AMBER Archive (2001) - By Author

1217 messages sorted by: [ date ] [ thread ] [ subject ]
About this archive

Starting: Tue Jan 02 2001 - 02:41:34 CST
Ending: Sun Dec 30 2001 - 21:24:17 CST

Jithesh P.V
- How to remove CIO from prmtop & crd (Thu Mar 29 2001 - 03:21:25 CST)
- makeDIST_RST (Wed Mar 07 2001 - 09:40:48 CST)
A. Ababou
- amber5 and 77000 atoms ... (Wed Jul 04 2001 - 13:20:38 CDT)
- amber5 and 77000 atoms ... (Wed Jul 04 2001 - 10:36:16 CDT)
- My input problem in amber6 ! (Mon Jun 25 2001 - 10:54:18 CDT)
- Ca2+ parameters and how ? ... (Mon Apr 02 2001 - 14:46:27 CDT)
- Ca2+ parameters and how ? ... (Sat Mar 31 2001 - 09:07:39 CST)
- Water Box ... (Fri Mar 09 2001 - 10:43:05 CST)
A.Madhumalar
- Err in equilibration run (Sun Oct 28 2001 - 04:02:55 CST)
- Err in equilibration run (Mon Oct 22 2001 - 01:22:09 CDT)
- (no subject) (Tue Sep 25 2001 - 05:36:46 CDT)
- Re: coordinate resetting ? (Mon Aug 27 2001 - 07:50:59 CDT)
- ERR IN MD RUN!! (Sun Aug 19 2001 - 03:40:19 CDT)
- constraining hydrogen bonds (Sun Jul 22 2001 - 10:19:02 CDT)
- ADDING IONS USING EDIT (Sat Jul 14 2001 - 12:54:31 CDT)
- C DNA MONOMER UNITS (Tue Jul 03 2001 - 02:38:11 CDT)
- tleap input format (Wed Jun 27 2001 - 08:20:02 CDT)
- compiling amber6 in linux clusters (Sun Jun 03 2001 - 11:35:16 CDT)
- Minimization inputs in AMBER6!! (Thu May 10 2001 - 12:09:27 CDT)
- Generating C-DNA using nucgen! (Sun Mar 11 2001 - 02:31:16 CST)
- Compilation of Amber6 in linux machine (Sun Feb 18 2001 - 02:08:48 CST)
- Compilation of AMBER6 (Thu Feb 15 2001 - 12:36:51 CST)
Abdo MALAC
- Info (Mon Jan 29 2001 - 10:39:58 CST)
Adrian E. Roitberg
- parameters (Mon May 07 2001 - 13:00:55 CDT)
Agnes Hahn
- Fe4S4 cluster (Thu Feb 22 2001 - 10:06:09 CST)
Alan Todd
- AMBER on alpha (Tue Jan 23 2001 - 07:34:23 CST)
Aldo Jongejan
- ANAL (Amber6.0) (Wed May 02 2001 - 08:01:31 CDT)
Alexander Issanin
- GIBBS on Cray (Tue Nov 20 2001 - 01:24:31 CST)
- DNA bend (Tue Jan 09 2001 - 03:11:29 CST)
Alexander Steudle
- Combination of two solvents (Wed Aug 15 2001 - 09:58:15 CDT)
amber mail account
- Re: how to create a bond (fwd) (Thu Dec 20 2001 - 14:37:11 CST)
- Re: Cl and H-bonding (fwd) (Thu Dec 20 2001 - 14:36:58 CST)
- Re: (fwd) (Thu Dec 20 2001 - 14:36:43 CST)
Amesh Patel
- fatal error during equilibration of solvated system (Mon Nov 19 2001 - 08:31:39 CST)
- equilibration (Thu Nov 01 2001 - 23:09:57 CST)
- escaping atoms.... (Wed May 09 2001 - 09:36:30 CDT)
Andrea Bernini
- sander_classic NPAIRS limit (Fri Dec 14 2001 - 03:12:56 CST)
- pyridoxal phosphate parameters (Thu Nov 15 2001 - 03:43:33 CST)
- Re: Problem, setting up AMBERHOME! (Tue Apr 24 2001 - 09:08:08 CDT)
- GIBBS (Thu Mar 01 2001 - 05:20:07 CST)
Andreas Svrcek-Seiler
- Re: File format convert (Thu Dec 20 2001 - 06:58:53 CST)
- Re: software to build molecules (Tue Dec 11 2001 - 12:44:58 CST)
- Re: Maxwell-Boltzmann distribution of velocities (Fri Oct 26 2001 - 05:46:36 CDT)
- GB and Ions, 2nd try (Tue Oct 02 2001 - 10:43:39 CDT)
- Re: generalized born model on protein or peptide (Fri Sep 07 2001 - 14:39:27 CDT)
- Re: MD run with constantly decreasing total energy (fwd) (Mon Jul 30 2001 - 04:06:55 CDT)
- Re: solvation energy calculation (Thu Jul 26 2001 - 07:10:27 CDT)
- Re: DelPhi's manual (Thu Jul 26 2001 - 06:55:11 CDT)
- Re: trajectory analysis (Tue Jul 24 2001 - 14:00:59 CDT)
- Is there a potential for speedup in the GB-code ? (Fri Jun 15 2001 - 10:05:36 CDT)
- a correction, sorry (Fri Jun 08 2001 - 08:43:39 CDT)
- Re: error message. (Fri Jun 08 2001 - 06:36:41 CDT)
- Re: ice cube flying through space (Sat Jun 02 2001 - 07:54:55 CDT)
- Re: sander 6 warming up (Fri Jun 01 2001 - 08:53:35 CDT)
- Re: topology description (Tue May 08 2001 - 10:18:12 CDT)
- AMBER parameters (Tue May 01 2001 - 08:58:13 CDT)
- GB and Ions (Mon Apr 09 2001 - 05:21:06 CDT)
- Re: Question about installing AMBER (Wed Mar 21 2001 - 04:31:22 CST)
- Principal component analysis (Fri Mar 09 2001 - 13:11:21 CST)
- parm94.dat vs parm99.dat (Mon Feb 26 2001 - 02:24:00 CST)
- Implicit solvent MD with small RNA's (Wed Feb 14 2001 - 10:52:56 CST)
- Re: Regarding MD (Mon Feb 12 2001 - 01:26:12 CST)
- MD with 'Solvated Ions' (Mon Jan 15 2001 - 08:19:30 CST)
Andrew Aird
- peek_ewald_inpcrd (Mon May 07 2001 - 11:48:59 CDT)
- minimization (Tue Apr 10 2001 - 11:05:27 CDT)
- (no subject) (Wed Jan 31 2001 - 13:46:10 CST)
- pressure regulation (Wed Jan 24 2001 - 12:51:37 CST)
Andrew Gordon Purkiss
- Re: A request regarding AMBER postings with attached files (fwd) (Tue Jul 24 2001 - 06:14:29 CDT)
- Re: leap and SP2 nitrogen (Mon Feb 26 2001 - 07:07:26 CST)
Andrew Hoofnagle
- What do the exit codes mean? (Fri Nov 16 2001 - 17:09:58 CST)
- Re: Problem minimizing on SGI (SHOULD NOT BE HERE). (Thu Sep 13 2001 - 15:39:29 CDT)
- Problem minimizing on SGI (SHOULD NOT BE HERE). (Thu Sep 13 2001 - 12:37:05 CDT)
- How is the random number used to generate random velocities? (Mon Jun 11 2001 - 12:02:37 CDT)
- GAMESS and RESP. (Mon Jan 29 2001 - 16:51:56 CST)
- Phosphorylated residues. (Mon Jan 22 2001 - 14:33:16 CST)
Andrew Petersen
- sander compilers (Mon Apr 09 2001 - 09:21:55 CDT)
- Machine_g77_lam-mpi (Mon Mar 26 2001 - 15:33:27 CST)
Anita Ilze Zvaigzne
- Re: block attachments? (Tue Jul 24 2001 - 10:06:07 CDT)
- A request regarding AMBER postings with attached files (Tue Jul 24 2001 - 05:18:42 CDT)
- Re: lipid bilayer MD simulations (Tue Mar 06 2001 - 18:45:45 CST)
- Re: AMBER mail reflector archive (Thu Feb 15 2001 - 18:31:43 CST)
Ann Hermone
- PME with octahedral box (Tue Mar 20 2001 - 12:01:05 CST)
- PME with octahedral box (Mon Mar 19 2001 - 15:31:16 CST)
- Gibbs (Mon Feb 12 2001 - 14:17:51 CST)
Anna Ferrari
- PROFEC (Fri Mar 02 2001 - 04:57:28 CST)
Anton B. Guliaev
- ISTAR option and performance (Tue Oct 09 2001 - 12:39:10 CDT)
- limit in xleap (Fri Sep 21 2001 - 17:13:03 CDT)
- movie for subset of atoms (Thu Aug 30 2001 - 15:42:14 CDT)
- sander input in Amber 6 (Fri Aug 17 2001 - 10:14:32 CDT)
- Npairs Exceeds Max (Mon Jul 23 2001 - 12:37:48 CDT)
- 2'-deoxy-uracil (Wed Jun 06 2001 - 17:36:01 CDT)
Anton Guliaev
- Dual Origin vs dual Alfa (Tue Feb 13 2001 - 18:06:37 CST)
- Cavity solvation (Mon Jan 29 2001 - 17:45:15 CST)
- X-ray vs. MD (Thu Jan 25 2001 - 16:28:34 CST)
Antonio Entrena Guadix
- Amber Parameters (Wed Feb 14 2001 - 05:04:54 CST)
Anwer Mujeeb
- Re: (No Subject) (Thu Mar 08 2001 - 12:30:17 CST)
arnaud
- problem with anal (Fri Sep 07 2001 - 11:47:24 CDT)
artem
- TIP3P/SPC VdW radius (Tue Apr 10 2001 - 11:00:18 CDT)
Artem Mamonov
- tree names in group spec. (Thu May 10 2001 - 18:49:02 CDT)
arubin_at_unmc.edu
- CUT in AMBER6 (Mon May 21 2001 - 17:53:41 CDT)
- RMSD calculation (Tue May 15 2001 - 14:43:46 CDT)
asit_at_frontierdomain.com
- Amber for SP (Tue Dec 11 2001 - 21:54:48 CST)
Assoc.Prof.Dr.Kritsana Sagarik
- Freze solute molecules in AMBER (Tue Jan 23 2001 - 06:58:34 CST)
B $BM4
- About the input of GIbbs and parm98 and Monte Carlo (Sorry for my mistake) (Fri Mar 09 2001 - 08:54:03 CST)
- About the input of GIbbs and parm98 and Monte Carlo (Fri Mar 09 2001 - 08:33:17 CST)
backy_at_ibms.sinica.edu.tw
- what should change in the parameter? (Wed Oct 31 2001 - 03:52:10 CST)
- questions for group specification... (Wed Aug 01 2001 - 04:11:59 CDT)
- About Delphi... (Wed Jul 25 2001 - 22:42:10 CDT)
- Question... (Tue Jul 24 2001 - 00:57:56 CDT)
Bayly, Christopher
- RE: residue numbering in dimers and trimers (Thu Aug 30 2001 - 13:30:47 CDT)
- RE: CCl4 ESP Grid problem with jaguar | 010628a (fwd) (Wed Jul 04 2001 - 10:50:19 CDT)
- RE: Lone Pairs. (Thu Feb 08 2001 - 10:39:39 CST)
Bill Ross
- Re: restraint (Thu Nov 01 2001 - 17:04:13 CST)
- Re: help for restrained minimization (Mon Oct 29 2001 - 03:32:16 CST)
- Re: (no subject) (Fri Oct 26 2001 - 17:51:36 CDT)
- Re: Xleap, PDB file format (Fri Oct 26 2001 - 11:31:16 CDT)
- Re: how to add Zn Ca parameters (Wed Oct 24 2001 - 19:04:58 CDT)
- Re: Define flexible residues during MD simulation (Tue Oct 23 2001 - 23:14:35 CDT)
- Re: Err in equilibration run (Mon Oct 22 2001 - 02:03:38 CDT)
- Re: generation of small organic molecules on xleap (Sun Oct 21 2001 - 23:48:53 CDT)
- Re: possible bug in carnal in AMBER5 (Wed Oct 17 2001 - 16:09:00 CDT)
- Re: distribution of Na+ around DNA (Wed Oct 17 2001 - 09:32:02 CDT)
- Re: ANAL (Mon Oct 15 2001 - 13:17:23 CDT)
- Re: torsional profile with MD (Mon Oct 15 2001 - 12:17:12 CDT)
- Re: torsional profile with MD (Mon Oct 15 2001 - 12:12:21 CDT)
- Re: Can amber calculate the gibbs perturb energy when a ligand added a group (Sat Oct 13 2001 - 23:50:14 CDT)
- Re: adding water (Sat Oct 13 2001 - 23:44:47 CDT)
- Re: trajectory analysis (Sat Oct 13 2001 - 14:50:04 CDT)
- re: energy decomposition (Sat Oct 13 2001 - 14:10:18 CDT)
- Re: NPSCAL parameter (Mon Oct 08 2001 - 10:36:10 CDT)
- Re: problem with ambpdb (Wed Oct 03 2001 - 03:16:23 CDT)
- Re: CMC/MD (Wed Sep 26 2001 - 19:34:45 CDT)
- Re: Velocity information in CARNAL generated restart files (Tue Sep 25 2001 - 14:32:51 CDT)
- Re: water model (Tue Sep 25 2001 - 01:21:44 CDT)
- Re: restraints and type (Fri Sep 21 2001 - 10:41:15 CDT)
- Re: about radius of gyration (Mon Sep 17 2001 - 11:14:53 CDT)
- Re: compile leap (Mon Sep 17 2001 - 02:28:12 CDT)
- Re: energies for part of the protein (Wed Sep 12 2001 - 19:07:32 CDT)
- Re: library files in leap (Thu Sep 06 2001 - 17:11:06 CDT)
- Re: residue numbering in dimers and trimers (Thu Aug 30 2001 - 12:00:44 CDT)
- Re: problem using xleap and tleap (Wed Aug 22 2001 - 12:23:27 CDT)
- Re: adding atoms and amino acid residues (Mon Aug 20 2001 - 20:10:48 CDT)
- Re: trajectory analysis (Tue Jul 24 2001 - 13:48:54 CDT)
- Re: constraining hydrogen bonds (Sun Jul 22 2001 - 17:50:24 CDT)
- Re: installing amber6 (Tue Jul 17 2001 - 13:18:06 CDT)
- Re: about ion concentration in protein simulation (Wed Jul 11 2001 - 17:49:27 CDT)
