Amber Archive Mar 2004: By Thread

AMBER: Jiten (Mon Mar 01 2004 - 06:04:17 PST)
- Re: AMBER: ML (Mon Mar 01 2004 - 06:49:18 PST)
(no subject) Job Success (Mon Mar 01 2004 - 06:17:29 PST)
Re: AMBER: sander + vlimit exceed... David A. Case (Mon Mar 01 2004 - 06:50:23 PST)
AMBER: GIBBS + vlimit exceeded Miguel de Federico (Mon Mar 01 2004 - 09:17:44 PST)
AMBER: ptraj Carsten Detering (Mon Mar 01 2004 - 09:23:26 PST)
- RE: AMBER: ptraj Ross Walker (Mon Mar 01 2004 - 15:25:41 PST)
  - Re: AMBER: ptraj Carsten Detering (Tue Mar 02 2004 - 10:48:35 PST)
Re: AMBER: Piotr Cieplak (Mon Mar 01 2004 - 09:38:49 PST)
- Re: AMBER: Jiten (Mon Mar 01 2004 - 16:14:13 PST)
  - AMBER: NMODE COMPILATION Obdulia Rabal (Mon Mar 15 2004 - 02:58:11 PST)
    - Re: AMBER: NMODE COMPILATION Anselm Horn (Mon Mar 15 2004 - 03:34:50 PST)
AMBER: production input file Ryan Ye (Mon Mar 01 2004 - 10:58:48 PST)
- Re: AMBER: production input file darden (Mon Mar 01 2004 - 14:32:35 PST)
RE: AMBER: Problems with xleap Ross Walker (Mon Mar 01 2004 - 15:25:23 PST)
Re: AMBER: Problems with xleap Rhonda Torres (Mon Mar 01 2004 - 16:02:23 PST)
Re: AMBER: xleap don't recognize my residue/atom scopio (Tue Mar 02 2004 - 00:00:31 PST)
- RE: AMBER: xleap don't recognize my residue/atom Ross Walker (Tue Mar 02 2004 - 09:44:13 PST)
  - RE: AMBER: xleap don't recognize my residue/atom Rhonda Torres (Tue Mar 02 2004 - 10:11:07 PST)
AMBER: error in minimization atchara.mercury.hec.utah.edu (Tue Mar 02 2004 - 09:47:14 PST)
- Re: AMBER: error in minimization David A. Case (Tue Mar 02 2004 - 11:41:36 PST)
AMBER: A question about RMSD calculation yonchen (Tue Mar 02 2004 - 11:05:13 PST)
- Re: AMBER: A question about RMSD calculation David A. Case (Tue Mar 02 2004 - 11:52:05 PST)
AMBER: How to use tleap convert *.pdb file to *.crd and *.top files yonchen (Tue Mar 02 2004 - 11:08:55 PST)
- Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files Carsten Detering (Tue Mar 02 2004 - 11:18:42 PST)
- Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files David A. Case (Tue Mar 02 2004 - 11:53:31 PST)
Re: AMBER: A question about RMSD calculation Bill Ross (Tue Mar 02 2004 - 11:53:11 PST)
- RE: AMBER: A question about RMSD calculation Obdulia Rabal (Thu Mar 11 2004 - 10:09:25 PST)
AMBER: diffusion coefficient with external applied electric field Ioana Cozmuta (Tue Mar 02 2004 - 12:36:35 PST)
AMBER: General Questions Sekwan Oh (Tue Mar 02 2004 - 16:07:08 PST)
- Re: AMBER: General Questions David A. Case (Wed Mar 03 2004 - 05:22:14 PST)
AMBER: HIV-RT Nevirapin Annette Höglund (Wed Mar 03 2004 - 07:37:40 PST)
AMBER: torsion term Guanglei Cui (Wed Mar 03 2004 - 08:48:36 PST)
AMBER: questions about mmpbsa xhu1.memphis.edu (Wed Mar 03 2004 - 11:48:12 PST)
- Re: AMBER: questions about mmpbsa Holger Gohlke (Thu Mar 04 2004 - 23:35:57 PST)
AMBER: pls forget my first question in my last email xhu1.memphis.edu (Wed Mar 03 2004 - 12:02:06 PST)
AMBER: compiling xleap on MAC OS X.3 Yunfeng Hu (Wed Mar 03 2004 - 14:19:57 PST)
- Re: AMBER: compiling xleap on MAC OS X.3 Bill Ross (Wed Mar 03 2004 - 15:16:53 PST)
Re: AMBER: compiling xleap on MAC OS X.3 Bill Ross (Wed Mar 03 2004 - 14:37:50 PST)
- Re: AMBER: compiling xleap on MAC OS X.3 Yunfeng Hu (Wed Mar 03 2004 - 14:43:53 PST)
AMBER: Use tleap convert *.pdb file to *.top and *.crd file yonchen (Wed Mar 03 2004 - 20:01:04 PST)
- Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file David A. Case (Thu Mar 04 2004 - 08:47:10 PST)
- Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file Carsten Detering (Fri Mar 05 2004 - 10:19:18 PST)
AMBER: Question about RMSD calculation yonchen (Wed Mar 03 2004 - 20:25:01 PST)
Re: AMBER: Question about RMSD calculation Carlos Simmerling (Wed Mar 03 2004 - 20:43:58 PST)
