AMBER Archive (2009) - By Subject

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About this archive

Starting: Thu Jan 01 2009 - 21:37:45 CST
Ending: Mon Nov 23 2009 - 13:51:08 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 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 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
- ÁÖÅÂ¼º (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 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 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 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’åŽ (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)
- ÁÎÇà»ª (Wed Mar 11 2009 - 04:19:28 CDT)
[AMBER] about mm-pbsa
- å»–é’åŽ (Mon Mar 23 2009 - 04:10:29 CDT)
- å»–é’åŽ (Thu Mar 19 2009 - 01:48:21 CDT)
- Wei Huang (Mon Mar 16 2009 - 10:17:30 CDT)
- å»–é’åŽ (Mon Mar 16 2009 - 10:02:49 CDT)
- å»–é’åŽ (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] addions
- Shubhra Gupta (Wed Jun 03 2009 - 00:47:11 CDT)
[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 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
- ÁÖÅÂ¼º (Thu Apr 23 2009 - 20:35:46 CDT)
- Ross Walker (Thu Apr 23 2009 - 08:16:18 CDT)
- ÁÖÅÂ¼º (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, 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
- 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 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
- 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 test faied
- case (Tue Aug 25 2009 - 06:39:16 CDT)
- subarna thakur (Tue Aug 25 2009 - 06:01:12 CDT)
[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 (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 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
- 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] 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
- 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] 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
- 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 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] 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] 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 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] 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] 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] 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] 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] 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’åŽ (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] 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’åŽ (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 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] 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] 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: 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’åŽ (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] 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 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 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
- 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 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
- 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: 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] 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 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 + 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] 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 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 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 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 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 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 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 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 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 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] 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 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] 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
- ÁÖÅÂ¼º (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] 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] 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 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] looking for parameters for DHFR substrates and inhibitors...
- Sidney Elmer (Sat Nov 21 2009 - 22:47:50 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] 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
- 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-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-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 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 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 in Amber 9
- Sean Zhao (Mon May 04 2009 - 04:09:14 CDT)
[AMBER] mm_pbsa- Decomposition: bad atom type
- Antonija TomiÄ‡ (Tue Oct 06 2009 - 08:53:25 CDT)
[AMBER] mm_pbsa-Binding and Stability tests?
- Antonija TomiÄ‡ (Wed Aug 26 2009 - 04:15:54 CDT)
- Niel Henriksen (Mon Aug 24 2009 - 12:24:09 CDT)
- Antonija TomiÄ‡ (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 TomiÄ‡ (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 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- 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 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] 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 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] 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] 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 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 standart residue library creation with tleap (Zn atom)
- 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-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] 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 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] 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 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’åŽ (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 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 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] 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] 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] 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
- 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] 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 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] 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 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
- 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
- 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 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 TomiÄ‡ (Mon Jun 29 2009 - 10:27:54 CDT)
- Carlos Simmerling (Mon Jun 29 2009 - 10:00:59 CDT)
- Antonija TomiÄ‡ (Mon Jun 29 2009 - 09:48:54 CDT)
[AMBER] Problems with running two separate jobs in the same time
- Antonija TomiÄ‡ (Thu Apr 09 2009 - 05:33:03 CDT)
- Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
- Antonija TomiÄ‡ (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 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?
- H