Amber Archive Oct 2010: by subject

[AMBER] 1D-RISM in NAB: compressibility units
- Tyler Luchko (Thu Oct 28 2010 - 07:50:07 PDT)
- Andrej Frolov (Thu Oct 28 2010 - 00:52:26 PDT)
[AMBER] 2drms in ptraj
- Daniel Sindhikara (Thu Oct 28 2010 - 23:24:10 PDT)
- Carlos Simmerling (Thu Oct 28 2010 - 08:48:38 PDT)
- Beale, John (Thu Oct 28 2010 - 06:03:37 PDT)
[AMBER] 3D-RISM in NAB: solvent susceptibility function support
- Tyler Luchko (Thu Oct 28 2010 - 08:54:41 PDT)
- Andrej Frolov (Thu Oct 28 2010 - 07:53:43 PDT)
- Tyler Luchko (Thu Oct 28 2010 - 07:35:38 PDT)
- Andrej Frolov (Thu Oct 28 2010 - 01:11:52 PDT)
[AMBER] a question about replica-exchange MD
- Carlos Simmerling (Sun Oct 17 2010 - 05:02:44 PDT)
- case (Sat Oct 16 2010 - 07:18:54 PDT)
- Cheng-I Lee (Fri Oct 15 2010 - 22:02:46 PDT)
- Carlos Simmerling (Fri Oct 15 2010 - 03:55:34 PDT)
- Cheng-I Lee (Thu Oct 14 2010 - 23:24:32 PDT)
[AMBER] about Error while mapping in energy decomposition (Amber 10)
- Liane Saiz Urra (Tue Oct 26 2010 - 02:42:44 PDT)
[AMBER] about replica exchange
- Cheng-I Lee (Mon Oct 25 2010 - 05:10:38 PDT)
- Daniel Roe (Mon Oct 25 2010 - 04:46:01 PDT)
- Cheng-I Lee (Sun Oct 24 2010 - 17:01:08 PDT)
[AMBER] About RMSD calculations
- hong-bin Xie (Thu Oct 14 2010 - 17:11:15 PDT)
- Bill Ross (Thu Oct 14 2010 - 17:01:58 PDT)
- hong-bin Xie (Thu Oct 14 2010 - 16:47:43 PDT)
[AMBER] adding ions to structures
- Andrew Jewett (Thu Oct 07 2010 - 19:06:38 PDT)
- Bill Ross (Thu Oct 07 2010 - 09:51:02 PDT)
- Bill Ross (Thu Oct 07 2010 - 09:44:53 PDT)
- Stefano Pieraccini (Thu Oct 07 2010 - 07:26:07 PDT)
[AMBER] advenced tutorial 13 (crystal simulations)
- Matthias Negri (Wed Oct 13 2010 - 04:32:34 PDT)
- Stefano Pieraccini (Wed Oct 13 2010 - 03:34:51 PDT)
[AMBER] amb2gmx.pl script ignores negative values of PK?
- Andrei Neamtu (Tue Oct 19 2010 - 05:27:02 PDT)
[AMBER] Amber heme parameters
- Nitu Bansal (Fri Oct 15 2010 - 09:01:11 PDT)
- case (Thu Oct 14 2010 - 12:18:32 PDT)
- Paul S. Nerenberg (Thu Oct 14 2010 - 11:37:36 PDT)
- Bill Ross (Thu Oct 14 2010 - 11:12:55 PDT)
- Nitu Bansal (Thu Oct 14 2010 - 11:07:08 PDT)
- case (Thu Oct 14 2010 - 04:37:52 PDT)
- Nitu Bansal (Wed Oct 13 2010 - 22:36:25 PDT)
- Bill Ross (Wed Oct 13 2010 - 10:22:10 PDT)
- Nitu Bansal (Wed Oct 13 2010 - 10:16:02 PDT)
[AMBER] AMBER parallel version
- ying yu (Sat Oct 16 2010 - 13:23:14 PDT)
- Jason Swails (Sat Oct 16 2010 - 06:41:12 PDT)
- Bill Miller III (Sat Oct 16 2010 - 05:00:30 PDT)
- ying yu (Fri Oct 15 2010 - 21:40:31 PDT)
[AMBER] AMBER support Red Hat Enterprise Linux (RHEL) Version 5.5?
- Ross Walker (Mon Oct 18 2010 - 21:21:15 PDT)
- ethan.chen (Mon Oct 18 2010 - 18:18:19 PDT)
[AMBER] AMBER support Red Hat Enterprise Linux (RHEL) Version5.5?
- ethan.chen (Mon Oct 18 2010 - 23:09:49 PDT)
[AMBER] Amber10 build/installation problems
- Yazlovitsky, Boris (Thu Oct 21 2010 - 11:21:29 PDT)
- Ross Walker (Tue Oct 19 2010 - 17:29:09 PDT)
- Bill Ross (Tue Oct 19 2010 - 17:22:20 PDT)
- Yazlovitsky, Boris (Tue Oct 19 2010 - 16:04:16 PDT)
[AMBER] amber84 ASH parameters
- Francesco Pietra (Mon Oct 18 2010 - 00:59:15 PDT)
[AMBER] antechamber error when processing the graphite structure
- Bongkeun Kim (Thu Oct 14 2010 - 14:48:58 PDT)
- Bill Ross (Thu Oct 14 2010 - 14:36:52 PDT)
- Gustavo Seabra (Thu Oct 14 2010 - 14:14:25 PDT)
- Bongkeun Kim (Thu Oct 14 2010 - 13:02:13 PDT)
[AMBER] Aromatic C and N atom type problems in Antechamber
- Gabriel Rocklin (Mon Oct 25 2010 - 15:21:00 PDT)
[AMBER] binding affinity calculation
- David A. Case (Tue Oct 19 2010 - 02:36:01 PDT)
- Sangita Kachhap (Mon Oct 18 2010 - 05:34:45 PDT)
[AMBER] binding free energy difference between PBTOT and GBTOT
- xue wang (Sun Oct 17 2010 - 07:07:39 PDT)
[AMBER] build starting structure with >250 residues
- Ross Walker (Thu Oct 14 2010 - 22:36:17 PDT)
- Cheng-I Lee (Thu Oct 14 2010 - 22:13:13 PDT)
[AMBER] calculate free energies using TI
- João Sardinha (Wed Oct 20 2010 - 04:01:55 PDT)
[AMBER] Can not addions with AMOEBA ff
- case (Wed Oct 20 2010 - 13:48:08 PDT)
- case (Wed Oct 20 2010 - 13:42:05 PDT)
- Igor Sizov (Wed Oct 20 2010 - 10:14:39 PDT)
[AMBER] Can we run sanders on GPU ?
