Amber Archive Aug 2010: by subject

[AMBER] (no subject)
- xqkong (Tue Aug 17 2010 - 17:47:28 PDT)
[AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
- Daniel Sindhikara (Sun Aug 01 2010 - 21:12:52 PDT)
[AMBER] About dipoles
- Ross Walker (Mon Aug 23 2010 - 12:16:19 PDT)
- Adrian Roitberg (Mon Aug 23 2010 - 11:38:12 PDT)
- Ross Walker (Mon Aug 23 2010 - 11:32:55 PDT)
- hong-bin Xie (Mon Aug 23 2010 - 09:25:44 PDT)
- Ross Walker (Mon Aug 23 2010 - 09:19:37 PDT)
- hong-bin Xie (Mon Aug 23 2010 - 09:08:47 PDT)
- Ross Walker (Mon Aug 23 2010 - 08:46:31 PDT)
- hong-bin Xie (Fri Aug 20 2010 - 14:32:59 PDT)
[AMBER] acceptance ration in rem.log
- Carlos Simmerling (Tue Aug 24 2010 - 05:47:18 PDT)
- Toshifumi Yui (Mon Aug 23 2010 - 22:12:35 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due October 15
- Dima A Sabbah (Mon Aug 23 2010 - 11:01:24 PDT)
- Carlos Simmerling (Mon Aug 23 2010 - 10:33:01 PDT)
- Carlos Simmerling (Mon Aug 23 2010 - 10:10:32 PDT)
- Carlos Simmerling (Mon Aug 23 2010 - 10:06:16 PDT)
[AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations
- g t (Thu Aug 19 2010 - 08:58:23 PDT)
- steinbrt.rci.rutgers.edu (Mon Aug 16 2010 - 12:13:52 PDT)
- g t (Mon Aug 16 2010 - 11:56:23 PDT)
[AMBER] addions causes "assertion failed" in sleap
- Jason Swails (Tue Aug 31 2010 - 06:39:55 PDT)
- Ben Roberts (Mon Aug 30 2010 - 18:26:41 PDT)
[AMBER] addions2 function missing from sleap
- Ben Roberts (Mon Aug 30 2010 - 17:15:14 PDT)
[AMBER] AMBER ff02 r1
- Neha Gandhi (Tue Aug 10 2010 - 02:14:08 PDT)
[AMBER] AMBER question
- Ross Walker (Sun Aug 22 2010 - 07:52:32 PDT)
[AMBER] amber ：FAD parameters and RESP charge
- xqkong (Tue Aug 17 2010 - 08:14:57 PDT)
[AMBER] amber11: Applying restraint weights
- case (Mon Aug 23 2010 - 05:24:55 PDT)
- Carlos Simmerling (Mon Aug 23 2010 - 04:30:26 PDT)
- George Tzotzos (Mon Aug 23 2010 - 03:57:50 PDT)
[AMBER] amber11: segmentation fault error
- Jason Swails (Mon Aug 30 2010 - 09:07:30 PDT)
- George Tzotzos (Mon Aug 30 2010 - 08:50:19 PDT)
[AMBER] Amber9 compilation/Westmere platform
- eric henon (Tue Aug 31 2010 - 06:41:43 PDT)
- Jason Swails (Tue Aug 31 2010 - 06:12:06 PDT)
- eric henon (Tue Aug 31 2010 - 01:11:29 PDT)
[AMBER] Amber: saveamberparm error
- case (Wed Aug 11 2010 - 12:47:49 PDT)
- Karan Mehra (Wed Aug 11 2010 - 12:38:11 PDT)
- case (Tue Aug 10 2010 - 04:48:24 PDT)
- Bill Ross (Mon Aug 09 2010 - 12:04:43 PDT)
- Karan Mehra (Mon Aug 09 2010 - 11:49:16 PDT)
[AMBER] AmberTools and OS X
- John McGuigan (Sun Aug 15 2010 - 13:44:40 PDT)
- Paul S. Nerenberg (Sat Aug 14 2010 - 23:45:46 PDT)
- John McGuigan (Sat Aug 14 2010 - 22:04:53 PDT)
[AMBER] analysis of mm_pbsa
- Asfa Ali (Wed Aug 04 2010 - 06:36:46 PDT)
- Jason Swails (Wed Aug 04 2010 - 06:27:18 PDT)
- Asfa Ali (Wed Aug 04 2010 - 06:19:02 PDT)
- Jason Swails (Wed Aug 04 2010 - 05:36:32 PDT)
- Asfa Ali (Tue Aug 03 2010 - 23:50:33 PDT)
[AMBER] Another missing sleap command: check
- Ben Roberts (Tue Aug 31 2010 - 07:49:36 PDT)
- Ben Roberts (Mon Aug 30 2010 - 17:28:36 PDT)
[AMBER] antechamber
- case (Mon Aug 02 2010 - 18:30:33 PDT)
- Philippe Pinard (Mon Aug 02 2010 - 11:56:26 PDT)
[AMBER] Antechamber issue
- David A. Case (Mon Aug 30 2010 - 14:28:37 PDT)
- P Bhattacharya (Mon Aug 30 2010 - 14:22:29 PDT)
- P Bhattacharya (Mon Aug 30 2010 - 10:12:12 PDT)
- Jason Swails (Mon Aug 30 2010 - 09:21:16 PDT)
- P Bhattacharya (Mon Aug 30 2010 - 08:58:38 PDT)
- case (Fri Aug 27 2010 - 18:34:31 PDT)
- P Bhattacharya (Fri Aug 27 2010 - 14:57:53 PDT)
- Jason Swails (Thu Aug 26 2010 - 16:38:51 PDT)
- P Bhattacharya (Thu Aug 26 2010 - 14:51:40 PDT)
- case (Thu Aug 26 2010 - 10:00:39 PDT)
- P Bhattacharya (Thu Aug 26 2010 - 09:07:59 PDT)
[AMBER] antechamber issue with gasteiger
- Jason Swails (Tue Aug 24 2010 - 08:39:54 PDT)
- Alan (Tue Aug 24 2010 - 08:33:23 PDT)
- Alan (Wed Aug 18 2010 - 08:55:16 PDT)
- Jason Swails (Wed Aug 18 2010 - 07:12:37 PDT)
- Alan (Wed Aug 18 2010 - 01:41:20 PDT)
[AMBER] average structre
- William Flak (Tue Aug 24 2010 - 18:58:48 PDT)
[AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations?
- Hegazy,Lamees (Thu Aug 19 2010 - 09:59:22 PDT)
- Jason Swails (Thu Aug 19 2010 - 09:51:21 PDT)
- George Tzotzos (Thu Aug 19 2010 - 09:45:33 PDT)
[AMBER] Binary trajectory format in Amber8
- Anselm Horn (Sat Aug 28 2010 - 08:40:06 PDT)
- case (Sat Aug 28 2010 - 06:32:05 PDT)
- Anselm Horn (Sat Aug 28 2010 - 01:32:23 PDT)
[AMBER] bond energy spikes in conjugent gradient minimization
- Jason Swails (Fri Aug 20 2010 - 04:56:37 PDT)
- case (Fri Aug 20 2010 - 04:48:47 PDT)
- Vickie Roberts (Fri Aug 20 2010 - 00:55:21 PDT)
[AMBER] BUG and FIX: pmemd crashes when vlimit exceeded
- Robert Duke (Tue Aug 10 2010 - 18:15:32 PDT)
- Don.Bashford.stjude.org (Tue Aug 10 2010 - 17:46:58 PDT)
[AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .
- Robert Duke (Thu Aug 12 2010 - 07:03:53 PDT)
- Jason Swails (Wed Aug 11 2010 - 14:45:41 PDT)
- Don.Bashford.stjude.org (Wed Aug 11 2010 - 14:29:48 PDT)
[AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. .
- Jason Swails (Thu Aug 12 2010 - 12:27:51 PDT)
- Don.Bashford.stjude.org (Thu Aug 12 2010 - 12:19:11 PDT)
[AMBER] Bug in MMPBSA.py.MPI
- Jason Swails (Wed Aug 11 2010 - 18:53:01 PDT)
- Matthias Negri (Wed Aug 11 2010 - 17:05:36 PDT)
[AMBER] Calculating diffusion coefficient in PTRAJ
- Hoshin Kim (Tue Aug 17 2010 - 22:10:13 PDT)
[AMBER] calculation of volume of active site
- Peter Schmidtke (Tue Aug 24 2010 - 03:03:14 PDT)
- Ganesh Kamath (Mon Aug 23 2010 - 10:20:58 PDT)
- Peter Schmidtke (Mon Aug 23 2010 - 10:15:41 PDT)
- Jia Xu (Mon Aug 23 2010 - 10:08:48 PDT)
- Ganesh Kamath (Mon Aug 23 2010 - 09:30:38 PDT)
[AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis?
