Amber Archive Jul 2005: by subject

David A. Case (Tue Jul 19 2005 - 19:46:48 PDT)
Andrew Box (Tue Jul 19 2005 - 19:07:44 PDT)
AMBER:
- Zhiguo Liu (Sun Jul 10 2005 - 00:37:36 PDT)
- Shan Jufang (Sat Jul 09 2005 - 12:37:54 PDT)
- glc0358.vip.sina.com (Sat Jul 09 2005 - 03:37:54 PDT)
- Zhiguo Liu (Sat Jul 09 2005 - 01:39:43 PDT)
- glc0358.vip.sina.com (Sat Jul 09 2005 - 00:03:23 PDT)
- glc0358.vip.sina.com (Fri Jul 08 2005 - 23:22:45 PDT)
AMBER: (no subject)
- Varsha Goyal (Sat Jul 02 2005 - 09:10:49 PDT)
- S.Sundar Raman (Sat Jul 02 2005 - 05:58:59 PDT)
- Varsha Goyal (Fri Jul 01 2005 - 14:46:55 PDT)
AMBER: 10-12 potential and create atom type
- David A. Case (Tue Jul 05 2005 - 15:03:09 PDT)
AMBER: [FWD] water minimalization problems
- blakrose.gazeta.pl (Wed Jul 27 2005 - 08:46:47 PDT)
AMBER: [OT] A nab programming question
- M. L. Dodson (Tue Jul 26 2005 - 07:32:47 PDT)
- David A. Case (Mon Jul 25 2005 - 14:35:49 PDT)
- M. L. Dodson (Thu Jul 21 2005 - 13:07:09 PDT)
AMBER: a bimolecular reaction
- Yong Duan (Fri Jul 22 2005 - 12:25:09 PDT)
- Yong Duan (Fri Jul 22 2005 - 10:44:23 PDT)
AMBER: Adding residues to a DNA sequence
- Kara Di Giorgio (Fri Jul 29 2005 - 09:39:43 PDT)
- David A. Case (Wed Jul 27 2005 - 14:31:16 PDT)
- Kara Di Giorgio (Mon Jul 25 2005 - 19:20:53 PDT)
- David A. Case (Mon Jul 25 2005 - 14:39:23 PDT)
- Kara Di Giorgio (Sun Jul 24 2005 - 18:50:45 PDT)
AMBER: Amber 7 Compiler Error
- Daniel Wetzler (Wed Jul 20 2005 - 02:38:25 PDT)
- Ross Walker (Tue Jul 19 2005 - 08:36:03 PDT)
- Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 05:26:14 PDT)
AMBER: Amber 8: create topology for solvent - PBC box size problem
- Angela Liu (Wed Jul 13 2005 - 11:41:04 PDT)
AMBER: Amber 8: heterogeneous multiple copy LES method
- Angela Liu (Fri Jul 15 2005 - 07:16:23 PDT)
- Carlos Simmerling (Thu Jul 14 2005 - 14:17:07 PDT)
- Angela Liu (Wed Jul 13 2005 - 11:47:08 PDT)
AMBER: AMBER on Mac OS X
- Kara Di Giorgio (Wed Jul 06 2005 - 09:46:11 PDT)
- David A. Case (Wed Jul 06 2005 - 08:36:08 PDT)
- Varsha Goyal (Wed Jul 06 2005 - 07:55:12 PDT)
AMBER: Amber parameters for ADP
- David A. Case (Sat Jul 30 2005 - 10:08:08 PDT)
- zgleo (Fri Jul 29 2005 - 22:22:19 PDT)
AMBER: AMBER-process_mdout.perl
- Ross Walker (Mon Jul 18 2005 - 08:24:18 PDT)
- mathew k varghese (Mon Jul 18 2005 - 04:22:56 PDT)
- julien (Mon Jul 18 2005 - 00:48:01 PDT)
- Praveena Gopal (Mon Jul 18 2005 - 00:26:19 PDT)
AMBER: ambpdb core dump
- David A. Case (Fri Jul 29 2005 - 07:56:42 PDT)
- David A. Case (Fri Jul 29 2005 - 07:40:03 PDT)
- Peter Gannett (Fri Jul 29 2005 - 04:27:46 PDT)
AMBER: An atom name with 4 characters is not compatible with Leap ?
