Amber Archive Sep 2011: by subject

[AMBER] 1st DNA tutorial cannot save parameter
- Ross Walker (Wed Sep 28 2011 - 21:49:17 PDT)
- Yao Yao (Wed Sep 28 2011 - 17:28:30 PDT)
[AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
- FyD (Mon Sep 26 2011 - 04:51:12 PDT)
- Yun Shi (Fri Sep 23 2011 - 22:26:22 PDT)
- Matthew Tessier (Fri Sep 23 2011 - 10:48:41 PDT)
- FyD (Fri Sep 23 2011 - 05:12:44 PDT)
- Karl N. Kirschner (Fri Sep 23 2011 - 03:10:57 PDT)
- FyD (Fri Sep 23 2011 - 02:37:32 PDT)
- Matthew Tessier (Thu Sep 22 2011 - 11:25:12 PDT)
- FyD (Wed Sep 21 2011 - 23:45:31 PDT)
- Matthew Tessier (Wed Sep 21 2011 - 06:46:14 PDT)
- FyD (Tue Sep 20 2011 - 01:19:34 PDT)
- Yun Shi (Mon Sep 19 2011 - 15:27:01 PDT)
- Matthew Tessier (Mon Sep 19 2011 - 07:41:30 PDT)
- Yun Shi (Fri Sep 16 2011 - 09:46:01 PDT)
- Yun Shi (Thu Sep 15 2011 - 15:30:28 PDT)
- Lachele Foley (Lists) (Thu Sep 15 2011 - 13:37:09 PDT)
- Matthew Tessier (Thu Sep 15 2011 - 11:53:30 PDT)
- Lachele Foley (Lists) (Thu Sep 15 2011 - 11:39:44 PDT)
- Yun Shi (Thu Sep 15 2011 - 11:07:33 PDT)
- Lachele Foley (Lists) (Thu Sep 15 2011 - 10:41:01 PDT)
- Yun Shi (Thu Sep 15 2011 - 10:03:47 PDT)
- Lachele Foley (Lists) (Thu Sep 15 2011 - 08:32:33 PDT)
- Yun Shi (Wed Sep 14 2011 - 15:53:43 PDT)
[AMBER] again GLYCAM06 + 99SB + GAFF ?
- FyD (Thu Sep 22 2011 - 00:12:38 PDT)
- Matthew Tessier (Wed Sep 21 2011 - 19:04:38 PDT)
- Yun Shi (Wed Sep 21 2011 - 07:41:36 PDT)
- FyD (Wed Sep 21 2011 - 00:08:17 PDT)
- Yun Shi (Tue Sep 20 2011 - 21:11:08 PDT)
- FyD (Mon Sep 19 2011 - 04:23:41 PDT)
- Yun Shi (Sun Sep 18 2011 - 21:38:55 PDT)
- FyD (Fri Sep 16 2011 - 03:42:46 PDT)
- Yun Shi (Thu Sep 15 2011 - 21:56:35 PDT)
- FyD (Tue Sep 13 2011 - 08:46:23 PDT)
- FyD (Tue Sep 13 2011 - 08:41:21 PDT)
- Yun Shi (Mon Sep 12 2011 - 23:55:50 PDT)
- Yun Shi (Mon Sep 12 2011 - 23:32:47 PDT)
- FyD (Wed Sep 07 2011 - 23:57:43 PDT)
- Yun Shi (Tue Sep 06 2011 - 22:28:44 PDT)
[AMBER] AMBER
- Jason Swails (Wed Sep 14 2011 - 10:19:24 PDT)
- Shesh Nath (Wed Sep 14 2011 - 00:00:24 PDT)
[AMBER] Amber 10/ambertool Installation error
- Jason Swails (Fri Sep 30 2011 - 07:22:43 PDT)
- Kshatresh Dutta Dubey (Fri Sep 30 2011 - 06:12:59 PDT)
[AMBER] Amber 11 configure error with openmpi
- Lianhu Wei (Tue Sep 13 2011 - 07:49:36 PDT)
- Jason Swails (Mon Sep 12 2011 - 13:37:48 PDT)
- David A Case (Mon Sep 12 2011 - 13:34:10 PDT)
- Jason Swails (Mon Sep 12 2011 - 10:23:48 PDT)
- Lianhu Wei (Mon Sep 12 2011 - 10:14:33 PDT)
[AMBER] AMBER expense
- David Condon (Fri Sep 16 2011 - 17:08:34 PDT)
- steinbrt.rci.rutgers.edu (Fri Sep 16 2011 - 16:16:20 PDT)
- David Condon (Fri Sep 16 2011 - 13:24:23 PDT)
[AMBER] Amber for GPUs
- Baker D.J. (Tue Sep 06 2011 - 05:06:42 PDT)
[AMBER] Amber parmbsc0
- Daniel Roe (Thu Sep 22 2011 - 04:58:12 PDT)
- Nadine Utz (Thu Sep 22 2011 - 00:52:00 PDT)
- souvik sur (Thu Sep 22 2011 - 00:35:03 PDT)
[AMBER] Amber parmbsc0 force field
- Jason Swails (Sat Sep 24 2011 - 07:33:29 PDT)
- souvik sur (Sat Sep 24 2011 - 07:09:53 PDT)
- case (Sat Sep 24 2011 - 06:04:47 PDT)
- Bruno Rodrigues (Fri Sep 23 2011 - 22:22:44 PDT)
- souvik sur (Fri Sep 23 2011 - 21:25:11 PDT)
[AMBER] Amber parmbsc0 vs ff99
- Jiri Sponer (Thu Sep 22 2011 - 11:36:51 PDT)
- Marek Maly (Thu Sep 22 2011 - 09:06:56 PDT)
- Jason Swails (Thu Sep 22 2011 - 09:15:28 PDT)
- Marek Maly (Thu Sep 22 2011 - 08:43:12 PDT)
- Brian Radak (Thu Sep 22 2011 - 08:24:56 PDT)
- Jason Swails (Thu Sep 22 2011 - 08:22:10 PDT)
- Thomas Cheatham (Thu Sep 22 2011 - 08:15:16 PDT)
- Marek Maly (Thu Sep 22 2011 - 07:54:45 PDT)
- Hugh Heldenbrand (Thu Sep 22 2011 - 08:02:40 PDT)
- Brian Radak (Thu Sep 22 2011 - 06:50:40 PDT)
- souvik sur (Thu Sep 22 2011 - 06:41:45 PDT)
[AMBER] Amber tools
- manikanthan bhavaraju (Tue Sep 06 2011 - 07:04:49 PDT)
- case (Mon Sep 05 2011 - 17:12:47 PDT)
- kirtana S (Sun Sep 04 2011 - 20:58:20 PDT)
- Jason Swails (Sat Sep 03 2011 - 23:04:11 PDT)
- manikanthan bhavaraju (Sat Sep 03 2011 - 22:09:45 PDT)
- KIRTANA S (Sat Sep 03 2011 - 22:05:35 PDT)
[AMBER] ambertool question !!!
- Dmitry Nilov (Mon Sep 26 2011 - 12:11:28 PDT)
- Brian Radak (Mon Sep 26 2011 - 11:36:16 PDT)
- Алексей Раевский (Mon Sep 26 2011 - 11:23:58 PDT)
- Алексей Раевский (Mon Sep 26 2011 - 11:22:14 PDT)
[AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
- Jason Swails (Sat Sep 24 2011 - 17:13:04 PDT)
- Daniel Roe (Sat Sep 24 2011 - 08:48:53 PDT)
- Mengjuei Hsieh (Sat Sep 24 2011 - 08:31:23 PDT)
- Jason Swails (Sat Sep 24 2011 - 07:50:40 PDT)
- Daniel Roe (Sat Sep 24 2011 - 05:44:13 PDT)
- George Tzotzos (Sat Sep 24 2011 - 04:08:22 PDT)
- George Tzotzos (Sat Sep 24 2011 - 02:41:03 PDT)
[AMBER] AmberTools Parallel Compilation Issue
- Matteo Guglielmi (Sat Sep 24 2011 - 08:03:03 PDT)
- Ross Walker (Fri Sep 23 2011 - 12:26:11 PDT)
- Matteo Guglielmi (Fri Sep 23 2011 - 12:06:59 PDT)
- Carlos Sosa (Fri Sep 23 2011 - 08:24:39 PDT)
- Matteo Guglielmi (Fri Sep 23 2011 - 08:21:53 PDT)
- Carlos Sosa (Fri Sep 23 2011 - 06:51:42 PDT)
- David A Case (Fri Sep 23 2011 - 06:15:59 PDT)
- Matteo Guglielmi (Fri Sep 23 2011 - 02:06:56 PDT)
- Jason Swails (Thu Sep 22 2011 - 18:10:18 PDT)
- Matteo Guglielmi (Thu Sep 22 2011 - 17:59:09 PDT)
[AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation?
- Jason Swails (Thu Sep 29 2011 - 07:18:31 PDT)
- George Tzotzos (Thu Sep 29 2011 - 07:07:51 PDT)
- Bill Miller III (Thu Sep 29 2011 - 06:59:20 PDT)
- George Tzotzos (Thu Sep 29 2011 - 06:54:50 PDT)
[AMBER] AMOEBA potentials
- David A Case (Thu Sep 15 2011 - 12:08:01 PDT)
- Neha Gandhi (Thu Sep 15 2011 - 02:43:14 PDT)
[AMBER] Announcing the NVIDIA MD SimCluster Program (Free test drives available)
- Ross Walker (Wed Sep 28 2011 - 14:29:36 PDT)
[AMBER] Antechamber
- case (Sun Sep 25 2011 - 14:09:14 PDT)
- Zachary Davis (Fri Sep 23 2011 - 10:17:38 PDT)
[AMBER] antechamber am1bcc stops with no error message
- case (Sun Sep 11 2011 - 18:48:34 PDT)
- Danny Xu (Mon Sep 05 2011 - 21:37:38 PDT)
[AMBER] antechamber error
- Soonmin Jang (Tue Sep 06 2011 - 07:04:50 PDT)
- Jason Swails (Sat Sep 03 2011 - 08:46:05 PDT)
- case (Sat Sep 03 2011 - 05:59:25 PDT)
- Soonmin Jang (Sat Sep 03 2011 - 01:45:47 PDT)
[AMBER] Aromatic bonds disappear during sdf creation with sleap
- Jason Swails (Mon Sep 12 2011 - 05:58:43 PDT)
- Guenegou, Guillaume [JRDFR] (Mon Sep 12 2011 - 05:10:29 PDT)
[AMBER] attachment for my previous mail
- Fredrick Devadoss (Wed Sep 14 2011 - 07:00:38 PDT)
[AMBER] Automatic creation of charge and radius files for Delphi
- Jan-Philip Gehrcke (Tue Sep 20 2011 - 03:13:21 PDT)
[AMBER] benchmarking Tesla S2050 1U system
- Sidney Elmer (Thu Sep 15 2011 - 17:08:27 PDT)
- Sidney Elmer (Wed Sep 14 2011 - 15:55:23 PDT)
- Ross Walker (Wed Sep 14 2011 - 12:41:19 PDT)
- Sidney Elmer (Wed Sep 14 2011 - 11:52:38 PDT)
[AMBER] Bond command using xleap or tleap
- case (Sat Sep 17 2011 - 06:18:04 PDT)
- Bill Ross (Fri Sep 16 2011 - 15:10:30 PDT)
- Sidney Elmer (Fri Sep 16 2011 - 09:23:57 PDT)
- Bill Ross (Thu Sep 15 2011 - 17:39:59 PDT)
- Sidney Elmer (Thu Sep 15 2011 - 17:14:38 PDT)
- David A Case (Thu Sep 15 2011 - 11:51:01 PDT)
- Fabrício Bracht (Wed Sep 14 2011 - 12:53:09 PDT)
[AMBER] bug in respgen ?