- Jason Swails (Fri Aug 06 2010 - 06:02:21 PDT)
- Catein Catherine (Fri Aug 06 2010 - 00:57:17 PDT)
[AMBER] Can I use LCOD command for umbrella sampling PMF calculation?
- Jason Swails (Fri Aug 06 2010 - 05:52:43 PDT)
- Catein Catherine (Fri Aug 06 2010 - 00:46:58 PDT)
[AMBER] combination of CPU + GPU for Amber 11
- CHAMI F. (Wed Aug 18 2010 - 02:58:01 PDT)
- CHAMI F. (Wed Aug 18 2010 - 02:53:42 PDT)
- Ross Walker (Tue Aug 17 2010 - 17:36:51 PDT)
- CHAMI F. (Tue Aug 17 2010 - 16:39:10 PDT)
[AMBER] Configure gnu
- P Bhattacharya (Mon Aug 16 2010 - 07:55:59 PDT)
- Daniel Roe (Mon Aug 16 2010 - 07:18:16 PDT)
- P Bhattacharya (Mon Aug 16 2010 - 07:03:01 PDT)
[AMBER] constant volume
- Jorgen Simonsen (Wed Aug 11 2010 - 05:45:27 PDT)
- Jorgen Simonsen (Wed Aug 11 2010 - 05:34:02 PDT)
- Andrew Purkiss-Trew (Wed Aug 11 2010 - 05:30:56 PDT)
- case (Wed Aug 11 2010 - 04:41:39 PDT)
- Jorgen Simonsen (Wed Aug 11 2010 - 01:06:26 PDT)
[AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe
- case (Mon Aug 02 2010 - 16:52:43 PDT)
- Francesca Cantini (Mon Aug 02 2010 - 09:35:31 PDT)
[AMBER] Created a new atom named: H within residue: .R<NASP 1>
- case (Tue Aug 17 2010 - 07:34:43 PDT)
- Jorgen Simonsen (Tue Aug 17 2010 - 05:47:32 PDT)
[AMBER] Creating new topology file from close.mdcrd file
- Jason Swails (Tue Aug 17 2010 - 05:52:18 PDT)
- Amor San Juan (Tue Aug 17 2010 - 02:42:40 PDT)
[AMBER] Creating new topology file from close.mdcrd file : SOLUTION found
- Amor San Juan (Tue Aug 17 2010 - 03:58:40 PDT)
[AMBER] cuda lauch time out error in Amber 11
- Ross Walker (Fri Aug 27 2010 - 06:01:31 PDT)
- Ross Walker (Fri Aug 27 2010 - 05:57:45 PDT)
- Scott Le Grand (Thu Aug 26 2010 - 18:21:29 PDT)
- Scott Le Grand (Thu Aug 26 2010 - 18:20:50 PDT)
- Sasha Buzko (Thu Aug 26 2010 - 18:07:36 PDT)
- Sergio R Aragon (Thu Aug 26 2010 - 17:45:05 PDT)
- Sasha Buzko (Thu Aug 26 2010 - 17:26:15 PDT)
- Sergio R Aragon (Thu Aug 26 2010 - 17:01:43 PDT)
[AMBER] cuda launch time out error in Amber 11
- Sergio R Aragon (Fri Aug 27 2010 - 22:46:59 PDT)
- Scott Le Grand (Fri Aug 27 2010 - 21:29:24 PDT)
- Sergio R Aragon (Fri Aug 27 2010 - 11:06:42 PDT)
- Sasha Buzko (Fri Aug 27 2010 - 10:26:25 PDT)
- Ross Walker (Fri Aug 27 2010 - 06:12:54 PDT)
- Sergio R Aragon (Thu Aug 26 2010 - 23:23:19 PDT)
[AMBER] Cut-off distance "in Closest" command of ptraj
- Jason Swails (Thu Aug 19 2010 - 07:04:56 PDT)
- Amor San Juan (Thu Aug 19 2010 - 00:14:28 PDT)
- Jason Swails (Wed Aug 18 2010 - 06:43:32 PDT)
- Amor San Juan (Tue Aug 17 2010 - 22:35:36 PDT)
[AMBER] dear sir
- Sushil Mishra (Sun Aug 08 2010 - 10:52:11 PDT)
- Sushil Mishra (Sun Aug 08 2010 - 10:50:50 PDT)
- selva raj (Sun Aug 08 2010 - 10:42:59 PDT)
[AMBER] Defining restraint by distance
- Olotu Odunayo (Wed Aug 18 2010 - 01:19:26 PDT)
[AMBER] Deleting bonds in sleap
- Ben Roberts (Mon Aug 16 2010 - 15:13:43 PDT)
- case (Sat Aug 14 2010 - 06:20:09 PDT)
- Ben Roberts (Fri Aug 13 2010 - 15:45:41 PDT)
- Ben Roberts (Fri Aug 13 2010 - 13:40:02 PDT)
- Bill Ross (Fri Aug 13 2010 - 13:19:03 PDT)
- Andreas Goetz (Fri Aug 13 2010 - 13:13:49 PDT)
- Ben Roberts (Fri Aug 13 2010 - 13:08:54 PDT)
- case (Fri Aug 13 2010 - 12:51:47 PDT)
- Ben Roberts (Fri Aug 13 2010 - 12:29:33 PDT)
[AMBER] determining closest water molecules
- Thomas Cheatham III (Tue Aug 10 2010 - 09:26:05 PDT)
- Beale, John (Tue Aug 10 2010 - 08:51:53 PDT)
[AMBER] Diffusion coefficient in PTRAJ.
- Hoshin Kim (Tue Aug 17 2010 - 00:52:41 PDT)
[AMBER] Dipole moment calculation from ptraj
- Thomas Cheatham III (Wed Aug 25 2010 - 09:09:12 PDT)
- v.satish.iitg.ernet.in (Tue Aug 24 2010 - 05:50:52 PDT)
- case (Mon Aug 23 2010 - 05:17:16 PDT)
- Siddharth Rastogi (Mon Aug 23 2010 - 02:33:46 PDT)
[AMBER] Dipole moment in QM/MM
- hong-bin Xie (Sun Aug 22 2010 - 10:14:48 PDT)
[AMBER] dipole moment of molecule of trans and cis azobenzene ?
- Chih-Ying Lin (Thu Aug 26 2010 - 10:01:58 PDT)
[AMBER] Double bonds ?
