Amber Archive Dec 2009: by subject

[AMBER] (No reply) Compatibility of ONIOM and Amber
- vaibhav dixit (Mon Dec 21 2009 - 05:58:03 PST)
[AMBER] .rst file error
- ZhaoLei (Mon Dec 28 2009 - 18:57:34 PST)
- Jason Swails (Mon Dec 28 2009 - 18:09:04 PST)
- ZhaoLei (Mon Dec 28 2009 - 17:37:40 PST)
- Jason Swails (Mon Dec 28 2009 - 07:44:38 PST)
- ZhaoLei (Mon Dec 28 2009 - 02:36:17 PST)
- Jia Xu (Mon Dec 28 2009 - 00:00:57 PST)
- ZhaoLei (Sun Dec 27 2009 - 19:09:24 PST)
- ZhaoLei (Sun Dec 27 2009 - 18:37:57 PST)
- ZhaoLei (Sun Dec 27 2009 - 06:46:37 PST)
[AMBER] a problem in building oligosaccharides using LEaP
- Song Lin (Thu Dec 24 2009 - 18:12:10 PST)
[AMBER] a question about ptraj
- qiaoyan (Fri Dec 25 2009 - 05:58:44 PST)
[AMBER] About APBS radiopt
- Robert Konecny (Mon Dec 28 2009 - 07:43:18 PST)
- Youn Kyeung Lee (Mon Dec 28 2009 - 02:12:07 PST)
[AMBER] Adding single distance restraint
- Jason Swails (Wed Dec 23 2009 - 19:11:48 PST)
- Adler, Marc (Wed Dec 23 2009 - 18:00:35 PST)
[AMBER] addles - neb error
- balaji nagarajan (Wed Dec 16 2009 - 19:20:22 PST)
- case (Wed Dec 16 2009 - 13:01:20 PST)
- balaji nagarajan (Tue Dec 15 2009 - 19:26:51 PST)
- Ross Walker (Tue Dec 15 2009 - 08:45:19 PST)
- balaji nagarajan (Tue Dec 15 2009 - 06:38:53 PST)
[AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found
- Jason Swails (Fri Dec 04 2009 - 09:42:19 PST)
- case (Fri Dec 04 2009 - 06:18:09 PST)
- Diego Javier Alonso de Armiño (Fri Dec 04 2009 - 04:09:04 PST)
- Jason Swails (Thu Dec 03 2009 - 18:55:09 PST)
- Mengjuei Hsieh (Thu Dec 03 2009 - 18:52:48 PST)
- Diego Javier Alonso de Armiño (Thu Dec 03 2009 - 17:47:08 PST)
[AMBER] amber.ambermd.org
- shumao.cqut.edu.cn (Sun Dec 13 2009 - 19:01:18 PST)
[AMBER] amber10 pmemd fail
- Ross Walker (Fri Dec 11 2009 - 19:43:53 PST)
- Robert Duke (Fri Dec 11 2009 - 13:40:31 PST)
- Aragorn Steiger (Fri Dec 11 2009 - 12:35:49 PST)
[AMBER] AMBER: segmentation fault when running parmchk
- Scott Brozell (Mon Dec 14 2009 - 10:14:15 PST)
[AMBER] ambertools and Snow Leopard 64 bits kernel
- Scott Brozell (Wed Dec 09 2009 - 13:48:30 PST)
[AMBER] AmberTools modifications for Ubuntu 9.10
- case (Fri Dec 04 2009 - 07:31:16 PST)
- peker milas (Thu Dec 03 2009 - 13:58:31 PST)
[AMBER] AmberTools-1.3 not compiling on MacOsX
- Jason Swails (Wed Dec 23 2009 - 03:38:08 PST)
- Mengjuei Hsieh (Wed Dec 23 2009 - 02:05:48 PST)
- Mengjuei Hsieh (Wed Dec 23 2009 - 01:12:19 PST)
- David Watson (Tue Dec 22 2009 - 22:59:09 PST)
- Cesar Millan (Tue Dec 22 2009 - 22:37:37 PST)
[AMBER] ambpdb water removal for rst files
- Bill Ross (Sun Dec 06 2009 - 12:09:26 PST)
- Bill Ross (Sun Dec 06 2009 - 12:03:00 PST)
- Andrew Voronkov (Sun Dec 06 2009 - 11:44:28 PST)
[AMBER] antechamber bond type error
- case (Sat Dec 19 2009 - 09:33:40 PST)
- Mark M Huntress (Fri Dec 18 2009 - 14:26:57 PST)
[AMBER] antechamber error
- case (Fri Dec 11 2009 - 04:51:44 PST)
- David Watson (Thu Dec 10 2009 - 15:26:00 PST)
- Mike Hanby (Thu Dec 10 2009 - 14:34:30 PST)
[AMBER] aromatic ring getting distorted
- Jio M (Sun Dec 06 2009 - 23:04:55 PST)
- case (Sun Dec 06 2009 - 12:14:45 PST)
- Jio M (Fri Dec 04 2009 - 02:03:49 PST)
[AMBER] atom type
- FyD (Wed Dec 23 2009 - 05:00:39 PST)
- shamoon siddiqui (Tue Dec 22 2009 - 21:31:42 PST)
[AMBER] ATP/GTP parameters
- E.M. (Tue Dec 08 2009 - 20:36:19 PST)
[AMBER] binding energy of multiple ligand-receptor complex
- 欧阳德方 (Fri Dec 04 2009 - 13:59:21 PST)
- Jason Swails (Fri Dec 04 2009 - 12:20:58 PST)
- steinbrt.rci.rutgers.edu (Fri Dec 04 2009 - 01:47:26 PST)
- Oliver Kuhn (Fri Dec 04 2009 - 01:10:39 PST)
- 欧阳德方 (Thu Dec 03 2009 - 02:51:17 PST)
[AMBER] branched aminoacids
- Alessandro Contini (Thu Dec 17 2009 - 03:22:56 PST)
- FyD (Thu Dec 17 2009 - 01:49:16 PST)
- Alessandro Contini (Thu Dec 17 2009 - 01:14:34 PST)
[AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5
- Nils Jan Daniel Drechsel (Fri Dec 18 2009 - 02:37:53 PST)
- case (Thu Dec 17 2009 - 05:03:27 PST)
- Nils Jan Daniel Drechsel (Thu Dec 17 2009 - 01:52:59 PST)
[AMBER] can I install amber11 on a windowsPC under cygwin?