- FyD (Wed Sep 28 2011 - 09:03:53 PDT)
- David A Case (Wed Sep 28 2011 - 07:11:30 PDT)
- FyD (Mon Sep 26 2011 - 04:33:35 PDT)
- FyD (Mon Sep 26 2011 - 03:19:08 PDT)
- thomas.fox.boehringer-ingelheim.com (Mon Sep 26 2011 - 00:00:06 PDT)
- FyD (Fri Sep 23 2011 - 07:27:13 PDT)
- thomas.fox.boehringer-ingelheim.com (Fri Sep 23 2011 - 05:59:04 PDT)
- FyD (Thu Sep 22 2011 - 00:25:43 PDT)
- thomas.fox.boehringer-ingelheim.com (Wed Sep 21 2011 - 00:06:21 PDT)
[AMBER] Can we extract information from out file for MBAR analysis for PMF analysis?
- Brian Radak (Wed Sep 14 2011 - 12:33:50 PDT)
- Catein Catherine (Wed Sep 14 2011 - 11:36:11 PDT)
[AMBER] Can we extract information from out file for MBAR analysis?
- Brian Radak (Wed Sep 14 2011 - 11:14:41 PDT)
- Catein Catherine (Wed Sep 14 2011 - 10:50:20 PDT)
[AMBER] CCA-Phe terminal using Antechamber
- David A Case (Thu Sep 01 2011 - 07:33:11 PDT)
- Sindrila Dutta banik (Thu Sep 01 2011 - 05:39:46 PDT)
[AMBER] charges on ligand
- steinbrt.rci.rutgers.edu (Tue Sep 20 2011 - 00:32:47 PDT)
- kamlesh sahu (Mon Sep 19 2011 - 22:58:18 PDT)
[AMBER] Chirality restraints
- Rajeswari A. (Thu Sep 29 2011 - 05:42:52 PDT)
- David A Case (Thu Sep 29 2011 - 05:35:59 PDT)
- Rajeswari A. (Thu Sep 29 2011 - 00:06:40 PDT)
[AMBER] Chromophore Building
- M. L. Dodson (Tue Sep 27 2011 - 12:55:49 PDT)
- Yao Yao (Tue Sep 27 2011 - 12:34:19 PDT)
[AMBER] Compiling Amber11 on Blue Gene/P
- Jason Swails (Fri Sep 30 2011 - 06:54:52 PDT)
- Garo Garabedyan (Fri Sep 30 2011 - 01:18:53 PDT)
- Ross Walker (Wed Sep 14 2011 - 12:20:45 PDT)
- Garo Garabedyan (Wed Sep 14 2011 - 11:33:23 PDT)
- Garo Garabedyan (Tue Sep 13 2011 - 23:12:20 PDT)
- Jed W Pitera (Tue Sep 13 2011 - 14:09:51 PDT)
- Garo Garabedyan (Tue Sep 13 2011 - 12:45:37 PDT)
[AMBER] cpptraj-segmentation fault
- Daniel Roe (Tue Sep 20 2011 - 04:18:48 PDT)
- Praapti Jayaswal (Mon Sep 19 2011 - 22:57:09 PDT)
- Daniel Roe (Thu Sep 15 2011 - 22:10:27 PDT)
- Praapti Jayaswal (Thu Sep 15 2011 - 21:19:40 PDT)
- Daniel Roe (Thu Sep 15 2011 - 05:42:56 PDT)
- Praapti Jayaswal (Mon Sep 12 2011 - 21:37:17 PDT)
- Daniel Roe (Mon Sep 12 2011 - 05:52:38 PDT)
- Praapti Jayaswal (Sun Sep 11 2011 - 23:58:39 PDT)
- Daniel Roe (Mon Sep 05 2011 - 17:26:46 PDT)
- Praapti Jayaswal (Sun Sep 04 2011 - 21:01:05 PDT)
- Daniel Roe (Fri Sep 02 2011 - 15:30:14 PDT)
- Praapti Jayaswal (Wed Aug 31 2011 - 23:02:24 PDT)
[AMBER] Creating prmtop and inpcrd files
- Jason Swails (Tue Sep 06 2011 - 08:44:43 PDT)
- Chidambar Kulkarni (Tue Sep 06 2011 - 06:45:43 PDT)
- case (Tue Sep 06 2011 - 05:37:21 PDT)
- Chidambar Kulkarni (Mon Sep 05 2011 - 23:57:53 PDT)
[AMBER] Difference between serial and parallel MMPBSA
- Osman, Roman (Thu Sep 22 2011 - 13:07:26 PDT)
- Mengjuei Hsieh (Thu Sep 22 2011 - 12:58:45 PDT)
- Osman, Roman (Sat Sep 17 2011 - 08:23:38 PDT)
- Ray Luo, Ph.D. (Fri Sep 16 2011 - 20:33:19 PDT)
- Osman, Roman (Fri Sep 16 2011 - 15:18:41 PDT)
[AMBER] Different Temps Coupling
- Ross Walker (Wed Sep 21 2011 - 12:42:53 PDT)
- Yao Yao (Wed Sep 21 2011 - 10:35:56 PDT)
[AMBER] Difficulties trying to derive charge for new acetylated serine
- FyD (Wed Sep 21 2011 - 08:55:17 PDT)
- M. L. Dodson (Wed Sep 21 2011 - 06:18:28 PDT)
- Fabrício Bracht (Tue Sep 20 2011 - 22:36:32 PDT)
[AMBER] dihedral parameters
- kirtana S (Tue Sep 27 2011 - 14:59:00 PDT)
- Chidambar Kulkarni (Tue Sep 27 2011 - 09:09:05 PDT)
- Jason Swails (Tue Sep 27 2011 - 05:01:07 PDT)
- Chidambar Kulkarni (Mon Sep 26 2011 - 20:51:18 PDT)
- Jason Swails (Mon Sep 26 2011 - 18:08:39 PDT)
- kirtana S (Mon Sep 26 2011 - 14:09:39 PDT)
- Chidambar Kulkarni (Thu Sep 15 2011 - 22:36:36 PDT)
- Dean Cuebas (Thu Sep 15 2011 - 15:08:36 PDT)
- Jason Swails (Thu Sep 15 2011 - 10:07:42 PDT)
- Chidambar Kulkarni (Thu Sep 15 2011 - 08:42:59 PDT)
- Jason Swails (Thu Sep 15 2011 - 07:39:54 PDT)
- Chidambar Kulkarni (Thu Sep 15 2011 - 07:14:55 PDT)
[AMBER] Dihedral Rotation
- Niel Henriksen (Mon Sep 19 2011 - 19:40:58 PDT)
- David Condon (Sat Sep 17 2011 - 12:27:11 PDT)
[AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
- Marek Maly (Thu Sep 15 2011 - 11:59:51 PDT)
- Scott Le Grand (Thu Sep 15 2011 - 12:05:50 PDT)
- Marek Maly (Thu Sep 15 2011 - 11:15:37 PDT)
- Ross Walker (Thu Sep 15 2011 - 10:37:01 PDT)
- Marek Maly (Thu Sep 15 2011 - 09:52:13 PDT)
[AMBER] Electrpostatic interaction vs Coulombic interaction
- Rilei Yu (Wed Sep 14 2011 - 23:52:17 PDT)
- David Case (Wed Sep 14 2011 - 18:34:22 PDT)
- Rilei Yu (Wed Sep 14 2011 - 17:48:08 PDT)
[AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
- Jason Swails (Fri Sep 30 2011 - 15:55:26 PDT)
- Marek Maly (Fri Sep 30 2011 - 14:26:23 PDT)
- Jason Swails (Fri Sep 30 2011 - 14:11:52 PDT)
- Marek Maly (Fri Sep 30 2011 - 13:35:23 PDT)
- Jason Swails (Fri Sep 30 2011 - 12:27:36 PDT)
- Marek Maly (Fri Sep 30 2011 - 09:23:27 PDT)
- Jason Swails (Thu Sep 29 2011 - 22:10:47 PDT)
- Marek Maly (Thu Sep 29 2011 - 19:34:43 PDT)
- Jason Swails (Thu Sep 29 2011 - 15:12:20 PDT)
- Marek Maly (Thu Sep 29 2011 - 14:32:09 PDT)
[AMBER] energy
- kirtana S (Wed Sep 14 2011 - 09:40:21 PDT)
- Bill Miller III (Wed Sep 14 2011 - 09:00:13 PDT)
- kirtana S (Wed Sep 14 2011 - 08:02:14 PDT)
- kirtana S (Mon Sep 05 2011 - 13:51:15 PDT)
- Bill Miller III (Mon Sep 05 2011 - 13:32:04 PDT)
- kirtana S (Mon Sep 05 2011 - 11:56:34 PDT)
[AMBER] Energy change
- Bill Miller III (Mon Sep 05 2011 - 13:59:29 PDT)
- manikanthan bhavaraju (Mon Sep 05 2011 - 13:58:41 PDT)
- kirtana S (Sun Sep 04 2011 - 22:31:45 PDT)
- Jason Swails (Fri Sep 02 2011 - 10:53:06 PDT)
- KIRTANA S (Fri Sep 02 2011 - 10:43:55 PDT)
- steinbrt.rci.rutgers.edu (Thu Sep 01 2011 - 23:43:24 PDT)
- KIRTANA S (Thu Sep 01 2011 - 13:09:19 PDT)
[AMBER] Energy of solute molecule
- Jason Swails (Mon Sep 05 2011 - 15:53:27 PDT)
- Ignacio J. General (Mon Sep 05 2011 - 07:15:14 PDT)
- Jason Swails (Fri Sep 02 2011 - 10:40:46 PDT)
- Mattei, Alessandra (Fri Sep 02 2011 - 10:31:35 PDT)
[AMBER] Error in computing entropy! problem with number of frames in NMODE
- hongphuc nguyen (Thu Sep 15 2011 - 20:12:42 PDT)
- Bill Miller III (Wed Sep 14 2011 - 04:24:46 PDT)
- hongphuc nguyen (Wed Sep 14 2011 - 02:50:58 PDT)
[AMBER] error using saveamberparm on pdb with nonstandard residues
- David A Case (Tue Sep 13 2011 - 04:51:18 PDT)
- Darren Jindal (Mon Sep 12 2011 - 19:32:18 PDT)
[AMBER] error when installing parallel sander / AmberTools1.5 Amber11
- matheus froeyen (Fri Sep 23 2011 - 01:49:50 PDT)
- Jason Swails (Thu Sep 22 2011 - 17:43:14 PDT)
- K T (Thu Sep 22 2011 - 17:28:31 PDT)
- Ross Walker (Thu Sep 22 2011 - 11:05:10 PDT)
- matheus froeyen (Thu Sep 22 2011 - 10:56:18 PDT)
[AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE
- case (Sun Sep 25 2011 - 14:03:34 PDT)
- Hirdesh Kumar (Tue Sep 20 2011 - 23:07:50 PDT)
[AMBER] Failure building Amber 11 parallel on AmberTools1.5
- Jason Swails (Tue Sep 27 2011 - 17:26:16 PDT)
- George Tzotzos (Tue Sep 27 2011 - 13:24:03 PDT)
[AMBER] Failure to compile AmberTools 1.5 on linux
- Francesco Pietra (Fri Sep 30 2011 - 08:34:02 PDT)
- David A Case (Fri Sep 30 2011 - 05:25:43 PDT)
- FyD (Fri Sep 30 2011 - 04:57:53 PDT)
- Francesco Pietra (Fri Sep 30 2011 - 02:43:18 PDT)
[AMBER] false positive on too large QM region?
