Amber Archive Apr 2010: by subject

[AMBER] "go" keyword in ptraj
- Ben Roberts (Fri Apr 30 2010 - 11:36:14 PDT)
- Thomas Cheatham III (Fri Apr 30 2010 - 08:39:21 PDT)
- Ross Walker (Fri Apr 30 2010 - 06:43:10 PDT)
- Ben Roberts (Fri Apr 30 2010 - 06:34:28 PDT)
[AMBER] (no subject)
- Waad RHAIEM (Wed Apr 14 2010 - 07:12:15 PDT)
[AMBER] 1-4 EEL
- Bill Ross (Fri Apr 16 2010 - 09:47:04 PDT)
- Jio M (Thu Apr 15 2010 - 23:32:36 PDT)
- Bill Ross (Thu Apr 15 2010 - 07:56:47 PDT)
- Jio M (Thu Apr 15 2010 - 00:47:40 PDT)
- Jio M (Wed Apr 14 2010 - 04:44:08 PDT)
[AMBER] A bugfix for thiazole-imidazole rings
- Hasan Alniss (Wed Apr 28 2010 - 04:55:08 PDT)
[AMBER] A possible pmemd bug
- Ross Walker (Thu Apr 22 2010 - 16:47:49 PDT)
- Scott Brozell (Thu Apr 22 2010 - 14:19:58 PDT)
- Robert Duke (Thu Apr 22 2010 - 07:01:24 PDT)
- Lijiang Yang (Thu Apr 22 2010 - 04:59:42 PDT)
[AMBER] a possible typo bug while building pmemd with mpi
- Jason Swails (Fri Apr 30 2010 - 20:12:30 PDT)
- Dean Cuebas (Fri Apr 30 2010 - 10:52:10 PDT)
- Alan (Thu Apr 29 2010 - 11:08:24 PDT)
- Ben Roberts (Thu Apr 29 2010 - 10:13:56 PDT)
- Jason Swails (Thu Apr 29 2010 - 09:57:46 PDT)
- Alan (Thu Apr 29 2010 - 09:46:22 PDT)
- David Watson (Thu Apr 29 2010 - 09:22:33 PDT)
- Alan (Thu Apr 29 2010 - 09:13:03 PDT)
- Jason Swails (Thu Apr 29 2010 - 08:50:28 PDT)
- Alan (Thu Apr 29 2010 - 08:18:29 PDT)
[AMBER] about IGB
- Carlos Simmerling (Mon Apr 26 2010 - 04:11:29 PDT)
- geyan (Sun Apr 25 2010 - 22:42:32 PDT)
- Carlos Simmerling (Sun Apr 25 2010 - 03:54:28 PDT)
- geyan (Sun Apr 25 2010 - 01:50:17 PDT)
- Ross Walker (Fri Apr 23 2010 - 22:55:43 PDT)
- geyan (Fri Apr 23 2010 - 18:08:51 PDT)
[AMBER] about parmjoin
- Alan (Wed Apr 21 2010 - 01:40:04 PDT)
[AMBER] About restart-job
- Matthias Wildauer (Wed Apr 14 2010 - 05:53:50 PDT)
- Rilei Yu (Tue Apr 13 2010 - 15:48:14 PDT)
[AMBER] about skinnb
- liu junjun (Wed Apr 28 2010 - 14:25:58 PDT)
- Robert Duke (Wed Apr 28 2010 - 14:04:36 PDT)
- liu junjun (Wed Apr 28 2010 - 13:27:35 PDT)
- liu junjun (Wed Apr 28 2010 - 13:02:42 PDT)
- Robert Duke (Wed Apr 28 2010 - 12:16:53 PDT)
- liu junjun (Wed Apr 28 2010 - 12:05:21 PDT)
- Robert Duke (Tue Apr 27 2010 - 10:32:34 PDT)
- liu junjun (Tue Apr 27 2010 - 10:08:48 PDT)
[AMBER] Addions grid ?
- Marek Maly (Tue Apr 27 2010 - 14:05:10 PDT)
- Bill Ross (Tue Apr 27 2010 - 11:32:29 PDT)
- Marek Maly (Tue Apr 27 2010 - 11:22:41 PDT)
- Bill Ross (Tue Apr 27 2010 - 11:09:49 PDT)
- Marek Maly (Tue Apr 27 2010 - 10:58:04 PDT)
- Bill Ross (Tue Apr 27 2010 - 10:01:36 PDT)
- Marek Maly (Tue Apr 27 2010 - 07:59:16 PDT)
[AMBER] amber 5 manual
- case (Thu Apr 08 2010 - 13:01:45 PDT)
- William Flak (Thu Apr 08 2010 - 12:48:33 PDT)
- case (Thu Apr 08 2010 - 11:36:03 PDT)
- William Flak (Wed Apr 07 2010 - 08:10:26 PDT)
[AMBER] amber <-> desmond conversion tools
- Cen Gao (Tue Apr 13 2010 - 22:25:43 PDT)
- Parish, Carol (Tue Apr 13 2010 - 11:13:22 PDT)
[AMBER] AMBER VS QM energy calculations for dihedrals
- Ilyas Yildirim (Wed Apr 28 2010 - 07:32:42 PDT)
- Palermo Giulia (Wed Apr 28 2010 - 07:09:50 PDT)
[AMBER] Amber10 Cuda compile failure
- Ross Walker (Wed Apr 14 2010 - 20:04:09 PDT)
- aapeters.ncsu.edu (Wed Apr 14 2010 - 14:16:28 PDT)
- Ross Walker (Tue Apr 13 2010 - 08:54:59 PDT)
- Ross Walker (Mon Apr 12 2010 - 14:57:36 PDT)
- Robert Duke (Mon Apr 12 2010 - 14:53:07 PDT)
- aapeters.ncsu.edu (Mon Apr 12 2010 - 14:35:49 PDT)
[AMBER] amber10 installation on SGI IRIX 6.5
- Atro Tossavainen (Mon Apr 05 2010 - 22:58:18 PDT)
- Bill Ross (Mon Apr 05 2010 - 13:44:33 PDT)
- Eruysal, Ferdi (Mon Apr 05 2010 - 13:37:49 PDT)
[AMBER] AMBER10 installation: make test error 1
- Anna Dejardin (Wed Apr 07 2010 - 02:47:39 PDT)
[AMBER] Amber11, pure QM PBC
- Ross Walker (Tue Apr 13 2010 - 08:57:12 PDT)
- case (Mon Apr 12 2010 - 09:18:05 PDT)
- aapeters.ncsu.edu (Mon Apr 12 2010 - 09:07:26 PDT)
[AMBER] Amber99FFSB parameter files for Gaussian
- Senthil Natesan (Wed Apr 07 2010 - 07:43:15 PDT)
[AMBER] AmberTool 1.4 with Intel 10.1.014 on snow leopard
- Yu Chen (Thu Apr 29 2010 - 11:54:16 PDT)
[AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
- Daniel Roe (Mon Apr 12 2010 - 08:12:29 PDT)
- Ibrahim Moustafa (Mon Apr 12 2010 - 06:39:07 PDT)
- Daniel Roe (Mon Apr 12 2010 - 05:12:44 PDT)
- Ibrahim Moustafa (Fri Apr 09 2010 - 16:14:25 PDT)
- Jason Swails (Fri Apr 09 2010 - 16:02:25 PDT)
- Ibrahim Moustafa (Fri Apr 09 2010 - 15:40:47 PDT)
[AMBER] ambertools 1.4, tests
- Mengjuei Hsieh (Tue Apr 27 2010 - 11:37:29 PDT)
- Jason Swails (Tue Apr 27 2010 - 09:05:33 PDT)
- Alan (Tue Apr 27 2010 - 08:12:49 PDT)
- David Watson (Tue Apr 27 2010 - 06:31:36 PDT)
- Alan (Tue Apr 27 2010 - 03:49:18 PDT)
[AMBER] AmberTools.pdf (AT 1.4)
- Alan (Thu Apr 29 2010 - 06:48:41 PDT)
[AMBER] analysis for solvation effect for protein
- Yunfen Wang (Sat Apr 17 2010 - 01:21:14 PDT)
[AMBER] angle between DNA (vector) and a plane
- Taufik Al-Sarraj (Thu Apr 15 2010 - 10:04:14 PDT)
[AMBER] angle force constants in GAFF
- João Sardinha (Thu Apr 08 2010 - 05:59:35 PDT)
- case (Thu Apr 08 2010 - 05:27:43 PDT)
- João Sardinha (Thu Apr 08 2010 - 04:11:00 PDT)
[AMBER] Announcement: release of Amber11 and AmberTools 1.4
- case (Mon Apr 26 2010 - 05:41:28 PDT)
[AMBER] antechamber
- case (Tue Apr 06 2010 - 04:46:21 PDT)
- Asfa Ali (Tue Apr 06 2010 - 00:30:13 PDT)
- case (Mon Apr 05 2010 - 04:41:14 PDT)
- monica.imtech.res.in (Sun Apr 04 2010 - 22:52:36 PDT)
- monica.imtech.res.in (Sun Apr 04 2010 - 21:41:48 PDT)
- case (Thu Apr 01 2010 - 05:14:19 PDT)
- Dmitry Nilov (Thu Apr 01 2010 - 03:05:48 PDT)
- monica.imtech.res.in (Thu Apr 01 2010 - 02:53:44 PDT)
- Dmitri Nilov (Thu Apr 01 2010 - 00:37:13 PDT)
- monica.imtech.res.in (Wed Mar 31 2010 - 23:57:43 PDT)
[AMBER] Antechamber, GAFF and methylimidazole typing
- Ben Roberts (Fri Apr 23 2010 - 14:32:57 PDT)
[AMBER] Asking help for some analysis section
- case (Tue Apr 13 2010 - 07:39:29 PDT)
- nicholus bhattacharjee (Tue Apr 13 2010 - 07:04:03 PDT)
[AMBER] Automatic assignment of HID, HIP, HIE??
