AMBER Archive (2007) - By Thread

Most recent messages
4765 messages sorted by: [ author ] [ date ] [ subject ]
About this archive

Starting: Mon Jan 01 2007 - 04:25:56 CST
Ending: Mon Dec 31 2007 - 15:27:41 CST

Re: AMBER: G5 OSX serial compile error Mengjuei Hsieh (Mon Jan 01 2007 - 04:16:12 CST)
- Re: AMBER: G5 OSX serial compile error Kevin Kelliher (Fri Jan 05 2007 - 12:58:56 CST)
  - Re: AMBER: G5 OSX serial compile error Mengjuei Hsieh (Mon Jan 08 2007 - 18:26:26 CST)
Re: AMBER: AMBER complile problem Chengwen Chen (Mon Jan 01 2007 - 21:19:08 CST)
AMBER: fluctuations Jardas sucuriba (Tue Jan 02 2007 - 09:21:22 CST)
AMBER: Deep energetics problem sai vikram (Tue Jan 02 2007 - 11:10:19 CST)
- RE: AMBER: Deep energetics problem Ross Walker (Tue Jan 02 2007 - 13:12:53 CST)
  - Re: AMBER: Deep energetics problem sai vikram (Wed Jan 03 2007 - 02:26:42 CST)
AMBER: Distance Restraints Problem Esther Brugger (Tue Jan 02 2007 - 16:00:16 CST)
- Re: AMBER: Distance Restraints Problem David A. Case (Tue Jan 02 2007 - 17:37:18 CST)
Re: AMBER: problems trying to modify Amber8 David A. Case (Tue Jan 02 2007 - 17:53:36 CST)
AMBER: assign atom hybrid xiaoqin huang (Tue Jan 02 2007 - 19:54:52 CST)
AMBER: amber9 installation error Seaclear Theory (Tue Jan 02 2007 - 20:10:12 CST)
- Re: AMBER: amber9 installation error David A. Case (Wed Jan 03 2007 - 01:00:50 CST)
  - Re: AMBER: amber9 installation error Seaclear Theory (Wed Jan 03 2007 - 09:55:51 CST)
  - Re: AMBER: amber9 installation error Seaclear Theory (Wed Jan 03 2007 - 12:04:27 CST)
AMBER: Re:tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Tue Jan 02 2007 - 20:41:13 CST)
Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file Bill Ross (Tue Jan 02 2007 - 22:26:14 CST)
- Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Wed Jan 03 2007 - 09:05:18 CST)
AMBER: H-bond in ptraj nag raj (Wed Jan 03 2007 - 06:17:51 CST)
- Re: AMBER: H-bond in ptraj Jianyin Shao (Thu Jan 04 2007 - 13:49:38 CST)
  - Re: AMBER: H-bond in ptraj nag raj (Thu Jan 04 2007 - 22:34:59 CST)
AMBER: torsion angle penalty calculation Mike Summers (Wed Jan 03 2007 - 09:18:34 CST)
- Re: AMBER: torsion angle penalty calculation David A. Case (Wed Jan 03 2007 - 10:54:33 CST)
  - Re: AMBER: torsion angle penalty calculationy Mike Summers (Wed Jan 03 2007 - 12:13:24 CST)
- AMBER: MPI is slower than single processor with water Mike Summers (Tue Jan 16 2007 - 10:30:18 CST)
  - RE: AMBER: MPI is slower than single processor with water Ross Walker (Tue Jan 16 2007 - 10:50:36 CST)
    - Re: AMBER: MPI is slower than single processor with water Mike Summers (Tue Jan 16 2007 - 11:32:53 CST)
    - RE: AMBER: MPI is slower than single processor with water Yu Chen (Tue Jan 16 2007 - 14:23:23 CST)
AMBER: installing amber 8 on 5 nodes cluster PC Syed Tarique Moin (Wed Jan 03 2007 - 10:44:54 CST)
- Re: AMBER: installing amber 8 on 5 nodes cluster PC David A. Case (Wed Jan 03 2007 - 11:26:17 CST)
