Amber Archive May 2011: by subject

[AMBER] A maximum of two parameters are acceptable
- kurisaki (Wed May 18 2011 - 05:57:53 PDT)
- case (Wed May 18 2011 - 05:47:31 PDT)
- kurisaki (Wed May 18 2011 - 02:41:40 PDT)
[AMBER] AMBER
- Shesh Nath (Tue May 31 2011 - 06:15:45 PDT)
- case (Mon May 30 2011 - 05:55:46 PDT)
- Shesh Nath (Mon May 30 2011 - 00:01:05 PDT)
[AMBER] Amber 10
- Eric Kaufmann (Tue May 17 2011 - 11:52:44 PDT)
[AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses
- Dean Cuebas (Fri May 20 2011 - 07:23:46 PDT)
- Bill Ross (Fri May 20 2011 - 00:25:03 PDT)
- case (Thu May 19 2011 - 19:35:36 PDT)
- Scott Le Grand (Thu May 19 2011 - 15:51:15 PDT)
- Ross Walker (Thu May 19 2011 - 14:16:16 PDT)
- filip fratev (Thu May 19 2011 - 13:19:46 PDT)
- Ross Walker (Thu May 19 2011 - 09:54:37 PDT)
- Scott Le Grand (Thu May 19 2011 - 07:52:27 PDT)
- filip fratev (Thu May 19 2011 - 07:23:13 PDT)
- Ross Walker (Wed May 18 2011 - 10:36:01 PDT)
- Qamar Nazir (Wed May 18 2011 - 03:38:21 PDT)
[AMBER] Amber 11 compilation
- Jason Swails (Mon May 09 2011 - 08:19:52 PDT)
- Guenegou, Guillaume [ORDFR] (Mon May 09 2011 - 07:52:31 PDT)
[AMBER] Amber order
- Jason Swails (Thu May 19 2011 - 11:29:33 PDT)
- Rupa Madyal (Thu May 19 2011 - 06:36:31 PDT)
[AMBER] AMBER scaling and Hardware Specs
- Ross Walker (Wed May 25 2011 - 09:29:45 PDT)
- David A. Case (Wed May 25 2011 - 02:10:00 PDT)
- Azat Mukhametov (Tue May 24 2011 - 19:03:46 PDT)
- Jason Swails (Tue May 24 2011 - 18:55:03 PDT)
- Azat Mukhametov (Tue May 24 2011 - 18:47:55 PDT)
- Carlos Simmerling (Tue May 24 2011 - 18:32:05 PDT)
- Ross Walker (Tue May 24 2011 - 18:31:25 PDT)
- Azat Mukhametov (Tue May 24 2011 - 18:15:09 PDT)
[AMBER] AMBER11 Installation on FEDORA 15
- Vivek Shankar Bharadwaj (Tue May 31 2011 - 19:35:34 PDT)
- case (Mon May 30 2011 - 18:43:38 PDT)
- Vivek Shankar Bharadwaj (Mon May 30 2011 - 09:36:02 PDT)
- case (Sun May 29 2011 - 10:54:46 PDT)
- Vivek Shankar Bharadwaj (Fri May 27 2011 - 10:00:21 PDT)
[AMBER] AmberTools 1.4 from Amber11 on MACOSX
- Jason Swails (Sat May 14 2011 - 15:02:57 PDT)
- Bruno Rodrigues (Sat May 14 2011 - 13:34:05 PDT)
- Jason Swails (Sat May 14 2011 - 12:56:22 PDT)
- Bruno Rodrigues (Sat May 14 2011 - 11:48:32 PDT)
[AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test
- Shan-ho Tsai (Tue May 03 2011 - 13:10:38 PDT)
[AMBER] AmberTools 1.5 and Amber11
- Ben Roberts (Wed May 25 2011 - 11:41:19 PDT)
- Daniel Roe (Wed May 25 2011 - 11:41:07 PDT)
- Massimiliano Porrini (Wed May 25 2011 - 11:35:30 PDT)
[AMBER] Ambertools 1.5 make install error
- David A. Case (Wed May 25 2011 - 07:44:27 PDT)
- Andre Serobian (Tue May 24 2011 - 13:31:04 PDT)
- Marc van der Kamp (Tue May 24 2011 - 09:22:14 PDT)
- Andre (Sun May 22 2011 - 03:04:15 PDT)
- Vlad Cojocaru (Sun May 22 2011 - 00:46:47 PDT)
- Andre Serobian (Sat May 21 2011 - 16:22:37 PDT)
[AMBER] ambpdb water removal for rst files
- Jason Swails (Sun May 29 2011 - 19:40:42 PDT)
- Bill Ross (Sun May 29 2011 - 17:27:36 PDT)
- Anselm Horn (Sun May 29 2011 - 13:00:12 PDT)
- Andrew Voronkov (Sun May 29 2011 - 10:35:32 PDT)
[AMBER] Amoeba Potential File Modifications
- David A Case (Thu May 12 2011 - 08:24:47 PDT)
- r smith (Mon May 09 2011 - 10:44:35 PDT)
[AMBER] Analysis of secondary structure
- Daniel Roe (Mon May 30 2011 - 12:36:15 PDT)
- Alessio Atzori (Mon May 30 2011 - 12:21:56 PDT)
[AMBER] antechamber ERROR
- Jason Swails (Wed May 18 2011 - 16:23:03 PDT)
- George Tzotzos (Wed May 18 2011 - 13:38:09 PDT)
- Jason Swails (Wed May 18 2011 - 12:49:07 PDT)
- George Tzotzos (Wed May 18 2011 - 12:27:37 PDT)
- Jason Swails (Wed May 18 2011 - 12:18:28 PDT)
- George Tzotzos (Wed May 18 2011 - 11:24:35 PDT)
[AMBER] Antechamber loading Problem
- Jason Swails (Sat May 07 2011 - 03:36:35 PDT)
- Jason Swails (Sat May 07 2011 - 03:04:08 PDT)
- Adrian Roitberg (Sat May 07 2011 - 00:48:04 PDT)
- souvik sur (Fri May 06 2011 - 21:01:27 PDT)
- David A Case (Fri May 06 2011 - 07:02:01 PDT)
- souvik sur (Fri May 06 2011 - 05:25:22 PDT)
[AMBER] Antechamber Problem
- Jason Swails (Mon May 02 2011 - 04:10:35 PDT)
- souvik sur (Mon May 02 2011 - 03:56:03 PDT)
- Jason Swails (Mon May 02 2011 - 03:02:57 PDT)
- souvik sur (Mon May 02 2011 - 01:59:52 PDT)
- Ross Walker (Mon May 02 2011 - 01:42:51 PDT)
- souvik sur (Sun May 01 2011 - 10:46:40 PDT)
[AMBER] calculation of interaction energy using mmpbsa
- dhilip kumar ramalingam (Mon May 23 2011 - 04:43:12 PDT)
- steinbrt.rci.rutgers.edu (Mon May 23 2011 - 04:30:33 PDT)
- dhilip kumar ramalingam (Mon May 23 2011 - 04:21:51 PDT)
[AMBER] CHAMBER
- Seibold, Stephen (Sat May 28 2011 - 08:52:17 PDT)
- Mark Williamson (Fri May 27 2011 - 01:38:34 PDT)
- Seibold, Stephen (Thu May 26 2011 - 11:20:03 PDT)
- Seibold, Stephen (Wed May 25 2011 - 11:18:00 PDT)
- Ross Walker (Wed May 25 2011 - 10:45:08 PDT)
- Seibold, Stephen (Wed May 25 2011 - 10:18:25 PDT)
[AMBER] closest command
- Sangita Kachhap (Wed May 11 2011 - 23:00:57 PDT)
- Marek Maly (Wed May 11 2011 - 11:02:25 PDT)
- Sangita Kachhap (Wed May 11 2011 - 10:29:30 PDT)
[AMBER] Clustering
- Anselm Horn (Sat May 07 2011 - 11:03:21 PDT)
- baljinder (Sat May 07 2011 - 08:57:42 PDT)
[AMBER] compilation of amber tools 1.5 with intel 11.1.059
- Vlad Cojocaru (Sat May 21 2011 - 02:59:11 PDT)
- Daniel Roe (Fri May 20 2011 - 12:32:58 PDT)
- Vlad Cojocaru (Fri May 20 2011 - 07:56:22 PDT)
- Vlad Cojocaru (Fri May 20 2011 - 06:35:49 PDT)
[AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits
- David A. Case (Thu May 26 2011 - 01:59:12 PDT)
- Jorge Iulek (Wed May 25 2011 - 16:01:04 PDT)
- Jorge Iulek (Wed May 25 2011 - 15:51:49 PDT)
- Jorge Iulek (Wed May 25 2011 - 16:06:39 PDT)
