulak (Tue Feb 10 2009 - 05:14:58 CST)
  • Carlos Simmerling (Mon Feb 09 2009 - 07:06:41 CST)
  • oguz gurbulak (Mon Feb 09 2009 - 07:03:47 CST)
  • Carlos Simmerling (Sun Feb 01 2009 - 12:11:51 CST)
  • oguz gurbulak (Sun Feb 01 2009 - 05:13:02 CST)
• [AMBER] The PDB file was not recognized by Amber, what can i do?
  • Houyang Chen (Wed Apr 29 2009 - 17:17:51 CDT)
  • Markus Kaukonen (Wed Apr 29 2009 - 02:16:30 CDT)
  • Barbault Florent (Wed Apr 29 2009 - 01:56:09 CDT)
  • Ross Walker (Tue Apr 28 2009 - 22:56:27 CDT)
  • Houyang Chen (Tue Apr 28 2009 - 22:42:39 CDT)
  • Barbault Florent (Tue Apr 28 2009 - 18:00:55 CDT)
  • Carlos Simmerling (Tue Apr 28 2009 - 17:03:57 CDT)
  • Houyang Chen (Tue Apr 28 2009 - 17:00:05 CDT)
• [AMBER] the problem of nucgen.dat
  • case (Sun Nov 08 2009 - 10:19:03 CST)
  • liangchen88_at_ucla.edu (Sat Nov 07 2009 - 21:48:54 CST)
  • case (Sat Nov 07 2009 - 08:51:57 CST)
  • liangchen88_at_ucla.edu (Sat Nov 07 2009 - 08:41:49 CST)
• [AMBER] The problem of restart file
  • Jeffrey (Wed Jul 01 2009 - 09:07:08 CDT)
  • Carlos Simmerling (Wed Jul 01 2009 - 07:49:32 CDT)
  • Jeffrey (Wed Jul 01 2009 - 07:15:34 CDT)
• [AMBER] The protein swell?
  • Chih-Ying Lin (Sun May 17 2009 - 17:17:51 CDT)
• [AMBER] The resonable way to create single strand DNA with NAB ?
  • Marek Malý (Mon May 11 2009 - 07:18:06 CDT)
  • David A. Case (Mon May 11 2009 - 06:34:16 CDT)
  • Marek Malý (Sun May 10 2009 - 12:12:09 CDT)
• [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
  • Andrew Voronkov (Tue Jul 28 2009 - 23:19:41 CDT)
  • Marek Maly (Fri Jul 17 2009 - 13:37:02 CDT)
  • Thomas Cheatham III (Fri Jul 17 2009 - 11:50:15 CDT)
  • Marek Maly (Fri Jul 17 2009 - 11:34:44 CDT)
• [AMBER] thermo, entropy by quasiharmonic method
  • David A. Case (Fri Jan 30 2009 - 17:40:38 CST)
  • Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 15:35:37 CST)
• [AMBER] Thermodynamic Integration and belly
  • Ignacio J. General (Mon Apr 13 2009 - 12:26:16 CDT)
  • steinbrt_at_rci.rutgers.edu (Mon Apr 13 2009 - 11:46:19 CDT)
  • Ignacio J. General (Mon Apr 13 2009 - 10:24:15 CDT)
  • Ignacio J. General (Wed Apr 08 2009 - 14:52:51 CDT)
• [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9
  • steinbrt_at_rci.rutgers.edu (Thu Mar 12 2009 - 19:37:08 CDT)
  • PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 16:56:59 CDT)
• [AMBER] Thermodynamic Integration calculation on an artificial anion receptor
  • steinbrt_at_rci.rutgers.edu (Thu Oct 29 2009 - 05:35:24 CDT)
  • Huifang (Wed Oct 28 2009 - 23:38:05 CDT)
• [AMBER] Thermodynamic Intergration problem
  • Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 11:00:06 CST)
  • Ross Walker (Wed Mar 04 2009 - 10:45:24 CST)
  • Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:36:14 CST)
• [AMBER] Thermodynamic parameters in mm_PBSA - NAB ?
  • Marek Maly (Wed Jun 10 2009 - 14:47:41 CDT)
  • David A. Case (Wed Jun 10 2009 - 11:01:26 CDT)
  • Marek Maly (Wed Jun 10 2009 - 05:33:59 CDT)
• [AMBER] thioglycoside
  • Lachele Foley (Lists) (Mon Jan 26 2009 - 09:36:26 CST)
  • FyD (Mon Jan 26 2009 - 09:07:37 CST)
  • Alexander Schierholt (Mon Jan 26 2009 - 08:46:28 CST)
• [AMBER] three trials to create topologies with sleap and tleap
  • Oliver Kuhn (Tue Nov 10 2009 - 03:34:36 CST)
• [AMBER] thymidine monophosphate parametrization
  • Yvonne.Westermaier_at_unige.ch (Tue Jul 28 2009 - 07:10:43 CDT)
  • case (Mon Jul 27 2009 - 09:47:38 CDT)
  • Yvonne.Westermaier_at_unige.ch (Fri Jul 24 2009 - 10:18:18 CDT)
• [AMBER] TI in Amber9/10
  • Ilyas Yildirim (Tue Sep 08 2009 - 13:07:40 CDT)
  • steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:41:32 CDT)
  • Alessandro S. Nascimento (Tue Sep 08 2009 - 10:47:26 CDT)
• [AMBER] TI production runs stop after a certain Step number
  • Hannes Wallnoefer (Wed Apr 08 2009 - 10:14:32 CDT)
  • steinbrt_at_rci.rutgers.edu (Wed Apr 08 2009 - 09:35:11 CDT)
  • Hannes Wallnoefer (Wed Apr 08 2009 - 06:48:31 CDT)
  • Ilyas Yildirim (Tue Apr 07 2009 - 14:08:31 CDT)
  • steinbrt_at_rci.rutgers.edu (Tue Apr 07 2009 - 09:49:57 CDT)
  • Hannes Wallnoefer (Tue Apr 07 2009 - 06:48:45 CDT)
• [AMBER] Time scale of the Protein domain motion ?
  • Chih-Ying Lin (Sat Oct 17 2009 - 14:46:37 CDT)
  • Carlos Simmerling (Sat Oct 17 2009 - 14:42:01 CDT)
  • Chih-Ying Lin (Sat Oct 17 2009 - 14:36:18 CDT)
  • Carlos Simmerling (Sat Oct 17 2009 - 14:23:34 CDT)
  • Chih-Ying Lin (Sat Oct 17 2009 - 14:18:34 CDT)
• [AMBER] Timescales and restraints for protein-small ligands movement simulations
  • Vivek Sharma (Sun Aug 02 2009 - 01:29:13 CDT)
  • Andrew Voronkov (Sat Aug 01 2009 - 09:14:49 CDT)
  • Andrew Voronkov (Sat Aug 01 2009 - 01:23:19 CDT)
• [AMBER] TiO2 modeling
  • stefano_elli_at_libero.it (Mon Oct 05 2009 - 11:00:59 CDT)
• [AMBER] tleap errors !!
  • David A. Case (Thu Feb 26 2009 - 07:45:49 CST)
  • Sampath Koppole (Thu Feb 26 2009 - 03:47:48 CST)
• [AMBER] Tleap input error, atom not found in residue template
  • Brothers, Michael Charles (Tue Jul 07 2009 - 11:08:00 CDT)
  • Ross Walker (Mon Jul 06 2009 - 23:28:46 CDT)
  • Brothers, Michael Charles (Mon Jul 06 2009 - 20:25:00 CDT)
• [AMBER] tleap maximum coordination exceeded
  • case (Tue Nov 17 2009 - 22:45:55 CST)
  • Jack Shultz (Tue Nov 17 2009 - 21:05:41 CST)
  • Jack Shultz (Tue Nov 17 2009 - 19:51:38 CST)
  • case (Tue Nov 17 2009 - 14:24:09 CST)
  • FyD (Tue Nov 17 2009 - 14:18:20 CST)
  • Jack Shultz (Tue Nov 17 2009 - 10:52:20 CST)
• [AMBER] TMD
  • balaji nagarajan (Wed Mar 18 2009 - 06:15:55 CDT)
  • Carlos Simmerling (Wed Mar 18 2009 - 05:32:14 CDT)
  • balaji nagarajan (Tue Mar 17 2009 - 23:58:37 CDT)
• [AMBER] TMD: solvation and equilibration questions
  • Jeffrey (Fri Jul 10 2009 - 20:07:55 CDT)
• [AMBER] to check basepair in ptraj
  • balaji nagarajan (Mon Jun 15 2009 - 09:23:28 CDT)
• [AMBER] To find radial distribution curve
  • nicholus bhattacharjee (Thu Mar 26 2009 - 12:16:07 CDT)
• [AMBER] to remove AMBER list
  • Ross Walker (Sat Jan 17 2009 - 15:32:19 CST)
  • Furia Gargano (Sat Jan 17 2009 - 12:02:26 CST)
• [AMBER] To stop the AMBER's list
  • Furia Gargano (Sat Jan 17 2009 - 11:59:48 CST)
• [AMBER] to understand multiplicity in antechamber
  • Alan (Fri Mar 13 2009 - 17:43:28 CDT)
  • Scott Brozell (Fri Mar 13 2009 - 14:05:06 CDT)
  • Alan (Fri Mar 13 2009 - 09:43:45 CDT)
  • Alan (Fri Mar 13 2009 - 07:06:45 CDT)
• [AMBER] to unsubscribe email
  • backy (Wed Jun 17 2009 - 03:22:19 CDT)
  • Ross Walker (Wed Jun 17 2009 - 03:09:39 CDT)
  • backy (Wed Jun 17 2009 - 02:13:02 CDT)
  • Ross Walker (Mon Jun 15 2009 - 11:59:06 CDT)
  • Urszula Uciechowska (Mon Jun 15 2009 - 07:59:46 CDT)
• [AMBER] too high in binding energy (MM-PBSA)
  • Maryam Hamzehee (Sat Jun 13 2009 - 04:53:43 CDT)
• [AMBER] too many missing parameters in frcmod for the prep of my ligand
  • FyD (Wed Sep 30 2009 - 05:30:32 CDT)
  • xueqin pang (Wed Sep 30 2009 - 04:21:31 CDT)
• [AMBER] too many undefined parameters in frcmod
  • xueqin pang (Thu Oct 29 2009 - 08:06:24 CDT)
  • Junmei Wang (Mon Oct 26 2009 - 09:45:04 CDT)
  • Jason Swails (Thu Oct 22 2009 - 06:59:55 CDT)
  • FyD (Thu Oct 22 2009 - 04:37:46 CDT)
  • xueqin pang (Thu Oct 22 2009 - 03:52:57 CDT)
• [AMBER] top2mol2
  • taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 17:39:34 CDT)
• [AMBER] topology file for GLY with amino and carboxyl group?
