Amber Archive Sep 2014: by subject

[AMBER] [ANN] MDTraj 1.0: Trajectory Analysis in Python
- Robert McGibbon (Mon Sep 08 2014 - 13:17:02 PDT)
[AMBER] about amoeba
- Jason Swails (Tue Sep 30 2014 - 04:28:23 PDT)
- m13654940810 (Tue Sep 30 2014 - 01:04:40 PDT)
[AMBER] about dihedral type
- Arun Srikanth (Sun Sep 14 2014 - 15:22:13 PDT)
- Arun Srikanth (Sun Sep 14 2014 - 14:03:39 PDT)
- Jason Swails (Sun Sep 14 2014 - 12:34:07 PDT)
- Arun Srikanth (Sun Sep 14 2014 - 11:47:20 PDT)
[AMBER] about MD
- David A Case (Sun Sep 28 2014 - 11:36:29 PDT)
- Jason Swails (Fri Sep 26 2014 - 20:51:03 PDT)
- m13654940810 (Fri Sep 26 2014 - 19:47:18 PDT)
[AMBER] ACS COMP Division travel awards for Spring 2015 National Meeting in Denver
- Carlos Simmerling (Fri Sep 12 2014 - 07:41:21 PDT)
[AMBER] Aligning a trajectory
- Jason Swails (Wed Sep 17 2014 - 05:39:41 PDT)
- Jonathan Gough (Wed Sep 17 2014 - 05:20:27 PDT)
[AMBER] amber course
- MOHD HOMAIDUR RAHMAN (Mon Sep 08 2014 - 09:25:33 PDT)
- Ross Walker (Mon Sep 08 2014 - 07:54:54 PDT)
- Fabian Glaser (Mon Sep 08 2014 - 06:35:04 PDT)
[AMBER] AMBER Digest, Vol 989, Issue 1
- Jason Swails (Mon Sep 29 2014 - 05:06:25 PDT)
- amirhossein taghavi (Mon Sep 29 2014 - 00:42:41 PDT)
[AMBER] amber force field
- Jason Swails (Wed Sep 03 2014 - 07:40:30 PDT)
- 王珍 (Wed Sep 03 2014 - 06:50:11 PDT)
[AMBER] amber-Gaussian find the transition
- Brian Radak (Sun Sep 07 2014 - 06:23:18 PDT)
- 王珍 (Sun Sep 07 2014 - 02:04:25 PDT)
[AMBER] Amber/ Orca problem
- Aixiao Li (Wed Sep 10 2014 - 02:01:41 PDT)
- David A Case (Tue Sep 09 2014 - 08:02:12 PDT)
- Aixiao Li (Tue Sep 09 2014 - 05:03:27 PDT)
- David A Case (Tue Sep 09 2014 - 05:14:18 PDT)
- Aixiao Li (Tue Sep 09 2014 - 04:11:12 PDT)
[AMBER] Amber12 serial test failure
- Jason Swails (Fri Sep 12 2014 - 11:27:06 PDT)
- Samaneh Ghassabi Kondalaji (Fri Sep 12 2014 - 11:01:07 PDT)
[AMBER] Ambertools14 sander_pbsa_decres test failure
- Ray Luo, Ph.D. (Fri Sep 19 2014 - 10:28:00 PDT)
- Ray Luo, Ph.D. (Fri Sep 19 2014 - 10:27:39 PDT)
- Shan-ho Tsai (Wed Sep 03 2014 - 18:38:41 PDT)
- David A Case (Wed Sep 03 2014 - 18:12:04 PDT)
- Shan-ho Tsai (Wed Sep 03 2014 - 12:31:53 PDT)
[AMBER] antechamber error message
- 전선희 (Mon Sep 01 2014 - 23:17:25 PDT)
[AMBER] Antechamber ligand parametrization
- James Starlight (Thu Sep 18 2014 - 06:33:29 PDT)
- David A Case (Thu Sep 18 2014 - 05:10:52 PDT)
- James Starlight (Thu Sep 18 2014 - 04:39:12 PDT)
- Parker de Waal (Thu Sep 18 2014 - 04:21:04 PDT)
- James Starlight (Thu Sep 18 2014 - 00:38:54 PDT)
- David A Case (Wed Sep 17 2014 - 12:41:28 PDT)
- James Starlight (Wed Sep 17 2014 - 06:02:52 PDT)
- David A Case (Wed Sep 17 2014 - 04:40:15 PDT)
- James Starlight (Wed Sep 17 2014 - 02:45:14 PDT)
- David A Case (Tue Sep 16 2014 - 12:53:36 PDT)
- James Starlight (Tue Sep 16 2014 - 07:46:15 PDT)
- Hannes Loeffler (Tue Sep 16 2014 - 04:55:55 PDT)
- James Starlight (Tue Sep 16 2014 - 04:14:59 PDT)
[AMBER] Any other way ?
- Jason Swails (Thu Sep 18 2014 - 19:27:45 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 19:13:16 PDT)
[AMBER] ask for help
- m13654940810 (Fri Sep 19 2014 - 18:01:28 PDT)
- David A Case (Fri Sep 19 2014 - 07:16:40 PDT)
- m13654940810 (Thu Sep 18 2014 - 19:39:58 PDT)
- Jason Swails (Thu Sep 18 2014 - 19:06:48 PDT)
- m13654940810 (Thu Sep 18 2014 - 18:18:52 PDT)
[AMBER] atom types for QM region in QM/MM
- Marc van der Kamp (Tue Sep 02 2014 - 01:35:49 PDT)
- Spelnikov Dmitriy (Tue Sep 02 2014 - 00:29:00 PDT)
[AMBER] average structure with RMSF or RMSD?