- Ross Walker (Tue Oct 26 2010 - 09:02:28 PDT)
- setyanto md (Mon Oct 25 2010 - 23:58:29 PDT)
- Ross Walker (Mon Oct 25 2010 - 23:00:10 PDT)
- c00jsw00 (Mon Oct 25 2010 - 22:59:58 PDT)
- Ross Walker (Mon Oct 25 2010 - 22:38:37 PDT)
- setyanto md (Mon Oct 25 2010 - 22:24:32 PDT)
[AMBER] cannot generate snapshot_statistics.in file
- Bill Miller III (Fri Oct 29 2010 - 07:41:31 PDT)
- bin wang (Fri Oct 29 2010 - 07:10:42 PDT)
- Dwight McGee (Wed Oct 27 2010 - 16:14:22 PDT)
- Dwight McGee (Wed Oct 27 2010 - 16:11:27 PDT)
- bin wang (Wed Oct 27 2010 - 15:58:03 PDT)
- Bill Miller III (Wed Oct 27 2010 - 08:57:58 PDT)
- bin wang (Wed Oct 27 2010 - 08:52:49 PDT)
[AMBER] charges in prmtop file
- Bill Ross (Tue Oct 05 2010 - 19:46:43 PDT)
- Bill Ross (Tue Oct 05 2010 - 19:43:31 PDT)
- amit dong (Tue Oct 05 2010 - 18:34:01 PDT)
[AMBER] Citations
- Jiri Sponer (Mon Oct 04 2010 - 02:13:24 PDT)
- Ross Walker (Sun Oct 03 2010 - 16:47:01 PDT)
- Jason Swails (Sun Oct 03 2010 - 16:41:33 PDT)
- William Flak (Sun Oct 03 2010 - 16:16:12 PDT)
[AMBER] cyclic_peptide
- Jason Swails (Thu Oct 28 2010 - 08:58:14 PDT)
- Carlos Simmerling (Thu Oct 28 2010 - 08:51:42 PDT)
- lara lara (Thu Oct 28 2010 - 08:50:24 PDT)
[AMBER] cz atom type
- case (Wed Oct 13 2010 - 06:59:26 PDT)
- Balazs Jojart (Tue Oct 12 2010 - 13:10:38 PDT)
[AMBER] DNA and igb=2, igb=5
- David A. Case (Wed Oct 06 2010 - 04:46:15 PDT)
- Ali M. Naserian-Nik (Wed Oct 06 2010 - 04:22:35 PDT)
[AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output
- Dmitry Nilov (Sat Oct 23 2010 - 06:53:06 PDT)
- Kshatresh Dutta Dubey (Fri Oct 22 2010 - 22:32:50 PDT)
- Andreas Goetz (Fri Oct 22 2010 - 11:37:56 PDT)
- Dmitry Nilov (Fri Oct 22 2010 - 05:27:48 PDT)
[AMBER] Enquiry about tutorial A5 - section 7 on nudged elastic band calculation
- Christina Bergonzo (Tue Oct 05 2010 - 06:59:14 PDT)
- Catein Catherine (Mon Oct 04 2010 - 14:12:25 PDT)
[AMBER] error in atomic charge calculation in RED server
- FyD (Wed Oct 20 2010 - 05:47:20 PDT)
- Chinh Su Tran To (Wed Oct 20 2010 - 04:21:57 PDT)
- Chinh Su Tran To (Tue Oct 12 2010 - 00:36:40 PDT)
- FyD (Tue Oct 12 2010 - 00:30:37 PDT)
- Chinh Su Tran To (Tue Oct 12 2010 - 00:06:10 PDT)
- FyD (Mon Oct 11 2010 - 23:55:21 PDT)
- FyD (Mon Oct 11 2010 - 23:37:36 PDT)
- Chinh Su Tran To (Mon Oct 11 2010 - 23:37:37 PDT)
- FyD (Mon Oct 11 2010 - 23:17:56 PDT)
- Chinh Su Tran To (Mon Oct 11 2010 - 22:19:34 PDT)
[AMBER] Error in running NM=1 with mmpbsa.pl
- Catein Catherine (Mon Oct 04 2010 - 07:59:43 PDT)
[AMBER] Error message (link) in running mmpbsa in amber11.
- Catein Catherine (Fri Oct 01 2010 - 11:47:04 PDT)
[AMBER] Error message from binding_energy.mmpbsa
- bin wang (Fri Oct 29 2010 - 13:35:28 PDT)
- Jason Swails (Fri Oct 29 2010 - 13:16:44 PDT)
- bin wang (Fri Oct 29 2010 - 13:10:44 PDT)
- Jason Swails (Fri Oct 29 2010 - 12:17:18 PDT)
- bin wang (Fri Oct 29 2010 - 12:13:58 PDT)
- Jason Swails (Fri Oct 29 2010 - 08:50:13 PDT)
- bin wang (Fri Oct 29 2010 - 08:46:13 PDT)
- Bill Miller III (Fri Oct 29 2010 - 08:09:03 PDT)
- bin wang (Fri Oct 29 2010 - 07:50:19 PDT)
[AMBER] extract distribution from PairwiseDistances
- Jianyin Shao (Fri Oct 29 2010 - 11:47:39 PDT)
- Yannick Spill (Fri Oct 29 2010 - 10:03:09 PDT)
- Jianyin Shao (Fri Oct 29 2010 - 09:02:28 PDT)
- Yannick SPILL (Fri Oct 29 2010 - 07:57:18 PDT)
[AMBER] fix the positions of EP
- case (Fri Oct 08 2010 - 08:24:47 PDT)
- William Flak (Fri Oct 08 2010 - 07:56:50 PDT)
[AMBER] free energy landscape
- Gustavo Seabra (Thu Oct 28 2010 - 09:41:06 PDT)
- Jason Swails (Thu Oct 28 2010 - 06:17:16 PDT)
- fancy2012 (Thu Oct 28 2010 - 01:11:42 PDT)
[AMBER] Fwd: Amber installation
- Hadrian Djohari (Tue Oct 05 2010 - 22:57:57 PDT)
- Paul S. Nerenberg (Mon Oct 04 2010 - 23:01:44 PDT)
- Hadrian Djohari (Mon Oct 04 2010 - 21:52:08 PDT)
- case (Mon Oct 04 2010 - 04:58:42 PDT)
- Paul S. Nerenberg (Sun Oct 03 2010 - 22:59:23 PDT)
- Paul S. Nerenberg (Sun Oct 03 2010 - 22:40:05 PDT)
- Hadrian Djohari (Sun Oct 03 2010 - 22:30:39 PDT)
[AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber
- Francesco Pietra (Wed Oct 06 2010 - 08:40:55 PDT)
- FyD (Wed Oct 06 2010 - 08:16:32 PDT)
- Francesco Pietra (Wed Oct 06 2010 - 06:54:07 PDT)
- FyD (Wed Oct 06 2010 - 04:51:48 PDT)
- Francesco Pietra (Wed Oct 06 2010 - 04:17:03 PDT)
- Francesco Pietra (Tue Oct 05 2010 - 13:10:55 PDT)
- Francesco Pietra (Mon Oct 04 2010 - 02:02:40 PDT)
[AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber
- Francesco Pietra (Thu Oct 07 2010 - 13:26:19 PDT)
- Paul S. Nerenberg (Thu Oct 07 2010 - 10:17:11 PDT)
- Paul S. Nerenberg (Thu Oct 07 2010 - 09:14:09 PDT)
- Jason Swails (Thu Oct 07 2010 - 08:36:07 PDT)
- Francesco Pietra (Thu Oct 07 2010 - 08:08:25 PDT)
- FyD (Wed Oct 06 2010 - 04:44:50 PDT)
- Francesco Pietra (Wed Oct 06 2010 - 03:07:28 PDT)
- FyD (Wed Oct 06 2010 - 02:29:05 PDT)
- Francesco Pietra (Wed Oct 06 2010 - 02:03:03 PDT)
- Francesco Pietra (Mon Oct 04 2010 - 01:56:32 PDT)
- Francesco Pietra (Sun Oct 03 2010 - 14:44:16 PDT)
- case (Fri Oct 01 2010 - 04:35:28 PDT)
- Francesco Pietra (Fri Oct 01 2010 - 03:04:57 PDT)
[AMBER] generating restraints
- David A. Case (Thu Oct 07 2010 - 04:38:56 PDT)
- Jorgen Simonsen (Wed Oct 06 2010 - 11:10:36 PDT)
[AMBER] GPU high temperature unfolding simulation
- Ross Walker (Sun Oct 31 2010 - 11:25:59 PDT)
- Carlos Simmerling (Sun Oct 31 2010 - 04:49:52 PDT)
- Ross Walker (Sat Oct 30 2010 - 22:47:36 PDT)
- andy ng (Sat Oct 30 2010 - 20:30:36 PDT)
[AMBER] H-Bonding
- case (Tue Oct 19 2010 - 11:51:39 PDT)
- Beale, John (Tue Oct 19 2010 - 09:15:20 PDT)
[AMBER] How to convert mdcrd to pdb for display?
