Amber Archive Jan 2003: by subject

'hot-solvent' and 'cold solute' problem
- David A. Case (Tue Jan 21 2003 - 08:38:14 PST)
- Stefan Jungblut (Tue Jan 21 2003 - 07:36:37 PST)
(no subject)
- Anke Eisenmann (Tue Jan 21 2003 - 06:07:25 PST)
- amkumar_at_post.its.mcw.edu (Fri Jan 10 2003 - 09:35:12 PST)
2drms command in ptraj
- Vlad Cojocaru (Tue Jan 28 2003 - 04:52:17 PST)
Amber parameters for Netropsin
- Manuel Rueda (Wed Jan 08 2003 - 15:48:12 PST)
Amber tutorial crown-ether
- David A. Case (Tue Jan 21 2003 - 08:48:47 PST)
- Dvira Segal (Tue Jan 21 2003 - 06:06:55 PST)
Amber Web page.
- caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 24 2003 - 08:45:00 PST)
AMBER7 & mpich
- FyD (Fri Jan 31 2003 - 06:05:41 PST)
antechamber and gamess
- David A. Case (Wed Jan 29 2003 - 08:16:03 PST)
- Arvid Soederhaell (Wed Jan 29 2003 - 07:08:00 PST)
average structure generated by carnal
- Andreas Svrcek-Seiler (Wed Jan 22 2003 - 07:16:53 PST)
- Kristina Furse (Tue Jan 21 2003 - 17:55:46 PST)
- eric hu (Tue Jan 21 2003 - 13:02:34 PST)
- Peter Gannett (Tue Jan 21 2003 - 12:14:38 PST)
- eric hu (Tue Jan 21 2003 - 10:53:49 PST)
Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
- David A. Case (Sun Jan 19 2003 - 23:26:16 PST)
- David A. Case (Sat Jan 18 2003 - 10:53:54 PST)
- John D. Chodera (Sat Jan 18 2003 - 01:26:12 PST)
building molecules by script files for leap
- David A. Case (Wed Jan 08 2003 - 09:27:13 PST)
- Dvira Segal (Wed Jan 08 2003 - 08:07:57 PST)
CARNAL
- Lepsa (Tue Jan 21 2003 - 10:07:18 PST)
- Lepsa (Tue Jan 21 2003 - 01:33:37 PST)
- Lepsa (Mon Jan 20 2003 - 07:22:22 PST)
CCL:electrostatic potential calculations
- Nathan A. Baker (Mon Jan 13 2003 - 14:27:00 PST)
CCL:MEAD on SuSE 8.1
- Szilveszter Juhos (Tue Jan 14 2003 - 08:22:08 PST)
Chloroform Parameters
- N. Jiten Singh (Thu Jan 23 2003 - 21:27:24 PST)
chloroform, dichlormethane f.f.
- Jose Ramon Blas (Tue Jan 14 2003 - 16:05:34 PST)
- David A. Case (Tue Jan 14 2003 - 08:19:24 PST)
- Arvid Soederhaell (Tue Jan 14 2003 - 02:24:33 PST)
compiling amber on myrinet
- Scott E. Boesch (Mon Jan 27 2003 - 12:12:31 PST)
compiling amber: Machine file for new 64 bit HP-Itanium II CPU
- Ying-Chieh Sun (Tue Jan 14 2003 - 17:40:40 PST)
conformational sampling
- Carlos Simmerling (Thu Jan 23 2003 - 15:45:58 PST)
- Robert G. Endres (Thu Jan 23 2003 - 06:17:57 PST)
coordinates for quasih
- Pratul Agarwal (Mon Jan 13 2003 - 07:48:17 PST)
- Jake Isaacs (Mon Jan 13 2003 - 06:43:54 PST)
crystal structure of DNA/RNA homopolymers
- Ioana Cozmuta (Mon Jan 27 2003 - 11:54:18 PST)
- David A. Case (Mon Jan 27 2003 - 11:48:35 PST)
- Ioana Cozmuta (Mon Jan 27 2003 - 11:34:13 PST)
Domain/Helix movement/MD
- Pratul Agarwal (Fri Jan 31 2003 - 13:00:54 PST)
- Lepsa (Fri Jan 31 2003 - 08:52:59 PST)
- Jianhui Wu (Fri Jan 31 2003 - 08:35:18 PST)
Dummy atoms in free energy calculation
- David A. Case (Sun Jan 12 2003 - 23:37:35 PST)
- Lepsa (Sat Jan 11 2003 - 10:18:44 PST)
Dummy-parameters in Amber?
