Amber Archive Sep 2006: By Thread

Re: AMBER: Question about free energy with mm_pbsa Thomas Cheatham (Thu Aug 31 2006 - 23:23:59 PDT)
- Re: AMBER: Question about free energy with mm_pbsa William Wei (Fri Sep 01 2006 - 06:32:29 PDT)
AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c Jiten (Thu Aug 31 2006 - 23:55:21 PDT)
- Re: AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c David A. Case (Fri Sep 01 2006 - 07:34:10 PDT)
AMBER: force fields for proflavine molecule sethl.gatech.edu (Fri Sep 01 2006 - 10:49:00 PDT)
AMBER: output file not generated bala (Fri Sep 01 2006 - 08:35:40 PDT)
AMBER: Gaussian, antechamber, RESP Ed Pate (Sat Sep 02 2006 - 14:42:11 PDT)
- Re: AMBER: Gaussian, antechamber, RESP Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Sun Sep 03 2006 - 05:57:57 PDT)
AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sat Sep 02 2006 - 18:52:45 PDT)
- Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sat Sep 02 2006 - 22:06:04 PDT)
  - Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sat Sep 02 2006 - 23:20:27 PDT)
    - Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sun Sep 03 2006 - 08:55:16 PDT)
    - Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Wed Sep 06 2006 - 01:46:57 PDT)
AMBER: Amber9: Free Energy Franck_Vendeix.ncsu.edu (Sun Sep 03 2006 - 16:11:44 PDT)
- Re: AMBER: Amber9: Free Energy David A. Case (Sun Sep 03 2006 - 18:57:50 PDT)
  - Re: AMBER: Amber9: Free Energy Franck_Vendeix.ncsu.edu (Sun Sep 03 2006 - 19:27:13 PDT)
AMBER: ligand file Fenghui Fan (Mon Sep 04 2006 - 11:20:27 PDT)
- Re: AMBER: ligand file David A. Case (Mon Sep 04 2006 - 12:02:34 PDT)
AMBER: cAMP ligand file Fenghui Fan (Mon Sep 04 2006 - 13:00:47 PDT)
AMBER: Implicit Water - Force field parameters Ramdas Pophale (Tue Sep 05 2006 - 12:22:49 PDT)
- Re: AMBER: Implicit Water - Force field parameters Fenghui Fan (Tue Sep 05 2006 - 13:16:37 PDT)
- Re: AMBER: Implicit Water - Force field parameters Ilyas Yildirim (Tue Sep 05 2006 - 13:22:13 PDT)
- Re: AMBER: Implicit Water - Force field parameters David A. Case (Wed Sep 06 2006 - 08:54:15 PDT)
AMBER: a ligand file Fenghui Fan (Tue Sep 05 2006 - 13:18:51 PDT)
- Re: AMBER: a ligand file David A. Case (Tue Sep 05 2006 - 13:55:26 PDT)
  - Re: AMBER: a ligand file Fenghui Fan (Wed Sep 06 2006 - 14:16:58 PDT)
    - Re: AMBER: a ligand file David A. Case (Wed Sep 06 2006 - 14:40:30 PDT)
AMBER: help with antechamber - creating ligand sethl.gatech.edu (Tue Sep 05 2006 - 14:10:08 PDT)
- Re: AMBER: help with antechamber - creating ligand Ilyas Yildirim (Tue Sep 05 2006 - 14:26:11 PDT)
- Re: AMBER: help with antechamber - creating ligand David A. Case (Tue Sep 05 2006 - 19:11:52 PDT)
AMBER: Amber parallel version Franck_Vendeix.ncsu.edu (Tue Sep 05 2006 - 23:05:20 PDT)
- Re: AMBER: Amber parallel version Jyh-Shyong Ho (Tue Sep 05 2006 - 23:43:08 PDT)
  - Re: AMBER: Amber parallel version Franck_Vendeix.ncsu.edu (Thu Sep 07 2006 - 11:45:47 PDT)
AMBER: PARAMETERISATION PROBLEM Claire Zerafa (Wed Sep 06 2006 - 07:12:04 PDT)
- Re: AMBER: PARAMETERISATION PROBLEM David A. Case (Wed Sep 06 2006 - 08:20:43 PDT)
AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 10:41:12 PDT)
- Re: AMBER: Question about using PMEMD and GB David A. Case (Wed Sep 06 2006 - 10:58:59 PDT)
  - Re: AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 11:31:20 PDT)
AMBER: improper torsion angle problem Fabian Alejandro Rodriguez (Wed Sep 06 2006 - 14:52:40 PDT)
- Re: AMBER: improper torsion angle problem David A. Case (Sun Sep 17 2006 - 16:52:38 PDT)
AMBER: trajout Weihua Li (Wed Sep 06 2006 - 20:22:28 PDT)
- Re: AMBER: trajout Carlos Simmerling (Thu Sep 07 2006 - 04:04:02 PDT)
AMBER: Ca2+ polarizability Martin LEPSIK (Thu Sep 07 2006 - 02:02:38 PDT)
AMBER: mdcrd file Jianhui (Thu Sep 07 2006 - 07:15:45 PDT)
- Re: AMBER: mdcrd file Mark Williamson (Thu Sep 07 2006 - 10:39:12 PDT)
  - Re: AMBER: mdcrd file Brent Krueger (Thu Sep 07 2006 - 19:55:27 PDT)
