Amber Archive Mar 2009: by subject

[AMBER] "rfree: End of file on unit 5"
- mathew k varghese (Mon Mar 30 2009 - 02:57:44 PDT)
- Remya S R (Sun Mar 29 2009 - 23:21:53 PDT)
[AMBER] .rst file generation problem.
- Carlos Simmerling (Tue Mar 31 2009 - 04:28:35 PDT)
- Aravind S (Tue Mar 31 2009 - 01:49:17 PDT)
- Carlos Simmerling (Mon Mar 30 2009 - 04:30:58 PDT)
- Aravind S (Sun Mar 29 2009 - 23:32:12 PDT)
- Aravind S (Sun Mar 29 2009 - 22:48:55 PDT)
[AMBER] 8Mureabox
- anna berteotti (Wed Mar 11 2009 - 01:45:03 PDT)
- David A. Case (Tue Mar 10 2009 - 05:51:08 PDT)
- anna berteotti (Mon Mar 09 2009 - 03:07:52 PDT)
[AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy?
- FyD (Sun Mar 22 2009 - 13:12:17 PDT)
- Youn Kyeung Lee (Thu Mar 19 2009 - 00:31:16 PDT)
[AMBER] A good way to use an Amber force field with NAMD?
- Sasha Buzko (Wed Mar 04 2009 - 09:58:09 PST)
- Robert Duke (Tue Mar 03 2009 - 20:26:59 PST)
- Sasha Buzko (Tue Mar 03 2009 - 18:55:56 PST)
- Ross Walker (Tue Mar 03 2009 - 17:33:58 PST)
- Sasha Buzko (Tue Mar 03 2009 - 16:26:44 PST)
- Adrian Roitberg (Tue Mar 03 2009 - 16:11:49 PST)
- Gustavo Seabra (Tue Mar 03 2009 - 16:08:33 PST)
- Sasha Buzko (Tue Mar 03 2009 - 13:37:29 PST)
[AMBER] About error of "vertex atom mismatch"
- 廖青华 (Wed Mar 18 2009 - 01:30:29 PDT)
[AMBER] About Free energy decomposition
- Rajesh Raju (Wed Mar 25 2009 - 07:08:00 PDT)
[AMBER] about MD simulation
- Carlos Simmerling (Wed Mar 11 2009 - 03:56:43 PDT)
- 廖青华 (Wed Mar 11 2009 - 02:19:28 PDT)
[AMBER] about mm-pbsa
- 廖青华 (Mon Mar 23 2009 - 02:10:29 PDT)
- 廖青华 (Wed Mar 18 2009 - 23:48:21 PDT)
- Wei Huang (Mon Mar 16 2009 - 08:17:30 PDT)
- 廖青华 (Mon Mar 16 2009 - 08:02:49 PDT)
- 廖青华 (Mon Mar 16 2009 - 07:59:40 PDT)
[AMBER] Actual force constant in SMD
- Dmitri Nilov (Mon Mar 16 2009 - 11:07:09 PDT)
[AMBER] adding chain id to ptraj pdb output
- Joe Krahn (Mon Mar 23 2009 - 16:20:30 PDT)
- Bala subramanian (Mon Mar 23 2009 - 04:37:43 PDT)
- Paul Brandt (Sat Mar 21 2009 - 19:09:59 PDT)
[AMBER] addles segmentation fault
- xiaonan zhang (Mon Mar 09 2009 - 06:08:47 PDT)
- Carlos Simmerling (Mon Mar 09 2009 - 04:45:24 PDT)
- gmail (Mon Mar 09 2009 - 01:28:56 PDT)
[AMBER] Amber 10 and core i7
- Supat Jiranusornkul (Thu Mar 26 2009 - 02:13:10 PDT)
[AMBER] AMBER installation : compilation error
- Catein Catherine (Wed Mar 04 2009 - 18:53:54 PST)
[AMBER] amber tools installation
- case (Mon Mar 30 2009 - 09:28:38 PDT)
- Jayalakshmi Sridhar (Mon Mar 30 2009 - 08:44:57 PDT)
[AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory
- Jeff Schwinefus (Wed Mar 04 2009 - 21:22:34 PST)
- Thomas Cheatham III (Wed Mar 04 2009 - 11:59:30 PST)
- Jeff Schwinefus (Tue Mar 03 2009 - 14:18:25 PST)
[AMBER] ambmol2?