  • FyD (Tue Jan 27 2009 - 14:02:14 CST)
  • Jose Borreguero (Tue Jan 27 2009 - 12:57:45 CST)
• [AMBER] Topology Reorder for EVB
  • Andrea Coletta (Tue Dec 08 2009 - 03:40:23 CST)
  • E.M. (Mon Dec 07 2009 - 13:17:44 CST)
  • Jason Swails (Mon Dec 07 2009 - 12:59:23 CST)
  • Andrea Coletta (Mon Dec 07 2009 - 09:58:50 CST)
• [AMBER] total charge for NPRO in ff03ua
  • Edyta Malolepsza (Tue Jun 16 2009 - 04:42:55 CDT)
  • Jun Wang (Mon Jun 15 2009 - 18:35:39 CDT)
  • Edyta Malolepsza (Mon Jun 15 2009 - 05:09:35 CDT)
• [AMBER] total number of hydrogen bonds of the system as a function of time
  • Jason Swails (Wed Nov 04 2009 - 08:08:21 CST)
  • Markus Kaukonen (Wed Nov 04 2009 - 07:59:17 CST)
• [AMBER] trajout problem
  • Anna Reymer (Tue Dec 01 2009 - 07:23:22 CST)
  • Daniel Roe (Tue Dec 01 2009 - 06:34:34 CST)
  • Sally Pias (Mon Nov 30 2009 - 13:01:52 CST)
  • Carlos Simmerling (Mon Nov 30 2009 - 07:56:43 CST)
  • Anna Reymer (Mon Nov 30 2009 - 06:58:39 CST)
  • Carlos Simmerling (Mon Nov 30 2009 - 06:09:05 CST)
  • Anna Reymer (Mon Nov 30 2009 - 06:03:38 CST)
• [AMBER] translate multiple residues
  • Bill Ross (Wed Oct 21 2009 - 17:40:51 CDT)
  • Taufik Al-Sarraj (Wed Oct 21 2009 - 16:32:30 CDT)
  • Bill Ross (Wed Oct 21 2009 - 15:53:20 CDT)
  • Taufik Al-Sarraj (Wed Oct 21 2009 - 15:33:12 CDT)
• [AMBER] transport properties
  • oguz gurbulak (Tue Apr 28 2009 - 09:11:05 CDT)
• [AMBER] Trouble saving amberparm files
  • Alison Saunders (Mon Jul 13 2009 - 16:43:40 CDT)
  • Tom Joseph (Mon Jul 13 2009 - 16:14:39 CDT)
  • Tom Joseph (Mon Jul 13 2009 - 16:13:14 CDT)
  • Alison Saunders (Mon Jul 13 2009 - 16:06:12 CDT)
  • Tom Joseph (Mon Jul 13 2009 - 15:16:27 CDT)
  • Alison Saunders (Mon Jul 13 2009 - 12:07:28 CDT)
• [AMBER] trouble using iAPBS
  • Robert Konecny (Thu Oct 01 2009 - 12:27:42 CDT)
  • Oliver Kuhn (Thu Oct 01 2009 - 06:31:51 CDT)
  • Robert Konecny (Mon Sep 28 2009 - 09:20:31 CDT)
  • Oliver Kuhn (Mon Sep 28 2009 - 07:08:27 CDT)
• [AMBER] trouble with antechamber
  • Jennifer L. Muzyka (Tue Dec 01 2009 - 09:10:40 CST)
  • case (Mon Nov 30 2009 - 08:57:26 CST)
  • Jennifer L. Muzyka (Mon Nov 30 2009 - 08:39:15 CST)
  • case (Tue Nov 24 2009 - 14:41:24 CST)
  • Jennifer L. Muzyka (Tue Nov 24 2009 - 14:13:46 CST)
• [AMBER] Trying to patch amber 9
  • Jack Shultz (Wed Jun 24 2009 - 10:25:41 CDT)
  • Jack Shultz (Wed Jun 24 2009 - 10:18:23 CDT)
  • case (Wed Jun 24 2009 - 09:58:48 CDT)
  • Jack Shultz (Wed Jun 24 2009 - 08:24:40 CDT)
• [AMBER] Tutorial 4 Parameter file was not saved
  • Ross Walker (Wed May 27 2009 - 12:31:30 CDT)
  • Workalemhu Berhanu (Wed May 27 2009 - 11:00:30 CDT)
• [AMBER] Tutorial 4 Please check the total charge and your -nc flag
  • David A. Case (Wed May 27 2009 - 06:42:29 CDT)
  • Workalemhu Berhanu (Tue May 26 2009 - 14:47:07 CDT)
• [AMBER] Tutorial A1
  • Workalemhu Berhanu (Tue May 19 2009 - 18:05:15 CDT)
• [AMBER] Tutorial A3
  • Ross Walker (Mon Jul 20 2009 - 14:03:44 CDT)
  • s. Bill (Sun Jul 19 2009 - 14:33:58 CDT)
• [AMBER] TWO restraints with different force constants
  • A. Gomez-Sicilia (Wed Aug 05 2009 - 07:20:54 CDT)
  • s. Bill (Wed Aug 05 2009 - 06:54:18 CDT)
• [AMBER] typo in AmberTools.pdf (release 1.3)
  • David A. Case (Wed Dec 23 2009 - 08:26:51 CST)
  • Alan (Wed Dec 23 2009 - 03:51:01 CST)
• [AMBER] Umbrella Sampling
  • Hemant Kumar (Sat Jul 18 2009 - 14:28:19 CDT)
  • Seetin, Matthew (Thu Jul 16 2009 - 15:13:59 CDT)
  • case (Thu Jul 16 2009 - 15:03:29 CDT)
  • Hemant Kumar (Thu Jul 16 2009 - 13:01:40 CDT)
• [AMBER] Umbrella test
  • David A. Case (Sat Apr 04 2009 - 08:12:13 CDT)
  • Arnaud (Thu Apr 02 2009 - 04:51:01 CDT)
• [AMBER] Unable to correctly identify element when running QM/MM in amber10
  • Ross Walker (Thu Oct 22 2009 - 14:03:40 CDT)
  • Jifeng Wang (Thu Oct 22 2009 - 11:20:30 CDT)
• [AMBER] unable to find mopac charges in mopac.out
  • Richard Tseng (Mon Nov 09 2009 - 13:25:11 CST)
  • case (Mon Nov 09 2009 - 10:47:01 CST)
  • Richard Tseng (Mon Nov 09 2009 - 10:39:51 CST)
  • case (Sat Nov 07 2009 - 07:59:43 CST)
  • Bill Ross (Fri Nov 06 2009 - 19:22:22 CST)
  • Richard Tseng (Fri Nov 06 2009 - 19:14:20 CST)
• [AMBER] unable to read MM charges
  • Vishal Maingi (Mon Jul 06 2009 - 04:32:29 CDT)
• [AMBER] unable to read MM charges (no reply yet)
  • Vishal Maingi (Mon Jul 06 2009 - 22:32:07 CDT)
• [AMBER] unable to start xleap
  • Wei Zhang (Fri May 01 2009 - 13:39:03 CDT)
  • Jayalakshmi Sridhar (Fri May 01 2009 - 13:32:27 CDT)
• [AMBER] uncharged c and n terminal amino acids
  • David A. Case (Wed Apr 22 2009 - 13:16:19 CDT)
  • Christopher Materese (Wed Apr 22 2009 - 13:05:38 CDT)
• [AMBER] Understanding the all.out file in the MM-PBSA output
  • Ray Luo (Thu Mar 12 2009 - 11:29:22 CDT)
  • Hannes Kopitz (Thu Mar 12 2009 - 05:54:27 CDT)
  • gmail (Wed Mar 11 2009 - 20:39:10 CDT)
• [AMBER] unexplained blow-up at restart
  • case (Mon Jul 13 2009 - 11:51:46 CDT)
  • Sally Pias (Mon Jul 13 2009 - 11:11:08 CDT)
  • Carlos Simmerling (Mon Jul 13 2009 - 05:24:23 CDT)
  • Sally Pias (Mon Jul 13 2009 - 02:01:29 CDT)
  • Sally Pias (Fri Jul 10 2009 - 13:59:24 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 12:58:15 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 12:25:10 CDT)
  • Sally Pias (Fri Jul 10 2009 - 12:20:27 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 12:02:39 CDT)
  • Sally Pias (Fri Jul 10 2009 - 11:31:59 CDT)
  • Sally Pias (Fri Jul 10 2009 - 10:29:01 CDT)
  • Simon Becker (Fri Jul 10 2009 - 08:24:13 CDT)
  • Carlos Simmerling (Fri Jul 10 2009 - 05:55:51 CDT)
  • Sally Pias (Fri Jul 10 2009 - 03:02:42 CDT)
• [AMBER] Unit 5 Error on OPEN: nan.in
  • Bill Ross (Tue Mar 17 2009 - 12:12:07 CDT)
  • Nancy (Tue Mar 17 2009 - 08:37:44 CDT)
  • Jenny Iskrenova (Tue Mar 17 2009 - 07:34:00 CDT)
  • mathew k varghese (Tue Mar 17 2009 - 06:22:08 CDT)
  • Nancy (Tue Mar 17 2009 - 04:11:10 CDT)
  • Nancy (Mon Mar 16 2009 - 20:02:09 CDT)
  • Carlos Simmerling (Mon Mar 16 2009 - 09:32:02 CDT)
  • Nancy (Mon Mar 16 2009 - 09:01:14 CDT)
  • mathew k varghese (Mon Mar 16 2009 - 08:36:57 CDT)
  • Nancy (Mon Mar 16 2009 - 07:49:31 CDT)
• [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun
  • Carlos Simmerling (Wed Feb 04 2009 - 05:16:34 CST)
  • drugdesign (Tue Feb 03 2009 - 23:46:19 CST)
  • Carlos Simmerling (Tue Feb 03 2009 - 11:39:58 CST)
  • Ross Walker (Tue Feb 03 2009 - 11:21:07 CST)
  • Carlos Simmerling (Tue Feb 03 2009 - 11:17:53 CST)
  • Ye MEI (Tue Feb 03 2009 - 11:12:54 CST)
  • drugdesign (Tue Feb 03 2009 - 11:03:20 CST)
• [AMBER] Unit 8 Error on OPEN: prmtop
  • Workalemhu Berhanu (Sun May 24 2009 - 17:12:00 CDT)
  • Peter Gannett (Sun May 24 2009 - 14:29:58 CDT)
  • Alessandro Nascimento (Sun May 24 2009 - 13:28:26 CDT)
  • Peter Gannett (Sun May 24 2009 - 12:46:47 CDT)
  • Workalemhu Berhanu (Sun May 24 2009 - 12:27:38 CDT)
• [AMBER] unit converter for force constants
  • GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:22:00 CDT)
• [AMBER] unit convertion for force constants
  • vhakkim boy (Mon Oct 12 2009 - 08:26:05 CDT)
  • GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:47:42 CDT)