- case (Tue Apr 13 2010 - 09:42:51 PDT)
- Dean Cuebas (Tue Apr 13 2010 - 09:36:09 PDT)
[AMBER] bond command
- Jason Swails (Thu Apr 22 2010 - 17:52:11 PDT)
- Siddharth Rastogi (Thu Apr 22 2010 - 17:31:02 PDT)
[AMBER] BOND TYPE
- Bill Ross (Fri Apr 16 2010 - 09:26:47 PDT)
- Dean Cuebas (Thu Apr 15 2010 - 19:08:43 PDT)
- Homa Azizian (Thu Apr 15 2010 - 18:46:49 PDT)
[AMBER] BOND TYPE corrections
- Dean Cuebas (Fri Apr 16 2010 - 09:02:20 PDT)
[AMBER] Chirality of amines in GAFF
- David A. Case (Wed Apr 14 2010 - 15:34:01 PDT)
- Dean Cuebas (Wed Apr 14 2010 - 15:12:51 PDT)
- FyD (Wed Apr 14 2010 - 12:51:52 PDT)
- Alan (Wed Apr 14 2010 - 06:23:28 PDT)
- Jason Swails (Wed Apr 14 2010 - 05:44:39 PDT)
- Dmitry Nilov (Wed Apr 14 2010 - 00:43:47 PDT)
[AMBER] Chirality Restraint
- Seetin, Matthew (Wed Apr 07 2010 - 10:58:47 PDT)
- Ilyas Yildirim (Wed Apr 07 2010 - 10:46:25 PDT)
[AMBER] chirality restraints for non-standard residue
- Jio M (Sun Apr 18 2010 - 01:57:05 PDT)
- Jio M (Fri Apr 16 2010 - 12:18:42 PDT)
- Jio M (Fri Apr 16 2010 - 11:54:12 PDT)
- Jason Swails (Fri Apr 16 2010 - 11:37:43 PDT)
- Jio M (Fri Apr 16 2010 - 04:15:08 PDT)
[AMBER] Comparing dihedral energy curves
- Lekpa Duukori (Mon Apr 26 2010 - 11:56:50 PDT)
- Ilyas Yildirim (Mon Apr 26 2010 - 10:15:53 PDT)
- Lekpa Duukori (Mon Apr 26 2010 - 09:34:24 PDT)
[AMBER] Compiling AmberTools 1.4 on MacOS10.5
- Dean Cuebas (Tue Apr 27 2010 - 12:42:16 PDT)
- Alan (Tue Apr 27 2010 - 10:43:06 PDT)
- Jason Swails (Tue Apr 27 2010 - 10:34:33 PDT)
- Dean Cuebas (Tue Apr 27 2010 - 10:26:37 PDT)
[AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc.
- Paul S. Nerenberg (Thu Apr 22 2010 - 16:50:57 PDT)
- Ross Walker (Thu Apr 22 2010 - 16:23:37 PDT)
- Paul S. Nerenberg (Thu Apr 22 2010 - 15:58:07 PDT)
[AMBER] Constraint minimisation before MD simulation
- Bill Ross (Tue Apr 27 2010 - 15:05:46 PDT)
- Carlos Simmerling (Tue Apr 27 2010 - 14:58:32 PDT)
- Amire-Brahimi Benjamin (Tue Apr 27 2010 - 14:48:31 PDT)
[AMBER] contiguous trajectory without iwrap=1
- Carlos Simmerling (Wed Apr 07 2010 - 18:13:24 PDT)
- Jacky Zhao (Wed Apr 07 2010 - 18:01:09 PDT)
- Bill Ross (Wed Apr 07 2010 - 17:02:50 PDT)
- Emmanuel Baribefe Naziga (Wed Apr 07 2010 - 16:56:42 PDT)
- Bill Ross (Wed Apr 07 2010 - 16:11:15 PDT)
- Emmanuel Baribefe Naziga (Wed Apr 07 2010 - 16:03:34 PDT)
[AMBER] COOH group:extra undesired bond
- Jio M (Tue Apr 06 2010 - 21:09:31 PDT)
[AMBER] COOH group:extra undesired bond::NO reply :-(
- Jio M (Sun Apr 04 2010 - 00:25:12 PDT)
- case (Sat Apr 03 2010 - 07:31:59 PDT)
- Jio M (Fri Apr 02 2010 - 23:34:45 PDT)
[AMBER] correct syntax for assinging scmask to two atoms of different molecules
- steinbrt.rci.rutgers.edu (Thu Apr 01 2010 - 07:14:04 PDT)
- imtiaz shafiq (Thu Apr 01 2010 - 07:00:47 PDT)
[AMBER] developing amber force field
- Diego Javier Alonso de Armiño (Fri Apr 09 2010 - 09:52:20 PDT)
- Necmettin Pirinccioglu (Fri Apr 09 2010 - 03:57:14 PDT)
- Karl N. Kirschner (Fri Apr 09 2010 - 03:12:14 PDT)
- Necmettin Pirinccioglu (Fri Apr 09 2010 - 02:03:51 PDT)
- InSuk Joung (Thu Apr 08 2010 - 18:44:14 PDT)
- Necmettin Pirinccioglu (Thu Apr 08 2010 - 12:46:10 PDT)
[AMBER] distance mapping
- monica.imtech.res.in (Fri Apr 30 2010 - 07:51:48 PDT)
[AMBER] distrbuting an excess charge
- Jason Swails (Mon Apr 12 2010 - 03:16:30 PDT)
- Homa Azizian (Sun Apr 11 2010 - 22:50:30 PDT)
[AMBER] Do molecular dynamics in the limited space
- Bill Ross (Fri Apr 23 2010 - 10:00:11 PDT)
- case (Fri Apr 23 2010 - 05:50:32 PDT)
- Yunjie Zhao (Thu Apr 22 2010 - 19:35:10 PDT)
- Bill Ross (Wed Apr 21 2010 - 09:59:39 PDT)
- Yunjie Zhao (Wed Apr 21 2010 - 06:40:31 PDT)
[AMBER] Does the frequency of output affect MD simulation in AMBER10?
- Jianing (Wed Apr 14 2010 - 18:33:07 PDT)
- Bill Ross (Wed Apr 14 2010 - 09:38:23 PDT)
- Jianing (Wed Apr 14 2010 - 06:13:22 PDT)
- Carlos Simmerling (Wed Apr 14 2010 - 05:37:48 PDT)
- Jianing (Wed Apr 14 2010 - 05:25:28 PDT)
- Carlos Simmerling (Tue Apr 13 2010 - 19:46:52 PDT)
- Jianing (Tue Apr 13 2010 - 19:44:33 PDT)
- Bill Ross (Tue Apr 13 2010 - 09:57:28 PDT)
- Jianing (Tue Apr 13 2010 - 06:25:29 PDT)
- Jianing (Tue Apr 13 2010 - 06:15:14 PDT)
- case (Tue Apr 13 2010 - 04:59:04 PDT)
- Carlos Simmerling (Tue Apr 13 2010 - 04:57:06 PDT)
- Jianing (Mon Apr 12 2010 - 22:17:46 PDT)
- Jianing (Mon Apr 12 2010 - 21:57:38 PDT)
- Bill Ross (Mon Apr 12 2010 - 11:13:25 PDT)
- Carlos Simmerling (Mon Apr 12 2010 - 07:02:01 PDT)
- Jianing (Mon Apr 12 2010 - 05:37:30 PDT)
- Carlos Simmerling (Mon Apr 12 2010 - 05:13:31 PDT)
- Jianing (Mon Apr 12 2010 - 05:12:08 PDT)
- Carlos Simmerling (Mon Apr 12 2010 - 04:09:45 PDT)
- Nancy (Mon Apr 12 2010 - 04:06:05 PDT)
[AMBER] dummy atom
- William Flak (Wed Apr 07 2010 - 08:21:31 PDT)
[AMBER] effect of pre-processor flags on pmemd?