- Re: Internal Restraints in Sander Problem (Wed Jul 11 2001 - 17:40:55 CDT)
- Re:problem in xleap (Wed Jul 11 2001 - 11:30:08 CDT)
- Re: Help with Leap! (Mon Jul 09 2001 - 19:34:52 CDT)
- Re: amber5/6 (Fri Jul 06 2001 - 15:18:23 CDT)
- Re: Problems with AMBER (Fri Jun 29 2001 - 18:23:06 CDT)
- Re: TIP3P (Fri Jun 29 2001 - 01:34:47 CDT)
- Re: Problems with AMBER (Thu Jun 28 2001 - 21:49:52 CDT)
- Re: Problems with AMBER (Thu Jun 28 2001 - 21:49:52 CDT)
- Re: Wrong compilation artifacts on ES40s? (Mon Jun 25 2001 - 01:51:20 CDT)
- Re: Wrong compilation artifacts on ES40s? (Sun Jun 24 2001 - 14:58:33 CDT)
- Re: Wrong compilation artifacts on ES40s? (Sun Jun 24 2001 - 12:59:27 CDT)
- Re: Linux stability (Fri Jun 22 2001 - 15:51:17 CDT)
- Re: Non-standard DNA bases (Wed Jun 13 2001 - 00:29:40 CDT)
- Re: Non-standard DNA bases (Tue Jun 12 2001 - 16:39:05 CDT)
- Re: atom coordinates (Mon Jun 11 2001 - 18:29:39 CDT)
- Re: AMBER on Hitachi SR8000 (Thu Jun 07 2001 - 16:43:48 CDT)
- Re: How to minimization of Average structure? (Sun Jun 03 2001 - 13:24:15 CDT)
- Re: Adding crystal water using tleap. (Sun Jun 03 2001 - 12:19:32 CDT)
- Re: add counterions (Wed May 30 2001 - 11:58:53 CDT)
- Re: problem in xleap (Wed May 30 2001 - 11:50:17 CDT)
- Re: AMBER compilation woes (Tue May 22 2001 - 02:01:52 CDT)
- Re: f2c.h (Mon May 21 2001 - 17:10:56 CDT)
- Re: CCL:Date: Wed, 16 May 2001 13:47:15 +0200 (Wed May 16 2001 - 14:59:11 CDT)
- Re: RMSD calculation (Tue May 15 2001 - 16:49:39 CDT)
- Re: Residue wise RMSD using carnal (Sun May 13 2001 - 12:28:05 CDT)
- Re: tree names in group spec. (Thu May 10 2001 - 20:37:01 CDT)
- Re: escaping atoms.... (Wed May 09 2001 - 17:34:27 CDT)
- Re: topology description (Wed May 09 2001 - 17:27:01 CDT)
- Re: addions in leap (Fri May 04 2001 - 09:23:44 CDT)
- Re: applying atom types (Fri Apr 27 2001 - 12:24:19 CDT)
- Re: 1-4 nonbonded interactions (Wed Apr 18 2001 - 14:58:59 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 14:22:19 CDT)
- Re: atom types for xleap (Tue Apr 17 2001 - 13:23:37 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 13:20:18 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 10:42:26 CDT)
- Re: odd display of ambpdb generated files (Fri Apr 13 2001 - 17:12:45 CDT)
- Re: Following Coordinates (Wed Apr 04 2001 - 19:24:54 CDT)
- Re: Pairlist error (Tue Apr 03 2001 - 23:23:29 CDT)
- Re: Ca2+ parameters and how ? ... (Mon Apr 02 2001 - 17:54:54 CDT)
- Re: saving a trajectory as individual pdb files (Mon Apr 02 2001 - 17:29:07 CDT)
- RE: terminal base pair opening (Mon Apr 02 2001 - 12:18:38 CDT)
- (no subject) (Mon Apr 02 2001 - 11:51:45 CDT)
- Re: parm warnings (Wed Mar 28 2001 - 13:58:17 CST)
- Re: loading prmtop and inpcrd into leap (Wed Mar 28 2001 - 12:37:38 CST)
- Re: Combining trajectories (Wed Mar 28 2001 - 11:35:54 CST)
- Re: PMF input file (Tue Mar 27 2001 - 13:18:18 CST)
- Re: Combining trajectories (Tue Mar 27 2001 - 10:53:58 CST)
- Re: How tleap does not add missing H atoms? (Mon Mar 26 2001 - 14:10:08 CST)
- Re: periodic box size (Mon Mar 26 2001 - 14:06:08 CST)
- Re: How tleap does not add missing H atoms? (Mon Mar 26 2001 - 11:54:34 CST)
- (no subject) (Thu Mar 22 2001 - 11:44:16 CST)
- Re: GIBBS error (Wed Mar 21 2001 - 18:07:56 CST)
- Re: amber6 compilation failure (fwd) (Tue Mar 20 2001 - 15:40:51 CST)
- Re: carnal problem (Fri Mar 16 2001 - 16:09:56 CST)
- Re: Selection (Wed Mar 14 2001 - 16:11:32 CST)
- Re: why the slowdown? (Wed Mar 14 2001 - 15:34:10 CST)
- Re: SHAKE (Thu Mar 08 2001 - 13:22:13 CST)
- Re: lipid bilayer MD simulations (Tue Mar 06 2001 - 13:48:02 CST)
- Re: lipid bilayer MD simulations (Tue Mar 06 2001 - 13:06:44 CST)
- re: leap adding terminal phosphates (Mon Mar 05 2001 - 14:27:27 CST)
- Re: PBC box problems (Wed Feb 28 2001 - 17:50:16 CST)
- Re: MD without SHAKE (Wed Feb 28 2001 - 13:25:50 CST)
- Re: MD without SHAKE (Tue Feb 27 2001 - 10:40:48 CST)
- Re: porphyrin parameters (Tue Feb 27 2001 - 02:50:34 CST)
- Re: MD without SHAKE (Mon Feb 26 2001 - 19:51:25 CST)
- Re: Linux 6.2 install problems (Mon Feb 26 2001 - 16:01:24 CST)
- Re: modified aminoacids using Leap (Thu Feb 22 2001 - 11:03:16 CST)
- Re: belly run (Wed Feb 21 2001 - 12:37:03 CST)
- RE: AMBER on SUN (Tue Feb 20 2001 - 13:17:50 CST)
- Re: periodic box size (Fri Feb 16 2001 - 14:35:36 CST)
- RE: AMBER mail reflector archive (Thu Feb 15 2001 - 17:47:31 CST)
- Re: dynamic memory allocation (Wed Feb 14 2001 - 12:21:22 CST)
- dynamic memory allocation (Tue Feb 13 2001 - 13:30:28 CST)
- Re: Ionic solutions (Mon Feb 12 2001 - 16:52:07 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 17:51:42 CST)
- Re: Cavity solvation (Mon Jan 29 2001 - 18:54:04 CST)
- Re: Measuring rigid-body rotation with AMBER (Fri Jan 26 2001 - 15:33:25 CST)
- Re: Incomplete coord file after crash (Thu Jan 25 2001 - 14:47:26 CST)
- Re: solvate cap (Fri Jan 19 2001 - 11:06:26 CST)
- Re: MD with 'Solvated Ions' (Mon Jan 15 2001 - 13:19:15 CST)
Boyd
- Emerging Technologies/COMP 2001 (Wed Mar 07 2001 - 08:58:54 CST)
bxiong
- (no subject) (Fri Jun 22 2001 - 21:11:09 CDT)
C. Klein
- sander crash / linux cluster (Mon Apr 30 2001 - 10:06:58 CDT)
C. Singer
- AMBER 6 on Linux - help (Tue Nov 13 2001 - 11:26:26 CST)
- Amber 6.0 on Linux Cluster (Sat Nov 10 2001 - 11:34:27 CST)
- AMBER Compile Question (Tue Nov 06 2001 - 20:07:31 CST)
- prowat test difficulties (Tue Oct 02 2001 - 13:37:39 CDT)
c724128
- PMF input file (Tue Mar 27 2001 - 13:14:18 CST)
- PMF input file (Tue Mar 27 2001 - 05:48:11 CST)
- PMF-input file (Tue Mar 27 2001 - 05:40:03 CST)
Carles Ferrer
- TOPOLOGY FILE PROCESSING (Thu Dec 20 2001 - 12:01:04 CST)
Carlos Simmerling
- Re: MD in vacuo (Mon Nov 05 2001 - 14:27:23 CST)
- Re: sander_classic (Wed Oct 31 2001 - 14:57:43 CST)
- Re: trajectory analysis (Tue Jul 24 2001 - 14:22:24 CDT)
- Re: AMBER box (Thu Jul 19 2001 - 06:24:35 CDT)
- Re: equilibriating LES (Thu Jul 19 2001 - 06:22:54 CDT)
- Re: addles (Thu Jul 05 2001 - 06:38:25 CDT)
- Re: coordinate blowup in sander (Fri Jun 15 2001 - 13:46:36 CDT)
- Re: RMSD calculation (Tue May 15 2001 - 18:13:47 CDT)
- Re: Compilation problem of AMBER6.0! (Mon Apr 16 2001 - 09:01:06 CDT)
- Re: Average structure (Thu Mar 29 2001 - 11:55:55 CST)
- Re: Problem of running sander on Linux cluster (Mon Mar 19 2001 - 11:03:02 CST)
- Re: LES analysis (Tue Feb 13 2001 - 12:39:47 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 21:59:16 CST)
Chigusa Kobayashi
- Unit of force constant (Thu Sep 06 2001 - 15:23:14 CDT)
chomsri upkaew
- Problem of running sander on Linux cluster (Mon Mar 19 2001 - 09:24:59 CST)
- Can't compile sander witk parallel on Linux cluster (Fri Mar 16 2001 - 05:54:27 CST)
- (no subject) (Fri Mar 16 2001 - 03:36:38 CST)
Chris Chipot
- Post-doctoral position available (Mon Jul 23 2001 - 18:32:19 CDT)
- [charmm-bbs] Post-doctoral position available (Mon Jul 23 2001 - 18:32:19 CDT)
- Post-doctoral position available (Sat Mar 17 2001 - 12:21:59 CST)
- [charmm-bbs] Post-doctoral position available (Sat Mar 17 2001 - 12:21:59 CST)
- Postdoctoral position (Tue Jan 30 2001 - 13:48:16 CST)
- Post-doctoral position (Wed Jan 17 2001 - 13:58:19 CST)
Christian Pilger
- summary: titratable amino acids and counter ions (Wed May 30 2001 - 07:23:30 CDT)
- titratable amino acids and counter ions (Mon May 28 2001 - 06:49:36 CDT)
- Amber 6 on parallel SUN (Thu Apr 19 2001 - 04:47:02 CDT)
- structure verification (Thu Apr 05 2001 - 08:22:29 CDT)
- compilation problems (Sun Mar 04 2001 - 09:03:34 CST)
- trajectory-problem (Wed Feb 14 2001 - 19:14:25 CST)
- Re: dynamic memory allocation (Wed Feb 14 2001 - 10:24:47 CST)
- Re: Amber Parameters (Wed Feb 14 2001 - 07:05:55 CST)
- (no subject) (Tue Feb 13 2001 - 13:33:31 CST)
Christine Bathelt
- P-N-parameters (Fri Sep 28 2001 - 08:15:36 CDT)
- restraints and type (Fri Sep 21 2001 - 11:24:57 CDT)
Christoph Sotriffer
- Re: sander_classic no mdcrd (Fri Jun 01 2001 - 08:53:27 CDT)
Chuck Schneider
- Re: Dual Athlon (Thu Sep 27 2001 - 06:12:06 CDT)
- re: Amber compiling on Alpha Clusters Redhat Linux (Thu Jun 28 2001 - 07:08:41 CDT)
- Re: compilation problems (Mon Mar 05 2001 - 07:20:18 CST)
- Re: dynamic memory allocation (Wed Feb 14 2001 - 10:20:02 CST)
cieplak_at_tiger.chem.uw.edu.pl
- Re: belly run (Thu Feb 22 2001 - 04:28:14 CST)
Craig Marhefka
- FW: about Owfeg in Amber 6.0 (Mon Apr 02 2001 - 08:19:18 CDT)
- AMBER on SUN (Tue Feb 20 2001 - 08:43:33 CST)
- Typo's in the Parm99.dat (Fri Jan 26 2001 - 14:19:45 CST)
Curt M. Breneman
- Re: CCL:MEP with GAMESS or GAUSSIAN (Fri Jan 26 2001 - 11:32:44 CST)
Daniel Flint
- sander_classic no mdcrd (Fri Jun 01 2001 - 09:06:10 CDT)
- sander_classic no mdcrd (Fri Jun 01 2001 - 09:06:10 CDT)
Daniel GENEST
- shared memory (Fri Jul 06 2001 - 11:33:10 CDT)
- db4 with amber5.0 (Fri Feb 23 2001 - 11:44:56 CST)
darden
- Re: NFFT (Tue Oct 30 2001 - 12:03:22 CST)
- Re: Ewald error estimation (Mon May 21 2001 - 15:58:17 CDT)
- Re: peek_ewald_inpcrd (Mon May 07 2001 - 16:01:08 CDT)
- Re: pressure regulation (Thu Jan 25 2001 - 10:50:13 CST)
Dat H. Nguyen
- Newton-Raphson minimization! (Thu Aug 30 2001 - 18:20:56 CDT)
- Problem with (Tue Jul 31 2001 - 18:22:21 CDT)
- Help with Leap! (Mon Jul 09 2001 - 19:17:58 CDT)
David Bevan
- Animating normal modes (Mon Jun 11 2001 - 12:36:39 CDT)
- Essential dynamics (Thu Apr 26 2001 - 06:18:25 CDT)
David Case
- Re: Gaussian to Amber (Wed Nov 21 2001 - 12:39:43 CST)
- Re: AMBER Compile Question (Tue Nov 06 2001 - 20:22:34 CST)
- Re: Xleap, PDB file format (Fri Oct 26 2001 - 10:59:14 CDT)
- Re: Temperature and pressure couplings (Wed Oct 03 2001 - 10:57:33 CDT)
- Re: dissociation of protein from DNA in MD (Sat Jul 21 2001 - 15:15:13 CDT)
- Re: stop COM motions in AMBER 5.0.1 question (Mon Jul 09 2001 - 10:06:21 CDT)
