Amber Archive Mar 2001: By Thread

Parm98 for amino acids? Sanjeev B.S. (Wed Feb 28 2001 - 22:09:16 PST)
GIBBS Andrea Bernini (Thu Mar 01 2001 - 03:20:07 PST)
about prep input Zhangxd (Thu Mar 01 2001 - 05:40:23 PST)
Dummy Atoms Matthew Davies (Thu Mar 01 2001 - 05:58:14 PST)
Pentium IV compiler in MD Jose Ramon Blas (Thu Mar 01 2001 - 13:11:08 PST)
PROFEC Anna Ferrari (Fri Mar 02 2001 - 02:57:28 PST)
imaging in amber6 Riccardo Nifosi (Fri Mar 02 2001 - 07:52:15 PST)
- Re: imaging in amber6 David Case (Fri Mar 02 2001 - 09:05:39 PST)
- compilation problems Christian Pilger (Sun Mar 04 2001 - 07:03:34 PST)
  - Re: compilation problems Chuck Schneider (Mon Mar 05 2001 - 05:20:18 PST)
  - Interface Svetlana Nolde (Mon Mar 05 2001 - 06:59:02 PST)
  - leap adding terminal phosphates Michael Cooney (Mon Mar 05 2001 - 10:20:00 PST)
    - re: leap adding terminal phosphates Bill Ross (Mon Mar 05 2001 - 12:27:27 PST)
  - Pentium 4 Robert Matthew Fesinmeyer (Mon Mar 05 2001 - 11:01:26 PST)
    - Re: Pentium 4 David Konerding (Mon Mar 05 2001 - 11:57:04 PST)
    - RE: Pentium 4 Heirich, Alan (Mon Mar 05 2001 - 12:47:08 PST)
    - recommended vs. default values Jake Isaacs (Mon Mar 05 2001 - 13:22:43 PST)
    - Amber Website - UK Mirror Ross Walker (Tue Mar 06 2001 - 02:47:28 PST)
    - (no subject) Yongxing Liu (Tue Mar 06 2001 - 09:42:54 PST)
  - Q about RESP Ramon Garduno (Mon Mar 05 2001 - 11:35:47 PST)
- curves Troy Bothwell (Sun Mar 04 2001 - 15:27:05 PST)
  - RE: curves Wing Lok Abe Kurtz (Sun Mar 04 2001 - 16:46:54 PST)
  - anal ouput Francois Dupradeau (Mon Mar 05 2001 - 00:40:14 PST)
Re: lipid bilayer MD simulations Bill Ross (Tue Mar 06 2001 - 11:06:44 PST)
- Re: lipid bilayer MD simulations Bill Ross (Tue Mar 06 2001 - 11:48:02 PST)
Re: SHAKE David Case (Thu Mar 08 2001 - 09:28:28 PST)
- Re: SHAKE Michael Cooney (Thu Mar 08 2001 - 09:39:51 PST)
sander VS sander_classic Khatcharin Siriwong (Thu Mar 08 2001 - 10:18:44 PST)
- Re: sander VS sander_classic David Case (Thu Mar 08 2001 - 10:53:51 PST)
- Re: sander VS sander_classic Jarrod Smith (Thu Mar 08 2001 - 11:03:59 PST)
Re: SHAKE Bill Ross (Thu Mar 08 2001 - 11:22:13 PST)
Re: using "radial" in PTRAJ Pascal Bonnet (Fri Mar 09 2001 - 09:26:17 PST)
Principal component analysis Andreas Svrcek-Seiler (Fri Mar 09 2001 - 11:11:21 PST)
variable NTWXM in Sander Michael Cooney (Fri Mar 09 2001 - 14:54:23 PST)
Again Gibbs... yu kaneko (Sat Mar 10 2001 - 00:12:10 PST)
Generating C-DNA using nucgen! A.Madhumalar (Sun Mar 11 2001 - 00:31:16 PST)
MM-PBSA Eoin Galligan (Mon Mar 12 2001 - 07:34:20 PST)
AMBER6 on IBMSP3 Sanjeev B.S. (Tue Mar 13 2001 - 03:59:55 PST)
- Re: AMBER6 on IBMSP3 David Skinner (Tue Mar 13 2001 - 08:18:19 PST)
  - Re: AMBER6 on IBMSP3 Sanjeev B.S. (Fri Mar 16 2001 - 10:03:22 PST)
  - carnal problem Joseph Nachman (Fri Mar 16 2001 - 11:58:45 PST)
  - AMBER6 on IBMSP3 Installation Sanjeev B.S. (Tue Mar 20 2001 - 06:07:05 PST)
    - RE: AMBER6 on IBMSP3 Installation Thomas A. Spraggins (Tue Mar 20 2001 - 05:09:27 PST)