- Taufik Al-Sarraj (Tue Mar 31 2009 - 15:28:51 PDT)
[AMBER] analysing DNA trajectory
- Bala subramanian (Fri Mar 20 2009 - 01:06:08 PDT)
[AMBER] analysis on Amber
- Thomas Cheatham (Sat Mar 07 2009 - 10:18:58 PST)
- oguz gurbulak (Sat Mar 07 2009 - 10:04:19 PST)
[AMBER] angle between ligand ring plane and axis
- Jia Xu (Wed Mar 04 2009 - 03:00:08 PST)
[AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany
- Harald Lanig (Fri Mar 20 2009 - 04:25:09 PDT)
[AMBER] Announcing NMR validation web interface iCing
- Alan (Mon Mar 30 2009 - 09:55:00 PDT)
[AMBER] Antechamber problem
- 欧阳德方 (Fri Mar 27 2009 - 17:55:03 PDT)
- Junmei Wang (Fri Mar 27 2009 - 14:21:33 PDT)
- David A. Case (Fri Mar 27 2009 - 05:29:48 PDT)
- 欧阳德方 (Thu Mar 26 2009 - 21:44:24 PDT)
[AMBER] assigning velocities to each atom without heating the system
- Ross Walker (Mon Mar 02 2009 - 12:23:22 PST)
- Parimal Kar (Mon Mar 02 2009 - 09:46:25 PST)
- Gustavo Seabra (Mon Mar 02 2009 - 09:31:09 PST)
- Parimal Kar (Mon Mar 02 2009 - 08:44:26 PST)
[AMBER] BINDER/xaLeap
- taufik.alsarraj.utoronto.ca (Mon Mar 30 2009 - 19:16:32 PDT)
- Ross Walker (Mon Mar 30 2009 - 18:29:46 PDT)
- Taufik Al-Sarraj (Mon Mar 30 2009 - 18:00:10 PDT)
[AMBER] binding free energy
- Ross Walker (Mon Mar 02 2009 - 12:16:55 PST)
- Robert Duke (Mon Mar 02 2009 - 05:22:22 PST)
- Ross Walker (Sun Mar 01 2009 - 09:29:35 PST)
- Don.Bashford.stjude.org (Sun Mar 01 2009 - 09:18:39 PST)
- Barbault Florent (Sun Mar 01 2009 - 04:20:39 PST)
[AMBER] calculate shear viscosity
- oguz gurbulak (Mon Mar 02 2009 - 05:35:06 PST)
[AMBER] catenan simulation problems
- David A. Case (Wed Mar 18 2009 - 04:47:32 PDT)
- David A. Case (Sat Mar 07 2009 - 15:25:07 PST)
- Cristina S.D. Sisu (Fri Mar 06 2009 - 07:35:46 PST)
- Cristina Sisu (Fri Mar 06 2009 - 07:28:00 PST)
- David A. Case (Fri Mar 06 2009 - 06:59:24 PST)
- Cristina Sisu (Fri Mar 06 2009 - 05:16:08 PST)
[AMBER] CCL4 simulation
- David A. Case (Wed Mar 18 2009 - 04:06:30 PDT)
- sudipta (Wed Mar 18 2009 - 00:47:48 PDT)
- David A. Case (Tue Mar 17 2009 - 19:14:51 PDT)
- sudipta (Tue Mar 17 2009 - 11:18:07 PDT)
[AMBER] change in protein ligand order
- Hannes Wallnoefer (Tue Mar 24 2009 - 13:45:16 PDT)
- Bill Ross (Tue Mar 24 2009 - 11:07:42 PDT)
- Hannes Wallnoefer (Tue Mar 24 2009 - 05:38:18 PDT)
- Hannes Loeffler (Tue Mar 24 2009 - 04:27:24 PDT)
- Hannes Wallnoefer (Tue Mar 24 2009 - 04:05:36 PDT)
[AMBER] Changing Force Fields in "Midstream"
- Hopkins, Robert (Thu Mar 12 2009 - 13:45:46 PDT)
- David A. Case (Wed Mar 11 2009 - 15:36:56 PDT)
- Kristina Furse (Wed Mar 11 2009 - 14:58:06 PDT)
- Wei Zhang (Wed Mar 11 2009 - 14:42:52 PDT)
- Hopkins, Robert (Wed Mar 11 2009 - 14:36:12 PDT)
- Hopkins, Robert (Tue Mar 10 2009 - 16:29:44 PDT)
- Ross Walker (Mon Mar 09 2009 - 17:21:15 PDT)
- Hopkins, Robert (Mon Mar 09 2009 - 17:12:27 PDT)
[AMBER] chemical shift penalty
- David A. Case (Thu Mar 05 2009 - 15:59:33 PST)
- Jacopo Sgrignani (Thu Mar 05 2009 - 01:47:03 PST)
[AMBER] combine many coord files into trajectory file
- Peter Gannett (Tue Mar 31 2009 - 07:25:00 PDT)
- Carlos Simmerling (Tue Mar 31 2009 - 06:55:58 PDT)
- Peter Gannett (Tue Mar 31 2009 - 06:51:16 PDT)
[AMBER] Compilation and qmmm_div
- Benjamin Roberts (Wed Mar 04 2009 - 16:15:37 PST)
- Ross Walker (Wed Mar 04 2009 - 08:36:07 PST)
- Benjamin Roberts (Wed Mar 04 2009 - 07:48:16 PST)
[AMBER] continuam water
- Carlos Simmerling (Tue Mar 24 2009 - 06:36:15 PDT)
- Mannan (Mon Mar 23 2009 - 21:11:50 PDT)
[AMBER] convert .mol2 file to .pdb with atomtype definitions
- Pankaj R. Daga (Tue Mar 17 2009 - 09:41:20 PDT)
- Wei Zhang (Tue Mar 17 2009 - 09:33:27 PDT)
- Pansy Patel (Tue Mar 17 2009 - 09:09:10 PDT)
- David A. Case (Tue Mar 17 2009 - 09:00:19 PDT)
- Pansy Patel (Tue Mar 17 2009 - 08:50:57 PDT)
[AMBER] create new crd files from transformed coordinates
- case (Wed Mar 25 2009 - 05:26:29 PDT)
- Donald Keidel (Tue Mar 24 2009 - 18:49:03 PDT)