AMBER: Leap atom removal bug? david.evans.ulsop.ac.uk (Thu Mar 04 2004 - 02:30:01 PST)
- Re: AMBER: Leap atom removal bug? david.evans.ulsop.ac.uk (Thu Mar 04 2004 - 03:30:00 PST)
- Re: AMBER: Leap atom removal bug? Bill Ross (Thu Mar 04 2004 - 05:06:44 PST)
- Re: AMBER: Leap atom removal bug? David A. Case (Thu Mar 04 2004 - 08:00:08 PST)
  - AMBER: Glycam_04.prep Karl N. Kirschner (Thu Mar 04 2004 - 08:20:24 PST)
  - AMBER: Sorry about that... Karl N. Kirschner (Thu Mar 04 2004 - 08:22:53 PST)
- Re: AMBER: Leap atom removal bug? Scott Brozell (Fri Mar 05 2004 - 18:34:16 PST)
Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file Bill Ross (Thu Mar 04 2004 - 05:11:45 PST)
AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Thu Mar 04 2004 - 14:31:43 PST)
- Re: AMBER: conversion of Amber 7 .pdb file to .bgf file David A. Case (Thu Mar 04 2004 - 14:59:21 PST)
  - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Thu Mar 04 2004 - 18:00:34 PST)
    - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file David A. Case (Fri Mar 05 2004 - 08:16:19 PST)
    - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Fri Mar 05 2004 - 12:47:59 PST)
  - AMBER: recovering total force array Dave S Walker (Thu Mar 11 2004 - 18:20:57 PST)
    - Re: AMBER: recovering total force array David A. Case (Fri Mar 12 2004 - 09:13:57 PST)
    - Re: AMBER: recovering total force array Dave S Walker (Tue Mar 30 2004 - 17:51:41 PST)
    - Re: AMBER: recovering total force array Carlos Simmerling (Tue Mar 30 2004 - 18:11:28 PST)
    - Re: AMBER: recovering total force array Dave S Walker (Wed Mar 31 2004 - 13:29:13 PST)
    - Re: AMBER: recovering total force array Carlos Simmerling (Wed Mar 31 2004 - 13:39:18 PST)
AMBER: PKA calculation hj zou (Thu Mar 04 2004 - 22:34:21 PST)
AMBER: positive binding free energy hj zou (Thu Mar 04 2004 - 22:53:18 PST)
- Re: AMBER: positive binding free energy Holger Gohlke (Fri Mar 05 2004 - 00:30:35 PST)
AMBER: MD at different pH !! Jiten (Thu Mar 04 2004 - 22:30:30 PST)
- Re: AMBER: MD at different pH !! David A. Case (Fri Mar 05 2004 - 08:23:27 PST)
  - AMBER: Ewald calculation using PME for charged system Byungchan Kim (Fri Mar 05 2004 - 10:13:43 PST)
    - AMBER: Ewald calculation using PME for charged system Byungchan Kim (Tue Mar 09 2004 - 13:04:31 PST)
    - Re: AMBER: Ewald calculation using PME for charged system David A. Case (Tue Mar 09 2004 - 14:58:29 PST)
    - Re: AMBER: Ewald calculation using PME for charged system Byungchan Kim (Tue Mar 09 2004 - 15:09:18 PST)
    - Re: AMBER: Ewald calculation using PME for charged system Wayne Dawson (Tue Mar 09 2004 - 19:28:36 PST)
    - Re: AMBER: Ewald calculation using PME for charged system David A. Case (Wed Mar 10 2004 - 00:11:54 PST)
  - Re: AMBER: MD at different pH !! Xin Chen (Fri Mar 05 2004 - 12:04:46 PST)
    - Re: AMBER: MD at different pH !! David A. Case (Fri Mar 05 2004 - 17:43:19 PST)
- Re: AMBER: MD at different pH !! Do Anh Tuan (Fri Mar 05 2004 - 13:11:25 PST)
  - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Fri Mar 05 2004 - 18:43:36 PST)
    - Re: AMBER: MD at different pH !! Do Anh Tuan (Fri Mar 05 2004 - 20:20:04 PST)
    - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Fri Mar 05 2004 - 20:58:39 PST)
    - Re: AMBER: MD at different pH !! Jiten (Fri Mar 05 2004 - 23:37:27 PST)
    - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Sat Mar 06 2004 - 04:18:15 PST)
AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite james.m.woolven.gsk.com (Fri Mar 05 2004 - 04:40:31 PST)
- Re: AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite David A. Case (Fri Mar 05 2004 - 10:20:26 PST)
AMBER: Sander problem with different CPU yuann (Fri Mar 05 2004 - 04:29:49 PST)