- newamber list (Wed Sep 17 2014 - 10:07:04 PDT)
- Daniel Roe (Wed Sep 17 2014 - 09:51:36 PDT)
- Matt Alegrete (Wed Sep 17 2014 - 09:27:01 PDT)
- newamber list (Wed Sep 17 2014 - 07:17:29 PDT)
[AMBER] bash scripting for MD tasks
- James Starlight (Mon Sep 29 2014 - 02:22:35 PDT)
- James Starlight (Mon Sep 29 2014 - 00:06:17 PDT)
- Ross Walker (Fri Sep 26 2014 - 08:57:15 PDT)
- James Starlight (Fri Sep 26 2014 - 04:14:05 PDT)
- James Starlight (Fri Sep 26 2014 - 02:43:22 PDT)
- James Starlight (Wed Sep 24 2014 - 07:41:05 PDT)
- Hannes Loeffler (Wed Sep 24 2014 - 06:27:50 PDT)
- Anselm Horn (Wed Sep 24 2014 - 05:45:11 PDT)
- James Starlight (Wed Sep 24 2014 - 05:35:35 PDT)
- Hannes Loeffler (Wed Sep 24 2014 - 05:18:00 PDT)
- Anselm Horn (Wed Sep 24 2014 - 03:43:17 PDT)
- Hannes Loeffler (Wed Sep 24 2014 - 02:46:40 PDT)
- James Starlight (Wed Sep 24 2014 - 02:21:40 PDT)
- Hannes Loeffler (Wed Sep 24 2014 - 02:14:55 PDT)
- James Starlight (Wed Sep 24 2014 - 01:59:04 PDT)
- James Starlight (Thu Sep 11 2014 - 02:15:54 PDT)
- James Maier (Wed Sep 10 2014 - 07:48:36 PDT)
- James Starlight (Mon Sep 08 2014 - 12:24:42 PDT)
[AMBER] Bridging Sodium ions using hbond
- DEBOSTUTI GHOSHDASTIDAR (Tue Sep 02 2014 - 09:19:07 PDT)
- Daniel Roe (Mon Sep 01 2014 - 08:11:54 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Mon Sep 01 2014 - 03:36:28 PDT)
[AMBER] Building Amber14 with -nofftw3
- Jason Swails (Fri Sep 19 2014 - 11:26:26 PDT)
- Lawrenz, Morgan (Fri Sep 19 2014 - 11:11:11 PDT)
- David A Case (Fri Sep 12 2014 - 10:35:22 PDT)
- Jason Swails (Fri Sep 12 2014 - 10:23:20 PDT)
- Lawrenz, Morgan (Fri Sep 12 2014 - 09:45:26 PDT)
[AMBER] building AmberTools14 to use with Amber12
- i iordanov (Thu Sep 04 2014 - 10:12:23 PDT)
- Jason Swails (Thu Sep 04 2014 - 04:02:15 PDT)
- i iordanov (Wed Sep 03 2014 - 19:34:53 PDT)
[AMBER] Calculation of Urea_Urea Interaction energy
- Daniel Roe (Mon Sep 08 2014 - 06:44:56 PDT)
- Jason Swails (Mon Sep 08 2014 - 04:49:43 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Sep 08 2014 - 00:56:30 PDT)
- Daniel Roe (Fri Sep 05 2014 - 19:41:15 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Sep 05 2014 - 11:06:27 PDT)
- Jason Swails (Fri Sep 05 2014 - 08:17:27 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Sep 05 2014 - 08:06:51 PDT)
[AMBER] Can (cp)ptraj calculate the diffusion of the center of mass?
- Jose Borreguero (Fri Sep 05 2014 - 11:13:00 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Sep 05 2014 - 11:09:20 PDT)
- Jose Borreguero (Fri Sep 05 2014 - 10:51:48 PDT)
- Daniel Roe (Thu Sep 04 2014 - 19:17:34 PDT)
- Jose Borreguero (Thu Sep 04 2014 - 15:59:21 PDT)
[AMBER] CHAMBER: problem with water and swissparam generated ligand
- Eric Lang (Thu Sep 18 2014 - 06:24:35 PDT)
- Jason Swails (Thu Sep 18 2014 - 05:52:30 PDT)
- Eric Lang (Thu Sep 18 2014 - 02:52:43 PDT)
- Jason Swails (Wed Sep 17 2014 - 11:53:21 PDT)
- Eric Lang (Wed Sep 17 2014 - 07:48:04 PDT)
- Jason Swails (Wed Sep 17 2014 - 07:31:57 PDT)
- Eric Lang (Wed Sep 17 2014 - 05:19:58 PDT)
- Jason Swails (Tue Sep 16 2014 - 12:20:12 PDT)
- Eric Lang (Tue Sep 16 2014 - 11:33:50 PDT)
- Sarah Witzke (Tue Sep 16 2014 - 07:20:25 PDT)
- Eric Lang (Tue Sep 16 2014 - 06:52:40 PDT)
- Jason Swails (Mon Sep 15 2014 - 18:05:48 PDT)
- Sarah Witzke (Mon Sep 15 2014 - 15:47:32 PDT)
- Eric Lang (Mon Sep 15 2014 - 13:59:53 PDT)
[AMBER] Charmmlipid2amber.py failure
- Julio Dominguez (Tue Sep 23 2014 - 13:20:05 PDT)
[AMBER] Clustering problem
- Lorenzo Gontrani (Wed Sep 17 2014 - 05:57:46 PDT)
- Lorenzo Gontrani (Wed Sep 17 2014 - 05:56:15 PDT)
- Alessandro Mariani (Wed Sep 17 2014 - 04:43:00 PDT)
[AMBER] Combined cartesian and NMR restraints
- Jason Swails (Fri Sep 26 2014 - 07:05:01 PDT)
- Parker de Waal (Fri Sep 26 2014 - 05:31:26 PDT)
- Parker de Waal (Thu Sep 25 2014 - 20:26:14 PDT)
- David A Case (Thu Sep 25 2014 - 19:56:31 PDT)
- Parker de Waal (Thu Sep 25 2014 - 19:37:44 PDT)
- Parker de Waal (Thu Sep 25 2014 - 18:43:54 PDT)
[AMBER] Compiling Amber14 using --with-netcdf
- Lawrenz, Morgan (Thu Sep 11 2014 - 17:46:35 PDT)
- Jason Swails (Thu Sep 11 2014 - 17:27:47 PDT)
- Lawrenz, Morgan (Thu Sep 11 2014 - 16:20:48 PDT)
[AMBER] cpptraj - atomicfluct
- Daniel Roe (Tue Sep 16 2014 - 07:30:36 PDT)
- Thomas Cheatham (Mon Sep 15 2014 - 18:47:37 PDT)
- David A Case (Mon Sep 15 2014 - 12:28:18 PDT)
- George Tzotzos (Mon Sep 15 2014 - 11:57:57 PDT)
[AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom
- Daniel Roe (Fri Sep 19 2014 - 06:47:16 PDT)
- Jason Swails (Fri Sep 19 2014 - 06:29:55 PDT)
- Oliver Grant (Fri Sep 19 2014 - 06:12:20 PDT)
[AMBER] Cpptraj hbond function - solvent bridge
- Daniel Roe (Wed Sep 17 2014 - 09:42:21 PDT)
- Miroslav Krepl (Wed Sep 17 2014 - 08:36:49 PDT)
[AMBER] cpptraj/parmbox
- Daniel Roe (Fri Sep 26 2014 - 10:21:42 PDT)
- Daniel Roe (Fri Sep 26 2014 - 06:59:59 PDT)
- Jason Swails (Fri Sep 26 2014 - 06:47:45 PDT)
- amirhossein taghavi (Fri Sep 26 2014 - 00:13:59 PDT)
[AMBER] CUDA 5.0 versus 5.5/6.0
- Carlos Sosa (Fri Sep 19 2014 - 05:42:58 PDT)
- Carlos Sosa (Fri Sep 19 2014 - 05:41:55 PDT)
- Marc van der Kamp (Fri Sep 19 2014 - 05:37:00 PDT)
- Marc van der Kamp (Fri Sep 19 2014 - 05:34:04 PDT)
- Carlos Sosa (Fri Sep 19 2014 - 05:31:40 PDT)
[AMBER] cuda version not working
- Fabian Glaser (Sun Sep 14 2014 - 07:07:49 PDT)
- David A Case (Sun Sep 14 2014 - 07:02:21 PDT)
- Fabian Glaser (Sat Sep 13 2014 - 21:55:35 PDT)
- Fabian Glaser (Sat Sep 13 2014 - 21:55:19 PDT)
