Amber Archive Oct 2012: by subject

[AMBER] "Bad value during floating point read" of processing dihedral using chamber
- baogen duan (Fri Oct 19 2012 - 05:56:57 PDT)
[AMBER] "istrng" option in MMPBSA calculation
- Jason Swails (Thu Oct 18 2012 - 05:00:50 PDT)
- baogen duan (Thu Oct 18 2012 - 03:57:29 PDT)
[AMBER] [PATCH 0/8] AmberTools cleanups
- Reinis (Tue Oct 23 2012 - 08:08:25 PDT)
- David A Case (Tue Oct 23 2012 - 05:43:36 PDT)
- Reinis Danne (Mon Oct 22 2012 - 15:14:53 PDT)
[AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj
- Reinis Danne (Mon Oct 22 2012 - 15:14:54 PDT)
[AMBER] [PATCH 2/8] dsarpack.f: Move into sff to allow build against arpack-ng
- Reinis Danne (Mon Oct 22 2012 - 15:14:55 PDT)
[AMBER] [PATCH 3/8] nab.c: Don't hardcode CPP path
- Reinis Danne (Mon Oct 22 2012 - 15:14:56 PDT)
[AMBER] [PATCH 4/8] sqm: Fix OpenMP build
- Reinis (Wed Oct 24 2012 - 15:55:05 PDT)
- Ross Walker (Wed Oct 24 2012 - 12:52:03 PDT)
- Reinis (Wed Oct 24 2012 - 11:30:25 PDT)
- Ross Walker (Wed Oct 24 2012 - 09:15:18 PDT)
- Reinis (Wed Oct 24 2012 - 01:09:25 PDT)
- Jason Swails (Tue Oct 23 2012 - 16:20:49 PDT)
- Reinis (Tue Oct 23 2012 - 13:55:26 PDT)
- Gustavo Seabra (Tue Oct 23 2012 - 12:51:43 PDT)
- Reinis (Tue Oct 23 2012 - 12:41:11 PDT)
- Gustavo Seabra (Tue Oct 23 2012 - 11:56:42 PDT)
- Ross Walker (Tue Oct 23 2012 - 10:00:36 PDT)
- Reinis (Tue Oct 23 2012 - 09:33:54 PDT)
- Ross Walker (Tue Oct 23 2012 - 09:26:34 PDT)
- Reinis (Tue Oct 23 2012 - 09:21:05 PDT)
- Gustavo Seabra (Tue Oct 23 2012 - 08:50:57 PDT)
- Reinis (Tue Oct 23 2012 - 08:37:25 PDT)
- David A Case (Tue Oct 23 2012 - 06:29:28 PDT)
- Reinis Danne (Mon Oct 22 2012 - 15:14:57 PDT)
[AMBER] [PATCH 5/8] test/nab: Use paths to scripts
- David A Case (Thu Oct 25 2012 - 16:58:56 PDT)
- Reinis Danne (Mon Oct 22 2012 - 15:14:58 PDT)
[AMBER] [PATCH 6/8] AmberTools: Tests should fail when they fail
- Reinis Danne (Mon Oct 22 2012 - 15:14:59 PDT)
[AMBER] [PATCH 7/8] AmberTools: Fix parallel tests
- Reinis Danne (Mon Oct 22 2012 - 15:15:00 PDT)
[AMBER] [PATCH 8/8] amber_outputs.py: Format floats in csv output
- Reinis Danne (Mon Oct 22 2012 - 15:15:01 PDT)
[AMBER] a question about replica exchange
- Carlos Simmerling (Mon Oct 15 2012 - 03:12:10 PDT)
- Albert (Sun Oct 14 2012 - 23:19:36 PDT)
[AMBER] about reproduction of HIS RESP charge
- FyD (Thu Oct 18 2012 - 12:39:39 PDT)
- Jocelyne Sogotongo (Wed Oct 17 2012 - 08:23:44 PDT)
[AMBER] about results
- Carlos Romero (Fri Oct 12 2012 - 18:28:18 PDT)
[AMBER] about salt concentration
- Thomas Evangelidis (Thu Oct 11 2012 - 02:23:28 PDT)
[AMBER] Accessible surface area
- Jason Swails (Wed Oct 17 2012 - 06:53:36 PDT)
- Esam Tolba (Wed Oct 17 2012 - 01:47:10 PDT)
[AMBER] ACS awards deadline Oct 23
- Carlos Simmerling (Tue Oct 16 2012 - 07:05:50 PDT)
[AMBER] AMBER
- davide.savy.unina.it (Tue Oct 16 2012 - 06:28:27 PDT)
[AMBER] Amber and P450 cytochromes
- Maximilian Ebert (Wed Oct 31 2012 - 08:53:56 PDT)
- David A Case (Wed Oct 31 2012 - 07:55:54 PDT)
- Maximilian Ebert (Wed Oct 31 2012 - 07:05:21 PDT)
[AMBER] AMBER Digest, Vol 292, Issue 2
- Julio Dominguez (Tue Oct 02 2012 - 21:03:57 PDT)
[AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ?
- Tomasz Borowski (Mon Oct 29 2012 - 05:25:45 PDT)
- Ross Walker (Tue Oct 23 2012 - 09:21:14 PDT)
- peter.stauffert.boehringer-ingelheim.com (Tue Oct 23 2012 - 05:42:10 PDT)
- Tomasz Borowski (Tue Oct 23 2012 - 04:40:02 PDT)
- Ross Walker (Fri Oct 19 2012 - 11:09:32 PDT)
- Aron Broom (Fri Oct 19 2012 - 07:45:13 PDT)
- Robert Crovella (Fri Oct 19 2012 - 06:50:05 PDT)
- Tomasz Borowski (Fri Oct 19 2012 - 01:13:38 PDT)
[AMBER] Amber12 installation and testing
- Ross Walker (Tue Oct 30 2012 - 10:59:58 PDT)
- Rahul Banerjee (Tue Oct 30 2012 - 10:47:09 PDT)
[AMBER] Amber12 Parrell Installation Error
- chenkai_szpku (Wed Oct 31 2012 - 04:52:01 PDT)
[AMBER] Amber12 uninitialized variable in sander/nmr.F90
- Jason Swails (Fri Oct 19 2012 - 15:21:51 PDT)
- Ake Sandgren (Fri Oct 19 2012 - 14:55:20 PDT)
[AMBER] AmberTools 12 Build Issue
- Jason Swails (Fri Oct 12 2012 - 08:23:46 PDT)
- Mark Zottola (Fri Oct 12 2012 - 07:57:54 PDT)
[AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90
- Andreas Goetz (Mon Oct 22 2012 - 15:02:28 PDT)
- Ake Sandgren (Mon Oct 22 2012 - 13:18:47 PDT)
- Andreas Goetz (Mon Oct 22 2012 - 13:11:24 PDT)
- Ake Sandgren (Fri Oct 19 2012 - 13:11:00 PDT)
[AMBER] ambpdb problems
- Jason Swails (Tue Oct 16 2012 - 10:17:24 PDT)
- Pyle, Ronald (Tue Oct 16 2012 - 07:59:00 PDT)
[AMBER] aMD with implicit solvent?
- Marc van der Kamp (Fri Oct 05 2012 - 08:30:52 PDT)
[AMBER] angle between axes of two helices
- vaibhav dixit (Wed Oct 10 2012 - 22:24:38 PDT)
[AMBER] Antechamber + SQM/DFTB
- Edgar Mixcoha (Mon Oct 01 2012 - 06:56:52 PDT)
- David A Case (Mon Oct 01 2012 - 05:32:28 PDT)
- Edgar Mixcoha (Mon Oct 01 2012 - 03:12:14 PDT)
[AMBER] antechamber limitation on molecule size
- Daniel Roe (Wed Oct 31 2012 - 17:06:57 PDT)
- Yi An (Wed Oct 31 2012 - 12:05:59 PDT)
- anyiphysics.gmail.com (Mon Oct 29 2012 - 12:37:25 PDT)
[AMBER] Antechamber preparartion
- FyD (Tue Oct 30 2012 - 01:35:31 PDT)
- David A Case (Mon Oct 29 2012 - 07:18:55 PDT)
- Алексей Раевский (Mon Oct 29 2012 - 04:57:10 PDT)
[AMBER] Antechamber Warning Atomtype
- Jason Swails (Wed Oct 24 2012 - 12:55:43 PDT)
- ashley chen (Tue Oct 23 2012 - 23:37:40 PDT)
[AMBER] Arsenic VDW parameters
- zhukk (Tue Oct 09 2012 - 01:11:34 PDT)
[AMBER] Asterisks in the restart file
- Ross Walker (Mon Oct 08 2012 - 05:44:25 PDT)
- David A Case (Mon Oct 08 2012 - 05:43:29 PDT)
- Cao Yang (Mon Oct 08 2012 - 05:08:41 PDT)
[AMBER] Atom selection for restraints
- Daniel Roe (Mon Oct 29 2012 - 16:10:52 PDT)
- Date, Mihir (Mon Oct 29 2012 - 15:41:10 PDT)
[AMBER] Atom selection for restraints. .