- David A. Case (Wed Jul 27 2005 - 10:39:08 PDT)
- Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 08:59:43 PDT)
- David A. Case (Wed Jul 27 2005 - 08:08:11 PDT)
- Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 00:20:27 PDT)
- David A. Case (Fri Jul 22 2005 - 10:27:31 PDT)
- David A. Case (Fri Jul 22 2005 - 10:24:58 PDT)
- Tim Meyer (Fri Jul 22 2005 - 08:06:52 PDT)
- ivan.mmb.pcb.ub.es (Fri Jul 22 2005 - 01:16:52 PDT)
- Arnoult, Eric [PRDFR] (Fri Jul 22 2005 - 00:53:24 PDT)
AMBER: Anal - problems with energy analysis
- David A. Case (Tue Jul 12 2005 - 15:00:45 PDT)
- Yogesh Sabnis (Tue Jul 12 2005 - 01:33:30 PDT)
AMBER: antechamber
- David A. Case (Mon Jul 25 2005 - 16:42:32 PDT)
- Dustin (Mon Jul 25 2005 - 13:30:40 PDT)
AMBER: Apologies - LMOD website down
- Istvan Kolossvary (Thu Jul 14 2005 - 07:39:54 PDT)
AMBER: Atom type :Si
- Ananda Rama Krishnan Selvaraj (Fri Jul 22 2005 - 12:45:30 PDT)
- Stefano.Pieraccini.unimi.it (Fri Jul 22 2005 - 01:37:50 PDT)
- Ananda Rama Krishnan Selvaraj (Thu Jul 21 2005 - 12:02:23 PDT)
AMBER: box size in explicit water
- David A. Case (Wed Jul 06 2005 - 10:30:59 PDT)
- Melinda Layten (Wed Jul 06 2005 - 09:52:55 PDT)
- Lwin, ThuZar (Wed Jul 06 2005 - 09:39:47 PDT)
AMBER: building nucleic acids
- David A. Case (Sun Jul 10 2005 - 21:51:46 PDT)
- mathew k varghese (Fri Jul 08 2005 - 22:55:00 PDT)
- Bill Ross (Fri Jul 08 2005 - 12:05:15 PDT)
- mathew k varghese (Thu Jul 07 2005 - 21:07:03 PDT)
AMBER: Can GB and MS work correctly together in mmpbsa?
- zhli_2000.126.com (Mon Jul 18 2005 - 18:09:23 PDT)
- zhli_2000.126.com (Mon Jul 18 2005 - 18:23:39 PDT)
- Alfonso Garcia-Sosa (Mon Jul 18 2005 - 12:16:21 PDT)
- Scott Pendley (Mon Jul 18 2005 - 10:31:29 PDT)
- zhli_2000.126.com (Sat Jul 16 2005 - 20:30:47 PDT)
- Scott Pendley (Fri Jul 15 2005 - 13:08:43 PDT)
- Scott Pendley (Fri Jul 15 2005 - 10:46:46 PDT)
- zhli_2000.126.com (Fri Jul 15 2005 - 00:10:41 PDT)
- Holger Gohlke (Thu Jul 14 2005 - 22:39:21 PDT)
- zhli_2000.126.com (Thu Jul 14 2005 - 19:38:08 PDT)
AMBER: cap and ptraj
- Fabien CAILLIEZ (Tue Jul 19 2005 - 15:14:50 PDT)
AMBER: cap simulations questions
- David A. Case (Mon Jul 18 2005 - 09:01:34 PDT)
- Fabien CAILLIEZ (Mon Jul 18 2005 - 07:50:32 PDT)
AMBER: Carbonane
- Kara Di Giorgio (Thu Jul 21 2005 - 17:55:26 PDT)
AMBER: cavity volume
- Germán Sciaini (Mon Jul 04 2005 - 03:29:59 PDT)
- Anthony Cruz (Fri Jul 01 2005 - 05:46:24 PDT)
AMBER: comparing md trajectories
- Carlos Simmerling (Tue Jul 19 2005 - 05:58:44 PDT)
- ayongye.chem.uga.edu (Mon Jul 18 2005 - 18:12:15 PDT)
AMBER: Comparison of AMBER against DL-POLY
- Devashish Kumar (Tue Jul 12 2005 - 15:32:03 PDT)
AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler
- Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 13:14:30 PDT)
AMBER: convert_trajectory
- Wei Chen (Wed Jul 27 2005 - 19:06:28 PDT)
- Thomas E. Cheatham, III (Wed Jul 27 2005 - 16:45:34 PDT)
- Wei Chen (Wed Jul 27 2005 - 16:07:55 PDT)
- Thomas E. Cheatham, III (Wed Jul 27 2005 - 14:27:57 PDT)
- Wei Chen (Wed Jul 27 2005 - 13:58:36 PDT)
AMBER: Create new Unit
- FyD (Thu Jun 30 2005 - 17:25:02 PDT)
AMBER: Critical PMEMD 8 Bugfix
- Robert Duke (Mon Jul 11 2005 - 05:38:59 PDT)