    - RE: AMBER6 on IBMSP3 Installation Sanjeev B.S. (Tue Mar 20 2001 - 11:53:07 PST)
    - RE: AMBER6 on IBMSP3 Installation Thomas Cheatham (Tue Mar 20 2001 - 10:45:40 PST)
    - amber6 compilation failure (fwd) Jamal G. Musaev (Tue Mar 20 2001 - 12:29:55 PST)
    - Re: amber6 compilation failure (fwd) David Skinner (Tue Mar 20 2001 - 13:09:49 PST)
  - PME with octahedral box Ann Hermone (Tue Mar 20 2001 - 10:01:05 PST)
    - Re: PME with octahedral box David Konerding (Tue Mar 20 2001 - 10:43:11 PST)
ptraj image for octahedral box Peter Varnai (Tue Mar 13 2001 - 07:47:28 PST)
- Re: ptraj image for octahedral box Pascal Bonnet (Tue Mar 13 2001 - 17:28:47 PST)
ATP+Mg, P-tyrosine a P-threonine Michal Otyepka (Wed Mar 14 2001 - 02:35:53 PST)
How to calculate energy from mdcrd output file Khatcharin Siriwong (Wed Mar 14 2001 - 06:23:47 PST)
Re: why the slowdown? Bill Ross (Wed Mar 14 2001 - 13:34:10 PST)
Re: Selection Bill Ross (Wed Mar 14 2001 - 14:11:32 PST)
ptraj resolved; irest=1? Peter Varnai (Thu Mar 15 2001 - 07:29:54 PST)
- RE: ptraj resolved; irest=1? Guanglei Cui (Thu Mar 15 2001 - 08:08:01 PST)
  - Re: PBC box problems Michael Ford (Tue Mar 20 2001 - 10:10:17 PST)
- LEAP kiyean.nam_at_pharma.Novartis.com (Thu Mar 15 2001 - 15:01:43 PST)
- (no subject) chomsri upkaew (Fri Mar 16 2001 - 01:36:38 PST)
  - (no subject) David Konerding (Fri Mar 16 2001 - 09:28:06 PST)
- Can't compile sander witk parallel on Linux cluster chomsri upkaew (Fri Mar 16 2001 - 03:54:27 PST)
  - Re: Can't compile sander witk parallel on Linux cluster Tru Huynh (Fri Mar 16 2001 - 04:14:14 PST)
  - RE: Can't compile sander witk parallel on Linux cluster Ross Walker (Fri Mar 16 2001 - 04:54:07 PST)
- summary: lipid bilayer MD simulations Xavier Deupi (Fri Mar 16 2001 - 04:01:46 PST)
RE: Can't compile Sander with parallel on Linux cluster Ross Walker (Fri Mar 16 2001 - 07:05:49 PST)
- RE: Can't compile Sander with parallel on Linux cluster Thomas A. Spraggins (Fri Mar 16 2001 - 09:37:24 PST)
- Re: Can't compile Sander with parallel on Linux cluster David Konerding (Fri Mar 16 2001 - 09:54:10 PST)
Re: carnal problem Bill Ross (Fri Mar 16 2001 - 14:09:56 PST)
DNA out of a box Xiaolin Chuang (Sat Mar 17 2001 - 05:08:56 PST)
- Re: DNA out of a box Michael Cooney (Wed Mar 21 2001 - 09:43:18 PST)
- SP3 name list Sanjeev B.S. (Wed Mar 21 2001 - 11:10:13 PST)
  - Correction: SP3 name list Sanjeev B.S. (Wed Mar 21 2001 - 22:47:53 PST)
  - Amber 6.0 Benchmarks Florian Barth (Thu Mar 22 2001 - 02:54:18 PST)
    - Re: Amber 6.0 Benchmarks Tru Huynh (Thu Mar 22 2001 - 05:26:10 PST)
  - (no subject) txyang (Thu Mar 22 2001 - 04:54:18 PST)
  - Re: SP3 name list David Case (Thu Mar 22 2001 - 07:43:37 PST)
  - (no subject) Bill Ross (Thu Mar 22 2001 - 09:44:16 PST)
- GIBBS error kiyean.nam_at_pharma.Novartis.com (Wed Mar 21 2001 - 14:02:35 PST)
[charmm-bbs] Post-doctoral position available Chris Chipot (Sat Mar 17 2001 - 10:21:59 PST)
Post-doctoral position available Chris Chipot (Sat Mar 17 2001 - 10:21:59 PST)
Problem of running sander on Linux cluster chomsri upkaew (Mon Mar 19 2001 - 07:24:59 PST)