- Miguel de Federico (Thu Jan 23 2003 - 03:07:14 PST)
- meiselba (Thu Jan 23 2003 - 02:39:17 PST)
electrostatic potential calculations
- Peter Gannett (Mon Jan 13 2003 - 09:32:19 PST)
- Andreas Svrcek-Seiler (Sat Jan 11 2003 - 08:43:33 PST)
- Vlad Cojocaru (Sat Jan 11 2003 - 08:05:07 PST)
equilibrated solvent box
- David A. Case (Wed Jan 22 2003 - 08:48:12 PST)
- pu xuemei (Mon Jan 20 2003 - 00:55:26 PST)
- pu xuemei (Mon Jan 20 2003 - 00:54:33 PST)
errors in MD trajectories
- Vlad Cojocaru (Fri Jan 10 2003 - 10:13:03 PST)
Ewald error
- David A. Case (Mon Jan 20 2003 - 09:31:49 PST)
- Miguel de Federico (Mon Jan 20 2003 - 07:32:21 PST)
Force Fields
- Colin Connelly (Fri Jan 10 2003 - 21:44:35 PST)
free energy perturbation (Gibbs/Amber 5)?
- Lepsa (Fri Jan 10 2003 - 01:56:50 PST)
- meiselba (Thu Jan 09 2003 - 08:49:09 PST)
freeware to visualize RMSD matrices creatde with Carnal
- Vlad Cojocaru (Mon Jan 27 2003 - 14:41:00 PST)
GIBBS - Routine TORCON failed. Required change is too large.
- Miguel de Federico (Thu Jan 09 2003 - 02:11:41 PST)
gibbs calculation
- David A. Case (Tue Jan 28 2003 - 12:03:37 PST)
- Xiang, Tian-Xiang (Tue Jan 28 2003 - 11:03:44 PST)
Gibbs dummy atom
- Paula Petrone (Fri Jan 31 2003 - 15:49:52 PST)
gibbs run
- David A. Case (Mon Jan 27 2003 - 10:38:13 PST)
- Xiang, Tian-Xiang (Mon Jan 27 2003 - 09:05:06 PST)
Gibbs tutorial question
- David A. Case (Wed Jan 22 2003 - 13:54:10 PST)
- Patricia Burgess (Wed Jan 22 2003 - 12:27:34 PST)
Gibbs, ewald and ifc
- David Smith (Fri Jan 31 2003 - 14:16:14 PST)
- David A. Case (Fri Jan 31 2003 - 13:56:25 PST)
Has anyone ever used MEAD?
- Vlad Cojocaru (Mon Jan 20 2003 - 05:58:30 PST)
High temperature MD
- Lepsa (Wed Jan 29 2003 - 23:27:19 PST)
- A.Madhumalar (Sun Jan 19 2003 - 08:02:41 PST)
How much is minimum distance
- pu xuemei (Thu Jan 23 2003 - 23:11:29 PST)
How to control box size
- David A. Case (Wed Jan 22 2003 - 08:53:02 PST)
- pu xuemei (Wed Jan 22 2003 - 04:58:53 PST)
how to stop mapping of N- and C-terminal residues in xleap
- David A. Case (Tue Jan 14 2003 - 11:59:52 PST)
- Michael Ford (Tue Jan 14 2003 - 11:37:27 PST)
how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution)
- Michael Ford (Wed Jan 15 2003 - 10:02:52 PST)
IDSX0 in free energy calculations
- Lepsa (Fri Jan 10 2003 - 05:29:04 PST)
Intramolecular H-bonds in charge fitting
- Bayly, Christopher (Tue Jan 28 2003 - 07:35:14 PST)
- Lepsa (Tue Jan 28 2003 - 01:05:58 PST)
JACS 125th and PAK
- David A. Case (Fri Jan 03 2003 - 10:36:47 PST)
- Carlos Simmerling (Fri Jan 03 2003 - 09:02:12 PST)
LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi
- Chuck Schneider (Thu Jan 23 2003 - 04:52:41 PST)
- Dr Chris L. Brown (Wed Jan 22 2003 - 19:10:34 PST)
lastrst
- David A. Case (Mon Jan 27 2003 - 10:33:12 PST)
- Steve Seibold (Mon Jan 27 2003 - 09:46:57 PST)
Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
- Jim Newhouse (Tue Jan 07 2003 - 11:07:32 PST)