AMBER: cutoff in ANAL
- David A. Case (Thu Jul 28 2005 - 09:26:40 PDT)
- Madjid Taghdir (Wed Jul 27 2005 - 01:06:54 PDT)
AMBER: dihedral term in prmtop file
- Carlos Simmerling (Thu Jul 28 2005 - 07:59:36 PDT)
- Ye Mei (Thu Jul 28 2005 - 07:38:55 PDT)
AMBER: Division by zero in sander
- Caleb S Howe (cshowe.Princeton.EDU) (Thu Jul 28 2005 - 07:57:00 PDT)
AMBER: DNA strands separate
- Angelo Pugliese (Wed Jul 06 2005 - 08:00:00 PDT)
- ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 07:39:04 PDT)
- Angelo Pugliese (Wed Jul 06 2005 - 07:04:36 PDT)
- ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 06:40:18 PDT)
- Angelo Pugliese (Wed Jul 06 2005 - 05:46:05 PDT)
- ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 03:39:24 PDT)
AMBER: doubt on the value of Pressure on MD run
- Carlos Simmerling (Tue Jul 12 2005 - 04:07:08 PDT)
- Ananda Rama Krishnan Selvaraj (Tue Jul 12 2005 - 01:21:07 PDT)
AMBER: Energy decomposition parameters
- Angelo Pugliese (Fri Jul 15 2005 - 01:57:21 PDT)
AMBER: Error in MD
- Guanglei Cui (Thu Jul 21 2005 - 21:08:56 PDT)
- mathew k varghese (Thu Jul 21 2005 - 20:53:08 PDT)
AMBER: estimation of interface size
- Carlos Simmerling (Mon Jul 04 2005 - 04:39:11 PDT)
- Ye Mei (Sun Jul 03 2005 - 19:19:55 PDT)
AMBER: example script for hbond calculation
- Thomas E. Cheatham, III (Fri Jul 01 2005 - 09:10:07 PDT)
AMBER: Failed sander runs for large systems
- David A. Case (Sat Jul 30 2005 - 09:57:14 PDT)
- Guanglei Cui (Fri Jul 29 2005 - 21:33:27 PDT)
- Pratul K. Agarwal (Fri Jul 29 2005 - 19:41:44 PDT)
AMBER: Fatal Error on loading a pdb in xLeap
- Ilyas Yildirim (Thu Jul 28 2005 - 20:56:32 PDT)
- David A. Case (Thu Jul 28 2005 - 15:17:14 PDT)
- Kara Di Giorgio (Thu Jul 28 2005 - 08:10:45 PDT)
AMBER: fit
- Kateryna Miroshnychenko (Mon Jul 25 2005 - 03:11:11 PDT)
- Yong Xu (Mon Jul 25 2005 - 02:04:57 PDT)
AMBER: how is truncated octahedron box calculated
- Chris Moth (Thu Jul 07 2005 - 14:50:24 PDT)
- Lwin, ThuZar (Thu Jul 07 2005 - 13:38:05 PDT)
AMBER: how to average the structure along md trajectory
- Angelo Pugliese (Wed Jul 06 2005 - 08:02:48 PDT)
- Ye Mei (Wed Jul 06 2005 - 06:51:56 PDT)
AMBER: How to insert a protein in lipid bilayer
- Yong Xu (Wed Jul 27 2005 - 18:47:22 PDT)
- nag raj (Wed Jul 27 2005 - 09:56:07 PDT)
AMBER: how to make cluster files?
- Ananda Rama Krishnan Selvaraj (Fri Jul 01 2005 - 00:10:05 PDT)
AMBER: how to reduce box size and delete excess solvent
- hj zou (Wed Jul 27 2005 - 06:36:40 PDT)
AMBER: how to see the box lines
- Ananda Rama Krishnan Selvaraj (Sat Jul 09 2005 - 11:10:50 PDT)
AMBER: infinite DNA
- David A. Case (Fri Jul 08 2005 - 17:26:04 PDT)
- Carlos Simmerling (Fri Jul 08 2005 - 16:33:59 PDT)
- Stern, Julie (Fri Jul 08 2005 - 14:44:25 PDT)
AMBER: LCPO SASA parameters for other elements when using gbsa=1 option
- David.Maxwell.di.mdacc.tmc.edu (Fri Jul 08 2005 - 13:10:00 PDT)
AMBER: Leap compilation issues
- Ross Walker (Tue Jul 12 2005 - 09:47:05 PDT)
- justin litchfield (Mon Jul 11 2005 - 18:55:54 PDT)
- Bill Ross (Mon Jul 11 2005 - 18:34:35 PDT)
- justin litchfield (Mon Jul 11 2005 - 18:25:10 PDT)
- Ross Walker (Mon Jul 11 2005 - 10:05:25 PDT)