- Gustavo Seabra (Wed Sep 07 2011 - 17:19:36 PDT)
- Brian Radak (Wed Sep 07 2011 - 14:37:58 PDT)
[AMBER] FATAL: allocation failure in vector(), please help me to fix that problem
- Bill Miller III (Fri Sep 16 2011 - 03:49:55 PDT)
- hongphuc nguyen (Fri Sep 16 2011 - 01:26:55 PDT)
[AMBER] fixing rmsd values
- InSuk Joung (Mon Sep 26 2011 - 10:29:35 PDT)
- Niel Henriksen (Mon Sep 26 2011 - 10:29:22 PDT)
- Massimiliano Porrini (Mon Sep 26 2011 - 10:18:47 PDT)
- Bruno Rodrigues (Mon Sep 26 2011 - 08:54:25 PDT)
- Massimiliano Porrini (Mon Sep 26 2011 - 07:46:52 PDT)
- Niel Henriksen (Sun Sep 25 2011 - 08:47:23 PDT)
- Massimiliano Porrini (Sun Sep 25 2011 - 08:22:13 PDT)
[AMBER] force field modification
- kirtana S (Thu Sep 29 2011 - 09:46:18 PDT)
[AMBER] force field of molecular crystals
- case (Mon Sep 19 2011 - 19:06:23 PDT)
- jun kit (Mon Sep 19 2011 - 12:05:20 PDT)
- David A Case (Mon Sep 19 2011 - 12:00:07 PDT)
- jun kit (Mon Sep 19 2011 - 11:20:25 PDT)
[AMBER] Format conversion
- aiswarya.pawar.gmail.com (Wed Sep 07 2011 - 11:18:12 PDT)
[AMBER] From amber to gromacs
- Ivan Gladich (Fri Sep 30 2011 - 05:02:04 PDT)
- madhumita das (Fri Sep 30 2011 - 01:31:44 PDT)
[AMBER] Fwd: amber
- steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 07:14:29 PDT)
- Gustavo Seabra (Tue Sep 13 2011 - 06:59:55 PDT)
[AMBER] Fwd: false positive on too large QM region?
- Brian Radak (Tue Sep 13 2011 - 11:59:53 PDT)
- Qiantao Wang (Thu Sep 08 2011 - 14:34:44 PDT)
- Brian Radak (Thu Sep 08 2011 - 13:42:56 PDT)
- Gustavo Seabra (Thu Sep 08 2011 - 13:13:22 PDT)
- Ross Walker (Thu Sep 08 2011 - 12:43:45 PDT)
- Brian Radak (Thu Sep 08 2011 - 11:52:43 PDT)
- Gustavo Seabra (Thu Sep 08 2011 - 11:30:18 PDT)
- Brian Radak (Thu Sep 08 2011 - 07:42:56 PDT)
[AMBER] Fwd: fixing rmsd values (follow-up)
- Jason Swails (Thu Sep 29 2011 - 17:55:15 PDT)
- Mariano Rech (Wed Sep 28 2011 - 23:34:46 PDT)
- Massimiliano Porrini (Wed Sep 28 2011 - 11:10:52 PDT)
- Massimiliano Porrini (Wed Sep 28 2011 - 04:26:29 PDT)
- Bruno Rodrigues (Tue Sep 27 2011 - 14:39:47 PDT)
- Carlos Simmerling (Tue Sep 27 2011 - 14:14:33 PDT)
- Thomas Cheatham III (Tue Sep 27 2011 - 13:55:40 PDT)
- Carlos Simmerling (Tue Sep 27 2011 - 11:51:37 PDT)
- Massimiliano Porrini (Tue Sep 27 2011 - 11:44:14 PDT)
[AMBER] Fwd: pbsa
- Ray Luo, Ph.D. (Mon Sep 12 2011 - 10:24:23 PDT)
[AMBER] GAMESS to RESP input file
- FyD (Mon Sep 26 2011 - 04:58:34 PDT)
- shome sankar bhunia (Mon Sep 26 2011 - 03:46:25 PDT)
[AMBER] GB protocol problems for large RNAs
- Ross Walker (Thu Sep 22 2011 - 09:30:46 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Thu Sep 22 2011 - 09:02:28 PDT)
[AMBER] GB protocol problems for large RNAs (follow-up)
- David A Case (Tue Sep 27 2011 - 12:43:12 PDT)
- Thomas Gaillard (Tue Sep 27 2011 - 10:38:43 PDT)
- Niel Henriksen (Tue Sep 27 2011 - 09:42:32 PDT)
- Carlos Simmerling (Tue Sep 27 2011 - 09:34:23 PDT)
- Ross Walker (Tue Sep 27 2011 - 09:13:32 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Sep 27 2011 - 07:09:10 PDT)
[AMBER] GBSW AMBER
- David A Case (Thu Sep 29 2011 - 05:37:30 PDT)
- Cindy Pembroke (Thu Sep 29 2011 - 00:52:16 PDT)
[AMBER] giving acceptor mask in ptraj for hbond utility
- Daniel Roe (Tue Sep 27 2011 - 11:36:32 PDT)
- Bala subramanian (Tue Sep 27 2011 - 11:16:05 PDT)
[AMBER] Global Minimum in Simulated Annealing using SANDER
- steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 07:18:36 PDT)
- Julian Zachmann (Tue Sep 13 2011 - 07:12:00 PDT)
[AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor)
- Lachele Foley (Lists) (Mon Sep 19 2011 - 06:56:41 PDT)
- mish (Sun Sep 18 2011 - 23:15:53 PDT)
- d944286.oz.nthu.edu.tw (Sun Sep 18 2011 - 22:50:38 PDT)
[AMBER] Glycam06g and ff99SB cause the difference of DIHED (notattributed to the scaling factor)
- d944286.oz.nthu.edu.tw (Tue Sep 20 2011 - 08:32:38 PDT)
[AMBER] Grid
- Thomas Cheatham (Fri Sep 16 2011 - 01:57:32 PDT)
- Aparna P (Fri Sep 16 2011 - 01:27:00 PDT)
[AMBER] Grid and SDF
- Thomas Cheatham III (Thu Sep 22 2011 - 11:28:18 PDT)
- Lorenzo Gontrani (Thu Sep 22 2011 - 00:40:41 PDT)
- Lorenzo Gontrani (Thu Sep 22 2011 - 00:28:08 PDT)
- Lorenzo Gontrani (Wed Sep 21 2011 - 06:24:50 PDT)
- Lorenzo Gontrani (Wed Sep 21 2011 - 03:53:47 PDT)
[AMBER] Grid and SDF - sorry for the mail spamming
- Lorenzo Gontrani (Thu Sep 22 2011 - 22:49:06 PDT)
[AMBER] hello
- steinbrt.rci.rutgers.edu (Wed Sep 14 2011 - 06:06:40 PDT)
- Linda catherine (Wed Sep 14 2011 - 05:16:27 PDT)
[AMBER] help ! zinc parameters
- Baldoni Hector Armando (Thu Sep 22 2011 - 07:02:00 PDT)
- Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 06:07:20 PDT)
- FyD (Wed Sep 21 2011 - 08:02:16 PDT)
- Kk Zhu (Wed Sep 21 2011 - 00:06:52 PDT)
- FyD (Tue Sep 20 2011 - 02:14:09 PDT)
- Bill Ross (Mon Sep 19 2011 - 13:30:19 PDT)
- zhukk (Mon Sep 19 2011 - 05:28:07 PDT)
- zhukk (Mon Sep 19 2011 - 05:25:39 PDT)
- zhukk (Mon Sep 19 2011 - 05:12:50 PDT)
- Ross Walker (Fri Sep 16 2011 - 09:18:15 PDT)
- Oteri Francesco (Fri Sep 16 2011 - 08:37:07 PDT)
- Bill Ross (Fri Sep 16 2011 - 08:39:20 PDT)
- Kk Zhu (Thu Sep 15 2011 - 23:46:06 PDT)
- FyD (Thu Sep 15 2011 - 00:23:58 PDT)
- Kk Zhu (Wed Sep 14 2011 - 19:48:36 PDT)
[AMBER] Help needed for Amber SCC-DFTB code
- Qiantao Wang (Wed Sep 21 2011 - 14:44:56 PDT)
- 杨立江 (Tue Sep 20 2011 - 22:45:23 PDT)
[AMBER] help! zinc parameters
- Kk Zhu (Mon Sep 19 2011 - 05:46:05 PDT)
[AMBER] help!!zinc parameters
- zhukk (Mon Sep 19 2011 - 04:55:16 PDT)
- steinbrt.rci.rutgers.edu (Fri Sep 16 2011 - 08:36:31 PDT)
- zhukk (Fri Sep 16 2011 - 08:16:17 PDT)
[AMBER] how NOT to label terminal residue
- David A Case (Fri Sep 30 2011 - 05:18:53 PDT)
- Victor Ma (Thu Sep 29 2011 - 14:24:45 PDT)
- Jason Swails (Thu Sep 29 2011 - 14:06:24 PDT)
- Victor Ma (Thu Sep 29 2011 - 13:54:44 PDT)
[AMBER] How to avoid Zn parametrization?
