Amber Archive Jul 2004: by subject

AMBER:
- Chen (Fri Jul 30 2004 - 20:55:14 PDT)
- Ross Walker (Fri Jul 30 2004 - 08:46:52 PDT)
- David A. Case (Fri Jul 30 2004 - 08:06:56 PDT)
- Guanglei Cui (Fri Jul 30 2004 - 06:39:51 PDT)
- csong.mail.sdu.edu.cn (Fri Jul 30 2004 - 02:08:40 PDT)
- Carlos Simmerling (Tue Jul 13 2004 - 04:59:08 PDT)
- Jiten (Tue Jul 13 2004 - 02:25:53 PDT)
- hj zou (Sat Jul 10 2004 - 23:16:17 PDT)
AMBER: "closestwater" algorithm
- Grace Li (Mon Jul 05 2004 - 15:42:08 PDT)
AMBER: (no subject)
- Ross Walker (Fri Jul 30 2004 - 14:09:25 PDT)
- David A. Case (Fri Jul 30 2004 - 13:42:15 PDT)
- HL Eastwood (Fri Jul 30 2004 - 11:12:34 PDT)
- Ross Walker (Fri Jul 30 2004 - 09:21:33 PDT)
- HL Eastwood (Fri Jul 30 2004 - 08:47:18 PDT)
- myunggi.csit.fsu.edu (Thu Jul 22 2004 - 10:10:09 PDT)
- FyD (Wed Jul 14 2004 - 12:30:04 PDT)
- Ross Walker (Wed Jul 14 2004 - 11:33:38 PDT)
- Ross Walker (Tue Jul 13 2004 - 10:32:22 PDT)
- anshul.imtech.res.in (Tue Jul 13 2004 - 20:40:08 PDT)
AMBER: .lib file error in tleap
- Sébastien Osborne (Mon Jul 19 2004 - 11:15:11 PDT)
- anita pachaimuthu (Mon Jul 19 2004 - 10:19:19 PDT)
AMBER: A problem regarding constant pH calculation in Amber 8
- Yongzhi Chen (Mon Jul 19 2004 - 18:54:43 PDT)
AMBER: about correlation calculation in ptraj
- jz7.duke.edu (Tue Jul 27 2004 - 14:20:53 PDT)
AMBER: about GLYCAM prep files in AMBER
- Ozlem Demir (Tue Jul 20 2004 - 10:34:07 PDT)
AMBER: about RDF calculation in action.c
- Grace Li (Fri Jul 23 2004 - 13:39:07 PDT)
AMBER: about running ptraj in ambber8 (re-post)
- jz7.duke.edu (Mon Jul 26 2004 - 13:47:52 PDT)
AMBER: about running ptraj in amber8
- jz7.duke.edu (Mon Jul 26 2004 - 09:30:42 PDT)
- Ross Walker (Mon Jul 26 2004 - 09:22:36 PDT)
- jz7.duke.edu (Mon Jul 26 2004 - 07:04:33 PDT)
AMBER: About the calculation of non-bond list
- Wu Lei (Sat Jul 10 2004 - 07:21:57 PDT)
AMBER: About the free energy difference in vacuum with GIBBS.
- David A. Case (Wed Jul 14 2004 - 13:51:38 PDT)
- Chunhu Tan (Mon Jul 12 2004 - 15:34:35 PDT)
AMBER: about the parameter of the cystein pair in MD simulation
- Thomas E. Cheatham, III (Sun Jul 25 2004 - 20:07:44 PDT)
- Yuhui Cheng (Sun Jul 25 2004 - 19:01:13 PDT)
AMBER: About TI with sander
- David A. Case (Mon Jul 05 2004 - 08:31:23 PDT)
- Chunhu Tan (Sun Jul 04 2004 - 18:18:48 PDT)
AMBER: AMBER 6 compilation problems!