- Andreas Svrcek-Seiler (Mon Jul 11 2005 - 03:43:39 PDT)
- justin litchfield (Sun Jul 10 2005 - 23:49:33 PDT)
- David A. Case (Sun Jul 10 2005 - 22:13:04 PDT)
- Bill Ross (Sun Jul 10 2005 - 19:11:43 PDT)
- justin litchfield (Sun Jul 10 2005 - 18:41:50 PDT)
AMBER: Leap problem
- Kara Di Giorgio (Fri Jul 15 2005 - 06:59:47 PDT)
- Oliver Hucke (Thu Jul 14 2005 - 18:48:52 PDT)
- Kara Di Giorgio (Thu Jul 14 2005 - 18:19:00 PDT)
- Furse, Kristina Elisabet (Thu Jul 14 2005 - 17:31:40 PDT)
- Kara Di Giorgio (Thu Jul 14 2005 - 17:06:50 PDT)
AMBER: Leap question
- David A. Case (Thu Jul 14 2005 - 08:39:59 PDT)
- Kara Di Giorgio (Thu Jul 14 2005 - 08:10:12 PDT)
AMBER: least square fit of snapshots in md trajectory to a reference frame
- David A. Case (Fri Jul 01 2005 - 08:51:21 PDT)
- Ye Mei (Thu Jun 30 2005 - 19:56:08 PDT)
AMBER: lib file for nonstandard residue
- David A. Case (Thu Jul 14 2005 - 15:35:47 PDT)
- Bill Ross (Thu Jul 14 2005 - 15:20:25 PDT)
- Eric Hu (Thu Jul 14 2005 - 15:02:35 PDT)
- Bill Ross (Thu Jul 14 2005 - 12:37:01 PDT)
- Bill Ross (Thu Jul 14 2005 - 12:08:03 PDT)
- Eric Hu (Wed Jul 13 2005 - 16:52:19 PDT)
AMBER: Lipid bilayer parameters
- nag raj (Fri Jul 22 2005 - 00:18:24 PDT)
AMBER: Lipid bilayer parameters and charmm force field parameters
- nag raj (Fri Jul 22 2005 - 20:15:35 PDT)
AMBER: Lipid parameters
- nag raj (Tue Jul 26 2005 - 03:55:22 PDT)
AMBER: Loading a macmodel file complex
- Ross Walker (Tue Jul 05 2005 - 08:54:57 PDT)
- Yogesh Sabnis (Mon Jul 04 2005 - 08:02:49 PDT)
AMBER: loading DNA-RNA hybrid in xleap
- Ilyas Yildirim (Sun Jul 03 2005 - 04:23:56 PDT)
- cbala.igib.res.in (Sat Jul 02 2005 - 12:57:33 PDT)
- David A. Case (Sat Jul 02 2005 - 10:30:58 PDT)
- cbala.igib.res.in (Sat Jul 02 2005 - 08:36:59 PDT)
AMBER: MD simulation on a protein solvated by a combination of some water mod
- David A. Case (Thu Jul 14 2005 - 08:29:20 PDT)
- 荒牧武志 (Thu Jul 14 2005 - 02:56:39 PDT)
AMBER: MD simulation on a protein solvated by a combination of some water models ?
- Ross Walker (Tue Jul 12 2005 - 09:41:44 PDT)
- 荒牧武志 (Mon Jul 11 2005 - 21:10:12 PDT)
AMBER: Minimized structure
- Yam (Thu Jul 28 2005 - 21:03:40 PDT)
- Thomas E. Cheatham, III (Thu Jul 28 2005 - 20:09:55 PDT)
- Yam (Thu Jul 28 2005 - 19:25:29 PDT)
- Vitor Manuel Sousa F?x (Thu Jul 28 2005 - 04:07:09 PDT)
- Carlos Simmerling (Thu Jul 28 2005 - 03:53:45 PDT)
- Linchen Gong (Wed Jul 27 2005 - 23:55:05 PDT)
- Thomas E. Cheatham, III (Wed Jul 27 2005 - 20:47:28 PDT)
- Yam (Wed Jul 27 2005 - 20:02:03 PDT)
AMBER: MM-PBSA-big energies
- Carlos Simmerling (Sun Jul 03 2005 - 15:13:48 PDT)
- John (Sun Jul 03 2005 - 14:31:56 PDT)
AMBER: mm_pbsa
- zgleo (Sun Jul 31 2005 - 08:26:02 PDT)
- Wei Chen (Fri Jul 29 2005 - 20:53:36 PDT)
- JunJun Liu (Fri Jul 29 2005 - 19:22:20 PDT)
- Wei Chen (Fri Jul 29 2005 - 18:09:13 PDT)
- JunJun Liu (Fri Jul 29 2005 - 17:58:53 PDT)
- Wei Chen (Fri Jul 29 2005 - 17:55:07 PDT)
- Suxin Zheng (Fri Jul 29 2005 - 17:39:15 PDT)
- Wei Chen (Fri Jul 29 2005 - 17:10:46 PDT)
AMBER: MM_PBSA help, please
- opitz.che.udel.edu (Tue Jul 12 2005 - 15:18:50 PDT)
- Scott Pendley (Tue Jul 12 2005 - 14:57:08 PDT)