- Marek Maly (Wed Aug 18 2010 - 04:55:29 PDT)
- case (Tue Aug 17 2010 - 15:18:00 PDT)
- Marek Maly (Tue Aug 17 2010 - 10:15:14 PDT)
[AMBER] drawing sphere in each frame and update
- steinbrt.rci.rutgers.edu (Thu Aug 12 2010 - 00:10:15 PDT)
- Sun, Yufang (Wed Aug 11 2010 - 13:31:20 PDT)
[AMBER] Energy abrupt rise in Energy minimization
- Jiang Yusheng (Thu Aug 05 2010 - 07:00:04 PDT)
- Bill Ross (Wed Aug 04 2010 - 13:25:40 PDT)
- Jiang Yusheng (Wed Aug 04 2010 - 12:31:15 PDT)
- Bill Ross (Wed Aug 04 2010 - 12:10:48 PDT)
- Jiang Yusheng (Wed Aug 04 2010 - 11:49:16 PDT)
- Bill Ross (Wed Aug 04 2010 - 11:33:21 PDT)
- Jiang Yusheng (Wed Aug 04 2010 - 10:37:32 PDT)
[AMBER] Enthalpy estimate
- case (Thu Aug 26 2010 - 04:48:37 PDT)
- Lekpa Duukori (Wed Aug 25 2010 - 13:50:57 PDT)
- Jason Swails (Wed Aug 25 2010 - 13:40:08 PDT)
- Lekpa Duukori (Wed Aug 25 2010 - 12:39:35 PDT)
[AMBER] entropies from nmode in MMPBSA
- Cristina Sisu (Mon Aug 23 2010 - 04:14:03 PDT)
- Bill Miller III (Mon Aug 23 2010 - 03:48:22 PDT)
- Cristina Sisu (Sun Aug 22 2010 - 17:28:24 PDT)
[AMBER] entropy calculation using nmode
- Asfa Ali (Wed Aug 04 2010 - 03:46:59 PDT)
[AMBER] entropy calculations MMPBSA.py.MPI
- Matthias Negri (Tue Aug 17 2010 - 15:45:34 PDT)
[AMBER] Equilibration
- Gustavo Seabra (Tue Aug 24 2010 - 06:40:35 PDT)
- M. Reza Ganjalikhany (Tue Aug 24 2010 - 00:48:38 PDT)
- Gustavo Seabra (Mon Aug 23 2010 - 18:28:29 PDT)
- manikanthan bhavaraju (Mon Aug 23 2010 - 15:18:36 PDT)
- M. Reza Ganjalikhany (Mon Aug 23 2010 - 13:03:15 PDT)
- Gustavo Seabra (Mon Aug 23 2010 - 07:26:59 PDT)
- M. Reza Ganjalikhany (Mon Aug 23 2010 - 02:01:39 PDT)
[AMBER] error in heating
- Bill Ross (Sun Aug 01 2010 - 22:52:25 PDT)
- Bill Ross (Sun Aug 01 2010 - 22:48:40 PDT)
- rameshwar prajapati (Sun Aug 01 2010 - 22:31:55 PDT)
[AMBER] error in mmpbsa
- Ray Luo (Fri Aug 27 2010 - 10:04:56 PDT)
- Asfa Ali (Fri Aug 27 2010 - 04:16:00 PDT)
- Amor San Juan (Fri Aug 27 2010 - 03:02:14 PDT)
- Asfa Ali (Fri Aug 27 2010 - 02:20:40 PDT)
[AMBER] Error in snader execution
- arikcohen (Wed Aug 18 2010 - 11:03:11 PDT)
- Jason Swails (Tue Aug 17 2010 - 19:11:40 PDT)
- arikcohen (Tue Aug 17 2010 - 18:53:00 PDT)
[AMBER] error message about memory in antechamber
- case (Wed Aug 11 2010 - 09:03:54 PDT)
- Guoxiong Su (Tue Aug 10 2010 - 12:26:20 PDT)
- case (Mon Aug 09 2010 - 11:47:52 PDT)
- Guoxiong Su (Mon Aug 09 2010 - 08:47:52 PDT)
- case (Thu Aug 05 2010 - 12:48:26 PDT)
- Guoxiong Su (Thu Aug 05 2010 - 11:16:27 PDT)
[AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10)
- Jason Swails (Wed Aug 04 2010 - 06:17:34 PDT)
- Catein Catherine (Wed Aug 04 2010 - 02:59:40 PDT)
[AMBER] Error message when doing A10 tutorial (SMD with LCOD) with AMBER 10.
- Catein Catherine (Fri Aug 06 2010 - 01:11:15 PDT)
[AMBER] error when compiling pmemd
- Jorgen Simonsen (Tue Aug 10 2010 - 11:37:19 PDT)
- Ross Walker (Tue Aug 10 2010 - 11:32:07 PDT)
- Daniel Roe (Tue Aug 10 2010 - 11:21:32 PDT)
- Jorgen Simonsen (Tue Aug 10 2010 - 11:14:43 PDT)
- Ross Walker (Tue Aug 10 2010 - 10:35:28 PDT)
- Jorgen Simonsen (Tue Aug 10 2010 - 09:37:08 PDT)
- Jason Swails (Tue Aug 10 2010 - 06:05:14 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 23:55:56 PDT)
- Jason Swails (Mon Aug 09 2010 - 12:57:40 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 09:20:42 PDT)
- Ross Walker (Mon Aug 09 2010 - 06:06:44 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 05:15:08 PDT)
- case (Mon Aug 09 2010 - 05:05:36 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 03:56:13 PDT)
[AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
- Majid Taghdir (Mon Aug 30 2010 - 03:43:05 PDT)
- Jason Swails (Mon Aug 30 2010 - 07:12:09 PDT)
- Majid Taghdir (Mon Aug 30 2010 - 06:26:29 PDT)
- Jason Swails (Mon Aug 30 2010 - 05:15:59 PDT)
- Jason Swails (Sun Aug 29 2010 - 07:52:23 PDT)
- Majid Taghdir (Sun Aug 29 2010 - 02:17:48 PDT)
[AMBER] errror in heating
- Bill Ross (Mon Aug 02 2010 - 08:28:21 PDT)
- Jason Swails (Mon Aug 02 2010 - 04:37:25 PDT)
- rameshwar prajapati (Sun Aug 01 2010 - 23:22:37 PDT)
- Bill Ross (Sun Aug 01 2010 - 22:56:46 PDT)
- rameshwar prajapati (Sun Aug 01 2010 - 22:47:51 PDT)
[AMBER] exchange probability in remd
- Lekpa Duukori (Fri Aug 20 2010 - 10:25:58 PDT)
- Carlos Simmerling (Fri Aug 20 2010 - 10:18:19 PDT)
- Lekpa Duukori (Fri Aug 20 2010 - 10:14:40 PDT)
[AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors?
- Jason Swails (Wed Aug 18 2010 - 23:13:05 PDT)
- Catein Catherine (Wed Aug 18 2010 - 21:32:46 PDT)
[AMBER] FAD parameters and RESP charge
- xqkong (Wed Aug 18 2010 - 18:40:20 PDT)
- Jason Swails (Wed Aug 18 2010 - 17:54:28 PDT)
- xqkong (Wed Aug 18 2010 - 17:36:45 PDT)
[AMBER] FEP help
- case (Sat Aug 21 2010 - 06:19:02 PDT)
- William Flak (Fri Aug 20 2010 - 21:50:14 PDT)
[AMBER] FEP with EP
- William Flak (Sat Aug 28 2010 - 18:53:51 PDT)
[AMBER] flying out
- case (Tue Aug 24 2010 - 04:28:20 PDT)
- manikanthan bhavaraju (Mon Aug 23 2010 - 21:14:43 PDT)
- William Flak (Mon Aug 23 2010 - 21:02:38 PDT)
[AMBER] force field parameters for ionic liquids
- Ganesh Kamath (Sat Aug 28 2010 - 06:27:55 PDT)
[AMBER] Free energy using MMPBSA
- Jason Swails (Mon Aug 30 2010 - 08:39:40 PDT)
- Bill Miller III (Mon Aug 30 2010 - 08:29:04 PDT)
- shenna shearin (Mon Aug 30 2010 - 07:12:35 PDT)
[AMBER] gbsa in pmemd
- Ross Walker (Thu Aug 12 2010 - 16:48:12 PDT)
- Yi Xue (Thu Aug 12 2010 - 14:00:57 PDT)
[AMBER] Gradually Compress Volume to Increase Density
- Bill Ross (Mon Aug 02 2010 - 08:21:10 PDT)
- Jason Swails (Mon Aug 02 2010 - 05:33:46 PDT)
- Shubhra Gupta (Mon Aug 02 2010 - 05:19:34 PDT)
- Jason Swails (Mon Aug 02 2010 - 04:17:55 PDT)
- Shubhra Gupta (Mon Aug 02 2010 - 01:59:45 PDT)
[AMBER] H-bonding analysis
- Bill Ross (Fri Aug 06 2010 - 09:52:37 PDT)
- Asfa Ali (Thu Aug 05 2010 - 23:19:19 PDT)
[AMBER] Horrific pmemd.cuda performance on an 8-GPU system
- Sasha Buzko (Thu Aug 12 2010 - 09:23:50 PDT)
- michael (Wed Aug 11 2010 - 14:48:36 PDT)
- Ross Walker (Wed Aug 11 2010 - 13:04:25 PDT)
- Sasha Buzko (Wed Aug 11 2010 - 12:15:59 PDT)
[AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10?
- Vlad Cojocaru (Mon Aug 09 2010 - 06:51:15 PDT)
- Jason Swails (Mon Aug 09 2010 - 05:51:42 PDT)
- Catein Catherine (Sun Aug 08 2010 - 22:58:09 PDT)
[AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction
- Jason Swails (Mon Aug 30 2010 - 08:50:03 PDT)
- Catein Catherine (Mon Aug 30 2010 - 07:44:27 PDT)
[AMBER] How to change fillratio in mm_pbsa.pl
- Jason Swails (Thu Aug 12 2010 - 08:04:04 PDT)
- pxq (Thu Aug 12 2010 - 07:59:13 PDT)
[AMBER] How to change temperature in mm_pbsa.pl script
- Bill Miller III (Thu Aug 12 2010 - 08:04:01 PDT)
- pxq (Thu Aug 12 2010 - 07:52:49 PDT)
- Jason Swails (Wed Aug 11 2010 - 08:03:06 PDT)
- pxq (Tue Aug 10 2010 - 18:28:29 PDT)
[AMBER] How to define "generalized distance coordinate restraint" in AMBER10?