  - Re: AMBER: installing amber 8 on 5 nodes cluster PC Syed Tarique Moin (Wed Jan 03 2007 - 12:25:45 CST)
- AMBER: mm_pbsa problems Jardas sucuriba (Tue Jan 30 2007 - 09:55:00 CST)
AMBER: How to get a periodic box of modified water molecules Li Su (Wed Jan 03 2007 - 11:25:11 CST)
- Re: AMBER: How to get a periodic box of modified water molecules David A. Case (Thu Jan 04 2007 - 00:04:10 CST)
  - AMBER: AMBER citation questions caoch_at_cherry.bio.titech.ac.jp (Thu Jan 04 2007 - 02:59:08 CST)
    - Re: AMBER: AMBER citation questions Carlos Simmerling (Thu Jan 04 2007 - 05:36:28 CST)
AMBER: Distance Restraints Esther Brugger (Wed Jan 03 2007 - 14:29:26 CST)
- Re: AMBER: Distance Restraints Esther Brugger (Wed Jan 03 2007 - 16:04:03 CST)
  - AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..." Mike Hanby (Wed Jan 03 2007 - 16:53:43 CST)
    - RE: AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..." Ross Walker (Wed Jan 03 2007 - 17:34:23 CST)
  - Re: AMBER: Distance Restraints Esther Brugger (Fri Jan 05 2007 - 09:17:38 CST)
AMBER: NH3 potential Jennie Thomas (Wed Jan 03 2007 - 15:00:28 CST)
AMBER: H-acceptors problem in ptraj nag raj (Wed Jan 03 2007 - 23:20:09 CST)
AMBER: The unperturbed charge of the unit: -20.999999 is not zero. saurabh agrawal (Thu Jan 04 2007 - 01:03:49 CST)
- Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. Nitin Bhardwaj (Thu Jan 04 2007 - 09:54:39 CST)
  - Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. Carlos Simmerling (Thu Jan 04 2007 - 13:31:29 CST)
    - AMBER: 22 improper torsions in old prep form saurabh agrawal (Fri Jan 05 2007 - 00:29:21 CST)
AMBER: intra-molecular h-bonds in ptraj lily ferreira (Thu Jan 04 2007 - 09:17:37 CST)
- Re: AMBER: intra-molecular h-bonds in ptraj Jianyin Shao (Thu Jan 04 2007 - 14:11:36 CST)
AMBER: enzyme kinetics in silico Sean Rathlef (Thu Jan 04 2007 - 11:24:46 CST)
- Re: AMBER: enzyme kinetics in silico Suxin Zheng (Thu Jan 04 2007 - 11:54:47 CST)
  - RE: AMBER: enzyme kinetics in silico Xu, Yong (Tue Apr 03 2007 - 14:26:45 CDT)
    - Re: AMBER: enzyme kinetics in silico Sean Rathlef (Tue Apr 03 2007 - 16:08:10 CDT)
- Re: AMBER: enzyme kinetics in silico Fenghui Fan (Thu Jan 04 2007 - 15:34:41 CST)
Fwd: AMBER: Atoms overlapping Nitin Bhardwaj (Thu Jan 04 2007 - 18:58:26 CST)
Re : AMBER: intra-molecular h-bonds in ptraj lily ferreira (Fri Jan 05 2007 - 07:37:52 CST)
- Re: Re : AMBER: intra-molecular h-bonds in ptraj Esther Brugger (Fri Jan 05 2007 - 09:11:43 CST)
- Re: Re : AMBER: intra-molecular h-bonds in ptraj Thomas Cheatham (Sun Jan 07 2007 - 22:51:29 CST)
Re: AMBER: 22 improper torsions in old prep form Bill Ross (Fri Jan 05 2007 - 12:39:23 CST)
AMBER: How to change the force field equation in amber by programming... Gobind Singh Bisht (Fri Jan 05 2007 - 13:55:22 CST)
- Re: AMBER: How to change the force field equation in amber by programming... David A. Case (Fri Jan 05 2007 - 15:34:41 CST)
  - Re: AMBER: How to change the force field equation in amber by programming... Gobind Singh Bisht (Sun Jan 07 2007 - 08:06:06 CST)