- David A. Case (Wed May 25 2011 - 14:37:02 PDT)
- Vlad Cojocaru (Wed May 25 2011 - 13:51:40 PDT)
- Daniel Roe (Wed May 25 2011 - 12:59:29 PDT)
- JORGE IULEK (Wed May 25 2011 - 12:11:34 PDT)
- JORGE IULEK (Wed May 25 2011 - 12:09:08 PDT)
- David A. Case (Wed May 25 2011 - 08:11:35 PDT)
- Vlad Cojocaru (Wed May 25 2011 - 07:15:42 PDT)
- JORGE IULEK (Wed May 25 2011 - 06:46:36 PDT)
[AMBER] compile errors with AmberTools1.5 + Amber11
- Robert Wohlhueter (Sun May 01 2011 - 18:46:14 PDT)
- Jason Swails (Sun May 01 2011 - 03:45:05 PDT)
[AMBER] Compiling AMBER on Windows 7 with CUDA
- Ross Walker (Wed May 11 2011 - 15:21:54 PDT)
- Starr Hazard (Wed May 11 2011 - 11:14:16 PDT)
[AMBER] compiling errors when using Intel compiler and AmberTools 1.5
- Bongkeun Kim (Mon May 30 2011 - 09:54:31 PDT)
- Daniel Roe (Mon May 30 2011 - 05:52:26 PDT)
- Bongkeun Kim (Mon May 30 2011 - 03:20:34 PDT)
[AMBER] Configuration Checking
- souvik sur (Tue May 31 2011 - 06:41:47 PDT)
[AMBER] configuring AmberTools 1.5 for Intel MKL
- Jason Swails (Thu May 12 2011 - 23:17:44 PDT)
- case (Thu May 12 2011 - 18:54:08 PDT)
- Brendan Duggan (Thu May 12 2011 - 18:24:01 PDT)
- Jason Swails (Thu May 12 2011 - 16:02:30 PDT)
- Brendan Duggan (Thu May 12 2011 - 09:13:02 PDT)
[AMBER] constrained atom minimization
- David A. Case (Wed May 25 2011 - 14:30:33 PDT)
- arikcohen (Wed May 25 2011 - 11:39:29 PDT)
[AMBER] contacts command in ptraj - amber 10
- g t (Fri May 13 2011 - 04:11:17 PDT)
- Thomas Cheatham III (Wed May 11 2011 - 11:38:23 PDT)
- g t (Wed May 11 2011 - 09:18:45 PDT)
[AMBER] continue simulation with extended conformation
- Carlos Simmerling (Tue May 31 2011 - 11:18:45 PDT)
- Daniel Schaal (Tue May 31 2011 - 07:06:48 PDT)
[AMBER] CUDA
- Francesco Pietra (Mon May 16 2011 - 09:28:57 PDT)
[AMBER] Defining molecules composed of new residues
- Jason Swails (Fri May 27 2011 - 09:03:44 PDT)
- Brian Radak (Fri May 27 2011 - 07:02:25 PDT)
[AMBER] defining the mixed 1-4 scaling in amber 11 and sleap
- Jason Swails (Tue May 03 2011 - 22:47:07 PDT)
- Jason Swails (Tue May 03 2011 - 11:05:14 PDT)
[AMBER] disappearing atoms using softcore TI - amber 11
- steinbrt.rci.rutgers.edu (Thu May 26 2011 - 01:16:32 PDT)
- Zora Strelcova (Thu May 26 2011 - 00:48:51 PDT)
- steinbrt.rci.rutgers.edu (Thu May 26 2011 - 00:28:58 PDT)
- Zora Strelcova (Wed May 25 2011 - 12:44:34 PDT)
- steinbrt.rci.rutgers.edu (Wed May 25 2011 - 07:10:36 PDT)
- Ignacio J. General (Wed May 25 2011 - 07:05:27 PDT)
- Zora Strelcova (Wed May 25 2011 - 06:32:55 PDT)
[AMBER] Energy is increasing during minimization
- Wook Lee (Fri May 13 2011 - 01:20:38 PDT)
[AMBER] Entropy calculation using MM_PBSA.py
- mish (Thu May 05 2011 - 14:35:08 PDT)
- Bill Miller III (Thu May 05 2011 - 14:31:26 PDT)
- mish (Thu May 05 2011 - 14:25:23 PDT)
[AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time
- Ross Walker (Thu May 26 2011 - 10:19:03 PDT)
- Daniel Aiello (Thu May 26 2011 - 09:49:26 PDT)
- David A. Case (Thu May 26 2011 - 09:31:53 PDT)
- Daniel Aiello (Thu May 26 2011 - 08:38:02 PDT)
- Daniel Roe (Thu May 26 2011 - 08:16:15 PDT)
- Daniel Aiello (Thu May 26 2011 - 07:07:30 PDT)
[AMBER] Error in creating a cpin file
- Jason Swails (Mon May 09 2011 - 07:48:29 PDT)
- pankhuri arora (Mon May 09 2011 - 02:55:25 PDT)
- Jason Swails (Fri May 06 2011 - 17:33:29 PDT)
- pankhuri arora (Wed May 04 2011 - 22:34:38 PDT)
[AMBER] error in protein miniminisation
- Ben Roberts (Fri May 13 2011 - 06:06:48 PDT)
- dhilip kumar ramalingam (Fri May 13 2011 - 02:17:58 PDT)
[AMBER] error preparing a ligand using antechamber
- Paul Rigor (Mon May 16 2011 - 18:50:35 PDT)
- case (Mon May 16 2011 - 18:31:19 PDT)
- Paul Rigor (Mon May 16 2011 - 17:31:11 PDT)
- case (Mon May 16 2011 - 17:13:57 PDT)
- Paul Rigor (Mon May 16 2011 - 16:45:40 PDT)
- Paul Rigor (Mon May 16 2011 - 14:18:17 PDT)
[AMBER] Estiblish
- steinbrt.rci.rutgers.edu (Thu May 19 2011 - 03:35:21 PDT)
- hanlu0366 (Thu May 19 2011 - 02:43:25 PDT)
[AMBER] Forcefield for Modified RNA
- Jason Swails (Thu May 05 2011 - 05:02:54 PDT)
- hari krishna (Thu May 05 2011 - 03:48:05 PDT)
- David A. Case (Tue May 03 2011 - 08:41:12 PDT)
- FyD (Tue May 03 2011 - 02:20:10 PDT)
- hari krishna (Mon May 02 2011 - 21:49:44 PDT)
[AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein
- Jason Swails (Tue May 17 2011 - 07:41:27 PDT)
- siddesh southekal (Tue May 17 2011 - 05:37:09 PDT)
- Jason Swails (Thu May 05 2011 - 06:36:01 PDT)
- David A Case (Thu May 05 2011 - 06:06:17 PDT)
- siddesh southekal (Thu May 05 2011 - 03:07:19 PDT)
[AMBER] forrtl: severe (64): input conversion error
- manikanthan bhavaraju (Tue May 03 2011 - 18:15:23 PDT)
- Jagur Lambix (Tue May 03 2011 - 14:17:03 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
- Jason Swails (Fri May 06 2011 - 09:12:16 PDT)
- Katharina Lang (Fri May 06 2011 - 07:54:07 PDT)
[AMBER] Fwd: parameters sodium phosfate
- Domenica Dibenedetto (Mon May 02 2011 - 03:40:33 PDT)
[AMBER] GLYCAM Users Please Read
- Lachele Foley (Lists) (Fri May 13 2011 - 11:53:20 PDT)
[AMBER] H-Bond %occupancy
- Thomas Cheatham (Tue May 03 2011 - 11:14:49 PDT)
- Sangita Kachhap (Tue May 03 2011 - 11:11:03 PDT)
[AMBER] H-bond analysis
- Wu Xu (Mon May 30 2011 - 15:25:46 PDT)
- Daniel Roe (Mon May 30 2011 - 06:19:43 PDT)
- Wu Xu (Mon May 30 2011 - 05:01:51 PDT)
[AMBER] Hardwares requirement
- Jason Swails (Wed May 04 2011 - 07:36:47 PDT)
- souvik sur (Wed May 04 2011 - 06:42:39 PDT)
- Paul S. Nerenberg (Mon May 02 2011 - 22:38:02 PDT)
- souvik sur (Mon May 02 2011 - 22:31:16 PDT)
- Jason Swails (Mon May 02 2011 - 04:11:29 PDT)
- souvik sur (Mon May 02 2011 - 00:38:51 PDT)
[AMBER] hbond solvent output problem ...