[AMBER] Creating conditions for biased MD
- Carlos Simmerling (Mon Mar 30 2009 - 04:56:36 PDT)
- Francesco Pietra (Mon Mar 30 2009 - 03:16:54 PDT)
[AMBER] divcon error during antechamber run, convergence problem
- Andrew Voronkov (Sat Mar 07 2009 - 07:58:19 PST)
- David A. Case (Fri Mar 06 2009 - 10:33:24 PST)
- Andrew Voronkov (Fri Mar 06 2009 - 10:04:55 PST)
- Martin Peters (Thu Mar 05 2009 - 06:21:19 PST)
- drugdesign (Thu Mar 05 2009 - 05:53:59 PST)
[AMBER] DNA simulation: Problem with RMSD
- BERGY (Thu Mar 05 2009 - 22:20:00 PST)
- Thomas Cheatham (Wed Mar 04 2009 - 20:04:53 PST)
- BERGY (Wed Mar 04 2009 - 19:44:26 PST)
[AMBER] doubt-reg_ Targeted molecular dynamics
- balaji nagarajan (Fri Mar 13 2009 - 09:20:41 PDT)
[AMBER] error for nmode
- David A. Case (Thu Mar 19 2009 - 04:31:24 PDT)
- Dechang Li (Thu Mar 19 2009 - 04:00:09 PDT)
[AMBER] error in constructing DNA from nucgen
- Bill Ross (Tue Mar 17 2009 - 15:47:07 PDT)
- Ross Walker (Tue Mar 17 2009 - 12:31:16 PDT)
- Pansy Patel (Tue Mar 17 2009 - 12:24:58 PDT)
- Carlos Simmerling (Tue Mar 17 2009 - 11:53:05 PDT)
- Pansy Patel (Tue Mar 17 2009 - 11:43:49 PDT)
[AMBER] errors about install amber9 on MAC OS
- David A. Case (Wed Mar 18 2009 - 04:08:44 PDT)
- zgong.hust (Wed Mar 18 2009 - 01:41:19 PDT)
[AMBER] errors on reading time series file in WHAM calculation
- Jenny Iskrenova (Tue Mar 24 2009 - 07:35:51 PDT)
- gmail (Mon Mar 23 2009 - 17:35:02 PDT)
[AMBER] Fail to allocate ff
- Gustavo Seabra (Tue Mar 03 2009 - 12:36:53 PST)
- Madhurima Jana (Tue Mar 03 2009 - 06:27:41 PST)
- Nicholas Musolino (Tue Mar 03 2009 - 05:10:21 PST)
- Madhurima Jana (Tue Mar 03 2009 - 03:17:57 PST)
[AMBER] Free Energy Decomposition Problem
- ozlem ulucan (Mon Mar 09 2009 - 06:55:45 PDT)
[AMBER] Fwd: AMBER: MM-PBSA in AMBER 10
- Ray Luo (Thu Mar 26 2009 - 16:54:17 PDT)
- Daniel Oehme (Thu Mar 26 2009 - 16:44:59 PDT)
[AMBER] Fwd: please help me out
- bharat lakhani (Wed Mar 04 2009 - 20:42:06 PST)
[AMBER] GBSA: dielectric symmetry
- David A. Case (Thu Mar 05 2009 - 16:05:51 PST)
- Giacomo Bastianelli (Thu Mar 05 2009 - 15:29:50 PST)
[AMBER] generalized distance restraint
- Rausch, Felix (Wed Mar 11 2009 - 00:39:05 PDT)
- M. L. Dodson (Mon Mar 09 2009 - 09:51:19 PDT)
- Carlos Simmerling (Mon Mar 09 2009 - 09:39:43 PDT)
- Rausch, Felix (Mon Mar 09 2009 - 09:15:11 PDT)
- Carlos Simmerling (Mon Mar 09 2009 - 08:13:50 PDT)
- Rausch, Felix (Mon Mar 09 2009 - 06:48:01 PDT)
[AMBER] H-Bonds
- Thomas Cheatham III (Wed Mar 04 2009 - 13:00:30 PST)
[AMBER] helical parameters
- Bala subramanian (Mon Mar 23 2009 - 11:14:29 PDT)
[AMBER] Help needed in amber parallel installation
- Ross Walker (Fri Mar 20 2009 - 08:40:30 PDT)
- Carlos Simmerling (Fri Mar 20 2009 - 04:34:31 PDT)
- sushobhan.iiar.res.in (Thu Mar 19 2009 - 23:39:36 PDT)
[AMBER] Help with torsions in parm99.dat file
- Wei Zhang (Mon Mar 09 2009 - 07:38:56 PDT)
- Astrid Maaß (Mon Mar 09 2009 - 06:27:30 PDT)
- Ross Walker (Fri Mar 06 2009 - 22:32:23 PST)
- Gregersen, Brent (Fri Mar 06 2009 - 18:15:11 PST)
- Ross Walker (Fri Mar 06 2009 - 16:52:05 PST)
- Gregersen, Brent (Fri Mar 06 2009 - 14:44:17 PST)
[AMBER] High RMSD for DNA: A to B transition study
- David A. Case (Fri Mar 13 2009 - 05:00:40 PDT)
- SENTHIL KUMAR (Thu Mar 12 2009 - 23:36:43 PDT)
- David A. Case (Fri Mar 06 2009 - 06:57:02 PST)
- BERGY (Thu Mar 05 2009 - 23:26:57 PST)
[AMBER] How can I use the charge I calculated (using mol2 file) ?
- FyD (Tue Mar 03 2009 - 06:12:18 PST)
- David A. Case (Tue Mar 03 2009 - 05:39:26 PST)
- David A. Case (Mon Mar 02 2009 - 06:56:54 PST)
[AMBER] how to convert secstruct output file into plot or pictorial representation
- Siddharth Rastogi (Tue Mar 31 2009 - 03:56:37 PDT)
[AMBER] How to reproduce a parallel PMEMD run?
- Robert Duke (Wed Mar 25 2009 - 16:45:49 PDT)
- Siang Yip (Wed Mar 25 2009 - 15:33:56 PDT)
[AMBER] How to restart the umbrella sampling jobs?