- Grace Li (Fri Jul 30 2004 - 13:42:03 PDT)
- Carlos Simmerling (Fri Jul 30 2004 - 12:03:31 PDT)
- Grace Li (Fri Jul 30 2004 - 11:52:15 PDT)
- Ross Walker (Fri Jul 30 2004 - 10:30:54 PDT)
- Carlos Simmerling (Fri Jul 30 2004 - 10:26:59 PDT)
- Grace Li (Fri Jul 30 2004 - 10:17:39 PDT)
AMBER: Amber 8 installation error
- fangyu liang (Thu Jul 01 2004 - 00:53:21 PDT)
AMBER: amber compilation
- Viktor Hornak (Mon Jul 26 2004 - 13:47:33 PDT)
- Livadaru, Lucian (Mon Jul 26 2004 - 13:15:50 PDT)
AMBER: Amber7 (8):FLUSH--FAILED:: Resource temporarily unavailable
- Jean-Christophe Ducom (Sat Jul 17 2004 - 13:01:47 PDT)
AMBER: Amber7 bugfix1
- David A. Case (Tue Jul 06 2004 - 11:37:04 PDT)
- Ross Walker (Tue Jul 06 2004 - 11:17:49 PDT)
- sachin patil (Tue Jul 06 2004 - 10:47:38 PDT)
AMBER: Amber8 on Digital UNIX
- Guillermo Mulliert Carlín (Wed Jul 07 2004 - 02:41:53 PDT)
- David A. Case (Mon Jul 05 2004 - 09:55:20 PDT)
- Guillermo Mulliert Carlín (Mon Jul 05 2004 - 08:30:15 PDT)
AMBER: Amber8: Vlimit problem again
- Ross Walker (Wed Jul 21 2004 - 16:55:59 PDT)
- Yuhui Cheng (Wed Jul 21 2004 - 16:44:09 PDT)
- David A. Case (Fri Jul 16 2004 - 09:26:06 PDT)
- German Sciaini (Fri Jul 16 2004 - 06:12:59 PDT)
- Yuhui Cheng (Thu Jul 15 2004 - 19:34:58 PDT)
AMBER: amparm
- Ross Walker (Wed Jul 21 2004 - 14:11:29 PDT)
- Vincent Bisetty (Wed Jul 21 2004 - 13:37:39 PDT)
AMBER: Angle restraint during MD
- Carlos Simmerling (Wed Jul 14 2004 - 06:39:38 PDT)
- Jiten (Tue Jul 13 2004 - 22:51:42 PDT)
- Carlos Simmerling (Tue Jul 13 2004 - 10:47:16 PDT)
- Jiten (Tue Jul 13 2004 - 09:21:28 PDT)
- Carlos Simmerling (Tue Jul 13 2004 - 05:00:42 PDT)
- Jiten (Tue Jul 13 2004 - 02:28:14 PDT)
AMBER: Angle restraint during MD and namelist problem in amber8
- Thomas E. Cheatham, III (Wed Jul 14 2004 - 09:22:26 PDT)
- Jiten (Wed Jul 14 2004 - 09:13:38 PDT)
AMBER: animation?
- aldo jongejan (Wed Jul 28 2004 - 05:36:21 PDT)
- Guanglei Cui (Wed Jul 28 2004 - 06:20:12 PDT)
- S. Frank Yan (Tue Jul 27 2004 - 23:29:51 PDT)
AMBER: anisotropic scaling
- David A. Case (Tue Jul 13 2004 - 13:43:02 PDT)
- Ross Walker (Tue Jul 13 2004 - 12:39:05 PDT)
- Xiang, Tian-Xiang (Tue Jul 13 2004 - 12:12:32 PDT)
AMBER: announcing normal mode analysis web server ElNemo
- Karsten Suhre (Thu Jul 15 2004 - 01:21:07 PDT)
AMBER: antechamber
- Bill Ross (Fri Jul 16 2004 - 10:48:07 PDT)
- David A. Case (Fri Jul 16 2004 - 09:16:14 PDT)
- Xin Hu (Thu Jul 15 2004 - 19:51:26 PDT)
- David A. Case (Thu Jul 15 2004 - 16:30:26 PDT)
- Xin Hu (Thu Jul 15 2004 - 13:57:09 PDT)
- Ross Walker (Thu Jul 15 2004 - 11:21:44 PDT)
- Xin Hu (Thu Jul 15 2004 - 11:03:44 PDT)
AMBER: antechamber - improper torsions
- Oliver Hucke (Tue Jul 20 2004 - 09:23:02 PDT)
AMBER: antechamber - missing improper torsions
- Junmei Wang (Wed Jul 21 2004 - 09:11:04 PDT)
- German Sciaini (Tue Jul 20 2004 - 06:04:17 PDT)
- O. Hucke (Mon Jul 19 2004 - 11:58:39 PDT)
AMBER: atom out of bounds
- Venkata S Koppuravuri (Wed Jul 21 2004 - 06:25:25 PDT)
AMBER: atom out of bounds (fwd)
- Ross Walker (Thu Jul 22 2004 - 13:54:52 PDT)
- Venkata S Koppuravuri (Thu Jul 22 2004 - 12:52:13 PDT)
AMBER: atoms not in residue templates
- Ross Walker (Sat Jul 24 2004 - 08:05:36 PDT)
- anshul.imtech.res.in (Sat Jul 24 2004 - 08:19:42 PDT)
AMBER: average structure using ptraj
- Chris Moth (Fri Jul 02 2004 - 10:11:42 PDT)
- NI AI (Fri Jul 02 2004 - 08:15:53 PDT)
- Thomas E. Cheatham, III (Thu Jul 01 2004 - 10:40:25 PDT)
- NI AI (Thu Jul 01 2004 - 09:18:34 PDT)
AMBER: average using ptraj
- Ross Walker (Thu Jul 08 2004 - 13:18:58 PDT)
- Holly Freedman (Thu Jul 08 2004 - 12:13:58 PDT)
AMBER: best PC laptop system to run Amber 8
- fangyu liang (Sun Jul 04 2004 - 22:04:41 PDT)
- Andreas Svrcek-Seiler (Sun Jul 04 2004 - 05:24:07 PDT)
- fangyu liang (Sat Jul 03 2004 - 14:05:35 PDT)
AMBER: Bondi radii for BR and F in mm_pbsa calculation
- Rhonda Torres (Tue Jul 20 2004 - 17:23:10 PDT)
- S. Frank Yan (Tue Jul 20 2004 - 16:01:03 PDT)
AMBER: charge problem in minimization
- David A. Case (Thu Jul 08 2004 - 13:54:54 PDT)
- Ross Walker (Thu Jul 08 2004 - 10:40:56 PDT)
AMBER: Co-ordination error while running tleap
- anita pachaimuthu (Wed Jul 21 2004 - 08:12:12 PDT)
AMBER: combination rules
- David A. Case (Mon Jul 05 2004 - 10:29:04 PDT)
- German Sciaini (Mon Jul 05 2004 - 05:31:43 PDT)
AMBER: Correl in Amber8: Diagonal elements not 1?