- Re: folding simulations (Thu Jun 28 2001 - 19:27:00 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 14:33:16 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 11:27:19 CDT)
- Re: your mail (Thu Mar 22 2001 - 16:11:32 CST)
- Re: SP3 name list (Thu Mar 22 2001 - 09:43:37 CST)
- Re: sander VS sander_classic (Thu Mar 08 2001 - 12:53:51 CST)
- Re: SHAKE (Thu Mar 08 2001 - 11:28:28 CST)
- Re: imaging in amber6 (Fri Mar 02 2001 - 11:05:39 CST)
- Re: Sander parallel compilation (Wed Feb 28 2001 - 12:46:04 CST)
- Re: Sander parallel compilation (Wed Feb 28 2001 - 12:27:40 CST)
- Re: Belly option in sander (Wed Jan 31 2001 - 13:28:43 CST)
David Konerding
- Re: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards (Thu Oct 18 2001 - 10:30:38 CDT)
- Re: Info about LEaP (Mon Sep 24 2001 - 10:29:16 CDT)
- Re: Utilizing Amber6 on Linux Cluster (Wed Aug 22 2001 - 14:41:13 CDT)
- Re: Utilizing Amber6 on Linux Cluster (Wed Aug 22 2001 - 10:31:56 CDT)
- Re: ewald bomb in amber 6 (Fri Jul 13 2001 - 17:07:41 CDT)
- Re: ewald bomb in amber 6 (Fri Jul 13 2001 - 09:28:30 CDT)
- Re: shared memory (Fri Jul 06 2001 - 11:26:43 CDT)
- Re: Non-standard DNA bases (Wed Jun 13 2001 - 09:41:09 CDT)
- Re: Amber, VMD and visualization (Thu May 24 2001 - 21:03:13 CDT)
- Re: sander compilers (Mon Apr 09 2001 - 11:13:23 CDT)
- Re: Average structure (Thu Mar 29 2001 - 10:27:08 CST)
- Re: Combining trajectories (Wed Mar 28 2001 - 10:10:30 CST)
- Re: parallel load difference under linux (long) (Thu Mar 22 2001 - 14:58:23 CST)
- Re: PME with octahedral box (Tue Mar 20 2001 - 12:43:11 CST)
- Re: Problem of running sander on Linux cluster (Mon Mar 19 2001 - 10:22:31 CST)
- Re: Can't compile Sander with parallel on Linux cluster (Fri Mar 16 2001 - 11:54:10 CST)
- (no subject) (Fri Mar 16 2001 - 11:28:06 CST)
- Re: Pentium 4 (Mon Mar 05 2001 - 13:57:04 CST)
- Re: Linux 6.2 install problems (Mon Feb 26 2001 - 17:32:07 CST)
- Re: update to 1GHz Athlon (Tue Feb 20 2001 - 12:25:14 CST)
- Re: Compilation of Amber6 in linux machine (Mon Feb 19 2001 - 09:46:55 CST)
- Re: update to 1GHz Athlon (Fri Feb 16 2001 - 10:06:38 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 16:54:13 CST)
- Re: process problem (Wed Jan 31 2001 - 11:48:08 CST)
- Re: nucgen (Mon Jan 08 2001 - 13:54:43 CST)
David L. Bostick
- 1-4 nonbonded interactions (Wed Apr 18 2001 - 13:37:12 CDT)
David Pearlman
- Re: Interface and Sander_classic (Tue Oct 30 2001 - 14:13:42 CST)
- Re: Interface and Sander_classic (Tue Oct 30 2001 - 12:34:31 CST)
- Re: Need some help with Amber/Linux (Thu Oct 25 2001 - 20:04:23 CDT)
- Re: Interface program installation (Fri Oct 19 2001 - 16:22:45 CDT)
- Re: Bang for the Buck (Fri Feb 09 2001 - 19:16:42 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 17:19:12 CST)
David Skinner
- Re: amber6 compilation failure (fwd) (Tue Mar 20 2001 - 15:09:49 CST)
- Re: AMBER6 on IBMSP3 (Tue Mar 13 2001 - 10:18:19 CST)
Dayle Smith
- MD without SHAKE (Mon Feb 26 2001 - 19:06:33 CST)
DeLano, Warren
- RE: software to build molecules (Tue Dec 11 2001 - 11:02:44 CST)
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards (Thu Oct 18 2001 - 11:48:53 CDT)
- RE: movie for subset of atoms (Thu Aug 30 2001 - 16:32:53 CDT)
- Announcing PyMOL v0.56 (+ Windows Installer) (Wed Jul 18 2001 - 14:14:45 CDT)
Didier Rognan
- parameters (Fri Oct 12 2001 - 11:12:37 CDT)
- special belly minimization (Wed Apr 25 2001 - 05:40:51 CDT)
- AMBER 6 on PME (Fri Apr 06 2001 - 11:41:19 CDT)
- AMBER6/PME on Origin 2000 (Fri Apr 06 2001 - 06:43:43 CDT)
dkon_at_email.arizona.edu
- quasih again (Tue Dec 18 2001 - 13:30:05 CST)
- quasih (Sun Dec 16 2001 - 19:50:44 CST)
- trajectory analysis (Tue Jul 24 2001 - 13:15:31 CDT)
- rigid body motion (Mon Jul 23 2001 - 12:20:27 CDT)
- AMBER box (Wed Jul 18 2001 - 18:20:00 CDT)
- ptraj diffusion (Thu Jul 12 2001 - 13:32:38 CDT)
Dow Hurst
- Re: I'm upset ! (Thu Feb 01 2001 - 09:40:12 CST)
Dr Chris L. Brown
- GFP chromophore force field parameters (Wed Jun 13 2001 - 20:31:56 CDT)
Dr David R V Buckley
- MAX_RSTACK (Fri Oct 26 2001 - 10:44:02 CDT)
Dr Richard Bryce
- AMBER parameter database (Fri Jun 29 2001 - 11:47:18 CDT)
Dr. Andrea Cavalli
- Protonated Water (Thu Aug 16 2001 - 02:37:33 CDT)
dwang
- problem in a short MD with protein fixed (Tue Oct 16 2001 - 20:00:26 CDT)
- i need help! (Mon Jan 15 2001 - 10:58:46 CST)
dynamic group
- Regarding the construction of gris in insightII (Mon Feb 12 2001 - 03:43:19 CST)
- Regarding MD (Sat Feb 10 2001 - 03:29:42 CST)
Elizabeth K. White
- ANAL (Mon Oct 15 2001 - 12:45:18 CDT)
- energy decomposition (Sat Oct 13 2001 - 08:51:40 CDT)
- energies for part of the protein (Wed Sep 12 2001 - 17:21:10 CDT)
- folding simulations (Thu Jun 28 2001 - 16:52:19 CDT)
- equilibrating water in sander (Wed Jun 20 2001 - 18:00:00 CDT)
- make test.all (Wed Jun 06 2001 - 16:22:46 CDT)
- machine/OS on which make test.all crashes in AMBER (Thu May 31 2001 - 19:51:22 CDT)
- make test.all crashes in AMBER (Thu May 31 2001 - 16:48:12 CDT)
- AMBER compilation woes (Tue May 22 2001 - 00:12:04 CDT)
Elsa de Sousa Henriques
- Re: (Tue Dec 11 2001 - 12:34:24 CST)
- Re: help (Mon Nov 05 2001 - 11:42:39 CST)
- Re:Re: (to "Xiaolin Chuang") (Fri Aug 24 2001 - 13:38:05 CDT)
Elsa Sousa Henriques
- Re: odd display of ambpdb generated files (Mon Apr 16 2001 - 12:49:03 CDT)
- Re: Resp (Wed Mar 28 2001 - 19:25:53 CST)
- Re: Ionic solutions (Tue Feb 13 2001 - 15:56:18 CST)
- Re: Ionic solutions (Tue Feb 13 2001 - 12:01:08 CST)
Eoin Galligan
- analysis problem (Mon Oct 08 2001 - 08:12:22 CDT)
- trajectory analysis (Wed Sep 12 2001 - 11:21:16 CDT)
- equilibriating LES (Thu Jul 19 2001 - 05:27:55 CDT)
- addles (Wed Jul 04 2001 - 08:18:59 CDT)
- gradual warming + partial solvation (Mon Jun 25 2001 - 09:59:44 CDT)
- PMF calculations (Tue Jun 19 2001 - 05:58:26 CDT)
- leap not reaing torsion from frcmod file (Thu Jun 07 2001 - 08:45:22 CDT)
- error msg in leap (Wed Jun 06 2001 - 12:30:43 CDT)
- free energy method (Wed Jun 06 2001 - 04:34:53 CDT)
- MM-PBSA (Mon Mar 12 2001 - 09:34:20 CST)
- calc free energy during dynamics (Thu Mar 08 2001 - 05:23:10 CST)
- not using SHAKE (Wed Feb 07 2001 - 07:27:24 CST)
- error msg (Mon Feb 05 2001 - 06:44:59 CST)
- error msg (Mon Feb 05 2001 - 06:44:59 CST)
- process problem (Wed Jan 31 2001 - 09:54:11 CST)
- solvate cap (Fri Jan 19 2001 - 08:33:37 CST)
- update to files (Thu Jan 11 2001 - 06:29:49 CST)
Eric ARNOULT
- Trosion parameters (Wed Jul 25 2001 - 03:34:25 CDT)
- parm94 (Fri Jul 13 2001 - 07:40:20 CDT)
Eric Aubanel
- LAPACK required by Amber (Fri Sep 14 2001 - 13:49:46 CDT)
- Problem with compilation of AMBER on IBM Power3 SP (Thu Sep 13 2001 - 15:05:50 CDT)
Erlend Moldrheim
- Parmscan and iron parameters (Fri Jan 19 2001 - 11:13:38 CST)
ess-ws_at_iwr.uni-heidelberg.de
- ESS Workshop - Flexibility and Function of Proteins (Fri Sep 07 2001 - 09:04:57 CDT)
Etienne ENGLER
- Re: Gibbs with Linux RH 7.0 (Wed Jan 17 2001 - 03:43:47 CST)
Eva Darian
- Constraining backbone dihedrals (Wed Nov 28 2001 - 12:14:38 CST)
- Re: how to add Zn Ca parameters (Thu Oct 25 2001 - 16:29:50 CDT)
- RESP charges (correction) (Tue Oct 09 2001 - 10:54:49 CDT)
- RESP charges (Mon Oct 08 2001 - 16:44:16 CDT)
- 8-Oxo-G (Wed Feb 28 2001 - 12:00:18 CST)
F. Ryjacek
- (no subject) (Fri Sep 14 2001 - 12:34:41 CDT)
- Re: how to write out... (Fri Sep 14 2001 - 12:23:20 CDT)
Fabio Schoen
- An Amber question (Thu Nov 15 2001 - 02:11:06 CST)
Fabrice YERLY
- Linux 2.2.19 Compil. Amber 4.1 with gcc 2.95.4 (Wed Nov 21 2001 - 10:18:59 CST)
Fabrizio Giordanetto
- phosphotyrosine (Tue May 15 2001 - 10:34:51 CDT)
Fernanda Camarinha
- batch mode (Mon Feb 12 2001 - 11:29:07 CST)
Filip Lankas
- Temperature and pressure couplings (Wed Oct 03 2001 - 10:38:56 CDT)
Filip Ryjacek
- Re: Gaussian to Amber (Thu Nov 22 2001 - 04:03:06 CST)
Florian Barth
- Re: movie for subset of atoms (Thu Aug 30 2001 - 16:16:00 CDT)
- Linux-cluster performance (Wed Aug 15 2001 - 08:07:51 CDT)
- AMBER on Hitachi SR8000 (Thu Jun 07 2001 - 15:22:32 CDT)
- Amber 6.0 Benchmarks (Thu Mar 22 2001 - 04:54:18 CST)
- Belly option in sander (Wed Jan 31 2001 - 12:17:51 CST)
Francois Dupradeau
- AmberFFC version 1.2 (Sun Jun 24 2001 - 15:49:29 CDT)
- anal ouput (Mon Mar 05 2001 - 02:40:14 CST)
- SUMMARY for GAMESS/GAUSSIAN MEP (Thu Feb 01 2001 - 01:37:36 CST)
- MEP with GAMESS or GAUSSIAN (Fri Jan 26 2001 - 06:16:55 CST)
Fred P. Arnold
- Minor correction (I think) on RESP input (Tue Feb 13 2001 - 11:23:22 CST)
- Lone Pairs. (Wed Feb 07 2001 - 16:19:32 CST)
Fumihito Mohri
- (no subject) (Tue Dec 11 2001 - 00:34:09 CST)
Garrett W Grahek
- MD integrator (Fri Feb 16 2001 - 11:35:43 CST)
Giulio Rastelli
- benchmarks (Wed Nov 28 2001 - 09:41:33 CST)
- torsional profile (Thu Oct 18 2001 - 10:29:12 CDT)
- torsional profile with MD (Mon Oct 15 2001 - 11:17:34 CDT)
- torsional profile (Thu Aug 30 2001 - 19:02:39 CDT)
- charge on protein (Wed Aug 15 2001 - 12:08:43 CDT)
- water molecules in a periodic box (Mon Aug 06 2001 - 12:03:41 CDT)
- box information (Tue Jul 31 2001 - 12:39:29 CDT)
- parm99 (Thu Jul 19 2001 - 06:01:41 CDT)
- isotropic scaling of coordinates during MD (Sat Apr 14 2001 - 06:35:48 CDT)
- Re: questions about Sander (Wed Mar 07 2001 - 04:52:16 CST)
- modified aminoacids using Leap (Thu Feb 22 2001 - 05:14:00 CST)
- parm96 (Tue Feb 06 2001 - 11:18:25 CST)
go5612gwe_at_arabia.com
- WHY NOT TRY IT? (Mon Jun 18 2001 - 14:02:17 CDT)
Gota Kawai
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 (Tue Jan 23 2001 - 21:30:29 CST)
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 (Tue Jan 23 2001 - 17:36:02 CST)
Guanglei Cui
- RE: plotting MD results for DNA (Tue Nov 27 2001 - 12:11:09 CST)
- error message (Mon Sep 03 2001 - 10:12:17 CDT)
- water cap (Tue Jul 24 2001 - 23:29:45 CDT)
- RE: constraining hydrogen bonds (Sun Jul 22 2001 - 11:02:45 CDT)
- RE: addles (Wed Jul 04 2001 - 09:11:51 CDT)