- Marek Maly (Fri May 06 2011 - 13:04:26 PDT)
[AMBER] help with antechamber
- tsurma.umich.edu (Mon May 09 2011 - 07:45:46 PDT)
- case (Sun May 08 2011 - 18:44:12 PDT)
- tsurma.umich.edu (Sun May 08 2011 - 13:22:29 PDT)
- tsurma.umich.edu (Sun May 01 2011 - 18:37:55 PDT)
[AMBER] help with ewald parameter
- Bill Ross (Tue May 03 2011 - 10:40:47 PDT)
- Ankita Kumari (Mon May 02 2011 - 22:25:12 PDT)
- tsurma.umich.edu (Mon May 02 2011 - 08:47:52 PDT)
- Ross Walker (Mon May 02 2011 - 01:41:57 PDT)
- tsurma.umich.edu (Sun May 01 2011 - 18:37:18 PDT)
[AMBER] hold H-bonds of ssRNA fixed
- Wu Xu (Mon May 30 2011 - 19:17:12 PDT)
- Bill Ross (Mon May 30 2011 - 18:43:49 PDT)
- Wu Xu (Mon May 30 2011 - 18:23:30 PDT)
[AMBER] how are you?
- scott.pendley.gmail.com (Tue May 24 2011 - 13:06:24 PDT)
[AMBER] How to add a new force field
- steinbrt.rci.rutgers.edu (Mon May 09 2011 - 06:23:02 PDT)
- hanlu0366 (Mon May 09 2011 - 06:13:10 PDT)
[AMBER] How to minimize buried bad contacts
- Scott Pendley (Wed May 18 2011 - 09:57:08 PDT)
[AMBER] How to restart the MM-PBSA?
- Jason Swails (Mon May 09 2011 - 08:29:53 PDT)
- geyan (Mon May 09 2011 - 08:00:12 PDT)
- Bill Miller III (Sun May 08 2011 - 06:20:34 PDT)
- geyan (Sun May 08 2011 - 06:16:50 PDT)
[AMBER] how to use Bennett acceptance ratio in Amber11?
- steinbrt.rci.rutgers.edu (Fri May 13 2011 - 05:51:00 PDT)
- David A Case (Fri May 13 2011 - 04:59:45 PDT)
- steinbrt.rci.rutgers.edu (Thu May 12 2011 - 00:52:22 PDT)
- xiaodong huang (Wed May 11 2011 - 21:45:51 PDT)
[AMBER] How to use mmpbsa.py for three-trajectory protocol?
- bin wang (Fri May 20 2011 - 08:23:06 PDT)
- Bill Miller III (Fri May 20 2011 - 07:46:37 PDT)
- bin wang (Fri May 20 2011 - 07:44:30 PDT)
- Bill Miller III (Fri May 20 2011 - 07:07:02 PDT)
- bin wang (Fri May 20 2011 - 07:00:55 PDT)
[AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer
- Lekpa Duukori (Tue May 24 2011 - 17:04:26 PDT)
- David A. Case (Tue May 24 2011 - 08:52:56 PDT)
- Lekpa Duukori (Mon May 23 2011 - 10:24:47 PDT)
- Lekpa Duukori (Mon May 16 2011 - 10:43:02 PDT)
[AMBER] Hydrogens Langevin dynamics
- case (Wed May 18 2011 - 05:53:46 PDT)
- Massimiliano Porrini (Wed May 18 2011 - 05:01:00 PDT)
[AMBER] ibelly error
- David A. Case (Thu May 26 2011 - 01:46:24 PDT)
- Marc van der Kamp (Thu May 26 2011 - 01:23:48 PDT)
- Jason Swails (Wed May 25 2011 - 19:21:42 PDT)
- qiaoyan (Wed May 25 2011 - 18:40:30 PDT)
[AMBER] implicit solvent positional restraint
- Carlos Simmerling (Wed May 11 2011 - 06:01:26 PDT)
- Sangita Kachhap (Wed May 11 2011 - 04:24:45 PDT)
[AMBER] In ff99SB, what does this SB stands for ?
- mish (Thu May 26 2011 - 06:40:05 PDT)
- Jiri Sponer (Thu May 26 2011 - 05:01:22 PDT)
- Carlos Simmerling (Thu May 26 2011 - 04:55:02 PDT)
- mish (Thu May 26 2011 - 04:46:57 PDT)
[AMBER] installing ambertools
- case (Sat May 07 2011 - 11:56:07 PDT)
- Jason Swails (Sat May 07 2011 - 11:55:20 PDT)
- Michael Forrester (Sat May 07 2011 - 11:24:00 PDT)
[AMBER] internal energy INT is not zero in mm_pbsa
- Jason Swails (Sun May 08 2011 - 03:28:42 PDT)
- mirage . (Sun May 08 2011 - 02:43:45 PDT)
- Jason Swails (Sun May 08 2011 - 01:56:07 PDT)
- mirage . (Sun May 08 2011 - 01:56:16 PDT)
- mirage . (Sun May 08 2011 - 01:43:03 PDT)
- Bill Miller III (Sat May 07 2011 - 10:21:27 PDT)
- mirage . (Sat May 07 2011 - 10:15:07 PDT)
- mirage . (Fri May 06 2011 - 01:24:11 PDT)
- Dwight McGee (Thu May 05 2011 - 12:31:04 PDT)
- Bill Miller III (Thu May 05 2011 - 12:26:59 PDT)
- mirage . (Thu May 05 2011 - 12:15:56 PDT)
[AMBER] kclust_SegFault
- Maura Catherine Mooney (Mon May 16 2011 - 12:25:39 PDT)
[AMBER] Large protein hydrogen bonding analysis
- Dmitry Osolodkin (Tue May 17 2011 - 13:14:13 PDT)
[AMBER] lennard Jones water parameters
- David A Case (Mon May 09 2011 - 10:47:03 PDT)
- Paul S. Nerenberg (Mon May 09 2011 - 10:32:20 PDT)
- Wong, Sergio E. (Mon May 09 2011 - 10:04:16 PDT)
[AMBER] Loading .mol2 file in sleap
- Jason Swails (Wed May 04 2011 - 19:05:21 PDT)
- r smith (Wed May 04 2011 - 13:01:24 PDT)
- Ben Roberts (Wed May 04 2011 - 11:26:37 PDT)
- r smith (Wed May 04 2011 - 06:04:52 PDT)
[AMBER] MCPB help
- Martin Peters (Fri May 27 2011 - 06:26:05 PDT)
- Hashem Taha (Thu May 26 2011 - 12:15:18 PDT)
- Hashem Taha (Thu May 26 2011 - 12:14:52 PDT)
- Hashem Taha (Thu May 26 2011 - 08:41:12 PDT)
- Hashem Taha (Wed May 25 2011 - 09:19:08 PDT)
- Martin Peters (Wed May 04 2011 - 01:02:40 PDT)
- Ben Roberts (Tue May 03 2011 - 14:21:07 PDT)
- Hashem Taha (Tue May 03 2011 - 08:51:19 PDT)
[AMBER] MCPB install problem
- setyanto md (Wed May 04 2011 - 00:48:35 PDT)
[AMBER] MCPB problem
- Martin Peters (Wed May 04 2011 - 08:39:55 PDT)
- Manish (Wed May 04 2011 - 08:22:00 PDT)
- Ben Roberts (Tue May 03 2011 - 14:20:18 PDT)