- opitz.che.udel.edu (Tue Jul 12 2005 - 10:29:19 PDT)
- David A. Case (Tue Jul 12 2005 - 09:34:56 PDT)
- opitz.che.udel.edu (Tue Jul 12 2005 - 07:19:05 PDT)
- Scott Pendley (Mon Jul 11 2005 - 14:37:50 PDT)
- opitz.che.udel.edu (Mon Jul 11 2005 - 14:15:19 PDT)
- Scott Pendley (Mon Jul 11 2005 - 11:30:34 PDT)
- opitz.che.udel.edu (Mon Jul 11 2005 - 08:55:47 PDT)
AMBER: mm_pbsa question
- Matthew Davies (Tue Jul 19 2005 - 03:07:51 PDT)
AMBER: mmpbsa test problem
- Suxin Zheng (Fri Jul 22 2005 - 18:41:11 PDT)
AMBER: Modeling of a radical
- Peter Gannett (Sat Jul 23 2005 - 07:21:25 PDT)
- David A. Case (Thu Jul 14 2005 - 08:48:54 PDT)
- L Jin (Thu Jul 14 2005 - 03:46:20 PDT)
AMBER: molecular dynamics
- Ross Walker (Sat Jul 09 2005 - 20:42:06 PDT)
- Vijay Manickam Achari (Sat Jul 09 2005 - 19:55:55 PDT)
AMBER: molecular dynamics course
- Ilan Samish (Sat Jul 09 2005 - 23:23:05 PDT)
AMBER: molecular dynamics simulation of protein containing Mg2+ cation
- David A. Case (Sun Jul 03 2005 - 16:34:14 PDT)
- Ye Mei (Fri Jul 01 2005 - 02:33:31 PDT)
AMBER: molsurf error in MM/PBSA calculation
- Paul Beroza (Thu Jul 14 2005 - 16:01:08 PDT)
- David A. Case (Tue Jul 12 2005 - 18:23:50 PDT)
- David A. Case (Tue Jul 12 2005 - 15:03:23 PDT)
- JunJun Liu (Tue Jul 12 2005 - 06:43:55 PDT)
AMBER: new residue
- Douali, Latifa (Wed Jul 27 2005 - 14:36:27 PDT)
- David A. Case (Wed Jul 27 2005 - 14:13:32 PDT)
- Douali, Latifa (Wed Jul 27 2005 - 13:45:17 PDT)
- David A. Case (Wed Jul 27 2005 - 10:20:42 PDT)
- Ross Walker (Wed Jul 27 2005 - 09:54:14 PDT)
- Douali, Latifa (Wed Jul 27 2005 - 09:09:01 PDT)
- Furse, Kristina Elisabet (Tue Jul 26 2005 - 18:40:51 PDT)
- Douali, Latifa (Tue Jul 26 2005 - 17:50:51 PDT)
AMBER: NTWPRY problem
- wenfei Li (Mon Jul 25 2005 - 18:51:09 PDT)
- wenfei Li (Mon Jul 25 2005 - 18:42:16 PDT)
- wenfei Li (Mon Jul 25 2005 - 18:39:21 PDT)
- David A. Case (Mon Jul 25 2005 - 16:54:25 PDT)
- wenfei Li (Mon Jul 25 2005 - 08:44:31 PDT)
AMBER: nucgen and nukit
- Bill Ross (Tue Jul 05 2005 - 09:33:04 PDT)
- dthomas.chem.uwa.edu.au (Tue Jul 05 2005 - 07:55:44 PDT)
AMBER: nucgen bdna types
- David A. Case (Sun Jul 24 2005 - 16:42:44 PDT)
- Stern, Julie (Fri Jul 22 2005 - 18:01:20 PDT)
AMBER: nucgen error (U not generated)
- Thomas E. Cheatham, III (Wed Jul 27 2005 - 20:49:33 PDT)
- mathew k varghese (Wed Jul 27 2005 - 20:28:51 PDT)
AMBER: nucgen H5T H3T
- David A. Case (Tue Jul 26 2005 - 07:54:32 PDT)
- Stern, Julie (Mon Jul 25 2005 - 18:55:52 PDT)
AMBER: P4 EM64T Intel Fortran Compile Problem
- Zhang Bing (Wed Jul 20 2005 - 19:24:20 PDT)
- Dawei Zhang (Fri Jul 15 2005 - 13:54:39 PDT)
- Andreas Svrcek-Seiler (Fri Jul 15 2005 - 10:49:47 PDT)
- Ross Walker (Fri Jul 15 2005 - 10:26:36 PDT)
- Dawei Zhang (Fri Jul 15 2005 - 10:04:49 PDT)
AMBER: parallel error
- Peter Varnai (Fri Jul 01 2005 - 08:51:18 PDT)
AMBER: pbsa problem
- Suxin Zheng (Wed Jul 27 2005 - 12:47:29 PDT)
AMBER: pdb file and xleap
- Wai Keat Yam (Wed Jul 20 2005 - 23:01:07 PDT)
- Ross Walker (Tue Jul 19 2005 - 08:33:44 PDT)
- Wai Keat Yam (Tue Jul 19 2005 - 03:06:50 PDT)
AMBER: pdb files from traj file
- Ross Walker (Wed Jul 13 2005 - 14:37:05 PDT)
- David LeBard (Wed Jul 13 2005 - 14:30:07 PDT)