- case (Tue Dec 29 2009 - 15:36:46 PST)
- Jason Swails (Tue Dec 29 2009 - 15:08:38 PST)
- Bill Ross (Tue Dec 29 2009 - 13:05:07 PST)
- case (Tue Dec 29 2009 - 11:44:18 PST)
- Mengjuei Hsieh (Tue Dec 29 2009 - 11:44:06 PST)
- Jason Swails (Tue Dec 29 2009 - 11:42:34 PST)
- Lixia Jin Day (Tue Dec 29 2009 - 10:06:30 PST)
[AMBER] CHARMM psf file to Amber prmtop file
- Ross Walker (Thu Dec 24 2009 - 15:11:36 PST)
- David A. Case (Wed Dec 23 2009 - 18:39:24 PST)
- Jason Swails (Wed Dec 23 2009 - 12:32:11 PST)
- xmzpzengs (Wed Dec 23 2009 - 08:40:28 PST)
- Sarvin Moghaddam (Wed Dec 23 2009 - 08:20:30 PST)
[AMBER] chemical shifts: nter and cter
- case (Wed Dec 16 2009 - 12:52:11 PST)
- Eliana Asciutto (Wed Dec 16 2009 - 11:55:14 PST)
[AMBER] clarification DNA forcefield
- Taufik Al-Sarraj (Mon Dec 07 2009 - 16:22:33 PST)
- Jiri Sponer (Fri Dec 04 2009 - 01:19:05 PST)
- Taufik Al-Sarraj (Thu Dec 03 2009 - 20:01:02 PST)
[AMBER] coarse grained
- Francesco Pietra (Sun Dec 27 2009 - 12:36:02 PST)
[AMBER] comparing coordinates from restart file and ptraj outputs
- Sidney Elmer (Tue Dec 15 2009 - 12:15:06 PST)
- Daniel Roe (Tue Dec 15 2009 - 07:45:20 PST)
- Jason Swails (Tue Dec 15 2009 - 04:00:41 PST)
- Sidney Elmer (Tue Dec 15 2009 - 00:21:35 PST)
- case (Mon Dec 14 2009 - 19:28:32 PST)
- Jason Swails (Mon Dec 14 2009 - 17:53:39 PST)
- Sidney Elmer (Mon Dec 14 2009 - 17:23:50 PST)
[AMBER] Comparison of the CHARMM and AMBER parameters for alkane
- FyD (Fri Dec 04 2009 - 12:02:17 PST)
- Ross Walker (Fri Dec 04 2009 - 11:16:50 PST)
- FyD (Fri Dec 04 2009 - 09:44:57 PST)
- intra\\sa175950 (Fri Dec 04 2009 - 01:54:55 PST)
- FyD (Thu Dec 03 2009 - 11:43:10 PST)
- Ross Walker (Thu Dec 03 2009 - 09:52:58 PST)
- intra\\sa175950 (Thu Dec 03 2009 - 08:49:28 PST)
[AMBER] Compatibility of ONIOM and Amber
- vaibhav dixit (Thu Dec 17 2009 - 22:30:32 PST)
[AMBER] COOH group troubling
- Bill Ross (Sun Dec 06 2009 - 11:07:44 PST)
- Jio M (Sun Dec 06 2009 - 10:53:22 PST)
- Bill Ross (Sun Dec 06 2009 - 08:46:58 PST)
- Jason Swails (Sun Dec 06 2009 - 07:05:07 PST)
- Jio M (Sun Dec 06 2009 - 05:57:06 PST)
[AMBER] Custom RNA modeling
- Jiri Sponer (Mon Dec 14 2009 - 14:08:07 PST)
- Carlos Simmerling (Mon Dec 14 2009 - 13:55:20 PST)
- Wallace Kunin (Mon Dec 14 2009 - 13:49:29 PST)
- Thomas Cheatham (Mon Dec 14 2009 - 10:35:44 PST)
- case (Mon Dec 14 2009 - 10:32:11 PST)
- Wallace Kunin (Mon Dec 14 2009 - 09:50:25 PST)
- Wallace Kunin (Wed Dec 09 2009 - 08:10:44 PST)
- Ilyas Yildirim (Tue Dec 08 2009 - 14:01:42 PST)
- Wallace Kunin (Tue Dec 08 2009 - 12:27:55 PST)
[AMBER] Different simulation times for similar systems
- Carlos Simmerling (Mon Dec 14 2009 - 10:11:56 PST)
- Oliver Kuhn (Mon Dec 14 2009 - 04:31:50 PST)
[AMBER] distance-dependent dielectric constant minimization
- Rilei Yu (Sat Dec 05 2009 - 23:37:13 PST)
- case (Sat Dec 05 2009 - 19:03:47 PST)
- Bill Ross (Sat Dec 05 2009 - 09:30:09 PST)
