Amber Archive May 2013: by subject

[AMBER] (nessun oggetto)
- David A Case (Mon May 13 2013 - 13:08:58 PDT)
- Maurizio CELENTANO (Mon May 13 2013 - 11:00:31 PDT)
- David A Case (Mon May 13 2013 - 09:08:29 PDT)
- Maurizio CELENTANO (Mon May 13 2013 - 07:52:58 PDT)
[AMBER] About addIonsRand
- Marc van der Kamp (Fri May 24 2013 - 06:03:33 PDT)
[AMBER] About free energy decomposition
- Bill Miller III (Fri May 10 2013 - 21:02:10 PDT)
- 赵媛 (Wed May 08 2013 - 20:23:32 PDT)
[AMBER] about halogen atom radius in MMPBSA calculation
- Nadine Homeyer (Sun May 05 2013 - 23:00:16 PDT)
- Wang Bo (Sat May 04 2013 - 21:05:00 PDT)
[AMBER] About water flags running parm7 with NAMD
- Francesco Pietra (Tue May 28 2013 - 08:42:21 PDT)
- George Giambasu (Tue May 28 2013 - 08:21:49 PDT)
- Jason Swails (Tue May 28 2013 - 07:55:19 PDT)
- Francesco Pietra (Tue May 28 2013 - 07:33:41 PDT)
- Daniel Sindhikara (Tue May 28 2013 - 02:08:58 PDT)
- Francesco Pietra (Tue May 28 2013 - 00:43:05 PDT)
[AMBER] Advice on length of production simulation
- Marc van der Kamp (Sat May 04 2013 - 04:08:34 PDT)
- Chris Chris (Fri May 03 2013 - 09:01:49 PDT)
[AMBER] Amber 12 installation on GPU
- Ross Walker (Thu May 02 2013 - 07:24:01 PDT)
- David A Case (Thu May 02 2013 - 06:29:48 PDT)
- hannes.loeffler.stfc.ac.uk (Thu May 02 2013 - 00:04:00 PDT)
- Shozeb Haider (Wed May 01 2013 - 23:51:46 PDT)
[AMBER] AMBER GPU Cooling/usage Question
- ET (Fri May 10 2013 - 08:49:23 PDT)
- Ross Walker (Thu May 09 2013 - 06:27:54 PDT)
- ET (Thu May 09 2013 - 05:44:08 PDT)
[AMBER] amber tutorial A15
- David A Case (Tue May 14 2013 - 03:35:12 PDT)
- yanyuna (Mon May 13 2013 - 19:30:21 PDT)
- yanyuna (Mon May 13 2013 - 19:04:04 PDT)
- David A Case (Mon May 13 2013 - 18:59:00 PDT)
- yanyuna (Mon May 13 2013 - 18:16:19 PDT)
[AMBER] AmberTools vs Amber
- Mandal, Sanat (Fri May 31 2013 - 06:20:44 PDT)
- David A Case (Fri May 31 2013 - 05:02:27 PDT)
[AMBER] Ambertools13 installation issue
- Jason Swails (Sun May 05 2013 - 08:26:44 PDT)
- Chinthaka Ratnaweera (Sun May 05 2013 - 06:46:40 PDT)
- Jason Swails (Sun May 05 2013 - 05:15:47 PDT)
- Chinthaka Ratnaweera (Sat May 04 2013 - 20:48:17 PDT)
- Jason Swails (Sat May 04 2013 - 20:07:59 PDT)
- Hector A. Baldoni (Sat May 04 2013 - 17:25:14 PDT)
- Chinthaka Ratnaweera (Sat May 04 2013 - 17:16:20 PDT)
- Jason Swails (Sat May 04 2013 - 17:14:46 PDT)
- Daniel Roe (Sat May 04 2013 - 16:13:33 PDT)
- Chinthaka Ratnaweera (Sat May 04 2013 - 13:21:17 PDT)
[AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges
- Franz Symalla (Thu May 23 2013 - 03:12:22 PDT)
- Andreas Goetz (Wed May 22 2013 - 14:28:21 PDT)
- Franz Symalla (Wed May 22 2013 - 05:56:42 PDT)
[AMBER] antechamber and sqm problem
- Jason Swails (Sun May 19 2013 - 12:26:31 PDT)
- Cenk \(Jenk\) Andac (Sun May 19 2013 - 11:07:40 PDT)
[AMBER] apbsgrid error during sander.APBS calculation
- Marek Maly (Fri May 10 2013 - 04:48:06 PDT)
- Robert Konecny (Thu May 09 2013 - 18:53:16 PDT)
- Marek Maly (Thu May 09 2013 - 17:18:54 PDT)
[AMBER] assistance required for bcl scripts
- BALA SUBRAMANI G L (Tue May 14 2013 - 05:24:41 PDT)
[AMBER] Assistance required for capActivesite program
- steinbrt.rci.rutgers.edu (Tue May 14 2013 - 04:54:03 PDT)
- BALA SUBRAMANI G L (Mon May 13 2013 - 06:08:23 PDT)
- Bala Subramani (Mon May 13 2013 - 06:09:05 PDT)
[AMBER] Assistance required for MCPB program
- BALA SUBRAMANI G L (Wed May 08 2013 - 05:19:51 PDT)
[AMBER] assistance required for MTK++
- BALA SUBRAMANI G L (Tue May 14 2013 - 00:20:27 PDT)
[AMBER] assistance required for prep & frcmod file preparation
- BALA SUBRAMANI G L (Wed May 15 2013 - 00:00:24 PDT)
[AMBER] Atom does not have a type.