- Re: AMBER: Sander problem with different CPU Carlos Simmerling (Fri Mar 05 2004 - 05:27:22 PST)
- Re: AMBER: Sander problem with different CPU Robert Duke (Fri Mar 05 2004 - 05:39:37 PST)
  - Re: AMBER: Sander problem with different CPU sychen (Sat Mar 06 2004 - 17:40:25 PST)
    - Re: AMBER: Sander problem with different CPU Carlos Simmerling (Mon Mar 08 2004 - 06:45:19 PST)
AMBER: Unbinding with different pH Volodymyr Nechiporuk-Zloy (Fri Mar 05 2004 - 06:10:23 PST)
AMBER: A Question about RESP ::©¾¸Û:: (Sat Mar 06 2004 - 04:39:22 PST)
- Re: AMBER: A Question about RESP Bimo Ario Tejo (Sat Mar 06 2004 - 05:31:51 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 05:58:44 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 06:42:01 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 06:41:15 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 07:28:25 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 18:54:52 PST)
    - RE: AMBER: A Question about RESP William Wei (Mon Mar 15 2004 - 07:23:57 PST)
    - AMBER: understanding SANDER source code myang (Sat Mar 20 2004 - 07:33:33 PST)
    - Re: AMBER: understanding SANDER source code Scott Brozell (Sun Mar 21 2004 - 11:47:40 PST)
    - RE: AMBER: understanding SANDER source code Yong Duan (Sun Mar 21 2004 - 18:32:03 PST)
    - Re: AMBER: understanding SANDER source code Andreas Svrcek-Seiler (Mon Mar 22 2004 - 04:15:42 PST)
    - Re: AMBER: understanding SANDER source code David E. Konerding (Mon Mar 22 2004 - 08:15:49 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 07:58:38 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 22:15:16 PST)
AMBER: pka questions hj zou (Sat Mar 06 2004 - 19:22:54 PST)
AMBER: antechamber prepin Guanglei Cui (Sun Mar 07 2004 - 11:03:22 PST)
- Re: AMBER: antechamber prepin David A. Case (Sun Mar 07 2004 - 22:49:48 PST)
  - Re: AMBER: antechamber prepin Guanglei Cui (Mon Mar 08 2004 - 08:22:40 PST)
AMBER: factor used in b-factor calculation Fabian Boes (Tue Mar 09 2004 - 00:12:11 PST)
- Re: AMBER: factor used in b-factor calculation ML (Tue Mar 09 2004 - 02:36:57 PST)
- Re: AMBER: factor used in b-factor calculation Bimo Ario Tejo (Wed Mar 10 2004 - 03:02:46 PST)
AMBER: a problem about alanine scan of proline luocheng (Tue Mar 09 2004 - 01:00:27 PST)
AMBER: Amber on RedHat 3.0 madeleine.richard.bull.net (Tue Mar 09 2004 - 01:39:47 PST)
AMBER: MD simulation of a DNA decamer Thomas Steinbrecher (Tue Mar 09 2004 - 02:10:15 PST)
- Re: AMBER: MD simulation of a DNA decamer Vlad Cojocaru (Tue Mar 09 2004 - 02:35:25 PST)
- RE: AMBER: MD simulation of a DNA decamer Ross Walker (Tue Mar 09 2004 - 10:07:35 PST)
AMBER: what's the meaning of parameter NRUN scopio (Tue Mar 09 2004 - 05:40:51 PST)
- Re: AMBER: what's the meaning of parameter NRUN Carlos Simmerling (Tue Mar 09 2004 - 06:04:29 PST)
  - Re: AMBER: what's the meaning of parameter NRUN scopio (Tue Mar 09 2004 - 17:25:07 PST)
    - Re: AMBER: what's the meaning of parameter NRUN David A. Case (Tue Mar 09 2004 - 22:31:33 PST)
- Re: AMBER: what's the meaning of parameter NRUN David A. Case (Tue Mar 09 2004 - 07:23:56 PST)
AMBER: NMR restraint in sander Lishan Yao (Tue Mar 09 2004 - 06:19:30 PST)
- Re: AMBER: NMR restraint in sander Guanglei Cui (Tue Mar 09 2004 - 06:55:15 PST)
AMBER: Residue question opitz.che.udel.edu (Tue Mar 09 2004 - 08:29:22 PST)
- Re: AMBER: Residue question David A. Case (Wed Mar 10 2004 - 08:10:11 PST)
AMBER: mol2 vs. prepin opitz.che.udel.edu (Tue Mar 09 2004 - 08:53:46 PST)
- Re: AMBER: mol2 vs. prepin Guanglei Cui (Tue Mar 09 2004 - 09:05:22 PST)
AMBER: sander + child process died Carsten Detering (Tue Mar 09 2004 - 18:18:21 PST)
AMBER: positive binding free energy hj zou (Tue Mar 09 2004 - 22:43:58 PST)