- Robert Duke (Wed Apr 21 2010 - 13:31:20 PDT)
- Thomas Zeiser (Wed Apr 21 2010 - 13:12:17 PDT)
[AMBER] elevated Temperature MD
- Steve Seibold (Tue Apr 20 2010 - 09:30:40 PDT)
- Nicholas Musolino (Mon Apr 19 2010 - 10:31:05 PDT)
- Carlos Simmerling (Mon Apr 19 2010 - 10:21:57 PDT)
- Steve Seibold (Mon Apr 19 2010 - 10:10:08 PDT)
[AMBER] energy decomposition
- Bill Miller III (Wed Apr 07 2010 - 14:45:18 PDT)
- Ganesh Kamath (Wed Apr 07 2010 - 14:29:08 PDT)
[AMBER] Energy units in mm-pbsa calculations
- Jason Swails (Thu Apr 08 2010 - 05:45:43 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Apr 07 2010 - 21:45:44 PDT)
- Jason Swails (Wed Apr 07 2010 - 06:36:13 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Apr 07 2010 - 05:42:24 PDT)
[AMBER] Entropy-problem
- Rilei Yu (Wed Apr 14 2010 - 18:47:02 PDT)
- Jason Swails (Wed Apr 14 2010 - 15:31:37 PDT)
- Rilei Yu (Wed Apr 14 2010 - 15:11:36 PDT)
[AMBER] error in reading namelist cntrl
- case (Mon Apr 05 2010 - 07:17:28 PDT)
- Hyma vathi (Mon Apr 05 2010 - 07:03:09 PDT)
- case (Mon Apr 05 2010 - 05:53:16 PDT)
- Carlos Simmerling (Mon Apr 05 2010 - 05:22:16 PDT)
- Hyma vathi (Mon Apr 05 2010 - 05:17:26 PDT)
[AMBER] error when running mmpbsa
- pxq (Sun Apr 18 2010 - 19:49:37 PDT)
- Bill Miller III (Sun Apr 18 2010 - 06:50:22 PDT)
- pxq (Sun Apr 18 2010 - 04:34:44 PDT)
- Jason Swails (Sat Apr 17 2010 - 07:58:41 PDT)
- pxq (Sat Apr 17 2010 - 07:25:35 PDT)
[AMBER] Error: Sander output is missing values
- Bill Miller III (Wed Apr 21 2010 - 09:25:28 PDT)
- Hyma vathi (Wed Apr 21 2010 - 08:50:33 PDT)
- Bill Ross (Tue Apr 20 2010 - 10:06:22 PDT)
- Jason Swails (Tue Apr 20 2010 - 08:41:03 PDT)
- Hyma vathi (Tue Apr 20 2010 - 08:08:31 PDT)
- Bill Miller III (Tue Apr 20 2010 - 04:36:52 PDT)
- Hyma vathi (Tue Apr 20 2010 - 03:31:32 PDT)
[AMBER] explicit water MMPBSA
- Cristina Sisu (Tue Apr 27 2010 - 06:54:56 PDT)
[AMBER] failed to compile Amber11 with mpi on Mac
- case (Thu Apr 29 2010 - 08:08:31 PDT)
- Alan (Thu Apr 29 2010 - 07:59:22 PDT)
- David Watson (Thu Apr 29 2010 - 07:54:08 PDT)
- Jason Swails (Thu Apr 29 2010 - 07:51:26 PDT)
- Alan (Thu Apr 29 2010 - 07:41:20 PDT)
[AMBER] ff99SB-ILDN
- Titus, Jamie (bairdje) (Tue Apr 27 2010 - 11:38:32 PDT)
[AMBER] Files for Charged serine in proteins?
- Dean Cuebas (Tue Apr 06 2010 - 09:39:04 PDT)
[AMBER] Force constant
- Nicholas Musolino (Sun Apr 18 2010 - 11:38:33 PDT)
- William Flak (Sun Apr 18 2010 - 09:56:53 PDT)
- Nicholas Musolino (Sun Apr 18 2010 - 09:08:14 PDT)
- William Flak (Sun Apr 18 2010 - 08:54:55 PDT)
[AMBER] forcefield parameters for TiO2/peptides?
- FyD (Thu Apr 29 2010 - 15:56:39 PDT)
- Tom Williams (Thu Apr 29 2010 - 14:03:48 PDT)
- Ben Roberts (Thu Apr 29 2010 - 08:11:40 PDT)
- Tom Williams (Wed Apr 28 2010 - 13:31:01 PDT)
[AMBER] Fortran runtime error :bad value duiring floating point read
- Yunfen Wang (Thu Apr 08 2010 - 05:02:43 PDT)
- Trevor Gokey (Thu Apr 08 2010 - 03:36:24 PDT)
- Yunfen Wang (Thu Apr 08 2010 - 03:05:50 PDT)
[AMBER] Fortran runtime error: Bad value during integer read
- João Henriques (Fri Apr 30 2010 - 05:28:51 PDT)
- Piotr Cieplak (Thu Apr 29 2010 - 13:56:54 PDT)
- Piotr Cieplak (Thu Apr 29 2010 - 13:50:51 PDT)
- FyD (Thu Apr 29 2010 - 12:55:05 PDT)
- João Henriques (Thu Apr 29 2010 - 11:39:39 PDT)
- Piotr Cieplak (Thu Apr 29 2010 - 10:56:59 PDT)
- Jason Swails (Thu Apr 29 2010 - 06:30:45 PDT)
- João Henriques (Thu Apr 29 2010 - 06:19:13 PDT)
- João Henriques (Thu Apr 29 2010 - 05:32:58 PDT)
- Jason Swails (Thu Apr 29 2010 - 05:10:25 PDT)
- João Henriques (Thu Apr 29 2010 - 04:20:00 PDT)
- Mengjuei Hsieh (Wed Apr 28 2010 - 18:33:42 PDT)
- João Henriques (Wed Apr 28 2010 - 09:09:35 PDT)
[AMBER] freezing selected residues
- Senthil Natesan (Fri Apr 30 2010 - 10:11:20 PDT)
[AMBER] Fwd: .rst file corrupted
- manikanthan bhavaraju (Fri Apr 09 2010 - 08:48:52 PDT)
[AMBER] H-bond analysis in ptraj
- Jason Swails (Sat Apr 24 2010 - 05:19:26 PDT)
- Yunfen Wang (Fri Apr 23 2010 - 17:56:38 PDT)
- Bill Ross (Fri Apr 23 2010 - 10:03:58 PDT)
- Shulin Zhuang (Thu Apr 22 2010 - 23:57:31 PDT)
- geyan (Thu Apr 22 2010 - 22:54:22 PDT)
- Yunfen Wang (Thu Apr 22 2010 - 20:30:27 PDT)
[AMBER] how do MM_PBSA without water
- Bill Ross (Thu Apr 22 2010 - 09:55:00 PDT)
- Bill Miller III (Thu Apr 22 2010 - 04:04:48 PDT)
- geyan (Thu Apr 22 2010 - 01:21:05 PDT)
- Jason Swails (Wed Apr 21 2010 - 04:55:36 PDT)
- geyan (Wed Apr 21 2010 - 01:44:53 PDT)
- Bill Miller III (Mon Apr 19 2010 - 06:25:40 PDT)
- geyan (Mon Apr 19 2010 - 00:33:23 PDT)
- Bill Miller III (Sun Apr 18 2010 - 08:36:56 PDT)
- geyan (Sun Apr 18 2010 - 08:20:57 PDT)
- Bill Miller III (Sun Apr 18 2010 - 06:18:53 PDT)
- geyan (Sun Apr 18 2010 - 00:48:06 PDT)
[AMBER] How do you know when to include improper dihedrals????