    - Re: AMBER: How to change the force field equation in amber by programming... David A. Case (Mon Jan 08 2007 - 17:00:10 CST)
  - AMBER: unsubscribe Perdita Barran (Sun Jan 07 2007 - 12:13:40 CST)
AMBER: Hydrogen in a phosphate ion Nitin Bhardwaj (Fri Jan 05 2007 - 16:00:09 CST)
- Re: AMBER: Hydrogen in a phosphate ion David A. Case (Tue Jan 09 2007 - 13:46:43 CST)
AMBER: Simulation of a charged system Kijeong Kwac (Fri Jan 05 2007 - 17:08:42 CST)
- Re: AMBER: Simulation of a charged system Carlos Simmerling (Fri Jan 05 2007 - 17:41:02 CST)
AMBER: question about the testing of AMBER9 Shaoqing.Zhang_at_mail.uh.edu (Fri Jan 05 2007 - 20:25:16 CST)
- Re: AMBER: question about the testing of AMBER9 David A. Case (Fri Jan 05 2007 - 22:54:53 CST)
  - Re: AMBER: question about the testing of AMBER9 Shaoqing.Zhang_at_mail.uh.edu (Sat Jan 06 2007 - 17:07:04 CST)
- RE: AMBER: question about the testing of AMBER9 Bill Ross (Mon Jan 08 2007 - 14:05:19 CST)
AMBER: entropy units Giulio Rastelli (Mon Jan 08 2007 - 04:33:19 CST)
AMBER: How to do minimization.. sai vikram (Mon Jan 08 2007 - 09:30:59 CST)
- RE: AMBER: How to do minimization.. Ross Walker (Mon Jan 08 2007 - 10:32:09 CST)
AMBER: improper torsions Ed Pate (Mon Jan 08 2007 - 13:08:36 CST)
- Re: AMBER: improper torsions Fenghui Fan (Mon Jan 08 2007 - 13:45:09 CST)
Re: AMBER: improper torsions Bill Ross (Mon Jan 08 2007 - 14:00:06 CST)
Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Tue Jan 09 2007 - 01:17:54 CST)
- RE: AMBER: Installation help - SGI Altix 350 Ross Walker (Tue Jan 09 2007 - 10:18:55 CST)
- Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra (Wed Jan 10 2007 - 10:07:26 CST)
AMBER: How many steps should be used for a MD calculation? Michel Becker (Tue Jan 09 2007 - 03:12:55 CST)
AMBER: image command venditti2_at_unisi.it (Tue Jan 09 2007 - 08:09:07 CST)
- Re: AMBER: image command Thomas Cheatham (Wed Jan 10 2007 - 00:25:48 CST)
  - Re: AMBER: image command Petr Kulhanek (Wed Jan 10 2007 - 02:45:45 CST)
AMBER: amber 9 Sophie Barbe (Tue Jan 09 2007 - 09:29:04 CST)
- RE: AMBER: amber 9 Ross Walker (Tue Jan 09 2007 - 10:31:36 CST)
  - RE: AMBER: amber 9 Sophie Barbe (Wed Jan 10 2007 - 11:54:36 CST)
AMBER: explicit implicit solvent Ji-Lai Li (Wed Jan 10 2007 - 08:24:20 CST)
- Re: AMBER: explicit implicit solvent Carlos Simmerling (Wed Jan 10 2007 - 08:53:53 CST)
AMBER: experimental phi-values as restraints rebeca_at_mmb.pcb.ub.es (Wed Jan 10 2007 - 10:06:11 CST)
- Re: AMBER: experimental phi-values as restraints Vladimir Tchoupakhine (Wed Jan 10 2007 - 10:23:58 CST)
AMBER: Steve Seibold (Wed Jan 10 2007 - 10:46:28 CST)
- Re: AMBER: Vladimir Tchoupakhine (Wed Jan 10 2007 - 10:51:46 CST)
- RE: AMBER: Ross Walker (Wed Jan 10 2007 - 11:17:11 CST)
  - RE: AMBER: Steve Seibold (Wed Jan 10 2007 - 13:03:30 CST)
AMBER: Section missing from AMBER 9 manual? Steven Winfield (Wed Jan 10 2007 - 10:57:36 CST)