- RE: AMBER: positive binding free energy Yong Duan (Wed Mar 10 2004 - 07:47:37 PST)
AMBER: Some questions in building a new residue Chung-Chien Wei (Wed Mar 10 2004 - 09:16:37 PST)
- Re: AMBER: Some questions in building a new residue Vlad Cojocaru (Wed Mar 10 2004 - 09:28:55 PST)
- Re: AMBER: Some questions in building a new residue Ilyas Yildirim (Wed Mar 10 2004 - 10:57:11 PST)
  - Re: AMBER: Some questions in building a new residue Chung-Chien Wei (Wed Mar 10 2004 - 11:49:33 PST)
    - Re: AMBER: Some questions in building a new residue FyD (Wed Mar 10 2004 - 12:31:25 PST)
AMBER: residue insertion Yunfeng Hu (Wed Mar 10 2004 - 16:24:52 PST)
- Re: AMBER: residue insertion David A. Case (Wed Mar 10 2004 - 23:00:39 PST)
  - Re: AMBER: residue insertion Scott Brozell (Fri Mar 19 2004 - 15:01:02 PST)
AMBER: positive binding free energy hj zou (Thu Mar 11 2004 - 05:59:09 PST)
- Re: AMBER: positive binding free energy Natasja Brooijmans (Thu Mar 11 2004 - 08:10:41 PST)
- Re: AMBER: positive binding free energy Jiri Sponer (Thu Mar 11 2004 - 09:02:18 PST)
AMBER: PMEMD COMPILATION REDHAT Obdulia Rabal (Thu Mar 11 2004 - 10:36:45 PST)
- Re: AMBER: PMEMD COMPILATION REDHAT Robert Duke (Thu Mar 11 2004 - 10:57:45 PST)
  - Re: AMBER: PMEMD COMPILATION REDHAT David Smith (Fri Mar 12 2004 - 05:55:13 PST)
AMBER: Atomic Charge in Residue opitz.che.udel.edu (Thu Mar 11 2004 - 11:29:21 PST)
AMBER: compiling on SGI Beale, John (Thu Mar 11 2004 - 13:26:22 PST)
- Re: AMBER: compiling on SGI Scott Brozell (Thu Mar 11 2004 - 14:24:36 PST)
AMBER: Resizing sizes.h and recompiling problem! Marco Aurelio Correia Preto (Sat Mar 13 2004 - 06:38:56 PST)
- Re: AMBER: Resizing sizes.h and recompiling problem! David A. Case (Sat Mar 13 2004 - 10:03:39 PST)
- Re: AMBER: Resizing sizes.h and recompiling problem! Stefano.Pieraccini.unimi.it (Sat Mar 13 2004 - 10:03:07 PST)
  - Re: AMBER: Resizing sizes.h and recompiling problem! Carlos Simmerling (Sat Mar 13 2004 - 11:24:44 PST)
AMBER: Anal module on PDBs Sanjeev B.S. (Sat Mar 13 2004 - 07:35:31 PST)
- RE: AMBER: Anal module on PDBs Sanjeev B.S. (Sat Mar 13 2004 - 11:25:07 PST)
Re: AMBER: Anal module on PDBs Bill Ross (Sat Mar 13 2004 - 16:17:25 PST)
AMBER: xleap couldn't display any word scopio (Sun Mar 14 2004 - 18:45:42 PST)
- Re: AMBER: xleap couldn't display any word John Bushnell (Mon Mar 15 2004 - 11:46:50 PST)
  - Re: AMBER: xleap couldn't display any word scopio (Mon Mar 15 2004 - 17:44:47 PST)
    - AMBER: About RESP Calculation Ilyas Yildirim (Thu Mar 18 2004 - 23:20:16 PST)
    - Re: AMBER: About RESP Calculation David A. Case (Fri Mar 19 2004 - 08:14:29 PST)
    - Re: AMBER: About RESP Calculation Ilyas Yildirim (Fri Mar 19 2004 - 11:50:13 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 12:10:19 PST)
    - Re: AMBER: About RESP Calculation David A. Case (Fri Mar 19 2004 - 12:15:39 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 12:30:00 PST)
    - Re: AMBER: About RESP Calculation Qing Zhang (Fri Mar 19 2004 - 22:43:03 PST)
    - Re: AMBER: About RESP Calculation FyD (Sat Mar 20 2004 - 23:30:41 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 09:45:22 PST)
AMBER: Release announcement for Amber 8 David A. Case (Sun Mar 14 2004 - 22:39:25 PST)
AMBER: new wed site for amber tutorials Juan Fernandez-Carmona (Mon Mar 15 2004 - 00:57:29 PST)
- Re: AMBER: new wed site for amber tutorials scopio (Mon Mar 15 2004 - 00:17:19 PST)
  - AMBER: Hydrogen Bond-statistics John (Mon Mar 15 2004 - 08:56:53 PST)
- Re: AMBER: new wed site for amber tutorials David A. Case (Mon Mar 15 2004 - 07:35:16 PST)
AMBER: How to convert charmm parameters to amber scopio (Mon Mar 15 2004 - 01:55:11 PST)
AMBER: [Fwd: No timings from jac test on opteron quad] Arvid Soderhall (Mon Mar 15 2004 - 05:28:02 PST)