- Dean Cuebas (Thu Apr 15 2010 - 08:33:31 PDT)
- Dean Cuebas (Thu Apr 15 2010 - 08:23:12 PDT)
- Karl N. Kirschner (Thu Apr 15 2010 - 06:18:02 PDT)
- Dmitry Nilov (Thu Apr 15 2010 - 05:42:21 PDT)
- Dmitry Nilov (Thu Apr 15 2010 - 03:05:13 PDT)
- Dean Cuebas (Mon Apr 12 2010 - 12:30:07 PDT)
[AMBER] how is pH treated in Amber - other than constant pH simulations
- Dean Cuebas (Tue Apr 20 2010 - 08:08:24 PDT)
- Andrew Voronkov (Tue Apr 20 2010 - 06:24:15 PDT)
- Andrew Voronkov (Tue Apr 20 2010 - 00:32:35 PDT)
- Dean Cuebas (Fri Apr 16 2010 - 13:05:43 PDT)
- Jason Swails (Fri Apr 16 2010 - 11:25:49 PDT)
- Andrew Voronkov (Fri Apr 16 2010 - 11:17:32 PDT)
- Dean Cuebas (Fri Apr 16 2010 - 09:53:34 PDT)
- Carlos Simmerling (Fri Apr 16 2010 - 09:10:42 PDT)
- Andrew Voronkov (Fri Apr 16 2010 - 08:44:36 PDT)
[AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
- Carlos Simmerling (Tue Apr 20 2010 - 06:01:58 PDT)
- Andrew Voronkov (Tue Apr 20 2010 - 05:28:37 PDT)
- Dmitry Nilov (Tue Apr 20 2010 - 04:46:20 PDT)
- Dmitry Nilov (Tue Apr 20 2010 - 04:41:26 PDT)
- Carlos Simmerling (Tue Apr 20 2010 - 04:36:50 PDT)
- Andrew Voronkov (Tue Apr 20 2010 - 04:27:50 PDT)
- Dmitry Nilov (Tue Apr 20 2010 - 03:43:52 PDT)
- Andrew Voronkov (Tue Apr 20 2010 - 03:23:15 PDT)
[AMBER] how to achieve the 2D periodic boundary
- kecy_w.sina.com (Fri Apr 02 2010 - 06:59:53 PDT)
[AMBER] how to add a gradually reduced restraint
- Jianing (Tue Apr 20 2010 - 00:49:14 PDT)
- Dmitry Nilov (Mon Apr 19 2010 - 07:45:22 PDT)
- Jianing (Mon Apr 19 2010 - 02:07:00 PDT)
[AMBER] how to load topology file
- Lachele Foley (Lists) (Tue Apr 27 2010 - 15:32:44 PDT)
- Bill Ross (Tue Apr 27 2010 - 15:27:00 PDT)
- Siddharth Rastogi (Tue Apr 27 2010 - 15:21:33 PDT)
[AMBER] How to perform backbone and residues restraint at the same time
- Rilei Yu (Sat Apr 03 2010 - 02:40:27 PDT)
- case (Fri Apr 02 2010 - 06:57:34 PDT)
- Rilei Yu (Thu Apr 01 2010 - 19:20:55 PDT)
[AMBER] how to pick certain water molecular from a .mdcrd
- Thomas Cheatham (Tue Apr 13 2010 - 20:00:27 PDT)
- Jason Swails (Tue Apr 13 2010 - 05:13:36 PDT)
- pxq (Mon Apr 12 2010 - 23:35:08 PDT)
- pxq (Mon Apr 12 2010 - 07:08:38 PDT)
[AMBER] How to prepare the two tolopogy files when doing TI calculation?
- fancy2012 (Tue Apr 13 2010 - 05:58:53 PDT)
- steinbrt.rci.rutgers.edu (Tue Apr 13 2010 - 05:35:46 PDT)
- fancy2012 (Tue Apr 13 2010 - 05:29:17 PDT)
[AMBER] How to prepare the two tolopogy files when doing TIcalculation?
- Ramu Anandakrishnan (Tue Apr 13 2010 - 05:40:46 PDT)
[AMBER] how to write one ptraj file into several smaller files
- monica.imtech.res.in (Fri Apr 30 2010 - 06:19:45 PDT)
- Jason Swails (Fri Apr 30 2010 - 05:08:37 PDT)
- Yunfen Wang (Fri Apr 30 2010 - 05:00:02 PDT)
[AMBER] Hydrogen Bond Analysis - explanation needed
- Srivatsan (Fri Apr 23 2010 - 02:42:33 PDT)
[AMBER] I do need your help, please
- Ross Walker (Thu Apr 08 2010 - 22:52:19 PDT)
- William Flak (Thu Apr 08 2010 - 12:04:50 PDT)
[AMBER] Install AMBER problem.
- Trojan 007 (Sat Apr 10 2010 - 17:55:43 PDT)
- Jason Swails (Fri Apr 09 2010 - 16:38:54 PDT)
- Trojan 007 (Fri Apr 09 2010 - 16:07:53 PDT)
[AMBER] Installation on sles11 on ibm-power6-cpus
- German Erlenkamp (Fri Apr 23 2010 - 00:35:04 PDT)
- German Erlenkamp (Mon Apr 12 2010 - 00:50:15 PDT)
[AMBER] Is the variation of C-Cl bond length normal?
- Ross Walker (Tue Apr 13 2010 - 12:57:03 PDT)
- Shulin Zhuang (Mon Apr 12 2010 - 15:26:12 PDT)
[AMBER] joining out files
- Jason Swails (Thu Apr 29 2010 - 14:40:21 PDT)
- Homa Azizian (Thu Apr 29 2010 - 14:29:47 PDT)
- Bill Ross (Thu Apr 29 2010 - 12:49:25 PDT)
- Bill Miller III (Thu Apr 29 2010 - 04:06:08 PDT)
- Homa Azizian (Thu Apr 29 2010 - 04:03:55 PDT)
- Homa Azizian (Wed Apr 28 2010 - 20:37:39 PDT)
[AMBER] ligand exchange
- John S (Mon Apr 05 2010 - 15:05:34 PDT)
[AMBER] loadmol2 Segmentation fault
- FyD (Thu Apr 15 2010 - 10:23:09 PDT)
- David A. Case (Thu Apr 15 2010 - 08:02:38 PDT)
- FyD (Thu Apr 15 2010 - 01:23:24 PDT)
- FyD (Thu Apr 15 2010 - 00:44:45 PDT)
- Rui Li (Wed Apr 14 2010 - 23:39:52 PDT)
- Scott Brozell (Wed Apr 14 2010 - 13:02:41 PDT)
- FyD (Wed Apr 14 2010 - 12:56:26 PDT)
- Scott Brozell (Wed Apr 14 2010 - 12:07:02 PDT)
- Rui Li (Tue Apr 13 2010 - 23:30:20 PDT)
- FyD (Tue Apr 13 2010 - 11:25:51 PDT)
- case (Tue Apr 13 2010 - 05:18:51 PDT)
- case (Tue Apr 13 2010 - 05:16:28 PDT)
- FyD (Tue Apr 13 2010 - 03:51:11 PDT)
- FyD (Tue Apr 13 2010 - 03:30:40 PDT)
- Rui Li (Tue Apr 13 2010 - 02:55:34 PDT)
[AMBER] make a new residue FAD-CYS
- 030081094 (Mon Apr 19 2010 - 00:29:26 PDT)
[AMBER] makeANG_rst values
- case (Tue Apr 06 2010 - 15:00:14 PDT)
- Andrew Olson (Tue Apr 06 2010 - 14:21:19 PDT)
- case (Sat Apr 03 2010 - 15:18:00 PDT)
- Andrew Olson (Sat Apr 03 2010 - 14:52:42 PDT)
[AMBER] MM parameters for TiO2
- Piotr Cieplak (Fri Apr 30 2010 - 14:57:28 PDT)
[AMBER] mm-pbsa *_com.all.out files
- Jason Swails (Wed Apr 21 2010 - 05:00:19 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Apr 20 2010 - 23:07:55 PDT)
[AMBER] mm-pbsa: self assembly
- Nicholas Musolino (Tue Apr 20 2010 - 04:59:17 PDT)
- vijayaraj.clri.res.in (Tue Apr 20 2010 - 04:45:42 PDT)
[AMBER] mmpbsa-job-killed
- Rilei Yu (Fri Apr 09 2010 - 16:57:49 PDT)
- Ross Walker (Thu Apr 08 2010 - 22:30:43 PDT)
- mish (Thu Apr 08 2010 - 04:17:11 PDT)
- Rilei Yu (Thu Apr 08 2010 - 04:07:25 PDT)
[AMBER] MMPBSA-ON-CLUSTER
- Bill Miller III (Sun Apr 04 2010 - 05:37:06 PDT)
- Rilei Yu (Sun Apr 04 2010 - 03:13:12 PDT)