- Jason Swails (Fri Oct 08 2010 - 11:05:45 PDT)
- Catein Catherine (Fri Oct 08 2010 - 09:55:07 PDT)
- Jason Swails (Fri Oct 08 2010 - 07:50:48 PDT)
- Catein Catherine (Fri Oct 08 2010 - 07:46:12 PDT)
[AMBER] How to genrate a movie from a trajectory?
- Eric Pettersen (Sat Oct 16 2010 - 08:29:21 PDT)
- Catein Catherine (Fri Oct 15 2010 - 07:47:06 PDT)
- Jason Swails (Fri Oct 15 2010 - 04:47:54 PDT)
- hirdesh kumar (Thu Oct 14 2010 - 21:30:59 PDT)
- Catein Catherine (Thu Oct 14 2010 - 20:54:16 PDT)
[AMBER] How to get the PDB file?
- Dima A Sabbah (Wed Oct 27 2010 - 08:02:23 PDT)
- Bill Miller III (Tue Oct 26 2010 - 18:31:15 PDT)
- xuemeiwang1103 (Tue Oct 26 2010 - 18:24:24 PDT)
[AMBER] HOW TO PREPARE MODIFIED NUCLEOSIDE
- Dmitry Nilov (Tue Oct 26 2010 - 05:59:13 PDT)
- Indrajit Deb (Tue Oct 26 2010 - 05:11:07 PDT)
[AMBER] how to stop printing restrt file in AMBER 11
- Bill Ross (Tue Oct 05 2010 - 17:07:08 PDT)
- Jason Swails (Tue Oct 05 2010 - 16:50:14 PDT)
- Dian Jiao (Tue Oct 05 2010 - 16:31:45 PDT)
[AMBER] Hydrogen Minimization and gradually relieving restraint on the DNA.
- Daniel Roe (Mon Oct 04 2010 - 05:01:33 PDT)
- abc def (Mon Oct 04 2010 - 00:11:38 PDT)
[AMBER] Incorrect handling of phenylalanine amide by antechamber
- Francesco Pietra (Thu Oct 07 2010 - 07:57:30 PDT)
- FyD (Thu Oct 07 2010 - 02:56:35 PDT)
- Francesco Pietra (Wed Oct 06 2010 - 01:21:35 PDT)
- FyD (Tue Oct 05 2010 - 23:19:20 PDT)
[AMBER] Infinite covalently bonded crystals
- David A. Case (Fri Oct 22 2010 - 05:28:40 PDT)
- Bill Ross (Thu Oct 21 2010 - 20:17:42 PDT)
- Andrew Jewett (Thu Oct 21 2010 - 17:31:58 PDT)
[AMBER] installation of pmemd
- fancy2012 (Fri Oct 08 2010 - 18:15:14 PDT)
- Jason Swails (Fri Oct 08 2010 - 06:03:01 PDT)
- fancy2012 (Fri Oct 08 2010 - 01:25:08 PDT)
[AMBER] interaction_energy
- Jason Swails (Tue Oct 19 2010 - 07:38:14 PDT)
- lara lara (Tue Oct 19 2010 - 01:11:24 PDT)
- Sushil Mishra (Tue Oct 19 2010 - 00:22:05 PDT)
- Daniel Sindhikara (Mon Oct 18 2010 - 22:02:03 PDT)
- Sushil Mishra (Mon Oct 18 2010 - 21:03:10 PDT)
- balaji nagarajan (Mon Oct 18 2010 - 20:13:49 PDT)
[AMBER] intra-molecular energies of a water molecule
- Dian Jiao (Wed Oct 06 2010 - 08:26:44 PDT)
- Carlos Simmerling (Wed Oct 06 2010 - 03:39:23 PDT)
- Dian Jiao (Wed Oct 06 2010 - 00:11:53 PDT)
[AMBER] Is it a typo in TUTORIAL A13: Simulation of a protein crystal?
- dcerutti.rci.rutgers.edu (Fri Oct 15 2010 - 08:56:27 PDT)
- Ye MEI (Thu Oct 14 2010 - 21:05:25 PDT)
[AMBER] Issue regarding buckling of planar ligand during simulations
- Andreas Goetz (Thu Oct 14 2010 - 07:12:38 PDT)
- abc def (Thu Oct 14 2010 - 04:43:31 PDT)
[AMBER] J-coupling restraints
- Mickey Richards (Thu Oct 21 2010 - 10:44:04 PDT)
- Bill Ross (Thu Oct 21 2010 - 10:01:49 PDT)
- Mickey Richards (Thu Oct 21 2010 - 09:45:27 PDT)
- David A. Case (Thu Oct 21 2010 - 08:42:20 PDT)
- Mickey Richards (Wed Oct 20 2010 - 19:12:03 PDT)
[AMBER] leap reading of pdb files
- case (Fri Oct 29 2010 - 05:51:43 PDT)
- Stefano Pieraccini (Fri Oct 29 2010 - 02:51:05 PDT)
[AMBER] ligand geometry after simulation
- Jason Swails (Sat Oct 09 2010 - 18:04:27 PDT)
- Bill Ross (Sat Oct 09 2010 - 13:03:29 PDT)
- Computational Chemist (Sat Oct 09 2010 - 12:59:59 PDT)
[AMBER] limitation of the protein size
- Bill Ross (Tue Oct 12 2010 - 21:04:42 PDT)
- Cheng-I Lee (Tue Oct 12 2010 - 20:44:42 PDT)
[AMBER] magnesium ion parametrization question
- Andrew Voronkov (Thu Oct 21 2010 - 00:15:04 PDT)
- Dmitry Nilov (Wed Oct 20 2010 - 10:11:27 PDT)
- InSuk Joung (Wed Oct 20 2010 - 10:10:52 PDT)
- Andrew Voronkov (Wed Oct 20 2010 - 09:18:52 PDT)
- Andrew Voronkov (Wed Oct 20 2010 - 09:02:56 PDT)
- Dmitry Nilov (Wed Oct 20 2010 - 06:36:15 PDT)
- Andrew Voronkov (Tue Oct 19 2010 - 07:12:33 PDT)
[AMBER] make.parallel test got stuck !! any updates?