• [AMBER] Unit name with loadMol2 command
  • David A. Case (Thu Apr 23 2009 - 17:54:02 CDT)
  • Nicholas Musolino (Thu Apr 23 2009 - 14:30:30 CDT)
• [AMBER] unit of charge in prep files
  • moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 20:18:58 CDT)
  • David A. Case (Tue Jun 09 2009 - 08:07:08 CDT)
  • moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 06:35:51 CDT)
• [AMBER] unit of force constant
  • balaji nagarajan (Tue Sep 08 2009 - 08:41:37 CDT)
  • Carlos Simmerling (Tue Sep 08 2009 - 08:21:40 CDT)
  • balaji nagarajan (Tue Sep 08 2009 - 08:16:08 CDT)
  • balaji nagarajan (Wed Sep 02 2009 - 11:57:25 CDT)
• [AMBER] units of measures
  • case (Thu Oct 22 2009 - 07:42:11 CDT)
  • lorenzo (Thu Oct 22 2009 - 06:20:26 CDT)
• [AMBER] Unknown residue: MOL number: 30 type: Terminal/last
  • David A. Case (Tue Jun 09 2009 - 06:51:42 CDT)
  • Workalemhu Berhanu (Mon Jun 08 2009 - 13:30:43 CDT)
• [AMBER] unnatural amino acid
  • FyD (Thu May 28 2009 - 13:46:27 CDT)
  • emiliawu_at_dicp.ac.cn (Fri May 29 2009 - 01:56:43 CDT)
• [AMBER] unning MMPBSA in CHCl3 environment
  • Ray Luo (Wed Mar 04 2009 - 11:15:55 CST)
  • SAFAK OZHAN (Wed Mar 04 2009 - 05:55:52 CST)
• [AMBER] unsolved verbosity when running minimization
  • Carlos Simmerling (Wed Jul 08 2009 - 06:34:20 CDT)
  • albert albert (Wed Jul 08 2009 - 06:10:43 CDT)
  • Carlos Simmerling (Mon Jul 06 2009 - 14:28:08 CDT)
  • albert albert (Mon Jul 06 2009 - 14:09:02 CDT)
• [AMBER] update on am1-bcc charge problem in antechamber
  • case (Fri Aug 21 2009 - 11:32:30 CDT)
• [AMBER] USE A VERSION COMPILED WITHOUT -DLES
  • s. Bill (Wed Aug 05 2009 - 06:55:55 CDT)
  • s. Bill (Wed Aug 05 2009 - 05:50:01 CDT)
• [AMBER] Use of Amber in distributed calculations
  • M. L. Dodson (Sat Jan 17 2009 - 08:01:36 CST)
  • M. L. Dodson (Sat Jan 17 2009 - 07:48:42 CST)
  • drugdesign (Sat Jan 17 2009 - 01:33:55 CST)
• [AMBER] use of random seed in multiple runs
  • Marek Maly (Fri Jun 05 2009 - 14:40:13 CDT)
  • Gustavo Seabra (Fri Jun 05 2009 - 14:18:35 CDT)
  • Robert Duke (Fri Jun 05 2009 - 10:45:09 CDT)
  • Naser Alijabbari (Fri Jun 05 2009 - 10:30:55 CDT)
  • Gustavo Seabra (Fri Jun 05 2009 - 10:16:00 CDT)
  • Robert Duke (Fri Jun 05 2009 - 09:45:32 CDT)
  • Robert Duke (Fri Jun 05 2009 - 09:37:14 CDT)
  • Marek Maly (Fri Jun 05 2009 - 08:49:14 CDT)
  • Gustavo Seabra (Fri Jun 05 2009 - 08:37:42 CDT)
  • Gustavo Seabra (Fri Jun 05 2009 - 08:28:03 CDT)
  • Marek Maly (Thu Jun 04 2009 - 15:01:54 CDT)
  • Carlos Simmerling (Thu Jun 04 2009 - 14:20:59 CDT)
  • Marek Maly (Thu Jun 04 2009 - 14:16:50 CDT)
  • Robert Duke (Thu Jun 04 2009 - 12:02:58 CDT)
  • Marek Maly (Thu Jun 04 2009 - 11:35:57 CDT)
  • Jifeng Wang (Thu Jun 04 2009 - 09:43:25 CDT)
  • Robert Duke (Thu Jun 04 2009 - 09:31:32 CDT)
  • Jifeng Wang (Thu Jun 04 2009 - 09:10:50 CDT)
  • Robert Duke (Wed Jun 03 2009 - 22:59:48 CDT)
  • Gustavo Seabra (Wed Jun 03 2009 - 21:00:51 CDT)
  • Andrew Voronkov (Wed Jun 03 2009 - 14:26:48 CDT)
  • Andrew Voronkov (Wed Jun 03 2009 - 12:00:32 CDT)
  • Gustavo Seabra (Wed Jun 03 2009 - 08:55:24 CDT)
  • Carlos Simmerling (Wed Jun 03 2009 - 05:13:23 CDT)
  • Andrew Voronkov (Wed Jun 03 2009 - 04:28:52 CDT)
• [AMBER] Using a restart file
  • Ross Walker (Thu Jan 15 2009 - 10:52:44 CST)
  • Carlos Simmerling (Thu Jan 15 2009 - 10:45:27 CST)
  • Simone Swift (Thu Jan 15 2009 - 10:40:38 CST)
• [AMBER] Using AMBER force fields in NAMD
  • Thomas Cheatham III (Tue Apr 28 2009 - 17:45:15 CDT)
  • Piotr Cieplak (Tue Apr 28 2009 - 17:23:15 CDT)
  • Ross Walker (Tue Apr 28 2009 - 17:17:06 CDT)
  • Michael Zimmermann (Tue Apr 28 2009 - 16:25:56 CDT)
• [AMBER] using binary trajectories from NAMD in PTRAJ
  • karthik s (Tue Jan 27 2009 - 00:49:13 CST)
  • Wei Huang (Mon Jan 26 2009 - 08:41:22 CST)
  • karthik s (Mon Jan 26 2009 - 01:11:29 CST)
• [AMBER] Using GAFF with a covalently bound ligand or label
  • FyD (Fri Jan 16 2009 - 03:13:43 CST)
  • Markus Kaukonen (Fri Jan 16 2009 - 00:31:53 CST)
  • David A. Case (Wed Jan 07 2009 - 20:42:27 CST)
  • Sale, Kenneth L (Wed Jan 07 2009 - 19:30:10 CST)
• [AMBER] using Gromacs for analysis
  • Bala subramanian (Fri Feb 27 2009 - 12:16:46 CST)
  • oguz gurbulak (Fri Feb 27 2009 - 11:03:54 CST)
• [AMBER] Using idecomp=3 with igb=10 (PB)
  • Chris Whittleston (Tue Oct 13 2009 - 05:02:17 CDT)
  • Hannes Kopitz (Mon Oct 12 2009 - 14:51:23 CDT)
  • Chris Whittleston (Mon Oct 12 2009 - 10:56:06 CDT)
  • Hannes Kopitz (Sun Oct 11 2009 - 16:13:45 CDT)
  • Chris Whittleston (Fri Oct 09 2009 - 10:16:53 CDT)
  • Hannes Kopitz (Thu Oct 08 2009 - 15:30:19 CDT)
  • Chris Whittleston (Thu Oct 08 2009 - 05:47:22 CDT)
  • Chris Whittleston (Wed Oct 07 2009 - 11:57:25 CDT)
  • Ashish Runthala (Tue Jul 28 2009 - 09:33:02 CDT)
  • Hannes Kopitz (Tue Jul 28 2009 - 07:47:15 CDT)
  • Chris Whittleston (Tue Jul 28 2009 - 05:54:09 CDT)
  • Hannes Kopitz (Tue Jul 28 2009 - 05:09:01 CDT)
  • Chris Whittleston (Mon Jul 27 2009 - 15:04:14 CDT)
• [AMBER] using ptraj
  • Carlos Simmerling (Tue Feb 17 2009 - 08:29:07 CST)
  • Molecular Dynamics (Tue Feb 17 2009 - 08:11:16 CST)
  • Carlos Simmerling (Tue Feb 17 2009 - 07:34:33 CST)
  • Molecular Dynamics (Tue Feb 17 2009 - 07:31:02 CST)
  • Carlos Simmerling (Tue Feb 17 2009 - 06:37:15 CST)
  • Molecular Dynamics (Tue Feb 17 2009 - 05:44:09 CST)
  • Carlos Simmerling (Mon Feb 16 2009 - 14:41:54 CST)
  • Molecular Dynamics (Mon Feb 16 2009 - 14:31:42 CST)
• [AMBER] using RESP program
  • FyD (Wed Oct 07 2009 - 15:04:38 CDT)
  • Ganesh Kamath (Wed Oct 07 2009 - 05:36:13 CDT)
  • gunajyoti das (Wed Oct 07 2009 - 05:30:27 CDT)
• [AMBER] Using smd with fixed atom
  • nandy_at_physics.iisc.ernet.in (Sun Apr 26 2009 - 09:57:45 CDT)
• [AMBER] using sqm from AmberTools 1.3
  • case (Tue Dec 29 2009 - 15:01:18 CST)
  • Alan (Tue Dec 29 2009 - 14:10:56 CST)
  • case (Tue Dec 29 2009 - 13:36:21 CST)
  • David Watson (Tue Dec 29 2009 - 13:34:28 CST)
  • Alan (Tue Dec 29 2009 - 11:35:06 CST)
  • Ross Walker (Thu Dec 24 2009 - 17:17:47 CST)
  • David A. Case (Wed Dec 23 2009 - 08:26:36 CST)
  • David A. Case (Wed Dec 23 2009 - 08:16:04 CST)
  • Alan (Wed Dec 23 2009 - 04:35:33 CST)
• [AMBER] validation of parameters and request of suggestions
  • Jeffrey (Mon Mar 23 2009 - 21:16:35 CDT)
• [AMBER] validation of parameters and request suggestions
  • Jeffrey (Tue Mar 24 2009 - 06:52:19 CDT)
• [AMBER] Van der Waals and electrostatic Forces
  • David A. Case (Wed Dec 23 2009 - 20:56:50 CST)
  • Frank X. Vázquez (Tue Dec 22 2009 - 11:42:33 CST)
• [AMBER] Van der Waals atom types
  • Antonio Morreale (Thu Apr 16 2009 - 09:39:14 CDT)
• [AMBER] variable header for ABMD
  • stephane acoca (Sun Sep 13 2009 - 22:03:00 CDT)
• [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj
  • Paul Frybarger (Mon Aug 17 2009 - 12:57:28 CDT)
  • workalemahu berhanu (Mon Aug 17 2009 - 08:26:35 CDT)
  • workalemahu berhanu (Sun Aug 16 2009 - 15:13:21 CDT)
• [AMBER] varying positional restraints with PMEMD
  • case (Sun Nov 08 2009 - 11:37:53 CST)
  • Julian Garrec (Thu Nov 05 2009 - 18:43:35 CST)
• [AMBER] Velocity rescaling and ig...