- David A Case (Thu Sep 11 2014 - 05:22:32 PDT)
- Jason Swails (Thu Sep 11 2014 - 04:48:51 PDT)
- Fabian Glaser (Thu Sep 11 2014 - 02:39:07 PDT)
[AMBER] CUDA version still not working
- Ross Walker (Sun Sep 21 2014 - 10:02:48 PDT)
- Daniel Roe (Sun Sep 21 2014 - 09:30:04 PDT)
- Fabian Glaser (Sun Sep 21 2014 - 06:57:09 PDT)
- Jason Swails (Sun Sep 21 2014 - 06:44:35 PDT)
- Fabian Glaser (Sun Sep 21 2014 - 05:51:21 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:31:34 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:30:39 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:20:52 PDT)
- Jason Swails (Thu Sep 18 2014 - 06:26:18 PDT)
- Fabian Glaser (Thu Sep 18 2014 - 06:04:38 PDT)
- Fabian Glaser (Thu Sep 18 2014 - 05:50:20 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:40:48 PDT)
- Fabian Glaser (Thu Sep 18 2014 - 01:39:32 PDT)
[AMBER] cuda versions advice
- Scott Le Grand (Thu Sep 04 2014 - 14:10:56 PDT)
- Scott Brozell (Thu Sep 04 2014 - 09:29:05 PDT)
- Ross Walker (Tue Sep 02 2014 - 14:02:43 PDT)
- Scott Le Grand (Tue Sep 02 2014 - 13:26:32 PDT)
- Scott Brozell (Tue Sep 02 2014 - 12:50:13 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
- Scott Le Grand (Wed Sep 10 2014 - 09:57:49 PDT)
- Ross Walker (Wed Sep 10 2014 - 09:51:22 PDT)
- Scott Brozell (Tue Sep 09 2014 - 23:23:18 PDT)
[AMBER] decomposition output file
- Nadia Li (Thu Sep 04 2014 - 07:19:11 PDT)
- Jason Swails (Thu Sep 04 2014 - 04:39:18 PDT)
- Bill Miller III (Wed Sep 03 2014 - 21:51:11 PDT)
- Nadia Li (Wed Sep 03 2014 - 21:47:06 PDT)
[AMBER] diffusion in octahedron box
- Jason Swails (Fri Sep 05 2014 - 05:40:45 PDT)
- newamber list (Fri Sep 05 2014 - 05:12:30 PDT)
- Jason Swails (Fri Sep 05 2014 - 05:09:50 PDT)
- newamber list (Fri Sep 05 2014 - 04:55:43 PDT)
[AMBER] dihedral in parmtop: negative third index vs ICP(H)
- Jason Swails (Fri Sep 05 2014 - 05:39:31 PDT)
- Hannes Loeffler (Fri Sep 05 2014 - 02:42:44 PDT)
- Jason Swails (Thu Sep 04 2014 - 04:11:01 PDT)
- Hannes Loeffler (Thu Sep 04 2014 - 01:57:53 PDT)
[AMBER] Distance command
- Daniel Roe (Wed Sep 03 2014 - 08:39:09 PDT)
[AMBER] Distance restraint
- Marc van der Kamp (Thu Sep 18 2014 - 08:15:09 PDT)
- David A Case (Thu Sep 18 2014 - 07:51:12 PDT)
- John Smith (Thu Sep 18 2014 - 07:24:21 PDT)
- Marc van der Kamp (Thu Sep 18 2014 - 07:09:34 PDT)
- John Smith (Thu Sep 18 2014 - 06:33:21 PDT)
- David A Case (Thu Sep 18 2014 - 05:19:55 PDT)
- Ilyas Yildirim (Thu Sep 18 2014 - 04:59:52 PDT)
- John Smith (Thu Sep 18 2014 - 04:50:04 PDT)
- Mary Varughese (Tue Sep 09 2014 - 20:01:40 PDT)
- Thomas Cheatham (Tue Sep 09 2014 - 19:40:15 PDT)
- Mary Varughese (Tue Sep 09 2014 - 19:34:01 PDT)
- David A Case (Tue Sep 09 2014 - 15:09:39 PDT)
- Mary Varughese (Tue Sep 09 2014 - 13:08:31 PDT)
[AMBER] DMPG lipid bilayer simulations?
- Dickson, Callum J (Thu Sep 11 2014 - 06:23:32 PDT)
- Smith, Jarrod A (Thu Sep 04 2014 - 13:28:34 PDT)
[AMBER] Enquiring about RMSD of small and large proteins
- newamber list (Wed Sep 17 2014 - 10:13:07 PDT)
- Daniel Roe (Wed Sep 17 2014 - 10:02:48 PDT)
- newamber list (Wed Sep 17 2014 - 07:56:23 PDT)
- Daniel Roe (Mon Sep 08 2014 - 06:54:02 PDT)
- Yip Yew Mun (Sun Sep 07 2014 - 19:52:54 PDT)
[AMBER] entropy
- David A Case (Thu Sep 25 2014 - 04:29:16 PDT)
- Asfa Ali (Thu Sep 25 2014 - 00:31:48 PDT)
[AMBER] Entropy calculation using nmode fails
- Neha Rana (Sun Sep 28 2014 - 07:35:27 PDT)
[AMBER] Equilibration of the membrane protein with the restrains
- James Starlight (Tue Sep 09 2014 - 00:33:34 PDT)
- James Starlight (Fri Sep 05 2014 - 05:30:45 PDT)
[AMBER] Equilibration phase and RMSD
- David A Case (Thu Sep 11 2014 - 12:30:31 PDT)
- Carlos Simmerling (Thu Sep 11 2014 - 12:23:52 PDT)
- Ibrahim Said (Thu Sep 11 2014 - 12:18:17 PDT)
- Carlos Simmerling (Thu Sep 11 2014 - 08:05:56 PDT)
- Ibrahim Said (Thu Sep 11 2014 - 07:56:30 PDT)
- Carlos Simmerling (Thu Sep 11 2014 - 05:43:59 PDT)
- David A Case (Thu Sep 11 2014 - 05:18:20 PDT)
- Ibrahim Said (Wed Sep 10 2014 - 13:22:17 PDT)
[AMBER] Error: cannot run
- David A Case (Thu Sep 18 2014 - 08:00:50 PDT)
- Daniel Roe (Thu Sep 18 2014 - 07:54:26 PDT)
- Vishal Nemaysh (Thu Sep 18 2014 - 07:37:34 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:57:55 PDT)
- Vishal Nemaysh (Thu Sep 18 2014 - 02:50:12 PDT)
[AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
- Pablo Ródenas (Fri Sep 12 2014 - 04:24:05 PDT)
- Jason Swails (Thu Sep 04 2014 - 06:48:04 PDT)
- Pablo Ródenas (Wed Sep 03 2014 - 23:17:05 PDT)
[AMBER] ESP fitting centers exist, but the fitting values are missing
- FyD (Wed Sep 17 2014 - 02:48:54 PDT)
- 张冬冬 (Tue Sep 16 2014 - 07:43:42 PDT)
- David A Case (Mon Sep 15 2014 - 06:17:42 PDT)
- 张冬冬 (Mon Sep 15 2014 - 05:29:08 PDT)
[AMBER] extract energies from trajectory
- Daniel Roe (Thu Sep 04 2014 - 19:19:34 PDT)
- Milo Westler (Thu Sep 04 2014 - 15:55:31 PDT)
[AMBER] failure to run MMPBSA job...
- Shashidhar Rao (Wed Sep 24 2014 - 11:00:37 PDT)
- Ray Luo, Ph.D. (Wed Sep 24 2014 - 10:40:52 PDT)
- Shashidhar Rao (Wed Sep 24 2014 - 08:13:17 PDT)
[AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type
- David A Case (Fri Sep 26 2014 - 08:54:02 PDT)
- Carlos Simmerling (Fri Sep 26 2014 - 08:26:22 PDT)
- Soumendranath Bhakat (Fri Sep 26 2014 - 08:21:04 PDT)
[AMBER] file contains 2 atoms not in residue templates
- Jason Swails (Tue Sep 23 2014 - 06:46:33 PDT)
- Vishal Nemaysh (Tue Sep 23 2014 - 06:22:57 PDT)
[AMBER] For Amber14 TI, how to perform only the discharge/recharge steps?