- David A Case (Tue May 07 2013 - 05:32:22 PDT)
- javier alejandro rendon carrillo (Tue May 07 2013 - 00:48:42 PDT)
[AMBER] atomicfluct
- David A Case (Tue May 28 2013 - 09:15:32 PDT)
- Daniel Roe (Tue May 28 2013 - 08:30:30 PDT)
- George Tzotzos (Mon May 27 2013 - 12:28:18 PDT)
- Daniel Roe (Mon May 27 2013 - 12:13:18 PDT)
- George Tzotzos (Mon May 27 2013 - 10:34:10 PDT)
[AMBER] ATTN: need revision
- Karl N. Kirschner (Mon May 13 2013 - 04:07:44 PDT)
- Karl N. Kirschner (Mon May 13 2013 - 00:32:00 PDT)
- seçkin Boz (Thu May 09 2013 - 04:45:46 PDT)
- Karl N. Kirschner (Wed May 08 2013 - 03:00:03 PDT)
- seçkin Boz (Wed May 08 2013 - 02:17:35 PDT)
[AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
- Daniel Roe (Fri May 10 2013 - 05:57:11 PDT)
- Andre C. Stiel (Fri May 10 2013 - 05:41:21 PDT)
- Daniel Roe (Fri May 10 2013 - 05:40:01 PDT)
- Andre C. Stiel (Fri May 10 2013 - 05:31:38 PDT)
- Andre C. Stiel (Fri May 10 2013 - 05:03:18 PDT)
- Daniel Roe (Thu May 09 2013 - 12:41:08 PDT)
- Andre C. Stiel (Thu May 09 2013 - 10:02:48 PDT)
[AMBER] Bug in cpptraj (AmberTools 13)
- Daniel Roe (Mon May 06 2013 - 07:15:12 PDT)
- Ake Sandgren (Sun May 05 2013 - 23:07:12 PDT)
[AMBER] by pmemd.cuda runs
- Jason Swails (Fri May 31 2013 - 11:11:01 PDT)
- Moth, Chris (Fri May 31 2013 - 09:09:03 PDT)
- Daniel Roe (Fri May 31 2013 - 07:27:55 PDT)
- Marc van der Kamp (Fri May 31 2013 - 06:12:46 PDT)
- Cenk \(Jenk\) Andac (Fri May 31 2013 - 05:32:37 PDT)
[AMBER] Chained AMBER jobs crash on Dual GPU compute node.
- ET (Thu May 30 2013 - 01:35:16 PDT)
- Jason Swails (Wed May 29 2013 - 11:16:24 PDT)
- ET (Wed May 29 2013 - 09:39:56 PDT)
- Jason Swails (Wed May 29 2013 - 07:15:33 PDT)
- ET (Tue May 28 2013 - 02:51:37 PDT)
- Jan-Philip Gehrcke (Mon May 27 2013 - 09:04:15 PDT)
- ET (Mon May 27 2013 - 03:41:40 PDT)
- Jan-Philip Gehrcke (Sun May 26 2013 - 11:30:10 PDT)
- ET (Sun May 26 2013 - 00:52:54 PDT)
[AMBER] cluster
- Daniel Roe (Tue May 21 2013 - 07:28:47 PDT)
- Mannan (Tue May 21 2013 - 03:48:43 PDT)
[AMBER] Convergence criterion
- Anselm Horn (Sat May 18 2013 - 18:06:07 PDT)
- Andreas Goetz (Sat May 18 2013 - 13:00:28 PDT)
- Anselm Horn (Sat May 18 2013 - 04:14:13 PDT)
- David A Case (Fri May 17 2013 - 17:21:40 PDT)
- Anselm Horn (Fri May 17 2013 - 12:46:16 PDT)
[AMBER] cpptraj and avgcoord
- Anselm Horn (Wed May 22 2013 - 07:10:16 PDT)
- Daniel Roe (Tue May 21 2013 - 16:03:01 PDT)
- Anselm Horn (Tue May 21 2013 - 14:37:35 PDT)
[AMBER] Cpptraj and hbonds
- Miguel Ortiz Lombardía (Tue May 28 2013 - 09:14:38 PDT)
- Daniel Roe (Tue May 28 2013 - 08:19:06 PDT)
- Miguel Ortiz Lombardía (Tue May 28 2013 - 07:56:42 PDT)
- Fernando Martín García (Tue May 28 2013 - 07:36:56 PDT)
- Daniel Roe (Tue May 28 2013 - 07:33:43 PDT)
- Fernando Martín García (Tue May 28 2013 - 07:06:26 PDT)
[AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics?
- Jan-Philip Gehrcke (Thu May 02 2013 - 08:02:56 PDT)
- Daniel Roe (Thu May 02 2013 - 07:22:02 PDT)
- Jan-Philip Gehrcke (Thu May 02 2013 - 05:30:36 PDT)
[AMBER] cpptraj strange warning with cluster command
- Miguel Ortiz Lombardía (Mon May 13 2013 - 09:08:40 PDT)
- Daniel Roe (Mon May 13 2013 - 08:35:59 PDT)
- Miguel Ortiz Lombardía (Mon May 13 2013 - 08:26:03 PDT)
[AMBER] create prmtop strcuture file for sumoylated residues
- crazylyf (Wed May 22 2013 - 06:18:50 PDT)
[AMBER] DNA basestep stacking energy/interaction energy
- BERGY (Wed May 01 2013 - 14:56:34 PDT)
[AMBER] DNA ligand system broke up- help please
- Mary Varughese (Thu May 09 2013 - 03:45:09 PDT)
[AMBER] drmsd
- Daniel Roe (Sat May 11 2013 - 08:17:38 PDT)
- Chris Chris (Fri May 10 2013 - 22:23:22 PDT)
[AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory.