- Rilei Yu (Sat Dec 05 2009 - 00:21:58 PST)
- Robert Duke (Tue Dec 01 2009 - 05:06:40 PST)
- case (Tue Dec 01 2009 - 04:48:32 PST)
- Rilei Yu (Mon Nov 30 2009 - 21:31:58 PST)
[AMBER] ERROR: Could not read coords from {filename}
- Paul Brandt (Tue Dec 29 2009 - 01:46:55 PST)
- ZhaoLei (Mon Dec 28 2009 - 18:58:53 PST)
- Carlos Simmerling (Mon Dec 28 2009 - 18:04:27 PST)
- ZhaoLei (Mon Dec 28 2009 - 17:34:29 PST)
- case (Mon Dec 28 2009 - 06:57:11 PST)
- ZhaoLei (Mon Dec 28 2009 - 06:12:54 PST)
- case (Mon Dec 28 2009 - 05:00:34 PST)
- Paul Brandt (Sun Dec 27 2009 - 20:14:50 PST)
[AMBER] exchange attempt in REMD
- Carlos Simmerling (Thu Dec 31 2009 - 07:50:24 PST)
- zgong.hust (Wed Dec 30 2009 - 20:22:54 PST)
- Carlos Simmerling (Wed Dec 30 2009 - 19:09:02 PST)
- zgong.hust (Wed Dec 30 2009 - 18:34:21 PST)
[AMBER] force field parameters
- Piotr Cieplak (Sun Dec 06 2009 - 23:25:03 PST)
[AMBER] Gaff compatible with ff899.SB
- Carlos Simmerling (Mon Dec 21 2009 - 07:32:40 PST)
- Pol Boudard (Mon Dec 21 2009 - 07:03:25 PST)
[AMBER] hbond analysis
- qiaoyan (Thu Dec 31 2009 - 00:40:22 PST)
[AMBER] heating system in NEB
- balaji nagarajan (Sat Dec 26 2009 - 03:29:35 PST)
[AMBER] help with TIP4P and mpi pmemd
- Lizzard Man (Fri Dec 04 2009 - 14:47:08 PST)
- Hashem Taha (Fri Dec 04 2009 - 13:44:44 PST)
- Robert Duke (Fri Dec 04 2009 - 13:26:41 PST)
- case (Fri Dec 04 2009 - 13:16:22 PST)
- Hashem Taha (Fri Dec 04 2009 - 13:01:50 PST)
- Robert Duke (Thu Dec 03 2009 - 21:58:58 PST)
- Hashem Taha (Thu Dec 03 2009 - 21:29:38 PST)
- Hashem Taha (Thu Dec 03 2009 - 18:26:57 PST)
- Robert Duke (Thu Dec 03 2009 - 14:37:14 PST)
- Hashem Taha (Thu Dec 03 2009 - 14:16:22 PST)
[AMBER] hi
- David Watson (Mon Dec 21 2009 - 01:09:53 PST)
- ashish pandey (Sun Dec 20 2009 - 22:45:40 PST)
[AMBER] how can i include ANP residue
- David Watson (Mon Dec 14 2009 - 14:44:30 PST)
- Bradley Dickson (Mon Dec 14 2009 - 14:00:32 PST)
- FyD (Mon Dec 14 2009 - 12:29:42 PST)
- Bradley Dickson (Mon Dec 14 2009 - 07:07:50 PST)
[AMBER] how to add desired number of water
- Ross Walker (Fri Dec 11 2009 - 19:47:19 PST)
- Bill Ross (Fri Dec 11 2009 - 14:19:57 PST)
- Hopkins, Robert (Fri Dec 11 2009 - 14:05:51 PST)
- Bill Ross (Wed Dec 09 2009 - 09:46:59 PST)
- Simon Becker (Wed Dec 09 2009 - 08:09:51 PST)
- balaji nagarajan (Tue Dec 08 2009 - 19:18:49 PST)
[AMBER] how to add desired numberof water
- Dean Cuebas (Mon Dec 14 2009 - 18:40:25 PST)
- Bill Ross (Fri Dec 11 2009 - 16:57:41 PST)
- Richard Owczarzy (Fri Dec 11 2009 - 16:19:31 PST)
- Hopkins, Robert (Fri Dec 11 2009 - 14:24:02 PST)
[AMBER] how to add desirednumberof water
- Hopkins, Robert (Sat Dec 12 2009 - 16:29:04 PST)
[AMBER] How to get total energy of a system from QM/MM
- steinbrt.rci.rutgers.edu (Wed Dec 02 2009 - 01:53:03 PST)
- gunajyoti das (Wed Dec 02 2009 - 00:56:06 PST)
[AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ?