- Lawrenz, Morgan (Fri Sep 19 2014 - 11:08:49 PDT)
- Ying-Chieh Sun (Tue Sep 16 2014 - 18:41:42 PDT)
- Lawrenz, Morgan (Tue Sep 16 2014 - 18:01:04 PDT)
[AMBER] Force field ff99SB*-ILDN request
- sunita.tifrh.res.in (Wed Sep 17 2014 - 09:03:07 PDT)
- Jason Swails (Wed Sep 17 2014 - 05:53:07 PDT)
- Vlad Cojocaru (Wed Sep 17 2014 - 05:07:23 PDT)
- Carlos Simmerling (Wed Sep 17 2014 - 04:31:10 PDT)
- sunita.tifrh.res.in (Tue Sep 16 2014 - 20:58:30 PDT)
- Jason Swails (Tue Sep 16 2014 - 14:42:45 PDT)
- David A Case (Tue Sep 16 2014 - 13:11:07 PDT)
- Jason Swails (Tue Sep 16 2014 - 10:30:21 PDT)
- Vlad Cojocaru (Tue Sep 16 2014 - 09:34:32 PDT)
- Carlos Simmerling (Tue Sep 16 2014 - 09:06:44 PDT)
- David A Case (Sun Sep 14 2014 - 16:46:57 PDT)
- Carlos Simmerling (Fri Sep 12 2014 - 18:17:28 PDT)
- Thomas Evangelidis (Fri Sep 12 2014 - 17:40:05 PDT)
- Carlos Simmerling (Fri Sep 12 2014 - 13:31:35 PDT)
- Hannes Loeffler (Fri Sep 12 2014 - 08:35:12 PDT)
- David A Case (Fri Sep 12 2014 - 08:16:55 PDT)
- Jason Swails (Fri Sep 12 2014 - 06:43:56 PDT)
- sunita.tifrh.res.in (Fri Sep 12 2014 - 06:18:22 PDT)
[AMBER] frcmod format file
- Maria Osorios (Wed Sep 10 2014 - 13:32:35 PDT)
- David A Case (Wed Sep 10 2014 - 04:43:47 PDT)
- Maria Osorios (Tue Sep 09 2014 - 18:57:53 PDT)
[AMBER] Fwd: file contains 2 atoms not in residue templates
- Vishal Nemaysh (Tue Sep 23 2014 - 06:24:57 PDT)
[AMBER] generate amoeba parameters for amber
- Lorenzo Gontrani (Mon Sep 15 2014 - 00:38:25 PDT)
- Jorgen Simonsen (Sat Sep 13 2014 - 21:34:19 PDT)
[AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure"
- Dieter Buyst (Tue Sep 23 2014 - 02:46:22 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:23:27 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:52:26 PDT)
- Dieter Buyst (Thu Sep 18 2014 - 01:51:19 PDT)
[AMBER] GTX780 versus K40?
- Carlos Sosa (Thu Sep 18 2014 - 14:04:50 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:46:15 PDT)
- Carlos Sosa (Thu Sep 18 2014 - 10:33:11 PDT)
[AMBER] h-bond
- erik.laurini.di3.units.it (Wed Sep 17 2014 - 05:20:28 PDT)
- Jason Swails (Wed Sep 17 2014 - 05:07:26 PDT)
- Soumendranath Bhakat (Wed Sep 17 2014 - 04:48:02 PDT)
- erik.laurini.di3.units.it (Wed Sep 17 2014 - 04:38:33 PDT)
[AMBER] Hbond Difference For Ambertools 12 and 14, or bug
- leexa.intern.bii.a-star.edu.sg (Tue Sep 23 2014 - 19:54:27 PDT)
- Daniel Roe (Mon Sep 22 2014 - 19:59:33 PDT)
- David A Case (Mon Sep 22 2014 - 18:30:29 PDT)
- leexa.intern.bii.a-star.edu.sg (Mon Sep 22 2014 - 17:56:55 PDT)
- Mary Varughese (Mon Sep 22 2014 - 10:05:38 PDT)
- Daniel Roe (Mon Sep 22 2014 - 07:24:06 PDT)
- leexa.intern.bii.a-star.edu.sg (Sun Sep 21 2014 - 23:37:41 PDT)
[AMBER] hbond lifetime
- Daniel Roe (Wed Sep 10 2014 - 19:51:06 PDT)
- George Tzotzos (Wed Sep 10 2014 - 13:52:46 PDT)
- Daniel Roe (Wed Sep 10 2014 - 13:27:08 PDT)
- George Tzotzos (Wed Sep 10 2014 - 13:13:13 PDT)
[AMBER] HID or HIE which one to consider?
- Marc van der Kamp (Wed Sep 10 2014 - 00:45:04 PDT)
- sunita.tifrh.res.in (Tue Sep 09 2014 - 23:49:13 PDT)
- Marc van der Kamp (Mon Sep 08 2014 - 06:45:54 PDT)
- sunita.tifrh.res.in (Mon Sep 08 2014 - 06:34:07 PDT)
[AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff?
- Jason Swails (Tue Sep 23 2014 - 05:04:53 PDT)
- Bikash Ranjan Sahoo (Tue Sep 23 2014 - 04:44:12 PDT)
- David A Case (Tue Sep 23 2014 - 04:01:32 PDT)
- Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:43:10 PDT)
- Hannes Loeffler (Tue Sep 23 2014 - 01:21:00 PDT)
- Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:06:31 PDT)
[AMBER] how to simulate a polyester?