- Re: Problem of running sander on Linux cluster David Konerding (Mon Mar 19 2001 - 08:22:31 PST)
- RE: Problem of running sander on Linux cluster Thomas A. Spraggins (Mon Mar 19 2001 - 08:23:12 PST)
  - Re: Problem of running sander on Linux cluster Carlos Simmerling (Mon Mar 19 2001 - 09:03:02 PST)
    - RE: Problem of running sander on Linux cluster Thomas A. Spraggins (Mon Mar 19 2001 - 10:54:49 PST)
    - (no subject) Yongxing Liu (Mon Mar 19 2001 - 10:58:49 PST)
    - PME with octahedral box Ann Hermone (Mon Mar 19 2001 - 13:31:16 PST)
    - Test Group - swarm.ca Mite51_at_hotmail.com (Mon Mar 19 2001 - 14:56:09 PST)
Re: amber6 compilation failure (fwd) Bill Ross (Tue Mar 20 2001 - 13:40:51 PST)
Question about installing AMBER jllo (Tue Mar 20 2001 - 19:46:40 PST)
- Re: Question about installing AMBER Andreas Svrcek-Seiler (Wed Mar 21 2001 - 02:31:22 PST)
- error in sander rathinavelan thenmalarchelvi (Wed Mar 21 2001 - 04:12:23 PST)
Re: GIBBS error Bill Ross (Wed Mar 21 2001 - 16:07:56 PST)
GIBSS pertType yu kaneko (Thu Mar 22 2001 - 04:58:28 PST)
Re: Correction: SP3 name list Michael Crowley (Thu Mar 22 2001 - 09:46:21 PST)
- Re: Correction: SP3 name list Michael Crowley (Thu Mar 22 2001 - 09:49:43 PST)
parallel load difference under linux (long) Tru Huynh (Thu Mar 22 2001 - 12:01:47 PST)
- Re: parallel load difference under linux (long) David Konerding (Thu Mar 22 2001 - 12:58:23 PST)
  - RE: parallel load difference under linux (long) Yong Duan (Thu Mar 22 2001 - 14:51:05 PST)
- Re: parallel load difference under linux (long) Michael Crowley (Thu Mar 22 2001 - 13:31:08 PST)
  - Re: parallel load difference under linux (long) Tru Huynh (Fri Mar 23 2001 - 03:43:28 PST)
Re: your mail David Case (Thu Mar 22 2001 - 14:11:32 PST)
- Re: your mail Jarrod Smith (Thu Mar 22 2001 - 14:38:16 PST)
- Re: your mail Nathalie Godbout (Fri Mar 23 2001 - 09:27:19 PST)
  - Re: SGI_MP (was "your mail") Jarrod Smith (Fri Mar 23 2001 - 10:27:09 PST)
    - Re: SGI_MP (was "your mail") Nathalie Godbout (Fri Mar 23 2001 - 11:54:14 PST)
    - Question about prep file Troy Bothwell (Fri Mar 23 2001 - 16:39:42 PST)
    - SP3 MACHINE file Sanjeev B.S. (Sat Mar 24 2001 - 04:59:50 PST)
    - SP3 benchmark Sanjeev B.S. (Mon Mar 26 2001 - 02:44:26 PST)
    - How tleap does not add missing H atoms? Xiaolin Chuang (Mon Mar 26 2001 - 08:07:19 PST)
    - Re: How tleap does not add missing H atoms? Jarrod Smith (Mon Mar 26 2001 - 10:47:50 PST)
    - Re: How tleap does not add missing H atoms? Bill Ross (Mon Mar 26 2001 - 12:10:08 PST)
    - Machine_g77_lam-mpi Andrew Petersen (Mon Mar 26 2001 - 13:33:27 PST)
    - Re: Machine_g77_lam-mpi Tru Huynh (Tue Mar 27 2001 - 01:39:53 PST)
    - Xleap Jean-François Gibrat (Tue Mar 27 2001 - 01:19:01 PST)
    - Re: Xleap Khatcharin Siriwong (Tue Mar 27 2001 - 01:42:34 PST)
    - Re: Xleap Jean-François Gibrat (Tue Mar 27 2001 - 01:55:16 PST)
    - RE: Xleap Ross Walker (Tue Mar 27 2001 - 02:12:09 PST)
    - PMF-input file c724128 (Tue Mar 27 2001 - 03:40:03 PST)