    - Re: AMBER: mdcrd file David A. Case (Thu Sep 07 2006 - 22:27:54 PDT)
    - Re: AMBER: mdcrd file Joseph Nachman (Fri Sep 08 2006 - 10:36:42 PDT)
    - Re: AMBER: mdcrd file Carlos Simmerling (Fri Sep 08 2006 - 13:54:34 PDT)
    - Re: AMBER: mdcrd file Joseph Nachman (Mon Sep 11 2006 - 11:00:21 PDT)
- RE: AMBER: mdcrd file Ross Walker (Thu Sep 07 2006 - 15:52:28 PDT)
AMBER: Re: FF problem: RG residue minimizes to non-planar structure David A. Case (Thu Sep 07 2006 - 11:53:33 PDT)
AMBER: leap - how to recognize my structure sethl.gatech.edu (Thu Sep 07 2006 - 15:16:06 PDT)
- Re: AMBER: leap - how to recognize my structure Carlos Simmerling (Thu Sep 07 2006 - 15:34:09 PDT)
AMBER: nmode memory allocation error AYTUG TUNCEL (Fri Sep 08 2006 - 01:41:35 PDT)
- Re: AMBER: nmode memory allocation error David A. Case (Sat Sep 09 2006 - 21:17:54 PDT)
- Re: AMBER: nmode memory allocation error Cenk Andac (Mon Sep 11 2006 - 02:48:30 PDT)
AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 07:15:32 PDT)
- Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 07:31:33 PDT)
  - Re: AMBER: hydronium ion parameters Jiten (Fri Sep 08 2006 - 08:12:03 PDT)
    - Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 09:09:55 PDT)
  - Re: AMBER: hydronium ion parameters Ilyas Yildirim (Fri Sep 08 2006 - 13:41:17 PDT)
AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 14:00:19 PDT)
- Re: AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 21:35:28 PDT)
- Re: AMBER: Problem with ptraj Thomas Cheatham (Tue Sep 12 2006 - 19:47:46 PDT)
AMBER: LEAP - "could not find type: NH" sethl.gatech.edu (Fri Sep 08 2006 - 14:08:11 PDT)
- Re: AMBER: LEAP - "could not find type: NH" Ilyas Yildirim (Fri Sep 08 2006 - 15:42:46 PDT)
AMBER: seg fault during test.serial Lachele Foley (Lists) (Fri Sep 08 2006 - 13:45:05 PDT)
- Re: AMBER: seg fault during test.serial David A. Case (Fri Sep 08 2006 - 18:19:16 PDT)
  - AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 18:31:59 PDT)
    - Re: AMBER: a ligand file David A. Case (Fri Sep 08 2006 - 18:53:18 PDT)
    - Re: AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 20:06:49 PDT)
    - Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 21:05:11 PDT)
    - Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 19:23:48 PDT)
  - Re: AMBER: seg fault during test.serial Lachele Foley (Lists) (Mon Sep 11 2006 - 07:50:57 PDT)
    - Re: AMBER: seg fault during test.serial David A. Case (Mon Sep 11 2006 - 08:54:43 PDT)
AMBER: pmf with respect to a surface Rahaman, Asif (Fri Sep 08 2006 - 15:35:22 PDT)
- Re: AMBER: pmf with respect to a surface David A. Case (Sat Sep 09 2006 - 21:14:30 PDT)
AMBER: post nmanal $B?y?9.5F;(B (Fri Sep 08 2006 - 23:03:47 PDT)
- Re: AMBER: post nmanal David A. Case (Sat Sep 09 2006 - 09:54:34 PDT)
  - Re: AMBER: post nmanal $B?y?9.5F;(B (Sun Sep 10 2006 - 23:09:28 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 02:00:08 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 01:57:43 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 02:01:34 PDT)
AMBER: protein-ligand interaction Fenghui Fan (Sat Sep 09 2006 - 09:59:51 PDT)
- Re: AMBER: protein-ligand interaction Ilyas Yildirim (Sat Sep 09 2006 - 14:58:10 PDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 18:03:06 PDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 18:07:48 PDT)
- Re: AMBER: resp FyD (Sun Sep 10 2006 - 00:46:11 PDT)
AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Sun Sep 10 2006 - 17:23:25 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Mon Sep 11 2006 - 13:48:51 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 08:54:08 PDT)
    - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 10:10:55 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 11:41:21 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 12:30:02 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Piotr Cieplak (Wed Sep 20 2006 - 20:46:19 PDT)