- FyD (Wed Sep 17 2014 - 03:12:35 PDT)
- David A Case (Tue Sep 16 2014 - 12:58:11 PDT)
- Jason Swails (Tue Sep 16 2014 - 08:18:58 PDT)
- 张冬冬 (Tue Sep 16 2014 - 07:52:19 PDT)
[AMBER] iwrap on very long simulation
- Jason Swails (Mon Sep 08 2014 - 07:02:46 PDT)
- sunita.tifrh.res.in (Mon Sep 08 2014 - 06:52:28 PDT)
- Jason Swails (Mon Sep 08 2014 - 06:34:51 PDT)
- sunita.tifrh.res.in (Mon Sep 08 2014 - 06:23:01 PDT)
- Jason Swails (Mon Sep 08 2014 - 06:07:11 PDT)
- sunita.tifrh.res.in (Mon Sep 08 2014 - 05:32:02 PDT)
- Setyanto Md (Sat Sep 06 2014 - 17:34:16 PDT)
- Setyanto Md (Sat Sep 06 2014 - 17:33:29 PDT)
- David A Case (Thu Sep 04 2014 - 05:01:17 PDT)
- Setyanto Md (Wed Sep 03 2014 - 18:12:31 PDT)
[AMBER] key word to pull out eigenvalues
- Daniel Roe (Tue Sep 30 2014 - 07:14:48 PDT)
- Nicole Ippolito (Mon Sep 29 2014 - 21:37:15 PDT)
[AMBER] learn more about cpptraj
- Daniel Roe (Tue Sep 30 2014 - 07:17:25 PDT)
- Jason Swails (Tue Sep 30 2014 - 04:20:25 PDT)
- amirhossein taghavi (Tue Sep 30 2014 - 02:53:48 PDT)
[AMBER] Lennard-Jones Parameters for Each Atom
- Jason Swails (Fri Sep 05 2014 - 10:11:09 PDT)
- Uday Midya (Fri Sep 05 2014 - 10:02:10 PDT)
- Jason Swails (Fri Sep 05 2014 - 06:59:08 PDT)
- Brian Radak (Fri Sep 05 2014 - 06:56:44 PDT)
- Uday Midya (Fri Sep 05 2014 - 06:46:54 PDT)
[AMBER] ligand shift
- Nadia Li (Wed Sep 10 2014 - 13:10:57 PDT)
- Carlos Simmerling (Mon Sep 08 2014 - 12:47:39 PDT)
- George Tzotzos (Mon Sep 08 2014 - 12:35:09 PDT)
- Daniel Roe (Mon Sep 08 2014 - 12:28:11 PDT)
- Carlos Simmerling (Mon Sep 08 2014 - 12:12:28 PDT)
- Nadia Li (Mon Sep 08 2014 - 12:03:00 PDT)
[AMBER] lipids14 pdb format
- Sergio Decherchi (Fri Sep 19 2014 - 04:31:45 PDT)
[AMBER] many initial systems for a two molecules system
- Fabian Glaser (Mon Sep 08 2014 - 08:01:16 PDT)
- Jason Swails (Mon Sep 08 2014 - 07:58:44 PDT)
- Fabian Glaser (Mon Sep 08 2014 - 07:51:57 PDT)
- Fabian Glaser (Mon Sep 08 2014 - 07:35:36 PDT)
- Jason Swails (Mon Sep 08 2014 - 07:22:30 PDT)
- Fabian Glaser (Mon Sep 08 2014 - 06:44:36 PDT)
- Fabian Glaser (Sun Sep 07 2014 - 05:05:23 PDT)
- Jason Swails (Thu Sep 04 2014 - 04:55:13 PDT)
- Fabian Glaser (Thu Sep 04 2014 - 04:37:13 PDT)
- Jason Swails (Thu Sep 04 2014 - 04:29:05 PDT)
- Fabian Glaser (Thu Sep 04 2014 - 00:44:45 PDT)
- Jason Swails (Wed Sep 03 2014 - 08:07:32 PDT)
- Fabian Glaser (Wed Sep 03 2014 - 04:26:10 PDT)
[AMBER] MD simulation at 1M or 2M salt concentration
- Jason Swails (Mon Sep 29 2014 - 06:01:11 PDT)
- Carlos Simmerling (Mon Sep 29 2014 - 05:47:28 PDT)
- Jason Swails (Mon Sep 29 2014 - 05:43:24 PDT)
- 张后今 (Mon Sep 29 2014 - 05:48:24 PDT)
- Jason Swails (Mon Sep 29 2014 - 05:23:05 PDT)
- 张后今 (Sat Sep 27 2014 - 18:59:03 PDT)
[AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory
- wliu (Wed Sep 03 2014 - 04:41:26 PDT)
- Jason Swails (Wed Sep 03 2014 - 03:43:57 PDT)
- wliu (Wed Sep 03 2014 - 02:58:57 PDT)
- wliu (Tue Sep 02 2014 - 07:08:44 PDT)
- Daniel Roe (Tue Sep 02 2014 - 06:59:33 PDT)
- wliu (Tue Sep 02 2014 - 06:40:19 PDT)
- Jason Swails (Tue Sep 02 2014 - 06:27:44 PDT)
- wliu (Tue Sep 02 2014 - 06:05:15 PDT)
[AMBER] metalloproteins modeling
- Spelnikov Dmitriy (Tue Sep 23 2014 - 02:22:58 PDT)
[AMBER] Minimizing Size of Membrane Simulation Box
- Parker de Waal (Tue Sep 23 2014 - 18:05:57 PDT)
[AMBER] mismatch pdb files when created using ambpdb and savepdb
- Daniel Roe (Wed Sep 10 2014 - 06:43:30 PDT)
- sunita.tifrh.res.in (Wed Sep 10 2014 - 06:21:50 PDT)
- Jason Swails (Wed Sep 10 2014 - 05:08:41 PDT)
- David A Case (Wed Sep 10 2014 - 04:49:04 PDT)
- Thomas Cheatham (Wed Sep 10 2014 - 02:22:18 PDT)
- sunita.tifrh.res.in (Wed Sep 10 2014 - 02:14:53 PDT)
- sunita.tifrh.res.in (Wed Sep 10 2014 - 01:47:21 PDT)
- Daniel Roe (Mon Sep 08 2014 - 08:22:53 PDT)
- David A Case (Mon Sep 08 2014 - 07:17:40 PDT)
- sunita.tifrh.res.in (Mon Sep 08 2014 - 06:13:05 PDT)
[AMBER] mm_pbsa vertex atom mismatch
- Fengxue Li (Wed Sep 10 2014 - 07:03:21 PDT)
- Ray Luo, Ph.D. (Tue Sep 09 2014 - 12:26:40 PDT)
- Fengxue Li (Tue Sep 09 2014 - 05:36:15 PDT)
[AMBER] MMGBSA giving to high VDW energies
- Ahmed Ayoub (Fri Sep 05 2014 - 12:12:00 PDT)
[AMBER] MMPBSA
- Daniel Roe (Thu Sep 18 2014 - 12:19:23 PDT)
- Ray Luo, Ph.D. (Thu Sep 18 2014 - 11:41:42 PDT)
- Asfa Ali (Thu Sep 18 2014 - 11:39:54 PDT)
- Ray Luo, Ph.D. (Thu Sep 18 2014 - 11:32:32 PDT)
- Asfa Ali (Thu Sep 18 2014 - 11:26:09 PDT)
- Daniel Roe (Thu Sep 18 2014 - 08:54:13 PDT)
- Jason Swails (Thu Sep 18 2014 - 09:27:17 PDT)
- Jason Swails (Thu Sep 18 2014 - 08:58:02 PDT)
- Sourav Purohit (Thu Sep 18 2014 - 08:47:18 PDT)
- Sourav Purohit (Thu Sep 18 2014 - 09:08:02 PDT)
- Jason Swails (Thu Sep 18 2014 - 07:42:22 PDT)
- Jason Swails (Thu Sep 18 2014 - 07:38:27 PDT)
- Sourav Purohit (Thu Sep 18 2014 - 07:24:31 PDT)
- Asfa Ali (Thu Sep 18 2014 - 07:10:13 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:37:07 PDT)
- Sourav Purohit (Thu Sep 18 2014 - 01:00:51 PDT)
- Sourav Purohit (Wed Sep 17 2014 - 17:04:12 PDT)
- Sourav Purohit (Wed Sep 17 2014 - 16:29:03 PDT)