- Jason Swails (Sat Apr 03 2010 - 21:18:23 PDT)
- Rilei Yu (Sat Apr 03 2010 - 20:42:57 PDT)
- Bill Miller III (Sat Apr 03 2010 - 19:09:15 PDT)
- Rilei Yu (Sat Apr 03 2010 - 18:56:49 PDT)
- Jason Swails (Sat Apr 03 2010 - 06:43:38 PDT)
- Bill Miller III (Sat Apr 03 2010 - 05:15:31 PDT)
- Rilei Yu (Sat Apr 03 2010 - 03:17:47 PDT)
- Rilei Yu (Sat Apr 03 2010 - 02:47:31 PDT)
[AMBER] mmpbsa-problem
- Dima A Sabbah (Fri Apr 09 2010 - 09:30:59 PDT)
[AMBER] molecular surface area
- Balazs Jojart (Thu Apr 22 2010 - 23:26:58 PDT)
- geyan (Thu Apr 22 2010 - 22:49:01 PDT)
[AMBER] MOPAC2009 output results into antechamber
- David A. Case (Wed Apr 21 2010 - 10:03:26 PDT)
- Alex Boncheff (Wed Apr 21 2010 - 08:14:58 PDT)
[AMBER] multiconformational RESP fitting with antechamber
- Ross Walker (Thu Apr 08 2010 - 22:54:41 PDT)
- Yi Shang (Thu Apr 08 2010 - 12:28:12 PDT)
[AMBER] mutate function in NAB
- Alessandro Nascimento (Tue Apr 20 2010 - 11:11:41 PDT)
[AMBER] new ambertools folder distribution and Makefile_at
- case (Mon Apr 26 2010 - 13:11:10 PDT)
- Alan (Mon Apr 26 2010 - 09:58:12 PDT)
[AMBER] nmr order parameter and autocorrelation
- Paul S. Nerenberg (Fri Apr 30 2010 - 15:19:51 PDT)
- luzhenw1.msu.edu (Fri Apr 30 2010 - 14:39:01 PDT)
- Carlos Simmerling (Fri Apr 30 2010 - 13:47:00 PDT)
- luzhenw1.msu.edu (Fri Apr 30 2010 - 13:43:00 PDT)
[AMBER] NMR refinment issues
- David A. Case (Sat Apr 17 2010 - 01:53:44 PDT)
- rolandmarques.aol.com (Thu Apr 15 2010 - 12:54:32 PDT)
- rolandmarques.aol.com (Wed Apr 14 2010 - 09:17:44 PDT)
[AMBER] non bonded interactions (vanderwaal and electrostatic)
- Barbault Florent (Wed Apr 07 2010 - 12:14:08 PDT)
- Ganesh Kamath (Wed Apr 07 2010 - 11:44:04 PDT)
[AMBER] not sure of the atomtype in .prep
- pxq (Mon Apr 05 2010 - 06:02:35 PDT)
[AMBER] Nucleic acid aperture
- Fernando Martín García (Fri Apr 16 2010 - 01:52:34 PDT)
[AMBER] OT: GLYLIB C libraries for molecular data
- Lachele Foley (Lists) (Wed Apr 28 2010 - 16:02:42 PDT)
[AMBER] periodic boundary condition
- juan zeng (Fri Apr 16 2010 - 00:34:53 PDT)
- Bill Ross (Thu Apr 15 2010 - 11:12:03 PDT)
- Jason Swails (Thu Apr 15 2010 - 09:39:25 PDT)
- Bill Ross (Thu Apr 15 2010 - 08:01:16 PDT)
- Jason Swails (Thu Apr 15 2010 - 04:02:39 PDT)
- juan zeng (Wed Apr 14 2010 - 22:11:52 PDT)
- juan zeng (Wed Apr 14 2010 - 02:34:40 PDT)
[AMBER] PMEMD compiling errors
- Dian Jiao (Fri Apr 23 2010 - 13:26:47 PDT)
- Ross Walker (Fri Apr 23 2010 - 12:09:19 PDT)
- Dian Jiao (Fri Apr 23 2010 - 11:25:47 PDT)
[AMBER] PMEMD missing type? - bugfix
- Ross Walker (Fri Apr 16 2010 - 09:11:50 PDT)
- Robert Duke (Fri Apr 16 2010 - 08:54:36 PDT)
- Ross Walker (Fri Apr 16 2010 - 08:48:03 PDT)
- Robert Duke (Fri Apr 16 2010 - 07:02:05 PDT)
- Josh Berryman (Fri Apr 16 2010 - 06:25:01 PDT)
[AMBER] PMEMD.CUDA on GTX275
- Ross Walker (Wed Apr 14 2010 - 23:31:54 PDT)
- Peter Schmidtke (Wed Apr 14 2010 - 23:14:38 PDT)
- Ross Walker (Wed Apr 14 2010 - 22:56:56 PDT)
- Levi Pierce (Wed Apr 14 2010 - 21:36:40 PDT)
[AMBER] pmemd.cuda problem
- Levi Pierce (Mon Apr 26 2010 - 09:19:46 PDT)
- Ross Walker (Mon Apr 26 2010 - 00:36:16 PDT)
- case (Sun Apr 25 2010 - 09:23:42 PDT)
- Levi Pierce (Sat Apr 24 2010 - 19:04:47 PDT)
- Ross Walker (Sat Apr 24 2010 - 18:43:24 PDT)
- Levi Pierce (Sat Apr 24 2010 - 16:18:57 PDT)
[AMBER] Printing the reaction field in pbsa
- steinbrt.rci.rutgers.edu (Tue Apr 20 2010 - 08:30:36 PDT)
[AMBER] Problem from ala scanning
- Bill Miller III (Fri Apr 30 2010 - 16:08:57 PDT)
- Bill Miller III (Fri Apr 30 2010 - 07:52:37 PDT)
- Rilei Yu (Fri Apr 30 2010 - 07:31:25 PDT)
[AMBER] problem in MMPBSA
- Jason Swails (Mon Apr 19 2010 - 04:28:06 PDT)
- Dima A Sabbah (Sun Apr 18 2010 - 12:02:11 PDT)
- Dima A Sabbah (Sun Apr 18 2010 - 11:52:55 PDT)
- zgong.hust (Sat Apr 17 2010 - 18:49:01 PDT)
- Jason Swails (Sat Apr 17 2010 - 13:53:06 PDT)
- Dima A Sabbah (Sat Apr 17 2010 - 10:09:05 PDT)
- zgong.hust (Sat Apr 17 2010 - 08:06:47 PDT)
- zgong.hust (Fri Apr 16 2010 - 06:23:57 PDT)
[AMBER] problem on running saveAmberParm
- Bill Ross (Fri Apr 23 2010 - 11:00:29 PDT)
- case (Fri Apr 23 2010 - 10:52:11 PDT)
- Bill Ross (Fri Apr 23 2010 - 10:27:27 PDT)
- tianyuan meng (Thu Apr 22 2010 - 18:54:39 PDT)
[AMBER] problem rejoining segmented out files in long simulation
- g t (Wed Apr 28 2010 - 09:10:20 PDT)
- Jason Swails (Wed Apr 28 2010 - 08:31:03 PDT)
- Carlos Simmerling (Wed Apr 28 2010 - 08:10:58 PDT)
- g t (Wed Apr 28 2010 - 08:04:59 PDT)
[AMBER] problem when doing bond in tleap
- pxq (Sun Apr 04 2010 - 08:09:38 PDT)
- case (Sat Apr 03 2010 - 07:34:05 PDT)
- pxq (Sat Apr 03 2010 - 00:32:59 PDT)
[AMBER] Problem with an output file
- Jason Swails (Thu Apr 01 2010 - 21:21:52 PDT)
- lee lior (Thu Apr 01 2010 - 21:00:49 PDT)
[AMBER] problem with frcmod parameter
- pxq (Fri Apr 02 2010 - 19:10:02 PDT)
- Bill Ross (Fri Apr 02 2010 - 10:03:37 PDT)
- case (Fri Apr 02 2010 - 08:16:53 PDT)
- pxq (Fri Apr 02 2010 - 07:50:59 PDT)
[AMBER] problem with paiwise energy decomposition using mm-pbsa
- moitrayee.mbu.iisc.ernet.in (Fri Apr 23 2010 - 11:50:14 PDT)
[AMBER] PROBLEM WITH PMEMD PERFORMANCE
- Ross Walker (Thu Apr 15 2010 - 23:38:11 PDT)
- Juan Carlos (Thu Apr 15 2010 - 02:03:46 PDT)
- Ross Walker (Tue Apr 13 2010 - 09:00:13 PDT)
- Tom Joseph (Mon Apr 12 2010 - 08:16:03 PDT)
- Juan Carlos (Mon Apr 12 2010 - 03:24:12 PDT)
[AMBER] Problem with solvationbox command
- monica.imtech.res.in (Thu Apr 01 2010 - 02:08:32 PDT)
[AMBER] problem with XLEAP on X-client run on windows machine...