    - Re: AMBER: Parmchk problems (parm99.dat) David A. Case (Wed Sep 20 2006 - 21:22:56 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 13:44:30 PDT)
AMBER: (no subject) Prashanth Athri (Sun Sep 10 2006 - 17:23:05 PDT)
AMBER: Oon Modeling the metalloprotein with GB model. wenfei Li (Mon Sep 11 2006 - 00:41:16 PDT)
- AMBER: mm_pbsa snapshots for "three-trajectory" In Hee Park (Thu Sep 14 2006 - 16:42:13 PDT)
AMBER: Error in Running Sander Jianhui Tian (Mon Sep 11 2006 - 06:52:39 PDT)
- Re: AMBER: Error in Running Sander David A. Case (Mon Sep 11 2006 - 08:59:45 PDT)
- Re: AMBER: Error in Running Sander Jianhui (Mon Sep 11 2006 - 10:10:55 PDT)
AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Mon Sep 11 2006 - 07:24:44 PDT)
- AMBER: How to get the ligand. ac file Fenghui Fan (Mon Sep 11 2006 - 07:46:54 PDT)
- Re: AMBER: set a trucated octahedron box in Leap David A. Case (Mon Sep 11 2006 - 08:56:59 PDT)
  - Re: AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Tue Sep 12 2006 - 01:30:06 PDT)
    - Re: AMBER: set a trucated octahedron box in Leap Ilyas Yildirim (Tue Sep 12 2006 - 01:48:56 PDT)
    - Re: AMBER: set a trucated octahedron box in Leap David A. Case (Tue Sep 12 2006 - 08:03:24 PDT)
AMBER: cAMP ligand charge Fenghui Fan (Mon Sep 11 2006 - 08:06:40 PDT)
- Re: AMBER: cAMP ligand charge David A. Case (Mon Sep 11 2006 - 08:35:53 PDT)
AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 08:38:00 PDT)
- Re: AMBER: Parallel compile: ld: cannot find -lfmpi David A. Case (Mon Sep 11 2006 - 11:19:12 PDT)
  - Re: AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 13:39:55 PDT)
AMBER: System in polarizable waters Martin LEPSIK (Mon Sep 11 2006 - 09:14:24 PDT)
- Re: AMBER: System in polarizable waters David A. Case (Mon Sep 11 2006 - 11:12:04 PDT)
AMBER: angle between helices ÕÅÓÂ (Mon Sep 11 2006 - 19:05:51 PDT)
AMBER: Installing AMBER9 on cygwin (WinXP) HARADA Makoto (Tue Sep 12 2006 - 02:38:19 PDT)
- Re: AMBER: Installing AMBER9 on cygwin (WinXP) Gobind Singh Bisht (Tue Sep 12 2006 - 04:57:06 PDT)
- Re: AMBER: Installing AMBER9 on cygwin (WinXP) David A. Case (Tue Sep 12 2006 - 08:01:41 PDT)
AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 14:09:34 PDT)
- RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ross Walker (Tue Sep 12 2006 - 14:35:47 PDT)
  - RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 15:49:33 PDT)
AMBER: about ligand charge Fenghui Fan (Tue Sep 12 2006 - 20:16:27 PDT)
AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 priya priya (Wed Sep 13 2006 - 02:02:33 PDT)
- AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Hannes Barsch (Wed Sep 13 2006 - 06:54:54 PDT)
- Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Ilyas Yildirim (Wed Sep 13 2006 - 10:59:10 PDT)
AMBER: 'lastrst' error for amber8 Arvind Marathe (Wed Sep 13 2006 - 05:52:07 PDT)
- Re: AMBER: 'lastrst' error for amber8 michael crowley (Wed Sep 13 2006 - 08:14:08 PDT)
  - Re: AMBER: 'lastrst' error for amber8 Robert Duke (Wed Sep 13 2006 - 08:28:16 PDT)
  - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Thu Sep 14 2006 - 06:08:08 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Thu Sep 14 2006 - 08:05:25 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Fri Sep 15 2006 - 13:01:43 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Sat Sep 16 2006 - 09:50:31 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Sun Sep 17 2006 - 05:02:09 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Sun Sep 17 2006 - 23:50:41 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 08:44:49 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 09:25:33 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 09:41:56 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 10:44:11 PDT)
AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 05:57:44 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Wed Sep 13 2006 - 09:32:39 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 20:21:07 PDT)
  - Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Wed Sep 13 2006 - 22:53:50 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 23:47:07 PDT)
AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Fenghui Fan (Wed Sep 13 2006 - 07:23:33 PDT)
- Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Thomas Cheatham (Wed Sep 13 2006 - 08:48:54 PDT)
  - AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 13:24:14 PDT)
    - Re: AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 14:07:52 PDT)
    - Re: AMBER: MAXM in nmode David A. Case (Wed Sep 13 2006 - 14:17:29 PDT)
AMBER: RDC refinement Young-Tae Lee (Wed Sep 13 2006 - 08:13:30 PDT)
- Re: AMBER: RDC refinement David A. Case (Wed Sep 13 2006 - 08:35:07 PDT)
AMBER: energy data for limited part of system Tanya Johannsen (Wed Sep 13 2006 - 10:57:15 PDT)
- Re: AMBER: energy data for limited part of system David A. Case (Sun Sep 17 2006 - 16:56:23 PDT)
  - AMBER: potential energy Fenghui Fan (Sun Sep 17 2006 - 17:38:44 PDT)
    - RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 08:52:23 PDT)
    - Re: RE: AMBER: potential energy linfu (Mon Sep 18 2006 - 18:44:18 PDT)
    - Re: [UCE]Re: RE: AMBER: potential energy Thomas Cheatham (Mon Sep 18 2006 - 19:16:20 PDT)
    - Re: [UCE]Re: RE: AMBER: potential energy Fenghui Fan (Mon Sep 18 2006 - 19:41:09 PDT)
    - RE: [UCE]Re: RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 21:01:04 PDT)
    - Re: RE: AMBER: potential energy Thomas Cheatham (Tue Sep 19 2006 - 09:57:47 PDT)
AMBER: residence time of water molecules venditti2.unisi.it (Wed Sep 13 2006 - 07:56:34 PDT)
- Re: AMBER: residence time of water molecules Angelo (Thu Sep 14 2006 - 01:57:38 PDT)
AMBER: the time length of the restricted MD Fenghui Fan (Wed Sep 13 2006 - 12:38:59 PDT)
AMBER: Mixed solvent? Mingfeng Yang (Wed Sep 13 2006 - 12:44:32 PDT)
AMBER: Error in reading RDC data Lee, Young-Tae (Wed Sep 13 2006 - 13:09:42 PDT)
- Re: AMBER: Error in reading RDC data David A. Case (Wed Sep 13 2006 - 14:44:14 PDT)
AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Wed Sep 13 2006 - 13:42:02 PDT)
- Re: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Thu Sep 14 2006 - 01:15:43 PDT)
AMBER: pqr from constant pH MD harianto (Wed Sep 13 2006 - 14:43:13 PDT)
AMBER: MD on protein-ligand interaction Fenghui Fan (Thu Sep 14 2006 - 07:04:20 PDT)
- Re: AMBER: MD on protein-ligand interaction Ilyas Yildirim (Thu Sep 14 2006 - 12:09:14 PDT)
AMBER: potential energy in the MD result Fenghui Fan (Thu Sep 14 2006 - 07:39:12 PDT)
AMBER: pmemd error bala (Thu Sep 14 2006 - 08:34:12 PDT)
- Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 09:46:40 PDT)
- Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 09:46:30 PDT)
AMBER: addions default settings. asli ertekin (Thu Sep 14 2006 - 08:37:47 PDT)
Re: AMBER: addions default settings. Bill Ross (Thu Sep 14 2006 - 10:14:18 PDT)
AMBER: acidifying a water box Eric Shamay (Thu Sep 14 2006 - 11:36:11 PDT)
- Re: AMBER: acidifying a water box David A. Case (Thu Sep 14 2006 - 15:21:01 PDT)
- Re: AMBER: acidifying a water box Thomas Cheatham (Thu Sep 14 2006 - 15:56:32 PDT)
  - Re: AMBER: acidifying a water box Eric Shamay (Fri Sep 15 2006 - 01:49:15 PDT)
AMBER: DPPC Bilayer size Akshay Patny (Thu Sep 14 2006 - 11:47:45 PDT)
AMBER: Denaturing MD Fenghui Fan (Thu Sep 14 2006 - 15:58:35 PDT)
- Re: AMBER: Denaturing MD Thomas Cheatham (Thu Sep 14 2006 - 16:55:59 PDT)
AMBER: on the rst file of the current ruuning Fenghui Fan (Thu Sep 14 2006 - 20:33:50 PDT)
- RE: AMBER: on the rst file of the current ruuning Ross Walker (Mon Sep 18 2006 - 08:58:01 PDT)
AMBER: Temperature not rising enough during simulated annealing Adam Pelzer (Thu Sep 14 2006 - 20:30:12 PDT)
- Re: [UCE]AMBER: Temperature not rising enough during simulated annealing Thomas Cheatham (Thu Sep 14 2006 - 21:33:42 PDT)
AMBER: cyclic AMP off and frcmod files? Daniel Lee (Thu Sep 14 2006 - 20:52:33 PDT)
- Re: AMBER: cyclic AMP off and frcmod files? Fenghui Fan (Fri Sep 15 2006 - 06:44:49 PDT)
