Amber Archive Jun 2010: by subject

#RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl
- Sushil Mishra (Mon Jun 07 2010 - 03:13:17 PDT)
[AMBER] "prepin", ".frcmod" and "pdb" files of 5-methylcytidine (for DNA (dC) no RNA)
- Ehsan Habibi (Sun Jun 20 2010 - 03:25:47 PDT)
[AMBER] #RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl
- Sushil Mishra (Sun Jun 06 2010 - 23:41:42 PDT)
[AMBER] (no subject)
- Thomas Cheatham III (Tue Jun 29 2010 - 10:53:33 PDT)
- Emmanuel Baribefe Naziga (Mon Jun 28 2010 - 08:26:32 PDT)
- Beale, John (Mon Jun 28 2010 - 04:54:02 PDT)
- shenna shearin (Fri Jun 25 2010 - 08:46:53 PDT)
- Steve Seibold (Thu Jun 24 2010 - 12:50:24 PDT)
- Paul S. Nerenberg (Thu Jun 24 2010 - 11:37:28 PDT)
- Paul S. Nerenberg (Thu Jun 24 2010 - 11:33:37 PDT)
- Bill Ross (Thu Jun 24 2010 - 11:27:28 PDT)
- Steve Seibold (Thu Jun 24 2010 - 11:14:19 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Jun 21 2010 - 22:16:45 PDT)
- Jason Swails (Sun Jun 13 2010 - 09:44:11 PDT)
- Catein Catherine (Sun Jun 13 2010 - 08:20:45 PDT)
[AMBER] 2drms
- case (Thu Jun 10 2010 - 18:27:15 PDT)
- Niel Henriksen (Thu Jun 10 2010 - 07:57:27 PDT)
- Beale, John (Thu Jun 10 2010 - 07:40:24 PDT)
[AMBER] a query about analysis
- Cenk \(Jenk\) Andac (Mon Jun 21 2010 - 00:59:15 PDT)
- Jason Swails (Fri Jun 18 2010 - 06:14:10 PDT)
- oguz gurbulak (Fri Jun 18 2010 - 04:37:51 PDT)
[AMBER] about alanine scanning
- lidansa.mail.ustc.edu.cn (Wed Jun 23 2010 - 01:57:22 PDT)
- Sushil Mishra (Tue Jun 22 2010 - 23:48:44 PDT)
- lidansa.mail.ustc.edu.cn (Tue Jun 22 2010 - 17:55:48 PDT)
- Dwight McGee (Tue Jun 22 2010 - 10:05:28 PDT)
- Sushil Mishra (Tue Jun 22 2010 - 09:42:24 PDT)
- lidansa.mail.ustc.edu.cn (Tue Jun 22 2010 - 08:47:53 PDT)
[AMBER] about atom type
- case (Tue Jun 15 2010 - 09:03:25 PDT)
- Navanath Kumbhar (Mon Jun 14 2010 - 22:25:29 PDT)
[AMBER] about ewald error estimate
- Navanath Kumbhar (Wed Jun 09 2010 - 02:45:53 PDT)
- case (Tue Jun 08 2010 - 11:36:35 PDT)
- Navanath Kumbhar (Tue Jun 08 2010 - 09:56:53 PDT)
- case (Mon Jun 07 2010 - 05:12:29 PDT)
- Navanath Kumbhar (Mon Jun 07 2010 - 02:32:43 PDT)
[AMBER] About md parameters for unuaual amino acid residues
- Rilei Yu (Tue Jun 15 2010 - 00:23:44 PDT)
- Jason Swails (Mon Jun 14 2010 - 22:44:27 PDT)
- Rilei Yu (Mon Jun 14 2010 - 22:12:57 PDT)
[AMBER] about sybylmol2 file
- Bill Ross (Sat Jun 12 2010 - 12:39:28 PDT)
- case (Sat Jun 12 2010 - 05:31:15 PDT)
- Navanath Kumbhar (Sat Jun 12 2010 - 03:29:08 PDT)
- case (Fri Jun 11 2010 - 06:19:52 PDT)
- FyD (Fri Jun 11 2010 - 06:08:30 PDT)
- Navanath Kumbhar (Fri Jun 11 2010 - 03:27:20 PDT)
- case (Thu Jun 10 2010 - 18:09:04 PDT)
- Jason Swails (Thu Jun 10 2010 - 17:14:46 PDT)
- Navanath Kumbhar (Thu Jun 10 2010 - 07:33:59 PDT)
[AMBER] About water molecule analysis
- gokul algates (Fri Jun 04 2010 - 04:19:38 PDT)
[AMBER] adding counterions
- Ping (Wed Jun 30 2010 - 19:58:34 PDT)
[AMBER] Adding Ions.
- Dean Cuebas (Wed Jun 30 2010 - 21:29:39 PDT)
- Hugh Heldenbrand (Wed Jun 30 2010 - 11:27:04 PDT)
- Bill Ross (Wed Jun 30 2010 - 11:19:37 PDT)
- case (Wed Jun 30 2010 - 11:15:56 PDT)
- Ajay Ummat (Wed Jun 30 2010 - 11:05:25 PDT)
[AMBER] ALASCAN (Alanine scanning mutagens )
- Dwight McGee (Fri Jun 04 2010 - 08:31:01 PDT)
- Sushil Mishra (Fri Jun 04 2010 - 08:03:35 PDT)
- Dwight McGee (Fri Jun 04 2010 - 07:52:10 PDT)
- Sushil Mishra (Thu Jun 03 2010 - 10:09:36 PDT)
[AMBER] Amber on BlueGene/P
- case (Fri Jun 04 2010 - 11:35:22 PDT)
- T. Andrew Binkowski (Fri Jun 04 2010 - 10:49:11 PDT)
[AMBER] AMBER, shenna shearin has invited you to open a Google mail account
- shenna shearin (Fri Jun 25 2010 - 08:47:42 PDT)
[AMBER] amber.cuda performance on Nvidia S2050?
- Sasha Buzko (Mon Jun 07 2010 - 11:10:32 PDT)
- Scott Le Grand (Mon Jun 07 2010 - 10:52:59 PDT)
- Sasha Buzko (Mon Jun 07 2010 - 09:23:57 PDT)
[AMBER] amber10 compilation
- Daniel Roe (Tue Jun 01 2010 - 10:34:58 PDT)
- Jason Swails (Tue Jun 01 2010 - 10:30:59 PDT)
- Sangita Kachhap (Tue Jun 01 2010 - 09:18:03 PDT)
[AMBER] amber10 installation problem
- Sudeep Narayan Banerjee (Thu Jun 17 2010 - 01:05:40 PDT)
- Indrajit Deb (Thu Jun 17 2010 - 00:22:06 PDT)
- case (Wed Jun 16 2010 - 09:58:16 PDT)
- Devlina Chakravarty (Wed Jun 16 2010 - 05:01:16 PDT)
[AMBER] Amber10 installation problem in linux
- Mark Williamson (Fri Jun 11 2010 - 10:09:54 PDT)
- Sangita Kachhap (Fri Jun 11 2010 - 09:28:11 PDT)
[AMBER] amber10 installtion error in parallel
- Jason Swails (Tue Jun 01 2010 - 06:32:29 PDT)
[AMBER] AMBER10 TI calculations
- case (Tue Jun 01 2010 - 13:22:30 PDT)
- manikanthan bhavaraju (Tue Jun 01 2010 - 12:20:48 PDT)
[AMBER] AMBER11 and AmberTools1.4 errors
- Jason Swails (Thu Jun 24 2010 - 10:30:00 PDT)
- Steve Seibold (Thu Jun 24 2010 - 10:18:46 PDT)
[AMBER] AMBER11 compilation
- case (Mon Jun 07 2010 - 07:15:51 PDT)
- Steve Seibold (Mon Jun 07 2010 - 06:46:03 PDT)
- case (Mon Jun 07 2010 - 05:51:53 PDT)
- Steve Seibold (Mon Jun 07 2010 - 05:23:32 PDT)
[AMBER] amber11 PMEMD cuda problem. (sometimes stopped...)
- Ross Walker (Thu Jun 03 2010 - 07:44:12 PDT)
[AMBER] Amber11: running ptraj
- case (Mon Jun 07 2010 - 04:53:43 PDT)
- George Tzotzos (Mon Jun 07 2010 - 03:10:05 PDT)
[AMBER] amberhome not set
- Jason Swails (Wed Jun 23 2010 - 14:26:50 PDT)
- Ping (Wed Jun 23 2010 - 14:07:09 PDT)
- Bill Ross (Wed Jun 23 2010 - 13:57:48 PDT)
- Heather Condurso (Wed Jun 23 2010 - 13:45:26 PDT)
- Ping (Wed Jun 23 2010 - 13:42:06 PDT)
[AMBER] AmberTool 1.4 ptraj error
- Steve Seibold (Thu Jun 24 2010 - 08:58:44 PDT)
[AMBER] AmberTools installation in Cygwin
- Yan Gao (Wed Jun 30 2010 - 20:12:03 PDT)
[AMBER] AmberTools-1.4 Test Problem
- Gustavo Seabra (Wed Jun 02 2010 - 05:45:35 PDT)
[AMBER] ambertools1.2 compilation error
- xueping chin (Fri Jun 11 2010 - 06:05:51 PDT)
- case (Fri Jun 11 2010 - 05:58:56 PDT)
- colvin (Thu Jun 10 2010 - 22:58:06 PDT)
- case (Thu Jun 10 2010 - 19:06:52 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 02:26:42 PDT)
- colvin (Thu Jun 10 2010 - 01:54:19 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 01:44:28 PDT)
- colvin (Thu Jun 10 2010 - 01:28:57 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 01:18:21 PDT)
- colvin (Thu Jun 10 2010 - 00:43:54 PDT)
[AMBER] antechamber
- monica.imtech.res.in (Mon Jun 14 2010 - 00:43:00 PDT)
[AMBER] antechamber failing with -mul option and sqm
- case (Wed Jun 09 2010 - 18:18:41 PDT)
- Alan (Wed Jun 09 2010 - 04:15:11 PDT)
[AMBER] antechamber issue and parameters for heme of cyp3a4
- vaibhav dixit (Sat Jun 19 2010 - 21:25:35 PDT)
- Jio M (Sat Jun 19 2010 - 11:03:27 PDT)
- vaibhav dixit (Fri Jun 18 2010 - 22:00:47 PDT)
[AMBER] antechamber/gasteiger problem with FMN
- Eric Pettersen (Tue Jun 22 2010 - 13:11:28 PDT)
- Eric Pettersen (Tue Jun 22 2010 - 13:08:46 PDT)
[AMBER] Any way to apply different dt(time/step) to different steps
- Daniel Roe (Wed Jun 30 2010 - 20:33:16 PDT)
- Yiyu Li (Wed Jun 30 2010 - 19:25:08 PDT)
[AMBER] bond angle and distance calculation
- Hoshin Kim (Thu Jun 17 2010 - 01:48:18 PDT)
[AMBER] bond angle and distance problem
- Hoshin Kim (Thu Jun 17 2010 - 21:54:01 PDT)
[AMBER] Building a slab between two vacuums?