- FyD (Thu Sep 15 2011 - 00:10:18 PDT)
- Andrew Voronkov (Wed Sep 14 2011 - 03:18:08 PDT)
[AMBER] How to build the surface of crystalline cellulose?
- Lachele Foley (Lists) (Wed Sep 21 2011 - 06:06:16 PDT)
- bin wang (Mon Sep 19 2011 - 20:19:31 PDT)
- bin wang (Mon Sep 19 2011 - 15:16:44 PDT)
[AMBER] How to extract time angle, time, Energy from for MBAR analysis?
- Brian Radak (Wed Sep 14 2011 - 07:01:18 PDT)
- Catein Catherine (Wed Sep 14 2011 - 06:37:53 PDT)
[AMBER] how to fill in missing parameters in tleap?
- Yun Shi (Wed Sep 14 2011 - 22:07:21 PDT)
- Astrid Maaß (Mon Sep 12 2011 - 06:11:15 PDT)
- Yun Shi (Fri Sep 09 2011 - 16:51:48 PDT)
- Astrid Maaß (Fri Sep 09 2011 - 04:24:22 PDT)
- Yun Shi (Thu Sep 08 2011 - 23:47:16 PDT)
- Astrid Maaß (Thu Sep 08 2011 - 23:24:15 PDT)
- Yun Shi (Thu Sep 08 2011 - 13:50:55 PDT)
- Astrid Maaß (Wed Sep 07 2011 - 00:14:07 PDT)
- Yun Shi (Tue Sep 06 2011 - 11:22:06 PDT)
- Yun Shi (Tue Sep 06 2011 - 08:21:18 PDT)
- Astrid Maaß (Tue Sep 06 2011 - 02:07:37 PDT)
- Yun Shi (Mon Sep 05 2011 - 16:22:19 PDT)
[AMBER] how to generate a correlation matrix for both protein and substrate atoms
- Daniel Roe (Fri Sep 23 2011 - 04:40:38 PDT)
- sunxi.comcast.net (Thu Sep 22 2011 - 22:08:13 PDT)
[AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1
- case (Wed Sep 07 2011 - 12:41:32 PDT)
- FyD (Tue Sep 06 2011 - 08:01:41 PDT)
- George A. Khoury (Tue Sep 06 2011 - 07:00:43 PDT)
[AMBER] How to interpret GLYCAM prep file?
- Lachele Foley (Lists) (Thu Sep 15 2011 - 07:37:15 PDT)
- FyD (Thu Sep 15 2011 - 00:54:20 PDT)
- Yun Shi (Wed Sep 14 2011 - 16:49:42 PDT)
- Lachele Foley (Lists) (Fri Sep 09 2011 - 07:52:18 PDT)
- Yun Shi (Thu Sep 08 2011 - 23:38:15 PDT)
[AMBER] How to mutate nucleobases
- Rajesh Raju (Sat Sep 17 2011 - 09:41:08 PDT)
- Sangita Kachhap (Sat Sep 17 2011 - 09:03:04 PDT)
- Rajesh Raju (Fri Sep 16 2011 - 13:42:13 PDT)
[AMBER] How to recover rst or can I readin mdcrd for a MD by -c?
- Catein Catherine (Sat Sep 24 2011 - 23:03:19 PDT)
- Bruno Rodrigues (Sat Sep 24 2011 - 05:37:50 PDT)
- Catein Catherine (Fri Sep 23 2011 - 19:18:57 PDT)
[AMBER] How to start with
- Jason Swails (Fri Sep 16 2011 - 09:51:16 PDT)
- aiswarya.pawar.gmail.com (Fri Sep 16 2011 - 06:19:24 PDT)
[AMBER] How to use WHAM to analysis Replica Exchange Simulations
- Andrew Jewett (Tue Sep 06 2011 - 15:47:21 PDT)
- Daniel Sindhikara (Tue Sep 06 2011 - 15:28:54 PDT)
- Brian Radak (Tue Sep 06 2011 - 08:49:57 PDT)
- Catein Catherine (Tue Sep 06 2011 - 07:20:41 PDT)
[AMBER] hydrogen boding and PBC
- Vijay Manickam Achari (Tue Sep 06 2011 - 03:19:02 PDT)
[AMBER] hydrogen bonding
- Vijay Manickam Achari (Fri Sep 23 2011 - 21:17:29 PDT)
- Daniel Roe (Fri Sep 23 2011 - 07:56:17 PDT)
- Vijay Manickam Achari (Fri Sep 23 2011 - 05:17:06 PDT)
- Sara Ahmadi (Thu Sep 08 2011 - 04:22:34 PDT)
[AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
- Jason Swails (Tue Sep 20 2011 - 21:39:16 PDT)
- Robert Konecny (Tue Sep 20 2011 - 20:22:46 PDT)
- Jason Swails (Tue Sep 20 2011 - 15:19:31 PDT)
- Kenneth Tussey (Tue Sep 20 2011 - 15:05:00 PDT)
- Jason Swails (Tue Sep 20 2011 - 14:50:51 PDT)
- Kenneth Tussey (Tue Sep 20 2011 - 13:12:07 PDT)
- Jason Swails (Mon Sep 19 2011 - 15:22:23 PDT)
- Kenneth Tussey (Mon Sep 19 2011 - 13:47:21 PDT)
[AMBER] ICST
- David A Case (Thu Sep 22 2011 - 06:13:56 PDT)
- truongco nguyen (Thu Sep 22 2011 - 02:10:49 PDT)
[AMBER] Initial plateau of the radial distribution function
- Massimiliano Porrini (Fri Sep 16 2011 - 03:16:23 PDT)
[AMBER] inpcrd file
- Emmanuel Baribefe Naziga (Wed Sep 14 2011 - 17:12:39 PDT)
- fatahiya (Tue Sep 13 2011 - 23:47:04 PDT)
[AMBER] Instantaneous temperature in TI simulation
- Qiantao Wang (Wed Sep 28 2011 - 13:12:44 PDT)
- Brian Radak (Mon Sep 26 2011 - 06:05:47 PDT)
- Qiantao Wang (Sun Sep 25 2011 - 06:26:54 PDT)
- case (Sat Sep 24 2011 - 05:51:43 PDT)
- Brian Radak (Fri Sep 23 2011 - 13:07:58 PDT)
- Qiantao Wang (Fri Sep 23 2011 - 12:25:06 PDT)
- Qiantao Wang (Fri Sep 23 2011 - 12:08:41 PDT)
- Qiantao Wang (Wed Sep 21 2011 - 14:12:01 PDT)
- Brian Radak (Wed Sep 21 2011 - 13:44:41 PDT)
- Qiantao Wang (Wed Sep 21 2011 - 12:43:09 PDT)
- Brian Radak (Wed Sep 21 2011 - 06:40:07 PDT)
- David A Case (Wed Sep 21 2011 - 04:52:54 PDT)
- Jason Swails (Tue Sep 20 2011 - 13:08:49 PDT)
- Qiantao Wang (Tue Sep 20 2011 - 12:33:51 PDT)
- Brian Radak (Tue Sep 20 2011 - 11:23:48 PDT)
- Brian Radak (Tue Sep 20 2011 - 07:59:36 PDT)
- David A Case (Tue Sep 20 2011 - 07:33:55 PDT)
- Brian Radak (Tue Sep 20 2011 - 06:01:54 PDT)
[AMBER] intermolecular interaction
- su He (Fri Sep 09 2011 - 07:58:06 PDT)
- Jason Swails (Thu Sep 08 2011 - 21:00:41 PDT)
- su He (Thu Sep 08 2011 - 13:02:17 PDT)
[AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8?