- case (Mon Oct 04 2010 - 06:59:10 PDT)
- Senthil Natesan (Mon Oct 04 2010 - 06:52:43 PDT)
- case (Mon Oct 04 2010 - 06:41:23 PDT)
- Senthil Natesan (Mon Oct 04 2010 - 06:25:40 PDT)
[AMBER] maximum coordination exceeded $ set pert true
- William Flak (Thu Oct 07 2010 - 07:25:50 PDT)
- Jason Swails (Thu Oct 07 2010 - 07:07:35 PDT)
- William Flak (Thu Oct 07 2010 - 06:58:38 PDT)
[AMBER] mdcrd file
- Carlos Simmerling (Mon Oct 04 2010 - 04:07:35 PDT)
- hirdesh kumar (Mon Oct 04 2010 - 04:07:47 PDT)
- subrata paul (Mon Oct 04 2010 - 04:04:22 PDT)
[AMBER] Measure relative orientations in amber 9
- Bill Ross (Sat Oct 23 2010 - 10:10:10 PDT)
- Neha Gandhi (Sat Oct 23 2010 - 01:38:22 PDT)
[AMBER] memory issue- CPHF- gamess calculation
- kamlesh sahu (Thu Oct 14 2010 - 19:38:42 PDT)
- Paul S. Nerenberg (Thu Oct 14 2010 - 18:57:43 PDT)
- kamlesh sahu (Thu Oct 14 2010 - 18:24:35 PDT)
[AMBER] Mimiciking infinite DNA
- David A. Case (Tue Oct 19 2010 - 02:53:28 PDT)
- abc def (Tue Oct 19 2010 - 02:15:03 PDT)
[AMBER] mm-pbsa
- Bill Miller III (Sun Oct 17 2010 - 07:35:38 PDT)
- yan zhang (Sun Oct 17 2010 - 07:19:21 PDT)
[AMBER] mm_pbsa dependence on GB 0 or GB 1
- Jason Swails (Mon Oct 18 2010 - 04:45:06 PDT)
- Antonija Tomić (Mon Oct 18 2010 - 01:32:15 PDT)
- case (Fri Oct 15 2010 - 11:10:41 PDT)
- Antonija Tomić (Fri Oct 15 2010 - 08:14:11 PDT)
[AMBER] MMBPSA residue selection
- Jason Swails (Tue Oct 05 2010 - 08:14:35 PDT)
- Federica Chiappori (Tue Oct 05 2010 - 08:01:05 PDT)
[AMBER] MMGBSA issue with covalently bound parameterized ligand
- Christopher Roberts (Thu Oct 28 2010 - 14:29:31 PDT)
[AMBER] mmpbsa error
- Jason Swails (Tue Oct 05 2010 - 17:24:15 PDT)
- Anuradha Mittal (Tue Oct 05 2010 - 17:06:49 PDT)
[AMBER] MMPBSA in AMBER11
- Jason Swails (Thu Oct 28 2010 - 14:01:38 PDT)
- Bill Miller III (Thu Oct 28 2010 - 13:56:26 PDT)
- zhihong ke (Thu Oct 28 2010 - 13:48:10 PDT)
- Jason Swails (Fri Oct 22 2010 - 18:03:19 PDT)
- Bill Miller III (Fri Oct 22 2010 - 12:54:25 PDT)
- zhihong ke (Fri Oct 22 2010 - 12:42:39 PDT)
[AMBER] MMPBSA ligand/receptor selections
- Jason Swails (Sun Oct 31 2010 - 15:30:57 PDT)
- Logan Ahlstrom (Sun Oct 31 2010 - 15:14:20 PDT)
[AMBER] MMPBSA protein-protein interaction
- David A. Case (Fri Oct 22 2010 - 07:33:43 PDT)
- Lars Skjærven (Wed Oct 20 2010 - 08:24:33 PDT)
- case (Sat Oct 16 2010 - 07:45:53 PDT)
- Jason Swails (Fri Oct 15 2010 - 11:49:05 PDT)
- Lars Skjærven (Fri Oct 15 2010 - 10:15:20 PDT)
- case (Thu Oct 14 2010 - 06:06:16 PDT)
- Oliver Grant (Thu Oct 14 2010 - 04:17:06 PDT)
- Lars Skjærven (Thu Oct 14 2010 - 02:59:23 PDT)
[AMBER] MMPBSA Warning
- Bill Miller III (Sun Oct 03 2010 - 11:18:09 PDT)
- William Flak (Sun Oct 03 2010 - 11:12:47 PDT)
[AMBER] MMPBSA.py - very high energy terms
- Jason Swails (Fri Oct 01 2010 - 07:33:06 PDT)
- Senthil Natesan (Fri Oct 01 2010 - 07:20:51 PDT)
- Jason Swails (Fri Oct 01 2010 - 06:47:36 PDT)
- Senthil Natesan (Fri Oct 01 2010 - 06:27:18 PDT)
[AMBER] mmpbsa.py error
- Jason Swails (Sun Oct 03 2010 - 14:51:17 PDT)
- Anuradha Mittal (Sat Oct 02 2010 - 23:17:22 PDT)
[AMBER] multi input for parmchk
- case (Mon Oct 11 2010 - 04:41:14 PDT)
- Xioling Chuang (Sun Oct 10 2010 - 20:31:50 PDT)
[AMBER] nab function transformmol() returned value docs are inconsistent
- David A. Case (Thu Oct 07 2010 - 06:27:47 PDT)
- M. L. Dodson (Wed Oct 06 2010 - 11:58:12 PDT)
[AMBER] ncsu input
- Daniel Sindhikara (Sat Oct 23 2010 - 18:44:12 PDT)
- eduardo.troche.uvigo.es (Fri Oct 22 2010 - 08:41:32 PDT)
- Daniel Sindhikara (Fri Oct 22 2010 - 05:25:06 PDT)
- eduardo.troche.uvigo.es (Fri Oct 22 2010 - 03:55:53 PDT)
- Daniel Sindhikara (Thu Oct 21 2010 - 21:40:40 PDT)
- eduardo.troche.uvigo.es (Thu Oct 21 2010 - 08:22:05 PDT)
[AMBER] new_solvent_type
- lara lara (Wed Oct 13 2010 - 09:23:53 PDT)
[AMBER] new_type_solvent
- lara lara (Wed Oct 13 2010 - 09:00:15 PDT)
[AMBER] Newton-Raphson minimization
- case (Mon Oct 11 2010 - 04:48:01 PDT)
- fancy2012 (Mon Oct 11 2010 - 02:22:40 PDT)
[AMBER] nmode calculation
- Jason Swails (Tue Oct 19 2010 - 07:40:33 PDT)
- rameshwar prajapati (Tue Oct 19 2010 - 00:22:11 PDT)
[AMBER] nmode problem
- Sabbah, Dima (Tue Oct 05 2010 - 09:02:12 PDT)
- Dima A Sabbah (Mon Oct 04 2010 - 06:51:35 PDT)
- Dima A Sabbah (Fri Oct 01 2010 - 13:55:48 PDT)
[AMBER] NMR refinement in explicite water
- Sabbah, Dima (Thu Oct 07 2010 - 07:51:15 PDT)
- Baptiste Legrand (Thu Oct 07 2010 - 07:15:00 PDT)
- Sabbah, Dima (Thu Oct 07 2010 - 06:55:22 PDT)
- Dima A Sabbah (Thu Oct 07 2010 - 06:53:23 PDT)
- Baptiste Legrand (Thu Oct 07 2010 - 05:26:14 PDT)
- David A. Case (Thu Oct 07 2010 - 04:45:01 PDT)
- Baptiste Legrand (Thu Oct 07 2010 - 02:53:39 PDT)
- Sabbah, Dima (Tue Oct 05 2010 - 09:31:57 PDT)
- Jason Swails (Mon Oct 04 2010 - 07:49:08 PDT)
- Dima A Sabbah (Mon Oct 04 2010 - 07:25:24 PDT)
- Baptiste Legrand (Mon Oct 04 2010 - 07:13:50 PDT)
[AMBER] NMR-restrained RNA structure refinement with amber
- Michael F. Summers (Wed Oct 20 2010 - 11:03:09 PDT)
[AMBER] NMR_ensemble
- Raman Parkesh (Tue Oct 19 2010 - 06:18:03 PDT)
- David A. Case (Tue Oct 19 2010 - 02:59:49 PDT)
- Raman Parkesh (Mon Oct 18 2010 - 15:20:41 PDT)
[AMBER] no nuclear spin in PIMD?
- case (Tue Oct 05 2010 - 11:50:49 PDT)
- aapeters.ncsu.edu (Tue Oct 05 2010 - 09:19:00 PDT)
[AMBER] Normal mode analysis with QM potential
- case (Wed Oct 13 2010 - 05:34:55 PDT)
- 전종구 (Tue Oct 12 2010 - 22:52:22 PDT)
[AMBER] Nose Hoover thermostat
- Sangita Kachhap (Thu Oct 28 2010 - 22:08:52 PDT)
- Francesco Paesani (Tue Oct 26 2010 - 07:19:45 PDT)
- case (Mon Oct 25 2010 - 05:32:14 PDT)
- Sangita Kachhap (Sat Oct 23 2010 - 11:43:21 PDT)
[AMBER] OpenMPI or MPICH2 for paralel installation?