- Date, Mihir (Tue Oct 30 2012 - 07:18:22 PDT)
[AMBER] Atom selection for restraints. .. .
- Bashford, Donald (Tue Oct 30 2012 - 14:07:50 PDT)
[AMBER] Atom-type for aromatic carbon attached by amide nitrogen
- Yun Shi (Tue Oct 16 2012 - 20:29:13 PDT)
- Yun Shi (Tue Oct 16 2012 - 16:07:01 PDT)
- Aron Broom (Tue Oct 16 2012 - 15:21:45 PDT)
- Yun Shi (Tue Oct 16 2012 - 12:39:15 PDT)
[AMBER] Average structure of trajectories as pdb file?
- Daniel Roe (Thu Oct 11 2012 - 07:40:37 PDT)
- Esam Tolba (Thu Oct 11 2012 - 06:44:01 PDT)
[AMBER] Bad atom type
- Osman, Roman (Sun Oct 21 2012 - 17:58:56 PDT)
- Jason Swails (Sat Oct 20 2012 - 19:42:49 PDT)
- Osman, Roman (Sat Oct 20 2012 - 17:12:46 PDT)
[AMBER] bad atom type: cl error in MMPBSA decomp
- Bill Miller III (Fri Oct 12 2012 - 05:12:05 PDT)
- vaibhav dixit (Fri Oct 12 2012 - 02:43:39 PDT)
[AMBER] Basis of sander of Amber11 and Amber9
- David A Case (Wed Oct 10 2012 - 05:49:05 PDT)
- Sindrila Dutta banik (Tue Oct 09 2012 - 13:12:27 PDT)
[AMBER] calculating intramolecular hydrogen bonding
- Daniel Roe (Wed Oct 17 2012 - 06:57:44 PDT)
- Vijay Manickam Achari (Mon Oct 15 2012 - 01:19:08 PDT)
- Daniel Roe (Fri Oct 05 2012 - 10:43:11 PDT)
- Vijay Manickam Achari (Fri Oct 05 2012 - 00:29:22 PDT)
[AMBER] Calculation of single atom radius of gyration
- Daniel Roe (Fri Oct 26 2012 - 14:34:40 PDT)
- Amy Davenport (Fri Oct 26 2012 - 14:04:04 PDT)
- Daniel Sindhikara (Thu Oct 25 2012 - 18:54:15 PDT)
- Amy Davenport (Thu Oct 25 2012 - 16:02:50 PDT)
- Jason Swails (Wed Oct 24 2012 - 15:52:22 PDT)
- Daniel Roe (Wed Oct 24 2012 - 15:51:46 PDT)
- Amy Davenport (Wed Oct 24 2012 - 14:50:20 PDT)
[AMBER] can i strip water energy from .out ?
- Jason Swails (Mon Oct 29 2012 - 06:12:03 PDT)
- Tong Zhu (Sun Oct 28 2012 - 21:45:19 PDT)
- Jason Swails (Fri Oct 26 2012 - 06:32:29 PDT)
- 千语千寻 (Thu Oct 25 2012 - 23:22:30 PDT)
[AMBER] Can not find dhfr containing 23,558 atoms in AMBER
- Ross Walker (Tue Oct 09 2012 - 01:11:59 PDT)
- 陶晓芳 (Mon Oct 08 2012 - 20:18:53 PDT)
[AMBER] Centering a multimeric protein with solvateOct
- Jonathan Sheehan (Sat Oct 06 2012 - 18:07:47 PDT)
- Bill Ross (Sat Oct 06 2012 - 15:09:05 PDT)
- Jonathan Sheehan (Thu Oct 04 2012 - 12:24:29 PDT)
[AMBER] CHAMBER: error in finding bond type
- Mark Williamson (Wed Oct 17 2012 - 05:29:17 PDT)
- Mark Williamson (Tue Oct 16 2012 - 05:24:38 PDT)
- Mike Limb (Tue Oct 16 2012 - 04:28:26 PDT)
[AMBER] cis form: avoiding atom overlap in all-atom modeling
- David A Case (Tue Oct 23 2012 - 05:26:28 PDT)
- Anselm Horn (Tue Oct 23 2012 - 00:50:07 PDT)
- Aron Broom (Fri Oct 19 2012 - 11:30:18 PDT)
- bio lab (Fri Oct 19 2012 - 10:11:16 PDT)
- Aron Broom (Thu Oct 18 2012 - 21:36:08 PDT)
- Aron Broom (Thu Oct 18 2012 - 18:30:02 PDT)
- bio lab (Thu Oct 18 2012 - 17:05:47 PDT)
- Aron Broom (Thu Oct 18 2012 - 12:30:30 PDT)
- bio lab (Thu Oct 18 2012 - 11:10:58 PDT)
- Aron Broom (Thu Oct 18 2012 - 09:53:40 PDT)
- bio lab (Thu Oct 18 2012 - 09:42:13 PDT)
[AMBER] clustering error message
- Daniel Roe (Wed Oct 17 2012 - 13:08:02 PDT)
- Catein Catherine (Wed Oct 17 2012 - 10:29:13 PDT)
[AMBER] clustering the trajectories
- Daniel Roe (Thu Oct 18 2012 - 08:57:52 PDT)
- Esam Tolba (Thu Oct 18 2012 - 00:38:24 PDT)
- Daniel Roe (Wed Oct 17 2012 - 13:09:42 PDT)
- Esam Tolba (Wed Oct 17 2012 - 12:49:09 PDT)
- David A Case (Wed Oct 17 2012 - 06:26:56 PDT)
- Esam Tolba (Wed Oct 17 2012 - 01:44:51 PDT)
- Daniel Roe (Thu Oct 11 2012 - 07:43:10 PDT)
- Esam Tolba (Thu Oct 11 2012 - 07:37:05 PDT)
[AMBER] Clustering VS constant rmsd
- George Tzotzos (Thu Oct 18 2012 - 10:33:57 PDT)
- David A Case (Thu Oct 18 2012 - 04:39:06 PDT)
- George Tzotzos (Wed Oct 17 2012 - 18:19:33 PDT)
- David A Case (Wed Oct 17 2012 - 18:09:53 PDT)
- vaibhav dixit (Wed Oct 17 2012 - 10:47:02 PDT)
- Catein Catherine (Wed Oct 17 2012 - 10:23:50 PDT)
[AMBER] compilation aborted for ncsu-umbrella.F90 (code 1)
- David A Case (Tue Oct 23 2012 - 06:18:41 PDT)
- Jason Swails (Tue Oct 23 2012 - 06:19:01 PDT)
- hari krishna (Tue Oct 23 2012 - 04:48:44 PDT)
[AMBER] compilation error on Amber 10
- David A Case (Wed Oct 17 2012 - 06:39:24 PDT)
- Abderezak-EXT.Mekfouldji.sanofi.com (Wed Oct 17 2012 - 03:41:44 PDT)
[AMBER] Compiling amber parallel
- Dickson, Callum (Fri Oct 26 2012 - 08:11:18 PDT)
[AMBER] completing C-term atoms after strip in ptraj
- Nihal Korkmaz (Fri Oct 12 2012 - 11:48:36 PDT)
- David A Case (Fri Oct 12 2012 - 04:56:18 PDT)
- Jason Swails (Thu Oct 11 2012 - 23:38:08 PDT)
- Nihal Korkmaz (Thu Oct 11 2012 - 16:53:56 PDT)
[AMBER] Computational methods to explain the small regioselectivity
- Mu Xia (Wed Oct 24 2012 - 01:21:55 PDT)
[AMBER] Computer specification for Amber 12
- Esam Tolba (Thu Oct 18 2012 - 02:03:32 PDT)
[AMBER] Concerning nonbonded exclusions and MMPBSA
- Aron Broom (Thu Oct 18 2012 - 09:35:24 PDT)
- Jason Swails (Thu Oct 18 2012 - 08:57:58 PDT)
- Aron Broom (Thu Oct 18 2012 - 08:45:25 PDT)
[AMBER] configure problem during installation
- vaibhav dixit (Sat Oct 20 2012 - 07:45:38 PDT)
- Jason Swails (Sat Oct 20 2012 - 05:41:26 PDT)
- vaibhav dixit (Sat Oct 20 2012 - 01:40:26 PDT)
[AMBER] Count number of frames in any trajectory file
- Shafinaz Chowdhury (Mon Oct 15 2012 - 13:14:39 PDT)
[AMBER] cuda pmemd failed
- Ross Walker (Fri Oct 19 2012 - 11:31:05 PDT)
- Scott Le Grand (Thu Oct 18 2012 - 11:02:15 PDT)
- Jason Swails (Thu Oct 18 2012 - 06:39:17 PDT)
- Yubo Fan (Thu Oct 18 2012 - 06:37:55 PDT)
- Yubo Fan (Thu Oct 18 2012 - 06:00:05 PDT)
- Yubo Fan (Thu Oct 18 2012 - 04:51:52 PDT)
- Yubo Fan (Thu Oct 18 2012 - 00:41:11 PDT)
[AMBER] Cuda test hangs with Amber12 compiled with CUDA5
- Ross Walker (Fri Oct 19 2012 - 11:19:59 PDT)
- Jean-Christophe Ducom (Fri Oct 19 2012 - 11:18:46 PDT)
- Ismail, Mohd F. (Fri Oct 19 2012 - 11:12:59 PDT)
- Jean-Christophe Ducom (Fri Oct 19 2012 - 10:40:27 PDT)
[AMBER] deprotonated serine
- Antonija Tomić (Mon Oct 29 2012 - 07:27:06 PDT)
[AMBER] details of energy values for individual frames in MMPBSA.py calculations...