  • Cihan Aydin (Sun Jun 28 2009 - 11:22:29 CDT)
  • Ross Walker (Sun Jun 28 2009 - 11:18:08 CDT)
  • Cihan Aydin (Sun Jun 28 2009 - 11:08:32 CDT)
  • Carlos Simmerling (Sun Jun 28 2009 - 10:35:37 CDT)
  • Cihan Aydin (Sun Jun 28 2009 - 09:52:30 CDT)
• [AMBER] Verlet update time in explicit water Replica Exchange MD
  • Ross Walker (Wed Nov 25 2009 - 14:29:03 CST)
  • Da-Wei Li (Wed Nov 25 2009 - 13:43:58 CST)
  • Robert Duke (Wed Nov 25 2009 - 11:38:24 CST)
  • Da-Wei Li (Wed Nov 25 2009 - 11:28:27 CST)
  • Da-Wei Li (Wed Nov 25 2009 - 11:14:17 CST)
  • Carlos Simmerling (Wed Nov 25 2009 - 11:10:56 CST)
  • Da-Wei Li (Wed Nov 25 2009 - 11:05:55 CST)
• [AMBER] vertex atom mismatch
  • Guillermo Mulliert Carlín (Fri Jul 31 2009 - 09:33:46 CDT)
  • Clark, Tiffany D (Fri Jul 31 2009 - 08:14:15 CDT)
• [AMBER] Vertex atom mismatch in Amber
  • Vikas Sharma (Wed Jun 10 2009 - 22:29:57 CDT)
  • Vikas Sharma (Tue Jun 09 2009 - 08:41:33 CDT)
• [AMBER] Very weird topology problem
  • Peter Gannett (Sat Jan 24 2009 - 17:17:26 CST)
  • ranqi zhu (Sat Jan 24 2009 - 15:14:24 CST)
• [AMBER] vlimit
  • Ross Walker (Wed Oct 28 2009 - 17:35:15 CDT)
  • Taufik Al-Sarraj (Wed Oct 28 2009 - 17:02:43 CDT)
  • Bill Ross (Wed Oct 28 2009 - 16:55:55 CDT)
  • Ross Walker (Wed Oct 28 2009 - 16:29:21 CDT)
  • Taufik Al-Sarraj (Wed Oct 28 2009 - 16:16:32 CDT)
• [AMBER] vlimit error after heating restart
  • AL Olson (Fri Jul 17 2009 - 09:26:05 CDT)
• [AMBER] vlimit exceeded....nscu_SMD!!
  • Hlengisizwe Ndlovu (Thu Jul 16 2009 - 07:53:50 CDT)
• [AMBER] vlimit in TI with soft core potential
  • Ye MEI (Wed Jun 17 2009 - 04:13:40 CDT)
  • steinbrt_at_rci.rutgers.edu (Wed Jun 17 2009 - 03:47:38 CDT)
  • Ye MEI (Wed Jun 17 2009 - 03:20:31 CDT)
• [AMBER] vs_vikassharma@yahoo.co.in has sent you a private message
  • Vikas S (Sun Jun 07 2009 - 14:28:00 CDT)
• [AMBER] warning in dispatchToken
  • case (Sun Sep 20 2009 - 08:14:49 CDT)
  • Jeff Yeo (Sun Sep 20 2009 - 05:30:57 CDT)
• [AMBER] Warning: name change in pdb file residue
  • Duggan, Brendan M. (Thu Mar 05 2009 - 14:42:21 CST)
  • Donald Keidel (Thu Mar 05 2009 - 13:25:38 CST)
• [AMBER] Warning: No sp2 improper torsion term for
  • Alan (Mon Jun 08 2009 - 09:54:50 CDT)
  • Ross Walker (Fri Jun 05 2009 - 09:13:53 CDT)
  • Alan (Fri Jun 05 2009 - 07:26:55 CDT)
• [AMBER] water bonding with protein
  • David A. Case (Wed Apr 15 2009 - 06:58:17 CDT)
  • Mark M Huntress (Tue Apr 14 2009 - 21:55:39 CDT)
• [AMBER] Water-molecules
  • case (Sun Apr 26 2009 - 17:35:36 CDT)
  • sikander azam (Sun Apr 26 2009 - 08:11:33 CDT)
• [AMBER] Watercap... some querries
  • Robert Duke (Wed Jan 28 2009 - 12:46:02 CST)
  • Waqas Nasir (Wed Jan 28 2009 - 09:10:48 CST)
  • David A. Case (Wed Jan 28 2009 - 09:01:46 CST)
  • Waqas Nasir (Wed Jan 28 2009 - 08:54:00 CST)
• [AMBER] WATERSHELL
  • Mannan (Mon Aug 31 2009 - 00:02:51 CDT)
• [AMBER] What are the elements to speed up the simulation?
  • Chih-Ying Lin (Tue May 19 2009 - 17:17:07 CDT)
• [AMBER] What is dual topology
  • case (Wed Sep 02 2009 - 10:48:51 CDT)
  • Ashish Runthala (Wed Sep 02 2009 - 10:25:19 CDT)
• [AMBER] What is the default position of the partial charges?
  • Thomas Cheatham III (Wed Mar 04 2009 - 15:44:20 CST)
  • Chih-Ying Lin (Wed Mar 04 2009 - 15:06:16 CST)
• [AMBER] What is the meaning of "rms first *"
  • Catein Catherine (Thu Jul 30 2009 - 22:49:17 CDT)
• [AMBER] What is the meaning of IED values for PCA analysis?
  • case (Wed Aug 05 2009 - 11:39:30 CDT)
  • Catein Catherine (Mon Aug 03 2009 - 09:30:15 CDT)
• [AMBER] What is the Optimum Ph for solvating a protein
  • case (Sun Sep 13 2009 - 16:19:24 CDT)
  • Ashish Runthala (Sun Sep 13 2009 - 08:08:40 CDT)
• [AMBER] What is the parallel efficiency of amber10
  • Gustavo Seabra (Mon Jun 08 2009 - 08:44:26 CDT)
  • David A. Case (Mon Jun 08 2009 - 07:23:11 CDT)
  • Tom Joseph (Mon Jun 08 2009 - 01:07:29 CDT)
  • Catein Catherine (Sun Jun 07 2009 - 22:19:37 CDT)
• [AMBER] What is the parameters for Mg2+?
  • Catein Catherine (Mon Aug 17 2009 - 00:59:23 CDT)
  • Tom Joseph (Sun Aug 16 2009 - 11:00:35 CDT)
  • Catein Catherine (Sat Aug 15 2009 - 23:21:46 CDT)
• [AMBER] What is the purpose to do the bond constraints?
  • Bill Ross (Mon May 18 2009 - 14:39:42 CDT)
  • Ross Walker (Sun May 17 2009 - 22:38:52 CDT)
  • Chih-Ying Lin (Sun May 17 2009 - 17:09:04 CDT)
• [AMBER] What is the unit of RMSF?
  • case (Sat Sep 12 2009 - 08:37:42 CDT)
  • Catein Catherine (Sat Sep 12 2009 - 03:13:02 CDT)
• [AMBER] What should be the standard input file when imin=5
  • Carlos Simmerling (Thu Sep 03 2009 - 06:55:48 CDT)
  • Ashish Runthala (Thu Sep 03 2009 - 02:25:49 CDT)
• [AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message.
  • B (Thu Dec 17 2009 - 03:59:29 CST)
• [AMBER] where to get leaprc.ff99sb?
  • Jason Swails (Sat Nov 28 2009 - 21:51:39 CST)
  • Jack Shultz (Sat Nov 28 2009 - 21:19:33 CST)
  • Jason Swails (Sat Nov 28 2009 - 19:39:20 CST)
  • Jack Shultz (Sat Nov 28 2009 - 18:20:03 CST)
• [AMBER] where to I get the parameters for Mg divalent ion
  • Tom Joseph (Thu Jun 18 2009 - 22:53:01 CDT)
  • Mannan (Wed Jun 17 2009 - 23:11:19 CDT)
• [AMBER] which is the best intel complier for amber 10?
  • jacky zhao (Tue Nov 17 2009 - 02:24:30 CST)
• [AMBER] which keyword
  • s. Bill (Sun Jul 19 2009 - 07:21:23 CDT)
• [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm
  • Alan (Sun Apr 12 2009 - 10:58:18 CDT)
  • Wei Zhang (Sun Apr 12 2009 - 08:24:47 CDT)
  • Alan (Sun Apr 12 2009 - 04:30:15 CDT)
• [AMBER] Why does protein carry charges?
  • Ross Walker (Sat May 23 2009 - 13:06:57 CDT)
  • Chih-Ying Lin (Fri May 22 2009 - 23:09:21 CDT)
• [AMBER] why is nonpolar solvation energy not implemented for dynamic in amber
  • TaoPaul (Wed Aug 19 2009 - 10:29:38 CDT)
• [AMBER] why is TAUTP scaled by "e" ?
  • Jose Borreguero (Fri Oct 16 2009 - 14:13:42 CDT)
  • case (Fri Oct 16 2009 - 08:30:53 CDT)
  • Ross Walker (Thu Oct 15 2009 - 17:08:52 CDT)
  • Jose Borreguero (Thu Oct 15 2009 - 15:49:18 CDT)
• [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide
  • Dongshan Wei (Thu Dec 10 2009 - 18:14:12 CST)
  • Ross Walker (Thu Dec 10 2009 - 18:02:16 CST)
  • Carlos Simmerling (Thu Dec 10 2009 - 17:52:40 CST)
  • Dongshan Wei (Thu Dec 10 2009 - 17:40:19 CST)
• [AMBER] Why NaCl or KCl solution?
  • Chih-Ying Lin (Wed May 27 2009 - 21:11:21 CDT)
  • Thomas Cheatham (Wed May 27 2009 - 19:50:56 CDT)
  • Chih-Ying Lin (Sat May 23 2009 - 11:41:33 CDT)
• [AMBER] why should one restrain the position of the counterions?
  • Jose Borreguero (Mon Sep 28 2009 - 13:28:20 CDT)
• [AMBER] Why the calculation ofen stop with the calculation process not end?
  • xuemeiwang1103 (Wed Oct 21 2009 - 09:04:57 CDT)
• [AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"?
  • Catein Catherine (Mon May 04 2009 - 10:16:08 CDT)
• [AMBER] Why..QM/MM
  • Ross Walker (Sat Aug 08 2009 - 12:00:27 CDT)
  • s. Bill (Sat Aug 08 2009 - 06:26:46 CDT)
• [AMBER] Writing out trajectory in NAB
  • David A. Case (Mon Jan 12 2009 - 11:22:58 CST)
  • xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 10:43:33 CST)
• [AMBER] wrong estimation of hydrogen velocities when using SHAKE?
  • Jose Borreguero (Wed Mar 11 2009 - 16:56:03 CDT)
  • steinbrt_at_rci.rutgers.edu (Wed Mar 11 2009 - 13:56:15 CDT)
  • Jose Borreguero (Wed Mar 11 2009 - 13:46:29 CDT)
  • steinbrt_at_rci.rutgers.edu (Wed Mar 11 2009 - 12:45:56 CDT)
  • Jose Borreguero (Wed Mar 11 2009 - 12:28:21 CDT)
  • David A. Case (Wed Mar 11 2009 - 06:08:17 CDT)
  • Jose Borreguero (Tue Mar 10 2009 - 11:09:48 CDT)
• [AMBER] Xleap - solvatebox - counterions
  • amirhossein taghavi (Sat Jan 31 2009 - 11:34:10 CST)
  • Bill Ross (Fri Jan 30 2009 - 12:40:07 CST)
  • David A. Case (Fri Jan 30 2009 - 10:04:23 CST)
  • Arnaud (Fri Jan 30 2009 - 04:44:58 CST)
• [AMBER] xleap editing window icons inactive
  • Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:32:46 CDT)
  • Niel Henriksen (Wed Oct 21 2009 - 13:21:54 CDT)
  • Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:20:01 CDT)
• [AMBER] XLEaP Error on Closing Edit
  • Ross Walker (Tue Dec 01 2009 - 13:02:58 CST)
  • Wallace Kunin (Tue Dec 01 2009 - 12:43:27 CST)
• [AMBER] xleap facility to insert a residue
  • Sergey Samsonov (Fri Jul 24 2009 - 08:07:27 CDT)
• [AMBER] xleap input pdb problem
  • David A. Case (Wed May 06 2009 - 21:16:10 CDT)
  • Majeed Shaik (Wed May 06 2009 - 13:47:45 CDT)
• [AMBER] xleap installation error
  • Scott Brozell (Mon Aug 03 2009 - 11:57:18 CDT)
  • Bokun Cho (Mon Aug 03 2009 - 00:18:00 CDT)
• [AMBER] xleap not reconizing inhibitor prepin
  • Junmei Wang (Mon Oct 26 2009 - 09:51:41 CDT)
  • Bill Ross (Fri Oct 23 2009 - 13:33:44 CDT)
  • Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:21:07 CDT)
• [AMBER] xleap problem
  • David A. Case (Sun Jan 25 2009 - 17:30:47 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 05:49:28 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 10:34:39 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 10:27:48 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 10:02:50 CST)
  • David A. Case (Sun Jan 25 2009 - 07:57:41 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 05:56:12 CST)
• [AMBER] xleap problem !