- Bill Ross (Thu Jun 10 2010 - 09:57:14 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 06:13:15 PDT)
[AMBER] Can I did MM/GBSA analysis for a partial equilibrated system?
- Jason Swails (Sun Jun 13 2010 - 09:57:44 PDT)
- Catein Catherine (Sun Jun 13 2010 - 09:00:44 PDT)
[AMBER] Can I neglect the error message of sleap in amber tool?
- case (Thu Jun 10 2010 - 18:09:10 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 13:24:30 PDT)
- Catein Catherine (Thu Jun 10 2010 - 08:10:22 PDT)
[AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help.
- case (Fri Jun 11 2010 - 06:01:08 PDT)
- Jason Swails (Thu Jun 10 2010 - 20:25:42 PDT)
- Catein Catherine (Thu Jun 10 2010 - 20:12:49 PDT)
[AMBER] Can i use DA instead of DA3/DA5 for teminal residues?
- case (Thu Jun 24 2010 - 07:30:01 PDT)
- Catein Catherine (Thu Jun 24 2010 - 07:02:03 PDT)
[AMBER] Can mm-pbsa be limited to simulating a fragment of a large protein?
- Sasha Buzko (Fri Jun 11 2010 - 10:50:35 PDT)
[AMBER] Can't locate mm_pbsa_global.pm in .INC
- fancy2012 (Fri Jun 25 2010 - 18:04:49 PDT)
- Jason Swails (Fri Jun 25 2010 - 06:47:04 PDT)
- fancy2012 (Fri Jun 25 2010 - 02:05:37 PDT)
[AMBER] center and image
- Jason Swails (Tue Jun 22 2010 - 06:39:49 PDT)
- Homa Azizian (Mon Jun 21 2010 - 22:55:49 PDT)
[AMBER] Checksums?
- Ross Walker (Fri Jun 25 2010 - 15:34:46 PDT)
- Marc Moreau (Fri Jun 25 2010 - 12:58:26 PDT)
[AMBER] cluster analysis
- shenna shearin (Fri Jun 25 2010 - 11:11:27 PDT)
[AMBER] Combine trajectory files error
- Steve Seibold (Fri Jun 25 2010 - 07:54:26 PDT)
[AMBER] comparing DeltaG, docking and IC50
- vaibhav dixit (Tue Jun 08 2010 - 03:21:36 PDT)
[AMBER] Compiling failure of Amber 9
- Jason Swails (Tue Jun 29 2010 - 12:27:29 PDT)
- Yubo Fan (Tue Jun 29 2010 - 11:41:44 PDT)
- Jason Swails (Tue Jun 29 2010 - 06:46:24 PDT)
- Yubo Fan (Tue Jun 29 2010 - 06:39:37 PDT)
[AMBER] Conserving water bridges?
- Jason Swails (Fri Jun 11 2010 - 10:00:21 PDT)
- steinbrt.rci.rutgers.edu (Fri Jun 11 2010 - 03:18:25 PDT)
- Waqas Nasir (Fri Jun 11 2010 - 02:56:46 PDT)
[AMBER] Conserving water bridges? need help...
- Bill Ross (Mon Jun 14 2010 - 09:35:51 PDT)
- steinbrt.rci.rutgers.edu (Mon Jun 14 2010 - 04:39:59 PDT)
- Waqas Nasir (Mon Jun 14 2010 - 03:20:36 PDT)
[AMBER] constant pH equilibration confusion
- Bill Ross (Sat Jun 19 2010 - 18:13:34 PDT)
- Jason Swails (Sat Jun 19 2010 - 14:11:23 PDT)
- Jason Swails (Sat Jun 19 2010 - 14:10:20 PDT)
- Sangita Kachhap (Sat Jun 19 2010 - 13:30:53 PDT)
- Sangita Kachhap (Sat Jun 19 2010 - 13:09:27 PDT)
- Jason Swails (Sat Jun 19 2010 - 13:07:37 PDT)
- Sangita Kachhap (Sat Jun 19 2010 - 12:59:26 PDT)
- Bill Ross (Sat Jun 19 2010 - 09:38:16 PDT)
- Jason Swails (Sat Jun 19 2010 - 08:49:15 PDT)
- manikanthan bhavaraju (Sat Jun 19 2010 - 02:32:30 PDT)
- Sangita Kachhap (Sat Jun 19 2010 - 00:55:52 PDT)
[AMBER] constant pH simulation (protonation state specification)
- Jason Swails (Sun Jun 13 2010 - 23:33:23 PDT)
- Sangita Kachhap (Sun Jun 13 2010 - 21:46:54 PDT)
- Jason Swails (Sun Jun 13 2010 - 09:40:57 PDT)
- Sangita Kachhap (Sun Jun 13 2010 - 09:16:34 PDT)
[AMBER] constant pH simulation (syn and anti position)
- Sangita Kachhap (Tue Jun 15 2010 - 06:50:36 PDT)
[AMBER] constant pH simulation ERROR "vlimit exceeded for step"
- Bill Ross (Wed Jun 23 2010 - 09:55:40 PDT)
- Sangita Kachhap (Tue Jun 22 2010 - 23:33:36 PDT)
- Bill Ross (Tue Jun 22 2010 - 13:44:34 PDT)
- Sangita Kachhap (Tue Jun 22 2010 - 13:30:05 PDT)
- Bill Ross (Tue Jun 22 2010 - 13:22:51 PDT)
- Sangita Kachhap (Tue Jun 22 2010 - 13:20:10 PDT)
- Sangita Kachhap (Tue Jun 22 2010 - 13:10:37 PDT)
- Bill Ross (Tue Jun 22 2010 - 12:53:33 PDT)
- Sangita Kachhap (Tue Jun 22 2010 - 12:42:18 PDT)
- Sangita Kachhap (Mon Jun 21 2010 - 09:20:35 PDT)
- Jason Swails (Mon Jun 21 2010 - 09:04:21 PDT)
- Sangita Kachhap (Mon Jun 21 2010 - 08:10:59 PDT)
- Jason Swails (Mon Jun 21 2010 - 07:25:26 PDT)
- Sangita Kachhap (Mon Jun 21 2010 - 04:10:28 PDT)
[AMBER] Constant protonation vs. constant pH simulation
- Jason Swails (Sat Jun 26 2010 - 06:41:48 PDT)
- nicholus bhattacharjee (Sat Jun 26 2010 - 05:50:51 PDT)
- Adrian Roitberg (Sat Jun 26 2010 - 05:24:17 PDT)
- nicholus bhattacharjee (Sat Jun 26 2010 - 05:19:18 PDT)
[AMBER] correlation
- luzhenw1.msu.edu (Thu Jun 10 2010 - 22:16:47 PDT)
[AMBER] correlation matrix in PTRAJ
- luzhenw1.msu.edu (Fri Jun 11 2010 - 06:54:18 PDT)
[AMBER] Creating topology files for protein-ligand complex
- Heather Condurso (Wed Jun 16 2010 - 20:26:28 PDT)
- case (Wed Jun 16 2010 - 19:51:26 PDT)
[AMBER] CUDA (GPU): Implementation does not support extra points.
- case (Mon Jun 14 2010 - 07:09:25 PDT)
- ashutosh shandilya (Sun Jun 13 2010 - 23:08:10 PDT)
- Ross Walker (Sat Jun 12 2010 - 11:42:30 PDT)
- ashutosh shandilya (Sat Jun 12 2010 - 11:18:06 PDT)
[AMBER] CUDA Segfault GTX470
- Levi Pierce (Tue Jun 01 2010 - 13:16:30 PDT)
- Ross Walker (Tue Jun 01 2010 - 12:28:14 PDT)
- Levi Pierce (Tue Jun 01 2010 - 12:23:04 PDT)
[AMBER] cutoff
- Dean Cuebas (Sun Jun 06 2010 - 18:23:44 PDT)
- Ross Walker (Sun Jun 06 2010 - 14:14:13 PDT)
- fancy2012 (Sun Jun 06 2010 - 00:50:34 PDT)
- Bill Ross (Sat Jun 05 2010 - 16:03:31 PDT)
- Dean Cuebas (Sat Jun 05 2010 - 15:39:27 PDT)
- Bill Ross (Sat Jun 05 2010 - 15:38:45 PDT)
- Bill Ross (Sat Jun 05 2010 - 15:21:31 PDT)
- Ross Walker (Sat Jun 05 2010 - 12:28:45 PDT)
- fancy2012 (Sat Jun 05 2010 - 06:20:38 PDT)
- Bill Ross (Fri Jun 04 2010 - 10:12:50 PDT)
- fancy2012 (Fri Jun 04 2010 - 02:03:38 PDT)
[AMBER] density
- John S (Tue Jun 15 2010 - 12:57:51 PDT)
[AMBER] discontinuous residues
- Jio M (Tue Jun 01 2010 - 12:10:35 PDT)
- Jason Swails (Tue Jun 01 2010 - 07:07:48 PDT)
- Jio M (Tue Jun 01 2010 - 00:05:02 PDT)
[AMBER] distance restraints
- Jason Swails (Wed Jun 02 2010 - 10:56:38 PDT)
- Bill Ross (Wed Jun 02 2010 - 10:24:55 PDT)
- Jason Swails (Wed Jun 02 2010 - 06:20:13 PDT)
- qiaoyan (Wed Jun 02 2010 - 06:14:00 PDT)
[AMBER] dna
- case (Mon Jun 28 2010 - 19:07:46 PDT)
- Kevin Hauser (Sun Jun 27 2010 - 09:56:03 PDT)
- monica.imtech.res.in (Sat Jun 26 2010 - 21:50:02 PDT)
- case (Fri Jun 25 2010 - 06:54:08 PDT)
- monica.imtech.res.in (Fri Jun 25 2010 - 00:54:33 PDT)
- Kevin Hauser (Wed Jun 23 2010 - 09:34:05 PDT)
- case (Wed Jun 23 2010 - 09:20:37 PDT)
- monica.imtech.res.in (Wed Jun 23 2010 - 08:40:18 PDT)
- case (Wed Jun 23 2010 - 07:02:42 PDT)
- Kevin Hauser (Wed Jun 23 2010 - 05:45:29 PDT)
- monica.imtech.res.in (Wed Jun 23 2010 - 02:16:48 PDT)
[AMBER] DNA analysis
- case (Thu Jun 10 2010 - 18:08:57 PDT)
- Robert Elder (Thu Jun 10 2010 - 08:13:48 PDT)
- ros (Thu Jun 10 2010 - 06:25:01 PDT)
[AMBER] entropy calculation failed again!