- Bimo Ario Tejo (Thu Jul 15 2004 - 04:47:43 PDT)
AMBER: correlation in Amber 8
- Bimo Ario Tejo (Thu Jul 08 2004 - 01:14:34 PDT)
AMBER: Cubic Ice
- Johnson Agbo (Fri Jul 16 2004 - 18:08:14 PDT)
AMBER: cut offs in amber?
- Ross Walker (Wed Jul 21 2004 - 15:10:09 PDT)
- Grace Li (Wed Jul 21 2004 - 15:03:05 PDT)
- Ross Walker (Wed Jul 21 2004 - 14:39:47 PDT)
- Carlos Simmerling (Wed Jul 21 2004 - 14:32:18 PDT)
- Grace Li (Wed Jul 21 2004 - 14:20:40 PDT)
- Ross Walker (Wed Jul 21 2004 - 14:05:02 PDT)
- Grace Li (Wed Jul 21 2004 - 13:47:43 PDT)
AMBER: cys protecting group parameters
- Stefano.Pieraccini.unimi.it (Fri Jul 09 2004 - 06:48:36 PDT)
AMBER: cys protecting groups parameters
- Stefano.Pieraccini.unimi.it (Fri Jul 09 2004 - 05:41:20 PDT)
AMBER: details for Namelist problem
- Vlad Cojocaru (Mon Jul 05 2004 - 06:22:33 PDT)
- Vlad Cojocaru (Mon Jul 05 2004 - 02:48:40 PDT)
AMBER: Disulfide bond command
- bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 11:51:46 PDT)
- Ross Walker (Fri Jul 09 2004 - 11:27:13 PDT)
- bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 11:16:13 PDT)
AMBER: Enthalpy of solvent-solute vanderWaals
- Scott (Wed Jul 14 2004 - 12:56:45 PDT)
AMBER: erroe in installing amber8
- Scott Brozell (Sun Jul 25 2004 - 17:58:58 PDT)
- David A. Case (Sat Jul 24 2004 - 01:40:06 PDT)
- anshul.imtech.res.in (Sat Jul 24 2004 - 10:11:02 PDT)
AMBER: Ewald parameter range
- Johnson Agbo (Fri Jul 23 2004 - 11:00:12 PDT)
- David A. Case (Fri Jul 23 2004 - 01:53:50 PDT)
- Johnson Agbo (Thu Jul 22 2004 - 17:16:08 PDT)
AMBER: execution time
- Ross Walker (Fri Jul 09 2004 - 11:52:08 PDT)
- cailliez (Fri Jul 09 2004 - 02:50:25 PDT)
AMBER: Fe parameter
- Ross Walker (Mon Jul 12 2004 - 11:19:23 PDT)
- scopio (Mon Jul 12 2004 - 07:18:52 PDT)
- Wu Lei (Mon Jul 12 2004 - 00:51:18 PDT)
- hj zou (Mon Jul 12 2004 - 00:09:29 PDT)
AMBER: found unknown atflg PB
- Holger Gohlke (Thu Jul 22 2004 - 07:56:38 PDT)
- Scott (Thu Jul 22 2004 - 06:38:33 PDT)
AMBER: How to apply OPLS force field?
- David A. Case (Thu Jul 15 2004 - 10:04:22 PDT)
- Bill Ross (Thu Jul 15 2004 - 09:08:22 PDT)
- Wu Lei (Thu Jul 15 2004 - 00:45:31 PDT)
- Ross Walker (Wed Jul 14 2004 - 21:20:58 PDT)
- Wu Lei (Wed Jul 14 2004 - 21:12:50 PDT)
- David A. Case (Wed Jul 14 2004 - 09:29:59 PDT)
- Sichun Yang (Wed Jul 14 2004 - 09:21:41 PDT)
- mcpreto.fc.up.pt (Wed Jul 14 2004 - 06:26:04 PDT)
- Wu Lei (Tue Jul 13 2004 - 20:23:04 PDT)
AMBER: how to calculate E-pot from restart file?
- David A. Case (Thu Jul 08 2004 - 21:07:49 PDT)
- J. Zhang, Dr (Thu Jul 08 2004 - 20:13:44 PDT)
AMBER: How to make leap recognise Zn2+?