- Manish (Tue May 03 2011 - 14:13:04 PDT)
- Hashem Taha (Tue May 03 2011 - 12:05:05 PDT)
- Manish (Tue May 03 2011 - 09:31:36 PDT)
[AMBER] MM-PB/SA calculation problem
- jiangxn (Tue May 24 2011 - 18:40:43 PDT)
- Bill Miller III (Tue May 24 2011 - 12:41:37 PDT)
- Ray Luo, Ph.D. (Tue May 24 2011 - 07:14:33 PDT)
- 姜笑楠 (Mon May 23 2011 - 23:03:32 PDT)
[AMBER] MMPBSA entropy calculation yields different Delta S values
- sunita gupta (Fri May 13 2011 - 04:42:35 PDT)
[AMBER] MMPBSA for trimerization process
- Lekpa Duukori (Sun May 01 2011 - 04:04:16 PDT)
- Jason Swails (Sun May 01 2011 - 03:48:52 PDT)
- Lekpa Duukori (Sun May 01 2011 - 03:19:32 PDT)
[AMBER] mmpbsa nmode problem
- Jason Swails (Sun May 01 2011 - 03:53:40 PDT)
[AMBER] MMPBSA nmode warning
- Jason Swails (Tue May 31 2011 - 09:15:08 PDT)
- Bill Miller III (Tue May 31 2011 - 09:09:58 PDT)
- Sangita Kachhap (Tue May 31 2011 - 09:06:45 PDT)
- Bill Miller III (Mon May 30 2011 - 18:53:56 PDT)
- Sangita Kachhap (Sat May 28 2011 - 09:45:37 PDT)
- Bill Miller III (Sat May 28 2011 - 04:59:21 PDT)
- Sangita Kachhap (Sat May 28 2011 - 02:41:11 PDT)
[AMBER] mmpbsa problems with amber 11
- Jason Swails (Tue May 03 2011 - 10:46:30 PDT)
- David A. Case (Mon May 02 2011 - 08:27:17 PDT)
- Jason Swails (Mon May 02 2011 - 01:45:29 PDT)
- Guenegou, Guillaume [ORDFR] (Mon May 02 2011 - 00:48:32 PDT)
[AMBER] mmpbsa, mdfil: Error unknown flag: not
- Jason Swails (Sun May 15 2011 - 15:03:50 PDT)
- Andrew Voronkov (Sun May 15 2011 - 14:40:47 PDT)
- Bill Miller III (Sun May 15 2011 - 09:21:30 PDT)
- Andrew Voronkov (Sun May 15 2011 - 09:18:04 PDT)
- Jason Swails (Tue May 10 2011 - 13:14:30 PDT)
- Andrew Voronkov (Tue May 10 2011 - 09:26:01 PDT)
- Bill Ross (Sun May 08 2011 - 11:10:10 PDT)
- Jason Swails (Sun May 08 2011 - 09:19:27 PDT)
- Andrew Voronkov (Sun May 08 2011 - 08:28:11 PDT)
- Andrew Voronkov (Sun May 08 2011 - 06:57:54 PDT)
- Jason Swails (Sat May 07 2011 - 11:54:01 PDT)
- Andrew Voronkov (Sat May 07 2011 - 11:08:41 PDT)
[AMBER] MMPBSA.py - entropy only?
- Jesper Sørensen (Fri May 13 2011 - 03:56:27 PDT)
- Jason Swails (Thu May 12 2011 - 16:07:22 PDT)
- Catein Catherine (Thu May 12 2011 - 07:50:14 PDT)
- Bill Miller III (Thu May 12 2011 - 07:40:19 PDT)
- Jesper Sørensen (Thu May 12 2011 - 07:26:36 PDT)
- Bill Miller III (Thu May 12 2011 - 04:27:22 PDT)
- Jesper Sørensen (Thu May 12 2011 - 04:15:24 PDT)
- Bill Miller III (Thu May 12 2011 - 03:54:39 PDT)
- Jesper Sørensen (Thu May 12 2011 - 02:27:21 PDT)
[AMBER] MMPBSA.py - entropy results
- Jesper Sørensen (Tue May 24 2011 - 02:27:36 PDT)
- Jason Swails (Mon May 23 2011 - 10:19:19 PDT)
- Jesper Sørensen (Mon May 23 2011 - 02:37:27 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj
- Oliver Kuhn (Mon May 16 2011 - 07:12:20 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj (in more detail)
- Oliver Kuhn (Mon May 16 2011 - 13:06:41 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj (in more detail) - add
- Jason Swails (Mon May 16 2011 - 13:46:46 PDT)
- Oliver Kuhn (Mon May 16 2011 - 13:22:23 PDT)
[AMBER] MMPBSA.py, systematic error in ptraj entropy results?
- Jesper Sørensen (Tue May 17 2011 - 03:41:34 PDT)
- Thomas Cheatham III (Mon May 16 2011 - 13:55:33 PDT)
- Jason Swails (Mon May 16 2011 - 13:48:44 PDT)
- Jesper Sørensen (Mon May 16 2011 - 06:06:31 PDT)
[AMBER] MMPBSA: protein-protein dimerisation
- Bill Miller III (Sat May 28 2011 - 04:57:37 PDT)
- George Tzotzos (Sat May 28 2011 - 02:03:26 PDT)
[AMBER] MMPBSA: Trajectory pre-processing
- George Tzotzos (Fri May 06 2011 - 07:33:13 PDT)
- Bill Miller III (Fri May 06 2011 - 07:28:31 PDT)
- George Tzotzos (Fri May 06 2011 - 07:21:25 PDT)
- Bill Miller III (Fri May 06 2011 - 04:38:06 PDT)
- George Tzotzos (Fri May 06 2011 - 03:30:05 PDT)
[AMBER] MTK++ MCPB Example: Creating Force Field Modification Files
- Ben Roberts (Wed May 04 2011 - 11:29:49 PDT)
- Naveen Samala (Wed May 04 2011 - 10:48:39 PDT)
[AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap
- Naveen Samala (Thu May 05 2011 - 13:26:26 PDT)
- Martin Peters (Thu May 05 2011 - 13:01:38 PDT)
- Bill Ross (Thu May 05 2011 - 11:42:33 PDT)
- Naveen Samala (Thu May 05 2011 - 08:53:56 PDT)
- Martin Peters (Thu May 05 2011 - 08:22:41 PDT)
- Naveen Samala (Thu May 05 2011 - 07:52:55 PDT)
- Martin Peters (Thu May 05 2011 - 01:27:45 PDT)
- Naveen Samala (Wed May 04 2011 - 13:47:17 PDT)
[AMBER] MTK++/MCPB Side Chain Model
- Yang, Yue (Fri May 06 2011 - 18:38:19 PDT)
- Naveen Samala (Fri May 06 2011 - 15:39:46 PDT)
[AMBER] MTK++/MCPB: Problem in converting prep to xml
- Naveen Samala (Tue May 31 2011 - 15:19:03 PDT)
[AMBER] NEB calculation using amber 11
- Carlos Simmerling (Mon May 23 2011 - 10:48:57 PDT)