- Jason Swails (Wed Sep 17 2014 - 16:23:45 PDT)
- Sourav Purohit (Wed Sep 17 2014 - 16:18:37 PDT)
- Jason Swails (Wed Sep 17 2014 - 16:08:35 PDT)
- Sourav Purohit (Wed Sep 17 2014 - 15:46:32 PDT)
[AMBER] mmpbsa amber error while running decomp
- Sucharita Dey (Tue Sep 02 2014 - 00:31:55 PDT)
- Jason Swails (Mon Sep 01 2014 - 07:51:16 PDT)
- Sucharita Dey (Sun Aug 31 2014 - 22:52:26 PDT)
[AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions
- Jason Swails (Thu Sep 18 2014 - 06:23:48 PDT)
- Thomas Evangelidis (Thu Sep 18 2014 - 06:07:41 PDT)
- Jason Swails (Thu Sep 18 2014 - 05:59:09 PDT)
- Thomas Evangelidis (Thu Sep 18 2014 - 05:15:42 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:55:46 PDT)
- Thomas Evangelidis (Thu Sep 18 2014 - 02:39:05 PDT)
- Jason Swails (Wed Sep 17 2014 - 08:42:17 PDT)
- Thomas Evangelidis (Wed Sep 17 2014 - 08:33:44 PDT)
- Jason Swails (Tue Sep 16 2014 - 09:13:44 PDT)
- Thomas Evangelidis (Tue Sep 16 2014 - 07:05:34 PDT)
[AMBER] MMPBSA: Default inp warnings
- Jason Swails (Wed Sep 17 2014 - 11:40:57 PDT)
- George Tzotzos (Wed Sep 17 2014 - 11:00:05 PDT)
- Jason Swails (Wed Sep 17 2014 - 10:57:24 PDT)
- George Tzotzos (Wed Sep 17 2014 - 10:39:25 PDT)
[AMBER] mmpbsa: PB Bomb in pb_aaradi()
- Wei Chen (Wed Sep 10 2014 - 15:03:57 PDT)
- Ray Luo, Ph.D. (Wed Sep 10 2014 - 14:57:56 PDT)
- Wei Chen (Wed Sep 10 2014 - 14:18:53 PDT)
[AMBER] ncsu_abmd qm/mm
- Fekete Attila (Wed Sep 03 2014 - 01:35:58 PDT)
[AMBER] negative values for the dihedral height barrier in GLYCAM
- Lachele Foley (Tue Sep 23 2014 - 15:24:30 PDT)
- Jason Swails (Tue Sep 23 2014 - 09:01:21 PDT)
- ABEL Stephane 175950 (Tue Sep 23 2014 - 08:09:30 PDT)
[AMBER] neutralizing systems for AMBER TI
- Lawrenz, Morgan (Thu Sep 25 2014 - 09:23:19 PDT)
- Jason Swails (Thu Sep 25 2014 - 07:20:41 PDT)
- Ying-Chieh Sun (Wed Sep 24 2014 - 20:05:01 PDT)
- Lawrenz, Morgan (Wed Sep 24 2014 - 16:02:09 PDT)
[AMBER] No hybrid REMD for cuda?
- Hugo Azurmendi (Wed Sep 03 2014 - 14:07:14 PDT)
- Jason Swails (Wed Sep 03 2014 - 13:30:18 PDT)
- Hugo Azurmendi (Wed Sep 03 2014 - 12:53:25 PDT)
[AMBER] Not getting solute-solvent hbond by cpptraj (AmberTools14)
- Daniel Roe (Wed Sep 10 2014 - 06:46:25 PDT)
- Indrajit Deb (Wed Sep 10 2014 - 04:27:44 PDT)
[AMBER] On combining different force-fields and charge-derivation methods
- Mohammad Salem (Wed Sep 03 2014 - 15:26:27 PDT)
[AMBER] One third of Amber 14's test.cuda tests are failing for me
- Jan-Philip Gehrcke (Fri Sep 05 2014 - 05:04:32 PDT)
- Ross Walker (Fri Sep 05 2014 - 04:50:49 PDT)
- Jan-Philip Gehrcke (Fri Sep 05 2014 - 03:18:27 PDT)
[AMBER] parallel cuda test errors
- Gard Nelson (Wed Sep 03 2014 - 13:46:43 PDT)
- Ross Walker (Wed Sep 03 2014 - 13:00:23 PDT)
- Gard Nelson (Wed Sep 03 2014 - 12:49:38 PDT)
[AMBER] Parameter bond and angle file could not find
- Jason Swails (Wed Sep 24 2014 - 07:26:39 PDT)
- Vishal Nemaysh (Wed Sep 24 2014 - 06:39:27 PDT)
[AMBER] Parameter file was not saved.
- ros (Mon Sep 29 2014 - 07:58:45 PDT)
- Jason Swails (Mon Sep 29 2014 - 07:13:50 PDT)
- Vishal Nemaysh (Mon Sep 29 2014 - 06:38:05 PDT)
[AMBER] Patches Installation Failure
- Jason Swails (Wed Sep 24 2014 - 04:52:28 PDT)
- 张后今 (Wed Sep 24 2014 - 01:42:12 PDT)
[AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files.
- Ray Luo, Ph.D. (Wed Sep 10 2014 - 16:53:11 PDT)
- Ray Luo, Ph.D. (Tue Sep 09 2014 - 12:28:16 PDT)
- Jan-Philip Gehrcke (Tue Sep 09 2014 - 03:28:05 PDT)
- Ray Luo, Ph.D. (Mon Sep 08 2014 - 15:22:12 PDT)
- Jan-Philip Gehrcke (Mon Sep 08 2014 - 06:57:00 PDT)
[AMBER] PHI Intel Compilation
- Jacopo Sgrignani (Thu Sep 04 2014 - 04:08:05 PDT)
- Ross Walker (Tue Sep 02 2014 - 10:34:15 PDT)
- Jacopo Sgrignani (Tue Sep 02 2014 - 10:16:53 PDT)
- Ross Walker (Tue Sep 02 2014 - 10:11:35 PDT)
- Jacopo Sgrignani (Tue Sep 02 2014 - 06:40:39 PDT)
[AMBER] pmemd cuda error
- Kshatresh Dutta Dubey (Mon Sep 22 2014 - 05:51:33 PDT)
- Ross Walker (Thu Sep 18 2014 - 10:28:24 PDT)
- Scott Le Grand (Thu Sep 18 2014 - 09:57:36 PDT)
- Kshatresh Dutta Dubey (Thu Sep 18 2014 - 04:47:41 PDT)
[AMBER] PMEMD Distance Restraints
- David A Case (Sun Sep 21 2014 - 07:20:59 PDT)
- Parker de Waal (Sat Sep 20 2014 - 13:55:44 PDT)
[AMBER] Postdoc Position Available
- Dirar Homouz (Tue Sep 09 2014 - 03:20:51 PDT)
[AMBER] Preparing a system of 7.4 PH
- Jason Swails (Thu Sep 18 2014 - 04:34:14 PDT)
- ammarah.ghaffar.comsats.edu.pk (Wed Sep 17 2014 - 23:12:02 PDT)
[AMBER] problem on minimization
- ZHAO Ruisheng (Thu Sep 25 2014 - 01:09:46 PDT)
- David A Case (Wed Sep 24 2014 - 06:43:48 PDT)
- ZHAO Ruisheng (Wed Sep 24 2014 - 05:18:48 PDT)
[AMBER] Problem running multiple GPU's
- Ross Walker (Wed Sep 10 2014 - 10:03:10 PDT)
- jon.maguire.louisville.edu (Wed Sep 10 2014 - 09:46:33 PDT)
- Jason Swails (Wed Sep 10 2014 - 09:45:14 PDT)
- jon.maguire.louisville.edu (Wed Sep 10 2014 - 08:53:26 PDT)
[AMBER] Problem running multiple GPU's - FIXED
- Ross Walker (Wed Sep 10 2014 - 11:06:10 PDT)
- jon.maguire.louisville.edu (Wed Sep 10 2014 - 10:56:20 PDT)