    - PMF input file c724128 (Tue Mar 27 2001 - 03:48:11 PST)
    - Combining trajectories Troy Bothwell (Tue Mar 27 2001 - 08:45:54 PST)
    - Re: Combining trajectories Peter Varnai (Wed Mar 28 2001 - 00:56:58 PST)
    - Re: Combining trajectories David Konerding (Wed Mar 28 2001 - 08:10:30 PST)
    - loading prmtop and inpcrd into leap Jake Isaacs (Wed Mar 28 2001 - 08:13:06 PST)
    - Re: Combining trajectories Bill Ross (Wed Mar 28 2001 - 09:35:54 PST)
Re: How tleap does not add missing H atoms? Bill Ross (Mon Mar 26 2001 - 09:54:34 PST)
periodic box size Jake Isaacs (Mon Mar 26 2001 - 10:40:49 PST)
Re: periodic box size Bill Ross (Mon Mar 26 2001 - 12:06:08 PST)
Re: Combining trajectories Bill Ross (Tue Mar 27 2001 - 08:53:58 PST)
nstlim in sander Michael Cooney (Tue Mar 27 2001 - 10:12:08 PST)
PMF input file c724128 (Tue Mar 27 2001 - 11:14:18 PST)
Re: PMF input file Bill Ross (Tue Mar 27 2001 - 11:18:18 PST)
Compilation of LEaP on SP3 Sanjeev B.S. (Wed Mar 28 2001 - 00:02:02 PST)
Resp Yanni Wang (Wed Mar 28 2001 - 05:24:04 PST)
- Re: Resp Elsa Sousa Henriques (Wed Mar 28 2001 - 17:25:53 PST)
- LEaP compilation Sanjeev B.S. (Wed Mar 28 2001 - 22:00:27 PST)
- How to remove CIO from prmtop & crd Jithesh P.V (Thu Mar 29 2001 - 01:21:25 PST)
- Average structure Khatcharin Siriwong (Thu Mar 29 2001 - 07:07:11 PST)
  - RE: Average structure Guanglei Cui (Thu Mar 29 2001 - 07:42:38 PST)
    - Re: Average structure Laurent Chiche (Thu Mar 29 2001 - 08:01:32 PST)
    - Re: Average structure David Konerding (Thu Mar 29 2001 - 08:27:08 PST)
    - Re: Average structure Carlos Simmerling (Thu Mar 29 2001 - 09:55:55 PST)
    - RE: Average structure Yongxing Liu (Thu Mar 29 2001 - 11:51:05 PST)
    - parameters for NADH marin (Thu Mar 29 2001 - 13:28:25 PST)
    - problem with Leap xin hu (Fri Mar 30 2001 - 05:08:41 PST)
    - how to get dials_and_windows thenmalar rathinavelan (Fri Mar 30 2001 - 00:23:41 PST)
    - Membrane Yanni Wang (Fri Mar 30 2001 - 00:31:34 PST)
    - helix analyse Yuguang Mu (Fri Mar 30 2001 - 09:20:21 PST)
    - Ca2+ parameters and how ? ... A. Ababou (Sat Mar 31 2001 - 07:07:39 PST)
    - Missing "ASH" parameters Jake Isaacs (Thu Mar 29 2001 - 10:09:01 PST)
Re: loading prmtop and inpcrd into leap Bill Ross (Wed Mar 28 2001 - 10:37:38 PST)
parm warnings Troy Bothwell (Wed Mar 28 2001 - 10:48:50 PST)
Minimization and NSNB Lillian Chong (Wed Mar 28 2001 - 10:59:15 PST)
Re: parm warnings Bill Ross (Wed Mar 28 2001 - 11:58:17 PST)
[charmm-bbs] Post-doctoral position available Heather A.Carlson (Wed Mar 28 2001 - 14:51:37 PST)
Post-doctoral position available Heather A.Carlson (Wed Mar 28 2001 - 14:51:37 PST)
[charmm-bbs] Post-doctoral Position Ronald Kuehne (Wed Mar 28 2001 - 16:51:26 PST)
Post-doctoral Position Ronald Kuehne (Wed Mar 28 2001 - 16:51:26 PST)
Re: LEaP adding an extra hydrogen to N-terminus Jake Isaacs (Thu Mar 29 2001 - 07:31:04 PST)
RE: LEaP adding an extra hydrogen to N-terminus Guanglei Cui (Thu Mar 29 2001 - 07:48:05 PST)

Amber Archive Mar 2001 By Thread