- case (Sat Jun 05 2010 - 05:03:43 PDT)
- Rilei Yu (Fri Jun 04 2010 - 21:30:06 PDT)
- Dwight McGee (Fri Jun 04 2010 - 20:02:59 PDT)
- Bill Miller III (Fri Jun 04 2010 - 20:02:37 PDT)
- Rilei Yu (Fri Jun 04 2010 - 19:44:09 PDT)
- Dwight McGee (Fri Jun 04 2010 - 19:04:18 PDT)
- Bill Miller III (Fri Jun 04 2010 - 18:35:20 PDT)
- Dwight McGee (Fri Jun 04 2010 - 18:32:34 PDT)
- Rilei Yu (Fri Jun 04 2010 - 18:28:10 PDT)
[AMBER] Entropy calculation using nmode in mm_pbsa.pl
- Sushil Mishra (Sun Jun 06 2010 - 05:22:26 PDT)
[AMBER] Entropy for my system works now
- Rilei Yu (Sat Jun 05 2010 - 19:15:58 PDT)
[AMBER] error - binding_energy.mmpbsa run
- Bill Miller III (Thu Jun 03 2010 - 04:34:13 PDT)
- Andrew Voronkov (Thu Jun 03 2010 - 03:33:21 PDT)
- Jason Swails (Wed Jun 02 2010 - 06:20:52 PDT)
- Andrew Voronkov (Wed Jun 02 2010 - 06:15:56 PDT)
[AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2
- Jason Swails (Thu Jun 24 2010 - 09:50:38 PDT)
- Catein Catherine (Thu Jun 24 2010 - 09:44:31 PDT)
- Jason Swails (Thu Jun 24 2010 - 07:02:01 PDT)
- Catein Catherine (Thu Jun 24 2010 - 06:57:43 PDT)
[AMBER] Error in estrogen-raloxifene tutorial
- Jason Swails (Tue Jun 01 2010 - 06:41:22 PDT)
- vaibhav dixit (Tue Jun 01 2010 - 02:34:21 PDT)
[AMBER] Error installing AMBER 10 on ubuntu
- case (Mon Jun 07 2010 - 07:20:00 PDT)
- Catein Catherine (Mon Jun 07 2010 - 07:04:45 PDT)
- case (Mon Jun 07 2010 - 05:22:16 PDT)
- Catein Catherine (Mon Jun 07 2010 - 01:58:13 PDT)
- Catein Catherine (Mon Jun 07 2010 - 01:43:31 PDT)
[AMBER] Error on running ptraj
- Daniel Roe (Tue Jun 08 2010 - 07:46:10 PDT)
- case (Tue Jun 08 2010 - 05:02:42 PDT)
- tianyuan meng (Tue Jun 08 2010 - 00:45:07 PDT)
[AMBER] Error while compiling AT1.4 on OS X
- Gustaf Olsson (Thu Jun 10 2010 - 13:18:48 PDT)
- Bill Ross (Thu Jun 10 2010 - 09:44:11 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 05:16:47 PDT)
- Gustaf Olsson (Thu Jun 10 2010 - 05:07:29 PDT)
- case (Thu Jun 10 2010 - 04:58:34 PDT)
- Gustaf Olsson (Wed Jun 09 2010 - 23:54:39 PDT)
[AMBER] error: mask from topology files!
- Bill Miller III (Tue Jun 01 2010 - 07:53:09 PDT)
- vaibhav dixit (Tue Jun 01 2010 - 07:46:52 PDT)
[AMBER] Error: No potential terms in sander output!
- vaibhav dixit (Wed Jun 02 2010 - 03:37:15 PDT)
[AMBER] Errors in installing amber10 in cygwin (winxp)
- case (Mon Jun 28 2010 - 18:32:22 PDT)
- Yan Gao (Mon Jun 28 2010 - 15:53:56 PDT)
[AMBER] force field parameter and resp charge calculation
- FyD (Wed Jun 30 2010 - 07:58:33 PDT)
- colvin (Wed Jun 30 2010 - 07:13:43 PDT)
- FyD (Wed Jun 30 2010 - 02:27:02 PDT)
- colvin (Wed Jun 30 2010 - 01:45:14 PDT)
- FyD (Wed Jun 30 2010 - 00:15:50 PDT)
- FyD (Tue Jun 29 2010 - 23:57:41 PDT)
- colvin (Tue Jun 29 2010 - 23:51:58 PDT)
- xueping chin (Tue Jun 29 2010 - 23:36:46 PDT)
- FyD (Tue Jun 29 2010 - 23:21:14 PDT)
- FyD (Tue Jun 29 2010 - 09:27:08 PDT)
- colvin (Tue Jun 29 2010 - 04:03:30 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit 9, file
- Bill Ross (Tue Jun 15 2010 - 09:39:50 PDT)
- Jason Swails (Mon Jun 14 2010 - 22:29:11 PDT)
- Homa Azizian (Mon Jun 14 2010 - 22:03:19 PDT)
[AMBER] Fourier terms
- Hector A. Baldoni (Sat Jun 05 2010 - 15:04:32 PDT)
[AMBER] frcdump for CHARMM
- Ross Walker (Wed Jun 16 2010 - 02:44:26 PDT)
- Mag. Thomas Taylor (Wed Jun 16 2010 - 02:08:00 PDT)
[AMBER] Free Energy profile
- Anna Reymer (Mon Jun 14 2010 - 02:47:57 PDT)
- steinbrt.rci.rutgers.edu (Thu Jun 10 2010 - 00:23:29 PDT)
- Lars Skjærven (Wed Jun 09 2010 - 15:42:25 PDT)
- steinbrt.rci.rutgers.edu (Wed Jun 09 2010 - 00:16:26 PDT)
- Lars Skjærven (Tue Jun 08 2010 - 12:47:49 PDT)
[AMBER] Fwd: Fwd: how to allign the protein with average pdb
- REENU KHATTRI (Tue Jun 29 2010 - 05:32:26 PDT)
[AMBER] Fwd: high bidning energy MMPBSA
- kamlesh sahu (Wed Jun 16 2010 - 18:51:11 PDT)
[AMBER] Fwd: how to allign the protein with average pdb
- Jason Swails (Mon Jun 28 2010 - 17:04:53 PDT)
- REENU KHATTRI (Mon Jun 28 2010 - 09:09:33 PDT)
[AMBER] Fwd: MMPBSA problem binding energy calculation
- Sushil Mishra (Mon Jun 07 2010 - 23:02:30 PDT)
- Bill Ross (Mon Jun 07 2010 - 18:26:14 PDT)
- kamlesh sahu (Mon Jun 07 2010 - 18:08:07 PDT)
[AMBER] GAFF 1.4
- Masahiro HIGASHI (Tue Jun 08 2010 - 00:20:53 PDT)
[AMBER] gb working but not pb & gives No potential terms in sander output! error
- vaibhav dixit (Fri Jun 04 2010 - 22:25:43 PDT)
[AMBER] gcc44 compiler
- Steve Seibold (Tue Jun 08 2010 - 07:29:04 PDT)
- Lachele Foley (Lists) (Tue Jun 08 2010 - 07:04:27 PDT)
- Steve Seibold (Tue Jun 08 2010 - 05:41:18 PDT)
- case (Tue Jun 08 2010 - 05:16:44 PDT)
- Steve Seibold (Tue Jun 08 2010 - 05:08:01 PDT)
[AMBER] graphical analysis of H-bond
- Homa Azizian (Fri Jun 18 2010 - 23:12:13 PDT)
[AMBER] high bidning energy MMPBSA
- kamlesh sahu (Wed Jun 16 2010 - 19:38:58 PDT)
- Bill Miller III (Wed Jun 16 2010 - 19:22:06 PDT)
- Jason Swails (Wed Jun 16 2010 - 19:21:42 PDT)
- kamlesh sahu (Wed Jun 16 2010 - 19:13:22 PDT)
- kamlesh sahu (Wed Jun 16 2010 - 18:56:25 PDT)
- Bill Miller III (Wed Jun 16 2010 - 18:49:05 PDT)
- kamlesh sahu (Wed Jun 16 2010 - 18:45:55 PDT)
[AMBER] how can i run min.in heat.in density.in equil.in as one sander job?