- Lachele Foley (Lists) (Sun Apr 11 2010 - 18:23:09 PDT)
- Babu Kannappan (Mon Apr 12 2010 - 06:22:37 PDT)
[AMBER] Problems during AMBER 10 compilation.
- Zuzanna K. Ścigacz (Tue Apr 06 2010 - 10:37:36 PDT)
- Bill Ross (Tue Apr 06 2010 - 10:14:44 PDT)
- Bill Ross (Tue Apr 06 2010 - 10:04:52 PDT)
- case (Tue Apr 06 2010 - 06:55:01 PDT)
- Zuzanna K. Ścigacz (Tue Apr 06 2010 - 06:13:54 PDT)
- case (Tue Apr 06 2010 - 05:55:40 PDT)
- Zuzanna K. Ścigacz (Tue Apr 06 2010 - 05:40:49 PDT)
- case (Tue Apr 06 2010 - 05:23:01 PDT)
- Zuzanna K. Ścigacz (Tue Apr 06 2010 - 05:09:28 PDT)
- case (Tue Apr 06 2010 - 04:58:02 PDT)
- Zuzanna K. Ścigacz (Tue Apr 06 2010 - 02:17:18 PDT)
- case (Thu Apr 01 2010 - 05:53:05 PDT)
- Zuzanna K. Scigacz (Thu Apr 01 2010 - 05:10:16 PDT)
[AMBER] Ptraj Problem
- Jason Swails (Wed Apr 07 2010 - 21:47:59 PDT)
- Jagdeesh C (Wed Apr 07 2010 - 21:35:57 PDT)
[AMBER] QM/MM + PIMD
- Gustavo Seabra (Fri Apr 16 2010 - 12:20:12 PDT)
- aapeters.ncsu.edu (Fri Apr 16 2010 - 10:36:19 PDT)
[AMBER] QM/MM cut problem
- Ross Walker (Thu Apr 29 2010 - 05:59:52 PDT)
- aapeters.ncsu.edu (Thu Apr 29 2010 - 04:58:49 PDT)
- Ross Walker (Thu Apr 29 2010 - 02:09:11 PDT)
- Ross Walker (Tue Apr 20 2010 - 15:43:51 PDT)
- aapeters.ncsu.edu (Tue Apr 20 2010 - 11:27:46 PDT)
- Ross Walker (Tue Apr 20 2010 - 10:20:07 PDT)
- M. L. Dodson (Tue Apr 20 2010 - 10:04:35 PDT)
- aapeters.ncsu.edu (Tue Apr 20 2010 - 09:36:18 PDT)
[AMBER] QMMM Iron
- Gustavo Seabra (Thu Apr 01 2010 - 11:20:37 PDT)
- Ross Walker (Thu Apr 01 2010 - 11:09:45 PDT)
- Ross Walker (Thu Apr 01 2010 - 09:00:32 PDT)
- Dmitry Mukha (Thu Apr 01 2010 - 03:07:08 PDT)
- Dmitry Mukha (Thu Apr 01 2010 - 02:15:23 PDT)
[AMBER] question about Amber Tutorial-A1
- Rui Li (Fri Apr 23 2010 - 21:57:54 PDT)
- Ross Walker (Fri Apr 23 2010 - 08:04:24 PDT)
- Rui Li (Fri Apr 23 2010 - 03:55:26 PDT)
[AMBER] question about cluster analysis
- Jianing (Tue Apr 27 2010 - 20:01:11 PDT)
[AMBER] question about EVB
- Ganesh Kamath (Tue Apr 06 2010 - 11:45:28 PDT)
[AMBER] question about mass card of frcmod file
- Bill Ross (Thu Apr 29 2010 - 16:07:25 PDT)
- Jim Miller (Thu Apr 29 2010 - 14:50:52 PDT)
[AMBER] Question about RMSD in AMBER
- Yi Shang (Wed Apr 28 2010 - 08:44:51 PDT)
- Yingjie Lin (Wed Apr 28 2010 - 07:57:04 PDT)
- Carlos Simmerling (Tue Apr 27 2010 - 18:14:46 PDT)
- Yingjie Lin (Tue Apr 27 2010 - 17:42:55 PDT)
[AMBER] question on section 2 of MM-PBSA tutorial
- Andrew Voronkov (Thu Apr 08 2010 - 00:14:17 PDT)
[AMBER] Question: ptraj masks
- Carlos Simmerling (Wed Apr 28 2010 - 14:28:37 PDT)
- Yingjie Lin (Wed Apr 28 2010 - 14:22:19 PDT)
[AMBER] radius of gyration
- Taufik Al-Sarraj (Fri Apr 16 2010 - 07:28:36 PDT)
- Ganesh Kamath (Thu Apr 15 2010 - 12:42:29 PDT)
- Ganesh Kamath (Tue Apr 06 2010 - 11:43:22 PDT)
[AMBER] RAMD
- Vlad Cojocaru (Mon Apr 12 2010 - 01:48:36 PDT)
- gokul algates (Sun Apr 11 2010 - 22:51:39 PDT)
[AMBER] RAMD random number generator
- Vlad Cojocaru (Thu Apr 15 2010 - 01:20:09 PDT)
- Waad RHAIEM (Wed Apr 14 2010 - 07:20:59 PDT)
[AMBER] reg-Generalized Born Approach
- Carlos Simmerling (Thu Apr 01 2010 - 05:12:13 PDT)
- case (Thu Apr 01 2010 - 05:12:03 PDT)
- maya maya (Wed Mar 31 2010 - 21:49:20 PDT)
[AMBER] regarding antechamber
- case (Mon Apr 12 2010 - 04:43:24 PDT)
- Asfa Ali (Sun Apr 11 2010 - 23:17:11 PDT)
[AMBER] regarding parameter file creation of dna-lig complex
- Asfa Ali (Tue Apr 13 2010 - 21:40:45 PDT)
- Bill Ross (Tue Apr 13 2010 - 13:29:25 PDT)
- Asfa Ali (Tue Apr 13 2010 - 12:37:15 PDT)
[AMBER] Regarding parameter files of dna-lig complex
- Bill Ross (Tue Apr 13 2010 - 10:01:14 PDT)
- Jason Swails (Tue Apr 13 2010 - 06:46:49 PDT)
- Asfa Ali (Mon Apr 12 2010 - 23:08:18 PDT)
[AMBER] Regarding RDF calculation in Ptraj
- Daniel Roe (Mon Apr 05 2010 - 05:04:31 PDT)
- aneesh cna (Fri Apr 02 2010 - 21:49:06 PDT)
[AMBER] regarding running Nudged Elastic Band Approach with amber10
- Jason Swails (Wed Apr 21 2010 - 05:10:58 PDT)
- jani vinod (Tue Apr 20 2010 - 20:12:28 PDT)
- Carlos Simmerling (Tue Apr 20 2010 - 03:20:28 PDT)
- jani vinod (Mon Apr 19 2010 - 21:11:52 PDT)
- Ross Walker (Mon Apr 19 2010 - 13:30:56 PDT)
- jani vinod (Mon Apr 19 2010 - 02:18:29 PDT)
[AMBER] regarding sqm
- Asfa Ali (Thu Apr 22 2010 - 06:17:13 PDT)
- Jason Swails (Thu Apr 22 2010 - 05:15:26 PDT)
- Asfa Ali (Wed Apr 21 2010 - 23:51:32 PDT)
[AMBER] regGB
- maya maya (Thu Apr 08 2010 - 23:37:53 PDT)
- case (Thu Apr 08 2010 - 07:59:47 PDT)
- maya maya (Thu Apr 08 2010 - 03:51:23 PDT)
[AMBER] remove water from system
- Jason Swails (Wed Apr 21 2010 - 04:37:47 PDT)
- Carlos Simmerling (Wed Apr 21 2010 - 03:29:56 PDT)
- Yunfen Wang (Wed Apr 21 2010 - 02:42:38 PDT)
- Yunfen Wang (Tue Apr 20 2010 - 17:53:36 PDT)
- Bill Ross (Tue Apr 20 2010 - 10:02:32 PDT)
- Jason Swails (Tue Apr 20 2010 - 05:16:42 PDT)
- Carlos Simmerling (Tue Apr 20 2010 - 03:06:21 PDT)
- Yunfen Wang (Tue Apr 20 2010 - 01:09:01 PDT)
[AMBER] Request for MD protocol
- steinbrt.rci.rutgers.edu (Tue Apr 20 2010 - 07:14:31 PDT)
- George Tzotzos (Tue Apr 20 2010 - 07:07:11 PDT)
[AMBER] RESP Iodine
- William Flak (Sun Apr 25 2010 - 04:52:21 PDT)
[AMBER] rna simulation
- Bill Ross (Mon Apr 05 2010 - 10:50:27 PDT)
- Bill Ross (Mon Apr 05 2010 - 10:32:50 PDT)
- Jason Swails (Mon Apr 05 2010 - 02:34:48 PDT)