- Jason Swails (Thu Aug 12 2010 - 04:40:00 PDT)
- Catein Catherine (Thu Aug 12 2010 - 02:57:55 PDT)
- Jason Swails (Wed Aug 11 2010 - 05:46:42 PDT)
- Catein Catherine (Wed Aug 11 2010 - 02:55:02 PDT)
[AMBER] How to define an unbiased reaction coordinate for potential of mean force calculations?
- Catein Catherine (Sun Aug 29 2010 - 23:09:31 PDT)
[AMBER] How to define center of mass for two separate residues in the restraint file?
- Jason Swails (Thu Aug 12 2010 - 20:18:19 PDT)
- Catein Catherine (Thu Aug 12 2010 - 20:04:09 PDT)
[AMBER] How to define putative reaction coordinates in AMBER?
- Jason Swails (Wed Aug 04 2010 - 05:29:45 PDT)
- Catein Catherine (Tue Aug 03 2010 - 23:09:01 PDT)
[AMBER] How to define twist angle with DOC?
- Catein Catherine (Wed Aug 18 2010 - 21:26:44 PDT)
[AMBER] how to extract temperatur and other data from mdout
- setyanto tri wahyudi (Mon Aug 02 2010 - 20:25:55 PDT)
- Bill Ross (Mon Aug 02 2010 - 09:52:08 PDT)
- Jason Swails (Mon Aug 02 2010 - 05:27:55 PDT)
- setyanto tri wahyudi (Sun Aug 01 2010 - 23:06:10 PDT)
- Bill Ross (Sun Aug 01 2010 - 22:24:04 PDT)
- setyanto tri wahyudi (Sun Aug 01 2010 - 20:45:20 PDT)
[AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
- danglena1411.gmail.com (Wed Aug 18 2010 - 00:40:55 PDT)
- Balazs Jojart (Tue Aug 17 2010 - 12:49:42 PDT)
- Jason Swails (Tue Aug 17 2010 - 10:49:53 PDT)
- Daniel Sindhikara (Tue Aug 17 2010 - 09:04:53 PDT)
- Jason Swails (Tue Aug 17 2010 - 09:04:01 PDT)
- Catein Catherine (Tue Aug 17 2010 - 08:36:35 PDT)
- Jason Swails (Tue Aug 17 2010 - 05:56:29 PDT)
- Catein Catherine (Tue Aug 17 2010 - 04:00:31 PDT)
[AMBER] how to generate porcupine plot
- Jia Xu (Sun Aug 01 2010 - 01:27:12 PDT)
[AMBER] How to identify water molecules at the interface ?
- Jason Swails (Mon Aug 16 2010 - 05:59:25 PDT)
- Amor San Juan (Sun Aug 15 2010 - 20:51:47 PDT)
[AMBER] How to identify water molecules at the interface ? follow up ....
- Jason Swails (Mon Aug 16 2010 - 06:03:42 PDT)
- Amor San Juan (Sun Aug 15 2010 - 23:19:59 PDT)
[AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files?
- Catein Catherine (Sun Aug 15 2010 - 22:44:22 PDT)
- Paul S. Nerenberg (Sat Aug 14 2010 - 23:39:45 PDT)
- Catein Catherine (Sat Aug 14 2010 - 20:52:09 PDT)
[AMBER] How to make parameter files of GTP from PDB file.
- Bill Ross (Thu Aug 05 2010 - 10:28:45 PDT)
- kurisaki ikuo (Wed Aug 04 2010 - 20:43:37 PDT)
- kurisaki ikuo (Wed Aug 04 2010 - 20:12:59 PDT)
[AMBER] how to overcome the memory issues in mm-gbsa calculation for DS analysis?
- Catein Catherine (Mon Aug 16 2010 - 02:36:11 PDT)
[AMBER] How to parametrize ligand using AMOEBA polarizable potential
- sunita gupta (Tue Aug 03 2010 - 04:43:25 PDT)
[AMBER] how to run entropy calculation using pmemd
- fancy2012 (Tue Aug 03 2010 - 04:36:05 PDT)
- Jason Swails (Tue Aug 03 2010 - 04:29:47 PDT)
- fancy2012 (Tue Aug 03 2010 - 02:50:13 PDT)
[AMBER] How to run LCOD in AMBER 10?
- M. L. Dodson (Mon Aug 09 2010 - 08:30:40 PDT)
- Catein Catherine (Mon Aug 09 2010 - 07:14:37 PDT)
- Jason Swails (Mon Aug 09 2010 - 06:10:37 PDT)
- Catein Catherine (Sun Aug 08 2010 - 21:26:17 PDT)
[AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI?
- Carlos Simmerling (Fri Aug 20 2010 - 09:25:05 PDT)
- Jason Swails (Fri Aug 20 2010 - 05:06:35 PDT)
- Catein Catherine (Fri Aug 20 2010 - 02:39:44 PDT)
[AMBER] How to solvate a molecule in a water spherocylinder in leap?
- Guoxiong Su (Tue Aug 31 2010 - 07:12:30 PDT)
- David A. Case (Mon Aug 30 2010 - 14:31:11 PDT)
- Guoxiong Su (Mon Aug 30 2010 - 14:07:29 PDT)
[AMBER] how we increase the number of sugar molecule in a system
- FyD (Thu Aug 26 2010 - 10:18:38 PDT)
- Lachele Foley (Lists) (Thu Aug 26 2010 - 09:16:53 PDT)
- ros (Thu Aug 26 2010 - 08:21:44 PDT)
- case (Thu Aug 26 2010 - 04:38:04 PDT)
- subrata paul (Thu Aug 26 2010 - 01:50:59 PDT)
- Lachele Foley (Lists) (Wed Aug 25 2010 - 06:42:37 PDT)
- subrata paul (Wed Aug 25 2010 - 00:22:19 PDT)
- subrata paul (Mon Aug 23 2010 - 02:46:11 PDT)
- Sushil Mishra (Mon Aug 23 2010 - 02:10:39 PDT)
- subrata paul (Mon Aug 23 2010 - 02:02:50 PDT)
[AMBER] hydration status
- monica.imtech.res.in (Sat Aug 21 2010 - 07:14:33 PDT)
[AMBER] Implicit Solvent Equation
- case (Sun Aug 22 2010 - 05:58:17 PDT)
- Hector Chang (Fri Aug 20 2010 - 13:17:44 PDT)
[AMBER] Installation_problem_Ambertools1.4_in Mac OSX
- Raman Parkesh (Thu Aug 12 2010 - 11:39:49 PDT)
- Jason Swails (Thu Aug 12 2010 - 11:32:26 PDT)
- Raman Parkesh (Thu Aug 12 2010 - 11:18:39 PDT)
[AMBER] Installing Amber9 on Ubuntu platform
- case (Mon Aug 23 2010 - 12:27:59 PDT)
- Bill Ross (Mon Aug 23 2010 - 12:25:41 PDT)
- Jason Swails (Mon Aug 23 2010 - 12:22:55 PDT)
- Arun Gupta (Mon Aug 23 2010 - 11:57:30 PDT)
[AMBER] Interaction energy_mm_pbsa
- moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:33:13 PDT)
- Bill Miller III (Mon Aug 23 2010 - 04:20:51 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:15:07 PDT)
- Bill Miller III (Mon Aug 23 2010 - 03:58:44 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 03:17:52 PDT)
[AMBER] Ionic Strength Limits for MMPBSA
- Hopkins, Robert (Wed Aug 11 2010 - 15:33:28 PDT)
[AMBER] Is there any training program in Europe in the future?