- Ross Walker (Wed Jun 16 2010 - 02:49:41 PDT)
- Gustavo Seabra (Wed Jun 16 2010 - 02:26:20 PDT)
- vaibhav dixit (Wed Jun 16 2010 - 01:57:00 PDT)
- Gustavo Seabra (Tue Jun 15 2010 - 04:00:16 PDT)
- vaibhav dixit (Tue Jun 15 2010 - 03:15:58 PDT)
[AMBER] how to allign the protein with average pdb
- Jason Swails (Mon Jun 28 2010 - 04:35:50 PDT)
- REENU KHATTRI (Sun Jun 27 2010 - 23:50:46 PDT)
[AMBER] How to build a TT dimer
- M. L. Dodson (Thu Jun 24 2010 - 07:11:06 PDT)
- Shi Choong (Wed Jun 23 2010 - 19:40:55 PDT)
[AMBER] how to cut phosphodiester bond
- Sangita Kachhap (Wed Jun 09 2010 - 02:13:49 PDT)
- case (Tue Jun 08 2010 - 11:33:12 PDT)
- Sangita Kachhap (Tue Jun 08 2010 - 09:30:04 PDT)
[AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation
- Sangita Kachhap (Thu Jun 10 2010 - 08:09:28 PDT)
- Jason Swails (Wed Jun 09 2010 - 10:31:41 PDT)
- Sangita Kachhap (Wed Jun 09 2010 - 10:06:38 PDT)
- Jason Swails (Wed Jun 09 2010 - 08:46:54 PDT)
- Sangita Kachhap (Wed Jun 09 2010 - 08:13:29 PDT)
[AMBER] How to insert a dimer into the pdb file
- Shi Choong (Mon Jun 28 2010 - 16:43:29 PDT)
[AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help.
- Catein Catherine (Tue Jun 08 2010 - 07:27:43 PDT)
- Jason Swails (Tue Jun 08 2010 - 04:23:56 PDT)
- Catein Catherine (Tue Jun 08 2010 - 00:35:20 PDT)
[AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ?
- Dongshan Wei (Tue Jun 22 2010 - 17:32:24 PDT)
- Gustavo Seabra (Tue Jun 22 2010 - 13:16:02 PDT)
- Jason Swails (Tue Jun 22 2010 - 10:09:24 PDT)
- Jason Swails (Tue Jun 22 2010 - 10:08:11 PDT)
- Dongshan Wei (Tue Jun 22 2010 - 09:16:16 PDT)
[AMBER] How to read the motion of PCA?
- Hannes Loeffler (Wed Jun 23 2010 - 02:19:34 PDT)
- Catein Catherine (Tue Jun 22 2010 - 08:16:36 PDT)
[AMBER] How to restart the remd simulation following the remd tutorial?
- Dongshan Wei (Wed Jun 09 2010 - 23:02:11 PDT)
- Daniel Roe (Fri Jun 04 2010 - 05:01:59 PDT)
- Dongshan Wei (Thu Jun 03 2010 - 13:29:43 PDT)
[AMBER] how to use a distant-dependent dielectric constant of "epsilon = 4r"
- case (Sat Jun 19 2010 - 06:36:56 PDT)
- DeChang Li (Fri Jun 18 2010 - 20:54:48 PDT)
[AMBER] improper for NH2 group in guanosine
- Dmitry Nilov (Wed Jun 23 2010 - 02:12:10 PDT)
- case (Tue Jun 22 2010 - 16:05:01 PDT)
- Dmitry Nilov (Tue Jun 22 2010 - 03:11:51 PDT)
[AMBER] info on ff10?
- case (Thu Jun 10 2010 - 18:09:19 PDT)
- Sidney Elmer (Thu Jun 10 2010 - 09:53:20 PDT)
[AMBER] Installing amber10 on ubunta, some hints please.
- David Dubins (Wed Jun 09 2010 - 12:58:17 PDT)
- Ye MEI (Wed Jun 09 2010 - 09:15:27 PDT)
- Paul S. Nerenberg (Wed Jun 09 2010 - 08:55:22 PDT)
- Jason Swails (Wed Jun 09 2010 - 08:49:43 PDT)
- Catein Catherine (Wed Jun 09 2010 - 08:24:39 PDT)
[AMBER] inter- intra energy
- balaji nagarajan (Mon Jun 28 2010 - 01:01:02 PDT)
[AMBER] inter_intra - energy
- balaji nagarajan (Thu Jun 24 2010 - 05:35:55 PDT)
[AMBER] intra-inter energy
- balaji nagarajan (Thu Jun 24 2010 - 09:05:38 PDT)
[AMBER] Invitation to connect on LinkedIn
- hyma srinivas (Fri Jun 11 2010 - 08:58:51 PDT)
[AMBER] Is AmberTools 1.4 compatible with AMBER10?
- Jason Swails (Sun Jun 20 2010 - 09:51:53 PDT)
- Catein Catherine (Sun Jun 20 2010 - 09:14:04 PDT)
[AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4.
- case (Tue Jun 22 2010 - 15:30:00 PDT)
- Catein Catherine (Tue Jun 22 2010 - 09:40:47 PDT)
- case (Mon Jun 21 2010 - 06:51:50 PDT)
- Catein Catherine (Sun Jun 20 2010 - 23:32:52 PDT)
[AMBER] is it possible to improve amino acids dihedral angles using Amber?
- Andrew Voronkov (Tue Jun 08 2010 - 05:21:58 PDT)
[AMBER] Is it possible to plot RMSd VS residue number for a protein?
- M. Reza Ganjalikhany (Tue Jun 01 2010 - 09:27:20 PDT)
- Homa Azizian (Mon May 31 2010 - 16:58:53 PDT)
[AMBER] Is it possible to revome water molecules during simulation?
- Bill Ross (Wed Jun 02 2010 - 14:26:43 PDT)
- Hoshin Kim (Thu Jun 03 2010 - 00:59:27 PDT)
- Jason Swails (Wed Jun 02 2010 - 12:57:59 PDT)
- Bill Ross (Wed Jun 02 2010 - 12:53:48 PDT)
- Hoshin Kim (Wed Jun 02 2010 - 23:40:11 PDT)
[AMBER] is there any command to superimpose/align a protein in amber8 to get less RMSD residue wise
- REENU KHATTRI (Sun Jun 27 2010 - 18:40:24 PDT)
[AMBER] Is xleap part of Ambertool or Amber10?
- Jason Swails (Sun Jun 20 2010 - 09:45:49 PDT)
- Catein Catherine (Sun Jun 20 2010 - 09:08:45 PDT)
[AMBER] Kinetic energy after heating is zero
- Jason Swails (Thu Jun 24 2010 - 07:28:30 PDT)
- case (Thu Jun 24 2010 - 07:22:57 PDT)
- Jason Swails (Thu Jun 24 2010 - 05:30:00 PDT)
- Ashutosh Shandilya (Thu Jun 24 2010 - 03:28:14 PDT)
[AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
- Yu Chen (Wed Jun 30 2010 - 20:19:27 PDT)
[AMBER] Lennard Jones calculation
- case (Sat Jun 19 2010 - 07:23:55 PDT)
- Antonios Samiotakis (Sat Jun 12 2010 - 08:15:13 PDT)
- Antonios Samiotakis (Fri Jun 11 2010 - 18:52:50 PDT)
- case (Fri Jun 11 2010 - 17:48:59 PDT)
- Antonios Samiotakis (Fri Jun 11 2010 - 16:01:24 PDT)
[AMBER] Lmod, NAB error
- Cristina Sisu (Thu Jun 03 2010 - 09:51:12 PDT)
- Bill Ross (Thu Jun 03 2010 - 09:49:01 PDT)
- Cristina Sisu (Thu Jun 03 2010 - 09:23:16 PDT)
- Jason Swails (Thu Jun 03 2010 - 09:17:50 PDT)
- Cristina Sisu (Thu Jun 03 2010 - 09:04:50 PDT)
[AMBER] make test.parallel
- Steve Seibold (Wed Jun 30 2010 - 05:00:43 PDT)
- case (Tue Jun 29 2010 - 07:23:50 PDT)
- Steve Seibold (Tue Jun 29 2010 - 07:14:34 PDT)
[AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file
- case (Tue Jun 15 2010 - 11:19:27 PDT)
- Bill Ross (Tue Jun 15 2010 - 10:36:18 PDT)
- Ehsan Habibi (Tue Jun 15 2010 - 10:23:45 PDT)
[AMBER] mm_pbsa error on ambertools 1.4 amber11
- Jason Swails (Fri Jun 04 2010 - 06:01:22 PDT)
- ANDREA.MEZGEZ.dicamp.units.it (Fri Jun 04 2010 - 03:59:55 PDT)
- Jason Swails (Thu Jun 03 2010 - 09:03:52 PDT)
- ANDREA.MEZGEZ.dicamp.units.it (Thu Jun 03 2010 - 08:39:30 PDT)
[AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures
- Jason Swails (Tue Jun 01 2010 - 14:33:16 PDT)
- Dwight McGee (Tue Jun 01 2010 - 13:25:31 PDT)
- Dwight McGee (Tue Jun 01 2010 - 13:21:19 PDT)
- Yuqin Cai (Tue Jun 01 2010 - 12:55:42 PDT)
[AMBER] mme and mme2 produce different energies
- case (Tue Jun 29 2010 - 07:59:52 PDT)
- Kevin Wiehe (Fri Jun 25 2010 - 11:36:50 PDT)
[AMBER] mmgbsa tricky output
- Amor San Juan (Wed Jun 30 2010 - 02:19:53 PDT)
[AMBER] mmpbsa
- RANAJIT SHINDE (Fri Jun 18 2010 - 22:28:19 PDT)
- Jason Swails (Fri Jun 18 2010 - 05:59:51 PDT)