- Re: AMBER: Section missing from AMBER 9 manual? David A. Case (Wed Jan 10 2007 - 15:02:12 CST)
AMBER: test submission through PBS queue Evan Kelly (Wed Jan 10 2007 - 13:20:45 CST)
- Re: AMBER: test submission through PBS queue Scott Brozell (Wed Jan 10 2007 - 13:33:09 CST)
- RE: AMBER: test submission through PBS queue Ross Walker (Wed Jan 10 2007 - 13:35:27 CST)
AMBER: sander crashes during minimization Seth Lilavivat (Wed Jan 10 2007 - 13:29:15 CST)
- RE: AMBER: sander crashes during minimization Ross Walker (Wed Jan 10 2007 - 13:40:05 CST)
AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Thu Jan 11 2007 - 08:12:09 CST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Thu Jan 11 2007 - 16:12:23 CST)
  - RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Fri Jan 12 2007 - 07:58:40 CST)
    - Re: AMBER: perturbed atoms are not bonded on using TIP5P water Steven Winfield (Fri Jan 12 2007 - 08:07:38 CST)
    - Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Sun Jan 14 2007 - 11:39:13 CST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 19:40:32 CST)
  - Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Mon Jan 15 2007 - 20:23:17 CST)
    - RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 21:33:18 CST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 21:19:59 CST)
- RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Tue Jan 16 2007 - 11:35:22 CST)
AMBER: Simulations with GB models Wei Chen (Thu Jan 11 2007 - 10:23:15 CST)
- Re: AMBER: Simulations with GB models Carlos Simmerling (Thu Jan 11 2007 - 12:28:16 CST)
AMBER: Leap adding 3 extra atoms Akshay Patny (Thu Jan 11 2007 - 11:35:00 CST)
AMBER: CYX residue missing from Amber 9 ff03ua (?) Chris Moth (Thu Jan 11 2007 - 13:32:04 CST)
- RE: AMBER: CYX residue missing from Amber 9 ff03ua (?) Ray Luo (Thu Jan 11 2007 - 16:59:29 CST)
Re: AMBER: Leap adding 3 extra atoms Bill Ross (Thu Jan 11 2007 - 13:33:14 CST)
- RE: AMBER: Leap adding extra atoms Akshay Patny (Thu Jan 11 2007 - 15:38:37 CST)
  - RE: AMBER: Leap adding extra atoms Scott Brozell (Mon Jan 15 2007 - 14:39:49 CST)
  - RE: AMBER: Leap adding extra atoms Scott Brozell (Mon Jan 15 2007 - 15:30:00 CST)
AMBER: Amber 8.0 : how to represent EPS with VMD? Guillaume Bollot (Fri Jan 12 2007 - 08:49:28 CST)
AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Sat Jan 13 2007 - 12:25:46 CST)
- Re: AMBER: solvation of protein using TIP3PBOX in amber 8 David A. Case (Sat Jan 13 2007 - 23:40:46 CST)
  - Re: AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Sun Jan 14 2007 - 03:59:32 CST)
AMBER: output khn _ (Sat Jan 13 2007 - 22:24:11 CST)
- Re: AMBER: output David A. Case (Sat Jan 13 2007 - 23:38:24 CST)
- Re: AMBER: output Thaison Tran (Sun Jan 14 2007 - 01:59:56 CST)
AMBER: problems in energy minimization using TIP5P water model sugino tatsuro (Sun Jan 14 2007 - 10:35:11 CST)
AMBER: problem compiling Amber 7 Kevin Cahill (Sun Jan 14 2007 - 20:35:00 CST)
- Re: AMBER: problem compiling Amber 7 Scott Brozell (Mon Jan 15 2007 - 11:29:10 CST)