- Marek Maly (Tue Dec 22 2009 - 10:49:42 PST)
[AMBER] How to put another 10 ligands into the simulation system?
- David A. Case (Thu Dec 24 2009 - 09:17:11 PST)
- Chih-Ying Lin (Wed Dec 23 2009 - 20:00:02 PST)
- Chih-Ying Lin (Wed Dec 23 2009 - 08:51:23 PST)
- Chih-Ying Lin (Wed Dec 23 2009 - 08:18:47 PST)
[AMBER] how to restart the stopped MM-GBSA job
- Zhongjie Liang (Sun Dec 06 2009 - 17:36:56 PST)
[AMBER] How to run LEaP in a shell file?
- SongLin (Mon Dec 14 2009 - 05:45:03 PST)
- case (Mon Dec 14 2009 - 04:44:29 PST)
- SongLin (Sun Dec 13 2009 - 23:10:00 PST)
[AMBER] implicit solvent MD with fixed residues
- David A. Case (Fri Dec 25 2009 - 12:22:31 PST)
- Hakan Gunaydin (Thu Dec 24 2009 - 15:43:13 PST)
[AMBER] Inorganic Phosphate Parameters
- Cihan Aydin (Fri Dec 18 2009 - 12:19:21 PST)
[AMBER] Inorganic Phosphate Parameters. .
- case (Sat Dec 19 2009 - 09:39:28 PST)
- Jason Swails (Fri Dec 18 2009 - 14:54:39 PST)
- Don.Bashford.stjude.org (Fri Dec 18 2009 - 14:12:58 PST)
[AMBER] Installation on MacOSX
- Alan (Tue Dec 15 2009 - 08:11:20 PST)
- David Watson (Tue Dec 15 2009 - 04:54:06 PST)
- Jason Swails (Tue Dec 15 2009 - 03:43:47 PST)
- Alan (Tue Dec 15 2009 - 02:26:48 PST)
- David Watson (Mon Dec 14 2009 - 12:01:52 PST)
- Freedman, Tanya (Mon Dec 14 2009 - 10:59:06 PST)
[AMBER] iron in prepi file generation for heme
- David A. Case (Thu Dec 24 2009 - 09:27:07 PST)
- Donald Keidel (Wed Dec 23 2009 - 14:27:10 PST)
[AMBER] look at Amber's slides, email
- Sally Pias (Wed Dec 02 2009 - 21:08:47 PST)
[AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try]
- FyD (Wed Dec 02 2009 - 00:19:00 PST)
[AMBER] MM PBSA stats
- Peter Jones (Mon Dec 21 2009 - 21:57:51 PST)
[AMBER] MM_PBSA Problem (no radius for ion)
- s. Bill (Fri Dec 18 2009 - 07:33:57 PST)
- Scott Brozell (Thu Dec 17 2009 - 19:07:21 PST)
- s. Bill (Thu Dec 17 2009 - 11:39:49 PST)
[AMBER] mm_pbsa- Decomposition: bad atom type
- Antonija Tomić (Fri Dec 04 2009 - 02:57:59 PST)
- Hannes Kopitz (Fri Dec 04 2009 - 02:45:10 PST)
- Antonija Tomić (Fri Dec 04 2009 - 01:27:31 PST)
[AMBER] MMGBSA
- Zhongjie Liang (Wed Dec 02 2009 - 17:17:44 PST)
[AMBER] MMGBSA error
- David A. Case (Fri Dec 25 2009 - 14:17:26 PST)
- Jason Swails (Fri Dec 25 2009 - 05:28:15 PST)
- Zhongjie Liang (Thu Dec 24 2009 - 22:59:16 PST)
- Carlos Simmerling (Tue Dec 22 2009 - 05:05:41 PST)
- Zhongjie Liang (Tue Dec 22 2009 - 05:04:09 PST)
[AMBER] MMPBSA on a selected region
- Jason Swails (Thu Dec 10 2009 - 11:15:58 PST)
- ERIK.LAURINI.phd.units.it (Thu Dec 10 2009 - 10:20:19 PST)
[AMBER] mpirun error
- Vijay Manickam Achari (Mon Dec 28 2009 - 19:00:11 PST)
[AMBER] myristate to palmitate transformation
- Anthony Pemberton (Tue Dec 08 2009 - 08:24:59 PST)
[AMBER] NAB example scripts in AmberTools (Amber 10)
- case (Thu Dec 03 2009 - 05:12:27 PST)
- Christopher Wassman (Thu Dec 03 2009 - 01:08:37 PST)
[AMBER] nab installation
- case (Tue Dec 29 2009 - 11:26:35 PST)
- Lixia Jin Day (Tue Dec 29 2009 - 09:32:37 PST)
[AMBER] NAMD dcd files in ptraj
- Ganesh Kamath (Wed Dec 16 2009 - 13:04:25 PST)
[AMBER] neb error while heating