- Yongzhi Chen (Tue Jul 06 2004 - 09:00:26 PDT)
- Guanglei Cui (Tue Jul 06 2004 - 06:58:27 PDT)
- Yongzhi Chen (Mon Jul 05 2004 - 18:41:26 PDT)
AMBER: idecomp
- Marcela Madrid (Thu Jul 08 2004 - 12:35:57 PDT)
- David A. Case (Tue Jul 06 2004 - 09:37:42 PDT)
- Marcela Madrid (Tue Jul 06 2004 - 08:42:20 PDT)
AMBER: Imaging problem
- Thomas E. Cheatham, III (Fri Jul 30 2004 - 13:41:45 PDT)
- Steve Seibold (Fri Jul 30 2004 - 12:05:12 PDT)
AMBER: Implicit MD problem
- Carlos Simmerling (Wed Jul 14 2004 - 09:53:31 PDT)
- David A. Case (Wed Jul 14 2004 - 09:29:47 PDT)
- Carlos Simmerling (Wed Jul 14 2004 - 06:42:18 PDT)
AMBER: Implicit MD simulation
- Carlos Simmerling (Thu Jul 01 2004 - 05:07:52 PDT)
AMBER: Is it a bug?(in prep file opls_unict.in)
- David A. Case (Wed Jul 21 2004 - 06:32:44 PDT)
- 吴磊 (Wed Jul 21 2004 - 03:59:13 PDT)
- David A. Case (Wed Jul 21 2004 - 01:52:22 PDT)
- Wu Lei (Fri Jul 16 2004 - 22:15:16 PDT)
- David A. Case (Fri Jul 16 2004 - 09:27:41 PDT)
- Wu Lei (Thu Jul 15 2004 - 20:44:09 PDT)
AMBER: Leap could not find atom type CK
- 吴磊 (Tue Jul 20 2004 - 21:35:54 PDT)
AMBER: leap problem in AMBER7 (residue insertion)
- Kuhn, Bernd {PRBD~Basel} (Wed Jul 14 2004 - 04:44:00 PDT)
- David A. Case (Mon Jul 05 2004 - 10:21:50 PDT)
- Kuhn, Bernd {PRBD~Basel} (Mon Jul 05 2004 - 04:26:34 PDT)
AMBER: lib file
- Furse, Kristina Elisabet (Fri Jul 30 2004 - 14:38:37 PDT)
- David A. Case (Fri Jul 30 2004 - 13:48:50 PDT)
AMBER: MAXRMSPT error in MOIL-view
- Carlos Simmerling (Thu Jul 01 2004 - 15:26:53 PDT)
- Robyn Ayscue (Thu Jul 01 2004 - 15:19:23 PDT)
AMBER: MD simulation : problem
- Ross Walker (Mon Jul 12 2004 - 10:55:33 PDT)
- sachin patil (Sun Jul 11 2004 - 21:53:51 PDT)
- Ross Walker (Sun Jul 11 2004 - 17:41:11 PDT)
- sachin patil (Sun Jul 11 2004 - 08:08:13 PDT)
- Ross Walker (Fri Jul 09 2004 - 22:35:14 PDT)
- sachin patil (Fri Jul 09 2004 - 22:08:15 PDT)
AMBER: MD simulation : problem :THANK YOU
- sachin patil (Tue Jul 13 2004 - 07:51:28 PDT)
AMBER: mm_pbsa Abmer8 example
- John (Tue Jul 27 2004 - 03:38:50 PDT)
AMBER: mm_pbsa problem
- David A. Case (Fri Jul 02 2004 - 07:52:46 PDT)
- david.evans.ulsop.ac.uk (Fri Jul 02 2004 - 03:53:23 PDT)
- steven.j.enoch.gsk.com (Fri Jul 02 2004 - 03:29:57 PDT)
AMBER: Molecular dynamic
- Joseph Nachman (Tue Jul 13 2004 - 08:21:09 PDT)
- Andy Purkiss (Tue Jul 13 2004 - 02:21:02 PDT)
- Ross Walker (Mon Jul 12 2004 - 11:12:53 PDT)
- bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 15:54:38 PDT)
- Ross Walker (Thu Jul 08 2004 - 10:24:21 PDT)
- bybaker.itsa.ucsf.edu (Wed Jul 07 2004 - 14:12:33 PDT)
AMBER: Molecular dynamic & Acknowledgement
- bybaker.itsa.ucsf.edu (Tue Jul 13 2004 - 11:20:50 PDT)
AMBER: multiple heat bath GB+LES
- Marcin Krol (Mon Jul 05 2004 - 09:53:31 PDT)
AMBER: mutation of atoms
- Nelson Fonseca (Thu Jul 22 2004 - 05:41:22 PDT)
AMBER: My strange result of TI.
- Chunhu Tan (Wed Jul 07 2004 - 16:35:19 PDT)
AMBER: N-terminal Arg charges in ff99 not 1.00
- Ross Walker (Thu Jul 01 2004 - 13:13:00 PDT)
- Michael Dolan (Thu Jul 01 2004 - 12:57:37 PDT)
- David A. Case (Thu Jul 01 2004 - 12:17:52 PDT)
- Ross Walker (Thu Jul 01 2004 - 12:17:02 PDT)
- Michael Dolan (Thu Jul 01 2004 - 12:04:37 PDT)
- Michael Dolan (Thu Jul 01 2004 - 12:00:45 PDT)
AMBER: name error
- David A. Case (Thu Jul 08 2004 - 13:54:48 PDT)
- Ross Walker (Thu Jul 08 2004 - 10:35:46 PDT)
- Prashansa Agrawal (Wed Jul 07 2004 - 15:57:53 PDT)
AMBER: Namelist problem
- David A. Case (Mon Jul 05 2004 - 08:21:12 PDT)
- Viktor Hornak (Mon Jul 05 2004 - 07:07:36 PDT)
- Vlad Cojocaru (Mon Jul 05 2004 - 06:10:51 PDT)
- Guanglei Cui (Mon Jul 05 2004 - 05:56:10 PDT)
- Vlad Cojocaru (Mon Jul 05 2004 - 02:25:07 PDT)
AMBER: namelist problem solved
- Vlad Cojocaru (Thu Jul 08 2004 - 10:50:10 PDT)
- Vlad Cojocaru (Wed Jul 07 2004 - 04:09:16 PDT)
AMBER: NB pairs exceeds?