[AMBER] Problem running pmemd.cuda.mpi REMD with different number of replicas
- Thiago Lipinski Paes (Wed Sep 10 2014 - 12:13:36 PDT)
- Christina Bergonzo (Wed Sep 10 2014 - 09:29:27 PDT)
- Thiago Lipinski Paes (Wed Sep 10 2014 - 09:21:40 PDT)
[AMBER] Problems to minimize with Sander
- Hector A. Baldoni (Wed Sep 17 2014 - 17:45:38 PDT)
- Jason Swails (Wed Sep 17 2014 - 11:45:28 PDT)
- Investigador Química (Wed Sep 17 2014 - 11:19:58 PDT)
- Jason Swails (Wed Sep 10 2014 - 18:39:17 PDT)
- Maria Osorios (Wed Sep 10 2014 - 14:54:18 PDT)
[AMBER] protein-peptide alanine scaning
- Jason Swails (Tue Sep 02 2014 - 14:02:01 PDT)
- Renato Freitas (Tue Sep 02 2014 - 12:41:16 PDT)
- Jason Swails (Tue Sep 02 2014 - 12:03:15 PDT)
- Renato Freitas (Tue Sep 02 2014 - 10:12:21 PDT)
[AMBER] QM/MM optimization error
- Jason Swails (Mon Sep 08 2014 - 04:52:25 PDT)
- 王珍 (Sun Sep 07 2014 - 19:46:32 PDT)
[AMBER] Query for Hbond lifetime analysis with AmberTools14
- Daniel Roe (Wed Sep 10 2014 - 06:52:37 PDT)
- Indrajit Deb (Wed Sep 10 2014 - 03:00:33 PDT)
[AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD
- Jason Swails (Mon Sep 29 2014 - 04:47:42 PDT)
- Levi Pierce (Sun Sep 28 2014 - 11:46:06 PDT)
- M Olivia Kim (Wed Sep 17 2014 - 13:00:42 PDT)
- Jason Swails (Wed Sep 17 2014 - 11:40:00 PDT)
- M Olivia Kim (Wed Sep 17 2014 - 11:11:32 PDT)
[AMBER] questions about Amber to run MD of Amoeba
- m13654940810 (Mon Sep 22 2014 - 07:45:30 PDT)
- Daniel Roe (Mon Sep 22 2014 - 07:06:12 PDT)
- Jason Swails (Mon Sep 22 2014 - 07:05:55 PDT)
- m13654940810 (Mon Sep 22 2014 - 06:28:08 PDT)
- m13654940810 (Mon Sep 22 2014 - 05:45:19 PDT)
- Jason Swails (Mon Sep 22 2014 - 05:36:29 PDT)
- m13654940810 (Mon Sep 22 2014 - 05:12:40 PDT)
[AMBER] Reaction profile calculation in Amber by QM/MM method
- Jason Swails (Tue Sep 02 2014 - 06:00:27 PDT)
- MOHD HOMAIDUR RAHMAN (Tue Sep 02 2014 - 00:24:31 PDT)
[AMBER] Reading Error
- Jason Swails (Mon Sep 01 2014 - 07:46:19 PDT)
- David A Case (Mon Sep 01 2014 - 05:18:48 PDT)
- Soumendranath Bhakat (Mon Sep 01 2014 - 02:39:14 PDT)
[AMBER] Removing periodicity from the restart file
- Daniel Roe (Thu Sep 25 2014 - 08:03:01 PDT)
- James Starlight (Thu Sep 25 2014 - 00:52:23 PDT)
- Daniel Roe (Wed Sep 24 2014 - 07:42:59 PDT)
- James Starlight (Wed Sep 24 2014 - 07:38:07 PDT)
[AMBER] Replica Exchange
- Jason Swails (Tue Sep 16 2014 - 05:31:47 PDT)
- Jacopo Sgrignani (Tue Sep 16 2014 - 01:39:34 PDT)
[AMBER] restart file
- David A Case (Mon Sep 22 2014 - 04:27:02 PDT)
- Sourav Purohit (Mon Sep 22 2014 - 02:44:47 PDT)
- Jacopo Sgrignani (Mon Sep 22 2014 - 02:26:31 PDT)
[AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously
- George Green (Tue Sep 23 2014 - 14:28:39 PDT)
- Jason Swails (Tue Sep 23 2014 - 13:27:20 PDT)
- Gerald Monard (Tue Sep 23 2014 - 13:18:30 PDT)
- George Green (Tue Sep 23 2014 - 12:20:42 PDT)
- Jason Swails (Tue Sep 23 2014 - 08:30:46 PDT)
- George Green (Tue Sep 23 2014 - 06:39:58 PDT)
[AMBER] Rewrapping restart file
- Geoffrey Gray (Mon Sep 08 2014 - 11:17:23 PDT)
- Daniel Roe (Mon Sep 08 2014 - 09:51:09 PDT)
- Geoffrey Gray (Mon Sep 08 2014 - 09:08:21 PDT)
[AMBER] RMSD on two slightly different structures
- Guillaume Roellinger (Fri Sep 26 2014 - 03:56:30 PDT)
- Daniel Roe (Thu Sep 25 2014 - 08:14:08 PDT)
- Guillaume Roellinger (Thu Sep 25 2014 - 01:39:49 PDT)
- Daniel Roe (Mon Sep 22 2014 - 07:03:16 PDT)
- Jason Swails (Mon Sep 22 2014 - 05:23:46 PDT)
- Guillaume Roellinger (Mon Sep 22 2014 - 00:18:47 PDT)
[AMBER] sander QM/MM with terachem using MPI
- Andreas Goetz (Thu Sep 18 2014 - 22:52:20 PDT)
[AMBER] setting up topology file using GLYCAM
- Lachele Foley (Thu Sep 11 2014 - 07:18:36 PDT)
- Vijyan Achari (Thu Sep 11 2014 - 06:59:53 PDT)
[AMBER] Simulating Silver Salt
- Jason Swails (Wed Sep 17 2014 - 05:03:38 PDT)
- Soumendranath Bhakat (Wed Sep 17 2014 - 03:56:31 PDT)
[AMBER] Slow dissociation of ligand from binding pocket of protein
- George Tzotzos (Mon Sep 08 2014 - 13:11:36 PDT)
[AMBER] Solvation and processing of lipid bilayers using tleap
- James Starlight (Fri Sep 12 2014 - 04:07:51 PDT)
- Dickson, Callum J (Fri Sep 12 2014 - 03:47:49 PDT)
- James Starlight (Thu Sep 11 2014 - 14:02:08 PDT)
[AMBER] Solvation of the membrane bilayer using tleap
- James Starlight (Tue Sep 09 2014 - 07:27:30 PDT)
- James Starlight (Sun Sep 07 2014 - 00:34:14 PDT)
[AMBER] some problems when using pmemd.cuda
- Jason Swails (Tue Sep 30 2014 - 04:11:32 PDT)
- xueqiaoup.gmail.com (Mon Sep 29 2014 - 19:33:39 PDT)
- Jason Swails (Mon Sep 29 2014 - 05:15:29 PDT)
- xueqiaoup.gmail.com (Mon Sep 29 2014 - 01:05:22 PDT)
[AMBER] Strip pdb from the hydrogens
- James Starlight (Thu Sep 25 2014 - 05:20:47 PDT)
- David A Case (Thu Sep 25 2014 - 04:34:54 PDT)
- James Starlight (Thu Sep 25 2014 - 01:25:05 PDT)
[AMBER] Sudden change of energies in min.out files
- Jason Swails (Mon Sep 22 2014 - 07:10:14 PDT)
- maryam azimzadehirani (Mon Sep 22 2014 - 03:15:40 PDT)
[AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory?