AMBER: antechamber/mopac question opitz.che.udel.edu (Mon Mar 15 2004 - 12:20:24 PST)
- Re: AMBER: antechamber/mopac question David A. Case (Mon Mar 15 2004 - 17:56:51 PST)
AMBER: rdparm/ptraj writeparm david.evans.ulsop.ac.uk (Tue Mar 16 2004 - 00:57:16 PST)
- Re: AMBER: rdparm/ptraj writeparm Thomas E. Cheatham, III (Tue Mar 16 2004 - 09:04:47 PST)
  - Re: AMBER: rdparm/ptraj writeparm + leap problem david.evans.ulsop.ac.uk (Wed Mar 17 2004 - 01:36:51 PST)
    - Re: AMBER: rdparm/ptraj writeparm + leap problem David A. Case (Wed Mar 17 2004 - 08:33:34 PST)
    - Re: AMBER: rdparm/ptraj writeparm + leap problem david.evans.ulsop.ac.uk (Wed Mar 17 2004 - 08:50:16 PST)
AMBER: re:can i get help from you? hj zou (Tue Mar 16 2004 - 05:53:48 PST)
AMBER: literature question/residue charges opitz.che.udel.edu (Tue Mar 16 2004 - 12:09:43 PST)
- AMBER: AMBER6 manual Joseph Nachman (Tue Mar 16 2004 - 13:09:53 PST)
  - Re: AMBER: AMBER6 manual David A. Case (Tue Mar 16 2004 - 13:30:52 PST)
- AMBER: trajectory file Joseph Nachman (Tue Mar 16 2004 - 13:11:58 PST)
Re: AMBER: trajectory file Bill Ross (Tue Mar 16 2004 - 12:54:10 PST)
- Re: AMBER: trajectory file Joseph Nachman (Tue Mar 23 2004 - 14:38:28 PST)
- Re: AMBER: trajectory file Bill Ross (Tue Mar 23 2004 - 14:20:31 PST)
- Re: AMBER: trajectory file Joseph Nachman (Mon Mar 29 2004 - 09:16:58 PST)
  - Re: AMBER: trajectory file Andy Purkiss (Mon Mar 29 2004 - 08:54:24 PST)
  - Re: AMBER: trajectory file Rhonda Torres (Mon Mar 29 2004 - 10:03:03 PST)
Re: AMBER: literature question/residue charges Piotr Cieplak (Tue Mar 16 2004 - 14:07:21 PST)
AMBER: How to use these parameters? scopio (Tue Mar 16 2004 - 17:15:15 PST)
- Re: AMBER: How to use these parameters? Juan Fernandez-Carmona (Wed Mar 17 2004 - 00:41:39 PST)
  - Re: AMBER: How to use these parameters? scopio (Wed Mar 17 2004 - 01:31:28 PST)
AMBER: description of toplogy file format? Oliver Hucke (Tue Mar 16 2004 - 17:44:10 PST)
- Re: AMBER: description of toplogy file format? David A. Case (Tue Mar 16 2004 - 17:57:26 PST)
AMBER: segmentation fault with sander Carsten Detering (Tue Mar 16 2004 - 18:29:55 PST)
AMBER: MD problem. Osman Gani (Wed Mar 17 2004 - 03:07:47 PST)
- Re: AMBER: MD problem. David A. Case (Wed Mar 17 2004 - 08:36:04 PST)
AMBER: amber98 with amberffc+INSIGHT II a b (Wed Mar 17 2004 - 06:28:58 PST)
- Re: AMBER: amber98 with amberffc+INSIGHT II FyD (Wed Mar 17 2004 - 07:50:28 PST)
AMBER: protein-protein interaction Oscar Rey i Puiggròs (Wed Mar 17 2004 - 06:50:06 PST)
- Re: AMBER: protein-protein interaction David A. Case (Wed Mar 17 2004 - 08:37:40 PST)
AMBER: Preparing complex in Xleap for Amber calculations warka.il.waw.pl (Wed Mar 17 2004 - 08:02:38 PST)
- Re: AMBER: Preparing complex in Xleap for Amber calculations David A. Case (Wed Mar 17 2004 - 08:39:27 PST)
AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 Tom Turner (Wed Mar 17 2004 - 10:49:18 PST)
- Re: AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 David A. Case (Wed Mar 17 2004 - 11:26:00 PST)
AMBER: segmentation fault Hailong Lin (Thu Mar 18 2004 - 04:48:24 PST)
- Re: AMBER: segmentation fault David A. Case (Thu Mar 18 2004 - 08:19:04 PST)
AMBER: segmentation fault when convert pdb to mol2 Ye Mei (Thu Mar 18 2004 - 05:02:44 PST)
- Re: AMBER: segmentation fault when convert pdb to mol2 David A. Case (Thu Mar 18 2004 - 08:13:42 PST)
  - Re: Re: AMBER: segmentation fault when convert pdb to mol2 Ye Mei (Thu Mar 18 2004 - 16:38:21 PST)
Re: AMBER: segmentation fault Bill Ross (Thu Mar 18 2004 - 10:22:24 PST)
- Re: AMBER: segmentation fault Hailong Lin (Fri Mar 19 2004 - 04:41:50 PST)
  - Re: AMBER: segmentation fault Scott Brozell (Mon Mar 22 2004 - 18:10:27 PST)