- Gustavo Seabra (Tue Mar 03 2009 - 12:41:25 PST)
- Ross Walker (Tue Mar 03 2009 - 08:00:04 PST)
- Catein Catherine (Mon Mar 02 2009 - 21:52:16 PST)
[AMBER] hydrogen bond
- Ross Walker (Wed Mar 04 2009 - 08:39:49 PST)
- Carlos Simmerling (Wed Mar 04 2009 - 03:20:53 PST)
- . .. (Wed Mar 04 2009 - 03:12:33 PST)
[AMBER] IG not change at each restart of NPT simulation
- Robert Duke (Fri Mar 20 2009 - 06:58:18 PDT)
- Rajesh Raju (Fri Mar 20 2009 - 06:20:09 PDT)
- Robert Duke (Thu Mar 19 2009 - 07:05:35 PDT)
- Adrian Roitberg (Thu Mar 19 2009 - 06:30:10 PDT)
- Robert Duke (Thu Mar 19 2009 - 06:24:02 PDT)
- Rajesh Raju (Thu Mar 19 2009 - 05:54:26 PDT)
- Hopkins, Robert (Wed Mar 18 2009 - 16:15:54 PDT)
- Ross Walker (Wed Mar 18 2009 - 16:07:07 PDT)
- Hopkins, Robert (Wed Mar 18 2009 - 15:55:33 PDT)
[AMBER] inpcrd and prmtop
- Gustavo Seabra (Tue Mar 03 2009 - 12:20:38 PST)
- FyD (Tue Mar 03 2009 - 02:19:43 PST)
- m m (Tue Mar 03 2009 - 02:08:51 PST)
- Hannes Loeffler (Tue Mar 03 2009 - 01:37:16 PST)
- m m (Tue Mar 03 2009 - 01:27:06 PST)
[AMBER] Input file of the second stage RESP fitting
- Cen Gao (Tue Mar 17 2009 - 14:24:24 PDT)
- FyD (Tue Mar 17 2009 - 06:32:58 PDT)
- Cen Gao (Mon Mar 16 2009 - 21:29:17 PDT)
[AMBER] installing AmberTools on Windows machines
- David A. Case (Wed Mar 11 2009 - 13:27:07 PDT)
[AMBER] installing resp on linux 64bit
- aditya chhikara (Thu Mar 26 2009 - 14:36:50 PDT)
- FyD (Thu Mar 26 2009 - 12:37:22 PDT)
- aditya chhikara (Thu Mar 26 2009 - 10:24:27 PDT)
[AMBER] leap and chirality
- Wei Zhang (Tue Mar 24 2009 - 05:55:47 PDT)
- Karl Kirschner (Tue Mar 24 2009 - 01:11:38 PDT)
- Wei Zhang (Mon Mar 23 2009 - 11:36:54 PDT)
- Karl Kirschner (Mon Mar 23 2009 - 07:05:56 PDT)
- David A. Case (Mon Mar 23 2009 - 06:16:14 PDT)
- Karl Kirschner (Mon Mar 23 2009 - 02:54:29 PDT)
[AMBER] lipid bliayers
- Hannes Loeffler (Wed Mar 18 2009 - 06:17:04 PDT)
- Urszula Uciechowska (Wed Mar 18 2009 - 06:00:32 PDT)
[AMBER] Load protein complex to Xleap (Combine)
- David A. Case (Sun Mar 29 2009 - 11:41:13 PDT)
- Rilei Yu (Sat Mar 28 2009 - 21:00:00 PDT)
- Rilei Yu (Sat Mar 28 2009 - 20:07:47 PDT)
- David A. Case (Sat Mar 28 2009 - 19:26:58 PDT)
- Rilei Yu (Sat Mar 28 2009 - 18:17:21 PDT)
- David A. Case (Sat Mar 28 2009 - 14:39:35 PDT)
- Rilei Yu (Fri Mar 27 2009 - 19:30:04 PDT)
[AMBER] Mass of LP
- David A. Case (Thu Mar 19 2009 - 04:27:48 PDT)
- PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 20:27:24 PDT)
[AMBER] Metal in MD simulation
- priya priya (Thu Mar 19 2009 - 23:15:06 PDT)
- Bill Ross (Thu Mar 19 2009 - 14:22:12 PDT)
- Ross Walker (Thu Mar 19 2009 - 08:12:24 PDT)
- Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 07:48:28 PDT)
- priya priya (Wed Mar 18 2009 - 23:25:09 PDT)
[AMBER] minimisation with igb=10
- Ray Luo (Mon Mar 16 2009 - 09:34:21 PDT)
- Carlos Simmerling (Mon Mar 16 2009 - 09:04:37 PDT)
- Bala subramanian (Mon Mar 16 2009 - 08:56:48 PDT)
- Carlos Simmerling (Mon Mar 16 2009 - 08:45:47 PDT)
- Bala subramanian (Mon Mar 16 2009 - 08:43:10 PDT)
[AMBER] MM-PBSA decomp by residue and snapshot?
- Bradshaw, Richard (Thu Mar 05 2009 - 09:55:05 PST)
[AMBER] mm_pbsa problem
- Ray Luo (Mon Mar 30 2009 - 10:27:59 PDT)
- Giorgos Lamprinidis (Mon Mar 30 2009 - 06:59:55 PDT)
- case (Mon Mar 30 2009 - 05:48:05 PDT)
- Giorgos Lamprinidis (Mon Mar 30 2009 - 03:02:07 PDT)
[AMBER] MMGBSA IG Value
- Carlos Simmerling (Fri Mar 20 2009 - 10:42:14 PDT)
- Rajesh Raju (Fri Mar 20 2009 - 10:36:37 PDT)
- Carlos Simmerling (Fri Mar 20 2009 - 10:25:38 PDT)
- Rajesh Raju (Fri Mar 20 2009 - 10:20:52 PDT)
[AMBER] modifying LYN
- Marius Retegan (Tue Mar 31 2009 - 09:58:06 PDT)
- FyD (Tue Mar 31 2009 - 08:41:56 PDT)
- Marius Retegan (Tue Mar 31 2009 - 06:36:21 PDT)
[AMBER] mol2 - pdb conversion
- David A. Case (Wed Mar 18 2009 - 14:53:06 PDT)
- Taufik Al-Sarraj (Wed Mar 18 2009 - 12:20:54 PDT)
- David A. Case (Tue Mar 17 2009 - 08:47:53 PDT)
- Taufik Al-Sarraj (Mon Mar 16 2009 - 14:38:09 PDT)
[AMBER] NAB md function prints strange output
- Scott Brozell (Thu Mar 12 2009 - 14:04:15 PDT)
[AMBER] nmoldyn2 with Amber
- Thomas Cheatham (Sun Mar 08 2009 - 13:10:17 PDT)
- David Watson (Sun Mar 08 2009 - 13:00:39 PDT)
- M. L. Dodson (Sun Mar 08 2009 - 11:34:03 PDT)
- M. L. Dodson (Sun Mar 08 2009 - 11:32:22 PDT)
- David Watson (Sun Mar 08 2009 - 08:02:55 PDT)
- David Watson (Sun Mar 08 2009 - 07:54:57 PDT)
- Adrien Delmont (Sun Mar 08 2009 - 07:37:40 PDT)
[AMBER] Parametrisation of Silicon based molecules for Amber simulations ?