- Jason Swails (Fri Oct 29 2010 - 06:01:05 PDT)
- Vitaly Chaban (Thu Oct 28 2010 - 21:31:24 PDT)
- Ye MEI (Thu Oct 28 2010 - 20:49:48 PDT)
- Shaandar Nyamtulga (Thu Oct 28 2010 - 19:31:41 PDT)
[AMBER] output pairwise energies
- Jason Swails (Wed Oct 13 2010 - 10:34:01 PDT)
- Dian Jiao (Wed Oct 13 2010 - 10:25:04 PDT)
[AMBER] Output problem on Amber 9
- Seren Soner (Sat Oct 30 2010 - 14:15:37 PDT)
- Jason Swails (Sat Oct 30 2010 - 13:51:00 PDT)
- Seren Soner (Sat Oct 30 2010 - 13:48:05 PDT)
- Jason Swails (Sat Oct 30 2010 - 13:46:12 PDT)
- Seren Soner (Sat Oct 30 2010 - 13:33:17 PDT)
- Jason Swails (Sat Oct 30 2010 - 13:28:23 PDT)
- Seren Soner (Sat Oct 30 2010 - 13:23:41 PDT)
- Jason Swails (Fri Oct 29 2010 - 10:33:41 PDT)
- Jason Swails (Fri Oct 29 2010 - 10:25:08 PDT)
- tanya singh (Fri Oct 29 2010 - 09:42:58 PDT)
- Seren Soner (Fri Oct 29 2010 - 09:33:16 PDT)
- Jason Swails (Fri Oct 29 2010 - 09:28:31 PDT)
- Ross Walker (Fri Oct 29 2010 - 09:21:26 PDT)
- Seren Soner (Fri Oct 29 2010 - 09:09:38 PDT)
- Adrian Roitberg (Mon Oct 18 2010 - 03:40:34 PDT)
- Seren Soner (Mon Oct 18 2010 - 02:16:44 PDT)
[AMBER] Parameters for succinimide
- FyD (Mon Oct 18 2010 - 06:46:05 PDT)
- Stephan Jakobi (Mon Oct 18 2010 - 05:17:57 PDT)
[AMBER] PARMSCAN
- Sarath Chandra Dantu (Fri Oct 29 2010 - 07:34:40 PDT)
[AMBER] partition error in shake
- case (Wed Oct 13 2010 - 07:05:44 PDT)
- xuemeiwang1103 (Tue Oct 12 2010 - 01:25:13 PDT)
- case (Mon Oct 11 2010 - 20:36:27 PDT)
- xuemeiwang1103 (Mon Oct 11 2010 - 18:36:11 PDT)
- case (Mon Oct 11 2010 - 04:40:30 PDT)
- xuemeiwang1103 (Sun Oct 10 2010 - 20:20:17 PDT)
[AMBER] Phosphorylated aspartate residue
- case (Mon Oct 11 2010 - 04:59:50 PDT)
- FyD (Mon Oct 11 2010 - 00:19:09 PDT)
- Rahul Banerjee (Sat Oct 09 2010 - 07:13:10 PDT)
[AMBER] phosphorylated residues
- priyanka (Thu Oct 07 2010 - 20:36:07 PDT)
- Jason Swails (Thu Oct 07 2010 - 10:54:39 PDT)
- priyanka (Thu Oct 07 2010 - 09:43:20 PDT)
[AMBER] PIMD average trajectory
- aapeters.ncsu.edu (Tue Oct 05 2010 - 12:58:08 PDT)
[AMBER] pmemd 11 (parallel) compilation error - revisiting
- Alok Juneja (Thu Oct 21 2010 - 08:35:53 PDT)
- Ross Walker (Wed Oct 20 2010 - 18:48:50 PDT)
- Alok Juneja (Wed Oct 20 2010 - 18:31:01 PDT)
- Alok Juneja (Wed Oct 20 2010 - 13:26:06 PDT)
- Ross Walker (Wed Oct 20 2010 - 13:12:00 PDT)
- Alok Juneja (Wed Oct 20 2010 - 12:41:55 PDT)
[AMBER] pmemd installation error
- Per Jr. Greisen (Thu Oct 28 2010 - 04:09:02 PDT)
- M. Reza Ganjalikhany (Thu Oct 28 2010 - 04:01:00 PDT)
- Jason Swails (Mon Oct 25 2010 - 04:23:19 PDT)
- M. Reza Ganjalikhany (Mon Oct 25 2010 - 02:29:10 PDT)
[AMBER] PMEMD terminated abnormally!
- Ashutosh Shandilya (Tue Oct 19 2010 - 04:26:34 PDT)
- Ashutosh Shandilya (Tue Oct 19 2010 - 02:45:37 PDT)
- Adrian Roitberg (Tue Oct 19 2010 - 01:40:40 PDT)
- Ashutosh Shandilya (Tue Oct 19 2010 - 01:37:30 PDT)
- Ross Walker (Mon Oct 18 2010 - 23:41:15 PDT)
- Ashutosh Shandilya (Mon Oct 18 2010 - 23:21:59 PDT)
- Jason Swails (Mon Oct 18 2010 - 04:33:35 PDT)
- Ashutosh Shandilya (Mon Oct 18 2010 - 00:12:11 PDT)
[AMBER] pmemd.cuda error with group restraint
- Ross Walker (Fri Oct 01 2010 - 16:59:30 PDT)
[AMBER] Potential Energy calculation in AMBER force field
- Ilyas Yildirim (Mon Oct 04 2010 - 19:00:06 PDT)
- Bill Ross (Mon Oct 04 2010 - 17:38:15 PDT)
- Ilyas Yildirim (Mon Oct 04 2010 - 16:59:41 PDT)
- Jason Swails (Mon Oct 04 2010 - 14:40:44 PDT)
- Bill Ross (Mon Oct 04 2010 - 13:58:55 PDT)
- Ilyas Yildirim (Mon Oct 04 2010 - 12:34:37 PDT)
[AMBER] prepare the heme parameters
- juan zeng (Mon Oct 11 2010 - 03:54:59 PDT)
- FyD (Mon Oct 11 2010 - 00:16:18 PDT)
- juan zeng (Sun Oct 10 2010 - 18:49:45 PDT)
- ros (Sat Oct 09 2010 - 10:35:36 PDT)
- juan zeng (Sat Oct 09 2010 - 06:54:45 PDT)
- case (Sat Oct 09 2010 - 05:52:03 PDT)
- juan zeng (Sat Oct 09 2010 - 00:18:08 PDT)
[AMBER] Pressure in bar or atm?
- Ben Roberts (Mon Oct 11 2010 - 10:05:11 PDT)
- case (Fri Oct 08 2010 - 11:18:04 PDT)
- Ben Roberts (Fri Oct 08 2010 - 08:34:36 PDT)
[AMBER] Problem in mm_pbsa
- Kshatresh Dutta Dubey (Thu Oct 21 2010 - 00:51:36 PDT)
- juzer stationwala (Wed Oct 20 2010 - 22:04:19 PDT)
- Kshatresh Dutta Dubey (Wed Oct 20 2010 - 01:14:49 PDT)
- Rubben Torella (Wed Oct 20 2010 - 00:41:40 PDT)
- Kshatresh Dutta Dubey (Wed Oct 20 2010 - 00:00:54 PDT)
[AMBER] Problem using graphite structure in equil MD
- Bill Ross (Thu Oct 21 2010 - 16:31:02 PDT)
- Bongkeun Kim (Thu Oct 21 2010 - 16:09:14 PDT)
[AMBER] Problem using graphite strucute in equil MD
- Bill Ross (Thu Oct 21 2010 - 11:39:25 PDT)
- Bongkeun Kim (Thu Oct 21 2010 - 11:13:45 PDT)
- Bill Ross (Thu Oct 21 2010 - 10:00:05 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 23:13:43 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 16:38:24 PDT)
- Bill Ross (Wed Oct 20 2010 - 16:34:21 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 15:48:09 PDT)
- Bill Ross (Wed Oct 20 2010 - 14:26:33 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 13:54:28 PDT)
- Bill Ross (Wed Oct 20 2010 - 11:44:38 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 11:19:35 PDT)
- Bill Ross (Wed Oct 20 2010 - 11:03:56 PDT)
- Bongkeun Kim (Wed Oct 20 2010 - 10:31:18 PDT)
- Bill Ross (Wed Oct 20 2010 - 10:02:35 PDT)
- InSuk Joung (Wed Oct 20 2010 - 09:46:54 PDT)
- Bongkeun Kim (Tue Oct 19 2010 - 22:24:19 PDT)
[AMBER] Problem with formyl group parameters
- Jason Swails (Mon Oct 18 2010 - 04:43:07 PDT)
- Carter M.K. (Mon Oct 18 2010 - 03:36:44 PDT)
[AMBER] Protein Folding
- Carlos Simmerling (Thu Oct 28 2010 - 11:34:02 PDT)
- Jordan, Brad (Thu Oct 28 2010 - 11:25:40 PDT)
[AMBER] Protocol for structure determination of DNA duplex by NMR
- David A. Case (Thu Oct 07 2010 - 04:36:22 PDT)
- Olivier Julien (Wed Oct 06 2010 - 10:53:23 PDT)
[AMBER] proton spin effects with Semi-empirical or DFTB qm/mm?