- Carlos Simmerling (Mon Dec 28 2009 - 09:34:56 PST)
- balaji nagarajan (Sat Dec 26 2009 - 19:09:00 PST)
[AMBER] NEB-error
- Carlos Simmerling (Wed Dec 23 2009 - 08:46:59 PST)
- xmzpzengs (Wed Dec 23 2009 - 08:44:36 PST)
- Carlos Simmerling (Wed Dec 23 2009 - 08:12:01 PST)
- balaji nagarajan (Wed Dec 23 2009 - 08:04:46 PST)
[AMBER] NEB-NAN error
- balaji nagarajan (Mon Dec 28 2009 - 07:16:43 PST)
[AMBER] Nmode "not running properly" problem in MM_PBSA
- case (Sun Dec 13 2009 - 07:06:36 PST)
- Du Yun (Tue Dec 08 2009 - 17:56:48 PST)
[AMBER] non standard residue and bond command
- Bill Ross (Wed Dec 16 2009 - 13:20:08 PST)
- case (Wed Dec 16 2009 - 13:06:34 PST)
- Neha Bharat Gajaria (Wed Dec 16 2009 - 01:50:02 PST)
[AMBER] Non-Standard Atoms
- Jack Shultz (Sun Dec 20 2009 - 16:40:26 PST)
- case (Sun Dec 20 2009 - 11:02:46 PST)
- Jason Swails (Sat Dec 19 2009 - 18:54:20 PST)
- Jack Shultz (Sat Dec 19 2009 - 17:56:28 PST)
[AMBER] note on Antechamber error
- Mark M Huntress (Fri Dec 18 2009 - 14:27:50 PST)
[AMBER] Number of Cycles
- Ross Walker (Tue Dec 15 2009 - 11:01:40 PST)
- Robert Duke (Tue Dec 15 2009 - 11:00:19 PST)
- Jason Swails (Tue Dec 15 2009 - 10:32:40 PST)
- Niel Henriksen (Tue Dec 15 2009 - 10:11:08 PST)
- Robert Duke (Tue Dec 15 2009 - 09:54:28 PST)
- Bill Ross (Tue Dec 15 2009 - 09:53:24 PST)
- Niel Henriksen (Tue Dec 15 2009 - 09:41:55 PST)
- Robert Duke (Tue Dec 15 2009 - 09:29:22 PST)
- Jason Swails (Tue Dec 15 2009 - 09:18:37 PST)
- Carlos Simmerling (Tue Dec 15 2009 - 09:13:17 PST)
- Jason Swails (Tue Dec 15 2009 - 09:10:31 PST)
- Robert Duke (Tue Dec 15 2009 - 09:09:42 PST)
- Carlos Simmerling (Tue Dec 15 2009 - 08:53:06 PST)
- Robert Duke (Tue Dec 15 2009 - 06:55:31 PST)
- Jason Swails (Tue Dec 15 2009 - 05:34:29 PST)
- Jason Swails (Tue Dec 15 2009 - 05:32:31 PST)
- Carlos Simmerling (Tue Dec 15 2009 - 05:31:09 PST)
- Robert Duke (Tue Dec 15 2009 - 05:23:04 PST)
- Robert Duke (Tue Dec 15 2009 - 05:16:51 PST)
- Jason Swails (Tue Dec 15 2009 - 04:10:02 PST)
- s. Bill (Tue Dec 15 2009 - 00:31:21 PST)
[AMBER] OE and CG types
- Jio M (Tue Dec 29 2009 - 20:18:51 PST)
- Carlos Simmerling (Mon Dec 28 2009 - 09:42:41 PST)
- Dean Cuebas (Sat Dec 26 2009 - 17:10:06 PST)
- Jason Swails (Fri Dec 25 2009 - 04:32:03 PST)
- Jio M (Thu Dec 24 2009 - 23:29:19 PST)
- Carlos Simmerling (Thu Dec 24 2009 - 07:38:24 PST)
- Jio M (Thu Dec 24 2009 - 07:18:31 PST)
- Jason Swails (Thu Dec 24 2009 - 04:46:35 PST)
- Jio M (Thu Dec 24 2009 - 01:26:43 PST)
[AMBER] Output Does Not Match in Tutorial B1
- Wallace Kunin (Tue Dec 01 2009 - 10:41:08 PST)
- Wallace Kunin (Tue Dec 01 2009 - 10:00:48 PST)
[AMBER] parameter file for the sulphate ion
- Fenghui Fan (Thu Dec 03 2009 - 16:02:30 PST)
[AMBER] Parameters for HYP and CGU
- Alessandro Contini (Thu Dec 17 2009 - 01:11:44 PST)
- FyD (Thu Dec 17 2009 - 00:46:55 PST)
- Rilei Yu (Wed Dec 16 2009 - 21:58:26 PST)
- Rilei Yu (Wed Dec 16 2009 - 21:57:13 PST)
- Jason Swails (Wed Dec 16 2009 - 19:58:02 PST)
- Adrian Roitberg (Wed Dec 16 2009 - 19:27:25 PST)
- Rilei Yu (Wed Dec 16 2009 - 19:17:40 PST)