- Rhoad, Jonathan S. (Wed Jul 13 2005 - 14:22:56 PDT)
- Carlos Simmerling (Wed Jul 13 2005 - 14:16:52 PDT)
- YoungJin Cho (Wed Jul 13 2005 - 14:06:30 PDT)
AMBER: Periodic box imaging using ptraj
- Ross Walker (Wed Jul 27 2005 - 09:28:05 PDT)
- Grzegorz Jezierski (Wed Jul 27 2005 - 04:28:29 PDT)
- Grzegorz Jezierski (Wed Jul 27 2005 - 02:27:24 PDT)
- Thomas E. Cheatham, III (Tue Jul 26 2005 - 13:11:39 PDT)
- Grzegorz Jezierski (Tue Jul 26 2005 - 06:25:53 PDT)
AMBER: please help us on partial charge calculation of PT complex using RESP
- FyD (Fri Jul 01 2005 - 09:07:40 PDT)
- peng79.email.unc.edu (Fri Jul 01 2005 - 08:10:31 PDT)
AMBER: pmemd - bug report
- David A. Case (Tue Jul 05 2005 - 10:43:18 PDT)
- David A. Case (Tue Jul 05 2005 - 10:38:09 PDT)
- Robert Duke (Tue Jul 05 2005 - 09:47:19 PDT)
- Petr Kulhanek (Tue Jul 05 2005 - 09:29:54 PDT)
- Petr Kulhanek (Tue Jul 05 2005 - 03:31:14 PDT)
- Robert Duke (Mon Jul 04 2005 - 20:58:14 PDT)
- Robert Duke (Mon Jul 04 2005 - 14:40:18 PDT)
- Robert Duke (Mon Jul 04 2005 - 13:30:54 PDT)
- Petr Kulhanek (Mon Jul 04 2005 - 09:33:05 PDT)
AMBER: PMF calculations with TI using the sander
- David A. Case (Mon Jul 18 2005 - 09:03:47 PDT)
- Vitor Manuel Sousa F?x (Mon Jul 18 2005 - 00:30:59 PDT)
AMBER: Position Restraints!
- justin litchfield (Sat Jul 09 2005 - 17:08:15 PDT)
- Karthikeyan Pasupathy (Sat Jul 09 2005 - 10:24:51 PDT)
AMBER: potential of mean force calculation along reaction coordinates
- Ye Mei (Tue Jul 26 2005 - 00:04:00 PDT)
AMBER: prepi format and question about it
- Ilyas Yildirim (Wed Jul 27 2005 - 22:10:36 PDT)
- David A. Case (Wed Jul 27 2005 - 07:57:30 PDT)
- Ilyas Yildirim (Wed Jul 27 2005 - 02:20:00 PDT)
AMBER: problem with addIons
- David A. Case (Wed Jul 06 2005 - 15:41:21 PDT)
- David LeBard (Wed Jul 06 2005 - 15:08:35 PDT)
- Lwin, ThuZar (Wed Jul 06 2005 - 14:41:25 PDT)
AMBER: Problem with building AMBER7 on SUSE Linux 9.2
- Daniel Wetzler (Tue Jul 12 2005 - 00:53:40 PDT)
- Daniel Wetzler (Fri Jul 08 2005 - 04:18:09 PDT)
AMBER: problem with protein ligand complex
- David A. Case (Sat Jul 16 2005 - 12:05:02 PDT)
- Claire Zerafa (Sat Jul 16 2005 - 09:31:56 PDT)
AMBER: problem with xleap
- David A. Case (Fri Jul 22 2005 - 08:59:24 PDT)
- Alessio Coi (Fri Jul 22 2005 - 06:47:23 PDT)
AMBER: problems with bonds in sander
- Fabien CAILLIEZ (Thu Jul 07 2005 - 11:18:19 PDT)
AMBER: Problems with parameter lib and prep püarameter files
- Daniel Wetzler (Wed Jul 06 2005 - 03:40:53 PDT)
- Ross Walker (Tue Jul 05 2005 - 08:47:22 PDT)
- Daniel Wetzler (Mon Jul 04 2005 - 02:14:56 PDT)
AMBER: Protein residue numbering
- Sukjoon Yoon (Wed Jul 27 2005 - 04:52:42 PDT)
AMBER: Ptraj and order of operations
- Furse, Kristina Elisabet (Wed Jul 13 2005 - 11:55:02 PDT)
- Petr Kulhanek (Wed Jul 13 2005 - 00:21:48 PDT)
- Furse, Kristina Elisabet (Tue Jul 12 2005 - 18:07:04 PDT)
- Scott Pendley (Tue Jul 12 2005 - 16:22:29 PDT)
- Furse, Kristina Elisabet (Mon Jul 11 2005 - 17:26:09 PDT)
AMBER: ptraj output missing
- opitz.che.udel.edu (Fri Jul 29 2005 - 08:05:19 PDT)
AMBER: ptraj-acceptor mask format
- Peter Gannett (Wed Jul 27 2005 - 13:54:50 PDT)
- Thomas E. Cheatham, III (Tue Jul 26 2005 - 13:06:08 PDT)