- Marek Malý (Thu Mar 19 2009 - 16:49:21 PDT)
[AMBER] Particle-mesh Ewald method
- Ross Walker (Mon Mar 09 2009 - 12:53:52 PDT)
- Yunjie Zhao (Mon Mar 09 2009 - 02:46:15 PDT)
[AMBER] PB Bomb from MM-PBSA of Amber 10
- Ray Luo (Tue Mar 10 2009 - 09:28:15 PDT)
- Wei Huang (Tue Mar 10 2009 - 09:20:29 PDT)
- Zhu, Yong-Liang (Tue Mar 10 2009 - 09:06:43 PDT)
- Wei Huang (Tue Mar 10 2009 - 03:30:50 PDT)
- Zhu, Yong-Liang (Mon Mar 09 2009 - 21:30:33 PDT)
[AMBER] please help me out
- bharat lakhani (Tue Mar 24 2009 - 06:57:18 PDT)
- bharat lakhani (Mon Mar 23 2009 - 00:58:52 PDT)
- Ross Walker (Sat Mar 14 2009 - 09:54:22 PDT)
- David A. Case (Sat Mar 14 2009 - 06:06:34 PDT)
- bharat lakhani (Sat Mar 14 2009 - 04:04:37 PDT)
- rpaduri.chem.wayne.edu (Thu Mar 12 2009 - 09:37:09 PDT)
- bharat lakhani (Wed Mar 11 2009 - 23:04:00 PDT)
- FyD (Mon Mar 09 2009 - 03:05:06 PDT)
- bharat lakhani (Mon Mar 09 2009 - 01:43:08 PDT)
- FyD (Mon Mar 09 2009 - 01:10:08 PDT)
- bharat lakhani (Sun Mar 08 2009 - 22:04:45 PDT)
- bharat lakhani (Thu Mar 05 2009 - 03:16:45 PST)
- FyD (Thu Mar 05 2009 - 01:22:20 PST)
- bharat lakhani (Thu Mar 05 2009 - 00:35:44 PST)
[AMBER] PMEMD 9 on MVAPICH / Infiniband problem
- Robert Duke (Tue Mar 31 2009 - 05:21:22 PDT)
- fohm fohm (Tue Mar 31 2009 - 04:04:10 PDT)
- Ross Walker (Fri Mar 27 2009 - 18:04:04 PDT)
- Nick Holway (Fri Mar 27 2009 - 08:55:38 PDT)
[AMBER] pmemd compile error
- Robert Duke (Mon Mar 23 2009 - 14:03:45 PDT)
- Giorgos Lamprinidis (Mon Mar 23 2009 - 13:54:37 PDT)
[AMBER] pmemd compile error....
- Robert Duke (Tue Mar 24 2009 - 05:19:45 PDT)
- case (Tue Mar 24 2009 - 05:12:46 PDT)
- Robert Duke (Thu Mar 19 2009 - 08:25:04 PDT)
- Robert Duke (Thu Mar 19 2009 - 08:24:29 PDT)
- Giorgos Lamprinidis (Thu Mar 19 2009 - 08:06:04 PDT)
[AMBER] PMEMD error message
- Robert Duke (Tue Mar 10 2009 - 08:39:38 PDT)
- neville forlemu (Tue Mar 10 2009 - 07:55:31 PDT)
- Ross Walker (Sun Mar 08 2009 - 14:52:01 PDT)
- Robert Duke (Sun Mar 08 2009 - 13:47:16 PDT)
- neville forlemu (Sun Mar 08 2009 - 13:37:09 PDT)
[AMBER] polarizable force field and solvent
- zeinab bagheri (Wed Mar 11 2009 - 22:40:33 PDT)
- zeinab bagheri (Wed Mar 11 2009 - 15:02:06 PDT)
[AMBER] POLARIZABLE WATER MODEL
- CHAMI F. (Tue Mar 24 2009 - 11:03:25 PDT)
[AMBER] Problem build pmemd
- Robert Duke (Wed Mar 18 2009 - 06:53:17 PDT)
- Giorgos Lamprinidis (Wed Mar 18 2009 - 06:28:06 PDT)
- Atro Tossavainen (Sat Mar 14 2009 - 12:10:53 PDT)
- Robert Duke (Fri Mar 13 2009 - 05:40:09 PDT)
- Yiannis Georgiadis (Fri Mar 13 2009 - 17:14:49 PDT)
[AMBER] problem in installing AMBER10
- David A. Case (Fri Mar 27 2009 - 05:05:31 PDT)
- Dr. Debaprasad Giri (Fri Mar 27 2009 - 03:16:47 PDT)
- David A. Case (Mon Mar 23 2009 - 04:07:17 PDT)
- Dr. Debaprasad Giri (Mon Mar 23 2009 - 03:31:26 PDT)
[AMBER] problem in rmsd
- Carlos Simmerling (Tue Mar 10 2009 - 03:29:20 PDT)
- Hannes Loeffler (Tue Mar 10 2009 - 01:30:16 PDT)
- Thomas Cheatham (Mon Mar 09 2009 - 20:48:53 PDT)
- Parimal Kar (Mon Mar 09 2009 - 20:36:13 PDT)
- Thomas Cheatham (Mon Mar 09 2009 - 20:25:18 PDT)
- Parimal Kar (Mon Mar 09 2009 - 20:18:48 PDT)
[AMBER] problem in running sander
- David A. Case (Thu Mar 19 2009 - 05:13:11 PDT)
- Kshatresh Dutta Dubey (Thu Mar 19 2009 - 00:17:21 PDT)
- Carlos Simmerling (Wed Mar 18 2009 - 08:51:07 PDT)
- Carlos Simmerling (Wed Mar 18 2009 - 07:58:04 PDT)
[AMBER] Problem reading PDB file into XLEAP
- David A. Case (Sat Mar 28 2009 - 06:28:53 PDT)
- Hopkins, Robert (Fri Mar 27 2009 - 15:09:11 PDT)
- David A. Case (Fri Mar 27 2009 - 05:39:26 PDT)
- Hopkins, Robert (Thu Mar 26 2009 - 17:01:26 PDT)