- RANAJIT SHINDE (Fri Jun 18 2010 - 04:30:25 PDT)
[AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error
- Ray Luo (Wed Jun 16 2010 - 11:08:35 PDT)
- Cristina Sisu (Wed Jun 16 2010 - 07:58:52 PDT)
[AMBER] MMPBSA binding calculations
- shenna shearin (Sat Jun 12 2010 - 16:02:02 PDT)
- Bill Miller III (Sat Jun 12 2010 - 15:06:20 PDT)
- shenna shearin (Sat Jun 12 2010 - 14:49:52 PDT)
- shenna shearin (Sat Jun 12 2010 - 14:13:08 PDT)
- Jason Swails (Sat Jun 12 2010 - 13:38:50 PDT)
- shenna shearin (Sat Jun 12 2010 - 13:13:13 PDT)
- shenna shearin (Sat Jun 12 2010 - 13:10:40 PDT)
- Jason Swails (Wed Jun 09 2010 - 13:52:26 PDT)
- shenna shearin (Wed Jun 09 2010 - 13:44:34 PDT)
[AMBER] mmpbsa error of missing SVIB, when nm=0
- Catein Catherine (Sun Jun 27 2010 - 08:56:07 PDT)
[AMBER] mmpbsa installation
- Jason Swails (Sun Jun 27 2010 - 07:55:59 PDT)
- rameshwar prajapati (Sun Jun 27 2010 - 04:53:48 PDT)
[AMBER] MMPBSA problem binding energy calculation
- Bill Miller III (Tue Jun 01 2010 - 18:35:03 PDT)
- kamlesh sahu (Tue Jun 01 2010 - 18:24:12 PDT)
- kamlesh sahu (Tue Jun 01 2010 - 18:21:41 PDT)
- Bill Miller III (Tue Jun 01 2010 - 18:18:39 PDT)
- kamlesh sahu (Tue Jun 01 2010 - 18:05:10 PDT)
- Jason Swails (Tue Jun 01 2010 - 17:43:14 PDT)
- kamlesh sahu (Tue Jun 01 2010 - 17:35:25 PDT)
- Dwight McGee (Tue Jun 01 2010 - 06:55:15 PDT)
- Bill Miller III (Tue Jun 01 2010 - 04:02:09 PDT)
- kamlesh sahu (Tue Jun 01 2010 - 02:42:35 PDT)
[AMBER] MMPBSA warning
- Jason Swails (Fri Jun 18 2010 - 06:09:18 PDT)
- George Tzotzos (Fri Jun 18 2010 - 03:54:54 PDT)
[AMBER] MMPBSA.py calculations...bad atom type
- RANAJIT SHINDE (Sun Jun 06 2010 - 21:49:37 PDT)
- Jason Swails (Sat Jun 05 2010 - 06:40:27 PDT)
- Bill Miller III (Sat Jun 05 2010 - 04:04:53 PDT)
- RANAJIT SHINDE (Fri Jun 04 2010 - 22:45:16 PDT)
- RANAJIT SHINDE (Fri Jun 04 2010 - 22:44:23 PDT)
[AMBER] MMPBSA.py error
- Jason Swails (Mon Jun 14 2010 - 23:52:06 PDT)
- George Tzotzos (Mon Jun 14 2010 - 23:42:56 PDT)
- Jason Swails (Mon Jun 14 2010 - 10:32:12 PDT)
- Dwight McGee (Mon Jun 14 2010 - 09:42:44 PDT)
- George Tzotzos (Mon Jun 14 2010 - 09:10:06 PDT)
[AMBER] MMPBSA.py install problem
- Bill Miller III (Wed Jun 23 2010 - 09:55:51 PDT)
- Oliver Grant (Wed Jun 23 2010 - 09:48:39 PDT)
[AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined
- Jason Swails (Fri Jun 25 2010 - 07:02:07 PDT)
- Jason Swails (Fri Jun 25 2010 - 06:45:12 PDT)
- Oliver Grant (Fri Jun 25 2010 - 04:12:12 PDT)
- Oliver Grant (Fri Jun 25 2010 - 01:58:14 PDT)
[AMBER] MMPBSA.py nmode maxcyc problem
- Jason Swails (Thu Jun 10 2010 - 21:19:47 PDT)
- Jason Swails (Thu Jun 10 2010 - 17:01:55 PDT)
- Jason Swails (Thu Jun 10 2010 - 16:24:16 PDT)
- Niel Henriksen (Thu Jun 10 2010 - 07:51:08 PDT)
[AMBER] MMPBSA.py update install problem
- Rilei Yu (Wed Jun 02 2010 - 17:37:44 PDT)
- Jason Swails (Wed Jun 02 2010 - 06:14:24 PDT)
- Bill Miller III (Wed Jun 02 2010 - 04:30:04 PDT)
- Rilei Yu (Wed Jun 02 2010 - 01:53:16 PDT)
- Dwight McGee (Wed Jun 02 2010 - 01:14:54 PDT)
- Rilei Yu (Tue Jun 01 2010 - 23:18:26 PDT)
- Rilei Yu (Mon May 31 2010 - 16:59:09 PDT)
[AMBER] Modifying the bond energy calculation - adding a cubic bond term (hacking the sander code)
- Eric Shamay (Fri Jun 11 2010 - 17:13:56 PDT)
[AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f
- Bill Ross (Tue Jun 08 2010 - 11:07:19 PDT)
- case (Tue Jun 08 2010 - 07:38:26 PDT)
- Ehsan Habibi (Tue Jun 08 2010 - 06:49:06 PDT)
[AMBER] nmr refinment problem
- shirishkumar pawar (Tue Jun 15 2010 - 22:05:33 PDT)
- case (Tue Jun 15 2010 - 06:21:12 PDT)
- shirishkumar pawar (Tue Jun 15 2010 - 03:16:12 PDT)
[AMBER] P450 ff from Rydberg et al.
- Adrian Roitberg (Tue Jun 08 2010 - 11:29:39 PDT)
- case (Tue Jun 08 2010 - 11:25:47 PDT)
- Renata KWIECIEN (Tue Jun 08 2010 - 07:50:16 PDT)
[AMBER] parallel compiling failure of Amber 11
- Bill Ross (Tue Jun 22 2010 - 22:10:40 PDT)
- case (Tue Jun 22 2010 - 21:33:52 PDT)
- Jason Swails (Tue Jun 22 2010 - 18:24:26 PDT)
- Yubo Fan (Tue Jun 22 2010 - 18:05:40 PDT)
- Yubo Fan (Tue Jun 22 2010 - 10:49:25 PDT)
- Jason Swails (Tue Jun 22 2010 - 09:58:16 PDT)
- Yubo Fan (Tue Jun 22 2010 - 09:13:46 PDT)
- Jason Swails (Tue Jun 22 2010 - 08:12:26 PDT)
- Yubo Fan (Tue Jun 22 2010 - 07:56:54 PDT)
- Gustavo Seabra (Tue Jun 22 2010 - 01:54:42 PDT)
- Yubo Fan (Mon Jun 21 2010 - 17:15:43 PDT)
- Jason Swails (Mon Jun 21 2010 - 13:29:43 PDT)
- Yubo Fan (Mon Jun 21 2010 - 13:25:10 PDT)
- case (Mon Jun 14 2010 - 09:34:13 PDT)
- Ross Walker (Mon Jun 14 2010 - 09:25:51 PDT)
- Yubo Fan (Mon Jun 14 2010 - 08:58:52 PDT)
[AMBER] Parallel installation of AMBER 11 on MacOSX
- George Tzotzos (Wed Jun 02 2010 - 10:48:26 PDT)
- Bill Ross (Wed Jun 02 2010 - 10:43:52 PDT)
- Jason Swails (Wed Jun 02 2010 - 10:42:34 PDT)
- George Tzotzos (Wed Jun 02 2010 - 10:37:56 PDT)
- Bill Ross (Wed Jun 02 2010 - 10:35:27 PDT)
- George Tzotzos (Wed Jun 02 2010 - 10:32:25 PDT)
- Jason Swails (Wed Jun 02 2010 - 10:28:55 PDT)
- George Tzotzos (Wed Jun 02 2010 - 10:14:14 PDT)
[AMBER] Parameters for Nickel
- Jason Swails (Thu Jun 17 2010 - 08:27:08 PDT)
- Dian Jiao (Thu Jun 17 2010 - 08:14:41 PDT)
[AMBER] PBC in umbrella sampling
- case (Fri Jun 18 2010 - 15:15:41 PDT)
- dhacademic (Fri Jun 18 2010 - 07:45:14 PDT)
[AMBER] peptide leaving box, image command not working
- Niel Henriksen (Tue Jun 15 2010 - 06:58:21 PDT)
- Omair A. Khan (Mon Jun 14 2010 - 10:51:08 PDT)
[AMBER] periodic images of truc. octahedron in vmd
- Paul Brandt (Mon Jun 21 2010 - 16:06:33 PDT)
- Paul Brandt (Mon Jun 21 2010 - 14:54:09 PDT)
- Bill Ross (Mon Jun 21 2010 - 14:10:37 PDT)
- Paul Brandt (Mon Jun 21 2010 - 13:52:06 PDT)
[AMBER] pH based conformational study
- Sangita Kachhap (Wed Jun 16 2010 - 06:34:01 PDT)
- Jason Swails (Wed Jun 16 2010 - 06:19:32 PDT)
- Sangita Kachhap (Tue Jun 15 2010 - 23:55:18 PDT)
[AMBER] picky nab compiler: is this really necessary?
- case (Wed Jun 16 2010 - 17:01:54 PDT)
- M. L. Dodson (Wed Jun 16 2010 - 10:54:37 PDT)
- case (Wed Jun 16 2010 - 09:57:52 PDT)
- M. L. Dodson (Tue Jun 15 2010 - 12:32:26 PDT)
[AMBER] plz help!!!
- Nicee (Tue Jun 15 2010 - 04:16:09 PDT)
- monica.imtech.res.in (Tue Jun 15 2010 - 03:20:52 PDT)
[AMBER] pmemd.cuda - ewald error estimate?
- Ross Walker (Tue Jun 01 2010 - 16:23:25 PDT)
- Paul Brandt (Tue Jun 01 2010 - 15:43:01 PDT)
[AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050?