- Florian Barth (Fri Jan 03 2003 - 22:36:27 PST)
- David Case (Fri Jan 03 2003 - 21:46:00 PST)
- Chris Switzer (Fri Jan 03 2003 - 19:18:11 PST)
looking for 'pdb_to_mass'
- CUI, Guanglei (Tue Jan 07 2003 - 06:06:05 PST)
- yuann (Mon Jan 06 2003 - 22:54:32 PST)
mail reflector
- caldwell_at_heimdal.compchem.ucsf.edu (Thu Jan 16 2003 - 13:07:10 PST)
MEAD on SuSE 8.1
- Vlad Cojocaru (Tue Jan 14 2003 - 07:10:18 PST)
mm-pbsa error message
- Thomas Steinbrecher (Tue Jan 28 2003 - 07:02:04 PST)
mm-pbsa problem & possible solution
- Holger Gohlke (Thu Jan 30 2003 - 09:22:39 PST)
- Thomas Steinbrecher (Thu Jan 30 2003 - 07:51:57 PST)
mm_gbsa error message
- Holger Gohlke (Wed Jan 08 2003 - 13:52:31 PST)
- Mahadevan Seetharaman (Wed Jan 08 2003 - 10:17:23 PST)
mm_gbsa: Unit 5 Error on OPEN: sander_com.in
- Michael Ford (Wed Jan 15 2003 - 10:00:34 PST)
- Michael Ford (Tue Jan 14 2003 - 09:34:33 PST)
- William Wei (Tue Jan 14 2003 - 09:19:36 PST)
MM_PBSA
- Holger Gohlke (Wed Jan 29 2003 - 07:24:58 PST)
- Lepsa (Wed Jan 29 2003 - 05:12:34 PST)
mm_pbsa -- COMPT must be specified (correctly)
- Lepsa (Tue Jan 14 2003 - 00:49:55 PST)
- William Wei (Mon Jan 13 2003 - 10:00:10 PST)
- William Wei (Mon Jan 13 2003 - 09:32:36 PST)
- Holger Gohlke (Mon Jan 13 2003 - 09:01:10 PST)
mm_pbsa and ALA scan
- Lepsa (Wed Jan 29 2003 - 08:31:41 PST)
- Ahammadunny Pathiaseril (Wed Jan 29 2003 - 08:24:06 PST)
MM_PBSA for Linux
- Ram�n Gardu�o-Ju�rez (Wed Jan 22 2003 - 16:53:55 PST)
MM_pbsa prmtop file
- David A. Case (Thu Jan 09 2003 - 15:53:53 PST)
- wentaofu (Thu Jan 09 2003 - 15:29:38 PST)
mm_pbsa question
- Holger Gohlke (Tue Jan 07 2003 - 16:41:30 PST)
- wentaofu (Tue Jan 07 2003 - 16:17:08 PST)
mm_pbsa Stop at statistics
- William Wei (Fri Jan 17 2003 - 10:52:48 PST)
Moil-view
- CUI, Guanglei (Tue Jan 14 2003 - 09:48:49 PST)
- Ling Zhang (Tue Jan 14 2003 - 09:47:14 PST)
morse potential
- David A. Case (Mon Jan 20 2003 - 09:29:59 PST)
- hagop demirdjian (Mon Jan 20 2003 - 08:22:03 PST)
naphthalene, anthracene force field
- yuann (Wed Jan 29 2003 - 06:58:47 PST)
new amino acid residues
- David A. Case (Thu Jan 30 2003 - 09:46:35 PST)
- Nick Polfer (Thu Jan 30 2003 - 04:58:41 PST)
nmanal & quasih question
- David A. Case (Thu Jan 09 2003 - 09:16:11 PST)
- yuann (Thu Jan 09 2003 - 08:13:30 PST)
- yuann (Tue Jan 07 2003 - 23:16:56 PST)
Nmode query
- kinsellg (Fri Jan 24 2003 - 07:00:40 PST)
nscm
- Kristina Furse (Wed Jan 15 2003 - 11:13:00 PST)
- David A. Case (Tue Jan 14 2003 - 16:55:14 PST)
- Kristina Furse (Tue Jan 14 2003 - 16:21:52 PST)
nucleic acid structures
- Ioana Cozmuta (Fri Jan 17 2003 - 17:12:35 PST)
octahedral volume
- David A. Case (Tue Jan 21 2003 - 09:03:23 PST)
- Peter Varnai (Fri Jan 17 2003 - 02:26:58 PST)
one question
- Holger Gohlke (Tue Jan 28 2003 - 08:17:02 PST)
- Lepsa (Tue Jan 28 2003 - 08:16:05 PST)
- Fan Gao (Tue Jan 28 2003 - 08:14:56 PST)
pdb_to_mass