- Peter Gannett (Mon Jul 25 2005 - 12:10:47 PDT)
AMBER: Question about "nmanal"
- David A. Case (Tue Jul 12 2005 - 09:29:46 PDT)
- Yen-Ting Lai (Tue Jul 12 2005 - 06:36:25 PDT)
- Yen-Ting Lai (Tue Jul 12 2005 - 03:09:24 PDT)
- David A. Case (Mon Jul 11 2005 - 09:15:32 PDT)
- Yen-Ting Lai (Mon Jul 11 2005 - 07:11:25 PDT)
AMBER: question about leaprc.gaff and xxx.top
- Vijay Manickam Achari (Thu Jun 30 2005 - 22:52:15 PDT)
AMBER: Question about Lennard-Jones Parameters in Topology file
- Linda Prengaman (Tue Jul 05 2005 - 10:40:44 PDT)
- Germán Sciaini (Mon Jul 04 2005 - 03:46:00 PDT)
- Linda Prengaman (Sat Jul 02 2005 - 11:15:51 PDT)
AMBER: Question about Prep file
- opitz.che.udel.edu (Fri Jul 22 2005 - 12:21:20 PDT)
- David A. Case (Fri Jul 22 2005 - 11:34:57 PDT)
- Marc Baaden (Thu Jul 21 2005 - 23:38:42 PDT)
- opitz.che.udel.edu (Thu Jul 21 2005 - 13:52:41 PDT)
AMBER: question about sander minimization error
- Ilyas Yildirim (Thu Jul 07 2005 - 01:59:13 PDT)
- drugdesign (Thu Jul 07 2005 - 01:37:51 PDT)
AMBER: question about spline in sander -- array size of eed_cub
- Cordova, Luis E. (Thu Jun 30 2005 - 21:33:25 PDT)
AMBER: question replica exchange acceptance ratio
- Carlos Simmerling (Tue Jul 12 2005 - 16:43:01 PDT)
- Zhuang (Tue Jul 12 2005 - 15:39:47 PDT)
- Carlos Simmerling (Tue Jul 12 2005 - 14:42:55 PDT)
- Zhuang (Tue Jul 12 2005 - 14:01:19 PDT)
AMBER: questions about MG ions
- Kara Di Giorgio (Sun Jul 31 2005 - 21:55:46 PDT)
- JIANING WANG (Sun Jul 31 2005 - 16:12:36 PDT)
AMBER: questions about topology file
- David A. Case (Fri Jul 01 2005 - 13:24:02 PDT)
- Fabien CAILLIEZ (Fri Jul 01 2005 - 08:49:20 PDT)
AMBER: random-coil polymer
- Varsha Goyal (Sat Jul 16 2005 - 15:35:19 PDT)
AMBER: Release of R.E.D-II
- FyD (Thu Jul 07 2005 - 10:58:54 PDT)
AMBER: Replica Exchange
- Carlos Simmerling (Thu Jul 07 2005 - 06:43:17 PDT)
- Anthony Cruz (Thu Jul 07 2005 - 08:27:51 PDT)
- Anthony Cruz (Fri Jul 01 2005 - 07:33:46 PDT)
AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
- Qing Zhang (Tue Jul 12 2005 - 12:59:01 PDT)
- Ilyas Yildirim (Mon Jul 11 2005 - 18:25:00 PDT)
- Qing Zhang (Thu Jul 07 2005 - 17:48:40 PDT)
- Ilyas Yildirim (Thu Jul 07 2005 - 14:56:14 PDT)
- FyD (Thu Jul 07 2005 - 08:54:00 PDT)
- Qing Zhang (Thu Jul 07 2005 - 01:30:14 PDT)
- Ilyas Yildirim (Wed Jul 06 2005 - 20:18:46 PDT)
- Ilyas Yildirim (Wed Jul 06 2005 - 15:24:45 PDT)
AMBER: restart file
- Carlos Simmerling (Tue Jul 05 2005 - 14:22:16 PDT)
- Ross Walker (Tue Jul 05 2005 - 14:15:49 PDT)
- Harianto Tjong (Tue Jul 05 2005 - 13:49:16 PDT)
- Carlos Simmerling (Tue Jul 05 2005 - 12:36:43 PDT)
- Ross Walker (Tue Jul 05 2005 - 12:29:27 PDT)
- Harianto Tjong (Tue Jul 05 2005 - 11:49:20 PDT)
AMBER: RESTARTED DUE TO LINMIN FAILURE
- David A. Case (Sat Jul 30 2005 - 09:59:19 PDT)
- Sukjoon Yoon (Fri Jul 29 2005 - 23:00:24 PDT)
AMBER: sander problem
- Anthony Cruz (Thu Jul 07 2005 - 08:25:29 PDT)
- David A. Case (Wed Jul 06 2005 - 15:30:59 PDT)
- Ross Walker (Wed Jul 06 2005 - 14:19:34 PDT)
- Anthony Cruz (Wed Jul 06 2005 - 16:05:44 PDT)
AMBER: segmentation fault in radial ptraj
- Kateryna Miroshnychenko (Mon Jul 18 2005 - 09:55:08 PDT)