[AMBER] Problem reading PDB file into XLEAP - SLEAP
- David A. Case (Sun Mar 29 2009 - 11:37:35 PDT)
- Hopkins, Robert (Sun Mar 29 2009 - 11:27:09 PDT)
- Wei Zhang (Sat Mar 28 2009 - 16:29:20 PDT)
- Hopkins, Robert (Sat Mar 28 2009 - 16:12:06 PDT)
[AMBER] Problem running test.pmemd.AMOEBA
- Robert Duke (Fri Mar 13 2009 - 07:33:55 PDT)
- mloureiro.cesga.es (Fri Mar 13 2009 - 04:45:30 PDT)
[AMBER] problem using amoeba
- Robert Duke (Fri Mar 27 2009 - 05:22:31 PDT)
- Hemant Gangwar (Fri Mar 27 2009 - 03:41:26 PDT)
[AMBER] Problem with "Atom does not have a type"
- case (Mon Mar 30 2009 - 05:46:59 PDT)
- Richard Tseng (Sun Mar 29 2009 - 12:20:37 PDT)
- David A. Case (Sat Mar 28 2009 - 06:25:33 PDT)
- Richard Tseng (Fri Mar 27 2009 - 15:08:34 PDT)
- Richard Tseng (Fri Mar 27 2009 - 14:51:32 PDT)
- David A. Case (Fri Mar 27 2009 - 04:44:22 PDT)
- Richard Tseng (Thu Mar 26 2009 - 16:17:19 PDT)
[AMBER] problem with amber installation
- nicholus bhattacharjee (Tue Mar 24 2009 - 10:14:10 PDT)
[AMBER] Problem with particle-mesh Ewald method
- Ross Walker (Fri Mar 06 2009 - 22:10:34 PST)
- steinbrt.rci.rutgers.edu (Fri Mar 06 2009 - 19:42:26 PST)
- Yunjie Zhao (Fri Mar 06 2009 - 19:29:02 PST)
[AMBER] Problem with REMD
- Carlos Simmerling (Thu Mar 12 2009 - 04:00:07 PDT)
- parul sharma (Thu Mar 12 2009 - 00:45:09 PDT)
[AMBER] problem with the results in the .out file!
- Gustavo Seabra (Tue Mar 31 2009 - 06:01:41 PDT)
- Aravind S (Mon Mar 30 2009 - 22:30:57 PDT)
[AMBER] problems compiling ambertool
- Per Jr. Greisen (Wed Mar 18 2009 - 05:45:53 PDT)
- David A. Case (Wed Mar 18 2009 - 05:39:38 PDT)
- Per Jr. Greisen (Wed Mar 18 2009 - 04:49:57 PDT)
- Bill Ross (Tue Mar 17 2009 - 10:24:48 PDT)
- Bill Ross (Tue Mar 17 2009 - 10:10:01 PDT)
- David A. Case (Tue Mar 17 2009 - 09:13:30 PDT)
- Per Jr. Greisen (Tue Mar 17 2009 - 09:06:00 PDT)
- David A. Case (Tue Mar 17 2009 - 05:49:20 PDT)
- Per Jr. Greisen (Tue Mar 17 2009 - 01:10:20 PDT)
- Bill Ross (Mon Mar 16 2009 - 15:50:44 PDT)
- Per Jr. Greisen (Mon Mar 16 2009 - 15:35:38 PDT)
- David A. Case (Mon Mar 16 2009 - 08:12:40 PDT)
- Per Jr. Greisen (Mon Mar 16 2009 - 07:41:26 PDT)
- David A. Case (Mon Mar 16 2009 - 07:27:26 PDT)
- Per Jr. Greisen (Mon Mar 16 2009 - 07:00:14 PDT)
- David A. Case (Mon Mar 16 2009 - 06:50:24 PDT)
- Per Jr. Greisen (Mon Mar 16 2009 - 06:29:37 PDT)
- David A. Case (Mon Mar 16 2009 - 05:13:23 PDT)
- Atro Tossavainen (Mon Mar 16 2009 - 03:18:58 PDT)
- Atro Tossavainen (Sat Mar 14 2009 - 12:09:36 PDT)
- Per Jr. Greisen (Fri Mar 13 2009 - 15:01:35 PDT)
- David A. Case (Fri Mar 13 2009 - 12:54:56 PDT)
- Per Jr. Greisen (Fri Mar 13 2009 - 12:08:36 PDT)
[AMBER] Problems with MM-PBSA Calculation after MD
- Hannes Kopitz (Thu Mar 12 2009 - 04:06:54 PDT)
- German Erlenkamp (Thu Mar 12 2009 - 02:28:23 PDT)
[AMBER] protein PDB
- Chih-Ying Lin (Thu Mar 19 2009 - 13:43:15 PDT)
[AMBER] protein protrudes from unit cell
- Carlos Simmerling (Wed Mar 18 2009 - 08:49:43 PDT)
- Ross Walker (Wed Mar 18 2009 - 08:39:23 PDT)
- Hannes Loeffler (Wed Mar 18 2009 - 02:08:41 PDT)
- Jeffrey (Wed Mar 18 2009 - 01:59:06 PDT)
[AMBER] Pseudoatoms
- David A. Case (Mon Mar 02 2009 - 15:25:29 PST)
- waleed zalloum (Mon Mar 02 2009 - 04:12:33 PST)
[AMBER] QM/MM charges
- Ross Walker (Fri Mar 20 2009 - 08:37:34 PDT)
- Jacopo Sgrignani (Fri Mar 20 2009 - 02:38:30 PDT)
[AMBER] Quality/size of HDD for Amber
- Gustavo Seabra (Mon Mar 09 2009 - 10:44:54 PDT)
- M. L. Dodson (Fri Mar 06 2009 - 07:44:45 PST)
- Francesco Pietra (Fri Mar 06 2009 - 01:26:03 PST)
[AMBER] Question
- David A. Case (Sat Mar 28 2009 - 06:38:49 PDT)