- case (Tue Sep 06 2011 - 05:38:45 PDT)
- wrong string (Tue Sep 06 2011 - 01:09:06 PDT)
[AMBER] Large pressure fluctuations over the whole run
- case (Mon Sep 26 2011 - 19:19:59 PDT)
- Adrian Roitberg (Mon Sep 26 2011 - 15:25:32 PDT)
- Hernán Meier (Mon Sep 26 2011 - 15:04:51 PDT)
- Jason Swails (Thu Sep 22 2011 - 19:49:14 PDT)
- Hernán Meier (Thu Sep 22 2011 - 16:14:54 PDT)
[AMBER] libmkl_ia32.a missing from MKL em64t
- case (Wed Sep 07 2011 - 12:57:56 PDT)
- Aaron Greenwood (Wed Sep 07 2011 - 09:57:33 PDT)
[AMBER] load parmbsc0 and X-Ol for RNA
- David Condon (Sun Sep 25 2011 - 14:03:06 PDT)
- Catein Catherine (Fri Sep 23 2011 - 19:14:09 PDT)
- David A Case (Fri Sep 23 2011 - 13:10:33 PDT)
- David Condon (Fri Sep 23 2011 - 06:25:16 PDT)
[AMBER] mbondi3
- Jason Swails (Wed Sep 07 2011 - 12:48:41 PDT)
- Peter Varnai (Wed Sep 07 2011 - 10:28:39 PDT)
- Jason Swails (Tue Sep 06 2011 - 22:36:56 PDT)
- Carlos Simmerling (Tue Sep 06 2011 - 11:38:25 PDT)
- Peter Varnai (Tue Sep 06 2011 - 10:56:31 PDT)
[AMBER] Minimum distance
- RANAJIT SHINDE (Wed Sep 07 2011 - 00:00:24 PDT)
[AMBER] MM/GBSA question - pairwise decomposition
- Anselm Horn (Mon Sep 26 2011 - 12:11:55 PDT)
[AMBER] MM_PBSA triple trajectory approch
- Sangita Kachhap (Sun Sep 04 2011 - 00:03:16 PDT)
- Jason Swails (Sat Sep 03 2011 - 08:23:55 PDT)
- Bill Miller III (Sat Sep 03 2011 - 06:14:27 PDT)
- Sangita Kachhap (Sat Sep 03 2011 - 06:08:57 PDT)
- Bill Miller III (Sat Sep 03 2011 - 05:19:17 PDT)
- Sangita Kachhap (Sat Sep 03 2011 - 05:00:33 PDT)
[AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
- Jason Swails (Tue Sep 13 2011 - 20:12:07 PDT)
- Rajesh Raju (Tue Sep 13 2011 - 17:59:59 PDT)
- Jason Swails (Tue Sep 13 2011 - 17:43:17 PDT)
- David Case (Tue Sep 13 2011 - 16:59:58 PDT)
- Rajesh Raju (Tue Sep 13 2011 - 16:48:12 PDT)
[AMBER] MMPBSA Ala scan error
- Jesper Sørensen (Tue Sep 06 2011 - 12:14:28 PDT)
- Bill Miller III (Tue Sep 06 2011 - 04:31:49 PDT)
- Jesper Sørensen (Tue Sep 06 2011 - 01:16:25 PDT)
- Bill Miller III (Mon Sep 05 2011 - 13:53:29 PDT)
- Jesper Sørensen (Sun Sep 04 2011 - 23:41:04 PDT)
[AMBER] MMPBSA.py 3DRISM error
- Jason Swails (Sat Sep 24 2011 - 07:29:38 PDT)
- Jesper Soerensen (Fri Sep 23 2011 - 09:58:02 PDT)
- Jason Swails (Wed Sep 14 2011 - 19:15:25 PDT)
- Jason Swails (Wed Sep 14 2011 - 19:09:18 PDT)
- Jesper Soerensen (Wed Sep 14 2011 - 18:52:49 PDT)
[AMBER] MMPBSA.py discrepancies in results
- Bill Miller III (Thu Sep 29 2011 - 04:16:04 PDT)
- George Tzotzos (Thu Sep 29 2011 - 02:31:07 PDT)
- Jason Swails (Wed Sep 28 2011 - 15:22:06 PDT)
- George Tzotzos (Wed Sep 28 2011 - 14:43:57 PDT)
- Jason Swails (Wed Sep 28 2011 - 11:43:01 PDT)
- George Tzotzos (Wed Sep 28 2011 - 09:04:58 PDT)
- Bill Miller III (Wed Sep 28 2011 - 09:03:04 PDT)
- George Tzotzos (Wed Sep 28 2011 - 08:44:13 PDT)
- Jason Swails (Wed Sep 28 2011 - 08:23:33 PDT)
- George Tzotzos (Wed Sep 28 2011 - 07:43:42 PDT)
- Jason Swails (Wed Sep 28 2011 - 07:16:55 PDT)
- George Tzotzos (Wed Sep 28 2011 - 06:33:16 PDT)
- Bill Miller III (Wed Sep 28 2011 - 06:27:31 PDT)
- George Tzotzos (Wed Sep 28 2011 - 06:20:28 PDT)
[AMBER] MMPBSA.py energy decomposition inconsistencies
- Jason Swails (Fri Sep 16 2011 - 09:40:44 PDT)
- Antje Wolf (Fri Sep 16 2011 - 09:13:21 PDT)
- Jason Swails (Fri Sep 16 2011 - 07:03:30 PDT)
- Antje Wolf (Thu Sep 15 2011 - 23:51:40 PDT)
- Jason Swails (Thu Sep 15 2011 - 10:05:54 PDT)
- Antje Wolf (Thu Sep 15 2011 - 08:34:24 PDT)
- Jason Swails (Thu Sep 15 2011 - 07:15:29 PDT)
- Antje Wolf (Thu Sep 15 2011 - 05:13:17 PDT)
[AMBER] MMPBSA: how to include only some residues
- Jason Swails (Fri Sep 30 2011 - 16:40:28 PDT)
- Victor Ma (Fri Sep 30 2011 - 14:02:01 PDT)
[AMBER] Model building
- Sangita Kachhap (Thu Sep 29 2011 - 10:54:09 PDT)
- Aparna P (Thu Sep 29 2011 - 04:16:46 PDT)
- Daniel Roe (Tue Sep 27 2011 - 04:47:16 PDT)
- Aparna P (Mon Sep 26 2011 - 22:01:58 PDT)
- Aparna P (Sat Sep 24 2011 - 21:31:03 PDT)
- Daniel Roe (Fri Sep 23 2011 - 04:33:19 PDT)
- Aparna P (Fri Sep 23 2011 - 01:05:29 PDT)
- Daniel Roe (Thu Sep 22 2011 - 04:54:50 PDT)
- Aparna P (Thu Sep 22 2011 - 01:00:57 PDT)
[AMBER] Mol2 file creation
- Chidambar Kulkarni (Tue Sep 27 2011 - 09:05:04 PDT)
- David A Case (Tue Sep 27 2011 - 04:53:35 PDT)
- Chidambar Kulkarni (Mon Sep 26 2011 - 20:57:36 PDT)
[AMBER] moment of inertia
- peker milas (Tue Sep 06 2011 - 11:51:04 PDT)
- John S (Tue Sep 06 2011 - 11:27:40 PDT)
[AMBER] MPI version of MMPBSA
- Jason Swails (Thu Sep 08 2011 - 08:36:49 PDT)
- Siavoush Dastmalchi (Thu Sep 08 2011 - 02:05:16 PDT)
- Siavoush Dastmalchi (Thu Sep 08 2011 - 00:35:59 PDT)
[AMBER] NAB Module compilation error cpp failed
- Jason Swails (Mon Sep 05 2011 - 15:43:17 PDT)
- Rajesh Raju (Mon Sep 05 2011 - 10:36:00 PDT)
- Rajesh Raju (Mon Sep 05 2011 - 10:49:53 PDT)
[AMBER] Need Help! (TMD - NSCM - IWRAP reg!)
- Jason Swails (Wed Sep 14 2011 - 07:14:20 PDT)
- Fredrick Devadoss (Wed Sep 14 2011 - 06:51:22 PDT)
[AMBER] new residue parameters transfer
- Yong Duan (Tue Sep 20 2011 - 05:46:13 PDT)
- David A Case (Tue Sep 20 2011 - 04:48:08 PDT)
- Yao Yao (Mon Sep 19 2011 - 22:37:30 PDT)
[AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
- Marek Maly (Thu Sep 22 2011 - 04:58:49 PDT)
- Jason Swails (Wed Sep 21 2011 - 21:58:09 PDT)
- Marek Maly (Wed Sep 21 2011 - 16:11:28 PDT)
- Marek Maly (Wed Sep 21 2011 - 16:00:48 PDT)
- Bill Ross (Wed Sep 21 2011 - 12:24:56 PDT)
- Jason Swails (Wed Sep 21 2011 - 11:58:53 PDT)
- Marek Maly (Wed Sep 21 2011 - 11:19:15 PDT)
- Jason Swails (Wed Sep 21 2011 - 11:21:05 PDT)
- Marek Maly (Wed Sep 21 2011 - 10:56:43 PDT)
[AMBER] nmode calculations
- case (Sun Sep 25 2011 - 13:59:09 PDT)
- kirtana S (Sun Sep 25 2011 - 09:58:52 PDT)
- Jason Swails (Sat Sep 24 2011 - 17:17:02 PDT)
- kirtana S (Fri Sep 23 2011 - 14:52:11 PDT)
[AMBER] Non standard residue parameterization
- case (Tue Sep 06 2011 - 05:29:55 PDT)
- madhumita das (Mon Sep 05 2011 - 23:22:26 PDT)
- madhumita das (Mon Sep 05 2011 - 23:15:46 PDT)
- Bill Ross (Mon Sep 05 2011 - 20:50:19 PDT)
- case (Mon Sep 05 2011 - 17:18:11 PDT)
- madhumita das (Mon Sep 05 2011 - 08:47:30 PDT)
- Jason Swails (Fri Sep 02 2011 - 20:29:37 PDT)
- madhumita das (Fri Sep 02 2011 - 03:20:19 PDT)
[AMBER] non-bond interaction
- steinbrt.rci.rutgers.edu (Tue Sep 27 2011 - 00:07:12 PDT)
- Anglea A. (Tue Sep 27 2011 - 00:01:24 PDT)
[AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
- Jason Swails (Thu Sep 01 2011 - 12:37:21 PDT)
- InSuk Joung (Thu Sep 01 2011 - 12:16:56 PDT)
- Keith Yarem (Thu Sep 01 2011 - 11:40:54 PDT)
- Keith Yarem (Thu Sep 01 2011 - 11:23:03 PDT)
[AMBER] October 20 deadline for ACS COMP division awards for junior faculty and graduate students
- Carlos Simmerling (Tue Sep 13 2011 - 10:46:56 PDT)
[AMBER] On Cationic Dummy Atom
- Jason Swails (Thu Sep 29 2011 - 22:12:19 PDT)
- francesco oteri (Thu Sep 29 2011 - 02:26:32 PDT)
[AMBER] Parallel compile error of Amber11
- kurisaki (Tue Sep 27 2011 - 23:29:01 PDT)
- Jason Swails (Tue Sep 27 2011 - 20:40:06 PDT)
- kurisaki (Tue Sep 27 2011 - 20:30:52 PDT)
[AMBER] Parallel limit?