- kurisaki (Wed May 22 2013 - 06:11:15 PDT)
- Daniel Roe (Wed May 22 2013 - 05:54:51 PDT)
- kurisaki (Wed May 22 2013 - 05:04:14 PDT)
[AMBER] Energy and gradient inconsistent between AMBER and NAB
- Jason Swails (Tue May 21 2013 - 10:26:58 PDT)
- Chris Whittleston (Tue May 21 2013 - 08:39:06 PDT)
[AMBER] Error in Membrane protein Simulation
- Ross Walker (Tue May 07 2013 - 16:42:53 PDT)
- David A Case (Tue May 07 2013 - 15:44:54 PDT)
- Dipankar Roy (Tue May 07 2013 - 09:39:40 PDT)
[AMBER] Error message when using mpirun on amber12_parallel
- 肖立 (Thu May 30 2013 - 19:54:52 PDT)
- Jason Swails (Thu May 30 2013 - 19:33:28 PDT)
- Mandal, Sanat (Thu May 30 2013 - 16:52:40 PDT)
- 肖立 (Thu May 30 2013 - 16:47:04 PDT)
- Jason Swails (Thu May 30 2013 - 16:37:17 PDT)
- 肖立 (Thu May 30 2013 - 16:31:33 PDT)
[AMBER] error running pmemd cuda tests
- ET (Fri May 10 2013 - 09:33:19 PDT)
- Jason Swails (Thu May 09 2013 - 07:28:54 PDT)
- Blake Mertz (Thu May 09 2013 - 06:15:57 PDT)
- ET (Thu May 09 2013 - 00:57:17 PDT)
- Blake Mertz (Wed May 08 2013 - 18:53:53 PDT)
- Jason Swails (Wed May 08 2013 - 12:19:55 PDT)
- Blake Mertz (Wed May 08 2013 - 11:32:46 PDT)
[AMBER] error while restart run
- Daniel Roe (Tue May 07 2013 - 07:19:44 PDT)
- David A Case (Tue May 07 2013 - 05:45:21 PDT)
- Subrata Paul (Tue May 07 2013 - 04:22:41 PDT)
[AMBER] error while using tleap with protein more than 248 residues
- Daniel Roe (Tue May 14 2013 - 07:48:39 PDT)
- David A Case (Tue May 14 2013 - 03:32:20 PDT)
- sandeep singh (Sun May 12 2013 - 22:05:11 PDT)
[AMBER] example karplus.txt file for cpptraj jcoupling command
- Daniel Roe (Fri May 31 2013 - 15:24:20 PDT)
- Duggan, Brendan (Fri May 31 2013 - 15:03:05 PDT)
- Daniel Roe (Fri May 24 2013 - 13:24:03 PDT)
- Duggan, Brendan (Fri May 24 2013 - 13:06:20 PDT)
- Daniel Roe (Thu May 23 2013 - 12:35:44 PDT)
- Duggan, Brendan (Thu May 23 2013 - 10:28:42 PDT)
[AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
- ET (Fri May 31 2013 - 15:45:42 PDT)
- Marek Maly (Fri May 31 2013 - 13:14:47 PDT)
- ET (Fri May 31 2013 - 13:02:34 PDT)
- Marek Maly (Fri May 31 2013 - 10:55:41 PDT)
- ET (Fri May 31 2013 - 10:17:03 PDT)
- Marek Maly (Fri May 31 2013 - 08:40:01 PDT)
- Marek Maly (Fri May 31 2013 - 08:30:02 PDT)
- filip fratev (Fri May 31 2013 - 08:30:57 PDT)
- Marek Maly (Fri May 31 2013 - 05:34:27 PDT)
- Marek Maly (Fri May 31 2013 - 03:29:59 PDT)
- ET (Fri May 31 2013 - 03:21:21 PDT)
- ET (Fri May 31 2013 - 03:17:07 PDT)
- Marek Maly (Thu May 30 2013 - 15:41:54 PDT)
- Scott Le Grand (Thu May 30 2013 - 15:45:49 PDT)
- Marek Maly (Thu May 30 2013 - 15:00:21 PDT)
- Scott Le Grand (Thu May 30 2013 - 12:27:17 PDT)
- Scott Le Grand (Thu May 30 2013 - 12:24:43 PDT)
- Jason Swails (Thu May 30 2013 - 12:13:29 PDT)
- filip fratev (Thu May 30 2013 - 11:46:01 PDT)
- Scott Le Grand (Thu May 30 2013 - 11:01:58 PDT)
- pavel.banas.upol.cz (Thu May 30 2013 - 10:56:15 PDT)
- ET (Thu May 30 2013 - 10:27:13 PDT)
- Scott Le Grand (Thu May 30 2013 - 09:55:44 PDT)
- Marek Maly (Thu May 30 2013 - 07:49:27 PDT)
- ET (Thu May 30 2013 - 07:06:17 PDT)
- Marek Maly (Thu May 30 2013 - 05:32:57 PDT)
- Marek Maly (Thu May 30 2013 - 05:14:55 PDT)
- ET (Thu May 30 2013 - 05:08:18 PDT)
- ET (Thu May 30 2013 - 01:33:13 PDT)
- Jason Swails (Wed May 29 2013 - 19:42:10 PDT)
- Marek Maly (Wed May 29 2013 - 18:24:30 PDT)
- Scott Le Grand (Wed May 29 2013 - 17:46:59 PDT)
- Marek Maly (Wed May 29 2013 - 16:30:53 PDT)
- Scott Le Grand (Wed May 29 2013 - 16:05:24 PDT)
- Marek Maly (Wed May 29 2013 - 15:00:19 PDT)
- Marek Maly (Wed May 29 2013 - 14:22:34 PDT)
- Scott Le Grand (Wed May 29 2013 - 13:46:58 PDT)
- Jason Swails (Wed May 29 2013 - 13:44:18 PDT)
- Scott Le Grand (Wed May 29 2013 - 13:41:46 PDT)
- Marek Maly (Wed May 29 2013 - 13:11:12 PDT)
- Ross Walker (Tue May 28 2013 - 18:44:33 PDT)
- Scott Le Grand (Tue May 28 2013 - 17:49:31 PDT)
- ET (Tue May 28 2013 - 17:41:05 PDT)
- Divi/GMAIL (Tue May 28 2013 - 17:12:19 PDT)
- ET (Tue May 28 2013 - 17:11:27 PDT)
- Scott Le Grand (Tue May 28 2013 - 13:46:30 PDT)
- Marek Maly (Tue May 28 2013 - 13:20:45 PDT)
- Robert Konecny (Tue May 28 2013 - 13:36:52 PDT)
- Scott Le Grand (Tue May 28 2013 - 13:13:36 PDT)
- Marek Maly (Tue May 28 2013 - 12:24:36 PDT)
- Scott Le Grand (Tue May 28 2013 - 12:01:20 PDT)
- ET (Tue May 28 2013 - 11:42:32 PDT)
- Scott Le Grand (Tue May 28 2013 - 08:57:33 PDT)
- Gould, Ian R (Tue May 28 2013 - 08:50:53 PDT)
- Robert Konecny (Tue May 28 2013 - 08:11:47 PDT)
- Scott Le Grand (Tue May 28 2013 - 07:59:33 PDT)
- Marek Maly (Mon May 27 2013 - 17:41:58 PDT)
- Scott Le Grand (Mon May 27 2013 - 16:25:24 PDT)
- Marek Maly (Mon May 27 2013 - 10:01:39 PDT)
[AMBER] ff10 from amber11 maybe not using OL3??