  • balaji nagarajan (Wed Sep 30 2009 - 13:40:58 CDT)
• [AMBER] xleap reading hydrogens giving error
  • David A. Case (Fri May 15 2009 - 11:25:11 CDT)
  • Jorgen Simonsen (Fri May 15 2009 - 10:54:17 CDT)
  • David A. Case (Fri May 15 2009 - 09:17:04 CDT)
  • Jorgen Simonsen (Fri May 15 2009 - 02:47:10 CDT)
• [AMBER] xleap segmentation fault
  • Jayalakshmi Sridhar (Fri May 29 2009 - 10:45:25 CDT)
  • David A. Case (Thu May 28 2009 - 15:05:12 CDT)
  • Jayalakshmi Sridhar (Thu May 28 2009 - 11:29:47 CDT)
  • Jayalakshmi Sridhar (Mon May 04 2009 - 10:50:06 CDT)
• [AMBER] xleap, mac number problem
  • Mark M Huntress (Sat May 09 2009 - 14:46:46 CDT)
• [AMBER] xleap-does not work
  • Rilei Yu (Sun Oct 11 2009 - 06:01:07 CDT)
  • Jason Swails (Sat Oct 10 2009 - 12:08:08 CDT)
  • case (Sat Oct 10 2009 - 08:53:57 CDT)
  • Rilei Yu (Sat Oct 10 2009 - 08:35:53 CDT)
  • case (Sat Oct 10 2009 - 07:27:01 CDT)
  • Rilei Yu (Sat Oct 10 2009 - 03:30:06 CDT)
• [AMBER] xleap-does not work(Being solved!)
  • Rilei Yu (Sat Oct 10 2009 - 09:13:28 CDT)
• [AMBER] xmgrace
  • Nancy (Sat Mar 21 2009 - 00:42:48 CDT)
  • mathew k varghese (Sat Mar 21 2009 - 00:18:32 CDT)
  • Nancy (Fri Mar 20 2009 - 23:41:33 CDT)
• [AMBER] xmgrace and plotting time evolution of a defined variable
  • Mark Williamson (Wed Jan 14 2009 - 18:38:17 CST)
  • Naser Alijabbari (Wed Jan 14 2009 - 18:20:31 CST)
• [AMBER] xmin
  • Scott Brozell (Mon May 18 2009 - 15:30:17 CDT)
  • Peter Varnai (Sun May 17 2009 - 19:58:00 CDT)
  • Scott Brozell (Sun May 17 2009 - 15:45:27 CDT)
  • Peter Varnai (Thu May 14 2009 - 16:29:09 CDT)
• [AMBER] XServe cluster
  • Jim Paugh (Thu Oct 22 2009 - 16:10:49 CDT)
  • Richard Owczarzy (Thu Oct 22 2009 - 15:02:24 CDT)
  • Abdul Rehman Gani (Thu Oct 22 2009 - 14:40:11 CDT)
  • Jim Paugh (Thu Oct 22 2009 - 14:24:37 CDT)
  • Abdul Rehman Gani (Thu Oct 22 2009 - 14:14:36 CDT)
• [AMBER] yacc parser
  • Francesco Pietra (Thu Apr 02 2009 - 10:37:53 CDT)
  • David A. Case (Thu Apr 02 2009 - 07:03:06 CDT)
  • Mark Williamson (Wed Apr 01 2009 - 12:15:56 CDT)
  • Francesco Pietra (Wed Apr 01 2009 - 09:58:01 CDT)
• [AMBER] Your help about ptraj in AmberTools!]]
  • Rosina Noto (Mon Sep 28 2009 - 04:59:09 CDT)
• [AMBER] Your private message from Vikas is about to expire
  • Vikas S (Sun Jun 21 2009 - 01:40:41 CDT)
• [AMBER] zeros in excluded atom list in topology file
  • Bill Ross (Fri Nov 06 2009 - 18:09:39 CST)
  • Peter Schmidtke (Fri Nov 06 2009 - 18:07:44 CST)
  • case (Fri Nov 06 2009 - 16:44:04 CST)
  • Peter Schmidtke (Fri Nov 06 2009 - 02:54:57 CST)
  • Carlos Simmerling (Thu Nov 05 2009 - 18:39:56 CST)
  • Peter Schmidtke (Thu Nov 05 2009 - 11:06:41 CST)
• [AMBER] Zinc
  • Roman Osman (Tue Sep 29 2009 - 19:08:28 CDT)
  • Rubben Torella (Tue Sep 29 2009 - 16:31:31 CDT)
  • Sel Ercan (Tue Sep 29 2009 - 16:26:53 CDT)
• [AMBER] zinc coordination of benzimidazole
  • Urszula Uciechowska (Thu Jun 11 2009 - 03:49:45 CDT)
  • Aust, Susanne (Thu Jun 11 2009 - 02:09:59 CDT)
• [AMBER] Zinc ion, help
  • FyD (Wed Jul 08 2009 - 04:43:26 CDT)
  • Mahmoud A. A. Ibrahim (Tue Jul 07 2009 - 09:26:48 CDT)
• [AMBER] Zinc parameters?
  • vhakkim boy (Thu Dec 31 2009 - 22:56:50 CST)
  • Ray Luo, Ph.D. (Thu Dec 31 2009 - 20:11:45 CST)
  • xuemeiwang1103 (Wed Dec 30 2009 - 21:37:21 CST)
• [AMBER] ZPVE simple question
  • case (Wed Aug 26 2009 - 06:41:27 CDT)
  • Jerome.GOLEBIOWSKI_at_unice.fr (Wed Aug 26 2009 - 06:15:00 CDT)
  • ondrej.prenosil_at_marge.uochb.cas.cz (Wed Aug 26 2009 - 04:42:04 CDT)
• [AMBER] zwitterionic form of ARG and antechamber
  • Alan (Mon Apr 06 2009 - 07:33:31 CDT)
• [Amber]: REMD using hybrid solvent model
  • Morad Mustafa (Fri Aug 14 2009 - 07:44:44 CDT)
  • Carlos Simmerling (Wed Aug 12 2009 - 18:54:20 CDT)
  • Carlos Simmerling (Wed Aug 12 2009 - 18:52:56 CDT)
  • Morad Mustafa (Wed Aug 12 2009 - 16:30:01 CDT)
• [AMBER]Amber10 + g95
  • jacky zhao (Tue Nov 17 2009 - 02:26:56 CST)
  • Abhishek Banerjee (Sat Nov 07 2009 - 21:41:54 CST)
  • Sudeep Narayan Banerjee (Sat Nov 07 2009 - 20:56:39 CST)
• [Amber]AMBER: MM_PBSA problems in AMBER10
  • Ray Luo (Wed Oct 14 2009 - 11:48:48 CDT)
  • He Hongqing (Tue Oct 13 2009 - 22:43:57 CDT)
• [Contact q4md] qurey reagarding RED Server
  • FyD (Sat Jun 13 2009 - 03:08:26 CDT)
• [q4md-fft] charge calculation
  • FyD (Mon Aug 17 2009 - 18:40:49 CDT)
• [q4md-fft] Charge calculation or non standard residue
  • FyD (Sun Jul 05 2009 - 03:30:50 CDT)
• [Subject Filtered] [AMBER] hbond-error in amber9 8%
  • Thomas Cheatham III (Fri May 01 2009 - 13:07:40 CDT)
  • Hopkins, Robert (Thu Apr 30 2009 - 19:02:34 CDT)
• About Amber installations
  • jacky zhao (Tue May 26 2009 - 06:18:25 CDT)
  • Alan (Tue May 26 2009 - 04:53:37 CDT)
• About Amber10 installation "Possible Failure"
  • Ross Walker (Thu May 28 2009 - 09:06:31 CDT)
  • Ross Walker (Tue May 26 2009 - 10:38:19 CDT)
• add magnesium
  • Ross Walker (Wed May 20 2009 - 16:30:09 CDT)
• addions
  • Shubhra Gupta (Thu Jun 04 2009 - 23:38:20 CDT)
  • Peter Gannett (Wed Jun 03 2009 - 09:17:57 CDT)
  • nicholus bhattacharjee (Wed Jun 03 2009 - 08:44:51 CDT)
  • Shubhra Gupta (Wed Jun 03 2009 - 06:12:32 CDT)
• amber force filed for RNA
  • Ross Walker (Wed Jan 07 2009 - 10:49:41 CST)
• Amber question
  • Ross Walker (Thu Dec 24 2009 - 17:44:54 CST)
• AMBER: a question about ff03ua
  • FyD (Fri Jan 02 2009 - 14:20:37 CST)
  • David A. Case (Fri Jan 02 2009 - 10:35:15 CST)
  • oguz gurbulak (Fri Jan 02 2009 - 09:30:46 CST)
• AMBER: apparent error in closest function in ptraj 10
  • Roman Osman (Fri Jan 02 2009 - 11:37:09 CST)
  • D.J. Cole (Fri Jan 02 2009 - 10:06:01 CST)
  • Roman Osman (Fri Jan 02 2009 - 09:54:48 CST)
• AMBER: bug of the mm_pbsa module in ambertools 1.2
  • Scott Brozell (Tue Jan 06 2009 - 12:59:15 CST)
  • Ye Mei (Mon Jan 05 2009 - 09:28:02 CST)
• AMBER: CHCl3 solvent box
  • WJ Ding (Mon Jan 05 2009 - 15:21:32 CST)
  • David A. Case (Mon Jan 05 2009 - 07:48:44 CST)
  • WJ Ding (Sun Jan 04 2009 - 16:24:48 CST)
• AMBER: Dielectric constant
  • musa özboyacý (Sat Jan 03 2009 - 12:54:06 CST)
• AMBER: energy jumps during molecule minimization
  • David A. Case (Fri Jan 02 2009 - 06:48:23 CST)
  • Paul Ledbetter (Thu Jan 01 2009 - 21:33:30 CST)
• AMBER: error in amber 10
  • David A. Case (Tue Jan 06 2009 - 06:28:54 CST)
  • David A. Case (Tue Jan 06 2009 - 06:18:23 CST)
  • archana sonawani (Tue Jan 06 2009 - 01:19:03 CST)
• AMBER: GBSA EGB = NaN
  • Markus Kaukonen (Thu Feb 19 2009 - 07:34:38 CST)
  • Markus Kaukonen (Wed Feb 18 2009 - 06:26:28 CST)
• AMBER: How do you evaluate forces on a fixed atom?