- Jason Swails (Mon Oct 15 2012 - 14:20:44 PDT)
- Shashidhar Rao (Mon Oct 15 2012 - 13:19:59 PDT)
- Shashidhar Rao (Mon Oct 15 2012 - 13:14:13 PDT)
- Jason Swails (Mon Oct 15 2012 - 12:42:00 PDT)
- Jason Swails (Mon Oct 15 2012 - 12:40:53 PDT)
- Shashidhar Rao (Mon Oct 15 2012 - 12:25:09 PDT)
- Shashidhar Rao (Mon Oct 15 2012 - 12:12:41 PDT)
[AMBER] diff. between avg/rep structures & connectivity problem in PDB files
- vaibhav dixit (Mon Oct 08 2012 - 08:15:44 PDT)
- Daniel Roe (Mon Oct 08 2012 - 07:39:42 PDT)
- vaibhav dixit (Sun Oct 07 2012 - 02:24:02 PDT)
[AMBER] Difference between ntx5 and ntx 7
- Jason Swails (Tue Oct 02 2012 - 04:36:44 PDT)
- Sindrila Dutta banik (Mon Oct 01 2012 - 23:01:14 PDT)
[AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM
- Sangeetha B (Wed Oct 10 2012 - 04:27:22 PDT)
- Sangeetha B (Wed Oct 10 2012 - 04:14:40 PDT)
- Ben Roberts (Tue Oct 09 2012 - 13:14:52 PDT)
- Jason Swails (Tue Oct 09 2012 - 04:47:48 PDT)
- Sangeetha B (Tue Oct 09 2012 - 03:59:19 PDT)
[AMBER] different between PBSA and MMPBSA ?
- setyanto md (Mon Oct 08 2012 - 04:01:13 PDT)
- Jason Swails (Mon Oct 08 2012 - 03:26:37 PDT)
- setyanto md (Mon Oct 08 2012 - 01:05:34 PDT)
- David A Case (Tue Oct 02 2012 - 05:25:30 PDT)
- Jason Swails (Tue Oct 02 2012 - 04:45:54 PDT)
- setyanto md (Tue Oct 02 2012 - 04:41:26 PDT)
- Jason Swails (Tue Oct 02 2012 - 04:31:00 PDT)
- setyanto md (Tue Oct 02 2012 - 02:59:49 PDT)
- setyanto md (Tue Oct 02 2012 - 02:00:20 PDT)
[AMBER] different Partial charges for CYM in amino94.xml (MCPB) and all_amino94.lib (leap)
- Sangeetha B (Mon Oct 01 2012 - 00:30:48 PDT)
[AMBER] different restraint_wt settings possble?
- hironori.kokubo.takeda.com (Thu Oct 18 2012 - 02:12:15 PDT)
[AMBER] Distance calculations with ptraj
- Daniel Roe (Mon Oct 08 2012 - 15:07:15 PDT)
- Kira Armacost (Mon Oct 08 2012 - 13:18:03 PDT)
- Daniel Roe (Mon Oct 08 2012 - 07:28:49 PDT)
- Kira Armacost (Sun Oct 07 2012 - 12:23:43 PDT)
[AMBER] distortion of the ligand during MD
- Jason Swails (Wed Oct 17 2012 - 08:35:52 PDT)
- Mu Xia (Wed Oct 17 2012 - 07:02:42 PDT)
- David A Case (Wed Oct 17 2012 - 06:44:06 PDT)
- Mu Xia (Wed Oct 17 2012 - 04:12:45 PDT)
[AMBER] Download problem of amber12
- David A Case (Wed Oct 31 2012 - 07:49:31 PDT)
- Sanjib Paul (Tue Oct 30 2012 - 23:25:35 PDT)
[AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model
- Brian Radak (Mon Oct 01 2012 - 13:58:22 PDT)
- Sajeewa Pemasinghe (Mon Oct 01 2012 - 13:36:09 PDT)
[AMBER] Error 'Created a new atom named:'
- Olguin, Marco A (Thu Oct 25 2012 - 18:43:24 PDT)
- Joaquin Barroso Flores (Thu Oct 25 2012 - 18:26:03 PDT)
[AMBER] Error Message in running MM/GBSA
- Catein Catherine (Mon Oct 29 2012 - 22:51:59 PDT)
[AMBER] error when Chamber dealing with DNA, RNA and ATP
- Ross Walker (Tue Oct 30 2012 - 11:03:56 PDT)
- Mark Williamson (Tue Oct 30 2012 - 04:48:27 PDT)
[AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top
- baogen duan (Thu Oct 11 2012 - 19:16:03 PDT)
- duanbg (Tue Oct 02 2012 - 20:05:09 PDT)
[AMBER] Errors in Amber12 installation
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:11:21 PDT)
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:10:58 PDT)
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:09:52 PDT)
- Ben Roberts (Mon Oct 08 2012 - 18:57:18 PDT)
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 17:30:25 PDT)
- Ben Roberts (Mon Oct 08 2012 - 16:46:09 PDT)
- David A Case (Mon Oct 08 2012 - 13:33:19 PDT)
- Ross Walker (Mon Oct 08 2012 - 13:26:49 PDT)
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 11:28:04 PDT)
[AMBER] Estimating time in AMD
- Soumya Lipsa Rath (Mon Oct 08 2012 - 07:19:30 PDT)
- Soumya Lipsa Rath (Mon Oct 08 2012 - 02:31:46 PDT)
- Adrian Roitberg (Mon Oct 08 2012 - 02:10:48 PDT)
- Romelia Salomon (Mon Oct 08 2012 - 01:25:49 PDT)
- Soumya Lipsa Rath (Sun Oct 07 2012 - 22:08:04 PDT)
[AMBER] extract velocities
- Brian Radak (Mon Oct 22 2012 - 13:47:05 PDT)
- Giulia (Mon Oct 22 2012 - 09:11:48 PDT)
[AMBER] files for RED
- FyD (Sun Oct 28 2012 - 09:53:44 PDT)
- Urszula Uciechowska (Sat Oct 27 2012 - 07:30:06 PDT)
- FyD (Thu Oct 25 2012 - 05:34:49 PDT)
- Urszula Uciechowska (Thu Oct 25 2012 - 04:10:02 PDT)
- FyD (Wed Oct 24 2012 - 05:13:03 PDT)
- Urszula Uciechowska (Wed Oct 24 2012 - 03:23:44 PDT)
- FyD (Mon Oct 22 2012 - 08:44:09 PDT)
- Urszula Uciechowska (Mon Oct 22 2012 - 01:52:17 PDT)
[AMBER] forefield for Pyridoxal 5-phosphate
- FyD (Fri Oct 12 2012 - 13:02:08 PDT)
- BALA SUBRAMANI G L (Fri Oct 12 2012 - 07:39:35 PDT)
[AMBER] Fwd: Notes and warnings in the generalized Born calculation
- Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:37:02 PDT)
- Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:36:20 PDT)
- David A Case (Fri Oct 12 2012 - 17:48:35 PDT)
- Carlos Simmerling (Fri Oct 12 2012 - 14:26:55 PDT)
- Sajeewa Pemasinghe (Fri Oct 12 2012 - 14:23:48 PDT)
[AMBER] genmetalFF.sh
- David A Case (Tue Oct 16 2012 - 18:33:18 PDT)
- Renuka Ganesan (Tue Oct 16 2012 - 07:34:19 PDT)
[AMBER] glyco
- Lachele Foley (Lists) (Wed Oct 17 2012 - 18:27:22 PDT)
- yanyuna (Mon Oct 15 2012 - 19:58:57 PDT)
- Lachele Foley (Lists) (Mon Oct 15 2012 - 17:26:50 PDT)
- yanyuna (Mon Oct 15 2012 - 01:59:46 PDT)
[AMBER] glycoprotein
- Lachele Foley (Lists) (Sun Oct 14 2012 - 20:54:55 PDT)
- yanyuna (Sun Oct 14 2012 - 19:59:01 PDT)
- Lachele Foley (Lists) (Sun Oct 14 2012 - 09:24:53 PDT)
- yanyuna (Sat Oct 13 2012 - 23:27:26 PDT)
[AMBER] GPU accelerated - accelerated MD (Was: Count number of frames in any trajectory file)
- Ross Walker (Mon Oct 15 2012 - 13:44:07 PDT)
[AMBER] How Can I modify a amino acid in Amber
- FyD (Sun Oct 21 2012 - 22:59:59 PDT)
- Changqing Yan (Sun Oct 21 2012 - 19:22:19 PDT)
[AMBER] How Can I modify a amino acid in Amber?