- high density spot (Mon Jul 02 2001 - 09:49:30 CDT)
- torsion parameters needed (Fri Jun 29 2001 - 00:40:06 CDT)
- TIP3P (Fri Jun 29 2001 - 00:22:57 CDT)
- gb with explicit water molecules (Fri Jun 22 2001 - 11:05:52 CDT)
- igb=1 error message: Unable to find bonded partner for atom 239 (Sat Jun 09 2001 - 15:46:03 CDT)
- Delphi Calculations (Tue Apr 10 2001 - 14:15:01 CDT)
- RE: producing a post-ptraj prmtop (Tue Apr 03 2001 - 20:13:27 CDT)
- RE: saving a trajectory as individual pdb files (Mon Apr 02 2001 - 17:23:51 CDT)
- RE: about dials_and_windows (Mon Apr 02 2001 - 08:34:24 CDT)
- RE: terminal base pair opening (Mon Apr 02 2001 - 08:27:19 CDT)
- RE: LEaP adding an extra hydrogen to N-terminus (Thu Mar 29 2001 - 09:48:05 CST)
- RE: Average structure (Thu Mar 29 2001 - 09:42:38 CST)
- RE: ptraj resolved; irest=1? (Thu Mar 15 2001 - 10:08:01 CST)
- GB protein simulation (Mon Feb 19 2001 - 10:58:23 CST)
- RE: periodic box size (Fri Feb 16 2001 - 13:48:50 CST)
- RE: periodic box size (Fri Feb 16 2001 - 12:30:27 CST)
Gudrun Schuerer
- Parameters for phosphonate available? (Thu Jul 12 2001 - 08:27:46 CDT)
Guido Hansen
- coordinate resetting ? (Mon Aug 27 2001 - 03:46:51 CDT)
GUILBAUD Philippe 153683
- RE: CCl4 ESP Grid problem with jaguar (Thu Jul 05 2001 - 04:09:07 CDT)
- Gibbs with Linux RH 7.0 (Tue Jan 16 2001 - 08:12:46 CST)
Guo, Jianxin
- sorry for the virus. (Thu May 10 2001 - 13:52:55 CDT)
Hai Long
- How to let IBELLY and NTR both on? (Tue Apr 24 2001 - 11:10:49 CDT)
Haitao Dong
- matrix diagonalizing subroutines (Mon May 21 2001 - 13:45:03 CDT)
- matrix diagonalizing subroutines (Mon May 21 2001 - 13:15:16 CDT)
Halima Amer
- RE: Binary mdcrd (Wed Oct 03 2001 - 01:43:41 CDT)
- RE: references (Tue Jan 02 2001 - 09:29:16 CST)
HAllawi_at_TWT.com
- MAXGRP parameter (Mon Aug 20 2001 - 12:18:33 CDT)
- running Amber on dual processor machine (Wed Feb 21 2001 - 13:24:07 CST)
Harald Lanig
- Model(l)ing 2001 in Erlangen/Germany: Bursaries and Awards available! (Mon Aug 06 2001 - 08:04:51 CDT)
- Model(l)ing 2001 in Erlangen/Germany: Speaker list (Mon Apr 23 2001 - 07:59:29 CDT)
Harshit Patel
- Re:problem in xleap (Wed Jul 11 2001 - 10:13:56 CDT)
hathaimard pongkasem
- (no subject) (Tue Nov 27 2001 - 19:40:33 CST)
Heather A.Carlson
- Post-doctoral position available (Wed Mar 28 2001 - 16:51:37 CST)
- [charmm-bbs] Post-doctoral position available (Wed Mar 28 2001 - 16:51:37 CST)
- params - ADP, neutral ARG (Mon Feb 26 2001 - 12:58:17 CST)
Heirich, Alan
- RE: Pentium 4 (Mon Mar 05 2001 - 14:47:08 CST)
Hermann von Grafenstein
- Amber, VMD and visualization (Thu May 24 2001 - 19:32:44 CDT)
Howard Feldman
- question about implicit solvation model with AMBER (Tue Oct 23 2001 - 09:55:36 CDT)
hparikh
- Request. (Tue Apr 24 2001 - 16:12:52 CDT)
Hungie Hungie
- no. of processors decrease (Thu Nov 22 2001 - 07:25:10 CST)
- E is not constant in NVE (Mon Nov 05 2001 - 03:03:10 CST)
- NPT to NVE ensemble (Wed Oct 31 2001 - 07:31:20 CST)
- How to turn off PME? (Tue Oct 30 2001 - 09:49:45 CST)
- NFFT (Tue Oct 30 2001 - 08:43:48 CST)
- input parameter for amber5 (Mon Sep 10 2001 - 07:03:26 CDT)
iec_at_emirates.net.ae
- An Invitation From The Middle East Chemical Industry (Sat Jun 16 2001 - 12:34:21 CDT)
Ireena Bagai
- Problem, setting up AMBERHOME! (Tue Apr 24 2001 - 05:42:04 CDT)
- Where to Start working in AMBER from? (Fri Apr 20 2001 - 08:07:23 CDT)
- Compilation problem of AMBER6.0! (Mon Apr 16 2001 - 07:24:25 CDT)
Irina Tikhonova
- Problems with analin (Wed Dec 05 2001 - 12:50:43 CST)
- how to form ljp-files for PROFEC ? (Tue Nov 13 2001 - 10:23:37 CST)
- Question (Thu Nov 08 2001 - 12:26:11 CST)
J Suggs
- Non-standard DNA bases (Tue Jun 12 2001 - 18:32:21 CDT)
Jake Isaacs
- plotting MD results for DNA (Tue Nov 27 2001 - 11:56:00 CST)
- 5-methyl deoxycytosine parameters (Fri Oct 12 2001 - 08:13:59 CDT)
- computing order parameters from an MD trajectory (Mon Aug 27 2001 - 09:45:58 CDT)
- block attachments? (Tue Jul 24 2001 - 08:22:46 CDT)
- odd display of ambpdb generated files (Fri Apr 13 2001 - 15:20:39 CDT)
- creating a restrt file from frames of mdcrd and mdvel (Wed Apr 04 2001 - 09:31:35 CDT)
- saving a trajectory as individual pdb files (Mon Apr 02 2001 - 16:42:38 CDT)
- Missing "ASH" parameters (Thu Mar 29 2001 - 12:09:01 CST)
- Re: LEaP adding an extra hydrogen to N-terminus (Thu Mar 29 2001 - 09:31:04 CST)
- loading prmtop and inpcrd into leap (Wed Mar 28 2001 - 10:13:06 CST)
- periodic box size (Mon Mar 26 2001 - 12:40:49 CST)
- recommended vs. default values (Mon Mar 05 2001 - 15:22:43 CST)
- Re: periodic box size (Fri Feb 16 2001 - 12:54:25 CST)
- how to handle a metal ion (Wed Feb 14 2001 - 09:43:14 CST)
- generating parameters for a small molecule ligand (Tue Feb 13 2001 - 10:48:03 CST)
- a few more questions (Mon Feb 12 2001 - 12:37:16 CST)
- Re: batch mode (Mon Feb 12 2001 - 12:18:28 CST)
Jamal G. Musaev
- amber6 compilation failure (fwd) (Tue Mar 20 2001 - 14:29:55 CST)
Jarrod A. Smith
- AMBER mail reflector archive (Thu Feb 15 2001 - 16:54:55 CST)
Jarrod Smith
- Re: Xleap, PDB file format (Fri Oct 26 2001 - 10:12:49 CDT)
- Re: ISTAR option and performance (Tue Oct 09 2001 - 13:30:22 CDT)
- Re: Linux-cluster performance (Wed Aug 15 2001 - 12:23:09 CDT)
- Re: Amber 6.0 on LINUX with absoft (Mon May 14 2001 - 09:22:42 CDT)
- Re: sander6/Linux compiled with pgf77 + mpipro (Thu May 03 2001 - 14:41:06 CDT)
- sander6/Linux compiled with pgf77 + mpipro (Thu May 03 2001 - 10:11:16 CDT)
- Wallclock on Intel/Linux sander (Tue May 01 2001 - 14:48:36 CDT)
- Re: AMBER6 on Alphas40 (fwd) (Mon Apr 30 2001 - 11:11:34 CDT)
- ISTAR2 and 64-bit sander (Wed Apr 18 2001 - 14:20:05 CDT)
- Re: AMBER 6 on PME (Fri Apr 06 2001 - 13:07:57 CDT)
- Re: saving a trajectory as individual pdb files (Mon Apr 02 2001 - 17:39:15 CDT)
- Re: How tleap does not add missing H atoms? (Mon Mar 26 2001 - 12:47:50 CST)
- Re: SGI_MP (was "your mail") (Fri Mar 23 2001 - 12:27:09 CST)
- Re: your mail (Thu Mar 22 2001 - 16:38:16 CST)
- Re: (No Subject) (Thu Mar 08 2001 - 13:59:36 CST)
- Re: sander VS sander_classic (Thu Mar 08 2001 - 13:03:59 CST)
- Re: (No Subject) (Thu Mar 08 2001 - 09:45:51 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 20:55:10 CST)
- Re: Bang for the Buck (Fri Feb 09 2001 - 20:13:31 CST)
Jean-François Gibrat
- Re: Xleap (Tue Mar 27 2001 - 03:55:16 CST)
- Xleap (Tue Mar 27 2001 - 03:19:01 CST)
Jeff Saxe
- Re: DNA bend (Tue Jan 09 2001 - 09:47:54 CST)
Jerry Greenberg
- protonate database (Wed Nov 28 2001 - 12:08:19 CST)
Jerry wu
- solvatebox (Wed Nov 21 2001 - 23:40:24 CST)
- supercritical water (Tue Nov 20 2001 - 20:28:46 CST)
- PME model (Sun Nov 11 2001 - 01:01:40 CST)
- water model (Mon Sep 24 2001 - 19:23:33 CDT)
- SPC water (Fri Aug 31 2001 - 09:01:32 CDT)
- polarization (Fri Aug 17 2001 - 04:29:07 CDT)
Jianxin Guo
- RE: AMBER mail reflector archive (Thu Feb 15 2001 - 17:13:09 CST)
Jie Guo
- question (Thu Aug 30 2001 - 12:58:37 CDT)
jim caldwell
- list filter (Thu Dec 20 2001 - 14:12:43 CST)
- Re: Gaussian to Amber (Wed Nov 21 2001 - 13:47:05 CST)
- Re: Linux 2.2.19 Compil. Amber 4.1 with gcc 2.95.4 (Wed Nov 21 2001 - 11:02:48 CST)
- IMPORTANT Amber mail list announcement (Tue Oct 30 2001 - 13:44:48 CST)
- Re: Amber6 on SuSE Linux (Wed Oct 17 2001 - 12:00:06 CDT)
- Re: parameters (Fri Sep 14 2001 - 16:35:10 CDT)
- Re: energies for part of the protein (Wed Sep 12 2001 - 17:33:59 CDT)
- reflector back on. (Tue Aug 14 2001 - 14:30:19 CDT)
- restarting gibbs (fwd) (Tue Jul 31 2001 - 10:00:25 CDT)
- is parm98 the same as parm99? (fwd) (Tue Jul 31 2001 - 09:59:54 CDT)
- problem with xleap and sander! (fwd) (Mon Jul 30 2001 - 13:56:23 CDT)
- vdW parameters for our friend, vanadium (fwd) (Mon Jul 30 2001 - 13:54:33 CDT)
- beginners problem (fwd) (Mon Jul 30 2001 - 10:16:28 CDT)
- simulating membranes with AMBER (fwd) (Mon Jul 30 2001 - 10:16:06 CDT)
- MD run with constantly decreasing total energy (fwd) (Sun Jul 29 2001 - 21:28:36 CDT)
- spam (Tue Jul 24 2001 - 16:11:45 CDT)
- gamess X resp : Conclusions. (fwd) (Thu Jul 05 2001 - 12:17:50 CDT)
- Re: CCl4 ESP Grid problem with jaguar | 010628a (fwd) (Tue Jul 03 2001 - 14:38:21 CDT)
- Re: gibbs_restrt (Mon Jul 02 2001 - 12:02:22 CDT)
- resp charges: ccl4 jag vs. g98 (Wed Jun 27 2001 - 17:51:49 CDT)
- Resp input confusion. (Tue Jun 26 2001 - 16:55:07 CDT)
- Re: begginer's question. (Tue Jun 26 2001 - 14:20:32 CDT)
- Re: CCl4 charge problem... (Fri Jun 22 2001 - 16:03:13 CDT)
- Re: AMBER (Tue Jun 19 2001 - 17:30:17 CDT)
- Re: water parameters+TIP3 water model (Tue Jun 19 2001 - 13:52:04 CDT)
- Re: coordinate blowup in sander (Fri Jun 15 2001 - 12:54:53 CDT)
- reflector limitations (Wed Jun 06 2001 - 09:51:05 CDT)
- Re: make test.all crashes in AMBER (Thu May 31 2001 - 17:29:52 CDT)
- Peter Kollman memorial (Wed May 30 2001 - 18:25:17 CDT)
- Peter Kollman (Fri May 25 2001 - 13:10:55 CDT)
- Important Address change (Wed May 02 2001 - 13:42:04 CDT)
- Re: Problem, setting up AMBERHOME! (Tue Apr 24 2001 - 10:04:42 CDT)
- Re: ISTAR2 and 64-bit sander (Wed Apr 18 2001 - 15:26:42 CDT)
- Re: Pairlist error (Tue Apr 03 2001 - 23:44:54 CDT)
- Re: pressure with polarizable potentials (Mon Apr 02 2001 - 16:51:10 CDT)
- Re: AMBER (Thu Mar 01 2001 - 10:42:03 CST)
- Re: MD without SHAKE (Tue Feb 27 2001 - 09:04:25 CST)
- Re: Compilation of AMBER6 (Thu Feb 15 2001 - 12:20:15 CST)
- Re: process problem (Wed Jan 31 2001 - 10:51:42 CST)
- Re: Serious Problem with parm99.dat (Fri Jan 26 2001 - 14:18:51 CST)
- Re: pressure regulation (Wed Jan 24 2001 - 13:47:48 CST)
- Re: AMBER on alpha (Tue Jan 23 2001 - 16:54:18 CST)
- Re: Freze solute molecules in AMBER (Tue Jan 23 2001 - 10:26:56 CST)
- Re: Gibbs with Linux RH 7.0 (Tue Jan 16 2001 - 10:28:00 CST)
- RE: references (Tue Jan 02 2001 - 10:54:17 CST)
Jithesh P.V.