  - Re: AMBER: segmentation fault Scott Brozell (Thu Mar 25 2004 - 14:33:32 PST)
AMBER: alignment problem using carnal xhu1.memphis.edu (Thu Mar 18 2004 - 11:48:55 PST)
AMBER: About RESP Calculation Chris Moth (Fri Mar 19 2004 - 13:38:40 PST)
- Re: AMBER: About RESP Calculation Piotr Cieplak (Fri Mar 19 2004 - 12:20:42 PST)
AMBER: EWALD BOMB? Ryan Ye (Sat Mar 20 2004 - 11:28:01 PST)
- Re: AMBER: EWALD BOMB? Martina Roeselova (Mon Mar 22 2004 - 11:42:01 PST)
- Re: AMBER: EWALD BOMB? scott.brown.abbott.com (Mon Mar 22 2004 - 12:21:21 PST)
- Re: AMBER: EWALD BOMB? Scott Brozell (Mon Mar 22 2004 - 12:44:51 PST)
AMBER: langevin dynamics Wei Fu (Sun Mar 21 2004 - 19:22:27 PST)
- Re: AMBER: langevin dynamics David A. Case (Tue Mar 23 2004 - 14:33:01 PST)
  - Re: AMBER: langevin dynamics Wei Fu (Tue Mar 23 2004 - 18:39:44 PST)
AMBER: Compilation problem in SUN OS 5.7! Pradipta Bandyopadhyay (Mon Mar 22 2004 - 00:48:59 PST)
- Re: AMBER: Compilation problem in SUN OS 5.7! Scott Brozell (Mon Mar 22 2004 - 13:57:03 PST)
AMBER: Assignment of parameters, missing parameters Julien Michel (Mon Mar 22 2004 - 07:47:15 PST)
- Re: AMBER: Assignment of parameters, missing parameters David A. Case (Tue Mar 23 2004 - 14:28:59 PST)
AMBER: gibbs dynamic memory error jwfang (Mon Mar 22 2004 - 08:43:46 PST)
AMBER: Re: About RESP Calculation FyD (Mon Mar 22 2004 - 09:09:00 PST)
AMBER: SANDER general questions. Osman Gani (Mon Mar 22 2004 - 09:37:18 PST)
- Re: AMBER: SANDER general questions. Scott Brozell (Mon Mar 22 2004 - 13:26:55 PST)
AMBER: [Fwd: KLAMBDA in amber7] Ahammadunny Pathiaseril (Mon Mar 22 2004 - 10:44:11 PST)
- Re: AMBER: [Fwd: KLAMBDA in amber7] David A. Case (Wed Mar 24 2004 - 17:38:10 PST)
AMBER: downloading antechamber astrid.maass (Mon Mar 22 2004 - 23:53:56 PST)
- Re: AMBER: downloading antechamber David A. Case (Tue Mar 23 2004 - 14:20:34 PST)
AMBER: M7G parameters Vlad Cojocaru (Tue Mar 23 2004 - 04:43:55 PST)
- Re: AMBER: M7G parameters David A. Case (Tue Mar 23 2004 - 14:16:24 PST)
AMBER: Residue Charges opitz.che.udel.edu (Tue Mar 23 2004 - 07:17:38 PST)
- Re: AMBER: Residue Charges Rhonda Torres (Tue Mar 23 2004 - 09:51:55 PST)
AMBER: About glycam2004 Javier Perez Miron (Wed Mar 17 2004 - 19:02:47 PST)
- RE: AMBER: About glycam2004 Ross Walker (Tue Mar 23 2004 - 10:11:01 PST)
AMBER: gibbs error Fang, Jianwen (Tue Mar 23 2004 - 08:27:22 PST)
AMBER: How to make leap recognise inosine? arvind.mbu.iisc.ernet.in (Tue Mar 23 2004 - 09:33:40 PST)
- Re: AMBER: How to make leap recognise inosine? Rhonda Torres (Tue Mar 23 2004 - 09:54:49 PST)
Re: AMBER: How to make leap recognise inosine? Bill Ross (Tue Mar 23 2004 - 09:57:27 PST)
AMBER: residence time Ioana Cozmuta (Tue Mar 23 2004 - 19:51:10 PST)
AMBER: fluorine in mmpbsa ferranna.unimore.it (Wed Mar 24 2004 - 01:49:27 PST)
AMBER: Amber: Equilibrated DMSO solvent box Marco Aurelio Correia Preto (Wed Mar 24 2004 - 03:32:31 PST)
- Re: AMBER: Amber: Equilibrated DMSO solvent box Jiten (Wed Mar 24 2004 - 05:37:30 PST)
AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 24 2004 - 04:38:08 PST)
- Re: AMBER: non-isotropic pressure scaling Robert Duke (Wed Mar 24 2004 - 05:44:35 PST)
  - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 24 2004 - 06:33:20 PST)
  - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 31 2004 - 11:44:19 PST)
    - Re: AMBER: non-isotropic pressure scaling Robert Duke (Wed Mar 31 2004 - 12:35:14 PST)
AMBER: Cadmium Beale, John (Wed Mar 24 2004 - 05:10:36 PST)
AMBER: make sure of the Magnesium parameters sychen (Wed Mar 24 2004 - 10:15:25 PST)
- Re: AMBER: make sure of the Magnesium parameters Rhonda Torres (Wed Mar 24 2004 - 10:53:55 PST)