- albert (Mon Aug 30 2010 - 00:22:33 PDT)
[AMBER] Latest Na+ and Cl- ion parameters
- Dean Cuebas (Fri Aug 27 2010 - 14:12:23 PDT)
- Ilyas Yildirim (Fri Aug 27 2010 - 13:08:41 PDT)
[AMBER] loading MG.off (./MG.off is not a valid database)
- case (Tue Aug 24 2010 - 04:37:54 PDT)
- Ehsan Habibi (Tue Aug 24 2010 - 01:16:48 PDT)
[AMBER] makeCHIR_RST and proline
- Jorgen Simonsen (Fri Aug 13 2010 - 06:53:37 PDT)
[AMBER] MD and LES
- Computational Chemist (Tue Aug 31 2010 - 23:13:45 PDT)
[AMBER] minimization segmentation fault
- Bill Ross (Mon Aug 02 2010 - 09:50:34 PDT)
- Jorgen Simonsen (Mon Aug 02 2010 - 00:59:46 PDT)
[AMBER] Mistake in using amber
- steinbrt.rci.rutgers.edu (Tue Aug 03 2010 - 00:32:53 PDT)
- Rilei Yu (Mon Aug 02 2010 - 18:10:40 PDT)
- Bill Ross (Mon Aug 02 2010 - 18:02:42 PDT)
- Gustavo Seabra (Mon Aug 02 2010 - 18:01:41 PDT)
- Rilei Yu (Mon Aug 02 2010 - 17:55:47 PDT)
[AMBER] MM-PBSA fails with a division by zero error
- Jason Swails (Thu Aug 19 2010 - 12:19:52 PDT)
- Sasha Buzko (Thu Aug 19 2010 - 11:32:54 PDT)
[AMBER] mm_pbsa analysis failure
- Anselm Horn (Fri Aug 13 2010 - 05:17:26 PDT)
- Sangita Kachhap (Fri Aug 13 2010 - 04:36:49 PDT)
[AMBER] mm_pbsa ERROR
- Sangita Kachhap (Sun Aug 22 2010 - 03:52:49 PDT)
[AMBER] mm_pbsa failure
- Sangita Kachhap (Fri Aug 20 2010 - 03:58:34 PDT)
[AMBER] MMPBSA Warnings
- Jason Swails (Wed Aug 18 2010 - 07:15:48 PDT)
- Bill Miller III (Wed Aug 18 2010 - 04:28:08 PDT)
- George Tzotzos (Wed Aug 18 2010 - 00:56:45 PDT)
[AMBER] MMPBSA.py error message.
- Jason Swails (Wed Aug 18 2010 - 23:07:35 PDT)
- Wookyung Yu (Wed Aug 18 2010 - 21:55:25 PDT)
[AMBER] MMPBSA.py indexError
- Amor San Juan (Wed Aug 25 2010 - 02:09:53 PDT)
- Jason Swails (Tue Aug 24 2010 - 05:30:57 PDT)
- Bill Miller III (Tue Aug 24 2010 - 04:59:55 PDT)
- Amor San Juan (Tue Aug 24 2010 - 04:53:30 PDT)
[AMBER] MMPBSA.py nmode
- Bill Miller III (Thu Aug 26 2010 - 04:22:24 PDT)
- Amor San Juan (Thu Aug 26 2010 - 04:18:57 PDT)
- Bill Miller III (Thu Aug 26 2010 - 03:51:51 PDT)
- Amor San Juan (Thu Aug 26 2010 - 03:36:39 PDT)
- Bill Miller III (Wed Aug 25 2010 - 04:05:13 PDT)
- Amor San Juan (Wed Aug 25 2010 - 02:40:02 PDT)
[AMBER] MMPBSA.py: minimization issue with nmode
- Nicolas SAPAY (Tue Aug 31 2010 - 06:24:56 PDT)
- Nicolas SAPAY (Tue Aug 31 2010 - 06:21:13 PDT)
- Jason Swails (Tue Aug 31 2010 - 06:04:33 PDT)
- Jason Swails (Tue Aug 31 2010 - 05:55:43 PDT)
- Bill Miller III (Tue Aug 31 2010 - 05:31:05 PDT)
- Nicolas SAPAY (Tue Aug 31 2010 - 05:14:47 PDT)
[AMBER] Name for Glucosamine
- Lachele Foley (Lists) (Tue Aug 10 2010 - 08:16:42 PDT)
- Shubhra Gupta (Tue Aug 10 2010 - 05:21:52 PDT)
- Shubhra Gupta (Mon Aug 09 2010 - 22:39:17 PDT)
[AMBER] NMR refinement = increase in RMSD
- case (Fri Aug 13 2010 - 04:39:28 PDT)
- Andrew Olson (Wed Aug 11 2010 - 08:59:55 PDT)
[AMBER] No solvent overlap
- case (Wed Aug 04 2010 - 04:23:44 PDT)
- Thomas Exner (Tue Aug 03 2010 - 04:12:31 PDT)
[AMBER] nonbond interactions
- Jason Swails (Tue Aug 10 2010 - 17:34:52 PDT)
- Philippe Pinard (Tue Aug 10 2010 - 15:46:17 PDT)
[AMBER] NVE
- Jason Swails (Mon Aug 02 2010 - 04:23:08 PDT)
- steinbrt.rci.rutgers.edu (Mon Aug 02 2010 - 00:59:02 PDT)
- Philippe Pinard (Sun Aug 01 2010 - 22:53:53 PDT)
[AMBER] O2'methyl RNA
- waleed zalloum (Fri Aug 20 2010 - 07:05:08 PDT)
- Jason Swails (Thu Aug 19 2010 - 08:04:14 PDT)
- waleed zalloum (Thu Aug 19 2010 - 07:34:26 PDT)
- Jason Swails (Thu Aug 19 2010 - 07:23:41 PDT)
- waleed zalloum (Thu Aug 19 2010 - 05:37:25 PDT)
[AMBER] obtain a .pdb file from a .prepin/.frcmod file
- Ehsan Habibi (Sat Jul 31 2010 - 12:42:29 PDT)
[AMBER] Packmol file cannot minimized
- Jason Swails (Thu Aug 26 2010 - 05:24:49 PDT)
- case (Thu Aug 26 2010 - 04:34:35 PDT)
- setyanto tri wahyudi (Thu Aug 26 2010 - 00:02:17 PDT)
- case (Tue Aug 24 2010 - 04:42:25 PDT)
- Jason Swails (Tue Aug 24 2010 - 04:39:50 PDT)
- setyanto tri wahyudi (Tue Aug 24 2010 - 03:34:10 PDT)
[AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
- Scott Le Grand (Mon Aug 02 2010 - 10:08:25 PDT)
- Thomas Zeiser (Sun Aug 01 2010 - 00:32:04 PDT)
[AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
- Ross Walker (Thu Aug 05 2010 - 18:26:26 PDT)
- Scott Le Grand (Thu Aug 05 2010 - 10:17:58 PDT)
- Sasha Buzko (Thu Aug 05 2010 - 10:10:10 PDT)
- Scott Le Grand (Thu Aug 05 2010 - 08:03:42 PDT)
- Ross Walker (Thu Aug 05 2010 - 07:02:57 PDT)
- Sasha Buzko (Wed Aug 04 2010 - 20:57:37 PDT)
[AMBER] Parameter extraction
- arikcohen (Wed Aug 25 2010 - 14:25:17 PDT)
- Jason Swails (Wed Aug 25 2010 - 13:16:07 PDT)
- arikcohen (Wed Aug 25 2010 - 13:01:14 PDT)
[AMBER] parameters for ionic liquids
- Ganesh Kamath (Mon Aug 30 2010 - 07:14:07 PDT)
[AMBER] Parametrization of Ligand using AMOEBA potential
- Dian Jiao (Thu Aug 05 2010 - 07:15:05 PDT)
- sunita gupta (Thu Aug 05 2010 - 00:32:55 PDT)
[AMBER] parmbsc0
- case (Tue Aug 17 2010 - 15:21:31 PDT)
- Jason Swails (Tue Aug 17 2010 - 12:25:23 PDT)
[AMBER] PBC
- arikcohen (Fri Aug 20 2010 - 14:38:18 PDT)
- arikcohen (Fri Aug 20 2010 - 14:36:50 PDT)
- case (Fri Aug 20 2010 - 13:38:01 PDT)
- Jason Swails (Fri Aug 20 2010 - 12:49:21 PDT)
- arikcohen (Fri Aug 20 2010 - 12:43:24 PDT)
- Jason Swails (Fri Aug 20 2010 - 04:31:52 PDT)
- arikcohen (Thu Aug 19 2010 - 17:35:21 PDT)
[AMBER] peptides not folding in remd with changing sequence of D and L isomer
- Carlos Simmerling (Mon Aug 09 2010 - 08:18:16 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 08:12:50 PDT)
- Carlos Simmerling (Mon Aug 09 2010 - 07:20:43 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 05:02:05 PDT)
- Carlos Simmerling (Mon Aug 09 2010 - 04:54:07 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 04:52:25 PDT)
- Carlos Simmerling (Mon Aug 09 2010 - 04:21:22 PDT)
- Jorgen Simonsen (Mon Aug 09 2010 - 00:02:03 PDT)
- Daniel Sindhikara (Sun Aug 08 2010 - 23:54:52 PDT)
- Jason Swails (Sun Aug 08 2010 - 10:47:53 PDT)
- Jorgen Simonsen (Sun Aug 08 2010 - 09:44:35 PDT)
[AMBER] Permission to post Admin processes?