- NRUN in AMBER 6 (Tue Dec 11 2001 - 00:27:07 CST)
- DNA strands separated... (Mon Oct 22 2001 - 02:07:09 CDT)
- PDB old to new (Wed Jun 27 2001 - 01:48:06 CDT)
- Charges for methylated residue (Mon May 28 2001 - 23:45:46 CDT)
jllo
- Question about installing AMBER (Tue Mar 20 2001 - 21:46:40 CST)
John D. Chodera
- Possible error in AMBER parm94 file? (Mon Oct 01 2001 - 19:01:37 CDT)
John Finke
- Code modification. (Mon Oct 08 2001 - 18:16:44 CDT)
- Creating capped peptides with AMBER (Tue Jul 10 2001 - 19:41:28 CDT)
- Re: Problems with AMBER (Fri Jun 29 2001 - 17:55:06 CDT)
- Problems with AMBER (Thu Jun 28 2001 - 20:04:52 CDT)
John Nicholas
- Re: Need some help with Amber/Linux (Fri Oct 26 2001 - 11:19:11 CDT)
- Need some help with Amber/Linux (Thu Oct 25 2001 - 16:42:52 CDT)
Jones de Andrade
- histidines normal-modes (Thu Jul 12 2001 - 09:04:23 CDT)
- begginer's question about RESP and GAMESS (Tue Jun 26 2001 - 12:44:02 CDT)
- RESP X GAMESS Dummie Question (Mon Jun 18 2001 - 12:22:11 CDT)
Jose Ramon Blas
- Pentium IV compiler in MD (Thu Mar 01 2001 - 15:11:08 CST)
- xleap silly thing (Wed Jan 31 2001 - 14:32:20 CST)
- (no subject) (Fri Jan 26 2001 - 12:18:20 CST)
Joseph Nachman
- residue numbering in dimers and trimers (Thu Aug 30 2001 - 11:41:48 CDT)
- carnal problem (Fri Mar 16 2001 - 13:58:45 CST)
- sader-classic (Tue Jan 23 2001 - 10:32:21 CST)
Jozef Hritz
- Hritz (Tue Jul 03 2001 - 06:58:18 CDT)
Jung-Hsing Lin
- Re: Error message (Thu Aug 23 2001 - 12:54:27 CDT)
- Re: Utilizing Amber6 on Linux Cluster (Wed Aug 22 2001 - 12:49:25 CDT)
- Structure with coordinates of C-alpha atoms only (Thu Jul 05 2001 - 21:23:48 CDT)
- Re: iwrap & TIP3P model water (Fri Jun 22 2001 - 11:53:00 CDT)
- Re: TIP3P/SPC VdW radius (Tue Apr 10 2001 - 15:43:52 CDT)
k. vengadesan
- amber-request@cgl.ucsf.edu (Sat Apr 21 2001 - 21:57:24 CDT)
Katherine Wallis Abold
- post-processing of energy analysis (Sun Oct 07 2001 - 15:58:30 CDT)
- summary of Zn+2 van der Waals radii responses (Fri Jun 08 2001 - 09:43:03 CDT)
- Zn+2 van der Waals radii (Thu Jun 07 2001 - 17:16:14 CDT)
- LIE method (Wed Jun 06 2001 - 16:14:10 CDT)
Kevin Van Workum
- L-J mixing rules? (Mon Aug 27 2001 - 11:10:24 CDT)
Khatcharin Siriwong
- Average structure (Thu Mar 29 2001 - 09:07:11 CST)
- Re: Xleap (Tue Mar 27 2001 - 03:42:34 CST)
- How to calculate energy from mdcrd output file (Wed Mar 14 2001 - 08:23:47 CST)
- sander VS sander_classic (Thu Mar 08 2001 - 12:18:44 CST)
- Can't run sander_classic with parallel machine (Fri Feb 23 2001 - 11:31:16 CST)
kian kani
- Machine file for sgi (Mon Jun 25 2001 - 12:25:21 CDT)
- Error in Gibbs (Tue Jun 05 2001 - 11:42:48 CDT)
- Sander minimization (Tue Apr 24 2001 - 20:50:44 CDT)
Kiyean Nam
- Gibbs input (Tue Feb 27 2001 - 22:24:44 CST)
kiyean.nam_at_pharma.Novartis.com
- GIBBS error (Wed Mar 21 2001 - 16:02:35 CST)
- LEAP (Thu Mar 15 2001 - 17:01:43 CST)
Koji YOSHIDA
- how to pay (Tue Nov 06 2001 - 21:53:18 CST)
Krishna Bisetty
- average structure (Wed May 16 2001 - 05:33:41 CDT)
Kristin Lynne Meagher
- 90 degree phase offset in AMBER? (Mon Jun 04 2001 - 12:14:27 CDT)
Kristin Maher
- porphyrin parameters (Tue Feb 27 2001 - 00:28:43 CST)
Krzysztof Murzyn
- Re: your mail (Thu Feb 22 2001 - 04:45:36 CST)
L. Renee Olano
- TIP4P (Mon Nov 26 2001 - 08:59:53 CST)
Lakshmi P. Kotra
- peek_ewad_inpcrd (Mon Sep 03 2001 - 12:57:31 CDT)
Laurent Chiche
- Re: Average structure (Thu Mar 29 2001 - 10:01:32 CST)
Lepsa
- Re: MM-PGBSA Question!! (Sat Dec 22 2001 - 08:46:53 CST)
- Re: dG of wild type/mutant (Wed Dec 19 2001 - 08:43:25 CST)
- Re: converting some files (Fri Dec 07 2001 - 05:36:22 CST)
- MD in vacuo (Mon Nov 05 2001 - 12:52:08 CST)
- Re: RESP charges (correction) (Wed Oct 31 2001 - 10:01:30 CST)
- Re: RESP charges (correction) (Wed Oct 10 2001 - 02:15:53 CDT)
- Re: RESP charges (Tue Oct 09 2001 - 02:56:49 CDT)
Lillian Chong
- Minimization and NSNB (Wed Mar 28 2001 - 12:59:15 CST)
Linjing Yang
- parameters for 5'-phosphate GUA (Wed Nov 14 2001 - 14:22:47 CST)
liz
- generalized born model on protein or peptide (Fri Sep 07 2001 - 11:43:02 CDT)
- Resp (Wed May 09 2001 - 14:14:32 CDT)
lkirnars_at_unmc.edu
- (no subject) (Tue Jan 30 2001 - 15:25:54 CST)
Long Hai
- Add electric field (Mon Sep 10 2001 - 13:41:12 CDT)
Lorenzo Gontrani
- Nitro group (Fri Dec 21 2001 - 03:47:48 CST)
- R: color in xleap (Sat Oct 20 2001 - 15:21:07 CDT)
Luckhana
- Amber 6 (Fri Jul 06 2001 - 13:23:35 CDT)
Lynn Amon
- (no subject) (Tue Feb 13 2001 - 13:39:20 CST)
M ESTA Laurent
- Cl and H-bonding (Wed Dec 19 2001 - 11:42:48 CST)
- chlorine parameters (Tue Sep 25 2001 - 03:06:31 CDT)
Mahadevan Seetharaman
- O6-methyl-guanine parameters (Mon Nov 26 2001 - 16:50:50 CST)
- EWALD BOMB (Thu Feb 15 2001 - 16:45:44 CST)
Manoj Cheriyan
- Internal Restraints in Sander Problem (Wed Jul 11 2001 - 17:19:31 CDT)
Marcela Madrid
- how to create a bond (Thu Dec 20 2001 - 13:15:36 CST)
- xleap for windows 98? (Wed Dec 19 2001 - 19:14:47 CST)
- software to build molecules (Tue Dec 11 2001 - 10:17:30 CST)
- amber6 in SGI Origin 2000 (Fri Dec 07 2001 - 15:15:56 CST)
- MD of DNA (Thu Dec 06 2001 - 14:38:04 CST)
- DNA force field (Tue Nov 20 2001 - 15:57:59 CST)
- Maxwell-Boltzmann distribution of velocities (Thu Oct 25 2001 - 14:23:08 CDT)
- Ewald Bomb (Tue Sep 18 2001 - 08:29:23 CDT)
- parameters (Fri Sep 14 2001 - 14:50:26 CDT)
- adding atoms and amino acid residues (Mon Aug 20 2001 - 16:52:31 CDT)
- ice cube flying through space (Fri Jun 01 2001 - 10:10:53 CDT)
- ice cube flying through space (Fri Jun 01 2001 - 10:10:53 CDT)
- box of water (Wed May 16 2001 - 17:04:01 CDT)
- atom types for xleap (Tue Apr 17 2001 - 11:08:59 CDT)
- how do I turn on the verbose option? (Fri Feb 02 2001 - 14:01:46 CST)
- intprt option in Thermodynamics integration (Wed Jan 10 2001 - 19:51:22 CST)
Marco Punta
- AMBER on mpi (Wed Jun 27 2001 - 12:39:46 CDT)
Margaret Cheung
- opinion about buying linux clusters. (Sat Nov 10 2001 - 14:00:46 CST)
- Re: Utilizing Amber6 on Linux Cluster (Wed Aug 22 2001 - 12:23:40 CDT)
- changing the g77 optimization for compiling sander_classic (Mon Aug 20 2001 - 19:25:41 CDT)
- changing the g77 optimization for compiling sander_classic (Mon Aug 20 2001 - 15:08:30 CDT)
- error message. (Fri Jun 08 2001 - 02:24:07 CDT)
- Re: Bang for the Buck (Sun Feb 11 2001 - 01:20:46 CST)
Margaret Doll
- Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 (Mon Jan 22 2001 - 09:52:32 CST)
Margit Mollhoff
- RMS matrix with CARNAL (Fri Nov 16 2001 - 13:09:22 CST)
marin
- parameters for NADH (Thu Mar 29 2001 - 15:28:25 CST)
Marjoribanks, Andrew G
- AMBER enquiry (Tue May 15 2001 - 12:21:03 CDT)
Mark Forster
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 10:58:49 CDT)
- leap and SP2 nitrogen (Mon Feb 26 2001 - 06:07:27 CST)
- Re: how to handle a metal ion (Thu Feb 15 2001 - 04:11:24 CST)
- references (Tue Jan 02 2001 - 08:39:38 CST)
Mark Markson
- Belly Atonms (Tue Feb 13 2001 - 12:52:53 CST)
Markus Drumm
- Windows Virus (Tue Jul 24 2001 - 05:42:07 CDT)
Martin Crnugelj
- ewald bomb (Wed May 16 2001 - 02:43:13 CDT)
Matthew Davies
- Dummy Atoms (Thu Mar 01 2001 - 07:58:14 CST)
Mausumi Mazumdar
- Problem in adding solvent other than water ... (Wed Apr 18 2001 - 23:56:42 CDT)
Michael Cooney
- ptraj to re-associate protein+DNA (Wed Jul 25 2001 - 16:34:29 CDT)
- Re: water cap (Wed Jul 25 2001 - 12:27:54 CDT)
- dissociation of protein from DNA in MD (Sat Jul 21 2001 - 14:50:27 CDT)
- coordinate blowup in sander (Fri Jun 15 2001 - 11:29:05 CDT)
- carnal error with crd files stripped of waters (Fri May 11 2001 - 15:52:47 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 11:56:36 CDT)
- Re: N-terminal and C-terminal hydrogens (Thu Apr 12 2001 - 15:55:06 CDT)
- nstlim in sander (Tue Mar 27 2001 - 12:12:08 CST)
- Re: DNA out of a box (Wed Mar 21 2001 - 11:43:18 CST)
- variable NTWXM in Sander (Fri Mar 09 2001 - 16:54:23 CST)
- Re: SHAKE (Thu Mar 08 2001 - 11:39:51 CST)
- leap adding terminal phosphates (Mon Mar 05 2001 - 12:20:00 CST)
- Re: not using SHAKE (Wed Feb 07 2001 - 10:32:51 CST)
- Re: PME (Wed Jan 31 2001 - 15:13:47 CST)
- Re: Incomplete coord file after crash (Thu Jan 25 2001 - 15:24:46 CST)
- Incomplete coord file after crash (Thu Jan 25 2001 - 13:09:47 CST)
- Re: "Goodness" of Trajectory (Thu Jan 18 2001 - 13:29:25 CST)
- Re: velocity-output (Fri Jan 12 2001 - 18:34:33 CST)
- Re: DNA Simulation (Mon Jan 08 2001 - 13:57:31 CST)
Michael Crowley
- Re: NFFT (Tue Oct 30 2001 - 10:24:38 CST)
- Re: ewald bomb in amber 6 (Fri Jul 13 2001 - 13:38:23 CDT)
- Re: AMBER6 on Alphas40 (fwd) (Mon Apr 30 2001 - 11:35:36 CDT)
- Re: parallel load difference under linux (long) (Thu Mar 22 2001 - 15:31:08 CST)
- Re: Correction: SP3 name list (Thu Mar 22 2001 - 11:49:43 CST)
- Re: Correction: SP3 name list (Thu Mar 22 2001 - 11:46:21 CST)
- Re: periodic box size (Mon Feb 19 2001 - 00:48:05 CST)
Michael Ford
- Re: PBC box problems (Tue Mar 20 2001 - 12:10:17 CST)
- sugguestion! (Thu Mar 08 2001 - 12:26:36 CST)
- PBC box problems (Wed Feb 28 2001 - 16:34:36 CST)
Michael G Cooney
- problem processing stripped RST/CRD files (Tue Dec 11 2001 - 10:25:20 CST)
- Re: MD of DNA (Thu Dec 06 2001 - 15:05:14 CST)
- NSCM setting to remove center of mass motion (Thu Oct 25 2001 - 11:52:09 CDT)
- possible bug in carnal in AMBER5 (Wed Oct 17 2001 - 16:00:01 CDT)
- Re: problem in a short MD with protein fixed (Wed Oct 17 2001 - 13:52:30 CDT)
- RESP demo files (Tue Sep 25 2001 - 11:05:09 CDT)
- xleap crashing on sgi's (Thu Sep 06 2001 - 15:36:46 CDT)
- library files in leap (Thu Sep 06 2001 - 14:35:15 CDT)
Michael Jakusch
- Re: LINMIN Failure (Mon Oct 01 2001 - 10:17:17 CDT)
- Perturbed internal coordinate parameters (Wed Sep 26 2001 - 14:40:36 CDT)
- Gibbs, PME, DynModW, ISDX0, etc. (Thu Sep 20 2001 - 07:39:47 CDT)
- Strange density behavior with tr. octahedral box and constant pressure (Fri Sep 07 2001 - 08:24:53 CDT)
Michal Otyepka
- PARMSCAN (Tue Nov 06 2001 - 14:59:42 CST)
- param CT-CT-CT-OH (Wed Oct 24 2001 - 13:54:56 CDT)
- substracting of MM nonbondeb potential from QM curve (Tue Oct 23 2001 - 12:24:44 CDT)
- MM-PBSA; E(internal) (Wed Oct 10 2001 - 11:58:19 CDT)
- how to write out ... (Thu Sep 13 2001 - 07:07:39 CDT)
- free energy contribution of selected atoms vs. MM-PB/GBSA (Fri Aug 17 2001 - 06:25:55 CDT)
- (no subject) (Wed Jul 04 2001 - 12:20:54 CDT)
- Re: titratable amino acids and counter ions (Wed May 30 2001 - 06:50:10 CDT)
- (no subject) (Mon Apr 02 2001 - 04:33:38 CDT)
- ATP+Mg, P-tyrosine a P-threonine (Wed Mar 14 2001 - 04:35:53 CST)
- LEAP and crystal waters (Tue Feb 27 2001 - 01:35:42 CST)
- (no subject) (Wed Feb 21 2001 - 14:23:01 CST)
- REMD (Wed Feb 14 2001 - 13:30:06 CST)
Miguel Cabrera Fuentes
- Amber installation on linux (Sat Jul 21 2001 - 18:13:59 CDT)
- Amber installation (Fri Jul 20 2001 - 13:47:35 CDT)
Mihaly Mezei
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 14:18:03 CDT)
- Re: TIP3P/SPC VdW radius (Tue Apr 10 2001 - 16:01:35 CDT)
- Re: force fields (Wed Mar 07 2001 - 13:44:26 CST)
- Re: Ionic solutions (Tue Feb 20 2001 - 16:18:45 CST)
Min Wu
- h-bond energy (Sun Oct 21 2001 - 09:07:15 CDT)
mite51