[AMBER] Parametrizing charges for modified DNA bases
- FyD (Mon Dec 07 2009 - 11:31:02 PST)
- Bob Johnson (Mon Dec 07 2009 - 10:05:09 PST)
[AMBER] phosphorus to carbon on minimization
- FyD (Mon Dec 07 2009 - 10:56:28 PST)
- Jason Swails (Mon Dec 07 2009 - 10:43:05 PST)
- Alexander Boncheff (Mon Dec 07 2009 - 07:48:45 PST)
[AMBER] PIMD test stalling
- peker milas (Tue Dec 08 2009 - 18:23:45 PST)
[AMBER] PQR file - HELP PLEASE
- s. Bill (Tue Dec 22 2009 - 13:27:48 PST)
- Jason Swails (Tue Dec 22 2009 - 09:21:41 PST)
- s. Bill (Tue Dec 22 2009 - 04:57:48 PST)
[AMBER] PQR files
- s. Bill (Fri Dec 25 2009 - 10:27:22 PST)
- Jason Swails (Fri Dec 25 2009 - 08:57:51 PST)
- s. Bill (Fri Dec 25 2009 - 06:38:36 PST)
[AMBER] preparation of small molecule libraries with most probable conformations using Amber
- Andrew Voronkov (Sat Dec 26 2009 - 03:38:09 PST)
[AMBER] pressure tensor components
- case (Sun Dec 13 2009 - 07:10:02 PST)
- Silvia Carlotto (Thu Dec 10 2009 - 05:12:51 PST)
[AMBER] problem in installing amber tools on Mac OSX 10.6
- case (Mon Dec 28 2009 - 05:07:48 PST)
- David Watson (Mon Dec 28 2009 - 05:06:30 PST)
- Chun-Wei Pao (Sun Dec 27 2009 - 23:54:26 PST)
[AMBER] Problem of MM-PBSA
- Ray Luo (Mon Dec 07 2009 - 14:44:53 PST)
- 欧阳德方 (Mon Dec 07 2009 - 14:30:41 PST)
- Ray Luo (Mon Dec 07 2009 - 10:19:02 PST)
- 欧阳德方 (Sun Dec 06 2009 - 21:09:47 PST)
[AMBER] problem with antechamber
- Junmei Wang (Wed Dec 09 2009 - 15:24:11 PST)
- sculiujl (Fri Dec 04 2009 - 04:18:24 PST)
- sculiujl (Fri Dec 04 2009 - 03:38:04 PST)
[AMBER] problem with FAD in tleap
- M. Shahid (Tue Dec 01 2009 - 03:54:04 PST)
[AMBER] ptraj image
- Daniel Roe (Wed Dec 09 2009 - 08:21:18 PST)
- Thomas Cheatham (Wed Dec 09 2009 - 05:41:54 PST)
- Neha Bharat Gajaria (Tue Dec 08 2009 - 22:13:36 PST)
- Bill Ross (Tue Dec 08 2009 - 16:29:03 PST)
- Taufik Al-Sarraj (Tue Dec 08 2009 - 15:54:46 PST)
- Bill Ross (Tue Dec 08 2009 - 14:08:42 PST)
- Thomas Cheatham (Tue Dec 08 2009 - 13:50:09 PST)
- Taufik Al-Sarraj (Tue Dec 08 2009 - 13:37:55 PST)
[AMBER] ptraj usage for clustering of protein ensembles manual or tutorial
- Carlos Simmerling (Tue Dec 08 2009 - 06:59:48 PST)
- Andrew Voronkov (Tue Dec 08 2009 - 06:48:56 PST)
- Thomas Cheatham (Sun Dec 06 2009 - 09:23:48 PST)
- Andrew Voronkov (Sun Dec 06 2009 - 05:39:39 PST)
- Andrew Voronkov (Sun Dec 06 2009 - 03:58:41 PST)
- Thomas Cheatham III (Fri Dec 04 2009 - 11:20:21 PST)
- Andrew Voronkov (Fri Dec 04 2009 - 11:09:58 PST)
- Thomas Cheatham III (Fri Dec 04 2009 - 09:01:35 PST)
- Andrew Voronkov (Fri Dec 04 2009 - 01:55:05 PST)
[AMBER] ptraj utility
- Neha Bharat Gajaria (Tue Dec 01 2009 - 18:13:41 PST)
- case (Tue Dec 01 2009 - 04:56:52 PST)
- Carlos Simmerling (Tue Dec 01 2009 - 04:48:27 PST)
- Daniel Roe (Tue Dec 01 2009 - 04:45:19 PST)
- Neha Bharat Gajaria (Tue Dec 01 2009 - 00:30:07 PST)
[AMBER] pupil and amber
- Ben Roberts (Tue Dec 22 2009 - 18:59:04 PST)
- davide branduardi (Tue Dec 22 2009 - 12:29:37 PST)
[AMBER] QM/MM input file error
- Ross Walker (Thu Dec 03 2009 - 09:36:47 PST)
- mahesh kumar (Thu Dec 03 2009 - 06:05:25 PST)