- Scott Le Grand (Thu Sep 29 2011 - 10:02:54 PDT)
- David A Case (Thu Sep 29 2011 - 05:32:26 PDT)
- Ross Walker (Wed Sep 28 2011 - 21:20:28 PDT)
- Jason Swails (Wed Sep 28 2011 - 21:14:09 PDT)
- Ross Walker (Wed Sep 28 2011 - 20:45:38 PDT)
- Hu Ge (Wed Sep 28 2011 - 20:31:37 PDT)
[AMBER] Parameter files :problem to save
- Ross Walker (Wed Sep 28 2011 - 21:48:40 PDT)
- Ross Walker (Wed Sep 28 2011 - 21:43:28 PDT)
- Jason Swails (Wed Sep 28 2011 - 21:39:38 PDT)
- souvik sur (Wed Sep 28 2011 - 21:20:48 PDT)
[AMBER] Parameters
- kirtana S (Fri Sep 30 2011 - 19:14:57 PDT)
[AMBER] Parameters for Boron containing molecules
- gal.fradin.live.biu.ac.il (Sat Sep 10 2011 - 21:57:43 PDT)
- Jason Swails (Thu Sep 08 2011 - 08:39:58 PDT)
- gal.fradin.live.biu.ac.il (Thu Sep 08 2011 - 05:08:16 PDT)
[AMBER] Parameters from Jaguar output
- Kshatresh Dutta Dubey (Mon Sep 12 2011 - 22:09:29 PDT)
[AMBER] PBS script
- Bruno Rodrigues (Thu Sep 08 2011 - 21:38:58 PDT)
- Bruno Rodrigues (Thu Sep 08 2011 - 21:36:12 PDT)
[AMBER] pbsa
- Ray Luo, Ph.D. (Tue Sep 13 2011 - 11:50:31 PDT)
- kirtana S (Mon Sep 12 2011 - 19:01:17 PDT)
- Jason Swails (Mon Sep 12 2011 - 12:22:37 PDT)
- kirtana S (Mon Sep 12 2011 - 11:42:44 PDT)
- kirtana S (Mon Sep 12 2011 - 09:05:17 PDT)
- Ray Luo, Ph.D. (Mon Sep 12 2011 - 09:00:20 PDT)
- kirtana S (Mon Sep 12 2011 - 08:56:44 PDT)
[AMBER] PCA
- Jason Swails (Wed Sep 28 2011 - 22:31:11 PDT)
- Linda catherine (Wed Sep 28 2011 - 04:44:31 PDT)
[AMBER] PMEMD job was aborted
- kurisaki (Wed Sep 28 2011 - 01:53:09 PDT)
- Ross Walker (Wed Sep 28 2011 - 00:09:52 PDT)
- kurisaki (Wed Sep 28 2011 - 00:00:15 PDT)
[AMBER] PNEB on GPUs
- Jason Swails (Thu Sep 29 2011 - 06:13:45 PDT)
- William Cantara (Thu Sep 29 2011 - 06:03:45 PDT)
- Christina Bergonzo (Thu Sep 29 2011 - 05:25:59 PDT)
- Jason Swails (Wed Sep 28 2011 - 21:35:29 PDT)
- Ross Walker (Wed Sep 28 2011 - 21:16:06 PDT)
- Jason Swails (Wed Sep 28 2011 - 21:09:36 PDT)
- Jason Swails (Wed Sep 28 2011 - 21:02:32 PDT)
- Ross Walker (Wed Sep 28 2011 - 21:01:50 PDT)
- William Cantara (Wed Sep 28 2011 - 20:20:30 PDT)
[AMBER] Print Dipole Moment in Centriod MD
- Wei Lin (Wed Sep 14 2011 - 20:56:20 PDT)
[AMBER] Proble related to correlation function
- InSuk Joung (Wed Sep 07 2011 - 11:26:16 PDT)
- Sindrila Dutta banik (Wed Sep 07 2011 - 10:51:17 PDT)
[AMBER] problem in installing xleap
- sonali dhindwal (Sat Sep 03 2011 - 07:08:30 PDT)
- case (Sat Sep 03 2011 - 05:57:44 PDT)
- sonali dhindwal (Sat Sep 03 2011 - 04:49:21 PDT)
- peker milas (Fri Sep 02 2011 - 10:21:38 PDT)
- Ismail, Mohd F. (Fri Sep 02 2011 - 09:20:04 PDT)
- sonali dhindwal (Fri Sep 02 2011 - 06:58:08 PDT)
- David A Case (Thu Sep 01 2011 - 05:07:57 PDT)
- Ismail, Mohd F. (Wed Aug 31 2011 - 23:35:56 PDT)
- sonali dhindwal (Wed Aug 31 2011 - 21:38:20 PDT)
[AMBER] problem while using Antechamber
- sonali dhindwal (Mon Sep 05 2011 - 22:19:17 PDT)
- case (Mon Sep 05 2011 - 17:16:34 PDT)
- sonali dhindwal (Mon Sep 05 2011 - 07:21:24 PDT)
[AMBER] problem with MM-PBSA
- Bill Miller III (Wed Sep 07 2011 - 10:56:31 PDT)
- Maryam Hamzehee (Wed Sep 07 2011 - 10:45:20 PDT)
- Bill Miller III (Tue Sep 06 2011 - 04:39:22 PDT)
- Maryam Hamzehee (Tue Sep 06 2011 - 01:55:41 PDT)
[AMBER] Problem with mmpbsa
- dhilip kumar ramalingam (Tue Sep 13 2011 - 05:50:09 PDT)
- Bill Miller III (Tue Sep 13 2011 - 05:50:37 PDT)
- Devlina Chakravarty (Tue Sep 13 2011 - 05:33:33 PDT)
[AMBER] problem with nmodes calculation-260-residue protein
- case (Sat Sep 24 2011 - 05:58:05 PDT)
- hongphuc nguyen (Fri Sep 23 2011 - 02:15:37 PDT)
[AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
- Ross Walker (Mon Sep 19 2011 - 08:05:02 PDT)
- Ross Walker (Mon Sep 19 2011 - 08:00:27 PDT)
- Himanshu Joshi (Mon Sep 19 2011 - 03:49:05 PDT)
- Himanshu Joshi (Mon Sep 19 2011 - 02:29:31 PDT)
- Ross Walker (Sat Sep 17 2011 - 16:50:40 PDT)
- Himanshu Joshi (Fri Sep 16 2011 - 23:29:40 PDT)
- Himanshu Joshi (Fri Sep 16 2011 - 23:24:49 PDT)
[AMBER] problem with TI calculations
- David A Case (Wed Sep 21 2011 - 04:50:38 PDT)
- Victor Ma (Tue Sep 20 2011 - 12:08:03 PDT)
[AMBER] Problems of Hbond calculation
- Bruno Rodrigues (Mon Sep 26 2011 - 05:39:53 PDT)
- qiao xue (Sun Sep 25 2011 - 19:30:33 PDT)
[AMBER] Problems with parsing .PSF files by ptraj
- Marc van der Kamp (Fri Sep 16 2011 - 03:14:02 PDT)
[AMBER] problems with prmtops & MMGBSA
- Jason Swails (Fri Sep 09 2011 - 20:12:44 PDT)
- Romelia Salomon (Fri Sep 09 2011 - 18:23:54 PDT)
- Irene Newhouse (Fri Sep 09 2011 - 18:05:58 PDT)
[AMBER] ptraj
- Thomas Cheatham (Fri Sep 16 2011 - 06:25:44 PDT)
- Linda catherine (Fri Sep 16 2011 - 06:03:14 PDT)
[AMBER] ptraj clustering
- Thomas Cheatham III (Mon Sep 12 2011 - 13:37:55 PDT)
- George Tzotzos (Mon Sep 12 2011 - 13:26:03 PDT)
- Thomas Cheatham (Mon Sep 12 2011 - 12:13:35 PDT)
- George Tzotzos (Mon Sep 12 2011 - 08:02:40 PDT)
[AMBER] PTRAJ strange behavior
- peker milas (Thu Sep 01 2011 - 12:39:38 PDT)
[AMBER] ptraj: problem with distance and multi-atom masks
- Marc van der Kamp (Tue Sep 20 2011 - 07:24:07 PDT)
- Daniel Roe (Tue Sep 20 2011 - 04:37:00 PDT)
- Marc van der Kamp (Tue Sep 20 2011 - 02:32:34 PDT)
- Daniel Roe (Mon Sep 19 2011 - 09:44:48 PDT)
- Marc van der Kamp (Mon Sep 19 2011 - 02:32:47 PDT)
[AMBER] pulling DNA
- amir abbasi (Wed Sep 14 2011 - 05:38:39 PDT)
[AMBER] QM-MM atoms input
- Jason Swails (Mon Sep 12 2011 - 06:00:13 PDT)
- Marc van der Kamp (Mon Sep 12 2011 - 05:12:26 PDT)
- Shruti Koulgi (Mon Sep 12 2011 - 04:18:03 PDT)
- Shruti Koulgi (Mon Sep 12 2011 - 04:00:58 PDT)
[AMBER] Query regarding MMPBSA in Amber11
- Jason Swails (Thu Sep 29 2011 - 22:11:13 PDT)
- Hirdesh Kumar (Thu Sep 29 2011 - 21:28:11 PDT)
- Jason Swails (Thu Sep 29 2011 - 06:53:18 PDT)
- Hirdesh Kumar (Thu Sep 29 2011 - 01:54:29 PDT)
- Jason Swails (Wed Sep 28 2011 - 22:36:25 PDT)
- Hirdesh Kumar (Wed Sep 28 2011 - 21:47:34 PDT)
[AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks
- Scott Le Grand (Fri Sep 30 2011 - 11:04:28 PDT)
- Gould, Ian R (Fri Sep 30 2011 - 08:15:36 PDT)
[AMBER] Radial distribution
- kirtana S (Fri Sep 16 2011 - 10:09:19 PDT)
[AMBER] radial distribution function
- Thomas Cheatham III (Mon Sep 19 2011 - 16:04:23 PDT)
- Massimiliano Porrini (Sun Sep 18 2011 - 10:15:21 PDT)
- Thomas Cheatham (Fri Sep 16 2011 - 06:13:47 PDT)
- Massimiliano Porrini (Thu Sep 15 2011 - 05:27:03 PDT)
[AMBER] Regarding Force field
- David A Case (Mon Sep 26 2011 - 05:03:26 PDT)
- souvik sur (Sun Sep 25 2011 - 22:28:36 PDT)
[AMBER] replace unit in leap
- tsurma.umich.edu (Tue Sep 06 2011 - 08:41:00 PDT)
- case (Mon Sep 05 2011 - 17:11:46 PDT)
- tsurma.umich.edu (Sun Sep 04 2011 - 10:56:05 PDT)
- tsurma.umich.edu (Sun Sep 04 2011 - 09:59:45 PDT)
[AMBER] Residence time
- Carlos Simmerling (Wed Sep 07 2011 - 11:53:49 PDT)
- aiswarya pawar (Wed Sep 07 2011 - 04:18:14 PDT)
- Carlos Simmerling (Wed Sep 07 2011 - 04:08:13 PDT)
- aiswarya pawar (Wed Sep 07 2011 - 00:14:18 PDT)
[AMBER] residue list
- Jason Swails (Sun Sep 11 2011 - 20:48:31 PDT)
- kirtana S (Sun Sep 11 2011 - 19:40:52 PDT)
[AMBER] Residue transformation
- M. L. Dodson (Mon Sep 12 2011 - 20:52:35 PDT)
- Bruno Rodrigues (Mon Sep 12 2011 - 20:16:48 PDT)
- Fabrício Bracht (Mon Sep 12 2011 - 15:10:10 PDT)
[AMBER] RESP charge fitting
- FyD (Fri Sep 23 2011 - 05:21:13 PDT)
- shome sankar bhunia (Fri Sep 23 2011 - 04:22:37 PDT)
[AMBER] Restart-Files in Sander
- Brian Radak (Thu Sep 22 2011 - 06:25:48 PDT)
- Julian Zachmann (Thu Sep 22 2011 - 06:11:00 PDT)
[AMBER] Restrain of atoms during MD simulation
- Sindrila Dutta banik (Wed Sep 07 2011 - 00:37:16 PDT)
[AMBER] results from independent simulations
- Wu Xu (Thu Sep 08 2011 - 05:18:55 PDT)
- Daniel Sindhikara (Wed Sep 07 2011 - 21:13:22 PDT)
- Jason Swails (Wed Sep 07 2011 - 09:02:18 PDT)
- Wu Xu (Wed Sep 07 2011 - 08:51:48 PDT)
- Simon Becker (Wed Sep 07 2011 - 02:58:54 PDT)
- Jason Swails (Wed Sep 07 2011 - 02:17:31 PDT)
- Wu Xu (Tue Sep 06 2011 - 17:37:25 PDT)
[AMBER] RMSD
- Daniel Roe (Tue Sep 27 2011 - 05:43:10 PDT)
- fatahiya (Mon Sep 26 2011 - 19:08:39 PDT)
- Bruno Rodrigues (Mon Sep 26 2011 - 05:35:51 PDT)
- fatahiya (Sun Sep 25 2011 - 22:00:59 PDT)
- Daniel Roe (Thu Sep 22 2011 - 04:42:56 PDT)
- Aparna P (Thu Sep 22 2011 - 02:14:39 PDT)
- fatahiya (Wed Sep 21 2011 - 23:13:02 PDT)
[AMBER] rst or mdcrd file to view the structures?