- David A Case (Fri May 17 2013 - 05:35:07 PDT)
- Amparo Garcia Lopez (Fri May 17 2013 - 00:58:45 PDT)
- pavel.banas.upol.cz (Thu May 16 2013 - 16:05:04 PDT)
- Ilyas Yildirim (Thu May 16 2013 - 15:18:31 PDT)
- Amparo Garcia Lopez (Thu May 16 2013 - 14:44:00 PDT)
- Amparo Garcia Lopez (Thu May 16 2013 - 14:16:09 PDT)
- pavel.banas.upol.cz (Thu May 16 2013 - 13:16:00 PDT)
- Niel Henriksen (Thu May 16 2013 - 11:57:32 PDT)
- Amparo Garcia Lopez (Thu May 16 2013 - 09:31:16 PDT)
[AMBER] force field parameters for acetylated lysine
- Senthil Natesan (Tue May 21 2013 - 06:28:15 PDT)
- Karl N. Kirschner (Tue May 21 2013 - 00:17:27 PDT)
- Senthil Natesan (Fri May 17 2013 - 11:03:52 PDT)
[AMBER] Free energy calculation of pyridine
- David A Case (Mon May 27 2013 - 18:35:56 PDT)
- Bishnu Thapa (Mon May 27 2013 - 14:35:58 PDT)
[AMBER] Free Energy for the G Quadruplex DNA including channel potassium ions
- Debayan Chakraborty (Tue May 14 2013 - 05:03:26 PDT)
[AMBER] Fwd:
- Robin Jain (Sun May 05 2013 - 22:33:23 PDT)
[AMBER] Fwd: unstable sytem-help
- Mary Varughese (Fri May 10 2013 - 16:44:16 PDT)
- David A Case (Fri May 10 2013 - 03:48:11 PDT)
- Mary Varughese (Thu May 09 2013 - 06:50:32 PDT)
- David A Case (Thu May 09 2013 - 06:03:28 PDT)
- Mary Varughese (Thu May 09 2013 - 02:05:19 PDT)
[AMBER] Glass Transition Temperature
- David A Case (Fri May 10 2013 - 08:42:23 PDT)
- Hector A. Baldoni (Thu May 09 2013 - 12:18:39 PDT)
[AMBER] GPU version availability on Gordon-SDSC and Kraken NICS
- Ross Walker (Thu May 23 2013 - 10:45:27 PDT)
- Senthil Natesan (Thu May 23 2013 - 10:39:28 PDT)
[AMBER] Grid command for water density
- Jason Swails (Tue May 21 2013 - 04:49:55 PDT)
- BERGY (Sun May 19 2013 - 02:08:08 PDT)
[AMBER] GTX780
- Scott Le Grand (Tue May 28 2013 - 10:48:26 PDT)
- Fabrício Bracht (Tue May 28 2013 - 10:36:58 PDT)
[AMBER] hbond in ptraj and cpptraj
- Daniel Roe (Fri May 31 2013 - 07:24:00 PDT)
- pmaj.nencki.gov.pl (Fri May 31 2013 - 06:14:21 PDT)
[AMBER] How to average rst ?
- Daniel Roe (Wed May 08 2013 - 08:02:01 PDT)
- 赵媛 (Tue May 07 2013 - 20:58:15 PDT)
[AMBER] How to construct a mol2 file from a PDB and RESP output files ?
- FyD (Thu May 23 2013 - 03:49:05 PDT)
- David A Case (Wed May 22 2013 - 06:08:22 PDT)
- Ayesha Fatima (Wed May 22 2013 - 05:25:41 PDT)
- ABEL Stephane 175950 (Wed May 22 2013 - 04:08:06 PDT)
[AMBER] how to create parameter file for Zn
- BALA SUBRAMANI G L (Thu May 09 2013 - 06:13:16 PDT)
[AMBER] How to dump distance information in the form of a vector file?
- Daniel Roe (Thu May 16 2013 - 15:48:18 PDT)
- Sajeewa Pemasinghe (Thu May 16 2013 - 15:38:27 PDT)
- Daniel Roe (Thu May 16 2013 - 14:53:19 PDT)
- Sajeewa Pemasinghe (Thu May 16 2013 - 14:19:53 PDT)
[AMBER] how to remove the overlap between molecules
- Jason Swails (Tue May 21 2013 - 04:44:38 PDT)
- Rasha Alqus (Tue May 21 2013 - 03:56:30 PDT)
[AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation?