- shamoon siddiqui (Sun Apr 04 2010 - 23:59:47 PDT)
- Asfa Ali (Sun Apr 04 2010 - 23:47:38 PDT)
- shamoon siddiqui (Sun Apr 04 2010 - 23:23:34 PDT)
- Asfa Ali (Sun Apr 04 2010 - 23:12:59 PDT)
- shamoon siddiqui (Sun Apr 04 2010 - 22:50:47 PDT)
- Asfa Ali (Sun Apr 04 2010 - 22:42:33 PDT)
[AMBER] SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate disagreement
- imtiaz shafiq (Thu Apr 01 2010 - 06:15:20 PDT)
[AMBER] SASA
- Chih-Ying Lin (Sun Apr 04 2010 - 17:39:45 PDT)
- case (Thu Apr 01 2010 - 05:17:36 PDT)
- Beale, John (Thu Apr 01 2010 - 03:39:26 PDT)
[AMBER] Second Request
- Dima A Sabbah (Mon Apr 12 2010 - 06:59:56 PDT)
[AMBER] Segmentation Fault
- Ross Walker (Thu Apr 01 2010 - 12:14:42 PDT)
- Beale, John (Thu Apr 01 2010 - 11:52:34 PDT)
[AMBER] Setup of defined salt concentrations
- Bill Ross (Tue Apr 20 2010 - 10:29:24 PDT)
- Bill Ross (Tue Apr 20 2010 - 10:13:06 PDT)
- Dean Cuebas (Tue Apr 20 2010 - 09:14:17 PDT)
- InSuk Joung (Tue Apr 20 2010 - 07:44:24 PDT)
- Anselm Horn (Tue Apr 20 2010 - 06:16:33 PDT)
[AMBER] Simulation of complex
- Bill Ross (Wed Apr 21 2010 - 09:34:02 PDT)
- Asfa Ali (Wed Apr 21 2010 - 04:39:34 PDT)
- N.R. Jena (Wed Apr 21 2010 - 04:10:20 PDT)
- N.R. Jena (Wed Apr 21 2010 - 04:05:31 PDT)
- steinbrt.rci.rutgers.edu (Wed Apr 21 2010 - 04:03:40 PDT)
- Asfa Ali (Wed Apr 21 2010 - 03:51:04 PDT)
- steinbrt.rci.rutgers.edu (Wed Apr 21 2010 - 02:24:12 PDT)
- Asfa Ali (Wed Apr 21 2010 - 00:19:23 PDT)
- Dean Cuebas (Mon Apr 19 2010 - 09:52:00 PDT)
- Bill Ross (Mon Apr 19 2010 - 09:48:56 PDT)
- steinbrt.rci.rutgers.edu (Mon Apr 19 2010 - 08:42:43 PDT)
- Shozeb Haider (Mon Apr 19 2010 - 08:26:21 PDT)
- Asfa Ali (Mon Apr 19 2010 - 08:22:17 PDT)
[AMBER] sleap from AT 1.4 doesn't seem ok
- case (Thu Apr 29 2010 - 06:43:59 PDT)
- Alan (Wed Apr 28 2010 - 11:35:12 PDT)
[AMBER] slightly off topic: suggestions for DNA single strand simulations
- Bill Ross (Wed Apr 14 2010 - 10:25:47 PDT)
- Asfa Ali (Wed Apr 14 2010 - 10:02:25 PDT)
- Bill Ross (Wed Apr 14 2010 - 09:43:10 PDT)
- Asfa Ali (Tue Apr 13 2010 - 21:21:44 PDT)
- Thomas Cheatham (Tue Apr 13 2010 - 20:13:55 PDT)
- Amedeo Capobianco (Sun Apr 11 2010 - 14:11:02 PDT)
[AMBER] Solvent
- Ganesh Kamath (Fri Apr 09 2010 - 08:53:36 PDT)
- Beale, John (Fri Apr 09 2010 - 08:41:51 PDT)
[AMBER] solvent accessible surface
- Bill Miller III (Wed Apr 21 2010 - 20:41:02 PDT)
- Yunfen Wang (Wed Apr 21 2010 - 20:27:11 PDT)
[AMBER] Sorry for my multiple-email (making mistake!)
- Rilei Yu (Sat Apr 03 2010 - 05:12:51 PDT)
[AMBER] Stability Calculation Using MMPBSA.py?
- Hopkins, Robert (Thu Apr 29 2010 - 13:24:31 PDT)
- Jason Swails (Thu Apr 29 2010 - 12:49:12 PDT)
- Hopkins, Robert (Thu Apr 29 2010 - 12:36:45 PDT)
[AMBER] Steered/Targeted MD
- Ahmad, Rafi (Thu Apr 15 2010 - 09:08:46 PDT)
[AMBER] Strange atom charge in topology file
- pellegrini (Tue Apr 20 2010 - 08:12:01 PDT)
- Yi Shang (Tue Apr 20 2010 - 07:21:07 PDT)
- Yi Shang (Tue Apr 20 2010 - 07:02:23 PDT)
- pellegrini (Tue Apr 20 2010 - 06:20:33 PDT)
[AMBER] TER dfinition at the middile of pdb file
- Jason Swails (Fri Apr 30 2010 - 20:29:23 PDT)
[AMBER] Tesla C2050 atom limit?
- Ross Walker (Thu Apr 29 2010 - 01:12:22 PDT)
- Scott Le Grand (Thu Apr 29 2010 - 00:02:17 PDT)
- ben rodriguez (Wed Apr 28 2010 - 17:44:43 PDT)
[AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
- Marek Maly (Tue Apr 27 2010 - 07:32:04 PDT)
- Ramu Anandakrishnan (Tue Apr 27 2010 - 05:43:17 PDT)
- Marek Maly (Wed Apr 21 2010 - 16:07:39 PDT)
- Jason Swails (Wed Apr 21 2010 - 13:02:10 PDT)
- Marek Maly (Wed Apr 21 2010 - 10:29:39 PDT)
- Jason Swails (Wed Apr 21 2010 - 06:35:38 PDT)
- Marek Maly (Tue Apr 20 2010 - 12:54:04 PDT)
[AMBER] The system has extended beyond the extent of the virtual box
- kamlesh sahu (Mon Apr 26 2010 - 17:23:17 PDT)
- Carlos Simmerling (Mon Apr 26 2010 - 03:50:00 PDT)
- kamlesh sahu (Mon Apr 26 2010 - 01:31:23 PDT)
[AMBER] the volume is always getting bigger and bigger until crash
- Carlos Simmerling (Wed Apr 14 2010 - 17:50:04 PDT)
- Yunfen Wang (Wed Apr 14 2010 - 17:47:38 PDT)
- Carlos Simmerling (Wed Apr 14 2010 - 03:05:14 PDT)
- Yunfen Wang (Wed Apr 14 2010 - 00:56:11 PDT)
[AMBER] thermodynamic integration
- steinbrt.rci.rutgers.edu (Sat Apr 03 2010 - 08:02:45 PDT)
- Hyma vathi (Fri Apr 02 2010 - 23:00:12 PDT)
[AMBER] Thole screening in sander
- case (Wed Apr 14 2010 - 08:09:49 PDT)
- Diddo Diddens (Wed Apr 14 2010 - 07:31:23 PDT)
[AMBER] to test nab with openmp
- Alan (Thu Apr 29 2010 - 00:42:59 PDT)
[AMBER] Traceback: not available, complile with -ftrace = frame
- Bill Ross (Fri Apr 09 2010 - 08:57:00 PDT)
- Jason Swails (Thu Apr 08 2010 - 18:52:24 PDT)
- Yunfen Wang (Thu Apr 08 2010 - 18:35:20 PDT)
- Bill Ross (Thu Apr 08 2010 - 09:44:24 PDT)
- Jason Swails (Thu Apr 08 2010 - 05:51:34 PDT)
- Yunfen Wang (Wed Apr 07 2010 - 23:33:58 PDT)
- Jason Swails (Wed Apr 07 2010 - 21:03:31 PDT)
- Yunfen Wang (Wed Apr 07 2010 - 20:51:39 PDT)
- Jason Swails (Wed Apr 07 2010 - 07:00:05 PDT)
- Yunfen Wang (Wed Apr 07 2010 - 06:56:33 PDT)
[AMBER] Trajectory Smoothing
- Ganesh Krishnan (Sun Apr 18 2010 - 13:22:43 PDT)
- Ganesh Krishnan (Sun Apr 18 2010 - 12:53:12 PDT)
- Carlos Simmerling (Sun Apr 18 2010 - 12:34:17 PDT)
- Bill Ross (Sun Apr 18 2010 - 12:12:56 PDT)