- FyD (Sun Oct 14 2012 - 22:22:59 PDT)
- Changqing Yan (Sun Oct 14 2012 - 20:11:17 PDT)
- Sajeewa Pemasinghe (Sat Oct 13 2012 - 05:33:52 PDT)
- FyD (Sat Oct 13 2012 - 03:42:41 PDT)
- Sajeewa Pemasinghe (Sat Oct 13 2012 - 00:48:49 PDT)
- Changqing Yan (Fri Oct 12 2012 - 19:17:02 PDT)
[AMBER] How do I generate prmtop files with bondi radii?
- Sajeewa Pemasinghe (Thu Oct 04 2012 - 15:52:22 PDT)
- Jason Swails (Thu Oct 04 2012 - 15:28:08 PDT)
- Sajeewa Pemasinghe (Thu Oct 04 2012 - 15:20:36 PDT)
[AMBER] How dose ptraj calculate diffusion
- Daniel Roe (Mon Oct 15 2012 - 14:23:57 PDT)
- Alan (Mon Oct 15 2012 - 04:56:51 PDT)
[AMBER] How to convert ptraj cluster commands to cpptraj
- Catein Catherine (Fri Oct 19 2012 - 10:49:28 PDT)
[AMBER] how to create crd file from my tra file?
- Daniel Roe (Tue Oct 09 2012 - 09:00:02 PDT)
- Esam Tolba (Tue Oct 09 2012 - 02:07:26 PDT)
[AMBER] How to express a right-handed amino acid in leap
- Jason Swails (Thu Oct 11 2012 - 07:03:04 PDT)
- Changqing Yan (Thu Oct 11 2012 - 05:36:49 PDT)
[AMBER] how to predict time for MMPBSA decomp analysis
- vaibhav dixit (Tue Oct 09 2012 - 23:25:06 PDT)
[AMBER] How to read the PairwiseDistance file after clustering analysis?
- Catein Catherine (Fri Oct 19 2012 - 10:54:28 PDT)
[AMBER] Hydrogen bond time series in cpptraj
- Daniel Roe (Thu Oct 25 2012 - 08:16:03 PDT)
- Diego Javier Alonso de Armiño (Thu Oct 25 2012 - 06:23:33 PDT)
[AMBER] Hydrophobic cleft is solvent-exposed
- Mannan (Sun Oct 21 2012 - 19:06:17 PDT)
[AMBER] idecomp and so on....
- Jason Swails (Tue Oct 09 2012 - 14:11:49 PDT)
- André C. Stiel (Tue Oct 09 2012 - 13:59:12 PDT)
- Jason Swails (Tue Oct 09 2012 - 12:26:07 PDT)
- André C. Stiel (Tue Oct 09 2012 - 09:35:56 PDT)
- Jason Swails (Mon Oct 08 2012 - 14:40:49 PDT)
- André C. Stiel (Mon Oct 08 2012 - 09:52:36 PDT)
[AMBER] If i strip water from the trajectory files, would it influence the analysis results?
- Daniel Roe (Mon Oct 29 2012 - 07:28:25 PDT)
- Tong Zhu (Sun Oct 28 2012 - 21:43:06 PDT)
- 千语千寻 (Sun Oct 28 2012 - 19:17:17 PDT)
[AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP
- Aron Broom (Tue Oct 16 2012 - 16:26:15 PDT)
- Aron Broom (Tue Oct 16 2012 - 11:40:04 PDT)
- Jason Swails (Tue Oct 16 2012 - 10:15:35 PDT)
- Aron Broom (Tue Oct 16 2012 - 09:59:55 PDT)
[AMBER] Input files for MMPBSA
- Jason Swails (Tue Oct 16 2012 - 04:25:43 PDT)
- Tommy Yap (Mon Oct 15 2012 - 18:59:35 PDT)
- Jason Swails (Mon Oct 15 2012 - 04:52:56 PDT)
- Tommy Yap (Sun Oct 14 2012 - 19:54:24 PDT)
[AMBER] Inquiry about how writing out pressure tensor
- Mo Chen (Mon Oct 29 2012 - 12:29:50 PDT)
- David A Case (Mon Oct 29 2012 - 07:10:30 PDT)
- Mo Chen (Mon Oct 29 2012 - 00:13:12 PDT)
- Mo Chen (Mon Oct 29 2012 - 00:04:03 PDT)
- Mo Chen (Fri Oct 26 2012 - 18:57:51 PDT)
- Ross Walker (Fri Oct 26 2012 - 16:48:16 PDT)
- Mo Chen (Fri Oct 26 2012 - 15:57:17 PDT)
[AMBER] intdiel / extdiel
- Gustavo Seabra (Thu Oct 18 2012 - 17:12:49 PDT)
- Daniel Roe (Thu Oct 18 2012 - 16:48:10 PDT)
- Jason Swails (Thu Oct 18 2012 - 15:59:25 PDT)
- Gustavo Seabra (Thu Oct 18 2012 - 15:35:40 PDT)
- Jason Swails (Thu Oct 18 2012 - 12:26:22 PDT)
- Gustavo Seabra (Thu Oct 18 2012 - 11:01:02 PDT)
[AMBER] job failed for REMD in cluster
- Scott Le Grand (Mon Oct 15 2012 - 13:47:04 PDT)
- Jason Swails (Mon Oct 15 2012 - 13:09:01 PDT)
- David A Case (Mon Oct 15 2012 - 12:53:18 PDT)
- Jason Swails (Mon Oct 15 2012 - 12:47:14 PDT)
- Ross Walker (Mon Oct 15 2012 - 12:07:41 PDT)
- Ross Walker (Mon Oct 15 2012 - 12:06:32 PDT)
- Carlos Simmerling (Mon Oct 15 2012 - 12:01:47 PDT)
- Albert (Mon Oct 15 2012 - 11:53:49 PDT)
- Albert (Mon Oct 15 2012 - 11:48:04 PDT)
[AMBER] join amber mailing list
- Yulin Huang (Fri Oct 26 2012 - 13:44:50 PDT)
[AMBER] Joining two files
- Lorenzo Gontrani (Wed Oct 31 2012 - 05:45:13 PDT)
- Marco Malvaldi (Wed Oct 31 2012 - 05:00:03 PDT)
- Lorenzo Gontrani (Mon Oct 29 2012 - 07:32:47 PDT)
- Jacopo Sgrignani (Mon Oct 29 2012 - 05:31:06 PDT)
- Marco Malvaldi (Mon Oct 29 2012 - 03:47:35 PDT)
[AMBER] Leap ditribution
- David A Case (Wed Oct 17 2012 - 09:37:02 PDT)
- Aron Broom (Wed Oct 17 2012 - 09:05:48 PDT)
- davide.savy.unina.it (Wed Oct 17 2012 - 08:49:01 PDT)
[AMBER] Maintaining Chain ID
- Daniel Roe (Wed Oct 17 2012 - 07:04:15 PDT)
- David A Case (Mon Oct 15 2012 - 12:45:36 PDT)
- Brown, Kyle (Mon Oct 15 2012 - 10:26:52 PDT)
[AMBER] Meaning of setting gbsa=0 in generalized Born calculations
- Sajeewa Pemasinghe (Fri Oct 05 2012 - 07:48:36 PDT)
- Jason Swails (Fri Oct 05 2012 - 07:27:42 PDT)
- Carlos Simmerling (Fri Oct 05 2012 - 04:48:26 PDT)