  • Bill Kowallis (Wed Feb 18 2009 - 19:55:47 CST)
• AMBER: IMPORTANT Information regarding AMBER Mailing List - please read.
  • Ross Walker (Tue Jan 06 2009 - 14:40:00 CST)
• AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address.
  • Ross Walker (Sat Jan 03 2009 - 16:12:19 CST)
• AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)
  • Scott Brozell (Tue Jan 06 2009 - 13:23:29 CST)
• AMBER: install amber10
  • Scott Brozell (Tue Jan 06 2009 - 13:33:21 CST)
  • wl2290_at_columbia.edu (Tue Jan 06 2009 - 11:23:01 CST)
• AMBER: ligand parameter
  • Yu Chen (Sun Jan 11 2009 - 19:25:41 CST)
  • Bo Baker (Sun Jan 11 2009 - 18:52:19 CST)
  • David Watson (Sun Jan 11 2009 - 18:39:02 CST)
  • Bo Baker (Sun Jan 11 2009 - 18:20:08 CST)
  • Ross Walker (Wed Jan 07 2009 - 22:10:20 CST)
  • Bo Baker (Wed Jan 07 2009 - 20:18:02 CST)
  • David A. Case (Wed Jan 07 2009 - 07:08:27 CST)
  • Bo Baker (Tue Jan 06 2009 - 23:05:00 CST)
  • Ross Walker (Tue Jan 06 2009 - 22:25:20 CST)
  • Bo Baker (Tue Jan 06 2009 - 21:59:19 CST)
  • Ross Walker (Mon Jan 05 2009 - 23:48:13 CST)
  • Bo Baker (Mon Jan 05 2009 - 16:05:18 CST)
• AMBER: mail list
  • M. L. Dodson (Wed Jan 07 2009 - 10:04:02 CST)
  • James W. Caldwell (Tue Jan 06 2009 - 19:24:12 CST)
  • Ross Walker (Tue Jan 06 2009 - 17:47:08 CST)
  • Mark M Huntress (Tue Jan 06 2009 - 17:06:57 CST)
• AMBER: periodic bondary condition
  • Markus Kaukonen (Mon Oct 26 2009 - 03:14:48 CDT)
  • case (Fri Oct 16 2009 - 08:13:49 CDT)
  • Markus Kaukonen (Fri Oct 16 2009 - 02:38:03 CDT)
• AMBER: problem with ptraj image command in Amber 10?
  • Carlos Simmerling (Tue Jan 06 2009 - 11:37:51 CST)
  • Ryan Pavlovicz (Tue Jan 06 2009 - 11:28:27 CST)
• AMBER: questions about equilibram
  • wei zhang (Tue Jan 13 2009 - 06:58:51 CST)
  • David A. Case (Wed Jan 07 2009 - 06:54:10 CST)
  • wei zhang (Tue Jan 06 2009 - 05:18:47 CST)
• AMBER: reg sander crashing on more than 32 cores over IB
  • David A. Case (Mon Jan 05 2009 - 06:47:01 CST)
  • Amit Bajaj (Mon Jan 05 2009 - 00:33:15 CST)
• AMBER: REMINDER: The amber@scripps.edu mailing list is now CLOSED
  • Ross Walker (Tue Jan 06 2009 - 17:40:50 CST)
• AMBER: RMS plot
  • Carlos Simmerling (Tue Jan 06 2009 - 13:57:50 CST)
  • Duggan, Brendan M. (Tue Jan 06 2009 - 13:54:04 CST)
  • Carlos Simmerling (Fri Jan 02 2009 - 08:08:44 CST)
• AMBER: SMD-related questions
  • Gustavo Seabra (Fri Jan 02 2009 - 07:21:53 CST)
• AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
  • Andrew Voronkov (Sun Aug 23 2009 - 08:48:07 CDT)
• AMBER: xleap problem
  • Bala subramanian (Wed Jan 07 2009 - 08:54:44 CST)
  • David A. Case (Wed Jan 07 2009 - 07:43:16 CST)
  • Bala subramanian (Wed Jan 07 2009 - 07:34:43 CST)
  • David A. Case (Wed Jan 07 2009 - 07:06:19 CST)
  • Bala subramanian (Wed Jan 07 2009 - 04:53:24 CST)
  • Ross Walker (Tue Jan 06 2009 - 21:58:26 CST)
  • Bala subramanian (Tue Jan 06 2009 - 13:43:00 CST)
  • Carlos Simmerling (Tue Jan 06 2009 - 13:05:31 CST)
  • Bala subramanian (Tue Jan 06 2009 - 12:57:53 CST)
• Ambertools 1.2 installation error
  • case (Mon Jul 27 2009 - 09:38:28 CDT)
  • Bokun Cho (Mon Jul 27 2009 - 01:51:49 CDT)
• angle with ptraj
  • E.M. (Wed Aug 19 2009 - 14:44:56 CDT)
• Antechamber
  • David Watson (Fri Feb 27 2009 - 16:01:49 CST)
  • rpaduri_at_chem.wayne.edu (Fri Feb 27 2009 - 14:44:59 CST)
  • David Watson (Fri Feb 27 2009 - 08:26:30 CST)
  • null (Fri Feb 27 2009 - 08:00:07 CST)
  • FyD (Fri Feb 27 2009 - 07:12:16 CST)
  • kureeckal ramesh (Fri Feb 27 2009 - 06:56:58 CST)
• antechamber am1-bcc issues
  • Khavrutskii, Ilja (Fri Aug 21 2009 - 14:32:34 CDT)
  • Khavrutskii, Ilja (Fri Aug 21 2009 - 11:27:28 CDT)
  • David Mobley (Thu Aug 13 2009 - 08:25:52 CDT)
  • case (Sat Aug 08 2009 - 14:20:44 CDT)
  • gilbert_at_bluemarble.net (Sat Aug 08 2009 - 08:55:40 CDT)
  • case (Fri Aug 07 2009 - 18:54:38 CDT)
• ask for help (zn parameters)
  • Ross Walker (Sun Jul 05 2009 - 21:56:50 CDT)
• ATP/GTP parameters
  • FyD (Wed Dec 09 2009 - 00:51:03 CST)
• Average structure over simulation
  • Olotu Odunayo (Mon Jul 27 2009 - 10:47:20 CDT)
  • Niel Henriksen (Mon Jul 27 2009 - 09:56:40 CDT)
• AW: [AMBER] 2 restraints with different force constants
  • Aust, Susanne (Fri Jun 19 2009 - 07:39:34 CDT)
  • Aust, Susanne (Fri Jun 19 2009 - 06:51:21 CDT)
• AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
  • Aust, Susanne (Mon Oct 19 2009 - 04:01:27 CDT)
• AW: [AMBER] Any Comment, please
  • s. Bill (Tue Aug 11 2009 - 03:22:16 CDT)
  • Aust, Susanne (Tue Aug 11 2009 - 03:17:18 CDT)
• AW: [AMBER] atomtypes in gaff
  • FyD (Fri Jun 26 2009 - 01:56:35 CDT)
  • Bill Ross (Thu Jun 25 2009 - 11:42:01 CDT)
  • Aust, Susanne (Thu Jun 25 2009 - 07:05:10 CDT)
  • FyD (Thu Jun 25 2009 - 05:32:33 CDT)
  • Aust, Susanne (Thu Jun 25 2009 - 04:24:07 CDT)
• AW: [AMBER] Conference or workshop on AMBER?
  • Aust, Susanne (Wed Aug 19 2009 - 03:16:21 CDT)
• AW: [AMBER] Steered MD---more than one pair of atoms
  • Aust, Susanne (Wed Jul 08 2009 - 01:47:56 CDT)
• AW: [AMBER] TWO restraints with different force constants
  • Aust, Susanne (Wed Aug 05 2009 - 07:31:38 CDT)
• AW: [AMBER] zinc coordination of benzimidazole
  • Aust, Susanne (Fri Jun 12 2009 - 01:13:19 CDT)
• AW: AW: [AMBER] Any Comment, please
  • Aust, Susanne (Tue Aug 11 2009 - 03:36:34 CDT)
• AW: AW: [AMBER] atomtypes in gaff
  • FyD (Thu Jun 25 2009 - 06:36:20 CDT)
  • Aust, Susanne (Thu Jun 25 2009 - 06:27:19 CDT)
• AW: AW: AW: [AMBER] atomtypes in gaff
  • Aust, Susanne (Thu Jun 25 2009 - 06:44:58 CDT)
• bug in antechamber
  • David Mobley (Mon Jul 13 2009 - 12:41:01 CDT)
• bugfix 10 failing for ambertools1.2
  • case (Mon Jul 27 2009 - 10:03:24 CDT)
  • Alan (Mon Jul 20 2009 - 03:25:55 CDT)
• charge consideration
  • Jio M (Mon Sep 14 2009 - 03:38:27 CDT)
• charge interaction
  • case (Sun Sep 13 2009 - 16:37:55 CDT)
  • case (Sun Sep 13 2009 - 16:13:19 CDT)
  • Jio M (Sun Sep 13 2009 - 09:38:43 CDT)
• charge not zero on group:''''.respin1 attached
  • FyD (Sun Jul 19 2009 - 02:41:17 CDT)
  • Jio M (Sat Jul 18 2009 - 09:40:18 CDT)
• connect
  • Ross Walker (Mon Jun 15 2009 - 20:43:46 CDT)
  • Bill Ross (Mon Jun 15 2009 - 15:39:32 CDT)
  • KIRTANA S (Mon Jun 15 2009 - 15:18:54 CDT)
• COOH group trouble
  • Jio M (Wed Dec 09 2009 - 10:38:09 CST)
• COOH troubling
  • Dean Cuebas (Sat Dec 12 2009 - 10:47:42 CST)
  • Jio M (Sat Dec 12 2009 - 00:27:25 CST)
  • Jio M (Fri Dec 11 2009 - 13:37:39 CST)
  • case (Fri Dec 11 2009 - 07:27:09 CST)
  • Dean Cuebas (Fri Dec 11 2009 - 00:41:27 CST)
  • Junmei Wang (Thu Dec 10 2009 - 15:45:43 CST)
  • Jio M (Thu Dec 10 2009 - 05:03:59 CST)
  • Jio M (Thu Dec 10 2009 - 00:21:24 CST)
  • Dean Cuebas (Wed Dec 09 2009 - 18:00:40 CST)
  • Junmei Wang (Wed Dec 09 2009 - 17:17:12 CST)
  • Jio M (Wed Dec 09 2009 - 09:01:30 CST)
  • case (Wed Dec 09 2009 - 07:40:10 CST)
  • Jio M (Wed Dec 09 2009 - 06:16:17 CST)
• DCCM
  • Duggan, Brendan M. (Mon Jul 20 2009 - 09:29:46 CDT)
• Directory - GAFF Parameter File?
  • Patrick Gedeon (Mon Jul 06 2009 - 18:38:57 CDT)
• EEL = *************
  • case (Thu Dec 10 2009 - 14:13:15 CST)
  • Taufik Al-Sarraj (Tue Dec 08 2009 - 12:34:35 CST)
• ERROR in ptrajInitializeState(): Attempting ....