- csong.mail.sdu.edu.cn (Sun Jul 18 2004 - 01:28:27 PDT)
- David A. Case (Sat Jul 17 2004 - 18:09:22 PDT)
- csong.mail.sdu.edu.cn (Sat Jul 17 2004 - 03:10:23 PDT)
- David A. Case (Fri Jul 16 2004 - 09:23:22 PDT)
- Chen (Fri Jul 16 2004 - 01:40:42 PDT)
- Wu Lei (Fri Jul 16 2004 - 01:07:56 PDT)
- Chen (Fri Jul 16 2004 - 00:35:16 PDT)
AMBER: no 'water.lib' in /amber8/dat/leap/
- Ross Walker (Thu Jul 01 2004 - 13:30:25 PDT)
- Rhonda Torres (Thu Jul 01 2004 - 13:25:15 PDT)
- fangyu liang (Thu Jul 01 2004 - 13:21:50 PDT)
AMBER: Normal mode calculation with periodic boundary condition
- David A. Case (Thu Jul 15 2004 - 10:04:07 PDT)
- Johnson Agbo (Wed Jul 14 2004 - 22:15:09 PDT)
AMBER: NSPSOL in parm file
- David A. Case (Thu Jul 29 2004 - 08:07:54 PDT)
- Sichun Yang (Wed Jul 28 2004 - 21:14:01 PDT)
AMBER: parameter development for nucleotide analogues
- Ross Walker (Thu Jul 08 2004 - 10:49:33 PDT)
- Vlad Cojocaru (Thu Jul 08 2004 - 10:49:42 PDT)
- Vlad Cojocaru (Wed Jul 07 2004 - 03:37:50 PDT)
AMBER: Parameter generation from RESP charges
- anshul.imtech.res.in (Tue Jul 13 2004 - 21:02:07 PDT)
AMBER: parametrization problem
- Carsten Detering (Fri Jul 23 2004 - 13:33:01 PDT)
- Carsten Detering (Fri Jul 23 2004 - 13:38:59 PDT)
- Ross Walker (Fri Jul 23 2004 - 12:32:15 PDT)
- Carsten Detering (Fri Jul 23 2004 - 11:16:13 PDT)
AMBER: PB Bomb in pb_reslist(): maxnbr too small
- Ray Luo (Mon Jul 19 2004 - 05:22:26 PDT)
- steven.j.enoch.gsk.com (Tue Jul 20 2004 - 06:00:59 PDT)
AMBER: PB bomb in pb_saarc
- steven.j.enoch.gsk.com (Wed Jul 28 2004 - 01:49:20 PDT)
- steven.j.enoch.gsk.com (Wed Jul 28 2004 - 01:26:38 PDT)
AMBER: peptide-DNA crosslink modeling
- M. L. Dodson (Fri Jul 02 2004 - 11:06:39 PDT)
- David A. Case (Thu Jul 01 2004 - 22:01:40 PDT)
- Carlos Simmerling (Thu Jul 01 2004 - 18:42:48 PDT)
- M. L. Dodson (Thu Jul 01 2004 - 14:51:24 PDT)
AMBER: pH effect on protein folding
- Bimo Ario Tejo (Thu Jul 15 2004 - 20:34:39 PDT)
- Rukman Hertadi (Thu Jul 15 2004 - 19:00:54 PDT)
AMBER: pmemd.
- Robert Duke (Fri Jul 23 2004 - 10:46:48 PDT)
- Osman Gani (Fri Jul 23 2004 - 10:09:55 PDT)
AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
- Jiten (Tue Jul 13 2004 - 02:52:06 PDT)
- Jiten (Tue Jul 13 2004 - 02:46:57 PDT)
- Scott Brozell (Mon Jul 12 2004 - 11:30:39 PDT)
- Jiten (Mon Jul 12 2004 - 02:36:36 PDT)
- Mark Williamson (Sun Jul 11 2004 - 13:52:45 PDT)
- Ross Walker (Sun Jul 11 2004 - 11:38:49 PDT)
- Jiten (Sat Jul 10 2004 - 22:24:27 PDT)
- Jiten (Sat Jul 10 2004 - 22:04:35 PDT)
- David A. Case (Sat Jul 10 2004 - 20:46:57 PDT)
- Mark Williamson (Sat Jul 10 2004 - 10:54:56 PDT)
- Jiten (Sat Jul 10 2004 - 08:30:15 PDT)
AMBER: Problem to converge minimization
- David A. Case (Mon Jul 05 2004 - 08:22:01 PDT)
- Jiten (Mon Jul 05 2004 - 05:38:26 PDT)
- Guillaume Bollot (Mon Jul 05 2004 - 01:41:06 PDT)
AMBER: Problem with divcon - increasing MXATTS?