[AMBER] QM/MM minimization
- Ross Walker (Fri Dec 11 2009 - 19:39:55 PST)
- Hashem Taha (Fri Dec 11 2009 - 10:24:25 PST)
[AMBER] question about failures
- peker milas (Mon Dec 07 2009 - 22:25:10 PST)
- Jason Swails (Mon Dec 07 2009 - 22:00:00 PST)
- peker milas (Mon Dec 07 2009 - 21:31:06 PST)
- Jason Swails (Mon Dec 07 2009 - 20:51:28 PST)
- peker milas (Mon Dec 07 2009 - 19:37:40 PST)
[AMBER] reg.changing velocity
- David A. Case (Sat Dec 26 2009 - 19:01:18 PST)
- balaji nagarajan (Sat Dec 26 2009 - 10:47:10 PST)
[AMBER] Regarding rigid bond
- Bill Ross (Wed Dec 02 2009 - 09:20:52 PST)
- aneesh cna (Tue Dec 01 2009 - 21:17:46 PST)
- Bill Ross (Tue Dec 01 2009 - 09:41:44 PST)
- Adrian Roitberg (Tue Dec 01 2009 - 09:40:30 PST)
- Bill Ross (Tue Dec 01 2009 - 09:37:27 PST)
- Carlos Simmerling (Tue Dec 01 2009 - 04:55:17 PST)
- case (Tue Dec 01 2009 - 04:50:15 PST)
- Carlos Simmerling (Tue Dec 01 2009 - 03:28:58 PST)
- aneesh cna (Mon Nov 30 2009 - 21:35:03 PST)
[AMBER] Release of AmberTools, version 1.3
- David A. Case (Mon Dec 21 2009 - 06:33:20 PST)
[AMBER] Sander crash, corrupt rst file...
- Waqas Nasir (Mon Dec 21 2009 - 03:44:42 PST)
[AMBER] Scripting tleap
- Jio M (Sun Dec 06 2009 - 22:56:59 PST)
- case (Sun Dec 06 2009 - 12:11:02 PST)
- Jio M (Thu Dec 03 2009 - 22:04:01 PST)
[AMBER] Segmentation fault
- gurunath katagi (Wed Dec 02 2009 - 22:45:20 PST)
[AMBER] Segmentation fault in antechamber
- Scott Brozell (Mon Dec 14 2009 - 21:34:39 PST)
[AMBER] semiempirical copper
- Ross Walker (Thu Dec 03 2009 - 09:28:45 PST)
- Jacopo Sgrignani (Thu Dec 03 2009 - 06:09:57 PST)
[AMBER] SGLD in pmemd??
- Robert Duke (Tue Dec 01 2009 - 12:04:14 PST)
- Dean Cuebas (Tue Dec 01 2009 - 11:31:21 PST)
[AMBER] sleap in AmberTools 1.3 is not working anymore for me
- case (Tue Dec 29 2009 - 19:40:26 PST)
- Alan (Tue Dec 29 2009 - 13:47:52 PST)
- David Watson (Tue Dec 29 2009 - 13:02:05 PST)
- Alan (Tue Dec 29 2009 - 12:27:57 PST)
[AMBER] sodium ions before or after solvation makes a difference
- Bill Ross (Fri Dec 04 2009 - 10:23:44 PST)
- Thomas Cheatham III (Fri Dec 04 2009 - 09:09:17 PST)
- Naser Alijabbari (Thu Dec 03 2009 - 21:01:13 PST)
[AMBER] SQM and AMBER
- Jio M (Fri Dec 18 2009 - 22:36:05 PST)
[AMBER] SQM and AMBER :again
- Jio M (Wed Dec 23 2009 - 21:18:37 PST)
[AMBER] sqm x mopac in AmberTools 1.3
- Alan (Tue Dec 29 2009 - 11:52:44 PST)
- case (Tue Dec 29 2009 - 11:49:26 PST)
- Alan (Tue Dec 29 2009 - 10:49:26 PST)
- David A. Case (Tue Dec 22 2009 - 19:53:20 PST)
- David A. Case (Tue Dec 22 2009 - 19:50:35 PST)
- David Watson (Tue Dec 22 2009 - 07:58:56 PST)
- David Watson (Tue Dec 22 2009 - 07:20:37 PST)
- Alan (Tue Dec 22 2009 - 07:02:22 PST)
[AMBER] Tests to check for proper MMPBSA.py installation
- case (Wed Dec 30 2009 - 06:23:57 PST)
- RANAJIT SHINDE (Wed Dec 30 2009 - 04:15:48 PST)
[AMBER] Topology Reorder for EVB
- Andrea Coletta (Tue Dec 08 2009 - 01:40:23 PST)
- E.M. (Mon Dec 07 2009 - 11:17:44 PST)
- Jason Swails (Mon Dec 07 2009 - 10:59:23 PST)
- Andrea Coletta (Mon Dec 07 2009 - 07:58:50 PST)
[AMBER] trajout problem