- Vlad Cojocaru (Mon Sep 22 2014 - 04:25:16 PDT)
- Keiran Rowell (Mon Sep 22 2014 - 03:49:15 PDT)
- Jason Swails (Sun Sep 21 2014 - 06:42:09 PDT)
- Vlad Cojocaru (Sun Sep 21 2014 - 03:36:06 PDT)
- Keiran Rowell (Sun Sep 21 2014 - 02:51:16 PDT)
[AMBER] system size more than 1000 residues
- Pengzhi Zhang (Wed Sep 03 2014 - 12:23:53 PDT)
- Jason Swails (Tue Sep 02 2014 - 14:39:51 PDT)
- Pengzhi Zhang (Tue Sep 02 2014 - 14:32:59 PDT)
[AMBER] Tetrazole: parameters
- Esra Bozkurt (Tue Sep 16 2014 - 08:23:11 PDT)
[AMBER] the out file of qm/mm in amber
- Jason Swails (Wed Sep 10 2014 - 05:25:14 PDT)
- 王珍 (Wed Sep 10 2014 - 05:09:22 PDT)
[AMBER] time scales for running MD
- Carlos Simmerling (Mon Sep 01 2014 - 11:36:20 PDT)
- Asmita Gupta (Mon Sep 01 2014 - 10:15:41 PDT)
- Carlos Simmerling (Mon Sep 01 2014 - 08:50:23 PDT)
- Daniel Roe (Mon Sep 01 2014 - 07:34:47 PDT)
- Asmita Gupta (Mon Sep 01 2014 - 06:38:17 PDT)
- David A Case (Mon Sep 01 2014 - 05:24:05 PDT)
- Asmita Gupta (Mon Sep 01 2014 - 03:42:21 PDT)
[AMBER] tleap neutralization bug?
- David A Case (Fri Sep 19 2014 - 08:45:06 PDT)
- Gulsevin,Alican (Thu Sep 18 2014 - 17:00:21 PDT)
- Jason Swails (Thu Sep 18 2014 - 09:44:25 PDT)
- Jason Swails (Tue Sep 16 2014 - 10:25:21 PDT)
- Gulsevin,Alican (Tue Sep 16 2014 - 08:54:11 PDT)
- Jason Swails (Mon Sep 15 2014 - 09:23:17 PDT)
- Marcus Arieno (Mon Sep 15 2014 - 08:45:06 PDT)
- Niel Henriksen (Sun Sep 14 2014 - 13:29:41 PDT)
- Gulsevin,Alican (Sun Sep 14 2014 - 11:28:53 PDT)
[AMBER] Total vs per-residue MMGBSA energies
- Jason Swails (Wed Sep 10 2014 - 12:07:47 PDT)
- Ahmed Ayoub (Wed Sep 10 2014 - 11:54:20 PDT)
[AMBER] Trajectory analysis using ptraj
- James Starlight (Wed Sep 10 2014 - 00:02:13 PDT)
- Daniel Roe (Tue Sep 09 2014 - 06:43:41 PDT)
- James Starlight (Mon Sep 08 2014 - 23:07:35 PDT)
- Daniel Roe (Mon Sep 08 2014 - 06:59:26 PDT)
- James Starlight (Mon Sep 08 2014 - 01:45:44 PDT)
[AMBER] trajout frames that statisfy hbond criteria
- George Green (Tue Sep 23 2014 - 07:06:44 PDT)
- Daniel Roe (Tue Sep 23 2014 - 07:01:25 PDT)
- George Green (Tue Sep 23 2014 - 04:57:01 PDT)
[AMBER] Two questions about Net charge and write frcmod in parmed.py
- Jason Swails (Fri Sep 19 2014 - 05:12:45 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 20:50:41 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 20:41:49 PDT)
- Jason Swails (Thu Sep 18 2014 - 19:27:04 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 18:43:17 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 13:36:34 PDT)
- Jason Swails (Thu Sep 18 2014 - 12:26:58 PDT)
- Arun Srikanth (Thu Sep 18 2014 - 11:32:16 PDT)
- Jason Swails (Thu Sep 18 2014 - 04:29:31 PDT)
- Arun Srikanth (Wed Sep 17 2014 - 18:36:39 PDT)
[AMBER] US AMBER Workshop - Save the date
- Ross Walker (Thu Sep 25 2014 - 21:27:26 PDT)
[AMBER] Using nvt production run after npt equilibration
- James Starlight (Wed Sep 24 2014 - 03:28:01 PDT)
[AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF
- FyD (Thu Sep 04 2014 - 05:02:24 PDT)
- David A Case (Thu Sep 04 2014 - 04:54:49 PDT)
- bipin singh (Thu Sep 04 2014 - 00:28:45 PDT)
[AMBER] why the same structure and same topology have different energies using CHARMM and AMBER ?
- wliu (Tue Sep 23 2014 - 07:52:11 PDT)
[AMBER] writing trr trajectory
- newamber list (Tue Sep 30 2014 - 15:50:43 PDT)
[AMBER] Wrong atom type in the JCTC paper of lipid 14 ?
- ABEL Stephane 175950 (Sat Sep 27 2014 - 11:45:16 PDT)
[AMBER] Wrong atom type in the JCTC paper of lipid 14 ? - update
- ABEL Stephane 175950 (Sat Sep 27 2014 - 12:09:50 PDT)
[AMBER] Xparmed.py
- Jason Swails (Wed Sep 24 2014 - 13:28:54 PDT)
- Arun Srikanth (Wed Sep 24 2014 - 12:07:26 PDT)
- Jason Swails (Wed Sep 24 2014 - 11:57:51 PDT)
- Arun Srikanth (Wed Sep 24 2014 - 09:25:18 PDT)
- Daniel Roe (Wed Sep 24 2014 - 09:05:15 PDT)
- Arun Srikanth (Wed Sep 24 2014 - 08:58:32 PDT)
- Arun Srikanth (Wed Sep 24 2014 - 08:22:23 PDT)
- Jason Swails (Wed Sep 24 2014 - 08:04:42 PDT)
- David A Case (Wed Sep 24 2014 - 07:49:23 PDT)
- Arun Srikanth (Wed Sep 24 2014 - 06:43:42 PDT)
[AMBER] Zn CCCH
- Pengfei Li (Wed Sep 24 2014 - 12:30:35 PDT)
- Esra Bozkurt (Wed Sep 24 2014 - 06:44:56 PDT)
- Fonti Giulia (Wed Sep 24 2014 - 00:49:55 PDT)
about trajectory unwrap
- Daniel Roe (Wed Sep 10 2014 - 08:32:50 PDT)
- Jason Swails (Wed Sep 10 2014 - 08:34:06 PDT)
- Kong, Ren (Wed Sep 10 2014 - 08:06:34 PDT)
Welcome to Beijing for the 15th International Congress of Quantum Chemistry
- 石文 (Fri Sep 26 2014 - 05:49:17 PDT)

Amber Archive Sep 2014 by subject