  - AMBER: have problems with restrained minimization Abhilash (Fri Sep 15 2006 - 11:10:50 PDT)
  - Re: AMBER: cyclic AMP off and frcmod files? Daniel Lee (Sun Sep 17 2006 - 19:10:28 PDT)
AMBER: restraints and constant pressure Joshua (Thu Sep 14 2006 - 22:44:09 PDT)
- Re: AMBER: restraints and constant pressure Thomas Cheatham (Thu Sep 14 2006 - 23:22:02 PDT)
- Re: AMBER: restraints and constant pressure Joshua (Fri Sep 15 2006 - 02:09:44 PDT)
  - Re: AMBER: restraints and constant pressure Myunggi Yi (Fri Sep 15 2006 - 12:52:21 PDT)
  - Re: AMBER: restraints and constant pressure Thomas Cheatham (Sat Sep 16 2006 - 21:38:06 PDT)
    - Re: AMBER: restraints and constant pressure Myunggi Yi (Sat Sep 16 2006 - 23:29:38 PDT)
    - Re: AMBER: restraints and constant pressure Carlos Simmerling (Sun Sep 17 2006 - 07:01:54 PDT)
    - Re: AMBER: restraints and constant pressure Myunggi Yi (Sun Sep 17 2006 - 07:23:33 PDT)
AMBER: About Lennard-Jones Parameters Jianhui (Fri Sep 15 2006 - 14:08:13 PDT)
- Re: AMBER: About Lennard-Jones Parameters David A. Case (Fri Sep 15 2006 - 17:07:35 PDT)
AMBER: distance between two atoms Fenghui Fan (Fri Sep 15 2006 - 13:49:11 PDT)
AMBER: Problems with a restrained minimization approach Abhilash (Fri Sep 15 2006 - 12:35:34 PDT)
- Re: AMBER: Problems with a restrained minimization approach David A. Case (Fri Sep 15 2006 - 17:41:04 PDT)
AMBER: new article on Amber force fields Carlos Simmerling (Fri Sep 15 2006 - 12:47:34 PDT)
AMBER: change mdcrd file to pdb file Fenghui Fan (Sat Sep 16 2006 - 22:02:54 PDT)
- Re: AMBER: change mdcrd file to pdb file Ilyas Yildirim (Sat Sep 16 2006 - 22:17:21 PDT)
- Re: AMBER: change mdcrd file to pdb file Jianhui (Sun Sep 17 2006 - 07:16:29 PDT)
  - Re: AMBER: change mdcrd file to pdb file Fenghui Fan (Sun Sep 17 2006 - 08:30:02 PDT)
    - Re: AMBER: change mdcrd file to pdb file Fabian Alejandro Rodriguez (Sun Sep 17 2006 - 09:04:22 PDT)
AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 00:36:26 PDT)
- Re: AMBER: lib-4324 : UNRECOVERABLE library error Robert Duke (Sun Sep 17 2006 - 05:30:08 PDT)
  - Re: AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 10:23:24 PDT)
AMBER: parameters for Nickel and iron Rachel (Mon Sep 18 2006 - 06:02:39 PDT)
- Re: AMBER: parameters for Nickel and iron Fenghui Fan (Mon Sep 18 2006 - 19:45:24 PDT)
  - Re: AMBER: parameters for Nickel and iron Rachel (Tue Sep 19 2006 - 09:00:45 PDT)
    - Re: AMBER: parameters for Nickel and iron Ken Merz (Tue Sep 19 2006 - 13:00:51 PDT)
    - Re: AMBER: parameters for Nickel and iron Rachel (Thu Sep 21 2006 - 04:50:23 PDT)
- RE: AMBER: parameters for Nickel and iron Junmei Wang (Tue Sep 19 2006 - 09:16:26 PDT)
- RE: AMBER: parameters for Nickel and iron Junmei Wang (Tue Sep 26 2006 - 14:38:08 PDT)
  - Re: AMBER: parameters for Nickel and iron Rachel (Wed Sep 27 2006 - 06:53:45 PDT)
    - AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 08:14:23 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 10:49:53 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 10:59:33 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Thomas Cheatham (Wed Sep 27 2006 - 11:05:25 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 11:26:35 PDT)
    - AMBER: WHATIF Check after MD Fenghui Fan (Wed Sep 27 2006 - 19:24:39 PDT)
    - Re: AMBER: WHATIF Check after MD FyD (Wed Sep 27 2006 - 21:06:30 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 11:33:01 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 12:44:08 PDT)
AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 10:46:35 PDT)
- Re: AMBER: Restart problem on PMEMD with position restraint. Robert Duke (Mon Sep 18 2006 - 11:20:27 PDT)
- RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 11:32:05 PDT)
- Re: AMBER: Restart problem on PMEMD with position restraint. David A. Case (Mon Sep 18 2006 - 12:09:46 PDT)
  - RE: AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 14:10:44 PDT)
    - RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 14:57:58 PDT)
AMBER: Questions Joseph Fernandez (Mon Sep 18 2006 - 11:48:25 PDT)
- AMBER: coordinate files Ed Pate (Tue Sep 19 2006 - 13:17:26 PDT)
  - AMBER: the sequence command in leap Shuting Wei (Wed Sep 20 2006 - 08:32:17 PDT)
  - Re: AMBER: coordinate files David A. Case (Wed Sep 20 2006 - 18:22:47 PDT)
AMBER: ptraj RMSD vs. RMSF Steve Seibold (Mon Sep 18 2006 - 12:54:02 PDT)
AMBER: Question about Streptavidin/Biotin Tutorial. Qingning Shu (Mon Sep 18 2006 - 13:39:38 PDT)
- RE: AMBER: Question about Streptavidin/Biotin Tutorial. Ross Walker (Mon Sep 18 2006 - 15:10:39 PDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 13:40:21 PDT)
- Re: AMBER: A question about Dynamics. David A. Case (Mon Sep 18 2006 - 13:55:47 PDT)
  - Re: AMBER: A question about Dynamics. Chunhu Tan (Mon Sep 18 2006 - 14:24:22 PDT)
    - Re: Re: AMBER: A question about Dynamics. Qingning Shu (Thu Sep 21 2006 - 07:38:47 PDT)
    - RE: Re: AMBER: A question about Dynamics. Ross Walker (Thu Sep 21 2006 - 08:58:08 PDT)
    - Re: RE: Re: AMBER: A question about Dynamics. Qingning Shu (Fri Sep 22 2006 - 15:28:54 PDT)
    - Re: RE: Re: AMBER: A question about Dynamics. David A. Case (Fri Sep 22 2006 - 17:57:46 PDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 13:57:17 PDT)
AMBER: Can salt effect be determined in GB medel? Xioling Chuang (Mon Sep 18 2006 - 21:04:03 PDT)
- Re: AMBER: Can salt effect be determined in GB medel? linfu (Mon Sep 18 2006 - 23:32:16 PDT)
AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? linfu (Mon Sep 18 2006 - 23:40:52 PDT)
- Re: AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? David A. Case (Tue Sep 19 2006 - 10:29:51 PDT)
AMBER: resolving a bad initial model wang.cbs.cnrs.fr (Tue Sep 19 2006 - 07:42:11 PDT)
- Re: AMBER: resolving a bad initial model Andy Purkiss-Trew (Tue Sep 19 2006 - 07:51:01 PDT)
- Re: AMBER: resolving a bad initial model Carlos Simmerling (Tue Sep 19 2006 - 07:53:47 PDT)
- Re: AMBER: resolving a bad initial model Stefano Pieraccini (Tue Sep 19 2006 - 08:25:46 PDT)
AMBER: ACML and MASS/MASSV for sander and pmemd Nicolas Lux Fawzi (Tue Sep 19 2006 - 12:36:21 PDT)
- Re: AMBER: ACML and MASS/MASSV for sander and pmemd Robert Duke (Tue Sep 19 2006 - 13:03:00 PDT)
- RE: AMBER: ACML and MASS/MASSV for sander and pmemd Ross Walker (Tue Sep 19 2006 - 13:24:02 PDT)
  - Re: AMBER: ACML and MASS/MASSV for sander and pmemd Robert Duke (Tue Sep 19 2006 - 13:42:05 PDT)
    - AMBER: installation error for pmemd in Amber 9/Opteron Sergio Aragon (Tue Sep 19 2006 - 14:25:53 PDT)
    - RE: AMBER: installation error for pmemd in Amber 9/Opteron Ross Walker (Tue Sep 19 2006 - 14:41:11 PDT)
    - AMBER: zzfft issue resolved -thanks! Sergio Aragon (Tue Sep 19 2006 - 16:09:25 PDT)
    - AMBER: zzfft error for pmemd in Amber 9/Opteron Sergio Aragon (Tue Sep 19 2006 - 15:53:10 PDT)
AMBER: Steve Seibold (Wed Sep 20 2006 - 09:56:00 PDT)
AMBER: GPCR-membrane issue Akshay Patny (Wed Sep 20 2006 - 10:30:24 PDT)
AMBER: Problems using rst distance constraints in Amber 8 Whitney Allen (Wed Sep 20 2006 - 11:30:05 PDT)
- Re: AMBER: Problems using rst distance constraints in Amber 8 David A. Case (Wed Sep 20 2006 - 12:12:20 PDT)
AMBER: Which POPC Bilayer to start? Akshay Patny (Wed Sep 20 2006 - 14:48:42 PDT)
AMBER: mm-pbsa output Stefano Pieraccini (Thu Sep 21 2006 - 01:51:28 PDT)
- Re: AMBER: mm-pbsa output alfredoq.fcq.unc.edu.ar (Thu Sep 21 2006 - 04:29:51 PDT)
AMBER: bad atom type: Li jitrayut jitonnom (Thu Sep 21 2006 - 03:30:24 PDT)
- Re: AMBER: bad atom type: Li David A. Case (Tue Sep 26 2006 - 23:03:56 PDT)
AMBER: proposed patch for ptraj/evec.c (Amber 9.0) Cameron Abrams (Thu Sep 21 2006 - 10:26:35 PDT)
AMBER: Temperature fluctuation BIG with ntt=3 Mingfeng Yang (Thu Sep 21 2006 - 16:14:24 PDT)
- Re: AMBER: Temperature fluctuation BIG with ntt=3 Carlos Simmerling (Thu Sep 21 2006 - 17:48:07 PDT)