AMBER: SHAKE error
- David A. Case (Mon Jul 25 2005 - 16:57:02 PDT)
- Agata Jurkiewicz (Fri Jul 22 2005 - 15:06:49 PDT)
- David A. Case (Fri Jul 22 2005 - 13:46:42 PDT)
- Carlos Simmerling (Fri Jul 22 2005 - 12:26:36 PDT)
- Ilyas Yildirim (Fri Jul 22 2005 - 12:23:06 PDT)
- Agata Jurkiewicz (Fri Jul 22 2005 - 12:12:10 PDT)
- Carlos Simmerling (Fri Jul 22 2005 - 10:24:46 PDT)
- Agata Jurkiewicz (Fri Jul 22 2005 - 10:01:16 PDT)
- David A. Case (Fri Jul 22 2005 - 09:04:15 PDT)
- Carlos Simmerling (Fri Jul 22 2005 - 07:56:53 PDT)
- Agata Jurkiewicz (Fri Jul 22 2005 - 07:09:34 PDT)
AMBER: simulation with Mg2+ ions and counter ions
- Jiri Sponer (Sat Jul 09 2005 - 01:50:10 PDT)
- Lihua Wang (Sat Jul 09 2005 - 01:11:42 PDT)
- Ye Mei (Fri Jul 08 2005 - 23:54:16 PDT)
AMBER: Stacking energy
- Jiri Sponer (Fri Jul 01 2005 - 08:00:03 PDT)
- Angelo Pugliese (Fri Jul 01 2005 - 07:38:37 PDT)
- Jiri Sponer (Fri Jul 01 2005 - 07:01:24 PDT)
- Angelo Pugliese (Fri Jul 01 2005 - 03:42:28 PDT)
- Jiri Sponer (Fri Jul 01 2005 - 02:52:45 PDT)
- ivan.mmb.pcb.ub.es (Fri Jul 01 2005 - 01:44:57 PDT)
- Angelo Pugliese (Fri Jul 01 2005 - 01:32:34 PDT)
AMBER: temperature keep increasing in high temp.
- Yong Duan (Fri Jul 29 2005 - 20:43:52 PDT)
- Carlos Simmerling (Fri Jul 29 2005 - 17:28:42 PDT)
- Hwankyu Lee (Fri Jul 29 2005 - 14:27:04 PDT)
AMBER: Temperature varible in MMPBSA script
- JunJun Liu (Fri Jul 01 2005 - 06:59:05 PDT)
AMBER: Thermodynamic Integration for conformational changes?
- David A. Case (Tue Jul 26 2005 - 11:42:54 PDT)
- Carlos Simmerling (Tue Jul 26 2005 - 11:02:57 PDT)
- Grzegorz Jezierski (Tue Jul 26 2005 - 10:33:00 PDT)
AMBER: TI - frcmod file
- Ilyas Yildirim (Wed Jul 13 2005 - 14:32:41 PDT)
- Oliver Hucke (Wed Jul 13 2005 - 14:18:08 PDT)
- David A. Case (Wed Jul 13 2005 - 14:10:56 PDT)
- Rhoad, Jonathan S. (Wed Jul 13 2005 - 14:03:17 PDT)
- Ilyas Yildirim (Wed Jul 13 2005 - 13:51:00 PDT)
- Ilyas Yildirim (Wed Jul 13 2005 - 13:42:49 PDT)
- Douali, Latifa (Wed Jul 13 2005 - 08:38:25 PDT)
- Oliver Hucke (Tue Jul 12 2005 - 16:54:11 PDT)
- Ilyas Yildirim (Tue Jul 12 2005 - 15:06:53 PDT)
- Oliver Hucke (Tue Jul 12 2005 - 12:21:44 PDT)
AMBER: Trouble with Amber8
- Ross Walker (Tue Jul 19 2005 - 13:41:27 PDT)
- Dustin (Tue Jul 19 2005 - 13:16:10 PDT)
AMBER: Tutoial 8 (Case Study)
- Ross Walker (Tue Jul 26 2005 - 10:03:37 PDT)
AMBER: tyrosyl charges
- Ilyas Yildirim (Thu Jul 07 2005 - 15:30:20 PDT)
- Ozlem Demir (Thu Jul 07 2005 - 10:07:24 PDT)
AMBER: units of mwcovar matrix befor conversion
- Kateryna Miroshnychenko (Thu Jul 14 2005 - 01:18:28 PDT)
AMBER: Using Antechamber with Gamess and other molecular manipulations
- Charles Karney (Mon Jul 18 2005 - 10:28:20 PDT)
AMBER: Water simulation
- David LeBard (Sat Jul 09 2005 - 17:30:55 PDT)
- David A. Case (Fri Jul 08 2005 - 17:13:37 PDT)
- David LeBard (Fri Jul 08 2005 - 16:44:12 PDT)
AMBER: why not minimize snapshots before MM/PBSA calculations
- Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 00:21:30 PDT)
- JunJun Liu (Tue Jul 26 2005 - 08:02:00 PDT)
Problems with ptraj/rdparm
- Thomas E. Cheatham, III (Fri Jul 15 2005 - 12:22:28 PDT)

Amber Archive Jul 2005 by subject