- Ross Walker (Mon Jun 14 2010 - 15:08:20 PDT)
- Scott Le Grand (Mon Jun 14 2010 - 14:02:23 PDT)
- Ross Walker (Mon Jun 14 2010 - 13:34:47 PDT)
- Ross Walker (Mon Jun 14 2010 - 13:30:39 PDT)
- michael bane (Mon Jun 14 2010 - 12:35:36 PDT)
- Sasha Buzko (Mon Jun 14 2010 - 12:09:38 PDT)
- Sasha Buzko (Fri Jun 11 2010 - 10:21:33 PDT)
- Scott Le Grand (Fri Jun 11 2010 - 09:41:35 PDT)
- Ross Walker (Fri Jun 11 2010 - 07:50:26 PDT)
- Sasha Buzko (Thu Jun 10 2010 - 09:21:18 PDT)
[AMBER] pmemd.cuda error: launch timeout..
- Sasha Buzko (Tue Jun 08 2010 - 17:55:23 PDT)
- Ross Walker (Tue Jun 08 2010 - 14:04:42 PDT)
- Sasha Buzko (Tue Jun 08 2010 - 13:51:42 PDT)
- Scott Le Grand (Tue Jun 08 2010 - 13:24:01 PDT)
- Scott Le Grand (Tue Jun 08 2010 - 11:23:32 PDT)
- Sasha Buzko (Tue Jun 08 2010 - 10:55:18 PDT)
- Scott Le Grand (Tue Jun 08 2010 - 10:25:44 PDT)
- Sasha Buzko (Tue Jun 08 2010 - 10:17:47 PDT)
- Scott Le Grand (Tue Jun 08 2010 - 10:15:37 PDT)
- Sasha Buzko (Tue Jun 08 2010 - 09:54:23 PDT)
[AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE
- case (Sun Jun 27 2010 - 18:53:59 PDT)
- Levi Pierce (Fri Jun 25 2010 - 19:22:12 PDT)
- Scott Le Grand (Fri Jun 25 2010 - 16:53:49 PDT)
- Levi Pierce (Thu Jun 10 2010 - 14:24:21 PDT)
- Sasha Buzko (Thu Jun 10 2010 - 14:01:06 PDT)
- Levi Pierce (Thu Jun 10 2010 - 14:01:29 PDT)
[AMBER] Polak Ribiere
- Bill Ross (Tue Jun 01 2010 - 10:44:33 PDT)
- Mengjuei Hsieh (Tue Jun 01 2010 - 02:31:37 PDT)
- Jagdeesh C (Tue Jun 01 2010 - 01:21:27 PDT)
[AMBER] Polarizability and induced dipoles
- Ross Walker (Tue Jun 15 2010 - 05:00:48 PDT)
- Mag. Thomas Taylor (Tue Jun 15 2010 - 03:47:47 PDT)
- Ross Walker (Tue Jun 15 2010 - 02:31:16 PDT)
- Mag. Thomas Taylor (Tue Jun 15 2010 - 01:53:33 PDT)
[AMBER] Postdoc position available at SDSC.
- Ross Walker (Sat Jun 12 2010 - 07:37:17 PDT)
[AMBER] pre-processing of trajectories
- case (Sun Jun 27 2010 - 18:39:07 PDT)
- monica.imtech.res.in (Sat Jun 26 2010 - 21:20:06 PDT)
- Hannes Loeffler (Fri Jun 25 2010 - 06:52:51 PDT)
- monica.imtech.res.in (Fri Jun 25 2010 - 00:37:30 PDT)
- Hannes Loeffler (Thu Jun 24 2010 - 03:04:25 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Jun 24 2010 - 00:20:46 PDT)
- hannes.loeffler.stfc.ac.uk (Wed Jun 23 2010 - 12:41:24 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Jun 23 2010 - 11:21:20 PDT)
- Hannes Loeffler (Wed Jun 23 2010 - 07:33:25 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Jun 23 2010 - 07:02:08 PDT)
[AMBER] Prepare the mutants file for ala scanning
- Gustavo Seabra (Tue Jun 01 2010 - 02:59:43 PDT)
- Rilei Yu (Mon May 31 2010 - 17:11:07 PDT)
[AMBER] Problem on B-factor Calculation
- tianyuan meng (Mon May 31 2010 - 19:06:52 PDT)
[AMBER] Problem with pmed installation: Amber 10
- Ross Walker (Mon Jun 21 2010 - 07:40:37 PDT)
- Jason Swails (Mon Jun 21 2010 - 07:18:19 PDT)
- Devlina Chakravarty (Mon Jun 21 2010 - 03:53:15 PDT)
[AMBER] problem with the energetics of the system
- case (Sat Jun 19 2010 - 13:47:55 PDT)
- Bill Ross (Sat Jun 19 2010 - 09:35:26 PDT)
- Jason Swails (Sat Jun 19 2010 - 08:53:57 PDT)
- Homa Azizian (Fri Jun 18 2010 - 23:04:51 PDT)
- Bill Ross (Fri Jun 18 2010 - 09:47:00 PDT)
- Jason Swails (Thu Jun 17 2010 - 18:26:55 PDT)
- Homa Azizian (Thu Jun 17 2010 - 18:02:09 PDT)
- Bill Ross (Wed Jun 16 2010 - 22:38:15 PDT)
- Bill Ross (Wed Jun 16 2010 - 22:33:59 PDT)
- Homa Azizian (Wed Jun 16 2010 - 21:37:56 PDT)
- Gustavo Seabra (Wed Jun 16 2010 - 20:09:48 PDT)
- Homa Azizian (Wed Jun 16 2010 - 20:05:48 PDT)
[AMBER] problems with NAB and SHIFTS
- case (Wed Jun 16 2010 - 06:37:43 PDT)
- Jason Swails (Wed Jun 16 2010 - 06:15:51 PDT)
- Jakob Toudahl Nielsen (Wed Jun 16 2010 - 00:56:43 PDT)
- case (Tue Jun 15 2010 - 12:19:24 PDT)
- Jason Swails (Tue Jun 15 2010 - 12:12:58 PDT)
- Eric Shamay (Tue Jun 15 2010 - 11:41:35 PDT)
- Bill Ross (Tue Jun 15 2010 - 11:23:18 PDT)
- Jakob Toudahl Nielsen (Tue Jun 15 2010 - 11:16:20 PDT)
- case (Tue Jun 15 2010 - 07:09:46 PDT)
- Jakob Toudahl Nielsen (Tue Jun 15 2010 - 06:43:59 PDT)
- case (Tue Jun 15 2010 - 06:17:28 PDT)
- Jakob Toudahl Nielsen (Tue Jun 15 2010 - 06:15:22 PDT)
- Jason Swails (Tue Jun 15 2010 - 05:41:12 PDT)
- Jakob Toudahl Nielsen (Tue Jun 15 2010 - 04:19:23 PDT)
[AMBER] protonation states of histidines - is there any way to treat it accurately.
- Jason Swails (Fri Jun 11 2010 - 10:18:33 PDT)
- Andrew Voronkov (Fri Jun 11 2010 - 09:01:23 PDT)
[AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
- Daniel Roe (Wed Jun 30 2010 - 06:46:56 PDT)
- Paul S. Nerenberg (Mon Jun 28 2010 - 14:35:01 PDT)
- Paul S. Nerenberg (Fri Jun 25 2010 - 16:55:26 PDT)
[AMBER] Ptraj error - ERROR in safe_malloc
- Siddharth Rastogi (Wed Jun 23 2010 - 13:24:31 PDT)
- case (Wed Jun 23 2010 - 11:01:07 PDT)
- Siddharth Rastogi (Wed Jun 23 2010 - 09:45:19 PDT)
[AMBER] Ptraj problems
- Samuel Genheden (Mon Jun 14 2010 - 03:56:46 PDT)
- Thomas Cheatham (Mon Jun 14 2010 - 02:46:47 PDT)
- Samuel Genheden (Mon Jun 14 2010 - 01:47:25 PDT)
[AMBER] ptraj rms error
- case (Thu Jun 17 2010 - 06:52:11 PDT)
- Beale, John (Thu Jun 17 2010 - 04:30:58 PDT)
- Beale, John (Thu Jun 17 2010 - 03:38:00 PDT)
- Daniel Roe (Wed Jun 16 2010 - 12:53:32 PDT)
- Beale, John (Wed Jun 16 2010 - 08:30:48 PDT)
[AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj
- Daniel Roe (Wed Jun 30 2010 - 07:16:14 PDT)
- M. Reza Ganjalikhany (Sun Jun 27 2010 - 14:10:13 PDT)
- Jason Swails (Sun Jun 27 2010 - 08:44:21 PDT)
- M. Reza Ganjalikhany (Sun Jun 27 2010 - 04:36:21 PDT)
- M. Reza Ganjalikhany (Sun Jun 27 2010 - 02:52:28 PDT)
[AMBER] PTRAJ: setting up donor and acceptor masks for ligands for hbond analysis
- George Tzotzos (Wed Jun 09 2010 - 06:40:31 PDT)
[AMBER] Query- Heating after Equilibration
- Jagdeesh C (Wed Jun 23 2010 - 04:28:15 PDT)
- Bill Ross (Tue Jun 22 2010 - 22:12:48 PDT)
- case (Tue Jun 22 2010 - 21:43:19 PDT)
- Jagdeesh C (Tue Jun 22 2010 - 19:59:54 PDT)
- Jason Swails (Sun Jun 20 2010 - 08:47:04 PDT)
- case (Sun Jun 20 2010 - 08:32:40 PDT)
- Jagdeesh C (Sat Jun 19 2010 - 23:16:19 PDT)
[AMBER] question about radial distribution function
- Ganesh Kamath (Wed Jun 09 2010 - 07:51:24 PDT)
[AMBER] Questions with input file in constant pH MD
- Bill Miller III (Wed Jun 30 2010 - 06:50:44 PDT)
- nicholus bhattacharjee (Tue Jun 29 2010 - 22:37:32 PDT)
[AMBER] radial distribution function
- Ganesh Kamath (Fri Jun 18 2010 - 13:39:33 PDT)
[AMBER] radial distribution function in amber
- Ganesh Kamath (Tue Jun 22 2010 - 10:10:24 PDT)
[AMBER] random number generators visible from nab: choice necessary?