  - AMBER: INtel Fortran 90 compiler Carsten Detering (Wed Mar 24 2004 - 11:03:17 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 12:36:35 PST)
    - Re: AMBER: INtel Fortran 90 compiler Scott Brozell (Wed Mar 24 2004 - 13:37:37 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 14:01:54 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 14:54:01 PST)
    - Re: AMBER: INtel Fortran 90 compiler Bill Ross (Wed Mar 24 2004 - 13:41:30 PST)
AMBER: vlimit and vmax problem Venkata S Koppuravuri (Wed Mar 24 2004 - 10:25:31 PST)
- Re: AMBER: vlimit and vmax problem Rhonda Torres (Wed Mar 24 2004 - 13:05:20 PST)
- Re: AMBER: vlimit and vmax problem Bill Ross (Wed Mar 24 2004 - 13:17:32 PST)
AMBER: Glycam04 Karl N. Kirschner (Wed Mar 24 2004 - 11:37:56 PST)
AMBER: PMEMD and myrinet trouble Chris Moth (Wed Mar 24 2004 - 13:25:57 PST)
- Re: AMBER: PMEMD and myrinet trouble Robert Duke (Wed Mar 24 2004 - 13:56:10 PST)
  - AMBER: PMEMD and myrinet trouble Chris Moth (Mon Mar 29 2004 - 11:05:07 PST)
    - Re: AMBER: PMEMD and myrinet trouble Robert Duke (Mon Mar 29 2004 - 11:16:36 PST)
AMBER: antechamber download files should now be available David A. Case (Wed Mar 24 2004 - 15:05:19 PST)
- AMBER: Antechamber license ? Julien Michel (Thu Mar 25 2004 - 02:24:30 PST)
AMBER: RE: Amber: Equilibrated DMSO solvent box Marco Aurelio Correia Preto (Thu Mar 25 2004 - 01:26:41 PST)
AMBER: MM_PBSA GB parameters david.evans.ulsop.ac.uk (Thu Mar 25 2004 - 02:54:59 PST)
- Re: AMBER: MM_PBSA GB parameters david.evans.ulsop.ac.uk (Thu Mar 25 2004 - 08:25:56 PST)
AMBER: phosphorylated serin / histidin Nadine Homeyer (Thu Mar 25 2004 - 05:04:38 PST)
AMBER: FW: Problems with antechamber innstallation Osman Gani (Thu Mar 25 2004 - 07:12:20 PST)
AMBER: Antechamber MOPAC Beale, John (Thu Mar 25 2004 - 07:24:56 PST)
- Re: AMBER: Antechamber MOPAC David A. Case (Thu Mar 25 2004 - 16:34:53 PST)
AMBER: hbond analysis in ptraj(%occupied>1) Lishan Yao (Thu Mar 25 2004 - 07:19:01 PST)
- Re: AMBER: hbond analysis in ptraj(%occupied>1) Thomas E. Cheatham, III (Thu Mar 25 2004 - 10:26:50 PST)
  - Re: AMBER: hbond analysis in ptraj(%occupied>1) Sichun Yang (Thu Mar 25 2004 - 10:46:01 PST)
  - Re: AMBER: hbond analysis in ptraj(%occupied>1) Lishan Yao (Thu Mar 25 2004 - 10:54:59 PST)
    - AMBER: GIBBS: FEP and TI Miguel de Federico (Mon Mar 29 2004 - 09:03:53 PST)
    - Re: AMBER: GIBBS: FEP and TI David A. Case (Wed Mar 31 2004 - 11:07:17 PST)
AMBER: undefined loops and protonate Stern, Julie (Thu Mar 25 2004 - 09:52:41 PST)
- Re: AMBER: undefined loops and protonate David A. Case (Thu Mar 25 2004 - 16:37:47 PST)
AMBER: eedmeth atchara.mercury.hec.utah.edu (Thu Mar 25 2004 - 10:53:23 PST)
- Re: AMBER: eedmeth David A. Case (Thu Mar 25 2004 - 16:46:44 PST)
AMBER: Error while protonating a PDB file Mike (Thu Mar 25 2004 - 15:47:54 PST)
- Re: AMBER: Error while protonating a PDB file David A. Case (Thu Mar 25 2004 - 17:34:43 PST)
  - Re: AMBER: Error while protonating a PDB file Madan (Thu Mar 25 2004 - 21:03:56 PST)
    - Re: AMBER: Error while protonating a PDB file David A. Case (Sat Mar 27 2004 - 14:46:43 PST)
AMBER: Pang-model of Zn2+ Oliver Hucke (Thu Mar 25 2004 - 17:04:48 PST)
- Re: AMBER: Pang-model of Zn2+ Peter Oelschlaeger (Thu Mar 25 2004 - 17:44:01 PST)
  - Re: AMBER: Pang-model of Zn2+ Kennie Merz (Fri Mar 26 2004 - 05:52:43 PST)
AMBER: Pang Zn2+ model - correction Oliver Hucke (Thu Mar 25 2004 - 17:32:30 PST)
AMBER: a question about anal Xiao He (Thu Mar 25 2004 - 19:06:10 PST)
- RE: AMBER: a question about anal Chris Moth (Thu Mar 25 2004 - 19:54:51 PST)
AMBER: nmanal - segmentation fault Sivakolundu, Sivashankar (Thu Mar 25 2004 - 22:11:16 PST)
AMBER: tleap error and warnings Mike (Thu Mar 25 2004 - 23:06:38 PST)