- Ross Walker (Wed Jul 14 2004 - 11:13:19 PDT)
- Kennie Merz (Wed Jul 14 2004 - 10:03:32 PDT)
- steven.j.enoch.gsk.com (Wed Jul 14 2004 - 09:45:54 PDT)
- Kennie Merz (Wed Jul 14 2004 - 09:01:54 PDT)
- steven.j.enoch.gsk.com (Wed Jul 14 2004 - 08:33:38 PDT)
AMBER: Problem with sander - Error on Open
- Thomas E. Cheatham, III (Thu Jul 08 2004 - 19:18:10 PDT)
- Mike (Thu Jul 08 2004 - 18:57:43 PDT)
- Ross Walker (Thu Jul 08 2004 - 15:15:04 PDT)
- Mike (Thu Jul 08 2004 - 14:38:37 PDT)
AMBER: Problem with sander tutorial.
- Scott (Thu Jul 22 2004 - 19:08:19 PDT)
- Ross Walker (Thu Jul 22 2004 - 13:57:20 PDT)
- tarek mahfouz (Thu Jul 22 2004 - 09:59:42 PDT)
- Ross Walker (Tue Jul 20 2004 - 13:16:28 PDT)
- tarek mahfouz (Tue Jul 20 2004 - 12:09:44 PDT)
AMBER: problems in using glycam
- Wen-Chi Tseng (Thu Jul 01 2004 - 05:44:27 PDT)
AMBER: Problems with amber8 and pgf90
- Scott Brozell (Thu Jul 15 2004 - 09:23:44 PDT)
- Marc Perea (Thu Jul 15 2004 - 03:30:36 PDT)
AMBER: Problems with CPU scaling on cluster
- David E. Konerding (Fri Jul 16 2004 - 08:46:01 PDT)
- Ross Walker (Thu Jul 15 2004 - 11:48:15 PDT)
- Ross Walker (Mon Jul 12 2004 - 11:38:27 PDT)
- Your Name (Mon Jul 12 2004 - 01:12:48 PDT)
AMBER: problems with mdcrd
- Ross Walker (Thu Jul 08 2004 - 12:54:08 PDT)
- Ross Walker (Thu Jul 08 2004 - 10:32:04 PDT)
- Carsten Detering (Thu Jul 08 2004 - 10:16:04 PDT)
AMBER: ptraj
- Wen Li (Wed Jul 14 2004 - 14:07:11 PDT)
- Ross Walker (Thu Jul 08 2004 - 10:01:43 PDT)
- Wen Li (Thu Jul 08 2004 - 09:06:01 PDT)
AMBER: ptraj-closestwaters command
- Thomas E. Cheatham, III (Mon Jul 12 2004 - 13:38:41 PDT)
- Grace Li (Sat Jul 10 2004 - 09:14:34 PDT)
AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)
- Raik Grünberg (Thu Jul 29 2004 - 03:34:44 PDT)
AMBER: question about antechamber program
- David A. Case (Fri Jul 02 2004 - 13:26:12 PDT)
- Sivanesan Dakshanamurthy (Fri Jul 02 2004 - 11:42:07 PDT)
AMBER: question about production runs
- opitz.che.udel.edu (Fri Jul 16 2004 - 12:42:06 PDT)
AMBER: question about ptraj
- Guanglei Cui (Wed Jul 21 2004 - 13:32:29 PDT)
- jz7.duke.edu (Wed Jul 21 2004 - 13:00:01 PDT)
- Thomas E. Cheatham, III (Thu Jul 08 2004 - 09:56:04 PDT)
- Ross Walker (Thu Jul 08 2004 - 09:47:28 PDT)
- jz7.duke.edu (Thu Jul 08 2004 - 09:32:07 PDT)
AMBER: question about Ptraj - AND OR
- Herr/Señor/Monsieur/Mister Gregory (Mon Jul 12 2004 - 09:15:47 PDT)
- Thomas E. Cheatham, III (Mon Jul 12 2004 - 08:15:13 PDT)
- james tomomi macdonald (Mon Jul 12 2004 - 08:06:59 PDT)
AMBER: Question on Clustering Analysis
- Chen, Ya (Tue Jul 27 2004 - 11:26:30 PDT)
AMBER: question on simulated annealing
- David A. Case (Tue Jul 27 2004 - 12:26:06 PDT)
- Carlos Simmerling (Tue Jul 27 2004 - 11:28:27 PDT)
- Venkata S Koppuravuri (Tue Jul 27 2004 - 11:21:52 PDT)
AMBER: RESP vs. AM1-BCC charges for isoprene
- ajakalian.lav.Boehringer-Ingelheim.com (Mon Jul 26 2004 - 08:09:31 PDT)
- Oliver Hucke (Fri Jul 23 2004 - 10:41:05 PDT)
- ajakalian.lav.Boehringer-Ingelheim.com (Thu Jul 22 2004 - 05:43:16 PDT)
- Joe Harriman (Sat Jul 17 2004 - 05:44:47 PDT)
- Ilyas Yildirim (Fri Jul 16 2004 - 15:36:22 PDT)
- Oliver Hucke (Fri Jul 16 2004 - 15:49:00 PDT)
- Carsten Detering (Fri Jul 16 2004 - 14:37:22 PDT)
- Carsten Detering (Fri Jul 16 2004 - 14:33:51 PDT)
- Rhonda Torres (Fri Jul 16 2004 - 14:20:42 PDT)
- Oliver Hucke (Fri Jul 16 2004 - 14:00:57 PDT)
AMBER: Rigid counteranion during MD !!