- case (Fri Jun 11 2010 - 18:39:25 PDT)
- M. L. Dodson (Tue Jun 08 2010 - 09:16:46 PDT)
- M. L. Dodson (Mon Jun 07 2010 - 15:47:17 PDT)
- case (Mon Jun 07 2010 - 15:10:47 PDT)
- M. L. Dodson (Mon Jun 07 2010 - 13:22:43 PDT)
[AMBER] Rdf and density
- John S (Tue Jun 15 2010 - 22:55:37 PDT)
[AMBER] reduce
- case (Fri Jun 11 2010 - 06:15:51 PDT)
- George Tzotzos (Fri Jun 11 2010 - 02:03:02 PDT)
[AMBER] reducing the fram for analysing
- Jason Swails (Mon Jun 28 2010 - 04:47:00 PDT)
- Homa Azizian (Sun Jun 27 2010 - 23:40:27 PDT)
[AMBER] reg REMD
- Daniel Roe (Tue Jun 01 2010 - 10:30:05 PDT)
- Dongshan Wei (Tue Jun 01 2010 - 09:21:13 PDT)
[AMBER] regarding forcefield for rna
- Asfa Ali (Sun Jun 13 2010 - 21:57:40 PDT)
- Bill Ross (Sat Jun 12 2010 - 12:57:04 PDT)
- Asfa Ali (Fri Jun 11 2010 - 23:03:38 PDT)
- Bill Ross (Fri Jun 11 2010 - 08:14:08 PDT)
- Jiri Sponer (Fri Jun 11 2010 - 04:17:03 PDT)
- Asfa Ali (Fri Jun 11 2010 - 04:09:24 PDT)
- Jiri Sponer (Fri Jun 11 2010 - 03:42:13 PDT)
- Bill Ross (Thu Jun 10 2010 - 19:36:48 PDT)
- Jiri Sponer (Thu Jun 10 2010 - 11:30:52 PDT)
- Bill Ross (Thu Jun 10 2010 - 10:14:43 PDT)
- Jiri Sponer (Thu Jun 10 2010 - 06:59:26 PDT)
- Jiri Sponer (Thu Jun 10 2010 - 06:55:14 PDT)
- Asfa Ali (Thu Jun 10 2010 - 06:47:52 PDT)
- Jiri Sponer (Wed Jun 09 2010 - 04:45:25 PDT)
- Jiri Sponer (Wed Jun 09 2010 - 04:25:08 PDT)
- case (Wed Jun 09 2010 - 17:23:30 PDT)
- Bill Ross (Wed Jun 09 2010 - 10:12:18 PDT)
- Ilyas Yildirim (Wed Jun 09 2010 - 07:40:02 PDT)
- Asfa Ali (Wed Jun 09 2010 - 06:55:39 PDT)
- Asfa Ali (Wed Jun 09 2010 - 06:51:15 PDT)
- Jason Swails (Wed Jun 09 2010 - 06:43:26 PDT)
- InSuk Joung (Wed Jun 09 2010 - 06:21:13 PDT)
- Monika Sharma (Wed Jun 09 2010 - 06:15:11 PDT)
- Asfa Ali (Wed Jun 09 2010 - 06:04:42 PDT)
- InSuk Joung (Wed Jun 09 2010 - 04:39:57 PDT)
- Asfa Ali (Wed Jun 09 2010 - 04:35:21 PDT)
- Gustavo Seabra (Wed Jun 09 2010 - 04:18:35 PDT)
- Asfa Ali (Wed Jun 09 2010 - 04:10:19 PDT)
[AMBER] regarding mmpbsa
- Jason Swails (Wed Jun 30 2010 - 08:07:12 PDT)
- Asfa Ali (Wed Jun 30 2010 - 07:40:44 PDT)
- Jason Swails (Wed Jun 30 2010 - 07:28:06 PDT)
- Bill Miller III (Wed Jun 30 2010 - 06:10:00 PDT)
- Asfa Ali (Wed Jun 30 2010 - 03:47:49 PDT)
[AMBER] regarding ptraj
- Bill Ross (Tue Jun 29 2010 - 09:41:52 PDT)
- Gustavo Seabra (Tue Jun 29 2010 - 03:27:47 PDT)
- Asfa Ali (Mon Jun 28 2010 - 22:09:02 PDT)
[AMBER] Regarding temperature accelerated MD
- Ramya Narasimhan (Tue Jun 08 2010 - 02:50:50 PDT)
[AMBER] RESP charge of heavy metal contained complex
- FyD (Thu Jun 24 2010 - 22:25:19 PDT)
- Jia Xu (Thu Jun 24 2010 - 08:37:00 PDT)
[AMBER] RESP fit calculation
- FyD (Thu Jun 10 2010 - 21:06:32 PDT)
- Valerie Fako (Thu Jun 10 2010 - 11:07:58 PDT)
[AMBER] Restraint
- case (Thu Jun 24 2010 - 07:34:30 PDT)
- John S (Wed Jun 23 2010 - 21:10:07 PDT)
[AMBER] restraint during constant pH
- Jason Swails (Wed Jun 23 2010 - 22:05:50 PDT)
- Sangita Kachhap (Wed Jun 23 2010 - 21:52:28 PDT)
- Jason Swails (Wed Jun 23 2010 - 10:48:52 PDT)
- Sangita Kachhap (Wed Jun 23 2010 - 09:49:03 PDT)
- Jason Swails (Wed Jun 23 2010 - 07:42:06 PDT)
- Sangita Kachhap (Wed Jun 23 2010 - 07:39:35 PDT)
[AMBER] restraint in umbrella sampling
- Jason Swails (Wed Jun 02 2010 - 11:25:55 PDT)
- dhacademic (Wed Jun 02 2010 - 11:17:57 PDT)
[AMBER] rhombicity
- case (Thu Jun 17 2010 - 19:29:06 PDT)
- Peter Podbevšek (Thu Jun 17 2010 - 02:18:57 PDT)
[AMBER] RMSD calculation per reside wise not rmse/time by ptraj
- Jason Swails (Sun Jun 27 2010 - 07:52:57 PDT)
- REENU KHATTRI (Sun Jun 27 2010 - 06:55:50 PDT)
[AMBER] Segmentation fault
- case (Wed Jun 30 2010 - 09:31:54 PDT)
- Jagdeesh C (Sat Jun 26 2010 - 23:01:18 PDT)
- case (Sat Jun 26 2010 - 15:53:18 PDT)
- Jagdeesh C (Sat Jun 26 2010 - 03:06:23 PDT)
[AMBER] sietraj
- Yossa Dwi Hartono (Wed Jun 16 2010 - 22:52:47 PDT)
- Purisima, Enrico (Wed Jun 16 2010 - 07:11:10 PDT)
- Yossa Dwi Hartono (Wed Jun 16 2010 - 00:10:14 PDT)
[AMBER] similarity of quasi-harmonic modes dependent on reference conformation
- Jose Borreguero (Wed Jun 30 2010 - 05:35:24 PDT)
- Jason Swails (Tue Jun 29 2010 - 20:37:57 PDT)
- Jose Borreguero (Tue Jun 29 2010 - 19:34:52 PDT)
[AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type.