- Re: AMBER: problem compiling Amber 7 David A. Case (Mon Jan 15 2007 - 11:38:26 CST)
AMBER: About the problem of the PMEMD and cutoff $BJ}b}(B (Sun Jan 14 2007 - 21:56:17 CST)
- Re: AMBER: About the problem of the PMEMD and cutoff Robert Duke (Sun Jan 14 2007 - 22:20:22 CST)
  - Re: AMBER: About the problem of the PMEMD and cutoff $BJ}b}(B (Mon Jan 15 2007 - 06:45:29 CST)
    - Re: AMBER: About the problem of the PMEMD and cutoff Robert Duke (Mon Jan 15 2007 - 07:19:26 CST)
Fwd: Re: AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Mon Jan 15 2007 - 23:14:12 CST)
AMBER: convert pdb files to restart files khn _ (Tue Jan 16 2007 - 04:50:47 CST)
- Re: AMBER: convert pdb files to restart files Stefano Pieraccini (Tue Jan 16 2007 - 06:57:41 CST)
- RE: AMBER: convert pdb files to restart files Ross Walker (Tue Jan 16 2007 - 09:19:54 CST)
AMBER: mm_pbsa_statistics.pl Antonio Morreale (Tue Jan 16 2007 - 06:28:52 CST)
AMBER: RE: help Ross Walker (Tue Jan 16 2007 - 10:23:44 CST)
AMBER: Radii for water hydrogens are different Steve Spronk (Tue Jan 16 2007 - 14:29:45 CST)
- Re: AMBER: Radii for water hydrogens are different David A. Case (Fri Jan 19 2007 - 12:13:41 CST)
AMBER: RESP charges for charged species Michel Becker (Tue Jan 16 2007 - 15:44:26 CST)
- Re: AMBER: RESP charges for charged species FyD (Tue Jan 16 2007 - 23:13:51 CST)
AMBER: How are water molecules at cutoff being treated? Li Su (Tue Jan 16 2007 - 16:48:47 CST)
- Re: AMBER: How are water molecules at cutoff being treated? David A. Case (Tue Jan 16 2007 - 17:36:07 CST)
AMBER: mm_pbsa vertex atom mismatch AYTUG TUNCEL (Tue Jan 16 2007 - 17:10:35 CST)
AMBER: calcium parameter for GB Wei Chen (Tue Jan 16 2007 - 17:21:08 CST)
- Re: AMBER: calcium parameter for GB David A. Case (Tue Jan 16 2007 - 17:33:43 CST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Wed Jan 17 2007 - 02:19:09 CST)
    - Re: AMBER: calcium parameter for GB Wei Chen (Wed Jan 17 2007 - 10:25:47 CST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Wed Jan 17 2007 - 11:06:36 CST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Wed Jan 17 2007 - 19:25:20 CST)
    - Re: AMBER: calcium parameter for GB Wei Chen (Thu Jan 18 2007 - 10:15:45 CST)
- Re: AMBER: calcium parameter for GB Bill Ross (Thu Jan 18 2007 - 12:36:01 CST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Tue Jan 23 2007 - 12:49:54 CST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Tue Jan 23 2007 - 20:07:21 CST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Wed Jan 24 2007 - 11:33:24 CST)
AMBER: DNA structure analysis Catein Catherine (Tue Jan 16 2007 - 21:12:42 CST)
- Re: AMBER: DNA structure analysis Jiri Sponer (Wed Jan 17 2007 - 04:39:36 CST)
  - Re: AMBER: DNA structure analysis Catein Catherine (Wed Jan 17 2007 - 10:23:08 CST)
- Re: AMBER: DNA structure analysis Fenghui Fan (Wed Jan 17 2007 - 09:31:00 CST)
  - Re: AMBER: DNA structure analysis Catein Catherine (Wed Jan 17 2007 - 10:24:16 CST)