- Andreas Goetz (Tue Oct 12 2010 - 13:21:29 PDT)
- aapeters.ncsu.edu (Tue Oct 12 2010 - 12:59:56 PDT)
[AMBER] ptraj box information
- Daniel Roe (Thu Oct 14 2010 - 06:46:27 PDT)
- Dickson, Callum (Wed Oct 13 2010 - 03:15:50 PDT)
[AMBER] ptraj closest command
- William Flak (Sat Oct 09 2010 - 08:44:17 PDT)
[AMBER] Ptraj Error- Analysis on Trajectory files
- Ajay Ummat (Wed Oct 06 2010 - 16:06:54 PDT)
- Bill Ross (Wed Oct 06 2010 - 15:43:23 PDT)
- Daniel Roe (Wed Oct 06 2010 - 15:20:58 PDT)
- Bill Ross (Wed Oct 06 2010 - 11:54:51 PDT)
- Ajay Ummat (Wed Oct 06 2010 - 11:45:44 PDT)
[AMBER] Ptraj LES split problem
- Bradshaw, Richard (Mon Oct 11 2010 - 05:08:35 PDT)
[AMBER] Ptraj LES split problem (followup)
- Carlos Simmerling (Wed Oct 13 2010 - 06:42:55 PDT)
- Bradshaw, Richard (Wed Oct 13 2010 - 06:39:45 PDT)
[AMBER] ptraj mask
- Jianyin Shao (Fri Oct 08 2010 - 20:35:45 PDT)
- Tyler Glembo (Fri Oct 08 2010 - 12:04:50 PDT)
- Jason Swails (Fri Oct 08 2010 - 11:00:00 PDT)
- Tyler Glembo (Fri Oct 08 2010 - 10:41:32 PDT)
- Jason Swails (Fri Oct 08 2010 - 05:15:51 PDT)
- Tyler Glembo (Thu Oct 07 2010 - 22:50:00 PDT)
[AMBER] ptraj- cluster analysis - Error
- Daniel Roe (Thu Oct 07 2010 - 14:13:07 PDT)
- Senthil Natesan (Mon Oct 04 2010 - 06:11:57 PDT)
- Daniel Roe (Mon Oct 04 2010 - 04:50:42 PDT)
- Senthil Natesan (Sun Oct 03 2010 - 10:15:01 PDT)
[AMBER] ptraj- cluster analysis - Error - fixed !
- Senthil Natesan (Fri Oct 08 2010 - 06:42:47 PDT)
[AMBER] QMMM: Unable to achieve self consistency to the tolerances specified
- Gustavo Seabra (Mon Oct 18 2010 - 05:29:32 PDT)
- sunita gupta (Mon Oct 18 2010 - 05:20:19 PDT)
[AMBER] Query regarding RMSD calculcation
- hirdesh kumar (Thu Oct 07 2010 - 06:36:21 PDT)
- Jason Swails (Thu Oct 07 2010 - 06:08:29 PDT)
- hirdesh kumar (Wed Oct 06 2010 - 21:42:06 PDT)
- Daniel Roe (Wed Oct 06 2010 - 15:44:55 PDT)
- hirdesh kumar (Tue Oct 05 2010 - 22:22:18 PDT)
- Daniel Roe (Tue Oct 05 2010 - 07:14:13 PDT)
- hirdesh kumar (Mon Oct 04 2010 - 23:25:36 PDT)
- Kshatresh Dutta Dubey (Mon Oct 04 2010 - 22:59:15 PDT)
- hirdesh kumar (Mon Oct 04 2010 - 22:51:22 PDT)
[AMBER] Query regarding solvent accessible surface area of individual residue
- Jason Swails (Tue Oct 05 2010 - 05:10:24 PDT)
- hirdesh kumar (Tue Oct 05 2010 - 01:49:57 PDT)
[AMBER] Question about limitations of the nudged elastic band method
- Carlos Simmerling (Thu Oct 07 2010 - 18:47:38 PDT)
- patrick wintrode (Thu Oct 07 2010 - 18:39:39 PDT)
- Carlos Simmerling (Thu Oct 07 2010 - 17:49:26 PDT)
- patrick wintrode (Thu Oct 07 2010 - 17:43:22 PDT)
[AMBER] question on antechamber parametrization / unable to find mopac charges error
- David A. Case (Wed Oct 20 2010 - 05:53:59 PDT)
- Andrew Voronkov (Tue Oct 19 2010 - 05:23:01 PDT)
- Andrew Voronkov (Sun Oct 17 2010 - 10:35:07 PDT)
[AMBER] radial distibution function
- M. L. Dodson (Wed Oct 27 2010 - 07:36:54 PDT)
- subrata paul (Tue Oct 26 2010 - 21:41:05 PDT)
[AMBER] regarding 'ambpdb' command in amber tools 1.4
- case (Thu Oct 28 2010 - 04:41:08 PDT)
- Dmitry Nilov (Thu Oct 28 2010 - 03:38:04 PDT)
- aneesh cna (Thu Oct 28 2010 - 03:33:51 PDT)
[AMBER] remap umbrella sampling free-energy
- Giuseppe De Marco (Mon Oct 11 2010 - 10:57:22 PDT)
[AMBER] Removing rotational motion
- Jason Swails (Wed Oct 27 2010 - 10:28:11 PDT)
- John S (Tue Oct 26 2010 - 07:08:00 PDT)
[AMBER] residence time of water molecule and life time of hydrogen bonds
- atila petrosian (Wed Oct 20 2010 - 07:19:19 PDT)
- atila petrosian (Mon Oct 18 2010 - 03:45:20 PDT)
[AMBER] Residue not recognized
- Bill Ross (Wed Oct 20 2010 - 09:52:19 PDT)
- Millen, Andrea (Wed Oct 20 2010 - 09:50:23 PDT)
- FyD (Wed Oct 20 2010 - 08:17:51 PDT)
- case (Wed Oct 20 2010 - 06:45:11 PDT)
[AMBER] restart file error
- case (Thu Oct 14 2010 - 05:55:56 PDT)
- Daniel Roe (Thu Oct 14 2010 - 05:18:57 PDT)
- shweta (Wed Oct 13 2010 - 10:57:43 PDT)
[AMBER] restraint between two centers of mass?
- Jose Borreguero (Sun Oct 10 2010 - 07:35:44 PDT)
[AMBER] RMSD doubt
- Soumya Lipsa Rath (Thu Oct 07 2010 - 20:41:07 PDT)
- Carlos Simmerling (Thu Oct 07 2010 - 10:48:59 PDT)
- Soumya Lipsa Rath (Thu Oct 07 2010 - 09:55:37 PDT)
- Soumya Lipsa Rath (Thu Oct 07 2010 - 00:49:22 PDT)
[AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure?