- Anna Reymer (Tue Dec 01 2009 - 05:23:22 PST)
- Daniel Roe (Tue Dec 01 2009 - 04:34:34 PST)
[AMBER] trouble with antechamber
- Jennifer L. Muzyka (Tue Dec 01 2009 - 07:10:40 PST)
[AMBER] typo in AmberTools.pdf (release 1.3)
- David A. Case (Wed Dec 23 2009 - 06:26:51 PST)
- Alan (Wed Dec 23 2009 - 01:51:01 PST)
[AMBER] using sqm from AmberTools 1.3
- case (Tue Dec 29 2009 - 13:01:18 PST)
- Alan (Tue Dec 29 2009 - 12:10:56 PST)
- case (Tue Dec 29 2009 - 11:36:21 PST)
- David Watson (Tue Dec 29 2009 - 11:34:28 PST)
- Alan (Tue Dec 29 2009 - 09:35:06 PST)
- Ross Walker (Thu Dec 24 2009 - 15:17:47 PST)
- David A. Case (Wed Dec 23 2009 - 06:26:36 PST)
- David A. Case (Wed Dec 23 2009 - 06:16:04 PST)
- Alan (Wed Dec 23 2009 - 02:35:33 PST)
[AMBER] Van der Waals and electrostatic Forces
- David A. Case (Wed Dec 23 2009 - 18:56:50 PST)
- Frank X. Vázquez (Tue Dec 22 2009 - 09:42:33 PST)
[AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message.
- 木野　亮平 (Thu Dec 17 2009 - 01:59:29 PST)
[AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide
- Dongshan Wei (Thu Dec 10 2009 - 16:14:12 PST)
- Ross Walker (Thu Dec 10 2009 - 16:02:16 PST)
- Carlos Simmerling (Thu Dec 10 2009 - 15:52:40 PST)
- Dongshan Wei (Thu Dec 10 2009 - 15:40:19 PST)
[AMBER] XLEaP Error on Closing Edit
- Ross Walker (Tue Dec 01 2009 - 11:02:58 PST)
- Wallace Kunin (Tue Dec 01 2009 - 10:43:27 PST)
[AMBER] Zinc parameters?
- Ray Luo, Ph.D. (Thu Dec 31 2009 - 18:11:45 PST)
- xuemeiwang1103 (Wed Dec 30 2009 - 19:37:21 PST)
Amber question
- Ross Walker (Thu Dec 24 2009 - 15:44:54 PST)
ATP/GTP parameters
- FyD (Tue Dec 08 2009 - 22:51:03 PST)
COOH group trouble
- Jio M (Wed Dec 09 2009 - 08:38:09 PST)
COOH troubling
- Dean Cuebas (Sat Dec 12 2009 - 08:47:42 PST)
- Jio M (Fri Dec 11 2009 - 22:27:25 PST)
- Jio M (Fri Dec 11 2009 - 11:37:39 PST)
- case (Fri Dec 11 2009 - 05:27:09 PST)
- Dean Cuebas (Thu Dec 10 2009 - 22:41:27 PST)
- Junmei Wang (Thu Dec 10 2009 - 13:45:43 PST)
- Jio M (Thu Dec 10 2009 - 03:03:59 PST)
- Jio M (Wed Dec 09 2009 - 22:21:24 PST)
- Dean Cuebas (Wed Dec 09 2009 - 16:00:40 PST)
- Junmei Wang (Wed Dec 09 2009 - 15:17:12 PST)
- Jio M (Wed Dec 09 2009 - 07:01:30 PST)
- case (Wed Dec 09 2009 - 05:40:10 PST)
- Jio M (Wed Dec 09 2009 - 04:16:17 PST)
EEL = *************
- case (Thu Dec 10 2009 - 12:13:15 PST)
- Taufik Al-Sarraj (Tue Dec 08 2009 - 10:34:35 PST)
how to change velocities
- Carlos Simmerling (Sat Dec 26 2009 - 05:26:17 PST)
- balaji nagarajan (Fri Dec 25 2009 - 22:02:58 PST)
- Carlos Simmerling (Fri Dec 25 2009 - 04:13:44 PST)
- balaji nagarajan (Fri Dec 25 2009 - 02:23:57 PST)
looking for parameters for DHFR substrates and inhibitors... [one more try]
- Sidney Elmer (Tue Dec 01 2009 - 15:34:36 PST)
nab normal mode analysis has imaginary frequencies
- case (Thu Dec 10 2009 - 06:46:20 PST)
- Junmei Wang (Wed Dec 09 2009 - 15:34:28 PST)
PIMD test stalling
- peker milas (Tue Dec 08 2009 - 19:11:44 PST)
答复: [AMBER] MMGBSA error
- Zhongjie Liang (Fri Dec 25 2009 - 20:30:00 PST)
- Zhongjie Liang (Wed Dec 23 2009 - 05:12:07 PST)

Amber Archive Dec 2009 by subject