RE: AMBER: perturbed atoms are not bonded on using TIP5P wate sugino tatsuro (Tue Jan 16 2007 - 23:47:51 CST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P wate David A. Case (Thu Jan 18 2007 - 11:40:37 CST)
AMBER: Drug bound to the protein Sophie Barbe (Wed Jan 17 2007 - 02:56:21 CST)
- Re: AMBER: Drug bound to the protein Guillermo Mulliert Carlín (Wed Jan 17 2007 - 09:27:45 CST)
- Re: AMBER: Drug bound to the protein David A. Case (Wed Jan 17 2007 - 10:57:02 CST)
AMBER: solaris 10 and compilers on X86_64 hardware M. L. Dodson (Wed Jan 17 2007 - 09:45:27 CST)
- Re: AMBER: solaris 10 and compilers on X86_64 hardware Knut Langsetmo (Wed Jan 17 2007 - 10:03:33 CST)
AMBER: vdW parameters for chlorine atom Austin B. Yongye (Wed Jan 17 2007 - 11:19:34 CST)
- Re: AMBER: vdW parameters for chlorine atom David A. Case (Wed Jan 17 2007 - 19:55:15 CST)
AMBER: (no subject) Yusheng Dou (Wed Jan 17 2007 - 11:29:10 CST)
Re: AMBER: Drug bound to the protein Bill Ross (Wed Jan 17 2007 - 13:28:15 CST)
AMBER: vertex atom mismatch saurabh agrawal (Thu Jan 18 2007 - 01:49:25 CST)
- AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0 saurabh agrawal (Thu Jan 18 2007 - 11:15:40 CST)
AMBER: (no subject) mahdi fathi (Thu Jan 18 2007 - 04:10:24 CST)
AMBER: sanger deepti nayar (Thu Jan 18 2007 - 05:29:19 CST)
- Re: AMBER: sanger Chupakhin Vladimir (Thu Jan 18 2007 - 08:05:01 CST)
  - Re: AMBER: sanger Carlos Simmerling (Thu Jan 18 2007 - 08:09:31 CST)
- Re: AMBER: sanger David A. Case (Thu Jan 18 2007 - 11:05:34 CST)
AMBER: issues with restrt file Amit Kumar (Thu Jan 18 2007 - 10:15:52 CST)
- Re: AMBER: issues with restrt file Carlos Simmerling (Thu Jan 18 2007 - 11:07:35 CST)
  - Re: AMBER: issues with restrt file Amit Kumar (Thu Jan 18 2007 - 11:59:40 CST)
AMBER: error when using sander.LES: exceeded MAXLES Kailee (Thu Jan 18 2007 - 10:33:18 CST)
- Re: AMBER: error when using sander.LES: exceeded MAXLES Carlos Simmerling (Thu Jan 18 2007 - 11:03:08 CST)
- Re: AMBER: error when using sander.LES: exceeded MAXLES David A. Case (Thu Jan 18 2007 - 11:12:23 CST)
AMBER: mm-pbsa, long distance free energy calculation problem Bing Liu (Thu Jan 18 2007 - 11:06:53 CST)
- Re: AMBER: mm-pbsa, long distance free energy calculation problem Wei Chen (Thu Jan 18 2007 - 14:24:26 CST)
  - Re: AMBER: mm-pbsa, long distance free energy calculation problem Bing Liu (Thu Jan 18 2007 - 15:09:38 CST)
AMBER: HF/6-31G* ESP Charges do not match with ff02 charges Pavan G (Fri Jan 19 2007 - 00:19:19 CST)
- Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges mernst_at_tricity.wsu.edu (Fri Jan 19 2007 - 01:02:10 CST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges FyD (Fri Jan 19 2007 - 02:31:46 CST)
- Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges mernst_at_tricity.wsu.edu (Fri Jan 19 2007 - 12:59:52 CST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges FyD (Fri Jan 19 2007 - 14:30:43 CST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges Pavan G (Sun Jan 28 2007 - 09:45:32 CST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Jan 19 2007 - 02:34:58 CST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand FyD (Fri Jan 19 2007 - 07:19:17 CST)