- Jiten (Sun Jul 11 2004 - 07:51:48 PDT)
- Jiten (Sun Jul 11 2004 - 01:26:35 PDT)
AMBER: RNA sequence with DNA backbone?
- Vlad Cojocaru (Wed Jul 14 2004 - 04:09:13 PDT)
- Arvind (Wed Jul 14 2004 - 03:50:29 PDT)
- David A. Case (Mon Jul 12 2004 - 13:35:43 PDT)
- Arvind (Mon Jul 12 2004 - 04:26:36 PDT)
AMBER: running MD simulatons
- David A. Case (Tue Jul 06 2004 - 11:40:50 PDT)
- sachin patil (Tue Jul 06 2004 - 09:52:58 PDT)
AMBER: sander : constraints to conserve hydrogen bonds
- Carlos Simmerling (Fri Jul 23 2004 - 05:08:43 PDT)
- Jiten (Thu Jul 22 2004 - 22:58:15 PDT)
- sachin patil (Thu Jul 22 2004 - 21:15:04 PDT)
AMBER: sander on multiprocessors
- Andreas Svrcek-Seiler (Tue Jul 06 2004 - 04:15:48 PDT)
- Stef (Tue Jul 06 2004 - 01:42:36 PDT)
- cailliez (Tue Jul 06 2004 - 00:38:39 PDT)
AMBER: sander tutorial
- Carlos Simmerling (Thu Jul 22 2004 - 05:33:08 PDT)
- mathew k varghese (Thu Jul 22 2004 - 05:16:33 PDT)
AMBER: segmentation fault in leap
- Ross Walker (Thu Jul 08 2004 - 10:07:28 PDT)
- anshul.imtech.res.in (Thu Jul 08 2004 - 18:17:40 PDT)
- Guillermo Mulliert Carlín (Thu Jul 08 2004 - 05:02:05 PDT)
- anshul.imtech.res.in (Thu Jul 08 2004 - 14:40:42 PDT)
AMBER: Setup for parallel computing
- fangyu liang (Sat Jul 10 2004 - 16:10:19 PDT)
- Stef (Sat Jul 10 2004 - 14:14:56 PDT)
- fangyu liang (Fri Jul 09 2004 - 10:00:32 PDT)
AMBER: simulated annealing
- Abd Ghani Bin Abd Aziz (Wed Jul 28 2004 - 06:22:37 PDT)
- Carlos Simmerling (Wed Jul 28 2004 - 05:17:55 PDT)
AMBER: simulated annealing..
- Carlos Simmerling (Wed Jul 28 2004 - 07:06:01 PDT)
- Abd Ghani Bin Abd Aziz (Wed Jul 28 2004 - 06:45:55 PDT)
AMBER: solvate proteins in xleap/amber8
- Ting Wang (Tue Jul 13 2004 - 05:23:51 PDT)
AMBER: solvation free energy
- Qizhi Cui (Mon Jul 19 2004 - 10:32:17 PDT)
- Ray Luo (Sun Jul 11 2004 - 19:25:44 PDT)
- hj zou (Fri Jul 09 2004 - 00:38:39 PDT)
- hj zou (Sat Jul 10 2004 - 23:16:19 PDT)
AMBER: Temperature Regulation
- Dawsonzhu.aol.com (Wed Jul 28 2004 - 17:44:56 PDT)
- David A. Case (Tue Jul 27 2004 - 08:24:31 PDT)
- Andreas Svrcek-Seiler (Tue Jul 27 2004 - 07:09:51 PDT)
- Johnson Agbo (Mon Jul 26 2004 - 21:40:44 PDT)
AMBER: tleap - FATAL error
- Scott Brozell (Wed Jul 14 2004 - 14:44:41 PDT)
- Sivanesan Dakshanamurthy (Wed Jul 14 2004 - 14:28:41 PDT)
AMBER: tleap input file error
- David A. Case (Thu Jul 01 2004 - 17:06:18 PDT)
- fangyu liang (Thu Jul 01 2004 - 16:26:18 PDT)
AMBER: tleap: automatically identify and connect disulfide bonds?