- RE: AMBER: tleap error and warnings Chris Moth (Fri Mar 26 2004 - 07:34:08 PST)
AMBER: How to compile antechamber? scopio (Thu Mar 25 2004 - 23:17:54 PST)
- Re: AMBER: How to compile antechamber? Julien Michel (Fri Mar 26 2004 - 02:35:11 PST)
  - Re: AMBER: How to compile antechamber? David A. Case (Fri Mar 26 2004 - 09:56:10 PST)
AMBER: Problem solved Xiao He (Fri Mar 26 2004 - 07:35:01 PST)
Be Smart job Access (Fri Mar 26 2004 - 09:26:13 PST)
AMBER: Xiaowei Li (Fri Mar 26 2004 - 12:21:08 PST)
- Re: AMBER: David A. Case (Fri Mar 26 2004 - 13:41:32 PST)
  - Re: AMBER: Xiaowei Li (Fri Mar 26 2004 - 19:53:54 PST)
Re: Fwd: Re: AMBER: Pang-model of Zn2+ Oliver Hucke (Fri Mar 26 2004 - 13:29:24 PST)
- Re: Fwd: Re: AMBER: Pang-model of Zn2+ David A. Case (Fri Mar 26 2004 - 14:18:35 PST)
AMBER: questions for PNA parameters Suwipa saen-oon (Fri Mar 26 2004 - 19:36:56 PST)
AMBER: erreo in sander Anshul Awasthi (Sat Mar 27 2004 - 05:15:54 PST)
- Re: AMBER: erreo in sander David A. Case (Sat Mar 27 2004 - 01:13:20 PST)
AMBER: solvation energy hj zou (Sun Mar 28 2004 - 09:36:31 PST)
- Re: AMBER: solvation energy David A. Case (Sun Mar 28 2004 - 21:15:25 PST)
AMBER: fix two groups Helios Chen (Sun Mar 28 2004 - 19:07:07 PST)
- Re: AMBER: fix two groups Carlos Simmerling (Sun Mar 28 2004 - 19:16:17 PST)
  - Re: AMBER: fix two groups Helios Chen (Sun Mar 28 2004 - 20:54:58 PST)
- Re: AMBER: fix two groups Bill Ross (Sun Mar 28 2004 - 21:35:00 PST)
- Re: AMBER: fix two groups Joseph Nachman (Mon Mar 29 2004 - 08:14:33 PST)
AMBER: pmemd machinefiles Lubos Vrbka (Mon Mar 29 2004 - 02:38:13 PST)
- Re: AMBER: pmemd machinefiles Robert Duke (Mon Mar 29 2004 - 04:51:56 PST)
  - Re: AMBER: pmemd machinefiles Lubos Vrbka (Mon Mar 29 2004 - 05:34:50 PST)
    - Re: AMBER: pmemd machinefiles Robert Duke (Mon Mar 29 2004 - 06:27:17 PST)
- AMBER: HBOND calculation John (Mon Mar 29 2004 - 09:40:26 PST)
  - Re: AMBER: HBOND calculation Rhonda Torres (Mon Mar 29 2004 - 10:28:19 PST)
AMBER: radial distribution franck (Mon Mar 29 2004 - 05:20:48 PST)
Re: AMBER: HBOND calculation Bill Ross (Mon Mar 29 2004 - 10:24:59 PST)
AMBER: segmentation fault of minimization scopio (Mon Mar 29 2004 - 18:57:39 PST)
- Re: AMBER: segmentation fault of minimization Thomas E. Cheatham, III (Mon Mar 29 2004 - 19:42:01 PST)
AMBER: gaff: hydrogen atom types astrid.maass (Mon Mar 29 2004 - 23:37:58 PST)
AMBER: segmentation fault when running parmchk Ye Mei (Tue Mar 30 2004 - 01:52:14 PST)
- Re: AMBER: segmentation fault when running parmchk David A. Case (Wed Mar 31 2004 - 09:50:54 PST)
AMBER: Bad atom symbol, K+ and IB in vacuum Skauge Tormod (Tue Mar 30 2004 - 04:50:42 PST)
- Re: AMBER: Bad atom symbol, K+ and IB in vacuum Rhonda Torres (Tue Mar 30 2004 - 10:30:23 PST)
  - Re: AMBER: Bad atom symbol, K+ and IB in vacuum Skauge Tormod (Wed Mar 31 2004 - 04:20:30 PST)
- Re: AMBER: Bad atom symbol, K+ and IB in vacuum David A. Case (Wed Mar 31 2004 - 10:38:47 PST)
AMBER: solvation energy hj zou (Tue Mar 30 2004 - 04:55:20 PST)
- AMBER: NMR refinement John (Tue Mar 30 2004 - 06:32:55 PST)
AMBER: pmemd speedup and interactions Lubos Vrbka (Wed Mar 31 2004 - 01:27:21 PST)
- RE: AMBER: pmemd speedup and interactions Ross Walker (Wed Mar 31 2004 - 09:42:32 PST)
AMBER: pmemd speedup and interactions Lubos Vrbka (Wed Mar 31 2004 - 01:55:14 PST)
- Re: AMBER: pmemd speedup and interactions Robert Duke (Wed Mar 31 2004 - 12:03:39 PST)
AMBER: Pasrameters for MAI Anshul Awasthi (Wed Mar 31 2004 - 13:46:18 PST)
AMBER: test output of amber8 Oliver Hucke (Wed Mar 31 2004 - 15:54:38 PST)
- Re: AMBER: test output of amber8 David A. Case (Wed Mar 31 2004 - 17:37:50 PST)
AMBER: about glycam 04 Javier Perez Miron (Mon Mar 29 2004 - 09:40:18 PST)

Amber Archive Mar 2004 By Thread