- Re: Bang for the Buck (Fri Feb 09 2001 - 16:33:44 CST)
Mite51_at_hotmail.com
- Test Group - swarm.ca (Mon Mar 19 2001 - 16:56:09 CST)
- Re: disk file larger than 2 GB (Thu Feb 15 2001 - 01:59:25 CST)
Miyashita, Osamu
- sander_classic: bond energy problem (Mon May 07 2001 - 16:28:03 CDT)
- Re: Can't run sander_classic with parallel machine (Fri Feb 23 2001 - 11:58:47 CST)
- Amber6 by g77 and mpich (Thu Feb 15 2001 - 14:54:10 CST)
- Re: trajectory-problem (Thu Feb 15 2001 - 11:14:02 CST)
Monica
- query (fwd) (Fri Nov 02 2001 - 22:56:30 CST)
- query (Thu Nov 01 2001 - 08:14:02 CST)
- problem in xleap (Tue Jul 10 2001 - 22:51:18 CDT)
- problem in xleap (Tue Jul 10 2001 - 22:51:18 CDT)
- problem in xleap (Mon Jul 09 2001 - 01:47:48 CDT)
- problem in xleap (fwd) (Wed May 30 2001 - 07:35:06 CDT)
- problem in xleap (Wed May 30 2001 - 06:15:00 CDT)
- compilation on linux6 (Wed May 23 2001 - 07:35:11 CDT)
- Query (Sat May 19 2001 - 07:09:24 CDT)
monica jain
- (No Subject) (Thu Mar 08 2001 - 02:50:03 CST)
Ms. Parul Kalra
- nmode analysis (Mon Dec 17 2001 - 00:30:11 CST)
Nada Spackova
- Re: Residence time (Thu May 17 2001 - 08:24:07 CDT)
nanook1000_at_web.de
- RESP fit: ivary -1 ? (Sat Nov 10 2001 - 05:47:39 CST)
Nathalie Duclert
- GDP/GTP (Mon May 21 2001 - 08:02:12 CDT)
Nathalie Godbout
- Re: opinions on supercomputer platforms (Fri Apr 06 2001 - 14:57:37 CDT)
- Re: SGI_MP (was "your mail") (Fri Mar 23 2001 - 13:54:14 CST)
- Re: your mail (Fri Mar 23 2001 - 11:27:19 CST)
- Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) (Wed Feb 14 2001 - 14:00:25 CST)
- Re: Dual Origin vs dual Alfa (Wed Feb 14 2001 - 10:18:23 CST)
- Re: sader-classic (Tue Jan 23 2001 - 13:10:54 CST)
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 (Mon Jan 22 2001 - 15:31:45 CST)
Nelson Brito
- Re: I'm upset ! (Thu Feb 01 2001 - 04:51:49 CST)
Nelson Teixeira Brito
- sense of justice (Thu Feb 01 2001 - 11:53:36 CST)
nepenthes_at_vplaces.net
- compile leap (Mon Sep 17 2001 - 02:16:51 CDT)
Ngai Ling Ida Ma
- parameters for neutral amino acids (Tue May 29 2001 - 00:42:45 CDT)
nicolas baurin
- Re: sander_classic: bellyrun with constraints (Thu Apr 05 2001 - 02:12:51 CDT)
- sander_classic: bellyrun with constraints (Wed Apr 04 2001 - 13:13:21 CDT)
- about OWFEG (Mon Apr 02 2001 - 04:36:11 CDT)
Nicolas Grima
- Re: Problem with compilation of AMBER on IBM Power3 SP (Fri Sep 14 2001 - 04:20:27 CDT)
- Re: compilation on linux6 (Wed May 23 2001 - 07:17:56 CDT)
Nicole Silvester
- emin after molecular dynamics (Fri Jun 22 2001 - 02:41:06 CDT)
Nicoletta Pucello
- zinc (Thu Jun 21 2001 - 03:39:03 CDT)
Nikolai Smolin
- secondary structure (Mon Dec 10 2001 - 12:20:34 CST)
- RMS calculations (Wed Nov 21 2001 - 07:34:54 CST)
- NPSCAL parameter (Mon Oct 08 2001 - 06:20:24 CDT)
- about pressure (Thu Sep 27 2001 - 08:33:56 CDT)
- about radius of gyration (Mon Sep 17 2001 - 09:49:10 CDT)
noor gaffoor
- (no subject) (Sun Feb 11 2001 - 23:08:17 CST)
Noriyuki Yamaotsu
- Re: AMBER on Hitachi SR8000 (Thu Jun 07 2001 - 21:19:09 CDT)
Numan Oezguen
- Parameter for abasic nucleotide (Wed Jun 27 2001 - 21:48:58 CDT)
Okimasa Okada
- ester (Mon Jan 29 2001 - 18:47:29 CST)
Olga Carvalho
- gibbs_restrt (Mon Jul 02 2001 - 07:21:00 CDT)
- CARNAL (Thu Jun 21 2001 - 09:27:14 CDT)
- electrostatic point charge (Mon Apr 09 2001 - 09:45:19 CDT)
Oliver Zerbe
- NAN errors during production runs (Wed Oct 03 2001 - 11:45:10 CDT)
Omer Katzenelson
- CARNAL (Tue Aug 21 2001 - 20:27:54 CDT)
- Re: adding atoms and amino acid residues (Tue Aug 21 2001 - 16:25:31 CDT)
- vdw parameters for:THR-HG1, TYR-HH (Mon Jul 02 2001 - 20:49:27 CDT)
oppie1_at_excite.co.jp
- Ewald sum (Sat Jan 20 2001 - 08:30:20 CST)
Osmar Norberto de Souza
- f2c.h (Mon May 21 2001 - 15:20:38 CDT)
Ostlund, Neil S.
- RE: Windows version of AMBER? (Tue Apr 17 2001 - 12:04:04 CDT)
Osvaldo A. Santos-Filho
- informations (Mon Jun 04 2001 - 15:31:11 CDT)
Osvaldo Andrade Santos Filho
- AMBER on LINUX (Wed Apr 25 2001 - 14:30:05 CDT)
Paolo Daniele
- Informations (Wed Dec 05 2001 - 09:54:24 CST)
- Info about LEaP (Mon Sep 24 2001 - 10:21:39 CDT)
paopao1188_at_hotmail.com
- New product creates custom e-mail lists! (Tue Nov 06 2001 - 06:18:24 CST)
- New product creates custom e-mail lists! (Fri Nov 02 2001 - 09:10:35 CST)
Pascal Bonnet
- Re: Help with new residue (Fri Dec 14 2001 - 03:18:56 CST)
- Re: RMS calculations (Wed Nov 21 2001 - 17:16:47 CST)
- unusual parameters (Fri Oct 26 2001 - 03:06:26 CDT)
- Re: zinc (Thu Jun 21 2001 - 03:11:24 CDT)
- create a parm.top file (Tue Apr 24 2001 - 12:18:51 CDT)
- Re: ptraj image for octahedral box (Tue Mar 13 2001 - 19:28:47 CST)
- Re: using "radial" in PTRAJ (Fri Mar 09 2001 - 11:26:17 CST)
- Re: AMBER (Thu Mar 01 2001 - 14:09:00 CST)
Paul A Wilson
- General install questions (Wed Nov 28 2001 - 11:48:06 CST)
Pavel Jungwirth
- pressure with polarizable potentials (Mon Apr 02 2001 - 07:21:26 CDT)
Penny Govender
- Help with new residue (Fri Dec 14 2001 - 01:15:33 CST)
Peter Gannett
- ethidium bromide parms (Thu Feb 15 2001 - 20:20:26 CST)
Peter Varnai
- Amber6 on AMD Athlon (Thu Dec 06 2001 - 08:06:47 CST)
- shake tricks? (Thu Aug 30 2001 - 08:57:00 CDT)
- OCCO in parm99 (Wed Apr 04 2001 - 03:52:32 CDT)
- Re: producing a post-ptraj prmtop (Wed Apr 04 2001 - 03:44:26 CDT)
- terminal base pair opening 2 (Mon Apr 02 2001 - 08:46:06 CDT)
- terminal base pair opening (Mon Apr 02 2001 - 07:19:54 CDT)
- Re: Combining trajectories (Wed Mar 28 2001 - 02:56:58 CST)
- ptraj resolved; irest=1? (Thu Mar 15 2001 - 09:29:54 CST)
- ptraj image for octahedral box (Tue Mar 13 2001 - 09:47:28 CST)
- NSCM in periodic simulations (Thu Feb 01 2001 - 09:24:55 CST)
- octahedral box in AMBER6 (Mon Jan 22 2001 - 06:32:17 CST)
Phil Cunningham
- AMBER (Tue Jun 19 2001 - 15:53:11 CDT)
Pierre Tran
- (no subject) (Wed Jan 31 2001 - 10:58:40 CST)
ponmalai kolandaivel
- program req (Wed Dec 12 2001 - 07:52:08 CST)
PRADIPTA Bandyopadhyay
- RESP charges! (Fri Oct 26 2001 - 15:24:45 CDT)
- Problem in GIBBS! (Fri Oct 19 2001 - 15:43:41 CDT)
- Problem in GIBBS! (Thu Sep 20 2001 - 13:38:05 CDT)
- Leap and parm/pert! (Mon Aug 06 2001 - 18:45:00 CDT)
- Gibbs and cutoff! (Sat Aug 04 2001 - 17:23:30 CDT)
- Problem in MD! (Thu Jun 14 2001 - 12:16:59 CDT)
Prem Raj Joseph
- Energy calculation (Tue Jun 26 2001 - 11:34:38 CDT)
Pricl Sabrina
- Amber & F90 (Fri Nov 23 2001 - 07:22:20 CST)
r ojha
- Request (Wed Jul 11 2001 - 13:06:23 CDT)
R. M. Fesinmeyer
- Re: ?s: Xeon vs. Athlon, latency (Mon Oct 08 2001 - 12:15:39 CDT)
- ?s: Xeon vs. Athlon, latency (Wed Oct 03 2001 - 22:36:38 CDT)
- producing a post-ptraj prmtop (Tue Apr 03 2001 - 19:20:41 CDT)
- Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) (Wed Feb 14 2001 - 14:16:51 CST)
- Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) (Wed Feb 14 2001 - 13:02:11 CST)
- Re: Bang for the Buck (Sat Feb 10 2001 - 05:10:46 CST)
Raik Grunberg
- Re: NRUN in AMBER 6 (Tue Dec 11 2001 - 04:53:00 CST)
- mm_pbsa on single structure (Wed Nov 14 2001 - 08:45:38 CST)
- Re: generalized born model on protein or peptide (Mon Sep 10 2001 - 07:14:58 CDT)
- Re: adding atoms and amino acid residues (Tue Aug 21 2001 - 03:20:50 CDT)
- varying cartesian restraint (Sun Aug 05 2001 - 04:48:28 CDT)
Raik Gruenberg
- sander energy data (Thu Mar 08 2001 - 11:24:28 CST)
Raja Swaminathan
- ion analysis (Wed Dec 26 2001 - 09:56:17 CST)
- diffusion (Wed Dec 19 2001 - 03:15:56 CST)
- group input (Tue Aug 28 2001 - 12:28:04 CDT)
- weights for DNA and ions (Wed Feb 21 2001 - 03:24:22 CST)
- periodic box size (Fri Feb 16 2001 - 11:25:25 CST)
- Analysis (Tue Jan 02 2001 - 02:41:34 CST)
Ramakrishna S (EPD-BLRSJP-PEG)
- Amber 6.0 on Intel IA-64 Server (Thu Nov 08 2001 - 21:08:51 CST)
Ramon Garduno
- Q about RESP (Mon Mar 05 2001 - 13:35:47 CST)
ramon kleber da rocha
- MPI version of Gibbs (Mon Dec 03 2001 - 11:18:04 CST)
rathinavelan thenmalarchelvi
- error in sander (Wed Mar 21 2001 - 06:12:23 CST)
Rebecca Ann Perlow
- Nucleic acid notation within Toolchest (Mon Feb 19 2001 - 15:59:59 CST)
Riccardo Nifosi
- problem with carnal on linux (Mon Apr 23 2001 - 10:03:40 CDT)
- imaging in amber6 (Fri Mar 02 2001 - 09:52:15 CST)
Richard Stefl
- dipolar couplings (Mon Jul 16 2001 - 07:30:07 CDT)
Richard W Dixon
- Re: sander_classic no mdcrd (Fri Jun 01 2001 - 10:41:10 CDT)
- Re: sander_classic no mdcrd (Fri Jun 01 2001 - 10:41:10 CDT)
- Re: odd display of ambpdb generated files (Tue Apr 17 2001 - 08:26:45 CDT)
Rino Ragno
- (no subject) (Wed May 16 2001 - 06:47:15 CDT)
robert
- (no subject) (Tue Feb 13 2001 - 18:35:21 CST)
Robert Matthew Fesinmeyer
- P4 benchmarks posted (Thu Oct 11 2001 - 15:10:14 CDT)
- Pentium 4 (Mon Mar 05 2001 - 13:01:26 CST)
- Bang for the Buck (Fri Feb 09 2001 - 15:50:57 CST)
Romina Oliva
- C-terminal amide (Thu Dec 20 2001 - 11:40:36 CST)
Ronald Kuehne
- Post-doctoral Position (Wed Mar 28 2001 - 18:51:26 CST)
- [charmm-bbs] Post-doctoral Position (Wed Mar 28 2001 - 18:51:26 CST)
Ross Walker
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards (Thu Oct 18 2001 - 14:29:56 CDT)
- Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards (Thu Oct 18 2001 - 09:00:48 CDT)
- Amber 6 MDCRD Files > 2GB in 32 bit Linux. (Mon Oct 08 2001 - 06:49:14 CDT)
- RE: Xleap (Tue Mar 27 2001 - 04:12:09 CST)
- RE: Can't compile Sander with parallel on Linux cluster (Fri Mar 16 2001 - 09:05:49 CST)
- RE: Can't compile sander witk parallel on Linux cluster (Fri Mar 16 2001 - 06:54:07 CST)
- Amber Website - UK Mirror (Tue Mar 06 2001 - 04:47:28 CST)
- RE: Linux 6.2 install problems (Mon Feb 26 2001 - 15:39:02 CST)
- RE: AMBER mail reflector archive (Thu Feb 15 2001 - 17:11:45 CST)
- RE: EWALD BOMB (Thu Feb 15 2001 - 17:10:02 CST)
Rozita Dara
- running Sander in 4 CPUs (Mon Dec 03 2001 - 11:31:17 CST)
- adding water (Sat Oct 13 2001 - 21:40:22 CDT)
- problem with ambpdb (Sun Sep 30 2001 - 11:16:24 CDT)
- problem with xleap (Wed Sep 26 2001 - 17:22:29 CDT)
- Segmentation fault (core dumped) (Tue Sep 25 2001 - 21:31:30 CDT)
- another error (Wed Sep 19 2001 - 10:01:11 CDT)
- analysis of the results (Tue Sep 18 2001 - 10:56:07 CDT)
- error (Fri Sep 14 2001 - 11:07:07 CDT)
- ... error message (Thu Aug 23 2001 - 14:14:07 CDT)
- Error message (Thu Aug 23 2001 - 12:46:12 CDT)
- Error message (Thu Aug 23 2001 - 10:59:57 CDT)
- Analysising the results (Wed Aug 22 2001 - 15:03:28 CDT)
- problem using xleap and tleap (Wed Aug 22 2001 - 12:13:08 CDT)
Ryan H. Lilien
- AMBER vdW (Fri Apr 13 2001 - 08:41:59 CDT)
Salinthip Thipayang
- Parameters for DMSO solvent (Tue Nov 06 2001 - 12:26:48 CST)
Samantha
- Re: Aqvist LJ parameters (Thu Oct 18 2001 - 13:34:46 CDT)
samantha hughes
- Re: residue numbering in dimers and trimers (Fri Aug 31 2001 - 02:43:55 CDT)
- Re: solvation energy calculation (Thu Jul 26 2001 - 01:54:11 CDT)
- Re: mm_pbsa (Thu Jun 14 2001 - 02:06:47 CDT)
- Re: Amber, VMD and visualization (Fri May 25 2001 - 00:34:41 CDT)
- Re: carnal error with crd files stripped of waters (Mon May 14 2001 - 03:20:17 CDT)
- Re: calc free energy during dynamics (Thu Mar 08 2001 - 04:48:20 CST)
- Re: I'm upset ! (Thu Feb 01 2001 - 04:17:16 CST)
- Measuring rigid-body rotation with AMBER (Fri Jan 19 2001 - 09:23:24 CST)
Sanjeev B.S.