- Ganesh Krishnan (Sun Apr 18 2010 - 12:02:34 PDT)
- David A. Case (Sun Apr 18 2010 - 11:19:56 PDT)
- Ganesh Krishnan (Sun Apr 18 2010 - 10:25:47 PDT)
- David A. Case (Sun Apr 18 2010 - 00:37:24 PDT)
- Ganesh Krishnan (Sat Apr 17 2010 - 23:50:58 PDT)
- Jason Swails (Sat Apr 17 2010 - 14:45:22 PDT)
- Daniel Roe (Sat Apr 17 2010 - 13:52:13 PDT)
- Ganesh Krishnan (Sat Apr 17 2010 - 09:43:41 PDT)
- Bill Ross (Thu Apr 15 2010 - 07:47:22 PDT)
- Bill Miller III (Thu Apr 15 2010 - 04:09:28 PDT)
- Ganesh Krishnan (Wed Apr 14 2010 - 19:23:15 PDT)
[AMBER] trying to use antechamber with -nc 0 for a molecule
- Alan (Mon Apr 12 2010 - 09:14:35 PDT)
- zoran matovic (Mon Apr 12 2010 - 08:50:03 PDT)
- Alan (Mon Apr 12 2010 - 08:29:57 PDT)
- case (Mon Apr 12 2010 - 07:23:50 PDT)
- Alan (Mon Apr 12 2010 - 07:03:13 PDT)
[AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint
- Matthias Wildauer (Wed Apr 07 2010 - 11:53:53 PDT)
- case (Wed Apr 07 2010 - 11:51:06 PDT)
- Seetin, Matthew (Wed Apr 07 2010 - 11:50:33 PDT)
- Matthias Wildauer (Wed Apr 07 2010 - 11:04:45 PDT)
[AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
- Yu Chen (Fri Apr 30 2010 - 11:20:30 PDT)
- Bill Ross (Fri Apr 30 2010 - 10:07:57 PDT)
- Yu Chen (Fri Apr 30 2010 - 08:46:55 PDT)
- Yu Chen (Fri Apr 30 2010 - 08:25:35 PDT)
- case (Fri Apr 30 2010 - 07:41:11 PDT)
- David Watson (Fri Apr 30 2010 - 07:29:35 PDT)
- Yu Chen (Fri Apr 30 2010 - 07:10:44 PDT)
[AMBER] undo iwrap wrapping
- Carlos Simmerling (Mon Apr 05 2010 - 03:30:53 PDT)
- Paul Brandt (Mon Apr 05 2010 - 00:21:22 PDT)
[AMBER] Unit of analyze modes with ptraj
- David A. Case (Thu Apr 15 2010 - 14:40:51 PDT)
- Samuel Genheden (Thu Apr 15 2010 - 11:22:21 PDT)
- Samuel Genheden (Tue Apr 06 2010 - 02:54:28 PDT)
[AMBER] Unit of atomic fluctuation unit
- Kshatresh Dutta Dubey (Mon Apr 05 2010 - 23:22:51 PDT)
- nicholus bhattacharjee (Mon Apr 05 2010 - 22:39:26 PDT)
[AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA
- Juan Carlos (Thu Apr 08 2010 - 03:49:08 PDT)
- Daniel Roe (Tue Apr 06 2010 - 09:25:53 PDT)
- Robert Duke (Tue Apr 06 2010 - 06:20:50 PDT)
- Juan Carlos (Tue Apr 06 2010 - 00:35:40 PDT)
[AMBER] vacuum bubbles generated after heating
- Nicee (Tue Apr 13 2010 - 05:53:40 PDT)
- jani vinod (Tue Apr 13 2010 - 02:26:34 PDT)
- Bill Ross (Mon Apr 12 2010 - 13:49:47 PDT)
- Bill Ross (Mon Apr 12 2010 - 10:41:30 PDT)
- Jason Swails (Mon Apr 12 2010 - 03:11:45 PDT)
- Nicee (Mon Apr 12 2010 - 02:59:32 PDT)
[AMBER] vdW question.
- Bill Ross (Thu Apr 22 2010 - 10:14:15 PDT)
- Bill Ross (Thu Apr 22 2010 - 09:40:33 PDT)
- ros (Thu Apr 22 2010 - 08:43:25 PDT)
- steinbrt.rci.rutgers.edu (Thu Apr 22 2010 - 00:22:14 PDT)
- Kevin Hauser (Wed Apr 21 2010 - 20:26:50 PDT)
- Jason Swails (Wed Apr 21 2010 - 19:29:39 PDT)
- ros (Wed Apr 21 2010 - 18:41:38 PDT)
[AMBER] Vlimit error in ABMD
- Emmanuel Baribefe Naziga (Mon Apr 12 2010 - 09:06:44 PDT)
[AMBER] vlimit exceeded for step
- Rilei Yu (Sat Apr 10 2010 - 00:47:33 PDT)
- Jason Swails (Fri Apr 09 2010 - 16:59:01 PDT)
- Rilei Yu (Fri Apr 09 2010 - 16:50:56 PDT)
- Ross Walker (Fri Apr 09 2010 - 11:59:53 PDT)
- Thomas Cheatham III (Fri Apr 09 2010 - 08:02:34 PDT)
- Jason Swails (Fri Apr 09 2010 - 05:36:33 PDT)
- Rilei Yu (Thu Apr 08 2010 - 23:52:31 PDT)
[AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
- Lachele Foley (Lists) (Mon Apr 12 2010 - 05:51:07 PDT)
- Daniel Roe (Mon Apr 12 2010 - 05:29:53 PDT)
- Carlos Simmerling (Mon Apr 12 2010 - 04:35:12 PDT)
- Silvia Carlotto (Mon Apr 12 2010 - 04:30:36 PDT)
- Jason Swails (Mon Apr 12 2010 - 03:03:35 PDT)
- Silvia Carlotto (Mon Apr 12 2010 - 02:08:50 PDT)
[AMBER] WARNING: There is a bond of 8.894214 angstroms between
- Bill Ross (Mon Apr 26 2010 - 10:23:21 PDT)
- Bill Ross (Mon Apr 26 2010 - 10:19:28 PDT)
- Hyma vathi (Mon Apr 26 2010 - 09:58:35 PDT)
- case (Mon Apr 26 2010 - 05:50:39 PDT)
- Dmitry Nilov (Mon Apr 26 2010 - 03:53:15 PDT)
- Hyma vathi (Mon Apr 26 2010 - 02:55:59 PDT)
- Dmitry Nilov (Mon Apr 26 2010 - 02:33:01 PDT)
- Hyma vathi (Mon Apr 26 2010 - 02:19:30 PDT)
[AMBER] Water models ?
- Carlos Simmerling (Thu Apr 01 2010 - 06:07:49 PDT)
- xuemeiwang1103 (Thu Apr 01 2010 - 06:01:05 PDT)
[AMBER] xgrid in opempi 1.4.1 still broken
- case (Fri Apr 30 2010 - 09:35:02 PDT)
- Alan (Fri Apr 30 2010 - 08:04:24 PDT)
[AMBER] 转发: MMPBSA-on-cluster
- Rilei Yu (Sat Apr 03 2010 - 03:15:25 PDT)
[AMBER]Fortran runtime error: Bad value during integer read
- Jason Swails (Tue Apr 27 2010 - 21:38:13 PDT)
- Jason Swails (Tue Apr 27 2010 - 21:15:45 PDT)
- Ying Yang (Tue Apr 27 2010 - 19:53:44 PDT)
- Jason Swails (Tue Apr 27 2010 - 05:15:37 PDT)
- Ying Yang (Mon Apr 26 2010 - 23:59:54 PDT)
a possible typo bug while building pmemd with mpi
- Alan (Thu Apr 29 2010 - 08:45:56 PDT)
failed to compile Amber11 with mpi on Mac
- Alan (Thu Apr 29 2010 - 07:51:56 PDT)
Is the variation of C-Cl bond length normal?
- Shulin Zhuang (Tue Apr 13 2010 - 11:25:58 PDT)
ligand exchange
- case (Tue Apr 06 2010 - 04:42:13 PDT)
- John S (Tue Apr 06 2010 - 01:35:39 PDT)
question on section 2 of MM-PBSA tutorial
- Ross Walker (Fri Apr 16 2010 - 18:29:31 PDT)
- Andrew Voronkov (Fri Apr 16 2010 - 13:57:54 PDT)
to test nab with openmp
- Alan (Thu Apr 29 2010 - 03:09:22 PDT)
- Alan (Thu Apr 29 2010 - 02:13:18 PDT)

Amber Archive Apr 2010 by subject