- Buddhadev Maiti (Mon May 23 2011 - 10:46:53 PDT)
- Ross Walker (Mon May 23 2011 - 10:21:56 PDT)
- Carlos Simmerling (Mon May 23 2011 - 10:16:47 PDT)
- Buddhadev Maiti (Mon May 23 2011 - 10:14:13 PDT)
[AMBER] need suggestion about NVIDIA GTX 590
- setyanto md (Wed May 18 2011 - 03:34:38 PDT)
- filip fratev (Mon May 16 2011 - 06:47:37 PDT)
- Jason Swails (Mon May 16 2011 - 04:29:02 PDT)
- setyanto md (Sun May 15 2011 - 19:34:36 PDT)
[AMBER] new lib loaded, but atom types are not recognized
- Chinh Su Tran To (Tue May 10 2011 - 01:05:53 PDT)
- Thomas Cheatham (Mon May 09 2011 - 20:49:34 PDT)
- Chinh Su Tran To (Mon May 09 2011 - 20:31:26 PDT)
- Thomas Cheatham III (Mon May 09 2011 - 10:27:11 PDT)
- Chinh Su Tran To (Mon May 09 2011 - 01:05:37 PDT)
[AMBER] nmode calculation
- Sangita Kachhap (Mon May 09 2011 - 21:08:31 PDT)
- Sangita Kachhap (Mon May 09 2011 - 20:40:50 PDT)
- Jason Swails (Mon May 09 2011 - 11:08:12 PDT)
- Sangita Kachhap (Mon May 09 2011 - 10:42:16 PDT)
[AMBER] NMODE calculations results doubtful
- Dwight McGee (Mon May 09 2011 - 00:10:54 PDT)
- vaibhav dixit (Sun May 08 2011 - 23:34:49 PDT)
- Dwight McGee (Sun May 08 2011 - 22:20:24 PDT)
- vaibhav dixit (Sun May 08 2011 - 21:46:43 PDT)
[AMBER] Normal Mode Analysis
- Deák Robi (Tue May 31 2011 - 00:48:56 PDT)
- case (Mon May 30 2011 - 18:32:47 PDT)
- Deák Robi (Mon May 30 2011 - 15:59:51 PDT)
[AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent
- Ross Walker (Wed May 04 2011 - 09:16:28 PDT)
[AMBER] parameter-for-peptide-blocking-group
- FyD (Fri May 06 2011 - 07:35:54 PDT)
- vhakkim boy (Fri May 06 2011 - 05:51:42 PDT)
[AMBER] Parametrizing a peptide ligand
- Gustavo Seabra (Fri May 20 2011 - 12:27:47 PDT)
- FyD (Fri May 20 2011 - 04:18:26 PDT)
- Gustavo Seabra (Fri May 20 2011 - 02:53:18 PDT)
- FyD (Fri May 20 2011 - 00:55:28 PDT)
- Gustavo Seabra (Thu May 19 2011 - 13:14:33 PDT)
[AMBER] PhD position in Computational Structural Biology at MPI Muenster
- Vlad Cojocaru (Fri May 13 2011 - 02:45:23 PDT)
[AMBER] phosphate group
- FyD (Wed May 18 2011 - 01:52:49 PDT)
- case (Tue May 17 2011 - 18:16:29 PDT)
- Wu Xu (Tue May 17 2011 - 15:21:46 PDT)
[AMBER] Please help with - closestwater - problem
- Marek Maly (Mon May 09 2011 - 16:13:33 PDT)
- Thomas Cheatham III (Mon May 09 2011 - 14:31:14 PDT)
- Marek Maly (Mon May 09 2011 - 13:02:34 PDT)
[AMBER] Please help with - closestwater - problem - problem is connected with NETCDF format
- Marek Maly (Mon May 09 2011 - 17:49:51 PDT)
[AMBER] Positive Energy
- Kshatresh Dutta Dubey (Sat May 07 2011 - 07:26:23 PDT)
- case (Sat May 07 2011 - 06:14:55 PDT)
- Kshatresh Dutta Dubey (Sat May 07 2011 - 03:22:04 PDT)
[AMBER] Possibility to define residues pairs for inter-residual hbond analysis ?
- Marek Maly (Wed May 04 2011 - 11:57:04 PDT)
[AMBER] Post-processing trajectories: ntpr - ntwx
- Jason Swails (Sat May 21 2011 - 14:03:37 PDT)
- George Tzotzos (Sat May 21 2011 - 08:28:01 PDT)
[AMBER] PRCSM
- baljinder (Sat May 07 2011 - 09:00:11 PDT)
[AMBER] Problem in preparation of log file
- case (Sat May 07 2011 - 06:37:25 PDT)
- Sindrila Dutta banik (Sat May 07 2011 - 00:50:08 PDT)
[AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS
- Sindrila Dutta banik (Sat May 28 2011 - 22:03:04 PDT)
- FyD (Thu May 26 2011 - 00:14:14 PDT)
- Sindrila Dutta banik (Wed May 25 2011 - 09:27:27 PDT)
- Sindrila Dutta banik (Wed May 25 2011 - 09:10:00 PDT)
- David A. Case (Wed May 25 2011 - 07:07:51 PDT)
- Sindrila Dutta banik (Tue May 24 2011 - 22:35:54 PDT)
[AMBER] Problem installing AMBER 11 (after installing AmberTools1.5)
- Jason Swails (Tue May 24 2011 - 08:57:13 PDT)
- Marc van der Kamp (Tue May 24 2011 - 06:52:16 PDT)
- Jason Swails (Tue May 24 2011 - 05:38:05 PDT)
- Marc van der Kamp (Tue May 24 2011 - 05:03:50 PDT)
- Daniel Roe (Tue May 24 2011 - 04:53:27 PDT)
- Marc van der Kamp (Tue May 24 2011 - 03:11:27 PDT)
[AMBER] Problem of PB calculation when running mmpbsa.py
- bin wang (Fri May 20 2011 - 13:07:54 PDT)
- Bill Miller III (Fri May 20 2011 - 12:41:36 PDT)
- bin wang (Fri May 20 2011 - 12:36:29 PDT)
[AMBER] Problem of PB calculation when running mmpbsa.py. .
- Ray Luo, Ph.D. (Fri May 20 2011 - 13:15:53 PDT)
- Jason Swails (Fri May 20 2011 - 13:11:47 PDT)
- Zheng, Zhong (Fri May 20 2011 - 13:06:15 PDT)
[AMBER] Problem of PB calculation when running mmpbsa.py. .. .
- Ray Luo (Sat May 21 2011 - 16:28:39 PDT)
- bin wang (Sat May 21 2011 - 13:42:38 PDT)
- Jason Swails (Sat May 21 2011 - 13:08:43 PDT)
- bin wang (Sat May 21 2011 - 13:02:34 PDT)
- Jason Swails (Fri May 20 2011 - 14:18:05 PDT)
- Ray Luo, Ph.D. (Fri May 20 2011 - 14:08:11 PDT)
- Zheng, Zhong (Fri May 20 2011 - 14:03:30 PDT)
[AMBER] Problem of PB calculation when running mmpbsa.py. .. .. .