- Jiri Sponer (Sat Oct 16 2010 - 00:11:52 PDT)
- Sasha Buzko (Fri Oct 15 2010 - 16:42:38 PDT)
- Jiri Sponer (Fri Oct 15 2010 - 16:29:22 PDT)
- Jiri Sponer (Fri Oct 15 2010 - 16:26:04 PDT)
- Sasha Buzko (Fri Oct 15 2010 - 16:03:37 PDT)
- Carlos Simmerling (Fri Oct 15 2010 - 15:58:53 PDT)
- Sasha Buzko (Fri Oct 15 2010 - 15:08:17 PDT)
[AMBER] runing mmpbsa.pl on cluster
- Jason Swails (Fri Oct 01 2010 - 05:13:08 PDT)
- Jason Swails (Fri Oct 01 2010 - 05:11:54 PDT)
- Oliver Grant (Fri Oct 01 2010 - 04:53:44 PDT)
- Oliver Grant (Fri Oct 01 2010 - 04:50:39 PDT)
- Giorgos Lamprinidis (Fri Oct 01 2010 - 04:46:39 PDT)
- Jason Swails (Fri Oct 01 2010 - 03:37:08 PDT)
- Giorgos Lamprinidis (Fri Oct 01 2010 - 01:58:54 PDT)
[AMBER] running mmpbsa.py
- Bill Miller III (Fri Oct 01 2010 - 03:49:10 PDT)
- Jason Swails (Fri Oct 01 2010 - 03:48:32 PDT)
- Mannan (Fri Oct 01 2010 - 02:51:32 PDT)
[AMBER] Running NAB
- Arun Gupta (Fri Oct 29 2010 - 13:22:09 PDT)
- Jason Swails (Fri Oct 29 2010 - 13:13:45 PDT)
- Arun Gupta (Fri Oct 29 2010 - 13:09:17 PDT)
- case (Fri Oct 29 2010 - 13:04:52 PDT)
- Arun Gupta (Fri Oct 29 2010 - 12:56:47 PDT)
[AMBER] sander gb post-processing fail
- Trevor Gokey (Fri Oct 01 2010 - 21:22:41 PDT)
- Trevor Gokey (Fri Oct 01 2010 - 21:14:36 PDT)
- Daniel Roe (Fri Oct 01 2010 - 18:15:55 PDT)
- Trevor Gokey (Fri Oct 01 2010 - 12:11:23 PDT)
[AMBER] sander is running...
- Ross Walker (Fri Oct 01 2010 - 11:55:09 PDT)
- nicholus bhattacharjee (Fri Oct 01 2010 - 09:41:43 PDT)
[AMBER] sander termination for large [NaCl] concentration
- Ben Roberts (Thu Oct 28 2010 - 06:12:56 PDT)
- Santosh Mogurampelly (Thu Oct 28 2010 - 05:17:50 PDT)
[AMBER] sander.MPI error
- Bill Ross (Sun Oct 03 2010 - 12:35:52 PDT)
- Jason Swails (Sat Oct 02 2010 - 08:04:28 PDT)
- Sangita Kachhap (Sat Oct 02 2010 - 07:52:42 PDT)
[AMBER] SCC-DFT orbitals
- arikcohen (Sun Oct 31 2010 - 22:24:38 PDT)
[AMBER] Searching for a keyword
- case (Sat Oct 09 2010 - 05:48:02 PDT)
- William Flak (Fri Oct 08 2010 - 14:27:17 PDT)
[AMBER] Segmentation fault
- Daniel Roe (Mon Oct 04 2010 - 20:31:49 PDT)
- Jason Swails (Mon Oct 04 2010 - 18:47:12 PDT)
- Seibold, Stephen (Mon Oct 04 2010 - 16:18:25 PDT)
- Jason Swails (Sat Oct 02 2010 - 18:56:53 PDT)
- Seibold, Stephen (Sat Oct 02 2010 - 15:53:54 PDT)
- Jason Swails (Sat Oct 02 2010 - 15:40:52 PDT)
- Seibold, Stephen (Sat Oct 02 2010 - 14:33:41 PDT)
[AMBER] Shake errors
- Bill Ross (Wed Oct 13 2010 - 11:17:07 PDT)
- Justine Shaw (Wed Oct 13 2010 - 11:09:23 PDT)
- Justine Shaw (Tue Oct 12 2010 - 14:53:06 PDT)
- case (Tue Oct 12 2010 - 12:15:03 PDT)
- Bill Ross (Tue Oct 12 2010 - 11:48:07 PDT)
- Justine Shaw (Tue Oct 12 2010 - 11:25:03 PDT)
- Bill Ross (Mon Oct 11 2010 - 13:07:48 PDT)
- Justine Shaw (Mon Oct 11 2010 - 12:43:01 PDT)
[AMBER] sidechain side chain interaction within one protein
- Rilei Yu (Tue Oct 26 2010 - 21:30:19 PDT)
[AMBER] Solvate water moleculer in a TIP3PBOX
- Dian Jiao (Wed Oct 13 2010 - 09:37:33 PDT)
- case (Wed Oct 13 2010 - 07:01:52 PDT)
- oscarjiao.gmail.com (Tue Oct 12 2010 - 13:59:32 PDT)
[AMBER] solvent_box_type
- lara lara (Thu Oct 14 2010 - 23:24:35 PDT)
[AMBER] solvent_shell_minimization_error
- Jason Swails (Mon Oct 18 2010 - 04:39:57 PDT)
- balaji nagarajan (Mon Oct 18 2010 - 01:28:40 PDT)
[AMBER] spc/e water
- case (Fri Oct 01 2010 - 05:05:44 PDT)
[AMBER] sphere_problem
- M. L. Dodson (Mon Oct 18 2010 - 10:13:24 PDT)
- M. L. Dodson (Mon Oct 18 2010 - 10:07:51 PDT)
- Jason Swails (Mon Oct 18 2010 - 09:54:56 PDT)
- balaji nagarajan (Mon Oct 18 2010 - 09:19:12 PDT)
[AMBER] Stability problem
- shweta (Thu Oct 07 2010 - 07:30:47 PDT)
- Carlos Simmerling (Thu Oct 07 2010 - 03:54:56 PDT)
- shweta (Wed Oct 06 2010 - 18:56:18 PDT)
[AMBER] Stitching amino acid templates- sequence command
- tanya singh (Sat Oct 30 2010 - 08:51:42 PDT)
[AMBER] Sugars flexibility vs ionic strength
- Sergey Samsonov (Wed Oct 06 2010 - 00:32:21 PDT)
- Lachele Foley (Lists) (Tue Oct 05 2010 - 11:36:24 PDT)
- Sergey Samsonov (Tue Oct 05 2010 - 08:07:32 PDT)
- Lachele Foley (Lists) (Tue Oct 05 2010 - 06:36:38 PDT)
- Sergey Samsonov (Tue Oct 05 2010 - 03:00:13 PDT)
[AMBER] Switching from NAMD to Amber for membrane Simulations
- Francesco Pietra (Sat Oct 23 2010 - 10:55:35 PDT)
- Ross Walker (Sat Oct 23 2010 - 10:30:10 PDT)
- Joshua Adelman (Sat Oct 23 2010 - 07:53:32 PDT)
[AMBER] Targeted MD
- Jordan, Brad (Thu Oct 28 2010 - 13:57:26 PDT)
[AMBER] Targeted MD - minimization problem
- Jason Swails (Fri Oct 29 2010 - 10:39:14 PDT)
- Carlos Simmerling (Fri Oct 29 2010 - 09:36:26 PDT)
- Jordan, Brad (Fri Oct 29 2010 - 09:33:51 PDT)
[AMBER] The result of entropy calculation
- Dima A Sabbah (Mon Oct 18 2010 - 07:59:41 PDT)
- DeChang Li (Mon Oct 18 2010 - 07:44:58 PDT)
[AMBER] TI +- variance is coming out to be very high
- sunita gupta (Thu Oct 07 2010 - 05:16:15 PDT)
- steinbrt.rci.rutgers.edu (Wed Oct 06 2010 - 05:48:26 PDT)
- sunita gupta (Wed Oct 06 2010 - 00:07:13 PDT)