- Chinh Su Tran To (Tue Sep 20 2011 - 22:30:17 PDT)
- Bill Ross (Tue Sep 20 2011 - 10:24:03 PDT)
- Chinh Su Tran To (Tue Sep 20 2011 - 00:54:30 PDT)
- steinbrt.rci.rutgers.edu (Tue Sep 20 2011 - 00:25:51 PDT)
- Chinh Su Tran To (Mon Sep 19 2011 - 22:47:38 PDT)
- Bill Ross (Mon Sep 19 2011 - 20:36:33 PDT)
- Chinh Su Tran To (Mon Sep 19 2011 - 19:44:37 PDT)
- steinbrt.rci.rutgers.edu (Mon Sep 19 2011 - 04:22:22 PDT)
- Chinh Su Tran To (Mon Sep 19 2011 - 03:00:53 PDT)
- steinbrt.rci.rutgers.edu (Mon Sep 19 2011 - 00:38:41 PDT)
- Chinh Su Tran To (Sun Sep 18 2011 - 22:34:54 PDT)
[AMBER] Run Amber on a system with multiple GPUs
- Sasha Buzko (Fri Sep 02 2011 - 16:27:21 PDT)
- peter.stauffert.boehringer-ingelheim.com (Fri Sep 02 2011 - 10:55:35 PDT)
[AMBER] Run amber on Cluster
- Lianhu Wei (Wed Sep 14 2011 - 11:10:28 PDT)
- Ross Walker (Wed Sep 14 2011 - 10:14:02 PDT)
- Lianhu Wei (Wed Sep 14 2011 - 08:01:37 PDT)
- Jason Swails (Tue Sep 13 2011 - 14:38:50 PDT)
- Lianhu Wei (Tue Sep 13 2011 - 12:46:17 PDT)
[AMBER] Running amber v11 over multiple gpus/nodes
- Ross Walker (Fri Sep 16 2011 - 09:30:58 PDT)
- Baker D.J. (Fri Sep 16 2011 - 00:47:39 PDT)
- Ross Walker (Wed Sep 14 2011 - 10:55:03 PDT)
- Baker D.J. (Wed Sep 14 2011 - 08:18:03 PDT)
- peter.stauffert.boehringer-ingelheim.com (Wed Sep 14 2011 - 04:37:00 PDT)
- Baker D.J. (Wed Sep 14 2011 - 04:14:25 PDT)
[AMBER] sander mpi error when unfolding the protein
- Chinh Su Tran To (Thu Sep 29 2011 - 03:00:46 PDT)
- steinbrt.rci.rutgers.edu (Thu Sep 29 2011 - 02:23:53 PDT)
- Chinh Su Tran To (Thu Sep 29 2011 - 01:10:59 PDT)
- steinbrt.rci.rutgers.edu (Thu Sep 29 2011 - 00:55:22 PDT)
- Chinh Su Tran To (Thu Sep 29 2011 - 00:43:24 PDT)
[AMBER] sander outout using mdin=5 and idecomp=2
- kurisaki (Wed Sep 28 2011 - 07:01:13 PDT)
- kurisaki (Wed Sep 28 2011 - 06:37:57 PDT)
- Jason Swails (Wed Sep 28 2011 - 05:58:29 PDT)
- kurisaki (Wed Sep 28 2011 - 02:13:18 PDT)
[AMBER] sander/amoeba parameter format
- Andrew Petersen (Thu Sep 22 2011 - 09:53:40 PDT)
[AMBER] SASA calculation in Amber
- Jason Swails (Wed Sep 21 2011 - 10:33:56 PDT)
- Horacio Pérez-Sánchez (Wed Sep 21 2011 - 09:45:19 PDT)
[AMBER] scaling factors in carbohydrate-protein interaction
- FyD (Tue Sep 20 2011 - 00:54:21 PDT)
- Ross Walker (Sun Sep 18 2011 - 18:13:59 PDT)
- Lachele Foley (Lists) (Sun Sep 18 2011 - 15:12:36 PDT)
- FyD (Sat Sep 17 2011 - 23:14:46 PDT)
- Lachele Foley (Lists) (Sat Sep 17 2011 - 19:22:31 PDT)
- Yun Shi (Sat Sep 17 2011 - 15:43:52 PDT)
[AMBER] Self-Diffusion coefficient
- Bruno Rodrigues (Tue Sep 20 2011 - 11:13:53 PDT)
- Thomas Cheatham III (Mon Sep 19 2011 - 15:50:20 PDT)
- Bruno Rodrigues (Mon Sep 19 2011 - 14:43:31 PDT)
[AMBER] Serial Version of libFpbsa.a
- Ross Walker (Fri Sep 16 2011 - 11:27:37 PDT)
- Aaron Greenwood (Fri Sep 16 2011 - 11:15:02 PDT)
[AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
- Rajesh Raju (Sun Sep 18 2011 - 11:34:22 PDT)
- Jason Swails (Sun Sep 18 2011 - 02:21:57 PDT)
- Rajesh Raju (Sat Sep 17 2011 - 14:16:34 PDT)
- Bill Miller III (Sat Sep 17 2011 - 13:55:51 PDT)
- Rajesh Raju (Sat Sep 17 2011 - 13:43:31 PDT)
[AMBER] SHAKE error help
- tsurma.umich.edu (Wed Sep 14 2011 - 08:21:23 PDT)
- case (Sat Sep 10 2011 - 17:17:26 PDT)
- tsurma.umich.edu (Sat Sep 10 2011 - 11:49:10 PDT)
- case (Fri Sep 09 2011 - 14:43:43 PDT)
- tsurma.umich.edu (Fri Sep 09 2011 - 12:35:42 PDT)
- tsurma.umich.edu (Tue Sep 06 2011 - 08:43:08 PDT)
- tsurma.umich.edu (Mon Sep 05 2011 - 07:43:45 PDT)
- case (Mon Sep 05 2011 - 05:51:58 PDT)
- tsurma.umich.edu (Sat Sep 03 2011 - 14:35:49 PDT)
- case (Sat Sep 03 2011 - 11:05:41 PDT)
- tsurma.umich.edu (Sat Sep 03 2011 - 09:22:39 PDT)
- case (Sat Sep 03 2011 - 05:50:13 PDT)
- Bill Ross (Fri Sep 02 2011 - 21:09:54 PDT)
- tsurma.umich.edu (Fri Sep 02 2011 - 19:28:08 PDT)
[AMBER] Sleap : amoeba and gaff
- Wei Zhang (Mon Sep 05 2011 - 14:13:20 PDT)
- Guenegou, Guillaume [JRDFR] (Mon Sep 05 2011 - 05:10:45 PDT)
[AMBER] Sleap and TIP4P BOX
- Guenegou, Guillaume [JRDFR] (Fri Sep 23 2011 - 06:48:05 PDT)
- David A Case (Fri Sep 23 2011 - 06:20:18 PDT)
- Guenegou, Guillaume [JRDFR] (Fri Sep 23 2011 - 00:22:42 PDT)
- David A Case (Thu Sep 22 2011 - 05:59:31 PDT)
- Guenegou, Guillaume [JRDFR] (Wed Sep 21 2011 - 07:07:57 PDT)
- David A Case (Wed Sep 21 2011 - 06:39:29 PDT)
- Guenegou, Guillaume [JRDFR] (Wed Sep 21 2011 - 04:42:51 PDT)
[AMBER] SMD: restraints on the pulled apart interacting proteins
- Sergey Samsonov (Fri Sep 09 2011 - 07:39:36 PDT)
[AMBER] solvateBox
- Ismail, Mohd F. (Fri Sep 02 2011 - 09:07:36 PDT)
- Jason Swails (Thu Sep 01 2011 - 22:42:52 PDT)
- Ismail, Mohd F. (Thu Sep 01 2011 - 21:02:52 PDT)
- Jason Swails (Thu Sep 01 2011 - 20:51:13 PDT)
- Ismail, Mohd F. (Thu Sep 01 2011 - 20:36:33 PDT)
- Jason Swails (Thu Sep 01 2011 - 18:54:44 PDT)
- Jason Swails (Thu Sep 01 2011 - 18:49:07 PDT)
- Ismail, Mohd F. (Thu Sep 01 2011 - 14:18:12 PDT)
[AMBER] solvateBox or setBox or set box
- David A Case (Wed Sep 28 2011 - 05:17:24 PDT)
- Neha Gandhi (Tue Sep 27 2011 - 23:36:29 PDT)
[AMBER] Solvent model charges off by factor of 18.2223 or typo?