- Marc Moreau (Wed Aug 04 2010 - 10:49:42 PDT)
[AMBER] phenylalanine amide
- Francesco Pietra (Tue Aug 31 2010 - 14:12:24 PDT)
- Paul S. Nerenberg (Tue Aug 31 2010 - 10:34:05 PDT)
- Francesco Pietra (Tue Aug 31 2010 - 09:59:05 PDT)
- Paul S. Nerenberg (Tue Aug 31 2010 - 09:40:14 PDT)
- Francesco Pietra (Tue Aug 31 2010 - 09:31:49 PDT)
[AMBER] pmemd installation problem
- Carra, Claudio (JSC-SK)[Universities Space Research Association] (Tue Aug 31 2010 - 16:21:21 PDT)
- Ross Walker (Tue Aug 31 2010 - 01:33:38 PDT)
- Jason Swails (Mon Aug 30 2010 - 21:30:42 PDT)
- Carra, Claudio (JSC-SK)[Universities Space Research Association] (Mon Aug 30 2010 - 16:09:50 PDT)
[AMBER] Post-processing error
- arikcohen (Thu Aug 05 2010 - 17:15:54 PDT)
[AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED
- arikcohen (Fri Aug 06 2010 - 18:02:09 PDT)
- Bill Ross (Fri Aug 06 2010 - 16:50:17 PDT)
- arikcohen (Fri Aug 06 2010 - 16:41:45 PDT)
[AMBER] problem of NM calculations
- fancy2012 (Sun Aug 15 2010 - 02:37:52 PDT)
- fancy2012 (Sat Aug 14 2010 - 01:31:01 PDT)
- Jason Swails (Fri Aug 13 2010 - 12:50:29 PDT)
- fancy2012 (Fri Aug 13 2010 - 06:01:27 PDT)
[AMBER] Problem with running PMEMD on a cluster
- ali naserian nik (Mon Aug 02 2010 - 00:37:12 PDT)
[AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
- Shulin Zhuang (Tue Aug 24 2010 - 05:32:19 PDT)
- case (Tue Aug 24 2010 - 04:21:56 PDT)
- Shulin Zhuang (Mon Aug 23 2010 - 18:20:43 PDT)
- Gustavo Seabra (Mon Aug 23 2010 - 18:17:24 PDT)
- Shulin Zhuang (Mon Aug 23 2010 - 18:06:43 PDT)
[AMBER] protein protein interaction
- Carlos Simmerling (Sun Aug 22 2010 - 15:33:02 PDT)
- manikanthan bhavaraju (Sun Aug 22 2010 - 15:13:34 PDT)
- Carlos Simmerling (Sun Aug 22 2010 - 13:08:41 PDT)
- manikanthan bhavaraju (Sun Aug 22 2010 - 12:46:43 PDT)
- case (Sat Aug 21 2010 - 06:20:29 PDT)
- manikanthan bhavaraju (Fri Aug 20 2010 - 22:28:58 PDT)
[AMBER] protonate
- kamlesh sahu (Mon Aug 16 2010 - 08:21:02 PDT)
- case (Mon Aug 16 2010 - 04:41:15 PDT)
- kamlesh sahu (Mon Aug 16 2010 - 00:43:21 PDT)
[AMBER] ptraj "closest"
- Amor San Juan (Tue Aug 24 2010 - 04:32:30 PDT)
- Daniel Roe (Mon Aug 23 2010 - 07:07:17 PDT)
- Amor San Juan (Mon Aug 23 2010 - 04:10:11 PDT)
[AMBER] ptraj and image
- steinbrt.rci.rutgers.edu (Tue Aug 03 2010 - 04:13:13 PDT)
- Thomas Exner (Tue Aug 03 2010 - 04:08:11 PDT)
[AMBER] ptraj help
- William Flak (Thu Aug 26 2010 - 19:45:40 PDT)
- Jason Swails (Thu Aug 26 2010 - 17:39:26 PDT)
- William Flak (Thu Aug 26 2010 - 16:58:48 PDT)
[AMBER] ptraj question
- Jason Swails (Tue Aug 03 2010 - 17:27:16 PDT)
- Jia Xu (Tue Aug 03 2010 - 15:29:36 PDT)
[AMBER] PTRAJ: closest & strip in one script or separate
- Jason Swails (Fri Aug 20 2010 - 05:03:24 PDT)
- Amor San Juan (Fri Aug 20 2010 - 02:33:50 PDT)
[AMBER] PTRAJ: problem with image command
- Xioling Chuang (Tue Aug 03 2010 - 20:43:39 PDT)
- InSuk Joung (Tue Aug 03 2010 - 11:05:56 PDT)
- InSuk Joung (Tue Aug 03 2010 - 11:04:32 PDT)
- Xioling Chuang (Tue Aug 03 2010 - 09:17:02 PDT)
- InSuk Joung (Tue Aug 03 2010 - 08:20:13 PDT)
- Xioling Chuang (Tue Aug 03 2010 - 07:30:46 PDT)
[AMBER] Quantifying Hydrophobic interaction
- case (Tue Aug 24 2010 - 09:35:52 PDT)
- aneesh cna (Tue Aug 24 2010 - 06:23:53 PDT)
- case (Tue Aug 24 2010 - 04:32:17 PDT)
- aneesh cna (Mon Aug 23 2010 - 22:16:28 PDT)
[AMBER] query on invoking ff99SB and ff99
- case (Thu Aug 12 2010 - 06:49:25 PDT)
- Alan (Thu Aug 12 2010 - 05:23:44 PDT)
- case (Thu Aug 12 2010 - 04:51:44 PDT)
- Alan (Thu Aug 12 2010 - 03:11:52 PDT)
- Bill Ross (Wed Aug 11 2010 - 10:26:50 PDT)
- case (Wed Aug 11 2010 - 09:12:30 PDT)
- Jason Swails (Wed Aug 11 2010 - 09:00:05 PDT)
- Bala subramanian (Wed Aug 11 2010 - 08:35:00 PDT)
[AMBER] Query regarding radius of H atoms of TIP3 water model
- case (Fri Aug 13 2010 - 06:53:41 PDT)
- sunita gupta (Fri Aug 13 2010 - 05:52:02 PDT)
[AMBER] question about empirical valence bond theory
- Ganesh Kamath (Mon Aug 09 2010 - 07:06:38 PDT)
[AMBER] Question about mdinfo file.