- Austin B. Yongye (Thu Jul 29 2004 - 06:13:46 PDT)
- Scott Brozell (Wed Jul 28 2004 - 13:22:52 PDT)
- Raik Grünberg (Wed Jul 28 2004 - 10:27:31 PDT)
AMBER: torsion scan
- Guanglei Cui (Tue Jul 13 2004 - 14:12:50 PDT)
- David A. Case (Tue Jul 13 2004 - 13:47:00 PDT)
- Furse, Kristina Elisabet (Tue Jul 13 2004 - 10:37:35 PDT)
- Guanglei Cui (Tue Jul 13 2004 - 08:18:32 PDT)
AMBER: umbrella sampling
- David A. Case (Thu Jul 29 2004 - 11:19:13 PDT)
- tang kwa (Thu Jul 29 2004 - 10:25:00 PDT)
AMBER: Use of ibelly with nmode analysis
- David A. Case (Tue Jul 13 2004 - 09:24:27 PDT)
- steven.j.enoch.gsk.com (Tue Jul 13 2004 - 06:30:30 PDT)
AMBER: user force
- Carlos Simmerling (Fri Jul 23 2004 - 04:47:17 PDT)
- myunggi.csit.fsu.edu (Thu Jul 22 2004 - 16:26:14 PDT)
- Ross Walker (Thu Jul 22 2004 - 15:40:16 PDT)
- Carlos Simmerling (Thu Jul 22 2004 - 15:28:42 PDT)
- myunggi.csit.fsu.edu (Thu Jul 22 2004 - 15:25:50 PDT)
- Ross Walker (Thu Jul 22 2004 - 15:08:04 PDT)
- Bill Ross (Thu Jul 22 2004 - 14:57:24 PDT)
- myunggi.csit.fsu.edu (Thu Jul 22 2004 - 14:48:28 PDT)
- Furse, Kristina Elisabet (Thu Jul 22 2004 - 14:07:46 PDT)
- Myunggi Yi (Thu Jul 22 2004 - 10:00:16 PDT)
AMBER: using ptraj
- Scott (Thu Jul 29 2004 - 15:48:19 PDT)
- Carsten Detering (Thu Jul 29 2004 - 15:11:11 PDT)
- Scott (Thu Jul 29 2004 - 14:15:17 PDT)
- Carsten Detering (Tue Jul 27 2004 - 14:10:02 PDT)
AMBER: vdw energy in minimization
- Carlos Simmerling (Mon Jul 19 2004 - 11:47:21 PDT)
- anshul.imtech.res.in (Mon Jul 19 2004 - 20:44:30 PDT)
- carlos (Mon Jul 19 2004 - 05:13:30 PDT)
- anshul.imtech.res.in (Mon Jul 19 2004 - 08:11:17 PDT)
AMBER: weird box expansion
- Herbert Georg (Thu Jul 08 2004 - 10:38:01 PDT)
- Thomas E. Cheatham, III (Thu Jul 08 2004 - 10:06:57 PDT)
- Herbert Georg (Thu Jul 08 2004 - 09:57:57 PDT)
AMBER: Weird compiling problem in Amber 8
- Ray Luo (Sun Jul 18 2004 - 22:34:03 PDT)
- Scott Brozell (Mon Jul 19 2004 - 10:08:54 PDT)
- fangyu liang (Sun Jul 18 2004 - 23:30:22 PDT)
- echanco.uci.edu (Sun Jul 18 2004 - 22:51:29 PDT)
AMBER: WHAM program
- David A. Case (Fri Jul 30 2004 - 10:16:02 PDT)
- tang kwa (Fri Jul 30 2004 - 09:09:02 PDT)
AMBER: What happen when sander reads charge increments from cpin file?
- Yongzhi Chen (Wed Jul 21 2004 - 14:59:40 PDT)
- Ross Walker (Wed Jul 21 2004 - 13:41:45 PDT)
- Yongzhi Chen (Wed Jul 21 2004 - 13:24:51 PDT)
AMBER: what is averaged RMS fluctuation?
- Ross Walker (Mon Jul 12 2004 - 13:40:23 PDT)
- Carlos Simmerling (Mon Jul 12 2004 - 13:37:13 PDT)
- Thomas E. Cheatham, III (Mon Jul 12 2004 - 13:28:21 PDT)
- jz7.duke.edu (Mon Jul 12 2004 - 12:59:26 PDT)
- Ross Walker (Mon Jul 12 2004 - 11:51:47 PDT)
- jz7.duke.edu (Mon Jul 12 2004 - 09:17:30 PDT)
AMBER: X-CA-CT-X dih. FF param ?
- Guanglei Cui (Fri Jul 16 2004 - 10:24:46 PDT)
- FyD (Fri Jul 16 2004 - 10:08:26 PDT)
AMBER: Xleap crash, problem with residue bonding
- opitz.che.udel.edu (Mon Jul 26 2004 - 08:39:51 PDT)
- Bill Ross (Thu Jul 22 2004 - 14:55:58 PDT)
- Ross Walker (Thu Jul 22 2004 - 14:31:22 PDT)
- opitz.che.udel.edu (Thu Jul 22 2004 - 07:24:35 PDT)
AMBER: xleap problem
- hj zou (Mon Jul 12 2004 - 07:56:55 PDT)
- scopio (Mon Jul 12 2004 - 07:09:47 PDT)
- hj zou (Sat Jul 10 2004 - 23:16:19 PDT)
AMBER: xleap solvatebox/oct problem
- Jiten (Fri Jul 16 2004 - 02:07:09 PDT)
- David A. Case (Thu Jul 15 2004 - 10:02:11 PDT)
- Jiten (Thu Jul 15 2004 - 08:18:59 PDT)
constant pH calculation in Amber8
- John Mongan (Thu Jul 29 2004 - 14:40:36 PDT)
missing bondi radii of Br and F for surface area calculation
- S. Frank Yan (Tue Jul 20 2004 - 10:30:13 PDT)
Results from RED-II beta
- FyD (Sun Jul 18 2004 - 09:11:41 PDT)

Amber Archive Jul 2004 by subject