- Re: NSCM setting to remove center of mass motion (Thu Oct 25 2001 - 22:44:41 CDT)
- Re: starting MD from t=0 (Mon Sep 24 2001 - 11:30:07 CDT)
- Re: Problem with compilation of AMBER on IBM Power3 SP (Thu Sep 13 2001 - 23:00:36 CDT)
- Re: Problem with carnal ... (Thu Sep 13 2001 - 11:43:56 CDT)
- Result: Dist restraints + Belly (Sat Sep 08 2001 - 06:24:37 CDT)
- Belly+Restraints (Fri Sep 07 2001 - 05:32:16 CDT)
- Dist restraints + Belly Dyn (Thu Sep 06 2001 - 07:05:41 CDT)
- Re: peek_ewad_inpcrd (Wed Sep 05 2001 - 02:07:10 CDT)
- COORDINATE RESETTING (Sun Sep 02 2001 - 07:56:12 CDT)
- NPT restart problem (Fri Aug 31 2001 - 08:19:48 CDT)
- NPT restart problem (Fri Aug 31 2001 - 05:16:37 CDT)
- Mystery protons! (Sun Aug 26 2001 - 07:03:11 CDT)
- Re: Utilizing Amber6 on Linux Cluster (Thu Aug 23 2001 - 00:31:58 CDT)
- Re: AMBER6 on IBMSP3 (again) (Fri Aug 17 2001 - 03:10:11 CDT)
- Re: AMBER6 on IBMSP3 (again) (Fri Aug 17 2001 - 02:06:11 CDT)
- Re: AMBER6 on IBMSP3 (again) (Thu Aug 16 2001 - 15:10:04 CDT)
- Re: rigid body motion (Wed Jul 25 2001 - 11:00:00 CDT)
- Essential Dynamics (Sun Jul 15 2001 - 10:48:12 CDT)
- Re: ewald bomb in amber 6 (Fri Jul 13 2001 - 13:30:38 CDT)
- Best Topolgy for Linux Cluster (Tue Jun 26 2001 - 07:17:51 CDT)
- Re: Wrong compilation artifacts on ES40s? (Sun Jun 24 2001 - 15:17:48 CDT)
- Wrong compilation artifacts on ES40s? (Sun Jun 24 2001 - 13:43:11 CDT)
- Re: parallel sander (Wed Jun 20 2001 - 12:39:23 CDT)
- Dual-processor performance. (Tue Jun 12 2001 - 01:45:24 CDT)
- benchmark on X-86 (Tue Jun 05 2001 - 03:23:37 CDT)
- Adding crystal water using tleap. (Sun Jun 03 2001 - 10:04:51 CDT)
- Ewalb bomb on SP3 (Sat May 05 2001 - 14:38:23 CDT)
- Why does water leak!? (Thu May 03 2001 - 04:07:51 CDT)
- Re: AMBER6 on Alphas40 (fwd) (Mon Apr 30 2001 - 02:31:14 CDT)
- AMBER6 on Alphas40 (Sat Apr 28 2001 - 03:06:22 CDT)
- sander on SP3 (Tue Apr 24 2001 - 16:59:16 CDT)
- test run (Sat Apr 21 2001 - 16:24:25 CDT)
- tleap but no xleap on IBM SP3 (Fri Apr 20 2001 - 09:44:04 CDT)
- Test run for gb_rna on AMBER6 (IBM SP3) (Thu Apr 19 2001 - 14:54:57 CDT)
- LEaP compilation (Thu Mar 29 2001 - 00:00:27 CST)
- Compilation of LEaP on SP3 (Wed Mar 28 2001 - 02:02:02 CST)
- SP3 benchmark (Mon Mar 26 2001 - 04:44:26 CST)
- SP3 MACHINE file (Sat Mar 24 2001 - 06:59:50 CST)
- Correction: SP3 name list (Thu Mar 22 2001 - 00:47:53 CST)
- SP3 name list (Wed Mar 21 2001 - 13:10:13 CST)
- RE: AMBER6 on IBMSP3 Installation (Tue Mar 20 2001 - 13:53:07 CST)
- AMBER6 on IBMSP3 Installation (Tue Mar 20 2001 - 08:07:05 CST)
- Re: AMBER6 on IBMSP3 (Fri Mar 16 2001 - 12:03:22 CST)
- AMBER6 on IBMSP3 (Tue Mar 13 2001 - 05:59:55 CST)
- Parm98 for amino acids? (Thu Mar 01 2001 - 00:09:16 CST)
sara nunez
- Gibbs (Fri Aug 17 2001 - 10:50:25 CDT)
sara nuñez
- Sander (Mon Jan 15 2001 - 09:55:29 CST)
Sarah Tschampel
- (no subject) (Thu May 31 2001 - 11:01:09 CDT)
Satyavani Vemparala
- water parameters+TIP3 water model (Mon Jun 18 2001 - 15:00:00 CDT)
schayg_at_puskin-a206.sote.hu
- Re: peek_ewad_inpcrd (Tue Sep 04 2001 - 16:13:22 CDT)
- Re: problem in xleap (Wed Jul 11 2001 - 17:25:18 CDT)
- Re: problem in xleap (Wed Jul 11 2001 - 17:25:18 CDT)
- Re: error msg in leap (Wed Jun 06 2001 - 14:27:49 CDT)
- Re: informations (Tue Jun 05 2001 - 10:39:03 CDT)
Scott A. Showalter
- 2-Amino Purine Parameters (Fri Jan 26 2001 - 09:43:29 CST)
Scott Boesch
- Gibbs/non-bonded pairs (Tue Jan 30 2001 - 14:50:17 CST)
Scott E. Boesch
- Utilizing Amber6 on Linux Cluster (Wed Aug 22 2001 - 09:24:42 CDT)
seema namboori
- help (Sat Nov 03 2001 - 11:06:29 CST)
- help (Sat Nov 03 2001 - 11:05:40 CST)
- help (Wed Oct 17 2001 - 08:50:53 CDT)
Shixiang Yan
- a funny problem about output for sander_classic (Tue Sep 11 2001 - 16:12:13 CDT)
- partial solvation using delphi (Sun Sep 09 2001 - 13:10:32 CDT)
- parameter regarding S-O (Fri Sep 07 2001 - 16:32:25 CDT)
- density in equilibration? (Tue Aug 21 2001 - 11:38:35 CDT)
- about ion concentration in protein simulation (Wed Jul 11 2001 - 08:48:16 CDT)
- number of atoms for large system (Tue Jun 05 2001 - 14:36:50 CDT)
- sander 6 warming up (Thu May 31 2001 - 21:06:20 CDT)
- about plevel in sander 6 (Fri Apr 27 2001 - 17:32:48 CDT)
Simon Cross
- Re: generating parameters for a small molecule ligand (Wed Feb 14 2001 - 06:40:15 CST)
Soonmin Jang
- the molecule rotates during the MD run (Tue Dec 04 2001 - 02:46:42 CST)
- generation of small organic molecules on xleap (Sun Oct 21 2001 - 18:55:17 CDT)
- color in xleap (Sat Oct 20 2001 - 21:35:30 CDT)
- Amber 6.0 on LINUX with absoft (Mon May 14 2001 - 02:43:16 CDT)
Sophia Kondratova
- idsx0 parameter (Tue Dec 18 2001 - 12:23:15 CST)
- re: parallel gibbs (Mon Nov 26 2001 - 13:54:00 CST)
- parallel gibbs (Mon Nov 26 2001 - 08:02:59 CST)
- Methane in water box FEP (Fri Nov 23 2001 - 13:33:25 CST)
- Gaussian 98 to RESP (Tue Nov 06 2001 - 13:04:59 CST)
- Interface and Sander_classic (Tue Oct 30 2001 - 07:06:03 CST)
- Xleap, PDB file format (Fri Oct 26 2001 - 10:00:26 CDT)
- Methane minimization using Interface (Wed Oct 24 2001 - 09:17:36 CDT)
- Interface program installation (Fri Oct 19 2001 - 12:25:19 CDT)
- defining states in Gibbs (Wed Aug 22 2001 - 14:39:35 CDT)
Stan
- Windows version of AMBER? (Tue Apr 17 2001 - 01:59:44 CDT)
stefania_at_mail.unimo.it
- Charges for a 2-iodine-phenol (Mon Jun 25 2001 - 11:29:27 CDT)
Stephane
- Re: help for restrained minimization (Mon Oct 29 2001 - 02:39:21 CST)
- [Fwd: ?s: Xeon vs. Athlon, latency] (Mon Oct 08 2001 - 02:43:24 CDT)
- Re: ?s: Xeon vs. Athlon, latency (Fri Oct 05 2001 - 03:34:15 CDT)
- Re: (Fri Sep 28 2001 - 03:18:21 CDT)
- Dual Athlon (Thu Sep 27 2001 - 03:38:09 CDT)
- Problem with carnal ... (Thu Sep 13 2001 - 11:25:38 CDT)
- Re: input parameter for amber5 (Mon Sep 10 2001 - 07:17:45 CDT)
- Program versoins (Wed Sep 05 2001 - 05:05:58 CDT)
- Linux stability (Fri Jun 22 2001 - 17:05:29 CDT)
- DNA strand flying (Thu May 10 2001 - 10:48:17 CDT)
- Re: Compilation problem of AMBER6.0! (Tue Apr 17 2001 - 04:46:44 CDT)
- I'm upset ! (Thu Feb 01 2001 - 03:55:15 CST)
Steve Heller
- Call for Papers: Special issue of MATCH (Wed Jan 10 2001 - 09:03:51 CST)
Stéphane
- Not able to do parallel run (Fri Nov 30 2001 - 09:36:37 CST)
Sue Heavner
- C8-methyl-guanine (Sun Nov 25 2001 - 11:58:51 CST)
- trajectory analysis (Sat Oct 13 2001 - 14:26:41 CDT)
- MD run with constantly decreasing total energy (Sat Sep 08 2001 - 17:00:25 CDT)
- (no subject) (Fri Jul 06 2001 - 12:08:38 CDT)
Svetlana Nolde
- Re: How to let IBELLY and NTR both on? (Wed Apr 25 2001 - 04:55:32 CDT)
- setting random velocities (Mon Apr 02 2001 - 11:17:01 CDT)
- Interface (Mon Mar 05 2001 - 08:59:02 CST)
sxzheng
- About :ERROR TERMINATION DUE TO SHAKE OR TORCON (Sun Dec 30 2001 - 21:24:17 CST)
- How to deal with the little molcule? (Fri Aug 24 2001 - 09:48:22 CDT)
- Can amber calculate the gibbs perturb energy when a ligand added a group (Mon Aug 06 2001 - 22:26:13 CDT)
thenmalar rathinavelan
- about ion-amino group non-bonded distance (Fri Dec 07 2001 - 23:30:00 CST)
- hydorgen bond life time (Fri Sep 07 2001 - 23:14:18 CDT)
- water density and rdf calculations (Wed Apr 11 2001 - 05:02:59 CDT)
- about dials_and_windows (Mon Apr 02 2001 - 07:13:41 CDT)
- about dials_and_windows (Mon Apr 02 2001 - 07:13:41 CDT)
- how to get dials_and_windows (Fri Mar 30 2001 - 02:23:41 CST)
Therese Malliavin
- internal variables in ptraj (Tue Apr 10 2001 - 03:29:44 CDT)
Thijs Beuming
- (no subject) (Wed Dec 12 2001 - 07:39:57 CST)
Thomas A. Spraggins
- RE: Problem, setting up AMBERHOME! (Tue Apr 24 2001 - 07:23:48 CDT)
- RE: AMBER6 on IBMSP3 Installation (Tue Mar 20 2001 - 07:09:27 CST)
- RE: Problem of running sander on Linux cluster (Mon Mar 19 2001 - 12:54:49 CST)
- RE: Problem of running sander on Linux cluster (Mon Mar 19 2001 - 10:23:12 CST)
- RE: Can't compile Sander with parallel on Linux cluster (Fri Mar 16 2001 - 11:37:24 CST)
- RE: Compilation of Amber6 in linux machine (Sun Feb 18 2001 - 13:06:14 CST)
Thomas C. Bishop
- ptraj: principal axes (Wed Jul 18 2001 - 08:23:30 CDT)
Thomas Cheatham
- Re: ptraj (Thu Aug 23 2001 - 11:36:51 CDT)
- Re: ewald bomb in amber 6 (Fri Jul 13 2001 - 16:51:42 CDT)
- Re: ptraj diffusion (Thu Jul 12 2001 - 14:15:46 CDT)
- Re: AMBER6 on Alphas40 (fwd) (Mon Apr 30 2001 - 12:05:37 CDT)
- RE: AMBER6 on IBMSP3 Installation (Tue Mar 20 2001 - 12:45:40 CST)
- Re: Ionic solutions (Tue Feb 13 2001 - 12:22:54 CST)
Thomas Huber
- Re: list filter (Thu Dec 20 2001 - 15:42:19 CST)
- Re: simulating membranes with AMBER (Tue Jul 31 2001 - 13:54:38 CDT)