- case (Thu Jun 10 2010 - 18:08:51 PDT)
- Bill Ross (Thu Jun 10 2010 - 10:03:37 PDT)
- Bill Ross (Thu Jun 10 2010 - 09:49:50 PDT)
- Andrew Voronkov (Thu Jun 10 2010 - 06:19:02 PDT)
- Andrew Voronkov (Thu Jun 10 2010 - 05:42:56 PDT)
- Bill Ross (Wed Jun 09 2010 - 10:27:10 PDT)
- Jason Swails (Wed Jun 09 2010 - 08:53:35 PDT)
- Andrew Voronkov (Wed Jun 09 2010 - 07:17:31 PDT)
[AMBER] simulating in urea
- monica.imtech.res.in (Wed Jun 23 2010 - 22:42:12 PDT)
- monica.imtech.res.in (Wed Jun 23 2010 - 22:36:46 PDT)
- Bill Ross (Wed Jun 23 2010 - 09:53:09 PDT)
- case (Wed Jun 23 2010 - 09:11:21 PDT)
- monica.imtech.res.in (Wed Jun 23 2010 - 08:24:15 PDT)
- case (Wed Jun 23 2010 - 06:53:26 PDT)
- monica.imtech.res.in (Tue Jun 22 2010 - 23:30:11 PDT)
[AMBER] simulation of DNA-protein interaction
- Ehsan Habibi (Fri Jun 11 2010 - 02:31:55 PDT)
[AMBER] simulation of protein
- Bill Ross (Fri Jun 04 2010 - 11:43:09 PDT)
- Jason Swails (Fri Jun 04 2010 - 11:13:41 PDT)
- ashutosh shandilya (Fri Jun 04 2010 - 11:05:50 PDT)
- ashutosh shandilya (Fri Jun 04 2010 - 10:58:29 PDT)
- Bill Ross (Fri Jun 04 2010 - 10:56:06 PDT)
- ashutosh shandilya (Fri Jun 04 2010 - 10:40:06 PDT)
- Gustavo Seabra (Fri Jun 04 2010 - 10:34:54 PDT)
- Bill Ross (Fri Jun 04 2010 - 10:22:59 PDT)
- ashutosh shandilya (Fri Jun 04 2010 - 09:45:44 PDT)
- ashutosh shandilya (Fri Jun 04 2010 - 09:32:48 PDT)
[AMBER] sleap log
- case (Thu Jun 03 2010 - 13:06:33 PDT)
- Omair A. Khan (Thu Jun 03 2010 - 12:14:29 PDT)
- case (Tue Jun 01 2010 - 15:28:15 PDT)
- Omair A. Khan (Tue Jun 01 2010 - 09:10:10 PDT)
[AMBER] Solute and solvent temperatures in mden
- case (Thu Jun 10 2010 - 18:32:03 PDT)
- Mickey Richards (Thu Jun 10 2010 - 16:10:02 PDT)
- Bill Ross (Thu Jun 10 2010 - 16:02:34 PDT)
- Adrian Roitberg (Thu Jun 10 2010 - 15:57:19 PDT)
- Mickey Richards (Thu Jun 10 2010 - 15:45:35 PDT)
[AMBER] solute ans solvation box
- Emmanuel Baribefe Naziga (Mon Jun 28 2010 - 13:40:49 PDT)
[AMBER] Solvation free energy of a capped 9mer peptide
- Ray Luo (Thu Jun 17 2010 - 16:32:03 PDT)
- Lekpa Duukori (Thu Jun 17 2010 - 15:52:14 PDT)
[AMBER] solvent-solute interaction energy
- vedat durmaz (Wed Jun 09 2010 - 01:19:41 PDT)
- Adrian Roitberg (Tue Jun 08 2010 - 16:51:41 PDT)
- Bill Ross (Tue Jun 08 2010 - 16:50:09 PDT)
- durmaz.zib.de (Tue Jun 08 2010 - 16:11:56 PDT)
- Bill Ross (Tue Jun 08 2010 - 15:42:28 PDT)
- Hoshin Kim (Tue Jun 08 2010 - 02:26:24 PDT)
[AMBER] speed of analysis
- Ross Walker (Tue Jun 22 2010 - 22:12:06 PDT)
- Homa Azizian (Tue Jun 22 2010 - 22:04:13 PDT)
[AMBER] Strange results for
- Bill Miller III (Fri Jun 11 2010 - 08:01:46 PDT)
- vaibhav dixit (Wed Jun 09 2010 - 04:24:31 PDT)
[AMBER] stripping water
- Ross Walker (Tue Jun 22 2010 - 22:14:28 PDT)
- Homa Azizian (Tue Jun 22 2010 - 17:58:20 PDT)
[AMBER] stripping water and cross-correlation analysis
- case (Tue Jun 22 2010 - 21:29:07 PDT)
- Homa Azizian (Tue Jun 22 2010 - 18:23:08 PDT)
[AMBER] Stuck on pmemd.f90
- case (Thu Jun 10 2010 - 18:09:26 PDT)
- Jason Swails (Thu Jun 10 2010 - 17:29:26 PDT)
- Paul Go (Thu Jun 10 2010 - 10:22:44 PDT)
[AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files
- Sushil Mishra (Tue Jun 08 2010 - 13:04:40 PDT)
- Dwight McGee (Tue Jun 08 2010 - 12:11:36 PDT)
- Sushil Mishra (Tue Jun 08 2010 - 11:44:34 PDT)
[AMBER] The charge
- Ray Luo (Wed Jun 02 2010 - 13:32:47 PDT)
- xuemeiwang1103 (Tue Jun 01 2010 - 23:27:58 PDT)
[AMBER] The err of sander.PUPIL
- Joan Torras (Mon Jun 07 2010 - 11:37:09 PDT)
- Aurum Bai (Mon Jun 07 2010 - 02:04:18 PDT)
- Jason Swails (Sun Jun 06 2010 - 23:19:36 PDT)
- Aurum Bai (Sun Jun 06 2010 - 22:13:32 PDT)
[AMBER] Thr -> Met in TI calculation
- Jason Swails (Sat Jun 05 2010 - 06:45:34 PDT)
- fancy2012 (Sat Jun 05 2010 - 06:33:12 PDT)
[AMBER] time-correlation fluctuation
- Homa Azizian (Thu Jun 03 2010 - 02:06:06 PDT)
[AMBER] tleap: C-N triple bond and sp1 hybridization
- Bill Ross (Fri Jun 04 2010 - 10:01:19 PDT)
- case (Fri Jun 04 2010 - 09:49:34 PDT)
- vedat durmaz (Fri Jun 04 2010 - 07:14:40 PDT)
- case (Fri Jun 04 2010 - 05:43:38 PDT)
- vedat durmaz (Fri Jun 04 2010 - 05:26:46 PDT)
[AMBER] to understand 1-4 interactions in Amber FF
- Bill Ross (Tue Jun 15 2010 - 09:56:12 PDT)
- Alan (Tue Jun 15 2010 - 06:13:28 PDT)
- Ross Walker (Tue Jun 15 2010 - 05:24:15 PDT)
- Alan (Tue Jun 15 2010 - 04:16:31 PDT)
[AMBER] torsion angle define
- Bill Ross (Sat Jun 12 2010 - 12:40:35 PDT)
- Bill Ross (Sat Jun 12 2010 - 12:37:41 PDT)
- Bill Ross (Sat Jun 12 2010 - 12:34:49 PDT)
- Ilyas Yildirim (Sat Jun 12 2010 - 05:54:03 PDT)
- Navanath Kumbhar (Sat Jun 12 2010 - 05:40:11 PDT)
- Ilyas Yildirim (Sat Jun 12 2010 - 04:16:23 PDT)
- Navanath Kumbhar (Sat Jun 12 2010 - 04:04:56 PDT)
[AMBER] TUTORIAL A7 Replica Exchange Simulations with AMBER 10
- Ross Walker (Mon Jun 28 2010 - 11:36:43 PDT)
[AMBER] two questions about Amber annealing
- Bill Ross (Sun Jun 20 2010 - 00:18:48 PDT)
- Ross Walker (Sat Jun 19 2010 - 21:55:47 PDT)
- Bill Ross (Sat Jun 19 2010 - 21:19:50 PDT)
- Yiyu Li (Sat Jun 19 2010 - 20:17:08 PDT)
[AMBER] unexpected "vlimit exceeded for step" error
- Cristina Sisu (Thu Jun 24 2010 - 03:23:15 PDT)
- Bill Ross (Wed Jun 23 2010 - 10:02:36 PDT)
- Ross Walker (Wed Jun 23 2010 - 09:46:31 PDT)
- Cristina Sisu (Wed Jun 23 2010 - 03:49:07 PDT)
- Bill Ross (Tue Jun 22 2010 - 12:19:50 PDT)
- Cristina Sisu (Tue Jun 22 2010 - 12:13:16 PDT)
- Bill Ross (Tue Jun 22 2010 - 10:10:26 PDT)
- Ross Walker (Tue Jun 22 2010 - 08:34:17 PDT)
- Cristina Sisu (Tue Jun 22 2010 - 06:20:15 PDT)
- Ross Walker (Mon Jun 21 2010 - 10:51:17 PDT)
- case (Mon Jun 21 2010 - 10:48:29 PDT)
- Cristina Sisu (Mon Jun 21 2010 - 10:25:49 PDT)
[AMBER] Unknown clustering algorithm_ptraj_ambertools1.4
- Fredrick Devadoss (Tue Jun 22 2010 - 07:59:42 PDT)
- Dwight McGee (Tue Jun 22 2010 - 07:18:42 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Jun 22 2010 - 06:56:23 PDT)
[AMBER] visualising frame of minimisation
- Jason Swails (Thu Jun 17 2010 - 06:39:17 PDT)
- Alan (Mon Jun 14 2010 - 09:02:42 PDT)
[AMBER] vlimit exceeded for step
- Bill Ross (Wed Jun 30 2010 - 16:48:38 PDT)
- Jason Swails (Wed Jun 30 2010 - 16:29:39 PDT)
- Le, Shu-Yun (NIH/NCI) [E] (Wed Jun 30 2010 - 13:58:57 PDT)
[AMBER] want to keep water from the pdb
- Bill Ross (Tue Jun 15 2010 - 09:46:04 PDT)
- vaibhav dixit (Tue Jun 15 2010 - 02:42:50 PDT)
- Jason Swails (Tue Jun 15 2010 - 00:00:44 PDT)
- vaibhav dixit (Mon Jun 14 2010 - 23:50:03 PDT)
[AMBER] What's the mean of this ptraj error message? thanks in advance.
- Paul S. Nerenberg (Thu Jun 17 2010 - 09:06:48 PDT)
- Jason Swails (Thu Jun 17 2010 - 09:06:52 PDT)
- Catein Catherine (Thu Jun 17 2010 - 09:01:23 PDT)
[AMBER] Why different binding energy is obtained from GBSA calculations?
- Catein Catherine (Mon May 31 2010 - 20:43:15 PDT)
[AMBER] Why different results were obtained for two runs using the same prmtop files?
- Catein Catherine (Sun Jun 13 2010 - 09:03:21 PDT)
[AMBER] xleap problem for terminal DNA base pairs.
- Bill Ross (Sun Jun 20 2010 - 10:18:37 PDT)
- Jason Swails (Sun Jun 20 2010 - 09:06:17 PDT)
- Catein Catherine (Sun Jun 20 2010 - 08:56:59 PDT)
Error: No potential terms in sander output!
- Jim Paugh (Wed Jun 02 2010 - 05:30:53 PDT)
- Bill Miller III (Wed Jun 02 2010 - 04:47:51 PDT)
frcdump for CHARMM
- Ross Walker (Wed Jun 16 2010 - 08:10:35 PDT)
gb working but not pb & gives No potential terms in sander output! error
- vaibhav dixit (Sun Jun 06 2010 - 22:15:02 PDT)
- Bill Miller III (Sun Jun 06 2010 - 04:15:30 PDT)
- vaibhav dixit (Sun Jun 06 2010 - 02:37:55 PDT)
- Bill Miller III (Sat Jun 05 2010 - 03:53:17 PDT)
pre-processing of trajectories]
- moitrayee.mbu.iisc.ernet.in (Thu Jun 24 2010 - 00:21:16 PDT)
Requesting your help in amber
- Jason Swails (Tue Jun 08 2010 - 06:32:19 PDT)
- Jenny Iskrenova (Tue Jun 08 2010 - 06:04:22 PDT)
- Jenny Iskrenova (Mon Jun 07 2010 - 07:26:49 PDT)
RESP charge of heavy metal contained complex
- Jia Xu (Wed Jun 30 2010 - 08:48:32 PDT)
- FyD (Tue Jun 29 2010 - 23:07:22 PDT)
- Jia Xu (Sun Jun 27 2010 - 20:29:37 PDT)

Amber Archive Jun 2010 by subject