- steinbrt.rci.rutgers.edu (Tue Oct 05 2010 - 03:31:27 PDT)
- sunita gupta (Tue Oct 05 2010 - 02:09:28 PDT)
- steinbrt.rci.rutgers.edu (Tue Oct 05 2010 - 00:34:16 PDT)
- sunita gupta (Tue Oct 05 2010 - 00:17:20 PDT)
[AMBER] TI - vacuum problems
- FCUP (Wed Oct 06 2010 - 03:45:55 PDT)
[AMBER] TI problem - Antechamber changes the atom order
- FCUP (Wed Oct 06 2010 - 03:34:10 PDT)
[AMBER] TI-Problems
- Kirsten Heitmann (Mon Oct 04 2010 - 03:01:10 PDT)
- steinbrt.rci.rutgers.edu (Sat Oct 02 2010 - 05:44:02 PDT)
- case (Sat Oct 02 2010 - 04:58:46 PDT)
- Kirsten Heitmann (Sat Oct 02 2010 - 02:30:21 PDT)
- Kirsten Heitmann (Sat Oct 02 2010 - 01:05:20 PDT)
- steinbrt.rci.rutgers.edu (Fri Oct 01 2010 - 21:28:50 PDT)
- Jason Swails (Fri Oct 01 2010 - 13:40:22 PDT)
- Kirsten Heitmann (Fri Oct 01 2010 - 13:30:08 PDT)
- case (Fri Oct 01 2010 - 04:55:45 PDT)
[AMBER] Time-average restraint question
- Mickey Richards (Wed Oct 27 2010 - 11:03:37 PDT)
[AMBER] Trajectory
- Carlos Simmerling (Wed Oct 27 2010 - 11:17:17 PDT)
- John S (Wed Oct 27 2010 - 10:15:23 PDT)
[AMBER] trajectory and topology file format
- Sangita Kachhap (Sun Oct 10 2010 - 06:49:08 PDT)
[AMBER] Trajectory Minimization
- Thomas Cheatham (Tue Oct 26 2010 - 09:33:49 PDT)
- John S (Tue Oct 26 2010 - 09:24:08 PDT)
- John S (Tue Oct 26 2010 - 07:43:53 PDT)
- Thomas Cheatham (Tue Oct 26 2010 - 07:26:00 PDT)
- John S (Tue Oct 26 2010 - 06:57:23 PDT)
[AMBER] Triclinic box condition for PBC
- Bongkeun Kim (Fri Oct 22 2010 - 12:04:24 PDT)
- Bill Ross (Fri Oct 22 2010 - 11:35:54 PDT)
- dcerutti.rci.rutgers.edu (Fri Oct 22 2010 - 11:14:56 PDT)
- Bill Ross (Fri Oct 22 2010 - 10:56:32 PDT)
- Bongkeun Kim (Fri Oct 22 2010 - 10:39:04 PDT)
[AMBER] tutorials of TMD and REMD
- Jason Swails (Fri Oct 08 2010 - 20:22:51 PDT)
- fancy2012 (Fri Oct 08 2010 - 20:15:31 PDT)
[AMBER] Umbrella sampling with temperature and pressure coupling method problem
- Andrew Jewett (Tue Oct 19 2010 - 20:19:50 PDT)
- Daniel Sindhikara (Tue Oct 19 2010 - 17:08:01 PDT)
- DeChang Li (Tue Oct 19 2010 - 08:29:29 PDT)
- Daniel Sindhikara (Tue Oct 19 2010 - 08:02:15 PDT)
- DeChang Li (Tue Oct 19 2010 - 05:57:33 PDT)
[AMBER] undefined reference in compiling amber10/gfortran
- case (Fri Oct 01 2010 - 09:45:37 PDT)
- Francesco Pietra (Fri Oct 01 2010 - 09:15:44 PDT)
[AMBER] unexpected numnghbr array
- case (Tue Oct 05 2010 - 11:50:09 PDT)
- William Flak (Tue Oct 05 2010 - 07:17:33 PDT)
[AMBER] Update of renamed "initial_traj" to"strip_mdcrd" for MMPBSA.py in AMBER 11 Manual.
- Jason Swails (Thu Oct 28 2010 - 07:15:03 PDT)
- Rafi Ahmad (Thu Oct 28 2010 - 06:58:26 PDT)
[AMBER] UREABOX tleap
- Bill Ross (Mon Oct 25 2010 - 10:02:04 PDT)
- M. L. Dodson (Mon Oct 25 2010 - 08:09:08 PDT)
- Michela Candotti (Mon Oct 25 2010 - 08:01:56 PDT)
[AMBER] V-limit exceeded in replica-exchang MD
- Paul S. Nerenberg (Fri Oct 08 2010 - 22:15:39 PDT)
- Cheng-I Lee (Fri Oct 08 2010 - 21:50:56 PDT)
[AMBER] Water box deformed after heating step
- Carlos Simmerling (Wed Oct 13 2010 - 09:37:29 PDT)
- xue wang (Wed Oct 13 2010 - 08:50:33 PDT)
- Carlos Simmerling (Wed Oct 13 2010 - 07:18:48 PDT)
- xue wang (Wed Oct 13 2010 - 07:09:41 PDT)
[AMBER] Water bridge - MMPBSA
- Jason Swails (Wed Oct 06 2010 - 13:16:47 PDT)
- Bill Miller III (Wed Oct 06 2010 - 13:09:24 PDT)
- William Flak (Wed Oct 06 2010 - 12:46:13 PDT)
- Bill Miller III (Tue Oct 05 2010 - 03:39:18 PDT)
- William Flak (Tue Oct 05 2010 - 02:31:56 PDT)
- Jason Swails (Mon Oct 04 2010 - 18:45:19 PDT)
- Bill Miller III (Mon Oct 04 2010 - 15:52:01 PDT)
- William Flak (Mon Oct 04 2010 - 15:25:09 PDT)
[AMBER] Water bridges
- Jason Swails (Mon Oct 04 2010 - 18:48:49 PDT)
- Lekpa Duukori (Mon Oct 04 2010 - 15:34:18 PDT)
[AMBER] water molecule positions
- Beale, John (Mon Oct 25 2010 - 06:03:47 PDT)
[AMBER] xleap
- Siavoush Dastmalchi (Tue Oct 12 2010 - 01:24:28 PDT)
- Siavoush Dastmalchi (Tue Oct 12 2010 - 01:21:48 PDT)
- Scott Brozell (Mon Oct 11 2010 - 23:22:02 PDT)
- Siavoush Dastmalchi (Mon Oct 11 2010 - 22:36:38 PDT)
- Scott Brozell (Mon Oct 11 2010 - 22:14:21 PDT)
- Siavoush Dastmalchi (Mon Oct 11 2010 - 21:54:48 PDT)
[AMBER] xleap menu bar problem
- Siavoush Dastmalchi (Tue Oct 12 2010 - 06:30:24 PDT)
- Jose Borreguero (Tue Oct 12 2010 - 06:20:48 PDT)
- Siavoush Dastmalchi (Tue Oct 12 2010 - 06:11:46 PDT)
[AMBER] xleap, xaLeap and X11
- Jason Swails (Wed Oct 27 2010 - 10:25:09 PDT)
- Shaandar Nyamtulga (Tue Oct 26 2010 - 22:49:32 PDT)
[AMBER] xleap, xaLeap is missing after Amber10 installation
- Shaandar Nyamtulga (Tue Oct 26 2010 - 05:55:08 PDT)
- Ross Walker (Mon Oct 25 2010 - 23:07:15 PDT)
- Shaandar Nyamtulga (Mon Oct 25 2010 - 22:54:49 PDT)
[AMBER] xleap: SegFault on loadpdb
- Maura Catherine Mooney (Wed Oct 13 2010 - 10:56:19 PDT)
- Jason Swails (Wed Oct 13 2010 - 10:52:08 PDT)
- Maura Catherine Mooney (Wed Oct 13 2010 - 10:41:40 PDT)
[AMBER] xmin fails with error in load_lbfgs()
- Don.Bashford.stjude.org (Tue Oct 19 2010 - 12:53:04 PDT)

Amber Archive Oct 2010 by subject