- David A Case (Fri May 17 2013 - 11:11:51 PDT)
- Sajeewa Pemasinghe (Fri May 17 2013 - 10:58:14 PDT)
- Daniel Roe (Fri May 17 2013 - 10:34:40 PDT)
- Sajeewa Pemasinghe (Fri May 17 2013 - 10:05:13 PDT)
[AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run
- Jonathan Gough (Sun May 05 2013 - 09:20:37 PDT)
- Daniel Roe (Sun May 05 2013 - 09:05:58 PDT)
- Jonathan Gough (Sun May 05 2013 - 05:46:24 PDT)
[AMBER] Improper atom order
- Bill Ross (Sat May 11 2013 - 11:51:40 PDT)
- Reinis Danne (Thu May 09 2013 - 00:21:05 PDT)
- Bill Ross (Wed May 08 2013 - 17:34:52 PDT)
- Reinis Danne (Wed May 08 2013 - 01:19:40 PDT)
- Karl N. Kirschner (Wed May 08 2013 - 01:16:20 PDT)
- Reinis Danne (Tue May 07 2013 - 05:26:53 PDT)
[AMBER] improper Dihedral Specification
- Bill Ross (Wed May 01 2013 - 15:51:21 PDT)
- David A Case (Wed May 01 2013 - 04:52:51 PDT)
[AMBER] Inconsistent results for TI calculations
- Antonios Kolocouris (Mon May 13 2013 - 09:48:58 PDT)
- steinbrt.rci.rutgers.edu (Mon May 13 2013 - 09:31:50 PDT)
- Thomas Exner (Mon May 13 2013 - 07:47:36 PDT)
[AMBER] Interpreting .prmtop files
- David Winogradoff (Tue May 28 2013 - 08:45:27 PDT)
- Jason Swails (Thu May 16 2013 - 09:15:16 PDT)
- David Winogradoff (Thu May 16 2013 - 08:49:12 PDT)
- David Winogradoff (Thu May 16 2013 - 06:07:14 PDT)
- Jason Swails (Wed May 15 2013 - 16:18:14 PDT)
- Hai Nguyen (Wed May 15 2013 - 14:18:33 PDT)
- David Winogradoff (Wed May 15 2013 - 14:13:54 PDT)
[AMBER] JAC benchmark tests on K20X
- Shan-ho Tsai (Tue May 21 2013 - 07:05:05 PDT)
- Jason Swails (Tue May 21 2013 - 04:32:31 PDT)
- Shan-ho Tsai (Mon May 20 2013 - 13:11:13 PDT)
- Ross Walker (Mon May 20 2013 - 12:21:49 PDT)
- Shan-ho Tsai (Mon May 20 2013 - 12:00:16 PDT)
[AMBER] Kind of RESTYPE
- David A Case (Wed May 08 2013 - 05:14:32 PDT)
- setyanto md (Tue May 07 2013 - 22:12:27 PDT)
[AMBER] Leap adding salt No solvent overlap
- Johannes Zuegg (Tue May 07 2013 - 16:51:44 PDT)
- Daniel Roe (Tue May 07 2013 - 07:52:01 PDT)
- Jason Swails (Mon May 06 2013 - 20:19:25 PDT)
- Johannes Zuegg (Mon May 06 2013 - 18:35:03 PDT)
[AMBER] memory failure
- Jonathan Gough (Tue May 14 2013 - 12:45:05 PDT)
- David A Case (Tue May 14 2013 - 11:15:08 PDT)
- Jonathan Gough (Tue May 14 2013 - 10:41:56 PDT)
- Jonathan Gough (Tue May 14 2013 - 10:39:27 PDT)
[AMBER] mmpbsa error msg
- Jason Swails (Mon May 06 2013 - 12:58:21 PDT)
- Chinthaka Ratnaweera (Mon May 06 2013 - 11:53:23 PDT)
- Jason Swails (Mon May 06 2013 - 11:41:57 PDT)
- Chinthaka Ratnaweera (Mon May 06 2013 - 07:26:05 PDT)
- Chinthaka Ratnaweera (Mon May 06 2013 - 07:23:34 PDT)
[AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions.
- Jason Swails (Sat May 04 2013 - 17:06:02 PDT)
- David A Case (Sat May 04 2013 - 09:56:37 PDT)
- Jan-Philip Gehrcke (Sat May 04 2013 - 08:59:59 PDT)
- Angelica Parente (Sat May 04 2013 - 02:08:02 PDT)
[AMBER] MMPBSA for stability analysis
- Jason Swails (Sat May 18 2013 - 18:12:07 PDT)
- Debayan Chakraborty (Sat May 18 2013 - 10:43:21 PDT)
[AMBER] MMPBSA.py
- Jason Swails (Mon May 13 2013 - 05:03:38 PDT)
- Urszula Uciechowska (Sun May 12 2013 - 23:24:35 PDT)
[AMBER] MMPBSA.py error
- Jason Swails (Mon May 06 2013 - 13:04:42 PDT)
- Kshatresh Dutta Dubey (Mon May 06 2013 - 13:01:57 PDT)
- Jason Swails (Mon May 06 2013 - 12:52:41 PDT)
- Kshatresh Dutta Dubey (Mon May 06 2013 - 12:09:36 PDT)
- Jason Swails (Mon May 06 2013 - 11:40:48 PDT)
- Kshatresh Dutta Dubey (Mon May 06 2013 - 08:21:11 PDT)
- Chris Chris (Mon May 06 2013 - 08:18:28 PDT)
- Kshatresh Dutta Dubey (Mon May 06 2013 - 07:16:27 PDT)
- Le,Huy Tuan (Mon May 06 2013 - 07:10:54 PDT)
- Jason Swails (Mon May 06 2013 - 06:50:45 PDT)
- Le,Huy Tuan (Mon May 06 2013 - 06:39:25 PDT)
[AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
- Jan-Philip Gehrcke (Fri May 03 2013 - 08:28:53 PDT)
- Jason Swails (Fri May 03 2013 - 07:12:15 PDT)
- Jan-Philip Gehrcke (Fri May 03 2013 - 02:53:36 PDT)
[AMBER] Molecular Shape Searching on GPUs
- MARK (Mon May 20 2013 - 11:09:06 PDT)