- Zheng, Zhong (Fri May 20 2011 - 14:46:54 PDT)
[AMBER] Problem related to the Amber
- Ross Walker (Sun May 08 2011 - 21:34:58 PDT)
[AMBER] Problem with AMBER 11 and distance restraints
- Pablo Dans Puiggròs (Mon May 09 2011 - 09:39:03 PDT)
- Jason Swails (Mon May 09 2011 - 08:42:53 PDT)
- Pablo Dans Puiggròs (Mon May 09 2011 - 08:23:31 PDT)
[AMBER] problem with dielectric constant
- case (Mon May 30 2011 - 08:25:42 PDT)
- Bernhard Poll (Mon May 30 2011 - 07:18:59 PDT)
- case (Mon May 30 2011 - 06:08:22 PDT)
- Bernhard Poll (Mon May 30 2011 - 00:40:57 PDT)
[AMBER] Problem with Equilibration
- Jason Swails (Fri May 13 2011 - 09:12:34 PDT)
- Sangita Kachhap (Fri May 13 2011 - 04:48:13 PDT)
- Jason Swails (Thu May 12 2011 - 16:13:11 PDT)
- Devlina Chakravarty (Thu May 12 2011 - 05:13:58 PDT)
[AMBER] problem with nmode
- Jason Swails (Thu May 05 2011 - 07:12:44 PDT)
- poll.chemie.uni-hamburg.de (Thu May 05 2011 - 06:59:13 PDT)
[AMBER] problem with running pmemd.mpi on cluster
- Daniel Roe (Mon May 30 2011 - 06:27:19 PDT)
- Zheng, Zhong (Mon May 30 2011 - 06:14:24 PDT)
[AMBER] problem with vector principal
- Daniel Roe (Mon May 30 2011 - 07:12:19 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri May 27 2011 - 12:28:02 PDT)
[AMBER] problems with AmberTools 1.5 compilation
- Anna Reymer (Mon May 30 2011 - 04:17:49 PDT)
- Bruno Rodrigues (Sun May 29 2011 - 13:30:30 PDT)
- case (Sun May 29 2011 - 10:45:18 PDT)
- Jason Swails (Sun May 29 2011 - 08:57:20 PDT)
- Bruno Rodrigues (Sun May 29 2011 - 08:32:30 PDT)
- Anna Reymer (Sun May 29 2011 - 03:35:00 PDT)
[AMBER] Problems with calcein and antechamber
- Maria Federica Sanasi (Sun May 22 2011 - 03:35:00 PDT)
[AMBER] Protein drifting out of the solvent box
- Sasha Buzko (Mon May 09 2011 - 13:51:56 PDT)
- InSuk Joung (Sat May 07 2011 - 21:01:04 PDT)
- Sasha Buzko (Thu May 05 2011 - 14:39:46 PDT)
- Jason Swails (Thu May 05 2011 - 14:10:17 PDT)
- Sasha Buzko (Thu May 05 2011 - 13:59:37 PDT)
- Carlos Simmerling (Thu May 05 2011 - 12:12:46 PDT)
- Sasha Buzko (Thu May 05 2011 - 12:03:27 PDT)
[AMBER] protein scoop
- Aiko Matsumoto (Tue May 31 2011 - 08:50:36 PDT)
[AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
- Jason Swails (Sun May 08 2011 - 05:56:47 PDT)
- Kamali Sripathi (Sun May 08 2011 - 05:44:08 PDT)
[AMBER] ptraj closest command
- supriyah.imtech.res.in (Fri May 20 2011 - 04:30:08 PDT)
[AMBER] ptraj clustering output
- Lekpa Duukori (Wed May 11 2011 - 11:40:05 PDT)
- Thomas Cheatham III (Wed May 11 2011 - 11:35:18 PDT)
- Lekpa Duukori (Wed May 11 2011 - 10:12:14 PDT)
[AMBER] ptraj command
- Sangita Kachhap (Wed May 18 2011 - 23:08:09 PDT)
- Thomas Cheatham III (Wed May 18 2011 - 13:34:11 PDT)
- Sangita Kachhap (Sun May 15 2011 - 05:28:23 PDT)
[AMBER] Ptraj Hbond query.
- Maura Catherine Mooney (Tue May 10 2011 - 19:58:52 PDT)
- Thomas Cheatham (Tue May 10 2011 - 19:49:05 PDT)
- Maura Catherine Mooney (Tue May 10 2011 - 19:23:59 PDT)
[AMBER] Ptraj NAMD dcd imaging
- George Madalin Giambasu (Thu May 19 2011 - 10:47:13 PDT)
- Marek Maly (Thu May 19 2011 - 10:30:13 PDT)
- Manish (Thu May 19 2011 - 10:01:34 PDT)
[AMBER] ptraj trajectory file size limits?
- Nicole A. Horenstein (Sun May 01 2011 - 08:42:01 PDT)
[AMBER] ptraj: rms
- Daniel Roe (Mon May 30 2011 - 08:56:59 PDT)
- George Tzotzos (Mon May 30 2011 - 08:45:56 PDT)
[AMBER] Question about ptraj artifacts
- Kamali Sripathi (Fri May 06 2011 - 09:04:46 PDT)
[AMBER] Question about ptraj hbond schematic
- Thomas Cheatham III (Fri May 06 2011 - 14:12:27 PDT)
- Kamali Sripathi (Thu May 05 2011 - 13:58:52 PDT)
[AMBER] question about REMD
- Carlos Simmerling (Wed May 11 2011 - 05:58:16 PDT)
- Jason Swails (Wed May 11 2011 - 05:55:33 PDT)
- Massimiliano Porrini (Wed May 11 2011 - 05:32:54 PDT)
- Daniel Sindhikara (Wed May 11 2011 - 05:01:57 PDT)
- Massimiliano Porrini (Wed May 11 2011 - 04:19:50 PDT)
[AMBER] question about scmask
- steinbrt.rci.rutgers.edu (Fri May 06 2011 - 01:23:28 PDT)
- Lishan Yao (Fri May 06 2011 - 01:05:37 PDT)
- steinbrt.rci.rutgers.edu (Fri May 06 2011 - 00:28:57 PDT)
- Lishan Yao (Thu May 05 2011 - 17:53:29 PDT)
- steinbrt.rci.rutgers.edu (Thu May 05 2011 - 03:33:56 PDT)
- Lishan Yao (Thu May 05 2011 - 02:29:43 PDT)
[AMBER] question regarding H-bond calculation
- Adrian Roitberg (Sun May 01 2011 - 08:18:27 PDT)
- juzer stationwala (Sun May 01 2011 - 08:15:48 PDT)
[AMBER] Questions about compiling AmberToolsv1.4
- Kamali Sripathi (Tue May 10 2011 - 05:09:58 PDT)
- David A Case (Mon May 09 2011 - 12:38:32 PDT)
- David A Case (Mon May 09 2011 - 11:18:13 PDT)
- Kamali Sripathi (Mon May 09 2011 - 11:07:20 PDT)
- Jason Swails (Sun May 08 2011 - 09:24:55 PDT)
- Kamali Sripathi (Sun May 08 2011 - 06:53:01 PDT)
[AMBER] RAM requirements
- Robert Duke (Fri May 27 2011 - 16:09:01 PDT)
- Scott Le Grand (Fri May 27 2011 - 11:13:28 PDT)
- Dmitry Osolodkin (Fri May 27 2011 - 11:01:29 PDT)
- Robert Duke (Fri May 27 2011 - 08:05:40 PDT)
- Jason Swails (Fri May 27 2011 - 04:29:47 PDT)
- Dmitry Osolodkin (Fri May 27 2011 - 04:21:05 PDT)
- Jason Swails (Thu May 26 2011 - 21:01:19 PDT)
- Dmitry Osolodkin (Thu May 26 2011 - 14:08:18 PDT)
[AMBER] rdf
- subrata paul (Fri May 27 2011 - 06:35:15 PDT)
- Lorenzo Gontrani (Fri May 27 2011 - 05:20:58 PDT)
- subrata paul (Fri May 27 2011 - 04:50:53 PDT)
[AMBER] RED conformation weights
- FyD (Tue May 03 2011 - 02:13:13 PDT)
[AMBER] regarding calculation of interaction energies
- steinbrt.rci.rutgers.edu (Mon May 23 2011 - 00:29:21 PDT)
- dhilip kumar ramalingam (Mon May 23 2011 - 00:19:38 PDT)
[AMBER] regarding LINMIN failure
- Ben Roberts (Wed May 18 2011 - 08:06:19 PDT)
- dhilip kumar ramalingam (Wed May 18 2011 - 06:25:46 PDT)