- Re: TIP3P/SPC VdW radius (Tue Apr 10 2001 - 15:02:43 CDT)
- Re: lipid bilayer MD simulations (Wed Mar 07 2001 - 12:19:12 CST)
- Re: lipid bilayer MD simulations (Tue Mar 06 2001 - 16:01:34 CST)
Thomas.Fox_at_bc.boehringer-ingelheim.com
- RE: CCl4 charge problem... (part II) (Wed Jun 27 2001 - 05:04:17 CDT)
- RE: CCl4 charge problem... (Wed Jun 27 2001 - 03:16:19 CDT)
tianxiao young
- box size (Wed Aug 15 2001 - 23:31:40 CDT)
- hybridization (Tue Jul 24 2001 - 09:10:55 CDT)
- potentials (Tue Jul 17 2001 - 21:58:28 CDT)
- addions (Thu Jul 12 2001 - 21:55:38 CDT)
Tikhonova Irina
- Prep.in (Thu Nov 08 2001 - 15:44:49 CST)
Todd J. Minehardt
- sander minimization problems with igb=3, ntb =0 (Mon Jul 16 2001 - 08:28:46 CDT)
- ewald bomb in amber 6 (Fri Jul 13 2001 - 09:21:50 CDT)
- dsp3 hybrid for P ? (Sun Jun 03 2001 - 14:47:41 CDT)
Tomoshi Kameda
- belly with GB term (Thu Oct 25 2001 - 14:54:22 CDT)
Toshikazu Matsuoka
- xleap: japanese keyboad (Mon Oct 22 2001 - 00:41:02 CDT)
- Amber6 on SuSE Linux (Wed Oct 17 2001 - 03:56:49 CDT)
Troy Bothwell
- atom coordinates (Mon Jun 11 2001 - 17:47:59 CDT)
- ptraj Vector command (Thu May 10 2001 - 17:36:04 CDT)
- ptraj correlation command (Sat Apr 21 2001 - 09:23:40 CDT)
- RE: odd display of ambpdb generated files (Fri Apr 13 2001 - 19:02:26 CDT)
- N-terminal and C-terminal hydrogens (Thu Apr 12 2001 - 13:10:16 CDT)
- Box info after minimization (Wed Apr 04 2001 - 22:38:58 CDT)
- Following Coordinates (Wed Apr 04 2001 - 18:23:16 CDT)
- Pairlist error (Tue Apr 03 2001 - 22:20:35 CDT)
- parm warnings (Wed Mar 28 2001 - 12:48:50 CST)
- Combining trajectories (Tue Mar 27 2001 - 10:45:54 CST)
- Question about prep file (Fri Mar 23 2001 - 18:39:42 CST)
- curves (Sun Mar 04 2001 - 17:27:05 CST)
- Fluorescent dyes (Wed Feb 28 2001 - 22:01:47 CST)
- ptraj (Tue Feb 06 2001 - 12:36:20 CST)
- Nonbonded Pair List (Fri Feb 02 2001 - 13:18:16 CST)
- Constant Pressure vs. Constant Volume (Tue Jan 16 2001 - 15:28:04 CST)
- "Goodness" of Trajectory (Tue Jan 16 2001 - 15:28:03 CST)
- Octahedral Box? (Fri Jan 12 2001 - 11:34:10 CST)
- DNA Simulation (Mon Jan 08 2001 - 15:20:16 CST)
- nucgen (Mon Jan 08 2001 - 14:53:52 CST)
Troy Wymore
- ptraj (Thu Aug 23 2001 - 10:30:23 CDT)
- PSC BIOMEDICAL WORKSHOPS 2001 (Wed May 16 2001 - 12:27:50 CDT)
- Re: MD without SHAKE (Wed Feb 28 2001 - 12:59:51 CST)
Tru
- Re: Amber & F90 (Mon Nov 26 2001 - 05:28:22 CST)
- Re: Amber 6.0 on Linux Cluster (Mon Nov 12 2001 - 04:17:19 CST)
Tru Huynh
- dual K7 (was Re: Linux-cluster performance) (Mon Aug 20 2001 - 14:09:18 CDT)
- Re: Machine_g77_lam-mpi (Tue Mar 27 2001 - 03:39:53 CST)
- Re: parallel load difference under linux (long) (Fri Mar 23 2001 - 05:43:28 CST)
- parallel load difference under linux (long) (Thu Mar 22 2001 - 14:01:47 CST)
- Re: Amber 6.0 Benchmarks (Thu Mar 22 2001 - 07:26:10 CST)
- Re: Can't compile sander witk parallel on Linux cluster (Fri Mar 16 2001 - 06:14:14 CST)
- Re: update to 1GHz Athlon (Tue Feb 20 2001 - 11:22:27 CST)
- update to 1GHz Athlon (Fri Feb 16 2001 - 04:35:59 CST)
- Athlon 1GHz (was: Dual Origin vs dual Alfa) (Wed Feb 14 2001 - 11:29:53 CST)
txyang
- RDF figure (Fri Apr 06 2001 - 02:19:20 CDT)
- Blowup problem (Thu Apr 05 2001 - 02:12:45 CDT)
- (no subject) (Thu Mar 22 2001 - 06:54:18 CST)
- questions about Sander (Wed Mar 07 2001 - 02:46:02 CST)
- questions about Sander (Wed Mar 07 2001 - 02:41:45 CST)
Ulf Ryde
- Intprt in PMF calculations (Mon Jul 23 2001 - 06:18:57 CDT)
UMEMOTO, Kimiko
- installing amber6 (Tue Jul 17 2001 - 03:37:13 CDT)
Uwe Richter
- charge fitting (Thu Nov 01 2001 - 06:36:35 CST)
- charges for non-standard AAs (Wed Oct 31 2001 - 07:46:15 CST)
- esp with gamess-usB (Wed Sep 19 2001 - 08:05:26 CDT)
Victor Anisimov
- protein ionization (Tue May 29 2001 - 05:07:59 CDT)
Walker, Jerrylaine
- problem in Leap (Fri Dec 14 2001 - 08:51:03 CST)
Warren DeLano
- Re: Amber, VMD and visualization (Thu May 24 2001 - 20:30:00 CDT)
- Re: [Amber]: Peptide torsions in Parm99.dat (Thu Jan 25 2001 - 19:06:04 CST)
- [Amber]: Peptide torsions in Parm99.dat (Thu Jan 25 2001 - 16:53:15 CST)
Wei Wang
- Re: mm_pbsa (Mon Nov 19 2001 - 19:27:10 CST)
- Re: LIE method (Wed Jun 06 2001 - 22:24:26 CDT)
Wenguang Zhu
- floating overflow in alpha Redhat 7.1 (Tue Dec 18 2001 - 03:16:25 CST)
- leap compile on alpha linux (Mon Dec 17 2001 - 22:17:09 CST)
- (no subject) (Mon Dec 17 2001 - 22:13:32 CST)
wentaofu
- mm_pbsa (Mon Nov 19 2001 - 17:32:14 CST)
- sander_classic (Wed Oct 31 2001 - 13:57:07 CST)
- Define flexible residues during MD simulation (Tue Oct 23 2001 - 16:59:59 CDT)
- CMC/MD (Wed Sep 26 2001 - 18:03:37 CDT)
Wing Lok Abe Kurtz
- RE: curves (Sun Mar 04 2001 - 18:46:54 CST)
Xavier Deupi
- ntc in sander6 (Sat Aug 25 2001 - 07:08:12 CDT)
- summary: AMBER6 on IBMSP3 (Fri Aug 24 2001 - 02:04:19 CDT)
- AMBER6 on IBMSP3 (again) (Fri Aug 17 2001 - 10:03:36 CDT)
- summary: lipid bilayer MD simulations (Fri Mar 16 2001 - 06:01:46 CST)
- lipid bilayer MD simulations (Wed Mar 07 2001 - 08:01:15 CST)
Xiaoliang Qian
- shake comparison (Fri Feb 23 2001 - 11:13:07 CST)
Xiaolin Chuang
- iwrap (Wed Oct 17 2001 - 07:27:39 CDT)
- image command of ptraj (Wed Oct 17 2001 - 07:22:20 CDT)
- distribution of Na+ around DNA (Wed Oct 17 2001 - 07:04:54 CDT)
- (no subject) (Thu Aug 23 2001 - 11:00:49 CDT)
- solvation energy calculation (Thu Jul 26 2001 - 04:12:07 CDT)
- DelPhi's manual (Wed Jul 25 2001 - 12:37:04 CDT)
- nucgen (Thu Jul 05 2001 - 07:06:39 CDT)
- iwrap & TIP3P model water (Fri Jun 22 2001 - 11:20:06 CDT)
- How to minimization of Average structure? (Sun Jun 03 2001 - 11:57:48 CDT)
- How tleap does not add missing H atoms? (Mon Mar 26 2001 - 10:07:19 CST)
- DNA out of a box (Sat Mar 17 2001 - 07:08:56 CST)
Xin Hu
- restraint (Thu Nov 01 2001 - 16:48:29 CST)
- how to add Zn Ca parameters (Wed Oct 24 2001 - 18:08:51 CDT)
- (no subject) (Thu Sep 27 2001 - 21:27:27 CDT)
- problem with Leap (Fri Mar 30 2001 - 05:08:41 CST)
- question about RESP calculation (Mon Jan 22 2001 - 16:45:37 CST)
xin.hu_at_ndsu.nodak.edu
- help for restrained minimization (Fri Oct 26 2001 - 23:10:19 CDT)
Yang Tom
- ask help (Sun Apr 08 2001 - 02:40:01 CDT)
Yanni Wang
- Diffusion constant (Thu May 10 2001 - 04:14:34 CDT)
- Membrane (Fri Mar 30 2001 - 02:31:34 CST)
- Resp (Wed Mar 28 2001 - 07:24:04 CST)
- QM/MM in roar (Mon Feb 26 2001 - 12:04:03 CST)
- Roar (Wed Feb 21 2001 - 03:34:47 CST)
- lower_bound and upper_bound (Fri Feb 16 2001 - 09:58:02 CST)
Yinghong Sheng
- (no subject) (Wed Feb 14 2001 - 11:45:43 CST)
- AMBER parameter for HCOO(-) and NCHCHNHC (Tue Feb 06 2001 - 17:18:00 CST)
Yong Duan
- RE: Xeon vs. Athlon, latency (Thu Oct 04 2001 - 12:19:29 CDT)
- Re: equilibrating water in sander (Wed Jun 20 2001 - 23:27:02 CDT)
- RE: parallel load difference under linux (long) (Thu Mar 22 2001 - 16:51:05 CST)
- RE: AMBER on SUN (Tue Feb 20 2001 - 12:29:41 CST)
- RE: Ionic solutions (Tue Feb 13 2001 - 14:49:58 CST)
Yongxing Liu
- RE: Average structure (Thu Mar 29 2001 - 13:51:05 CST)
- (no subject) (Mon Mar 19 2001 - 12:58:49 CST)
- (no subject) (Tue Mar 06 2001 - 11:42:54 CST)
yu kaneko
- File format convert (Thu Dec 20 2001 - 06:19:01 CST)
- GIBSS pertType (Thu Mar 22 2001 - 06:58:28 CST)
- Again Gibbs... (Sat Mar 10 2001 - 02:12:10 CST)
Yuguang Mu
- roar-cp crashed (Wed Oct 24 2001 - 16:25:38 CDT)
- Re: Adding ions in xleap (Fri Jul 27 2001 - 01:25:38 CDT)
- Re: parallel sander (Fri Jun 22 2001 - 01:43:07 CDT)
- parallel sander (Wed Jun 20 2001 - 09:58:39 CDT)
- parameters forms (Tue May 08 2001 - 03:13:32 CDT)
- helix analyse (Fri Mar 30 2001 - 11:20:21 CST)
- disk file larger than 2 GB (Thu Feb 15 2001 - 01:12:47 CST)
- DMSO ? (Tue Feb 13 2001 - 10:22:42 CST)
ZHANG RB
- consult (Sun Feb 25 2001 - 05:50:47 CST)
- consult (Sun Feb 25 2001 - 05:50:11 CST)
Zhangxd
- question (Thu Jul 19 2001 - 09:05:18 CDT)
- limit the distance (Mon Jul 02 2001 - 15:13:08 CDT)
- the program and references (Tue May 15 2001 - 10:33:01 CDT)
- question about mm-pbsa (Mon May 07 2001 - 07:32:26 CDT)
- question about mm-pbsa (Wed May 02 2001 - 15:02:50 CDT)
- parameter (Tue Mar 06 2001 - 16:20:35 CST)
- about prep input (Thu Mar 01 2001 - 07:40:23 CST)
- question (Mon Jan 22 2001 - 12:24:48 CST)
- EWALD (Wed Jan 17 2001 - 13:13:44 CST)
- (no subject) (Mon Jan 15 2001 - 09:46:08 CST)
- define the QM (Wed Jan 10 2001 - 14:35:57 CST)
- software (Thu Jan 04 2001 - 12:30:53 CST)
Zhiyong Zhang
- One article (Tue Feb 13 2001 - 05:46:42 CST)

Last message date: Sun Dec 30 2001 - 21:24:17 CST
Archived on: Thu May 05 2005 - 14:17:15 CDT

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