- MARK (Mon May 20 2013 - 11:05:45 PDT)
[AMBER] mpi4py installation error
- Kshatresh Dutta Dubey (Mon May 13 2013 - 12:24:21 PDT)
- Daniel Roe (Mon May 13 2013 - 12:15:39 PDT)
- Kshatresh Dutta Dubey (Mon May 13 2013 - 11:18:50 PDT)
[AMBER] NAMD TO AMBER
- Rasha Alqus (Wed May 15 2013 - 03:37:32 PDT)
[AMBER] NaN from Mg2+ near ASP while running aMD
- Jonathan Gough (Sun May 12 2013 - 12:38:51 PDT)
- Jonathan Gough (Sun May 12 2013 - 12:34:31 PDT)
[AMBER] Need your help
- David A Case (Fri May 03 2013 - 11:56:51 PDT)
- Poornima Iyer (Fri May 03 2013 - 10:43:22 PDT)
[AMBER] Nonpolar contribution in MMPBSA is very large
- Kshatresh Dutta Dubey (Tue May 14 2013 - 07:38:19 PDT)
- Jason Swails (Tue May 14 2013 - 07:21:02 PDT)
- Kshatresh Dutta Dubey (Tue May 14 2013 - 05:48:14 PDT)
- Jan-Philip Gehrcke (Tue May 14 2013 - 05:39:16 PDT)
- Kshatresh Dutta Dubey (Tue May 14 2013 - 05:32:33 PDT)
- Jason Swails (Tue May 14 2013 - 05:04:22 PDT)
- Kshatresh Dutta Dubey (Tue May 14 2013 - 03:34:19 PDT)
[AMBER] normal modes and intensity for raman spectrum
- Adrian Roitberg (Wed May 08 2013 - 10:54:46 PDT)
- Rasha Alqus (Wed May 08 2013 - 08:51:56 PDT)
[AMBER] occasional distortion of solute molecule
- crazylyf (Wed May 01 2013 - 21:23:15 PDT)
[AMBER] Open MPI failure
- Daniel Roe (Tue May 07 2013 - 13:41:46 PDT)
- David Winogradoff (Tue May 07 2013 - 11:27:10 PDT)
- Daniel Roe (Tue May 07 2013 - 10:38:44 PDT)
- David Winogradoff (Tue May 07 2013 - 09:17:50 PDT)
- David A Case (Mon May 06 2013 - 12:49:25 PDT)
- Ross Walker (Mon May 06 2013 - 10:30:03 PDT)
- David Winogradoff (Mon May 06 2013 - 10:25:29 PDT)
- Daniel Roe (Mon May 06 2013 - 09:30:52 PDT)
- David Winogradoff (Mon May 06 2013 - 09:18:43 PDT)
[AMBER] Optimal APBS parameters - Amber OR APBS defaults ?
- Marek Maly (Tue May 07 2013 - 20:20:00 PDT)
- Ray Luo, Ph.D. (Tue May 07 2013 - 14:52:26 PDT)
- Marek Maly (Tue May 07 2013 - 11:27:06 PDT)
[AMBER] pairwise decomposition using mmpbsa.py
- Jason Swails (Wed May 22 2013 - 05:52:38 PDT)
- dilrajl.bii.a-star.edu.sg (Wed May 22 2013 - 05:34:45 PDT)
[AMBER] Paper detailing GPU Simulations Compared to CPU code
- ET (Wed May 08 2013 - 17:12:19 PDT)
[AMBER] Parameters for Aluminum Ion
- Sun (Thu May 16 2013 - 21:00:48 PDT)
[AMBER] PM6 fails for DMSO system
- Andreas Goetz (Sat May 04 2013 - 18:43:36 PDT)
- me, Nancy (Fri May 03 2013 - 18:14:52 PDT)
- me, Nancy (Thu May 02 2013 - 16:34:05 PDT)
- Jason Swails (Thu May 02 2013 - 15:25:46 PDT)
- me, Nancy (Thu May 02 2013 - 14:48:59 PDT)
[AMBER] PME and vdW cutoffs
- Andreas Goetz (Tue May 07 2013 - 13:22:38 PDT)
- George Tzotzos (Tue May 07 2013 - 09:37:59 PDT)
[AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
- Ross Walker (Wed May 08 2013 - 13:15:31 PDT)
- Scott Le Grand (Wed May 08 2013 - 12:51:30 PDT)
- Sergio R Aragon (Wed May 08 2013 - 12:19:20 PDT)
- sun (Wed May 08 2013 - 09:40:23 PDT)
[AMBER] pmemd.CUDA installation problem
- Cenk \(Jenk\) Andac (Thu May 16 2013 - 00:24:56 PDT)
- Cenk \(Jenk\) Andac (Wed May 15 2013 - 23:11:12 PDT)
- Jason Swails (Wed May 15 2013 - 10:03:29 PDT)
- Cenk \(Jenk\) Andac (Wed May 15 2013 - 09:38:14 PDT)
[AMBER] preferred nucleic acids pbsa model
- Le,Huy Tuan (Tue May 14 2013 - 06:55:40 PDT)
[AMBER] problem in cpptraj installation
- Daniel Roe (Mon May 06 2013 - 08:45:35 PDT)
- Kshatresh Dutta Dubey (Mon May 06 2013 - 08:15:09 PDT)
- Daniel Roe (Mon May 06 2013 - 07:54:20 PDT)
- Kshatresh Dutta Dubey (Sun May 05 2013 - 10:58:09 PDT)
- Daniel Roe (Sun May 05 2013 - 09:26:19 PDT)
- Kshatresh Dutta Dubey (Sun May 05 2013 - 09:07:54 PDT)
- Daniel Roe (Sun May 05 2013 - 08:59:03 PDT)
- Kshatresh Dutta Dubey (Sun May 05 2013 - 07:56:57 PDT)
[AMBER] Problem in updating AmberTools 12
- Jason Swails (Thu May 23 2013 - 15:32:25 PDT)
- Kshatresh Dutta Dubey (Thu May 23 2013 - 06:33:03 PDT)
[AMBER] problem on compiling sander
- me, Nancy (Mon May 27 2013 - 09:40:31 PDT)
- David A Case (Sun May 26 2013 - 16:29:48 PDT)
- me, Nancy (Sat May 25 2013 - 11:41:16 PDT)