[AMBER] Regarding MTK++/MCPB program to derive parameters using side chain model
- Naveen Samala (Mon May 16 2011 - 13:00:22 PDT)
- Naveen Samala (Thu May 12 2011 - 11:26:53 PDT)
[AMBER] Residue Template
- case (Sat May 07 2011 - 06:50:53 PDT)
- Sindrila Dutta banik (Sat May 07 2011 - 05:51:57 PDT)
[AMBER] Restraints during relaxation
- Oliver Kuhn (Tue May 31 2011 - 04:40:13 PDT)
[AMBER] Restraints during relaxation - add
- Oliver Kuhn (Tue May 31 2011 - 11:50:05 PDT)
- Carlos Simmerling (Tue May 31 2011 - 11:41:19 PDT)
- Oliver Kuhn (Tue May 31 2011 - 06:03:22 PDT)
[AMBER] rst problem
- Sel Ercan (Tue May 17 2011 - 01:44:52 PDT)
- selami ercan (Tue May 17 2011 - 01:23:47 PDT)
- Sel Ercan (Tue May 17 2011 - 00:31:23 PDT)
[AMBER] SANDER ERROR: forrtl: severe (64): input conversion error
- Bill Ross (Thu May 05 2011 - 15:52:19 PDT)
- Carlos Simmerling (Thu May 05 2011 - 15:42:42 PDT)
- Jason Swails (Thu May 05 2011 - 15:42:22 PDT)
- Jagur Lambix (Thu May 05 2011 - 15:35:21 PDT)
[AMBER] sander.MPI
- Bruno Rodrigues (Wed May 25 2011 - 12:04:27 PDT)
- Jason Swails (Wed May 25 2011 - 10:11:51 PDT)
- Ross Walker (Wed May 25 2011 - 09:42:49 PDT)
- Jason Swails (Wed May 25 2011 - 06:01:37 PDT)
- Bruno Rodrigues (Wed May 25 2011 - 05:18:02 PDT)
- Bruno Rodrigues (Tue May 24 2011 - 19:48:07 PDT)
- Jason Swails (Tue May 24 2011 - 13:11:16 PDT)
- Bruno Rodrigues (Tue May 24 2011 - 12:21:52 PDT)
[AMBER] SASA parameters Amber99
- Osvaldo Martin (Tue May 10 2011 - 09:45:44 PDT)
- David A Case (Tue May 10 2011 - 09:41:17 PDT)
- Jason Swails (Tue May 10 2011 - 08:34:44 PDT)
- Osvaldo Martin (Tue May 10 2011 - 08:22:32 PDT)
- Jason Swails (Tue May 10 2011 - 07:52:46 PDT)
- Osvaldo Martin (Tue May 10 2011 - 07:10:28 PDT)
[AMBER] secundary structure analysis
- Jorgen Simonsen (Wed May 18 2011 - 10:22:07 PDT)
[AMBER] segmentation fault when running sander
- Chinh Su Tran To (Fri May 20 2011 - 02:02:49 PDT)
- Jason Swails (Thu May 19 2011 - 04:18:54 PDT)
- Chinh Su Tran To (Wed May 18 2011 - 21:48:39 PDT)
- Thomas Cheatham (Wed May 18 2011 - 21:16:15 PDT)
- Chinh Su Tran To (Wed May 18 2011 - 21:04:51 PDT)
- Jason Swails (Wed May 18 2011 - 20:30:27 PDT)
- Chinh Su Tran To (Wed May 18 2011 - 19:31:49 PDT)
- Chinh Su Tran To (Wed May 18 2011 - 18:49:22 PDT)
- Jason Swails (Wed May 18 2011 - 11:14:31 PDT)
- Chinh Su Tran To (Tue May 17 2011 - 22:00:29 PDT)
- Chinh Su Tran To (Mon May 16 2011 - 04:46:47 PDT)
- Jason Swails (Mon May 16 2011 - 04:27:20 PDT)
- Chinh Su Tran To (Mon May 16 2011 - 04:12:36 PDT)
- Santosh Mogurampelly (Mon May 16 2011 - 00:26:56 PDT)
- Chinh Su Tran To (Sun May 15 2011 - 21:42:40 PDT)
[AMBER] selecting hydrogens in -NH groups for the hydrogen bonding facility in PTRAJ
- Jose Borreguero (Sat May 07 2011 - 12:05:48 PDT)
[AMBER] set UNIT box
- Bill Ross (Mon May 09 2011 - 12:45:51 PDT)
- George Tzotzos (Mon May 09 2011 - 12:30:43 PDT)
- Jason Swails (Mon May 09 2011 - 12:17:56 PDT)
- George Tzotzos (Mon May 09 2011 - 11:48:36 PDT)
- Jason Swails (Mon May 09 2011 - 11:04:42 PDT)
- George Tzotzos (Mon May 09 2011 - 11:00:13 PDT)
[AMBER] Simulated annealing
- Bill Ross (Mon May 09 2011 - 13:46:50 PDT)
- david condon (Mon May 09 2011 - 07:45:49 PDT)
- Guenegou, Guillaume [ORDFR] (Mon May 09 2011 - 07:41:12 PDT)
[AMBER] Size limit of traj file
- Jason Swails (Tue May 24 2011 - 18:57:52 PDT)
- Jagur Lambix (Tue May 24 2011 - 14:34:42 PDT)
[AMBER] solvatebox
- Bill Ross (Fri May 27 2011 - 21:44:48 PDT)
- M. L. Dodson (Fri May 27 2011 - 17:21:19 PDT)
- Jason Swails (Fri May 27 2011 - 16:17:36 PDT)
- George Tzotzos (Thu May 26 2011 - 12:38:07 PDT)
- Bill Ross (Thu May 26 2011 - 12:06:31 PDT)
- Carlos Simmerling (Thu May 26 2011 - 09:41:33 PDT)
- Gustavo Seabra (Thu May 26 2011 - 08:39:07 PDT)
- Bill Ross (Thu May 26 2011 - 08:34:30 PDT)
- Bill Ross (Thu May 26 2011 - 08:27:40 PDT)
- George Tzotzos (Thu May 26 2011 - 06:44:18 PDT)
- Carlos Simmerling (Thu May 26 2011 - 06:36:32 PDT)
- George Tzotzos (Thu May 26 2011 - 06:20:25 PDT)
[AMBER] Solvation
- Sindrila Dutta banik (Mon May 23 2011 - 05:56:42 PDT)
- Sindrila Dutta banik (Thu May 19 2011 - 04:11:05 PDT)
- Carlos Simmerling (Thu May 19 2011 - 05:34:29 PDT)
- Jason Swails (Thu May 19 2011 - 05:23:01 PDT)
- Sindrila Dutta banik (Thu May 19 2011 - 05:20:56 PDT)
- Carlos Simmerling (Thu May 19 2011 - 05:06:46 PDT)
- Sindrila Dutta banik (Thu May 19 2011 - 05:01:56 PDT)
[AMBER] Solvent box
- John S (Thu May 05 2011 - 11:22:15 PDT)
[AMBER] strange dihedral assignment by leap
- Thomas Gaillard (Fri May 20 2011 - 06:27:43 PDT)
- Jason Swails (Fri May 20 2011 - 05:27:11 PDT)
- Thomas Gaillard (Fri May 20 2011 - 05:04:29 PDT)
- Jason Swails (Fri May 20 2011 - 04:16:53 PDT)
- Thomas Gaillard (Fri May 20 2011 - 03:47:17 PDT)
- Jason Swails (Thu May 19 2011 - 20:21:19 PDT)
- Thomas Gaillard (Thu May 19 2011 - 17:16:53 PDT)
[AMBER] strange volume contraction
- case (Sat May 14 2011 - 10:19:27 PDT)
- Massimiliano Porrini (Sat May 14 2011 - 08:37:39 PDT)
- case (Sat May 14 2011 - 06:55:25 PDT)
- Massimiliano Porrini (Fri May 13 2011 - 05:51:34 PDT)
[AMBER] stripping of water
- Sangita Kachhap (Mon May 30 2011 - 08:49:52 PDT)
- Daniel Roe (Mon May 30 2011 - 05:41:06 PDT)
- Sangita Kachhap (Fri May 27 2011 - 00:13:15 PDT)
[AMBER] System configuration requirement for installing Amber9 in cluster
- souvik sur (Wed May 04 2011 - 20:57:38 PDT)
[AMBER] system extended beyond the virtual box
- David Case (Tue May 31 2011 - 18:30:05 PDT)
- David A. Case (Wed May 25 2011 - 00:15:43 PDT)
- Ross Walker (Mon May 23 2011 - 22:06:12 PDT)
- Qian Wang (Mon May 23 2011 - 21:18:00 PDT)
- Ross Walker (Mon May 23 2011 - 20:42:27 PDT)