- sychen (Fri Jan 10 2003 - 17:53:37 PST)
- Jake Isaacs (Fri Jan 10 2003 - 12:42:35 PST)
pi-pi in AMBER
- Lepsa (Tue Jan 21 2003 - 09:53:27 PST)
polarization + ewald
- darden (Mon Jan 27 2003 - 16:58:10 PST)
- GUILBAUD Philippe 153683 (Mon Jan 27 2003 - 03:21:44 PST)
Polarization charges -geometry
- David A. Case (Tue Jan 21 2003 - 08:56:07 PST)
- Lepsa (Fri Jan 17 2003 - 00:21:30 PST)
Polymers
- Ndubuisi Emmanuel Okoro (Wed Jan 29 2003 - 13:40:53 PST)
- Ndubuisi Emmanuel Okoro (Thu Jan 23 2003 - 19:12:10 PST)
posphinic acid parameters
- Alfonso Garcia Sosa (Sun Jan 26 2003 - 08:28:11 PST)
Predefined Water_cap with xleap
- Jose Ramon Blas (Wed Jan 08 2003 - 10:42:16 PST)
Probelm with the generation of topology file
- Jash, Panchatapa (Tue Jan 21 2003 - 10:01:45 PST)
problem with antechamber
- David A. Case (Sun Jan 12 2003 - 14:01:06 PST)
- Craig A Bayse (Sun Jan 12 2003 - 10:54:05 PST)
problems in equilibrating NaCl solution
- Seongeun Yang (Fri Jan 24 2003 - 16:13:41 PST)
- David A. Case (Fri Jan 24 2003 - 14:20:12 PST)
- Seongeun Yang (Tue Jan 21 2003 - 14:48:04 PST)
Proper torsion parameters missing?
- Miguel de Federico (Fri Jan 24 2003 - 01:27:21 PST)
- Heike Meiselbach (Thu Jan 23 2003 - 11:05:05 PST)
ptraj distanse question
- Lepsa (Fri Jan 31 2003 - 04:16:25 PST)
- Sichun Yang (Thu Jan 30 2003 - 20:16:06 PST)
ptraj on Methane in water box
- Dvira Segal (Fri Jan 31 2003 - 02:45:03 PST)
Quasi-harmonic analysis
- Miyashita, Osamu (Fri Jan 31 2003 - 10:25:23 PST)
- David A. Case (Thu Jan 30 2003 - 17:58:32 PST)
- Pratul Agarwal (Thu Jan 30 2003 - 15:48:22 PST)
question about ligand
- David A. Case (Fri Jan 31 2003 - 15:14:41 PST)
- Lishan Yao (Fri Jan 31 2003 - 14:43:39 PST)
question on ptraj
- Ioana Cozmuta (Wed Jan 22 2003 - 13:01:26 PST)
Question: about restarting Energy
- David A. Case (Mon Jan 27 2003 - 18:33:14 PST)
- vannajan_at_chiangmai.ac.th (Mon Jan 27 2003 - 17:53:30 PST)
reduce the disk space
- eric hu (Tue Jan 21 2003 - 10:48:14 PST)
reducing restrains
- David A. Case (Tue Jan 07 2003 - 09:08:24 PST)
- Luis Gracia (Tue Jan 07 2003 - 08:14:43 PST)
Request
- johneluwa_at_eircom.net (Wed Jan 29 2003 - 18:42:28 PST)
RESP-group constraint
- Artur Galstyan (Fri Jan 24 2003 - 06:38:53 PST)
roar-cp : input for QM part ; output for CM2 charges
- hagop demirdjian (Fri Jan 31 2003 - 07:38:29 PST)
Sander box error and thanks on previous mdin error
- kxg2248_at_njit.edu (Fri Jan 03 2003 - 09:37:05 PST)
- David A. Case (Fri Jan 03 2003 - 07:40:07 PST)
- kxg2248_at_njit.edu (Thu Jan 02 2003 - 19:41:49 PST)
SASA and H-bond over trajectories
- Bimo Ario Tejo (Mon Jan 20 2003 - 20:59:12 PST)
script for H-bonds extracting
- Bayly, Christopher (Tue Jan 28 2003 - 10:40:53 PST)
- Bimo Ario Tejo (Tue Jan 28 2003 - 02:00:52 PST)
script for Potential/kinectic energy
- Luis Gracia (Mon Jan 20 2003 - 10:16:52 PST)
- Holger Gohlke (Mon Jan 20 2003 - 08:44:13 PST)
- Layi Adekoya (Mon Jan 20 2003 - 08:30:09 PST)