[AMBER] Problem with cpptraj vs ptraj
- imarcos (Thu May 16 2013 - 03:55:15 PDT)
- Daniel Roe (Tue May 14 2013 - 07:12:12 PDT)
- imarcos (Tue May 14 2013 - 06:33:50 PDT)
[AMBER] problem with parmchk and a big organic molecule
- Rebeca García Fandiño (Tue May 21 2013 - 05:29:04 PDT)
[AMBER] Problem with the SMD aplication to proton transfer
- Brian Radak (Fri May 10 2013 - 05:55:58 PDT)
- Santi Tolosa (Fri May 10 2013 - 04:05:56 PDT)
[AMBER] problems solvating
- Daniel Roe (Tue May 07 2013 - 07:16:14 PDT)
- Jonathan Gough (Tue May 07 2013 - 05:58:05 PDT)
[AMBER] Protein-ligand docking
- David A Case (Mon May 06 2013 - 05:25:33 PDT)
- kanika sharma (Mon May 06 2013 - 04:27:45 PDT)
[AMBER] psf files from cellulose builder
- Rasha Alqus (Wed May 01 2013 - 08:59:05 PDT)
[AMBER] Ptraj_segmentation fault
- Jason Swails (Mon May 06 2013 - 05:36:30 PDT)
- KAMAKSHI SHARMA (Mon May 06 2013 - 00:26:22 PDT)
[AMBER] Qm/mm gaussian template=1
- Andreas Goetz (Thu May 23 2013 - 07:21:17 PDT)
- jcgt (Thu May 23 2013 - 02:13:57 PDT)
- jcgt (Wed May 22 2013 - 00:39:00 PDT)
- Andreas Goetz (Tue May 21 2013 - 16:48:51 PDT)
- jcgt (Tue May 21 2013 - 03:32:36 PDT)
[AMBER] Query regarding mechanical unfolding of protein
- Manish Paul (Wed May 22 2013 - 11:22:12 PDT)
[AMBER] Question about the normalization of velocity autocorrelation function
- Sajeewa Pemasinghe (Thu May 23 2013 - 05:12:43 PDT)
- David A Case (Thu May 23 2013 - 04:46:02 PDT)
- Sajeewa Pemasinghe (Wed May 22 2013 - 15:15:59 PDT)
[AMBER] radial distribution function problem
- Daniel Roe (Sat May 04 2013 - 09:10:52 PDT)
- Jio M (Sat May 04 2013 - 02:35:28 PDT)
[AMBER] Random Acceleration Molecular Dynamics (RAMD)
- Vlad Cojocaru (Tue May 14 2013 - 03:55:48 PDT)
- Lars Skjærven (Tue May 14 2013 - 03:16:50 PDT)
[AMBER] random seed not in output file -> run not reproducible
- Jason Swails (Tue May 14 2013 - 05:20:43 PDT)
- Jan-Philip Gehrcke (Tue May 14 2013 - 05:15:51 PDT)
- Ross Walker (Tue May 14 2013 - 05:04:20 PDT)
- Jason Swails (Tue May 14 2013 - 05:02:20 PDT)
- Ross Walker (Tue May 14 2013 - 04:35:08 PDT)
- Jan-Philip Gehrcke (Tue May 14 2013 - 04:02:30 PDT)
[AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
- Ayesha Fatima (Thu May 23 2013 - 21:26:57 PDT)
- FyD (Thu May 23 2013 - 04:53:21 PDT)
- ABEL Stephane 175950 (Thu May 23 2013 - 03:55:16 PDT)
- Ayesha Fatima (Wed May 22 2013 - 08:32:03 PDT)
- ABEL Stephane 175950 (Wed May 22 2013 - 06:26:51 PDT)
- ABEL Stephane 175950 (Wed May 22 2013 - 05:52:54 PDT)
[AMBER] reference group and pulled group in umbrella sampling
- Jio M (Fri May 31 2013 - 03:38:17 PDT)
[AMBER] References abou FF12SB
- Carlos Simmerling (Tue May 21 2013 - 04:52:44 PDT)
- Alan (Thu May 16 2013 - 05:35:56 PDT)
[AMBER] Regarding mmpbsa.py
- Jason Swails (Mon May 13 2013 - 05:00:28 PDT)
- David A Case (Mon May 13 2013 - 04:54:25 PDT)
- dilrajl.bii.a-star.edu.sg (Mon May 13 2013 - 03:55:57 PDT)
[AMBER] Relationship of time-autocorrelation plots for two lengths of time
- Sajeewa Pemasinghe (Thu May 23 2013 - 14:31:04 PDT)
- George Giambasu (Thu May 23 2013 - 06:42:08 PDT)
- Sajeewa Pemasinghe (Wed May 22 2013 - 14:28:27 PDT)
- George Giambasu (Wed May 22 2013 - 14:20:07 PDT)
- Sajeewa Pemasinghe (Wed May 22 2013 - 13:35:16 PDT)
[AMBER] repeat MD simulations
- Vlad Cojocaru (Sat May 18 2013 - 04:34:24 PDT)
- Kanin Wichapong (Sat May 18 2013 - 03:19:55 PDT)
[AMBER] restart a md simulation
- Anselm Horn (Thu May 02 2013 - 02:04:40 PDT)
- 纪晓峰 (Wed May 01 2013 - 18:53:03 PDT)
- 纪晓峰 (Wed May 01 2013 - 18:42:34 PDT)
[AMBER] RMSD calculation between trajectories
- Daniel Roe (Thu May 30 2013 - 05:56:56 PDT)
- dilrajl.bii.a-star.edu.sg (Thu May 30 2013 - 05:27:31 PDT)
- Daniel Roe (Wed May 29 2013 - 07:11:18 PDT)
- dilrajl.bii.a-star.edu.sg (Wed May 29 2013 - 05:10:58 PDT)
- Daniel Roe (Tue May 28 2013 - 07:24:01 PDT)
- Niel Henriksen (Tue May 28 2013 - 06:13:30 PDT)
- Niel Henriksen (Tue May 28 2013 - 05:59:50 PDT)
- dilrajl.bii.a-star.edu.sg (Tue May 28 2013 - 05:42:42 PDT)