- Jason Swails (Tue Aug 17 2010 - 13:02:52 PDT)
- Mayank Daga (Tue Aug 17 2010 - 12:51:46 PDT)
- Ross Walker (Tue Aug 17 2010 - 11:56:31 PDT)
- Mayank Daga (Tue Aug 17 2010 - 11:41:02 PDT)
- Ross Walker (Tue Aug 17 2010 - 10:39:18 PDT)
- Robert Duke (Tue Aug 17 2010 - 10:25:17 PDT)
- Robert Duke (Tue Aug 17 2010 - 10:08:06 PDT)
- Mayank Daga (Tue Aug 17 2010 - 10:19:11 PDT)
- Ross Walker (Tue Aug 17 2010 - 10:04:23 PDT)
- Ross Walker (Tue Aug 17 2010 - 09:52:19 PDT)
- Mayank Daga (Tue Aug 17 2010 - 09:42:21 PDT)
- Jason Swails (Tue Aug 17 2010 - 09:00:16 PDT)
- Robert Duke (Tue Aug 17 2010 - 08:58:42 PDT)
- Mayank Daga (Tue Aug 17 2010 - 08:55:11 PDT)
- Robert Duke (Tue Aug 17 2010 - 08:49:38 PDT)
- Jason Swails (Tue Aug 17 2010 - 08:31:11 PDT)
- Mayank Daga (Tue Aug 17 2010 - 08:10:26 PDT)
[AMBER] question on improper dihedrals
- Jason Swails (Tue Aug 24 2010 - 13:04:10 PDT)
- case (Tue Aug 24 2010 - 12:55:57 PDT)
- Jason Swails (Tue Aug 24 2010 - 12:19:07 PDT)
[AMBER] questions about installing pmend.cuda
- 宋德寿 (Tue Aug 03 2010 - 20:03:24 PDT)
- 宋德寿 (Tue Aug 03 2010 - 19:59:02 PDT)
- Ross Walker (Tue Aug 03 2010 - 11:04:15 PDT)
- case (Tue Aug 03 2010 - 06:20:09 PDT)
- 宋德寿 (Tue Aug 03 2010 - 05:07:32 PDT)
- Jason Swails (Tue Aug 03 2010 - 04:26:21 PDT)
- 宋德寿 (Mon Aug 02 2010 - 23:39:45 PDT)
- 宋德寿 (Mon Aug 02 2010 - 22:26:25 PDT)
- maluyao (Mon Aug 02 2010 - 21:55:06 PDT)
- 宋德寿 (Mon Aug 02 2010 - 21:45:49 PDT)
[AMBER] questions for the different atom style and resp charge
- xqkong (Wed Aug 25 2010 - 02:53:30 PDT)
- FyD (Tue Aug 24 2010 - 12:01:05 PDT)
- xqkong (Mon Aug 23 2010 - 23:44:10 PDT)
- FyD (Mon Aug 23 2010 - 23:08:36 PDT)
- xqkong (Mon Aug 23 2010 - 18:46:38 PDT)
- xqkong (Mon Aug 23 2010 - 18:31:21 PDT)
- FyD (Mon Aug 23 2010 - 12:22:06 PDT)
- xqkong (Mon Aug 23 2010 - 08:00:11 PDT)
- FyD (Mon Aug 23 2010 - 00:28:37 PDT)
- xqkong (Sun Aug 22 2010 - 03:11:50 PDT)
- xqkong (Sun Aug 22 2010 - 01:59:48 PDT)
[AMBER] random number seed - range
- Ross Walker (Fri Aug 13 2010 - 15:22:11 PDT)
- Ross Walker (Fri Aug 13 2010 - 15:16:43 PDT)
- Dean Cuebas (Fri Aug 13 2010 - 15:16:27 PDT)
- Ross Walker (Fri Aug 13 2010 - 15:08:39 PDT)
- Robert Duke (Fri Aug 13 2010 - 15:05:34 PDT)
- Robert Duke (Fri Aug 13 2010 - 14:59:42 PDT)
- Paul S. Nerenberg (Fri Aug 13 2010 - 14:58:55 PDT)
- Ross Walker (Fri Aug 13 2010 - 14:55:20 PDT)
- Robert Duke (Fri Aug 13 2010 - 14:40:35 PDT)
- Hopkins, Robert (Fri Aug 13 2010 - 14:03:53 PDT)
[AMBER] RDPARM
- case (Wed Aug 04 2010 - 17:37:18 PDT)
- Philippe Pinard (Wed Aug 04 2010 - 17:24:56 PDT)
- case (Wed Aug 04 2010 - 14:48:36 PDT)
- Philippe Pinard (Wed Aug 04 2010 - 09:35:49 PDT)
- case (Tue Aug 03 2010 - 15:26:49 PDT)
- Thomas Cheatham III (Tue Aug 03 2010 - 15:00:07 PDT)
- Philippe Pinard (Tue Aug 03 2010 - 14:40:03 PDT)
- Philippe Pinard (Tue Aug 03 2010 - 14:32:10 PDT)
- Thomas Cheatham III (Tue Aug 03 2010 - 14:11:58 PDT)
- Philippe Pinard (Tue Aug 03 2010 - 08:41:54 PDT)
- Thomas Cheatham III (Mon Aug 02 2010 - 16:24:40 PDT)
- Philippe Pinard (Mon Aug 02 2010 - 16:12:20 PDT)
[AMBER] Regarding protein diffusion
- aneesh cna (Mon Aug 30 2010 - 01:24:12 PDT)
[AMBER] regarding random number generator
- Sangita Kachhap (Sat Aug 14 2010 - 12:22:34 PDT)
- Ross Walker (Sat Aug 14 2010 - 11:28:22 PDT)
- Sangita Kachhap (Sat Aug 14 2010 - 09:07:41 PDT)
[AMBER] regarding trap simulation
- Jason Swails (Tue Aug 31 2010 - 06:49:51 PDT)
- Jorgen Simonsen (Tue Aug 31 2010 - 06:44:43 PDT)
- Jason Swails (Tue Aug 31 2010 - 06:30:45 PDT)
- Jorgen Simonsen (Tue Aug 31 2010 - 06:27:26 PDT)
[AMBER] Residue name problem in PTRAJ
- Hoshin Kim (Tue Aug 31 2010 - 15:32:19 PDT)
[AMBER] Resource for trying out various GPU setups with AMBER
- Ross Walker (Tue Aug 10 2010 - 08:26:20 PDT)
[AMBER] restart reimage
- Jason Swails (Thu Aug 19 2010 - 07:07:32 PDT)
- manikanthan bhavaraju (Wed Aug 18 2010 - 23:24:01 PDT)
[AMBER] restrain group specification for GPU
- Scott Le Grand (Wed Aug 11 2010 - 08:32:30 PDT)
- Scott Le Grand (Tue Aug 10 2010 - 17:15:20 PDT)
- Qizhi Cui (Tue Aug 10 2010 - 15:26:39 PDT)
- Qizhi Cui (Tue Aug 10 2010 - 12:59:37 PDT)
- Ross Walker (Tue Aug 10 2010 - 10:30:02 PDT)
- Bill Ross (Tue Aug 10 2010 - 09:59:08 PDT)
- Scott Le Grand (Tue Aug 10 2010 - 09:33:08 PDT)
- Qizhi Cui (Tue Aug 10 2010 - 08:40:11 PDT)
[AMBER] restraining only heavy atoms in PMEMD
- Senthil Natesan (Mon Aug 02 2010 - 11:37:33 PDT)
[AMBER] RE : Regarding protein diffusion
- ABEL Stephane 175950 (Mon Aug 30 2010 - 07:04:33 PDT)
[AMBER] Running AMBER on a GPU Cluster.
- Mayank Daga (Tue Aug 24 2010 - 10:56:39 PDT)
- Ross Walker (Tue Aug 24 2010 - 10:34:15 PDT)
- Sasha Buzko (Tue Aug 24 2010 - 10:13:40 PDT)
- Mayank Daga (Mon Aug 23 2010 - 18:35:30 PDT)
[AMBER] sander.MPI error
- Jason Swails (Fri Aug 20 2010 - 08:37:20 PDT)
- George Tzotzos (Fri Aug 20 2010 - 07:31:40 PDT)
- case (Fri Aug 20 2010 - 07:03:19 PDT)
- George Tzotzos (Fri Aug 20 2010 - 06:43:41 PDT)
[AMBER] SASA over trajectory
- Carlos Simmerling (Mon Aug 09 2010 - 08:01:06 PDT)
- Beale, John (Mon Aug 09 2010 - 07:58:22 PDT)
[AMBER] segmentation fault - ptrajin image familiar
- Jason Swails (Mon Aug 16 2010 - 06:06:18 PDT)
- Jorgen Simonsen (Mon Aug 16 2010 - 06:00:10 PDT)
- Daniel Roe (Mon Aug 16 2010 - 05:18:12 PDT)
- case (Mon Aug 16 2010 - 04:45:06 PDT)
- manikanthan bhavaraju (Mon Aug 16 2010 - 01:56:33 PDT)
- Jorgen Simonsen (Mon Aug 16 2010 - 01:01:25 PDT)
[AMBER] simulation of a restrained protein fragment + pmemd.cuda issues
- Ross Walker (Wed Aug 25 2010 - 11:29:26 PDT)
- Sasha Buzko (Tue Aug 24 2010 - 17:09:06 PDT)
[AMBER] simulation of a restrained protein fragment +pmemd.cuda issues
- Ross Walker (Thu Aug 26 2010 - 04:40:26 PDT)
- Paul Mortenson (Thu Aug 26 2010 - 02:33:09 PDT)
[AMBER] simulation output for explicit and implicit model
- Jason Swails (Tue Aug 10 2010 - 15:45:17 PDT)
- Yan Gao (Tue Aug 10 2010 - 15:32:27 PDT)
[AMBER] simulation output for explicit and implicit model--please disregard the previous message
- Bill Ross (Tue Aug 10 2010 - 16:11:48 PDT)
- Yan Gao (Tue Aug 10 2010 - 15:43:57 PDT)
[AMBER] simulation with multiple docked ligand
- steinbrt.rci.rutgers.edu (Wed Aug 04 2010 - 05:55:10 PDT)
- Ashutosh Shandilya (Wed Aug 04 2010 - 05:47:07 PDT)
[AMBER] single-point energy calculation on selected atoms
- Yi Xue (Mon Aug 16 2010 - 17:43:36 PDT)
[AMBER] slowly releasing restraint_wt force
- Sangita Kachhap (Mon Aug 23 2010 - 08:29:13 PDT)
[AMBER] snapshots
- Jason Swails (Wed Aug 11 2010 - 16:27:41 PDT)
- arikcohen (Wed Aug 11 2010 - 15:33:47 PDT)
- Philippe Pinard (Wed Aug 11 2010 - 15:30:48 PDT)
[AMBER] Soft-core Coulomb potential
- case (Mon Aug 09 2010 - 04:58:59 PDT)
- Samuel Genheden (Mon Aug 09 2010 - 00:52:31 PDT)
[AMBER] Solid surface simulation in Amber
- Tom Williams (Wed Aug 04 2010 - 09:35:57 PDT)
- Marek Maly (Wed Aug 04 2010 - 08:03:54 PDT)
- case (Wed Aug 04 2010 - 04:23:11 PDT)
- Tom Williams (Tue Aug 03 2010 - 23:06:47 PDT)
- Marek Maly (Tue Aug 03 2010 - 16:00:24 PDT)
- Bill Ross (Tue Aug 03 2010 - 16:08:20 PDT)
- Bill Ross (Tue Aug 03 2010 - 16:03:49 PDT)
- Marek Maly (Tue Aug 03 2010 - 15:23:34 PDT)
- Bill Ross (Tue Aug 03 2010 - 12:14:57 PDT)
[AMBER] Solid surface simulation in Amber - the recommended approach ?