- Jason Swails (Fri Oct 05 2012 - 04:45:19 PDT)
- Sajeewa Pemasinghe (Thu Oct 04 2012 - 21:01:50 PDT)
[AMBER] Meaning of the term "pre-equilibrated" waters
- Bill Ross (Sun Oct 21 2012 - 17:31:24 PDT)
- Sajeewa Pemasinghe (Sun Oct 21 2012 - 09:54:10 PDT)
[AMBER] Misleading leaprc with ff12
- David A Case (Fri Oct 26 2012 - 04:49:47 PDT)
- Jesper Sørensen (Thu Oct 25 2012 - 10:00:24 PDT)
[AMBER] missing bonds and angles
- Mary Varughese (Sun Oct 07 2012 - 22:36:17 PDT)
[AMBER] MMPBSA error
- Nadine Homeyer (Mon Oct 01 2012 - 05:49:38 PDT)
- Jason Swails (Mon Oct 01 2012 - 04:23:46 PDT)
- BERGY (Mon Oct 01 2012 - 02:15:17 PDT)
[AMBER] MMPBSA.py
- Federica Chiappori (Wed Oct 17 2012 - 02:03:17 PDT)
- Jason Swails (Tue Oct 16 2012 - 10:01:29 PDT)
- Federica Chiappori (Tue Oct 16 2012 - 08:58:16 PDT)
[AMBER] MMPBSA.py error in AmberTools 12 fixed
- Jason Swails (Mon Oct 22 2012 - 08:57:10 PDT)
[AMBER] Molecular Dynamic production
- Jason Swails (Tue Oct 02 2012 - 04:42:15 PDT)
- Anogna (Mon Oct 01 2012 - 22:51:28 PDT)
[AMBER] NaN question
- mhclewett.msn.com (Sat Oct 20 2012 - 08:43:59 PDT)
- Ross Walker (Fri Oct 19 2012 - 11:19:04 PDT)
- Jason Swails (Fri Oct 19 2012 - 10:07:32 PDT)
- mhclewett.msn.com (Fri Oct 19 2012 - 09:48:09 PDT)
- mhclewett.msn.com (Fri Oct 19 2012 - 09:46:58 PDT)
- Aron Broom (Fri Oct 19 2012 - 07:51:35 PDT)
- Jason Swails (Fri Oct 19 2012 - 07:49:50 PDT)
- mhclewett.msn.com (Fri Oct 19 2012 - 07:36:49 PDT)
[AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27
- Miguel Ortiz Lombardia (Fri Oct 26 2012 - 14:39:17 PDT)
- Jason Swails (Fri Oct 26 2012 - 09:19:44 PDT)
- Miguel Ortiz Lombardía (Fri Oct 26 2012 - 08:42:51 PDT)
[AMBER] NMR restraints based on order parameters
- Guanglei Cui (Thu Oct 11 2012 - 07:42:45 PDT)
[AMBER] no prmtop created with closest
- Andre Serobian (Wed Oct 10 2012 - 22:33:47 PDT)
- Daniel Roe (Wed Oct 10 2012 - 21:56:45 PDT)
- Andre Serobian (Wed Oct 10 2012 - 19:26:46 PDT)
[AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py
- Ray Luo, Ph.D. (Fri Oct 12 2012 - 10:25:22 PDT)
- Ray Luo, Ph.D. (Thu Oct 11 2012 - 14:25:38 PDT)
- Tong Zhu (Wed Oct 10 2012 - 23:55:07 PDT)
[AMBER] Nonstandard residue: phosphotyrosine
- steinbrt.rci.rutgers.edu (Mon Oct 29 2012 - 11:22:41 PDT)
- Jason Swails (Mon Oct 29 2012 - 08:05:43 PDT)
- PAUL NEWMAN (Mon Oct 29 2012 - 07:46:41 PDT)
- Anselm Horn (Mon Oct 29 2012 - 07:24:02 PDT)
- PAUL NEWMAN (Mon Oct 29 2012 - 07:03:47 PDT)
[AMBER] Notes and warnings in the generalized Born calculation
- Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:35:39 PDT)
- Jason Swails (Fri Oct 12 2012 - 17:12:25 PDT)
- Sajeewa Pemasinghe (Fri Oct 12 2012 - 11:24:45 PDT)
[AMBER] NPA charge for the ligand
- FyD (Mon Oct 15 2012 - 01:37:11 PDT)
- Mu Xia (Mon Oct 15 2012 - 00:58:30 PDT)
[AMBER] NVE ensemble for solvation
- David A Case (Wed Oct 10 2012 - 04:08:50 PDT)
- marawan hussain (Tue Oct 09 2012 - 17:12:04 PDT)
[AMBER] Obtain trajectory in NAB
- Sangmin Lee (Thu Oct 04 2012 - 22:17:58 PDT)
- David A Case (Thu Oct 04 2012 - 07:10:02 PDT)
- Sangmin Lee (Thu Oct 04 2012 - 01:13:46 PDT)
[AMBER] on salt bridge affinity by AMBER
- Carlos Simmerling (Sat Oct 13 2012 - 06:08:02 PDT)
- Acoot Brett (Fri Oct 12 2012 - 20:28:31 PDT)
[AMBER] Pairwise decoposition (MMPBSA)
- Bill Miller III (Wed Oct 17 2012 - 08:19:51 PDT)
- Xioling Chuang (Tue Oct 16 2012 - 19:34:41 PDT)
[AMBER] PairwiseDistance file location
- vaibhav dixit (Fri Oct 05 2012 - 18:58:53 PDT)
- Daniel Roe (Fri Oct 05 2012 - 10:47:55 PDT)
- vaibhav dixit (Thu Oct 04 2012 - 22:10:40 PDT)
- Daniel Roe (Thu Oct 04 2012 - 07:35:35 PDT)
- vaibhav dixit (Thu Oct 04 2012 - 01:28:11 PDT)
[AMBER] parallel MMPBSA: no of cores versus no of frames analyzed
- Jason Swails (Mon Oct 01 2012 - 10:18:21 PDT)
- Vlad Cojocaru (Mon Oct 01 2012 - 09:39:06 PDT)
- Jason Swails (Mon Oct 01 2012 - 09:32:04 PDT)
- Vlad Cojocaru (Mon Oct 01 2012 - 09:10:47 PDT)
[AMBER] Part 2 of xleap
- Mark Zottola (Fri Oct 12 2012 - 10:57:45 PDT)
[AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU
- pavel.banas.upol.cz (Tue Oct 16 2012 - 13:57:04 PDT)
- Niel Henriksen (Tue Oct 16 2012 - 10:06:17 PDT)
- Niel Henriksen (Mon Oct 15 2012 - 12:58:48 PDT)
- Jason Swails (Mon Oct 15 2012 - 12:38:16 PDT)
- Niel Henriksen (Mon Oct 15 2012 - 12:07:39 PDT)
- pavel.banas.upol.cz (Mon Oct 15 2012 - 11:25:17 PDT)
- Scott Le Grand (Mon Oct 15 2012 - 10:56:46 PDT)
- Niel Henriksen (Mon Oct 15 2012 - 09:39:12 PDT)
- pavel.banas.upol.cz (Mon Oct 15 2012 - 00:22:33 PDT)
[AMBER] phosphate moiety & igb model
- Carlos Simmerling (Fri Oct 05 2012 - 04:43:50 PDT)