[AMBER] rmsd vs rmsf
- nguyentb.bii.a-star.edu.sg (Tue May 21 2013 - 05:30:08 PDT)
- Jason Swails (Tue May 21 2013 - 04:36:55 PDT)
- Carlos Simmerling (Tue May 21 2013 - 04:17:08 PDT)
- nguyentb.bii.a-star.edu.sg (Tue May 21 2013 - 02:36:08 PDT)
[AMBER] Sample LMOD program (nab section of AmberTools manual)
- Chris Moth (Thu May 30 2013 - 12:56:25 PDT)
[AMBER] sander.MPI is extremely slow
- Ross Walker (Mon May 13 2013 - 03:23:14 PDT)
- Kshatresh Dutta Dubey (Sun May 12 2013 - 21:48:15 PDT)
[AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
- Jacob Monroe (Mon May 27 2013 - 09:07:44 PDT)
- FyD (Sat May 25 2013 - 09:00:09 PDT)
- David A Case (Sat May 25 2013 - 05:30:20 PDT)
- Jacob Monroe (Fri May 24 2013 - 13:02:49 PDT)
- David A Case (Fri May 24 2013 - 05:11:12 PDT)
- FyD (Thu May 23 2013 - 23:56:28 PDT)
- Jacob Monroe (Thu May 23 2013 - 20:38:13 PDT)
[AMBER] SMD calculation
- Jason Swails (Fri May 31 2013 - 07:24:57 PDT)
- Santi Tolosa (Fri May 31 2013 - 03:00:40 PDT)
[AMBER] SMD for proton transfer
- M. L. Dodson (Tue May 14 2013 - 06:47:30 PDT)
- Santi Tolosa (Tue May 14 2013 - 06:19:54 PDT)
[AMBER] SMD pulling GPU
- Ross Walker (Thu May 16 2013 - 09:59:41 PDT)
- José Guilherme Vilhena Albuquerque d'Orey (Thu May 16 2013 - 08:29:39 PDT)
- Ross Walker (Thu May 16 2013 - 07:58:09 PDT)
- James Murdock (Thu May 16 2013 - 03:42:30 PDT)
- José Guilherme Vilhena Albuquerque d'Orey (Thu May 16 2013 - 01:44:07 PDT)
[AMBER] SQM: How to extract the charge density of sqm runs?
- Andreas Goetz (Fri May 24 2013 - 16:13:26 PDT)
- David A Case (Fri May 24 2013 - 05:15:07 PDT)
- Franz Symalla (Thu May 23 2013 - 14:33:04 PDT)
[AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint
- David A Case (Tue May 28 2013 - 17:55:33 PDT)
- Adrian Roitberg (Tue May 28 2013 - 12:32:19 PDT)
- Emmanuel (Tue May 28 2013 - 12:29:54 PDT)
[AMBER] Steered Molecular dynamics
- Santi Tolosa (Fri May 24 2013 - 10:01:42 PDT)
[AMBER] Test for NTP, ntt=3
- David A Case (Tue May 07 2013 - 15:44:25 PDT)
- Jason Swails (Tue May 07 2013 - 05:54:27 PDT)
- Deák Robert (Tue May 07 2013 - 02:52:22 PDT)
- Deák Robert (Tue May 07 2013 - 02:47:41 PDT)
- Jason Swails (Mon May 06 2013 - 07:00:15 PDT)
- Deák Robert (Mon May 06 2013 - 06:25:38 PDT)
- Deák Robert (Mon May 06 2013 - 06:23:46 PDT)
[AMBER] the best APS is not zero, bonds involved by this atom are frozen
- Ashutosh Shandilya (Mon May 06 2013 - 08:24:40 PDT)
- Ashutosh Shandilya (Mon May 06 2013 - 08:15:43 PDT)
[AMBER] The force constants of bond and angle items are zero when the MCPB program reads the internal force constant matrix
- JiYuan Liu (Mon May 13 2013 - 00:43:43 PDT)
[AMBER] TI erro - atom coordinate disagreement
- steinbrt.rci.rutgers.edu (Thu May 23 2013 - 12:05:07 PDT)
- Kumar Sonu (Thu May 23 2013 - 10:50:30 PDT)
[AMBER] TR : [PROVENANCE INTERNET] RE : How to construct a mol2 file from a PDB and RESP outputfiles ?
- ABEL Stephane 175950 (Wed May 22 2013 - 06:31:43 PDT)
[AMBER] unstable sytem-help
- Mary Varughese (Wed May 08 2013 - 04:01:52 PDT)
[AMBER] vlimit exceed followed by SHAKE failure
- seçkin Boz (Thu May 09 2013 - 04:06:22 PDT)
- David A Case (Tue May 07 2013 - 05:49:28 PDT)
- seçkin Boz (Tue May 07 2013 - 01:48:18 PDT)
- David A Case (Fri May 03 2013 - 11:59:33 PDT)
- seçkin Boz (Fri May 03 2013 - 05:47:52 PDT)
- David A Case (Fri May 03 2013 - 04:59:20 PDT)
- seçkin Boz (Fri May 03 2013 - 03:43:24 PDT)
[AMBER] when doing accelerated MD...
- Jonathan Gough (Tue May 07 2013 - 15:16:57 PDT)
- Jesper Sørensen (Tue May 07 2013 - 15:09:22 PDT)
- Jonathan Gough (Tue May 07 2013 - 14:01:20 PDT)
Busco informacion sobre AMBER
- Sergio R Aragon (Sat May 04 2013 - 23:11:18 PDT)
- ros (Sat May 04 2013 - 23:09:29 PDT)
- Patricia Castro Gutierrez (Sat May 04 2013 - 22:32:22 PDT)
hey
- Wholly Peach (Wed May 08 2013 - 06:32:28 PDT)
Trouble generating topology files
- David A Case (Fri May 31 2013 - 05:08:24 PDT)
- Teo, Theodosia Hua Swan - teohy004 (Thu May 30 2013 - 17:58:04 PDT)

Amber Archive May 2013 by subject