- Marek Maly (Fri Aug 06 2010 - 18:26:22 PDT)
- Marek Maly (Tue Aug 03 2010 - 11:35:28 PDT)
[AMBER] solvateBox - what is the suitable value for distance?
- Brent Krueger (Tue Aug 24 2010 - 10:07:10 PDT)
- case (Tue Aug 24 2010 - 09:40:23 PDT)
- colvin (Mon Aug 23 2010 - 18:23:43 PDT)
[AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation
- g t (Thu Aug 19 2010 - 12:45:24 PDT)
- Jason Swails (Thu Aug 19 2010 - 12:29:09 PDT)
- g t (Thu Aug 19 2010 - 12:05:59 PDT)
[AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable
- Andreas Goetz (Wed Aug 11 2010 - 03:03:28 PDT)
- Alan (Wed Aug 11 2010 - 02:52:49 PDT)
[AMBER] the modified Bondi radii
- Asfa Ali (Tue Aug 31 2010 - 05:36:31 PDT)
- Jason Swails (Mon Aug 30 2010 - 15:55:34 PDT)
- zhihong ke (Mon Aug 30 2010 - 10:30:29 PDT)
- Jason Swails (Mon Aug 30 2010 - 10:20:16 PDT)
- zhihong ke (Mon Aug 30 2010 - 10:15:24 PDT)
[AMBER] The Result of PARMCHK
- setyanto tri wahyudi (Wed Aug 11 2010 - 19:41:19 PDT)
- case (Tue Aug 10 2010 - 04:33:20 PDT)
- setyanto tri wahyudi (Mon Aug 09 2010 - 20:09:34 PDT)
- case (Mon Aug 09 2010 - 04:57:37 PDT)
- setyanto tri wahyudi (Sun Aug 08 2010 - 23:32:47 PDT)
[AMBER] To obtain academic license of AMBER 11 program package
- sonali dhindwal (Thu Aug 26 2010 - 06:45:28 PDT)
- case (Thu Aug 26 2010 - 04:40:59 PDT)
- sonali dhindwal (Thu Aug 26 2010 - 03:47:59 PDT)
- sonali dhindwal (Tue Aug 24 2010 - 23:57:25 PDT)
[AMBER] too many titratable groups
- Jason Swails (Fri Aug 20 2010 - 11:43:20 PDT)
- piotrek.vega.umcs.lublin.pl (Fri Aug 20 2010 - 11:26:42 PDT)
[AMBER] Trivial syntax problem ?
- Marek Maly (Thu Aug 19 2010 - 09:50:05 PDT)
- case (Wed Aug 18 2010 - 18:33:27 PDT)
- Marek Maly (Wed Aug 18 2010 - 13:29:43 PDT)
[AMBER] Tutorial 3: MM-PBSA
- Jason Swails (Wed Aug 25 2010 - 04:27:22 PDT)
- George Tzotzos (Tue Aug 24 2010 - 23:46:29 PDT)
[AMBER] Tutorial3
- George Tzotzos (Thu Aug 05 2010 - 10:22:02 PDT)
- George Tzotzos (Thu Aug 05 2010 - 09:52:37 PDT)
[AMBER] Unit for Van der Waals and Electrostatic Eq.
- Bill Ross (Thu Aug 19 2010 - 09:42:04 PDT)
- Hector Chang (Thu Aug 19 2010 - 09:34:20 PDT)
- Jason Swails (Mon Aug 16 2010 - 11:48:32 PDT)
- case (Mon Aug 16 2010 - 08:37:15 PDT)
- Paul S. Nerenberg (Mon Aug 16 2010 - 08:32:56 PDT)
- Hector Chang (Mon Aug 16 2010 - 08:26:55 PDT)
[AMBER] using nab to create peptides and minimise
- case (Mon Aug 09 2010 - 07:54:15 PDT)
- Alan (Mon Aug 09 2010 - 07:32:33 PDT)
[AMBER] very slow work of ptraj on cluster
- Andrew Voronkov (Mon Aug 30 2010 - 02:10:24 PDT)
- Daniel Roe (Sat Aug 28 2010 - 15:47:30 PDT)
- Andrew Voronkov (Sat Aug 28 2010 - 09:36:31 PDT)
- Daniel Roe (Sat Aug 28 2010 - 05:54:54 PDT)
- Andrew Voronkov (Sat Aug 28 2010 - 04:33:06 PDT)
- Daniel Roe (Fri Aug 27 2010 - 13:08:26 PDT)
- Andrew Voronkov (Fri Aug 27 2010 - 09:33:09 PDT)
[AMBER] vlimit and shake
- Daniel Roe (Thu Aug 26 2010 - 22:31:56 PDT)
- manikanthan bhavaraju (Thu Aug 26 2010 - 19:32:25 PDT)
- Jason Swails (Thu Aug 26 2010 - 18:31:00 PDT)
- manikanthan bhavaraju (Thu Aug 26 2010 - 13:45:50 PDT)
- manikanthan bhavaraju (Thu Aug 26 2010 - 13:25:30 PDT)
[AMBER] volume in a cavity
- Ganesh Kamath (Sat Aug 21 2010 - 07:21:19 PDT)
[AMBER] Water deeply buried for MMPBSA calculations
- Amor San Juan (Thu Aug 26 2010 - 04:05:43 PDT)
- Jason Swails (Wed Aug 25 2010 - 04:19:55 PDT)
- Amor San Juan (Wed Aug 25 2010 - 03:54:54 PDT)
[AMBER] Where to apply find computer resources to run AMBER?
- Catein Catherine (Mon Aug 09 2010 - 07:21:04 PDT)
- Ross Walker (Mon Aug 09 2010 - 06:20:15 PDT)
- Catein Catherine (Sun Aug 08 2010 - 21:55:33 PDT)
[AMBER] Workaround for gfortran-4.1.2?
- Marc Moreau (Wed Aug 25 2010 - 21:23:49 PDT)
- Lachele Foley (Lists) (Wed Aug 25 2010 - 15:18:11 PDT)
- Jason Swails (Wed Aug 25 2010 - 13:10:50 PDT)
- Richard Owczarzy (Wed Aug 25 2010 - 12:51:15 PDT)
[AMBER] Writing trajectory for C-alpha atoms
- Ibrahim Moustafa (Mon Aug 02 2010 - 12:16:48 PDT)
- Ibrahim Moustafa (Mon Aug 02 2010 - 11:56:57 PDT)
- Bill Ross (Mon Aug 02 2010 - 11:54:57 PDT)
- Jason Swails (Mon Aug 02 2010 - 11:35:47 PDT)
- Ibrahim Moustafa (Mon Aug 02 2010 - 10:38:25 PDT)
- Daniel Roe (Mon Aug 02 2010 - 08:43:59 PDT)
- Ibrahim Moustafa (Mon Aug 02 2010 - 08:31:33 PDT)
Interaction energy_mm_pbsa]
- moitrayee.mbu.iisc.ernet.in (Tue Aug 24 2010 - 02:11:05 PDT)
- Jason Swails (Mon Aug 23 2010 - 06:27:50 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:47:21 PDT)
- Bill Miller III (Mon Aug 23 2010 - 04:37:31 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:35:40 PDT)

Amber Archive Aug 2010 by subject