- Kshatresh Dutta Dubey (Sat Mar 28 2009 - 02:16:03 PDT)
- Rausch, Felix (Fri Mar 27 2009 - 06:37:29 PDT)
- Kshatresh Dutta Dubey (Fri Mar 27 2009 - 06:06:09 PDT)
[AMBER] Question about NAB module
- Andreas Svrcek-Seiler (Mon Mar 02 2009 - 01:23:52 PST)
- Wei Huang (Sun Mar 01 2009 - 06:57:50 PST)
- David A. Case (Sun Mar 01 2009 - 05:52:19 PST)
[AMBER] question about pair wise per-residue energy decomposition; idecomp=3
- case (Wed Mar 25 2009 - 11:58:02 PDT)
- wfli.biophy.nju.edu.cn (Wed Mar 25 2009 - 02:48:29 PDT)
[AMBER] radial distribution function mask
- iccy liu (Wed Mar 04 2009 - 10:57:08 PST)
[AMBER] Regarding leap
- Gustavo Seabra (Thu Mar 05 2009 - 07:32:56 PST)
- aneesh cna (Wed Mar 04 2009 - 20:29:17 PST)
- Gustavo Seabra (Wed Mar 04 2009 - 14:05:25 PST)
- Carlos Simmerling (Wed Mar 04 2009 - 03:48:30 PST)
- aneesh cna (Wed Mar 04 2009 - 03:43:52 PST)
[AMBER] regarding tutorial on united atom force field
- Ray Luo (Tue Mar 17 2009 - 09:22:01 PDT)
- jani sahil (Mon Mar 16 2009 - 21:51:16 PDT)
[AMBER] Regarding use of PME along with Implict solvation
- jani sahil (Mon Mar 23 2009 - 06:04:15 PDT)
- parul sharma (Mon Mar 23 2009 - 03:55:24 PDT)
- jani sahil (Mon Mar 23 2009 - 03:38:39 PDT)
[AMBER] removing center of mass
- Bala subramanian (Tue Mar 17 2009 - 08:21:28 PDT)
[AMBER] Restraint Mask length restriction !!
- Ross Walker (Mon Mar 09 2009 - 12:50:08 PDT)
- Sampath Koppole (Mon Mar 09 2009 - 07:39:38 PDT)
- David A. Case (Mon Mar 09 2009 - 07:30:16 PDT)
- Sampath Koppole (Mon Mar 09 2009 - 07:06:23 PDT)
- David A. Case (Mon Mar 09 2009 - 06:43:34 PDT)
- Sampath Koppole (Mon Mar 09 2009 - 06:32:35 PDT)
[AMBER] Rosetta Academic Training Webinar
- Nir London (Wed Mar 25 2009 - 09:14:21 PDT)
[AMBER] sander.MPI and pmemd.MPI in Fedora 8
- John Bennett (Sun Mar 15 2009 - 14:23:16 PDT)
[AMBER] secstruct
- Carlos Simmerling (Thu Mar 05 2009 - 06:27:18 PST)
- Beale, John (Thu Mar 05 2009 - 05:54:20 PST)
[AMBER] Seeking for suggestion related to plot the cluster out file
- S.Sundar Raman (Wed Mar 11 2009 - 09:07:25 PDT)
- Ross Walker (Wed Mar 11 2009 - 08:55:38 PDT)
- S.Sundar Raman (Wed Mar 11 2009 - 07:57:40 PDT)
- Ross Walker (Wed Mar 11 2009 - 07:33:38 PDT)
- S.Sundar Raman (Wed Mar 11 2009 - 05:44:17 PDT)
[AMBER] Segmentation faults
- Benjamin Roberts (Wed Mar 04 2009 - 16:17:50 PST)
[AMBER] simulation in water-oil (or water/hydrophobic-solvent) box
- ranga nath (Sat Mar 21 2009 - 19:04:13 PDT)
- David A. Case (Thu Mar 19 2009 - 10:38:52 PDT)
- ranga nath (Wed Mar 18 2009 - 21:27:54 PDT)
[AMBER] sleap and check
- Alan (Wed Mar 18 2009 - 14:23:51 PDT)
- Wei Zhang (Wed Mar 18 2009 - 07:40:57 PDT)
- Alan (Wed Mar 18 2009 - 04:18:27 PDT)
[AMBER] SMD in Amber10
- Dmitri Nilov (Fri Mar 13 2009 - 08:17:44 PDT)
- Adrian Roitberg (Fri Mar 13 2009 - 08:01:31 PDT)
- Dmitri Nilov (Fri Mar 13 2009 - 07:54:07 PDT)
- Adrian Roitberg (Fri Mar 13 2009 - 06:45:39 PDT)
- Dmitri Nilov (Fri Mar 13 2009 - 01:52:26 PDT)
- Adrian Roitberg (Thu Mar 12 2009 - 11:46:14 PDT)
- Dmitri Nilov (Thu Mar 12 2009 - 11:12:13 PDT)
[AMBER] Solvate Box od amoeba water
- Hemant Kumar (Sun Mar 22 2009 - 09:06:01 PDT)
- Wei Zhang (Fri Mar 06 2009 - 06:20:09 PST)
- Hemant Gangwar (Fri Mar 06 2009 - 01:50:01 PST)
[AMBER] solvent and counter ions
- Bill Ross (Thu Mar 05 2009 - 15:29:50 PST)
- Taufik Al-Sarraj (Thu Mar 05 2009 - 15:16:24 PST)
- Bill Ross (Wed Mar 04 2009 - 16:20:45 PST)
- Thomas Cheatham III (Wed Mar 04 2009 - 13:49:35 PST)
- Taufik Al-Sarraj (Wed Mar 04 2009 - 13:36:36 PST)
[AMBER] specification of antechamber AC file format?