  • Siavoush Dastmalchi (Sat May 30 2009 - 12:11:55 CDT)
• Error in REDIII
  • FyD (Fri Jul 03 2009 - 09:59:30 CDT)
• Error on equilibriation of Amber10
  • case (Fri Jun 26 2009 - 07:17:42 CDT)
  • Masakazu SEKIJIMA (Thu Jun 25 2009 - 12:41:39 CDT)
  • case (Thu Jun 25 2009 - 07:07:20 CDT)
  • Masakazu SEKIJIMA (Thu Jun 25 2009 - 05:45:31 CDT)
• errors on remd
  • Ross Walker (Fri Jan 23 2009 - 10:38:06 CST)
• essential dynamics
  • Niel Henriksen (Wed May 13 2009 - 13:28:22 CDT)
  • David A. Case (Wed May 13 2009 - 12:48:42 CDT)
  • Chunliyan (Wed May 13 2009 - 12:25:57 CDT)
• Etot positive
  • Jio M (Mon Nov 16 2009 - 22:59:26 CST)
• force units
  • Brad Dickson (Fri Jun 19 2009 - 08:22:40 CDT)
  • Catein Catherine (Thu Jun 18 2009 - 09:01:40 CDT)
  • David A. Case (Thu Jun 18 2009 - 06:32:18 CDT)
  • Brad Dickson (Thu Jun 18 2009 - 04:31:16 CDT)
• Fwd: [AMBER] MM-GBSA Free enegy decomposition
  • Rajesh Raju (Tue Apr 28 2009 - 06:28:17 CDT)
• Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so
  • Atro Tossavainen (Wed Apr 08 2009 - 18:36:53 CDT)
  • Francesco Pietra (Wed Apr 08 2009 - 18:20:02 CDT)
  • Atro Tossavainen (Wed Apr 08 2009 - 17:25:54 CDT)
  • Francesco Pietra (Wed Apr 08 2009 - 10:23:58 CDT)
• Help required in Amber10 Installation
  • Bill Ross (Thu Oct 15 2009 - 11:28:26 CDT)
  • Abhishek Banerjee (Thu Oct 15 2009 - 10:51:56 CDT)
  • case (Thu Oct 15 2009 - 08:45:42 CDT)
  • Sudeep Narayan Banerjee (Thu Oct 15 2009 - 08:30:25 CDT)
  • Sudeep Narayan Banerjee (Thu Oct 15 2009 - 08:13:27 CDT)
  • Jason Swails (Thu Oct 15 2009 - 08:01:38 CDT)
  • Jason Swails (Thu Oct 15 2009 - 07:55:31 CDT)
  • Sudeep Narayan Banerjee (Thu Oct 15 2009 - 07:53:42 CDT)
  • Nicolas Sapay (Thu Oct 15 2009 - 07:34:28 CDT)
  • Sudeep Narayan Banerjee (Thu Oct 15 2009 - 07:11:01 CDT)
  • Chris Whittleston (Wed Oct 07 2009 - 12:48:18 CDT)
  • Bill Ross (Wed Oct 07 2009 - 11:59:21 CDT)
  • David Watson (Wed Oct 07 2009 - 10:53:26 CDT)
  • Sudeep Narayan Banerjee (Wed Oct 07 2009 - 10:48:02 CDT)
• Help with xleap
  • Taufik Al-Sarraj (Tue May 26 2009 - 18:58:00 CDT)
• how to change velocities
  • Carlos Simmerling (Sat Dec 26 2009 - 07:26:17 CST)
  • balaji nagarajan (Sat Dec 26 2009 - 00:02:58 CST)
  • Carlos Simmerling (Fri Dec 25 2009 - 06:13:44 CST)
  • balaji nagarajan (Fri Dec 25 2009 - 04:23:57 CST)
• How to compile and recompile ptraj?
  • case (Sun Nov 29 2009 - 19:41:24 CST)
  • cyk5056 (Sun Nov 29 2009 - 16:53:37 CST)
• How to creat .frcmod file
  • FyD (Thu Mar 05 2009 - 00:22:56 CST)
• How to know that the md is stable in equilibration run
  • nicholus bhattacharjee (Mon May 25 2009 - 11:11:39 CDT)
• how to select force field
  • Ross Walker (Sun Mar 08 2009 - 12:52:56 CDT)
  • Nancy (Sun Mar 08 2009 - 09:07:48 CDT)
• How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
  • Bill Ross (Mon Aug 10 2009 - 20:30:07 CDT)
  • Jianping Lin (Mon Aug 10 2009 - 20:23:44 CDT)
  • Bill Ross (Mon Aug 10 2009 - 20:17:05 CDT)
  • Jianping Lin (Mon Aug 10 2009 - 18:18:44 CDT)
• implicit solvent simulation with new ligand
  • Carlos Simmerling (Mon Aug 10 2009 - 09:42:33 CDT)
  • Manish Kumar (Fri Aug 07 2009 - 14:08:59 CDT)
  • Carlos Simmerling (Fri Aug 07 2009 - 13:29:46 CDT)
  • Manish Kumar (Fri Aug 07 2009 - 13:22:57 CDT)
• install and test Amber 10 parallel on Ubuntu 8.10
  • Jim Parker (Sat Apr 11 2009 - 23:47:19 CDT)
• join two units in amber9 or amber10
  • Bill Ross (Mon Mar 16 2009 - 17:56:01 CDT)
  • Taufik Al-Sarraj (Mon Mar 16 2009 - 16:11:30 CDT)
• Listing gaff parameters in frcmod
  • steinbrt_at_rci.rutgers.edu (Fri May 08 2009 - 09:23:45 CDT)
  • Bokun Cho (Fri May 08 2009 - 00:00:47 CDT)
  • Ross Walker (Thu May 07 2009 - 23:34:08 CDT)
  • Bokun Cho (Thu May 07 2009 - 23:20:46 CDT)
• looking for parameters for DHFR substrates and inhibitors... [one more try]
  • Sidney Elmer (Tue Dec 01 2009 - 17:34:36 CST)
• Missing X11 Libraries
  • Wallace Kunin (Fri Oct 02 2009 - 11:55:34 CDT)
• MM-PBSA delphi.crg and delphi.siz
  • Manish Kumar (Thu Jul 23 2009 - 02:10:51 CDT)
  • Ray Luo (Tue Jul 21 2009 - 09:24:40 CDT)
  • Manish Kumar (Mon Jul 20 2009 - 16:11:20 CDT)
  • Ray Luo (Sun Jul 19 2009 - 17:45:29 CDT)
  • Manish Kumar (Sun Jul 19 2009 - 14:36:35 CDT)
  • Ray Luo (Fri Jul 10 2009 - 11:32:18 CDT)
  • suhaib sh (Fri Jul 10 2009 - 09:17:52 CDT)
  • Manish Kumar (Thu Jul 09 2009 - 22:33:01 CDT)
• MM-PBSA test jobs error messages
  • Catein Catherine (Tue Jul 28 2009 - 04:24:31 CDT)
• MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?)
  • Catein Catherine (Wed Jul 29 2009 - 04:39:02 CDT)
• MM-PBSA test jobs error messages (with bugfix.all)
  • Catein Catherine (Wed Jul 29 2009 - 00:50:50 CDT)
• MM-PBSA with explicit water
  • mathew k varghese (Fri May 15 2009 - 01:43:46 CDT)
• MM_PBSA error
  • Ray Luo (Sat Nov 28 2009 - 12:07:26 CST)
  • Jagdeesh C (Fri Nov 27 2009 - 04:13:36 CST)
  • Mengjuei Hsieh (Fri Nov 27 2009 - 03:39:54 CST)
  • Jagdeesh C (Fri Nov 27 2009 - 03:20:27 CST)
• mpirun noticed that process rank 1 ... on signal 1 (Hangup).
  • Naser Alijabbari (Tue Jul 14 2009 - 11:30:55 CDT)
  • Ross Walker (Tue Jul 14 2009 - 07:33:49 CDT)
  • Naser Alijabbari (Tue Jul 14 2009 - 05:49:14 CDT)
• nab normal mode analysis has imaginary frequencies
  • case (Thu Dec 10 2009 - 08:46:20 CST)
  • Junmei Wang (Wed Dec 09 2009 - 17:34:28 CST)
• net charge
  • Junmei Wang (Tue Jun 23 2009 - 15:41:24 CDT)
  • case (Tue Jun 23 2009 - 14:22:28 CDT)
  • Vishal Maingi (Tue Jun 23 2009 - 13:56:52 CDT)
• nmode error: bad nonbon (amber 10)
  • David A. Case (Wed Jan 14 2009 - 07:13:18 CST)
  • Jeremy Harris (Tue Jan 13 2009 - 15:58:36 CST)
  • David A. Case (Tue Jan 06 2009 - 08:32:48 CST)
  • Jeremy Harris (Tue Jan 06 2009 - 07:37:21 CST)
• non aminoacid Residue
  • Ross Walker (Mon Jul 06 2009 - 11:21:44 CDT)
  • Neha Gandhi (Mon Jul 06 2009 - 03:43:56 CDT)
• PIMD test stalling
  • peker milas (Tue Dec 08 2009 - 21:11:44 CST)
• pls help and suggest
  • Gustavo Seabra (Fri Jul 17 2009 - 11:50:59 CDT)
  • Vishal Maingi (Thu Jul 09 2009 - 13:45:21 CDT)
  • Gustavo Seabra (Thu Jul 09 2009 - 11:14:42 CDT)
• pmemd parallel
  • Jun Dong (Wed Jul 15 2009 - 10:00:49 CDT)
  • Ross Walker (Tue Jul 14 2009 - 07:24:06 CDT)
• problem of installation of amber10
  • Mengjuei Hsieh (Wed Jul 29 2009 - 14:41:52 CDT)
• Problem with GROUP input
  • Jordan, Brad (Wed Sep 09 2009 - 19:11:51 CDT)
• ptraj imaging of namd generated trajectories
  • Vlad Cojocaru (Thu Aug 13 2009 - 05:10:54 CDT)
• query
  • Ashish Runthala (Sat Aug 01 2009 - 07:21:47 CDT)
  • bharat lakhani (Sat Aug 01 2009 - 07:07:24 CDT)
• question
  • rrd (Thu Nov 05 2009 - 18:09:11 CST)
  • Marek Maly (Thu Nov 05 2009 - 07:28:03 CST)
  • steinbrt_at_rci.rutgers.edu (Thu Nov 05 2009 - 02:12:47 CST)
  • rrd (Wed Nov 04 2009 - 20:52:04 CST)
  • Marek Maly (Tue Nov 03 2009 - 14:22:16 CST)
  • Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
• question about ff
  • FyD (Thu Jun 25 2009 - 04:12:40 CDT)
• question about TUTORIAL A1
  • Ross Walker (Mon Jul 06 2009 - 11:58:47 CDT)
  • Ross Walker (Sun Jul 05 2009 - 21:29:38 CDT)
• question_on_MMPBSA