- Re: AMBER: Temperature fluctuation BIG with ntt=3 David A. Case (Thu Sep 21 2006 - 18:39:46 PDT)
  - Re: AMBER: Temperature fluctuation BIG with ntt=3 Mingfeng Yang (Thu Sep 21 2006 - 21:59:54 PDT)
AMBER: Amber8: problem related to antechamber priya priya (Thu Sep 21 2006 - 21:11:23 PDT)
- Re: AMBER: Amber8: problem related to antechamber David A. Case (Fri Sep 22 2006 - 07:52:35 PDT)
- RE: AMBER: Amber8: problem related to antechamber Junmei Wang (Tue Sep 26 2006 - 14:15:07 PDT)
  - AMBER: RE: Amber8: problem related to antechamber priya priya (Tue Sep 26 2006 - 20:49:34 PDT)
AMBER: RMSd vs RMSf Steve Seibold (Fri Sep 22 2006 - 06:42:28 PDT)
AMBER: TI-FEP : strange result for different clambda values Biswa Ranjan Meher (Fri Sep 22 2006 - 08:26:30 PDT)
- Re: AMBER: TI-FEP : strange result for different clambda values Thomas Steinbrecher (Fri Sep 22 2006 - 08:38:10 PDT)
- Re: AMBER: TI-FEP : strange result for different clambda values David Mobley (Fri Sep 22 2006 - 09:38:19 PDT)
AMBER: center of mass dihedral restraints Lauren O'Neil (Fri Sep 22 2006 - 12:03:32 PDT)
- Re: AMBER: center of mass dihedral restraints Carlos Simmerling (Mon Sep 25 2006 - 04:43:49 PDT)
  - Re: AMBER: center of mass dihedral restraints Lauren O'Neil (Mon Sep 25 2006 - 08:39:19 PDT)
    - Re: AMBER: center of mass dihedral restraints venditti2.unisi.it (Mon Sep 25 2006 - 10:44:01 PDT)
AMBER: build a polymer with sequence command Shuting Wei (Fri Sep 22 2006 - 13:41:43 PDT)
- Re: AMBER: build a polymer with sequence command David A. Case (Fri Sep 22 2006 - 14:01:27 PDT)
  - Re: AMBER: build a polymer with sequence command Shuting Wei (Fri Sep 22 2006 - 14:42:04 PDT)
    - Re: AMBER: build a polymer with sequence command David A. Case (Fri Sep 22 2006 - 17:03:35 PDT)
    - Re: AMBER: build a polymer with sequence command Shuting Wei (Mon Sep 25 2006 - 10:15:10 PDT)
    - Re: AMBER: build a polymer with sequence command David A. Case (Mon Sep 25 2006 - 14:37:54 PDT)
AMBER: leap can't assign CALA Myunggi Yi (Fri Sep 22 2006 - 15:09:06 PDT)
- Re: AMBER: leap can't assign CALA David A. Case (Fri Sep 22 2006 - 17:53:29 PDT)
  - Re: AMBER: leap can't assign CALA Myunggi Yi (Sat Sep 23 2006 - 08:36:12 PDT)
AMBER: pbsa segmentation faults Thomas Steinbrecher (Fri Sep 22 2006 - 16:46:11 PDT)
- Re: AMBER: pbsa segmentation faults Ray Luo (Sat Sep 23 2006 - 23:40:58 PDT)
- AMBER: mm_pbsa segmentation faults Thomas Steinbrecher (Mon Sep 25 2006 - 11:24:17 PDT)
  - Re: AMBER: mm_pbsa segmentation faults linfu (Mon Sep 25 2006 - 17:56:08 PDT)
  - Re: AMBER: mm_pbsa segmentation faults Ray Luo (Mon Sep 25 2006 - 18:17:54 PDT)
  - Re: AMBER: mm_pbsa segmentation faults Ray Luo (Tue Sep 26 2006 - 09:29:26 PDT)
    - Re: AMBER: mm_pbsa segmentation faults Thomas Steinbrecher (Tue Sep 26 2006 - 10:31:34 PDT)
    - Re: AMBER: mm_pbsa segmentation faults Mark Williamson (Tue Sep 26 2006 - 14:41:06 PDT)
AMBER: Picking up water molecules around one molecule Atsutoshi Okabe (Sat Sep 23 2006 - 01:26:12 PDT)
AMBER: one question on MD Fenghui Fan (Sat Sep 23 2006 - 18:03:11 PDT)
- Re: AMBER: one question on MD Carlos Simmerling (Sat Sep 23 2006 - 18:32:46 PDT)
AMBER: the RMSD of MD Fenghui Fan (Sun Sep 24 2006 - 10:07:56 PDT)
- Re: AMBER: the RMSD of MD Adrian Roitberg (Sun Sep 24 2006 - 10:49:52 PDT)
AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS Zhihong Yu (Sun Sep 24 2006 - 20:03:28 PDT)
- Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS Carlos Simmerling (Mon Sep 25 2006 - 04:30:57 PDT)
- Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS JunJun Liu (Mon Sep 25 2006 - 12:28:55 PDT)
AMBER: polarizable ff for ligand bala (Mon Sep 25 2006 - 06:53:02 PDT)
AMBER: question on Lennard-Jones fitting in FF94 and 96 David Mobley (Mon Sep 25 2006 - 10:07:45 PDT)
Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS Zhihong Yu (Mon Sep 25 2006 - 18:20:14 PDT)
AMBER: from ADP-small protein complex to GTP-protein complex Fenghui Fan (Mon Sep 25 2006 - 21:00:53 PDT)