- Qian Wang (Mon May 23 2011 - 20:28:59 PDT)
[AMBER] system imaging
- Alex Rodriguez (Tue May 10 2011 - 10:31:38 PDT)
- InSuk Joung (Tue May 10 2011 - 09:49:38 PDT)
- Thomas Cheatham III (Tue May 10 2011 - 09:24:42 PDT)
- Alex Rodriguez (Tue May 10 2011 - 09:09:36 PDT)
[AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070
- Ross Walker (Fri May 27 2011 - 09:02:22 PDT)
- Paul Rigor (Thu May 26 2011 - 23:34:27 PDT)
- Ross Walker (Wed May 25 2011 - 22:28:59 PDT)
- Paul Rigor (Wed May 25 2011 - 20:33:39 PDT)
- Jason Swails (Wed May 25 2011 - 19:54:07 PDT)
- Paul Rigor (Wed May 25 2011 - 19:41:32 PDT)
- Paul Rigor (Wed May 25 2011 - 19:25:56 PDT)
- Jason Swails (Wed May 25 2011 - 19:25:40 PDT)
- Paul Rigor (Wed May 25 2011 - 19:19:21 PDT)
- Jason Swails (Wed May 25 2011 - 19:17:08 PDT)
- Jason Swails (Wed May 25 2011 - 19:12:22 PDT)
- Paul Rigor (Wed May 25 2011 - 18:51:43 PDT)
- Paul Rigor (Wed May 25 2011 - 17:53:37 PDT)
- Ross Walker (Wed May 25 2011 - 16:18:44 PDT)
- Jason Swails (Wed May 25 2011 - 15:35:34 PDT)
- Ross Walker (Wed May 25 2011 - 14:43:26 PDT)
- Jason Swails (Wed May 25 2011 - 14:30:19 PDT)
- Scott Le Grand (Wed May 25 2011 - 13:52:39 PDT)
- Scott Le Grand (Wed May 25 2011 - 13:47:44 PDT)
- Paul Rigor (Wed May 25 2011 - 13:35:10 PDT)
- Scott Le Grand (Wed May 25 2011 - 10:54:24 PDT)
- Jason Swails (Wed May 25 2011 - 10:27:27 PDT)
- Scott Le Grand (Wed May 25 2011 - 10:06:29 PDT)
- Ross Walker (Wed May 25 2011 - 09:38:44 PDT)
- Paul Rigor (Wed May 25 2011 - 00:49:18 PDT)
[AMBER] Topology File
- Sindrila Dutta banik (Tue May 24 2011 - 07:21:58 PDT)
[AMBER] TS calculation
- Mahmoud Soliman (Fri May 06 2011 - 03:05:36 PDT)
- Ross Walker (Fri May 06 2011 - 03:15:51 PDT)
- Jason Swails (Fri May 06 2011 - 03:11:10 PDT)
- Mahmoud Soliman (Fri May 06 2011 - 00:39:52 PDT)
- Mahmoud Soliman (Thu May 05 2011 - 13:40:07 PDT)
[AMBER] typo in parm99.dat?
- case (Sat May 28 2011 - 07:31:34 PDT)
- Mark Williamson (Fri May 27 2011 - 08:56:16 PDT)
- Thomas Gaillard (Fri May 27 2011 - 08:41:29 PDT)
[AMBER] umbrella sampling on a difference of distances RC.
- dacase.rci.rutgers.edu (Wed May 04 2011 - 07:51:37 PDT)
- M. L. Dodson (Wed May 04 2011 - 07:11:00 PDT)
- Adrian Roitberg (Wed May 04 2011 - 06:57:34 PDT)
- David A. Case (Wed May 04 2011 - 06:33:48 PDT)
[AMBER] Usage non-zero IVCAP in MM-PBSA ?
- Marek Maly (Tue May 03 2011 - 05:48:57 PDT)
[AMBER] Use of uninitialized value $ENV{"AMBERHOME"}
- Jason Swails (Thu May 19 2011 - 20:24:13 PDT)
- Jagur Lambix (Thu May 19 2011 - 11:46:02 PDT)
[AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue?
- Chiba Shuntaro (Fri May 20 2011 - 02:18:55 PDT)
- FyD (Fri May 20 2011 - 00:43:23 PDT)
- Chiba Shuntaro (Thu May 19 2011 - 01:12:25 PDT)
- FyD (Wed May 18 2011 - 04:24:17 PDT)
- FyD (Wed May 18 2011 - 04:17:02 PDT)
- Chiba Shuntaro (Wed May 18 2011 - 03:16:22 PDT)
- FyD (Wed May 18 2011 - 02:03:33 PDT)
- Chiba Suntaro (Tue May 17 2011 - 19:51:07 PDT)
- FyD (Sun May 15 2011 - 23:07:23 PDT)
- Chiba Suntaro (Sun May 15 2011 - 22:00:19 PDT)
[AMBER] vacuum in Ewald
- Ross Walker (Tue May 24 2011 - 09:30:22 PDT)
- Ignacio J. General (Tue May 24 2011 - 07:44:27 PDT)
- Ross Walker (Mon May 23 2011 - 13:46:47 PDT)
- Ignacio J. General (Mon May 23 2011 - 13:19:18 PDT)
[AMBER] visualization of large .mdcrd files
- Jason Swails (Mon May 09 2011 - 14:38:03 PDT)
- Bozell, Joseph John (Mon May 09 2011 - 12:46:26 PDT)
[AMBER] watershell
- Daniel Roe (Thu May 26 2011 - 08:06:44 PDT)
- subrata paul (Thu May 26 2011 - 07:46:02 PDT)
[AMBER] Where to send patches?
- case (Mon May 30 2011 - 05:56:12 PDT)
- Ake Sandgren (Mon May 30 2011 - 00:03:50 PDT)
[AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2
- Andrew Voronkov (Mon May 30 2011 - 12:28:28 PDT)
- case (Sun May 29 2011 - 10:45:23 PDT)
- Andrew Voronkov (Sun May 29 2011 - 08:16:08 PDT)
- David A. Case (Fri May 27 2011 - 18:38:33 PDT)
- Jason Swails (Thu May 26 2011 - 14:56:48 PDT)
- Andrew Voronkov (Thu May 26 2011 - 12:59:14 PDT)
- David A. Case (Wed May 25 2011 - 02:30:47 PDT)
- Andrew Voronkov (Tue May 24 2011 - 23:05:08 PDT)
[AMBER] xleap as a molecular viewer
- Gustavo Seabra (Tue May 17 2011 - 10:12:08 PDT)
- Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:46:54 PDT)
- Daniel Roe (Tue May 17 2011 - 07:26:01 PDT)
- Jason Swails (Tue May 17 2011 - 07:26:20 PDT)
- Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:24:31 PDT)
- Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:09:06 PDT)
- David A Case (Tue May 17 2011 - 07:05:31 PDT)
- Daniel Roe (Tue May 17 2011 - 07:03:24 PDT)
- Jason Swails (Tue May 17 2011 - 07:01:55 PDT)
- Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 06:12:05 PDT)
[AMBER] xleap as a molecular viewer 2
- Paul Rigor (Wed May 18 2011 - 11:43:03 PDT)
- Bill Ross (Wed May 18 2011 - 11:37:28 PDT)
- Guenegou, Guillaume [ORDFR] (Wed May 18 2011 - 02:54:18 PDT)
- steinbrt.rci.rutgers.edu (Wed May 18 2011 - 02:18:52 PDT)
- Guenegou, Guillaume [ORDFR] (Wed May 18 2011 - 01:06:49 PDT)
[AMBER] Xleap trouble
- souvik sur (Wed May 04 2011 - 23:53:11 PDT)
[AMBER] XLEaP: Could not find type: Cl-
- Jason Swails (Tue May 31 2011 - 20:31:43 PDT)
- Zheng (Tue May 31 2011 - 16:17:42 PDT)
Ambertools1.5 installing problems.
- Daniel Roe (Tue May 31 2011 - 13:33:55 PDT)
- ning-shiuan.lee.yale.edu (Tue May 31 2011 - 12:03:57 PDT)
Estiblish
- David A. Case (Wed May 25 2011 - 00:15:32 PDT)
- Ross Walker (Mon May 23 2011 - 20:46:28 PDT)
- hanlu0366 (Mon May 23 2011 - 20:40:38 PDT)
NEB on a large system
- Carlos Simmerling (Wed May 25 2011 - 08:31:05 PDT)
- patrick wintrode (Wed May 25 2011 - 07:49:02 PDT)

Amber Archive May 2011 by subject