  • jackie (Thu Aug 27 2009 - 10:41:28 CDT)
  • Catein Catherine (Thu Aug 27 2009 - 00:55:59 CDT)
  • jackie (Wed Aug 26 2009 - 10:08:01 CDT)
• Questions about QMMM
  • Ross Walker (Tue Jul 21 2009 - 17:47:49 CDT)
• R.E.D. error message
  • FyD (Thu Jun 18 2009 - 15:13:41 CDT)
• R: [AMBER] Amber10 Parallel Installation
  • sgrignani_at_cerm.unifi.it (Sat Jun 20 2009 - 15:14:38 CDT)
• RDC and alignment tensor
  • case (Mon Oct 19 2009 - 13:22:47 CDT)
  • Eliana Asciutto (Mon Oct 19 2009 - 12:51:50 CDT)
• reference re. size of dt
  • case (Mon Jul 13 2009 - 11:56:46 CDT)
• Regd: Fe4S4
  • case (Mon Jun 22 2009 - 13:39:57 CDT)
• Request to mailing list AMBER rejected
  • E.M. (Mon Jul 13 2009 - 22:37:46 CDT)
• residue
  • KIRTANA S (Fri Jun 19 2009 - 10:03:31 CDT)
• Residues
  • KIRTANA S (Fri Jun 12 2009 - 20:15:20 CDT)
• RESP with -a and witout -a flag
  • Jio M (Wed Nov 04 2009 - 00:47:55 CST)
  • Junmei Wang (Mon Nov 02 2009 - 10:48:48 CST)
  • Jio M (Sun Nov 01 2009 - 23:58:58 CST)
• RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND]
  • ABEL Stephane 175950 (Tue Feb 10 2009 - 08:39:17 CST)
• RE : [AMBER] script to convert GLYCAM ff in CHARMM format
  • ABEL Stephane 175950 (Fri Feb 06 2009 - 09:03:19 CST)
• same result
  • zgong.hust (Thu Jan 08 2009 - 02:49:29 CST)
  • Ross Walker (Wed Jan 07 2009 - 10:59:39 CST)
• Seg-fault when creating residue
  • Valla Fatemi (Wed Jun 17 2009 - 12:41:47 CDT)
• showing error when creating topology and coordinate file
  • Olotu Odunayo (Tue Aug 04 2009 - 08:08:32 CDT)
  • bharat lakhani (Mon Aug 03 2009 - 23:54:36 CDT)
• Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT
  • s. Bill (Wed Jul 29 2009 - 07:14:02 CDT)
• suggestions
  • Cihan Aydin (Mon Jul 06 2009 - 20:29:22 CDT)
  • Ross Walker (Mon Jul 06 2009 - 20:01:51 CDT)
• the copper paramter
  • Ross Walker (Mon Jul 20 2009 - 16:38:14 CDT)
• Tutorial 5
  • George Tzotzos (Sun Feb 01 2009 - 15:04:36 CST)
  • Ross Walker (Fri Jan 30 2009 - 19:32:03 CST)
  • George Tzotzos (Fri Jan 16 2009 - 14:31:11 CST)
  • Ross Walker (Fri Jan 16 2009 - 11:10:51 CST)
• using Gromacs for analysis
  • oguz gurbulak (Mon Mar 02 2009 - 10:17:45 CST)
• VDW and TI for free energy
  • Qicun Shi (Sat Oct 10 2009 - 23:05:20 CDT)
  • steinbrt_at_rci.rutgers.edu (Sat Oct 10 2009 - 03:44:31 CDT)
  • Qicun Shi (Fri Oct 09 2009 - 21:00:08 CDT)
  • Ross Walker (Thu Oct 08 2009 - 19:43:48 CDT)
• Verlet update time in explicit water Replica Exchange MD
  • Da-Wei Li (Wed Nov 25 2009 - 11:12:23 CST)
• xleap problem
  • M. L. Dodson (Thu Jan 29 2009 - 10:22:22 CST)
  • oguz gurbulak (Thu Jan 29 2009 - 09:53:30 CST)
  • David A. Case (Tue Jan 27 2009 - 09:18:53 CST)
  • oguz gurbulak (Mon Jan 26 2009 - 15:40:22 CST)
  • M. L. Dodson (Mon Jan 26 2009 - 14:47:26 CST)
  • oguz gurbulak (Mon Jan 26 2009 - 13:48:11 CST)
  • oguz gurbulak (Sun Jan 25 2009 - 10:08:26 CST)
• xleap, mac number problem
  • Mark M Huntress (Sat May 09 2009 - 17:29:50 CDT)
• ´ð¸´: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
  • Zhongjie Liang (Thu Jul 16 2009 - 04:16:02 CDT)
• ´ð¸´: [AMBER] MMGBSA error
  • Zhongjie Liang (Fri Dec 25 2009 - 22:30:00 CST)
  • Zhongjie Liang (Wed Dec 23 2009 - 07:12:07 CST)
• »Ø¸´£º [AMBER] antechamber
  • ÁÎÇ໪ (Thu Jul 02 2009 - 19:45:41 CDT)
• »Ø¸´£º [AMBER] parallel error
  • Tom Joseph (Mon Jun 15 2009 - 07:51:49 CDT)
• »Ø¸´£º [AMBER] Problem about adding a small residue to DNA
  • Yikan Chen (Fri Sep 04 2009 - 15:03:54 CDT)
  • Yikan Chen (Fri Sep 04 2009 - 14:51:38 CDT)
• »Ø¸´£º »Ø¸´£º [AMBER] parallel error
  • Tom Joseph (Mon Jun 15 2009 - 08:25:30 CDT)
• »Ø¸´£º »Ø¸´£º [AMBER] too high in binding energy (MM-PBSA)
  • Ilyas Yildirim (Sat Jun 13 2009 - 13:19:09 CDT)
• »Ø¸´£º »Ø¸´£º »Ø¸´£º [AMBER] parallel error
  • Tom Joseph (Mon Jun 15 2009 - 09:06:05 CDT)
• 回å¤�： [AMBER] about MD simulation
  • å»–é�’å�Ž (Wed Mar 11 2009 - 11:25:05 CDT)
• 回å¤�： [AMBER] amber10 parallel compiling error
  • å»–é�’å�Ž (Thu Jul 16 2009 - 20:27:05 CDT)
• 回å¤�： [AMBER] Error in MM PBSA
  • David A. Case (Tue Jun 02 2009 - 09:36:39 CDT)
  • å»–é�’å�Ž (Tue Jun 02 2009 - 09:30:47 CDT)
• 回å¤�： [AMBER] Error running MM _PBSA.pl script
  • Vikas Sharma (Mon May 18 2009 - 09:06:49 CDT)
  • å»–é�’å�Ž (Mon May 18 2009 - 07:08:47 CDT)
• 回å¤�： [AMBER] errors of PMEMD installation
  • Qinghua Liao (Fri Jul 24 2009 - 20:24:10 CDT)
  • Mengjuei Hsieh (Fri Jul 24 2009 - 13:12:00 CDT)
  • Qinghua Liao (Fri Jul 24 2009 - 04:59:03 CDT)
  • Qinghua Liao (Fri Jul 24 2009 - 04:18:44 CDT)
  • Mengjuei Hsieh (Fri Jul 24 2009 - 03:41:05 CDT)
  • å»–é�’å�Ž (Thu Jul 23 2009 - 20:27:51 CDT)
• 回å¤�： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
  • å»–é�’å�Ž (Thu Jul 02 2009 - 23:53:09 CDT)
• 回å¤�： [AMBER] MM PBSA output
  • Vikas Sharma (Wed May 20 2009 - 12:54:32 CDT)
  • å»–é�’å�Ž (Wed May 20 2009 - 07:15:04 CDT)
• 回å¤�： [AMBER] number_rec_numbers in mm_pbsa
  • å»–é�’å�Ž (Mon Apr 06 2009 - 19:18:54 CDT)
• 回å¤�： [AMBER] parallel error
  • å»–é�’å�Ž (Mon Jun 15 2009 - 07:08:27 CDT)
• 回å¤�： [AMBER] Problem about adding a small residue to DNA
  • Yikan Chen (Sun Sep 06 2009 - 10:47:04 CDT)
  • case (Sun Sep 06 2009 - 07:30:23 CDT)
  • Yikan Chen (Fri Sep 04 2009 - 16:38:27 CDT)
  • case (Fri Sep 04 2009 - 15:37:23 CDT)
  • Rilei Yu (Fri Sep 04 2009 - 01:33:50 CDT)
• 回å¤�： [AMBER] question of mm_pbsa
  • å»–é�’å�Ž (Sat Jul 11 2009 - 19:03:33 CDT)
  • å»–é�’å�Ž (Fri Jul 10 2009 - 20:22:25 CDT)
  • å»–é�’å�Ž (Fri Jul 10 2009 - 19:50:55 CDT)
• 回å¤�： [AMBER] the different RMSD?
  • Rilei Yu (Tue Nov 17 2009 - 23:25:17 CST)
• 回å¤�： [AMBER] too high in binding energy (MM-PBSA)
  • Maryam Hamzehee (Sat Jun 13 2009 - 08:56:16 CDT)
  • å»–é�’å�Ž (Sat Jun 13 2009 - 07:44:31 CDT)
• 回å¤�： [Amber]AMBER: MM_PBSA problems in AMBER10
  • Rilei Yu (Wed Oct 14 2009 - 03:18:34 CDT)
  • He Hongqing (Wed Oct 14 2009 - 02:32:25 CDT)
  • Rilei Yu (Wed Oct 14 2009 - 00:47:02 CDT)
• 回å¤�： [Amber]AMBER: MM_PBSA problemsin AMBER10
  • Bill Ross (Wed Oct 14 2009 - 11:56:41 CDT)
  • Qinghua Liao (Wed Oct 14 2009 - 04:22:41 CDT)
  • He Hongqing (Wed Oct 14 2009 - 03:39:33 CDT)
• 回å¤�： 回å¤�： [AMBER] antechamber
  • å»–é�’å�Ž (Thu Jul 02 2009 - 19:53:06 CDT)
• 回å¤�： 回å¤�： [AMBER] Error running MM _PBSA.pl script
  • å»–é�’å�Ž (Mon May 18 2009 - 09:41:14 CDT)
• 回å¤�： 回å¤�： [AMBER] parallel error
  • å»–é�’å�Ž (Mon Jun 15 2009 - 08:13:56 CDT)
• 回å¤�： 回å¤�： [AMBER] too high in binding energy (MM-PBSA)
  • Maryam Hamzehee (Sat Jun 13 2009 - 13:02:57 CDT)
  • Maryam Hamzehee (Sat Jun 13 2009 - 13:02:16 CDT)
  • Maryam Hamzehee (Sat Jun 13 2009 - 13:02:06 CDT)
  • å»–é�’å�Ž (Sat Jun 13 2009 - 10:23:38 CDT)
• 回å¤�： 回å¤�： 回å¤�： [AMBER] parallel error
  • å»–é�’å�Ž (Mon Jun 15 2009 - 08:35:58 CDT)
• 回å¤�： 回å¤�： 回å¤�： [AMBER] too high in binding energy (MM-PBSA)
  • Maryam Hamzehee (Mon Jun 15 2009 - 05:00:50 CDT)
  • å»–é�’å�Ž (Sat Jun 13 2009 - 19:48:59 CDT)
• 回å¤�： 回å¤�： 回å¤�： 回å¤�： [AMBER] parallel error
  • å»–é�’å�Ž (Mon Jun 15 2009 - 09:20:59 CDT)
• 回å¤�： 回å¤�： 回å¤�： 回å¤�： [AMBER] too high in binding energy (MM-PBSA)
  • å»–é�’å�Ž (Mon Jun 15 2009 - 05:45:09 CDT)