- Daniel Sindhikara (Sun Sep 25 2011 - 23:57:08 PDT)
[AMBER] Some common doubts about MMPBSA.py decomposition
- Rajesh Raju (Mon Sep 26 2011 - 18:13:08 PDT)
- Jason Swails (Mon Sep 26 2011 - 17:45:24 PDT)
- Rajesh Raju (Mon Sep 26 2011 - 12:24:36 PDT)
[AMBER] Some question regarding force field for periodic system
- Carlos Simmerling (Wed Sep 07 2011 - 04:09:38 PDT)
- jun kit (Tue Sep 06 2011 - 21:24:02 PDT)
[AMBER] some questions on GAFF
- su He (Fri Sep 02 2011 - 13:25:22 PDT)
- Chirag Vora (Fri Sep 02 2011 - 13:13:07 PDT)
- su He (Fri Sep 02 2011 - 12:58:06 PDT)
[AMBER] Sufficient CPU cores/GPU ratio ?
- Marek Maly (Wed Sep 21 2011 - 11:10:06 PDT)
- Jodi Ann Hadden (Wed Sep 21 2011 - 10:54:08 PDT)
- Marek Maly (Sun Sep 18 2011 - 07:34:21 PDT)
- Ross Walker (Sat Sep 17 2011 - 17:01:49 PDT)
- Marek Maly (Sat Sep 17 2011 - 16:08:48 PDT)
- Jodi Ann Hadden (Fri Sep 16 2011 - 11:39:03 PDT)
- Marek Maly (Wed Sep 14 2011 - 18:01:15 PDT)
- Scott Le Grand (Wed Sep 14 2011 - 17:51:33 PDT)
- Marek Maly (Wed Sep 14 2011 - 17:15:32 PDT)
- Jodi Ann Hadden (Wed Sep 14 2011 - 08:50:21 PDT)
- Marek Maly (Tue Sep 13 2011 - 13:47:09 PDT)
- Scott Le Grand (Tue Sep 13 2011 - 12:50:30 PDT)
- Marek Maly (Tue Sep 13 2011 - 11:41:28 PDT)
- Ross Walker (Tue Sep 13 2011 - 11:40:56 PDT)
- Ross Walker (Tue Sep 13 2011 - 11:40:56 PDT)
- Marek Maly (Tue Sep 13 2011 - 11:06:09 PDT)
- Marek Maly (Tue Sep 13 2011 - 11:00:47 PDT)
- Scott Le Grand (Tue Sep 13 2011 - 11:15:27 PDT)
- Marek Maly (Tue Sep 13 2011 - 10:50:02 PDT)
- Gould, Ian R (Tue Sep 13 2011 - 11:04:32 PDT)
- peter.stauffert.boehringer-ingelheim.com (Tue Sep 13 2011 - 10:57:29 PDT)
- Marek Maly (Tue Sep 13 2011 - 10:17:12 PDT)
- Ross Walker (Tue Sep 13 2011 - 10:25:20 PDT)
- Marek Maly (Tue Sep 13 2011 - 09:52:55 PDT)
- Ross Walker (Tue Sep 13 2011 - 09:53:34 PDT)
- Marek Maly (Tue Sep 13 2011 - 07:34:01 PDT)
- dhilip kumar ramalingam (Tue Sep 13 2011 - 07:45:57 PDT)
- Marek Maly (Tue Sep 13 2011 - 07:19:29 PDT)
[AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
- Ross Walker (Thu Sep 29 2011 - 07:38:08 PDT)
- Jan-Philip Gehrcke (Thu Sep 29 2011 - 04:00:16 PDT)
- Ross Walker (Wed Sep 28 2011 - 19:01:08 PDT)
[AMBER] the result of pseudorotation angle
- case (Sat Sep 10 2011 - 06:01:47 PDT)
- clwg (Sat Sep 10 2011 - 01:31:08 PDT)
[AMBER] thermodynamic integration on protein mutation
- Jorge Iulek (Tue Sep 27 2011 - 09:09:59 PDT)
- case (Mon Sep 26 2011 - 19:22:06 PDT)
- Jorge Iulek (Mon Sep 26 2011 - 17:34:51 PDT)
[AMBER] TI and MM-GBSA results
- Jason Swails (Wed Sep 14 2011 - 10:49:33 PDT)
- manikanthan bhavaraju (Wed Sep 14 2011 - 10:46:04 PDT)
- Ray Luo, Ph.D. (Wed Sep 14 2011 - 10:21:32 PDT)
- manikanthan bhavaraju (Tue Sep 13 2011 - 17:33:06 PDT)
[AMBER] tleap command "set default Dielectric constant" not valid?
- Yongmei Wang (ywang) (Thu Sep 15 2011 - 12:13:22 PDT)
- David A Case (Thu Sep 15 2011 - 12:04:17 PDT)
- Yongmei Wang (ywang) (Wed Sep 14 2011 - 21:33:29 PDT)
[AMBER] topology and coordinate files
- madhumita das (Tue Sep 20 2011 - 04:14:58 PDT)
[AMBER] turning on 1-2 and 1-3 interactions
- Jason Swails (Thu Sep 08 2011 - 11:54:22 PDT)
- Bill Ross (Thu Sep 08 2011 - 10:54:42 PDT)
- Steven Burger (Thu Sep 08 2011 - 10:46:26 PDT)
[AMBER] tx/LEaP numlock.
- Ross Walker (Tue Sep 20 2011 - 09:38:01 PDT)
[AMBER] umbrella sampling with amber10
- Qian Wang (Tue Sep 06 2011 - 13:42:28 PDT)
[AMBER] undefined reference
- David A Case (Tue Sep 13 2011 - 10:01:42 PDT)
- Lars Skjærven (Tue Sep 13 2011 - 07:03:39 PDT)
- David A Case (Tue Sep 13 2011 - 06:45:10 PDT)
- Lars Skjærven (Tue Sep 13 2011 - 05:48:56 PDT)
[AMBER] Unit of the partial charge as given in the topology file
- Jason Swails (Mon Sep 19 2011 - 11:56:29 PDT)
- Sindrila Dutta banik (Mon Sep 19 2011 - 11:47:26 PDT)
[AMBER] unsubscribe
- Yongmei Wang (ywang) (Fri Sep 16 2011 - 09:48:03 PDT)
[AMBER] velocity modification in PMEMD, CUDA version
- Chen, Changjun (Fri Sep 09 2011 - 03:04:15 PDT)
- Jason Swails (Tue Sep 06 2011 - 22:34:27 PDT)
- Chen, Changjun (Tue Sep 06 2011 - 20:15:42 PDT)
- Ross Walker (Tue Sep 06 2011 - 20:10:29 PDT)
- Chen, Changjun (Mon Sep 05 2011 - 19:29:29 PDT)
[AMBER] visualization of secstruc with e.g. gnuplot
- Anselm Horn (Tue Sep 13 2011 - 11:23:50 PDT)
- steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 06:20:05 PDT)
- Nadine Utz (Tue Sep 13 2011 - 04:07:16 PDT)
[AMBER] vlimit exeeding problem
- Aparna P (Tue Sep 13 2011 - 04:24:07 PDT)
- Ross Walker (Mon Sep 12 2011 - 22:57:43 PDT)
- Aparna P (Mon Sep 12 2011 - 22:46:22 PDT)
- Ross Walker (Mon Sep 12 2011 - 22:16:19 PDT)
- Aparna P (Mon Sep 12 2011 - 22:04:17 PDT)
- manikanthan bhavaraju (Mon Sep 12 2011 - 08:05:30 PDT)
- Aparna P (Sun Sep 11 2011 - 23:46:33 PDT)
[AMBER] Water density/potential visualization
- Daniel Sindhikara (Thu Sep 08 2011 - 22:16:49 PDT)
- Ozen, Aysegul (Thu Sep 08 2011 - 10:57:03 PDT)
- Abhishek Mukhopadhyay (Thu Sep 08 2011 - 09:56:54 PDT)
[AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation?
- Catein Catherine (Mon Sep 12 2011 - 10:33:58 PDT)
- Jason Swails (Mon Sep 12 2011 - 05:54:51 PDT)
- Catein Catherine (Sun Sep 11 2011 - 23:30:13 PDT)
[AMBER] writing box info to pdb file extracted from an mdcrd trajectory
- CHAMI F. (Wed Sep 07 2011 - 09:01:06 PDT)
- Mark Williamson (Wed Sep 07 2011 - 06:51:42 PDT)
- CHAMI F. (Fri Sep 02 2011 - 07:28:59 PDT)
[AMBER] X-PLOR formatted .psf in CHAMBER
- Marc van der Kamp (Thu Sep 15 2011 - 07:09:02 PDT)
- Marc van der Kamp (Thu Sep 15 2011 - 06:26:14 PDT)
- Thomas Cheatham (Thu Sep 15 2011 - 05:21:46 PDT)
- Marc van der Kamp (Thu Sep 15 2011 - 05:19:29 PDT)
[AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER
- Jiri Sponer (Fri Sep 23 2011 - 08:32:52 PDT)
- Qiantao Wang (Fri Sep 23 2011 - 07:41:08 PDT)
- Jason Swails (Thu Sep 22 2011 - 16:42:37 PDT)
- Rajesh Raju (Thu Sep 22 2011 - 16:24:39 PDT)
[AMBER] Xleap Installation
- Ben Roberts (Wed Sep 21 2011 - 06:51:05 PDT)
- Yao Yao (Tue Sep 20 2011 - 15:40:07 PDT)

Amber Archive Sep 2011 by subject