scripts for compiling UHBD/MEAD with amber 7.0
- eric hu (Mon Jan 20 2003 - 09:54:37 PST)
SCSL
- Roberto Gomperts (Thu Jan 23 2003 - 07:52:06 PST)
- Joffre Heredia (Wed Jan 22 2003 - 12:23:12 PST)
- David A. Case (Wed Jan 22 2003 - 08:37:33 PST)
shake and belly
- GUILLERMINA L ESTIU (Wed Jan 22 2003 - 10:47:30 PST)
- David A. Case (Wed Jan 22 2003 - 10:17:22 PST)
- GUILLERMINA L ESTIU (Tue Jan 21 2003 - 13:38:59 PST)
shake and H-O-H angle
- Andreas Svrcek-Seiler (Tue Jan 21 2003 - 11:29:22 PST)
- Luis Gracia (Tue Jan 21 2003 - 08:57:16 PST)
Shake problem in organic solvent
- David A. Case (Fri Jan 24 2003 - 13:43:20 PST)
- yuan bo (Fri Jan 24 2003 - 04:03:48 PST)
single point mutations to investigate the conformational change
- Sichun Yang (Mon Jan 27 2003 - 19:43:29 PST)
Small organic molecules
- David A. Case (Tue Jan 07 2003 - 08:16:48 PST)
- Dvira Segal (Tue Jan 07 2003 - 07:55:31 PST)
solvatecap
- GUILLERMINA L ESTIU (Wed Jan 15 2003 - 06:48:05 PST)
- David A. Case (Tue Jan 14 2003 - 14:29:43 PST)
- GUILLERMINA L ESTIU (Tue Jan 14 2003 - 12:33:16 PST)
solvent free energy, GB
- David A. Case (Thu Jan 16 2003 - 16:25:16 PST)
- Robert G. Endres (Thu Jan 16 2003 - 13:33:36 PST)
structure image
- A.Madhumalar (Mon Jan 27 2003 - 17:51:35 PST)
- Xiang, Tian-Xiang (Mon Jan 27 2003 - 08:25:34 PST)
- Xiang, Tian-Xiang (Mon Jan 27 2003 - 07:31:46 PST)
Summary: mm_pbsa -- COMPT must be specified (correctly)
- William Wei (Tue Jan 14 2003 - 07:31:07 PST)
terminal phosphate group in RNA
- David A. Case (Fri Jan 24 2003 - 16:03:06 PST)
- Mahadevan Seetharaman (Thu Jan 16 2003 - 14:10:13 PST)
the unit of velocity
- Jian Zhang (Wed Jan 08 2003 - 18:12:15 PST)
- David A. Case (Wed Jan 08 2003 - 08:09:43 PST)
- Jian Zhang (Tue Jan 07 2003 - 20:36:58 PST)
UCSF Network changes to affect Amber Web site.
- David A. Case (Fri Jan 17 2003 - 12:14:59 PST)
- Ross Walker (Fri Jan 17 2003 - 12:07:29 PST)
- caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 17 2003 - 11:41:19 PST)
virtual box
- eric hu (Tue Jan 07 2003 - 23:35:21 PST)
- eric hu (Tue Jan 07 2003 - 23:35:09 PST)
- David A. Case (Tue Jan 07 2003 - 15:56:29 PST)
- eric hu (Tue Jan 07 2003 - 15:26:15 PST)
water reordering in sander
- David A. Case (Tue Jan 07 2003 - 08:03:58 PST)
- Michael Trieb (Tue Jan 07 2003 - 05:43:38 PST)
xleap crashes
- Layi Adekoya (Tue Jan 14 2003 - 00:46:49 PST)
- David A. Case (Mon Jan 13 2003 - 09:08:15 PST)
- Layi Adekoya (Sun Jan 12 2003 - 23:54:20 PST)
- David Case (Fri Jan 10 2003 - 22:05:45 PST)
- Layi Adekoya (Fri Jan 10 2003 - 04:16:26 PST)
xleap in Amber7
- arubin_at_unmc.edu (Mon Jan 27 2003 - 16:56:16 PST)
- arubin_at_unmc.edu (Mon Jan 27 2003 - 16:54:46 PST)
your mail
- David A. Case (Tue Jan 21 2003 - 08:35:52 PST)
Zn2+ parameters
- Robert G. Endres (Sat Jan 25 2003 - 12:25:36 PST)
- Xiang, Tian-Xiang (Fri Jan 24 2003 - 13:42:07 PST)

Amber Archive Jan 2003 by subject