- Marc van der Kamp (Fri Oct 05 2012 - 03:10:21 PDT)
[AMBER] pmemd installation error
- Jason Swails (Thu Oct 11 2012 - 05:11:42 PDT)
- mehdi bagherpoor (Thu Oct 11 2012 - 04:10:30 PDT)
[AMBER] positional restraint to within stipulated distance
- Eng H Yap (Mon Oct 29 2012 - 20:00:01 PDT)
[AMBER] Possible bug in LEaP with ff12SB
- Bill Ross (Thu Oct 25 2012 - 23:47:25 PDT)
- Aronica, Pietro (Thu Oct 25 2012 - 05:36:11 PDT)
- David A Case (Thu Oct 25 2012 - 05:32:43 PDT)
- Aronica, Pietro (Thu Oct 25 2012 - 04:23:32 PDT)
[AMBER] Probelms encountered when creating non-standard residue
- Aron Broom (Thu Oct 18 2012 - 21:25:20 PDT)
- Changqing Yan (Thu Oct 18 2012 - 20:07:59 PDT)
[AMBER] Problem in Installing Amber12/Tools in parallel
- Jason Swails (Thu Oct 04 2012 - 05:12:16 PDT)
- Sajeewa Pemasinghe (Wed Oct 03 2012 - 23:40:55 PDT)
[AMBER] Problem in running parallel
- David A Case (Wed Oct 31 2012 - 07:46:17 PDT)
- Terry (Tue Oct 30 2012 - 22:33:15 PDT)
- hari krishna (Tue Oct 30 2012 - 21:56:22 PDT)
[AMBER] Problem related to the Amber11 installation in user account
- Jason Swails (Tue Oct 09 2012 - 05:15:53 PDT)
- Sindrila Dutta banik (Tue Oct 09 2012 - 02:19:36 PDT)
- Jason Swails (Tue Oct 09 2012 - 02:03:25 PDT)
- Sindrila Dutta banik (Tue Oct 09 2012 - 01:25:52 PDT)
- Jason Swails (Tue Oct 09 2012 - 01:06:30 PDT)
- Sindrila Dutta banik (Tue Oct 09 2012 - 00:59:16 PDT)
- Jason Swails (Tue Oct 09 2012 - 00:22:37 PDT)
- Sindrila Dutta banik (Mon Oct 08 2012 - 21:39:46 PDT)
[AMBER] Problem related to the analysis of mdcrd
- Daniel Roe (Thu Oct 04 2012 - 07:39:29 PDT)
- Sindrila Dutta banik (Wed Oct 03 2012 - 23:48:59 PDT)
[AMBER] Problem related to the parallel installation of Amber11
- Sindrila Dutta banik (Mon Oct 01 2012 - 13:21:16 PDT)
- Jason Swails (Mon Oct 01 2012 - 13:10:09 PDT)
- Sindrila Dutta banik (Mon Oct 01 2012 - 12:57:42 PDT)
- Jason Swails (Mon Oct 01 2012 - 12:14:54 PDT)
- Sindrila Dutta banik (Mon Oct 01 2012 - 11:49:35 PDT)
- Jason Swails (Mon Oct 01 2012 - 11:04:19 PDT)
- Sindrila Dutta banik (Mon Oct 01 2012 - 10:39:24 PDT)
- Jason Swails (Mon Oct 01 2012 - 04:25:52 PDT)
- Sindrila Dutta banik (Mon Oct 01 2012 - 02:11:47 PDT)
[AMBER] Problem related to the parallel installation og Amber11
- Ben Roberts (Sun Sep 30 2012 - 20:55:32 PDT)
- Ben Roberts (Sun Sep 30 2012 - 14:15:10 PDT)
- Sindrila Dutta banik (Sun Sep 30 2012 - 09:36:23 PDT)
[AMBER] Problem related to the radial distribution function
- Daniel Roe (Wed Oct 10 2012 - 10:41:53 PDT)
- Sindrila Dutta banik (Wed Oct 10 2012 - 04:55:31 PDT)
[AMBER] Problem related to the trajectory analysis
- Jason Swails (Wed Oct 03 2012 - 18:38:23 PDT)
- Sindrila Dutta banik (Wed Oct 03 2012 - 11:20:10 PDT)
[AMBER] problem restraint
- Elisa Frezza (Thu Oct 11 2012 - 08:12:04 PDT)
- Jason Swails (Thu Oct 11 2012 - 08:10:06 PDT)
- Elisa Frezza (Thu Oct 11 2012 - 07:51:17 PDT)
- Elisa Frezza (Thu Oct 11 2012 - 07:45:43 PDT)
- Jason Swails (Thu Oct 11 2012 - 07:30:43 PDT)
- Elisa Frezza (Thu Oct 11 2012 - 06:53:45 PDT)
[AMBER] problem umbrella sampling and gpus
- Jason Swails (Thu Oct 18 2012 - 07:15:08 PDT)
- Elisa Frezza (Wed Oct 17 2012 - 06:08:38 PDT)
[AMBER] Problem with "make install" after "./configure -mpi -cuda gnu"
- Tru Huynh (Mon Oct 08 2012 - 06:27:14 PDT)
- Jason Swails (Mon Oct 08 2012 - 03:37:18 PDT)
- Su, Shiquan (Sun Oct 07 2012 - 14:35:48 PDT)
- David A Case (Fri Oct 05 2012 - 05:13:04 PDT)
- Tru Huynh (Fri Oct 05 2012 - 00:42:03 PDT)
- Jason Swails (Thu Oct 04 2012 - 11:42:50 PDT)
- Su, Shiquan (Thu Oct 04 2012 - 10:21:25 PDT)
- Jason Swails (Wed Oct 03 2012 - 18:33:04 PDT)
- Su, Shiquan (Wed Oct 03 2012 - 12:57:54 PDT)
[AMBER] problem with antechamber and ESP
- David A Case (Thu Oct 11 2012 - 06:57:25 PDT)
- Rebeca García Fandiño (Thu Oct 11 2012 - 05:31:12 PDT)
[AMBER] problem with calculating decomposition energy
- Jason Swails (Mon Oct 15 2012 - 04:50:34 PDT)
- Maryam Hamzehee (Sun Oct 14 2012 - 23:23:27 PDT)
[AMBER] Problem with CHAMBER (for RNA molecule)
- Marc van der Kamp (Tue Oct 30 2012 - 05:09:20 PDT)
- Mark Williamson (Fri Oct 26 2012 - 08:28:04 PDT)
- Marc van der Kamp (Fri Oct 26 2012 - 01:59:17 PDT)
[AMBER] problem with decompostion energy
- Bill Miller III (Wed Oct 17 2012 - 08:36:05 PDT)
- Maryam Hamzehee (Wed Oct 17 2012 - 08:27:14 PDT)
[AMBER] Problems in Amber12 parallel installation
- Sajeewa Pemasinghe (Tue Oct 09 2012 - 11:56:45 PDT)
- David A Case (Tue Oct 09 2012 - 07:26:32 PDT)
- Sajeewa Pemasinghe (Mon Oct 08 2012 - 20:38:34 PDT)
[AMBER] problems with the keyword "append" in trajout command...