AMBER: lifetime and maxocc Sergey Samsonov (Tue Sep 26 2006 - 08:56:26 PDT)
AMBER: structure from MD Fenghui Fan (Tue Sep 26 2006 - 09:42:14 PDT)
- Re: AMBER: structure from MD Carlos Simmerling (Tue Sep 26 2006 - 09:43:58 PDT)
AMBER: chemical shift restrains Emilia Sikorska (Tue Sep 26 2006 - 11:22:05 PDT)
AMBER: missing benchmark files Mark H. Schofield (Tue Sep 26 2006 - 15:32:38 PDT)
- Re: AMBER: missing benchmark files David A. Case (Tue Sep 26 2006 - 23:50:49 PDT)
AMBER: job crashes Xiaowei (David) Li (Tue Sep 26 2006 - 20:09:04 PDT)
- Re: AMBER: job crashes JunJun Liu (Tue Sep 26 2006 - 20:39:52 PDT)
  - Re: AMBER: job crashes Xiaowei (David) Li (Tue Sep 26 2006 - 20:57:18 PDT)
AMBER: RE: Amber8: problem related to antechamber priya priya (Wed Sep 27 2006 - 00:29:01 PDT)
AMBER: kclust Fabiana Caporuscio (Wed Sep 27 2006 - 01:32:51 PDT)
AMBER: Error in compiling Amber 8 parallel Jianhui Tian (Wed Sep 27 2006 - 13:28:48 PDT)
- AMBER: Multiple Timestep MD David LeBard (Wed Sep 27 2006 - 18:03:35 PDT)
- RE: AMBER: Error in compiling Amber 8 parallel Ross Walker (Thu Sep 28 2006 - 08:36:25 PDT)
  - AMBER: running sander on several nodes Fenghui Fan (Thu Sep 28 2006 - 09:45:34 PDT)
    - Re: AMBER: running sander on several nodes Fenghui Fan (Thu Sep 28 2006 - 10:21:26 PDT)
    - RE: AMBER: running sander on several nodes Ross Walker (Thu Sep 28 2006 - 10:37:28 PDT)
AMBER: Questions/observations about Nudged Elastic Band (NEB) Pietro Amodeo (Thu Sep 28 2006 - 03:56:36 PDT)
- RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) Ross Walker (Thu Sep 28 2006 - 08:29:29 PDT)
  - AMBER: Machine File for Intel Core 2 Duo E6400 Osmar Norberto de Souza (Thu Sep 28 2006 - 11:47:06 PDT)
    - RE: AMBER: Machine File for Intel Core 2 Duo E6400 Ross Walker (Thu Sep 28 2006 - 12:05:02 PDT)
    - Re: AMBER: Machine File for Intel Core 2 Duo E6400 Osmar Norberto de Souza (Thu Sep 28 2006 - 12:22:15 PDT)
  - RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) Pietro Amodeo (Fri Sep 29 2006 - 02:21:43 PDT)
AMBER: NAD parameters Uni-Halle (Thu Sep 28 2006 - 06:06:06 PDT)
- Re: AMBER: NAD parameters cristian obiol (Thu Sep 28 2006 - 06:56:43 PDT)
- RE: AMBER: NAD parameters Ross Walker (Thu Sep 28 2006 - 08:32:48 PDT)
  - AMBER: Problem about installing amber9 on Mac OS X gtg549i.mail.gatech.edu (Thu Sep 28 2006 - 09:28:51 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Ross Walker (Thu Sep 28 2006 - 10:40:26 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X gtg549i.mail.gatech.edu (Thu Sep 28 2006 - 11:32:18 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Ross Walker (Thu Sep 28 2006 - 11:52:30 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Shuting Wei (Fri Sep 29 2006 - 14:08:42 PDT)
AMBER: parm*.dat Ivelin Georgiev (Thu Sep 28 2006 - 09:39:23 PDT)
- Re: AMBER: parm*.dat Jianhui (Thu Sep 28 2006 - 14:24:49 PDT)
AMBER: Parameterization of ethidium - phenyl ring sethl.gatech.edu (Thu Sep 28 2006 - 13:02:08 PDT)
- AMBER: WHAT IF CHeck after MD Fenghui Fan (Thu Sep 28 2006 - 15:06:04 PDT)
  - Re: AMBER: WHAT IF CHeck after MD David Mobley (Thu Sep 28 2006 - 15:58:32 PDT)
AMBER: problem to center solvateshell Bonnet, Pascal [PRDBE] (Fri Sep 29 2006 - 02:30:49 PDT)
AMBER: Problem using antechamber Gustavo Seabra (Fri Sep 29 2006 - 09:19:12 PDT)
- RE: AMBER: Problem using antechamber Junmei Wang (Fri Sep 29 2006 - 11:17:37 PDT)
  - Re: AMBER: Problem using antechamber Gustavo Seabra (Fri Sep 29 2006 - 12:06:34 PDT)
AMBER: Electrostatic Energy Constant Ivelin Georgiev (Fri Sep 29 2006 - 10:50:03 PDT)
- Re: AMBER: Electrostatic Energy Constant Thomas Cheatham (Fri Sep 29 2006 - 11:19:00 PDT)
  - Re: AMBER: Electrostatic Energy Constant Fenghui Fan (Fri Sep 29 2006 - 12:23:03 PDT)
    - Re: AMBER: Electrostatic Energy Constant Thomas Cheatham (Fri Sep 29 2006 - 12:44:25 PDT)
- Re: AMBER: Electrostatic Energy Constant Carlos Simmerling (Fri Sep 29 2006 - 13:20:24 PDT)

Amber Archive Sep 2006 By Thread