- David A. Case (Wed Mar 04 2009 - 14:39:44 PST)
- Nicholas Musolino (Mon Mar 02 2009 - 23:53:23 PST)
[AMBER] suggestions for PB simulation
- Bala subramanian (Sat Mar 14 2009 - 09:41:19 PDT)
[AMBER] sulfotyrosine parameters
- Ryan Pavlovicz (Tue Mar 10 2009 - 08:05:59 PDT)
[AMBER] temperature rises with igb=1
- David A. Case (Thu Mar 19 2009 - 05:04:54 PDT)
- Bala subramanian (Thu Mar 19 2009 - 04:24:45 PDT)
- Carlos Simmerling (Tue Mar 17 2009 - 09:58:05 PDT)
- Ross Walker (Tue Mar 17 2009 - 09:53:04 PDT)
- Bala subramanian (Tue Mar 17 2009 - 09:35:41 PDT)
- Carlos Simmerling (Tue Mar 17 2009 - 09:44:32 PDT)
[AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9
- steinbrt.rci.rutgers.edu (Thu Mar 12 2009 - 17:37:08 PDT)
- PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 14:56:59 PDT)
[AMBER] Thermodynamic Intergration problem
- Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:00:06 PST)
- Ross Walker (Wed Mar 04 2009 - 08:45:24 PST)
- Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 07:36:14 PST)
[AMBER] TMD
- Carlos Simmerling (Wed Mar 18 2009 - 03:32:14 PDT)
[AMBER] To find radial distribution curve
- nicholus bhattacharjee (Thu Mar 26 2009 - 10:16:07 PDT)
[AMBER] to understand multiplicity in antechamber
- Alan (Fri Mar 13 2009 - 15:43:28 PDT)
- Scott Brozell (Fri Mar 13 2009 - 12:05:06 PDT)
- Alan (Fri Mar 13 2009 - 07:43:45 PDT)
- Alan (Fri Mar 13 2009 - 05:06:45 PDT)
[AMBER] Understanding the all.out file in the MM-PBSA output
- Ray Luo (Thu Mar 12 2009 - 09:29:22 PDT)
- Hannes Kopitz (Thu Mar 12 2009 - 03:54:27 PDT)
- gmail (Wed Mar 11 2009 - 18:39:10 PDT)
[AMBER] Unit 5 Error on OPEN: nan.in
- Bill Ross (Tue Mar 17 2009 - 10:12:07 PDT)
- Nancy (Tue Mar 17 2009 - 06:37:44 PDT)
- Jenny Iskrenova (Tue Mar 17 2009 - 05:34:00 PDT)
- mathew k varghese (Tue Mar 17 2009 - 04:22:08 PDT)
- Nancy (Tue Mar 17 2009 - 02:11:10 PDT)
- Nancy (Mon Mar 16 2009 - 18:02:09 PDT)
- Carlos Simmerling (Mon Mar 16 2009 - 07:32:02 PDT)
- Nancy (Mon Mar 16 2009 - 07:01:14 PDT)
- mathew k varghese (Mon Mar 16 2009 - 06:36:57 PDT)
- Nancy (Mon Mar 16 2009 - 05:49:31 PDT)
[AMBER] unning MMPBSA in CHCl3 environment
- Ray Luo (Wed Mar 04 2009 - 09:15:55 PST)
- SAFAK OZHAN (Wed Mar 04 2009 - 03:55:52 PST)
[AMBER] validation of parameters and request of suggestions
- Jeffrey (Mon Mar 23 2009 - 19:16:35 PDT)
[AMBER] validation of parameters and request suggestions
- Jeffrey (Tue Mar 24 2009 - 04:52:19 PDT)
[AMBER] Warning: name change in pdb file residue
- Duggan, Brendan M. (Thu Mar 05 2009 - 12:42:21 PST)
- Donald Keidel (Thu Mar 05 2009 - 11:25:38 PST)
[AMBER] What is the default position of the partial charges?
- Thomas Cheatham III (Wed Mar 04 2009 - 13:44:20 PST)
- Chih-Ying Lin (Wed Mar 04 2009 - 13:06:16 PST)
[AMBER] wrong estimation of hydrogen velocities when using SHAKE?
- Jose Borreguero (Wed Mar 11 2009 - 14:56:03 PDT)
- steinbrt.rci.rutgers.edu (Wed Mar 11 2009 - 11:56:15 PDT)
- Jose Borreguero (Wed Mar 11 2009 - 11:46:29 PDT)
- steinbrt.rci.rutgers.edu (Wed Mar 11 2009 - 10:45:56 PDT)
- Jose Borreguero (Wed Mar 11 2009 - 10:28:21 PDT)
- David A. Case (Wed Mar 11 2009 - 04:08:17 PDT)
- Jose Borreguero (Tue Mar 10 2009 - 09:09:48 PDT)
[AMBER] xmgrace
- Nancy (Fri Mar 20 2009 - 22:42:48 PDT)
- mathew k varghese (Fri Mar 20 2009 - 22:18:32 PDT)
- Nancy (Fri Mar 20 2009 - 21:41:33 PDT)
How to creat .frcmod file
- FyD (Wed Mar 04 2009 - 22:22:56 PST)
how to select force field
- Ross Walker (Sun Mar 08 2009 - 10:52:56 PDT)
- Nancy (Sun Mar 08 2009 - 07:07:48 PDT)
join two units in amber9 or amber10
- Bill Ross (Mon Mar 16 2009 - 15:56:01 PDT)
- Taufik Al-Sarraj (Mon Mar 16 2009 - 14:11:30 PDT)
using Gromacs for analysis
- oguz gurbulak (Mon Mar 02 2009 - 08:17:45 PST)
回复： [AMBER] about MD simulation
- 廖青华 (Wed Mar 11 2009 - 09:25:05 PDT)

Amber Archive Mar 2009 by subject