- Jason Swails (Sat Oct 13 2012 - 11:39:43 PDT)
- Shashidhar Rao (Fri Oct 12 2012 - 11:46:24 PDT)
[AMBER] QM method
- FyD (Tue Oct 09 2012 - 09:03:48 PDT)
- Brian Radak (Tue Oct 09 2012 - 08:45:20 PDT)
- Mannan (Tue Oct 09 2012 - 06:24:04 PDT)
[AMBER] Queastions Regarding Tutorial A11 NCSU Method
- Γιώργος Λαμπρινίδης (Mon Oct 08 2012 - 23:43:48 PDT)
- Jason Swails (Mon Oct 08 2012 - 14:26:44 PDT)
- Γιώργος Λαμπρινίδης (Mon Oct 08 2012 - 12:48:17 PDT)
[AMBER] Question regarding COM and atom pulling
- Jason Swails (Tue Oct 09 2012 - 12:54:09 PDT)
- Fabrício Bracht (Tue Oct 09 2012 - 10:11:25 PDT)
[AMBER] questions about thermodynamic integration atom name and order
- Yulin Huang (Wed Oct 31 2012 - 19:10:16 PDT)
- Yulin Huang (Wed Oct 31 2012 - 09:17:59 PDT)
- Daniel Roe (Wed Oct 31 2012 - 08:43:24 PDT)
- Yulin Huang (Wed Oct 31 2012 - 08:30:36 PDT)
- Yulin Huang (Wed Oct 31 2012 - 08:27:49 PDT)
- steinbrt.rci.rutgers.edu (Wed Oct 31 2012 - 01:35:56 PDT)
- Jodi Ann Hadden (Tue Oct 30 2012 - 13:48:16 PDT)
- 千语千寻 (Mon Oct 29 2012 - 07:59:04 PDT)
- Yulin Huang (Mon Oct 29 2012 - 07:35:55 PDT)
[AMBER] radgyr of ptraj or cpptraj
- Daniel Roe (Mon Oct 29 2012 - 11:17:23 PDT)
- Binwu Zhao (Mon Oct 29 2012 - 09:57:45 PDT)
[AMBER] Random Seed
- Brian Radak (Wed Oct 17 2012 - 10:39:14 PDT)
- Jordan, Brad (Wed Oct 17 2012 - 10:08:09 PDT)
[AMBER] RE : RE : Reference for the AMBER12SB force field
- ABEL Stephane 175950 (Thu Oct 11 2012 - 04:36:44 PDT)
[AMBER] RE : Reference for the AMBER12SB force field
- Carlos Simmerling (Thu Oct 11 2012 - 04:28:58 PDT)
- ABEL Stephane 175950 (Mon Oct 08 2012 - 05:05:02 PDT)
[AMBER] Reference for the AMBER12SB force field
- Carlos Simmerling (Mon Oct 08 2012 - 04:57:33 PDT)
- ABEL Stephane 175950 (Mon Oct 08 2012 - 04:13:57 PDT)
[AMBER] Reg: error in equilibration
- David A Case (Mon Oct 08 2012 - 05:47:49 PDT)
- subramanian boopathi (Mon Oct 08 2012 - 05:09:02 PDT)
[AMBER] Release of the R.E.D.-III.52 tools
- FyD (Mon Oct 01 2012 - 02:32:02 PDT)
[AMBER] Request for MMPBSA files.
- Jason Swails (Tue Oct 30 2012 - 07:15:25 PDT)
- Anogna (Tue Oct 30 2012 - 04:50:45 PDT)
[AMBER] Request: Tell us your CUDA story
- Ross Walker (Tue Oct 16 2012 - 10:19:30 PDT)
[AMBER] residue split
- Carlos Romero (Thu Oct 18 2012 - 00:22:36 PDT)
- David A Case (Wed Oct 17 2012 - 06:19:14 PDT)
- Carlos Romero (Tue Oct 16 2012 - 22:11:04 PDT)
- David A Case (Tue Oct 16 2012 - 18:27:34 PDT)
- Carlos Romero (Tue Oct 16 2012 - 07:20:33 PDT)
- Carlos Simmerling (Tue Oct 16 2012 - 03:13:57 PDT)
- Carlos Romero (Mon Oct 15 2012 - 22:16:42 PDT)
[AMBER] RESP charge of the ligand
- FyD (Tue Oct 16 2012 - 01:44:50 PDT)
- Mu Xia (Mon Oct 15 2012 - 07:08:17 PDT)
[AMBER] RESTARTED DUE TO LINMIN FAILURE
- Jason Swails (Mon Oct 15 2012 - 05:05:55 PDT)
- Chris Chris (Sun Oct 14 2012 - 21:55:55 PDT)
[AMBER] restraint and NMR
- Elisa Frezza (Thu Oct 11 2012 - 04:38:59 PDT)
[AMBER] rmsd rmsf
- Yanyan MENG (Tue Oct 30 2012 - 00:50:10 PDT)
[AMBER] RNA - build a mismatch and a loop with NAB
- Jason Swails (Wed Oct 24 2012 - 04:30:27 PDT)
- Amparo Garcia Lopez (Wed Oct 24 2012 - 02:58:44 PDT)
- M. L. Dodson (Tue Oct 23 2012 - 05:31:59 PDT)
- David A Case (Tue Oct 23 2012 - 05:20:17 PDT)
- Amparo Garcia Lopez (Tue Oct 23 2012 - 01:06:39 PDT)
- Jason Swails (Mon Oct 22 2012 - 11:40:34 PDT)
- Amparo Garcia Lopez (Mon Oct 22 2012 - 07:11:13 PDT)
[AMBER] Setting the random seed in Langevin dynamics
- Sajeewa Pemasinghe (Wed Oct 03 2012 - 08:53:53 PDT)
- Deák Robert (Wed Oct 03 2012 - 07:25:50 PDT)
- Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:38:18 PDT)
- Adrian Roitberg (Wed Oct 03 2012 - 06:25:00 PDT)
- Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:19:55 PDT)
- Deák Robert (Wed Oct 03 2012 - 02:54:52 PDT)
- Sajeewa Pemasinghe (Tue Oct 02 2012 - 20:57:37 PDT)
[AMBER] short bonds in average pdb
- Carlos Simmerling (Thu Oct 18 2012 - 07:52:39 PDT)
- vaibhav dixit (Thu Oct 18 2012 - 07:37:44 PDT)
- Carlos Simmerling (Thu Oct 18 2012 - 07:24:47 PDT)
- steinbrt.rci.rutgers.edu (Thu Oct 18 2012 - 07:09:54 PDT)
- Jason Swails (Thu Oct 18 2012 - 06:44:31 PDT)
- Mu Xia (Thu Oct 18 2012 - 02:40:34 PDT)
[AMBER] Should we exclude "equilibri?um state" conformers?
- Catein Catherine (Wed Oct 17 2012 - 19:48:54 PDT)
[AMBER] Side chain correction for Asp
- David A Case (Wed Oct 17 2012 - 09:32:16 PDT)
- Steven Neumann (Wed Oct 17 2012 - 08:35:06 PDT)
- Steven Neumann (Wed Oct 17 2012 - 07:43:35 PDT)
[AMBER] simulation box shape changed
- Syed Tarique Moin (Thu Oct 11 2012 - 02:10:47 PDT)
- Jason Swails (Thu Oct 04 2012 - 04:44:00 PDT)
- Syed Tarique Moin (Wed Oct 03 2012 - 23:46:41 PDT)
[AMBER] space-time correlation in AMBER
- 강현아 (Tue Oct 30 2012 - 19:38:58 PDT)
[AMBER] spce water
- Elisa Frezza (Wed Oct 10 2012 - 04:40:51 PDT)
- David A Case (Wed Oct 10 2012 - 04:13:36 PDT)
- Elisa Frezza (Wed Oct 10 2012 - 02:02:06 PDT)
[AMBER] Temperature in TI run
- steinbrt.rci.rutgers.edu (Wed Oct 17 2012 - 00:48:13 PDT)
- Brian Radak (Tue Oct 16 2012 - 12:07:39 PDT)
- Fabrício Bracht (Tue Oct 16 2012 - 11:49:36 PDT)
[AMBER] the origin of ELEC DV/DL in the case of softcore TI calculation of the solute with no charge by crgmask
- David A Case (Thu Oct 04 2012 - 07:16:44 PDT)
[AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask
- David A Case (Thu Oct 11 2012 - 07:45:40 PDT)
- hironori.kokubo.takeda.com (Thu Oct 04 2012 - 20:27:07 PDT)
[AMBER] the origin of ELEC DV/DL in the case of softcoreTIcalculation of the solute with no charge by crgmask
- hironori.kokubo.takeda.com (Sun Oct 14 2012 - 23:11:49 PDT)
[AMBER] TI problem
- David A Case (Fri Oct 12 2012 - 08:13:00 PDT)
- Fabrício Bracht (Fri Oct 12 2012 - 06:12:53 PDT)
- David A Case (Thu Oct 11 2012 - 18:37:14 PDT)
- Fabrício Bracht (Thu Oct 11 2012 - 11:15:04 PDT)
[AMBER] TI Softcore potentials and SHAKE
- Kepa K. Burusco (Mon Oct 01 2012 - 09:02:03 PDT)
- David A Case (Mon Oct 01 2012 - 05:25:21 PDT)
- Kepa K. Burusco (Mon Oct 01 2012 - 03:17:52 PDT)
- Kepa K. Burusco (Sun Sep 30 2012 - 16:12:10 PDT)
[AMBER] TI with shake
- Abhishek Mukhopadhyay (Wed Oct 03 2012 - 14:37:28 PDT)
[AMBER] tleap has error by applying amber ff03ua
- Yu-Ming Huang (Tue Oct 30 2012 - 17:04:29 PDT)
[AMBER] To which ensemble does generalized Born trajectory fall?
- Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:31:03 PDT)
- David A Case (Wed Oct 03 2012 - 04:56:17 PDT)
- Sajeewa Pemasinghe (Tue Oct 02 2012 - 20:43:44 PDT)
[AMBER] Trajectory Clustering
- Chiara Pallara (Fri Oct 26 2012 - 09:04:24 PDT)
- Daniel Roe (Fri Oct 26 2012 - 07:22:05 PDT)
- Gannett, Peter (Fri Oct 26 2012 - 05:47:03 PDT)
- George Tzotzos (Fri Oct 26 2012 - 05:47:16 PDT)
- Ilyas Yildirim (Fri Oct 26 2012 - 05:47:15 PDT)
- David Condon (Fri Oct 26 2012 - 05:43:40 PDT)
- Gustavo Seabra (Fri Oct 26 2012 - 05:39:06 PDT)
- Chiara Pallara (Fri Oct 26 2012 - 05:08:38 PDT)
[AMBER] umbrella sampling
- Ignacio J. General (Wed Oct 17 2012 - 07:22:31 PDT)
- Elisa Frezza (Wed Oct 17 2012 - 07:13:55 PDT)
- Elisa Frezza (Wed Oct 17 2012 - 07:06:42 PDT)
- Ignacio J. General (Wed Oct 17 2012 - 07:04:39 PDT)
- Elisa Frezza (Wed Oct 17 2012 - 06:16:56 PDT)
- Ignacio J. General (Wed Oct 17 2012 - 05:13:19 PDT)
- Elisa Frezza (Wed Oct 17 2012 - 02:32:01 PDT)
- Elisa Frezza (Mon Oct 15 2012 - 05:13:28 PDT)
- Jason Swails (Mon Oct 15 2012 - 05:07:24 PDT)
- Elisa Frezza (Mon Oct 15 2012 - 00:32:26 PDT)
[AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate
- Dail Chapman (Sun Oct 14 2012 - 22:23:00 PDT)
- Jason Swails (Mon Oct 08 2012 - 03:38:44 PDT)
- Dail Chapman (Sun Oct 07 2012 - 16:57:08 PDT)
[AMBER] unable to find mopac charges
- Anselm Horn (Mon Oct 15 2012 - 00:07:38 PDT)
- David A Case (Thu Oct 11 2012 - 05:00:01 PDT)
- Jason Swails (Thu Oct 11 2012 - 01:22:20 PDT)
- Anogna (Wed Oct 10 2012 - 23:07:45 PDT)
- David A Case (Wed Oct 10 2012 - 05:47:53 PDT)
- Jason Swails (Wed Oct 10 2012 - 05:42:29 PDT)
- Anogna (Wed Oct 10 2012 - 03:39:36 PDT)
- David A Case (Fri Oct 05 2012 - 05:07:58 PDT)
- Jason Swails (Fri Oct 05 2012 - 04:59:54 PDT)
- Anogna (Thu Oct 04 2012 - 23:55:20 PDT)
- David A Case (Wed Oct 03 2012 - 04:58:18 PDT)
- Anogna (Wed Oct 03 2012 - 03:03:53 PDT)
[AMBER] Updated GLYCAM parameters
- Lachele Foley (Lists) (Mon Oct 29 2012 - 11:15:04 PDT)
[AMBER] Using NMR restraints for G-Quadruplex structure
- David A Case (Wed Oct 10 2012 - 04:11:37 PDT)
- Rajiv (Tue Oct 09 2012 - 23:07:48 PDT)
[AMBER] Vina Docking model is not accepted in Antechamber
- Aldo Segura (Wed Oct 17 2012 - 07:36:11 PDT)
- Chris Chris (Tue Oct 16 2012 - 21:09:12 PDT)
- Aldo Segura (Tue Oct 16 2012 - 15:52:02 PDT)
- Chris Chris (Tue Oct 16 2012 - 14:55:02 PDT)
- Aldo Segura (Tue Oct 16 2012 - 13:35:43 PDT)
- Chris Chris (Tue Oct 16 2012 - 11:47:09 PDT)
[AMBER] vlimit exceeded on step.. error
- Jitesh Doshi (Thu Oct 18 2012 - 04:39:35 PDT)
- Anna Bauß (Thu Oct 11 2012 - 01:43:38 PDT)
- Jitesh Doshi (Wed Oct 10 2012 - 05:24:00 PDT)
- David A Case (Wed Oct 10 2012 - 04:16:51 PDT)
- Jitesh Doshi (Wed Oct 10 2012 - 03:19:16 PDT)
- Daniel Roe (Tue Oct 09 2012 - 09:05:55 PDT)
- Jitesh Doshi (Tue Oct 09 2012 - 04:18:50 PDT)
- Jitesh Doshi (Fri Oct 05 2012 - 05:11:37 PDT)
- David A Case (Fri Oct 05 2012 - 04:58:43 PDT)
- Jitesh Doshi (Thu Oct 04 2012 - 23:44:22 PDT)
- David A Case (Wed Oct 03 2012 - 06:53:42 PDT)
- Jitesh Doshi (Wed Oct 03 2012 - 06:19:52 PDT)
[AMBER] What does the word 'DIPGRP - 1' mean?
- Sanjib Paul (Thu Oct 04 2012 - 05:50:37 PDT)
[AMBER] X11 problems on Mac OS X 10.8
- David A Case (Tue Oct 16 2012 - 18:38:01 PDT)
- Maria Ana Castro (Tue Oct 16 2012 - 08:11:51 PDT)
- Jonathan Gough (Thu Oct 04 2012 - 10:24:51 PDT)
- David A Case (Thu Oct 04 2012 - 09:30:29 PDT)
- Jason Swails (Thu Oct 04 2012 - 09:02:56 PDT)
- Jonathan Gough (Thu Oct 04 2012 - 08:08:32 PDT)
- Julio Dominguez (Wed Oct 03 2012 - 19:47:31 PDT)
- David A Case (Wed Oct 03 2012 - 04:49:30 PDT)
- Jonathan Gough (Tue Oct 02 2012 - 19:36:45 PDT)
- David A Case (Tue Oct 02 2012 - 18:01:37 PDT)
- Julio Dominguez (Tue Oct 02 2012 - 15:09:29 PDT)
- Jason Swails (Mon Oct 01 2012 - 16:14:17 PDT)
- Julio Dominguez (Mon Oct 01 2012 - 13:59:59 PDT)
[AMBER] XLeap Install Issue
- David A Case (Sat Oct 13 2012 - 06:05:18 PDT)
- Bill Ross (Fri Oct 12 2012 - 18:58:41 PDT)
- Mark Zottola (Fri Oct 12 2012 - 18:11:00 PDT)
- Jason Swails (Fri Oct 12 2012 - 16:47:40 PDT)
- Mark Zottola (Fri Oct 12 2012 - 10:32:52 PDT)
files for RED
- FyD (Wed Oct 31 2012 - 03:57:55 PDT)
- Urszula Uciechowska (Wed Oct 31 2012 - 00:55:35 PDT)
- FyD (Tue Oct 30 2012 - 03:54:57 PDT)
- Urszula Uciechowska (Tue Oct 30 2012 - 01:54:51 PDT)
- FyD (Sun Oct 28 2012 - 09:58:34 PDT)

Amber Archive Oct 2012 by subject