  - AMBER: Dihedral FF parameters FyD (Fri Jan 19 2007 - 09:40:10 CST)
    - Re: AMBER: Dihedral FF parameters Ye Mei (Fri Jan 19 2007 - 09:44:14 CST)
- RE: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Mon Jan 29 2007 - 10:57:45 CST)
AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) Chengwen Chen (Fri Jan 19 2007 - 03:37:53 CST)
- Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) David A. Case (Fri Jan 19 2007 - 10:36:34 CST)
  - Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) Chengwen Chen (Sat Jan 20 2007 - 21:55:46 CST)
AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Fri Jan 19 2007 - 07:15:56 CST)
- RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f Ray Luo (Fri Jan 19 2007 - 11:50:19 CST)
  - Re: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Fri Jan 19 2007 - 19:54:27 CST)
AMBER: (no subject) Yusheng Dou (Fri Jan 19 2007 - 08:51:51 CST)
AMBER: Steve Seibold (Fri Jan 19 2007 - 13:53:47 CST)
- RE: AMBER: Ross Walker (Fri Jan 19 2007 - 14:47:24 CST)
AMBER: equilibration with amber5, production of MD with amber7 Carlos Javier Nuñez Aguero (Fri Jan 19 2007 - 14:47:05 CST)
- Re: AMBER: equilibration with amber5, production of MD with amber7 David A. Case (Sun Jan 21 2007 - 23:28:46 CST)
AMBER: a question about analysis of DNA duplex after MD simulation with curves wendy chen (Sat Jan 20 2007 - 21:28:19 CST)
AMBER: deformation of DNA duplex after MD simulation (AMBER9) Chengwen Chen (Sat Jan 20 2007 - 22:28:59 CST)
AMBER: Can't run Normal Mode Analysis !!! jitrayut jitonnom (Sun Jan 21 2007 - 23:09:48 CST)
- Fwd: AMBER: Can't run Normal Mode Analysis !!! jitrayut jitonnom (Mon Jan 22 2007 - 06:58:24 CST)
- Re: AMBER: Can't run Normal Mode Analysis !!! Scott Pendley (Mon Jan 22 2007 - 11:05:26 CST)
AMBER: MM-PBSA problem: Why jitrayut jitonnom (Sun Jan 21 2007 - 23:20:38 CST)
- Re: AMBER: MM-PBSA problem: Why vanessa wai (Mon Jan 22 2007 - 04:47:30 CST)
AMBER: Can't run decompose energy in MM-PBSA jitrayut jitonnom (Mon Jan 22 2007 - 08:20:51 CST)
- RE: AMBER: Can't run decompose energy in MM-PBSA Ray Luo (Mon Jan 22 2007 - 11:27:03 CST)
  - Re: AMBER: Can't run decompose energy in MM-PBSA vanessa wai (Mon Jan 22 2007 - 19:37:02 CST)
AMBER: problem with distance restraints Ed Pate (Mon Jan 22 2007 - 13:43:58 CST)
- Re: AMBER: problem with distance restraints David A. Case (Mon Jan 22 2007 - 14:10:12 CST)
  - Re: AMBER: problem with distance restraints Ed Pate (Mon Jan 22 2007 - 16:29:15 CST)
    - Re: AMBER: problem with distance restraints David A. Case (Mon Jan 22 2007 - 17:41:50 CST)
AMBER: united atom parameters for -NH2 and -OH groups emine cebe (Mon Jan 22 2007 - 13:47:12 CST)
AMBER: how much restraint ? AYTUG TUNCEL (Mon Jan 22 2007 - 16:09:12 CST)
AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 22 2007 - 19:19:20 CST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 22 2007 - 20:10:47 CST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Tue Jan 23 2007 - 11:30:06 CST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Fri Jan 26 2007 - 17:38:48 CST)
  - RE: AMBER: ADDIONS do not neutralize to ZERO Ross Walker (Sun Jan 28 2007 - 22:38:25 CST)
    - RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 29 2007 - 11:04:58 CST)
    - Re: AMBER: ADDIONS do not neutralize to ZERO Chris Moth (Mon Jan 29 2007 - 15:30:20 CST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Sun Jan 28 2007 - 14:41:43 CST)
  - RE: AMBER: ADDIONS do not neutralize to ZERO saurabh agrawal (Sun Jan 28 2007 - 22:07:37 CST)
Re: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Mon Jan 22 2007 - 19:58:11 CST)
AMBER: Defining BOX INFO during TLEAP Akshay Patny (Mon Jan 22 2007 - 21:02:15 CST)
- Re: AMBER: Defining BOX INFO during TLEAP David A. Case (Wed Jan 24 2007 - 09:04:24 CST)
- RE: AMBER: Defining BOX INFO during TLEAP Akshay Patny (Wed Jan 24 2007 - 13:54:37 CST)
  - RE: AMBER: Defining BOX INFO during TLEAP Ross Walker (Wed Jan 24 2007 - 14:09:30 CST)
AMBER: Antechamber esp calculation mathew k varghese (Mon Jan 22 2007 - 22:44:42 CST)
- Re: AMBER: Antechamber esp calculation Ilyas Yildirim (Tue Jan 23 2007 - 00:07:31 CST)
- Re: AMBER: Antechamber esp calculation FyD (Tue Jan 23 2007 - 00:05:46 CST)
AMBER: pmemd install error Ji-Lai Li (Tue Jan 23 2007 - 00:59:27 CST)
- AMBER: Re: pmemd install error Ji-Lai Li (Tue Jan 23 2007 - 01:03:33 CST)
- Re: AMBER: pmemd install error Robert Duke (Tue Jan 23 2007 - 07:01:46 CST)
  - Re: AMBER: pmemd install error David A. Case (Fri Jan 26 2007 - 17:45:14 CST)
    - Re: AMBER: pmemd install error Ji-Lai Li (Sun Jan 28 2007 - 21:18:05 CST)
    - Re: AMBER: pmemd install error Robert Duke (Tue Jan 30 2007 - 14:24:19 CST)
AMBER: nuc.in file deepti nayar (Tue Jan 23 2007 - 02:21:27 CST)
- Re: AMBER: nuc.in file David A. Case (Thu Jan 25 2007 - 13:59:12 CST)
AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 03:50:58 CST)
- Re: AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Gustavo Seabra (Tue Jan 23 2007 - 10:54:09 CST)
AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Cenk Andac (Tue Jan 23 2007 - 06:03:37 CST)
- Re: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Steven Winfield (Tue Jan 23 2007 - 06:11:12 CST)
- Re: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 David A. Case (Wed Jan 24 2007 - 09:09:36 CST)
  - RE: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Ross Walker (Wed Jan 24 2007 - 11:49:20 CST)
AMBER: Molecular dynamic issues Sophie Barbe (Tue Jan 23 2007 - 08:34:50 CST)
- Re: AMBER: Molecular dynamic issues Chupakhin Vladimir (Tue Jan 23 2007 - 08:50:56 CST)
  - Re: AMBER: Molecular dynamic issues Carlos Simmerling (Tue Jan 23 2007 - 08:54:24 CST)
    - Re: AMBER: Molecular dynamic issues Sophie Barbe (Wed Jan 24 2007 - 08:41:19 CST)
AMBER: coordinates ****** kepa koldo burusco (Tue Jan 23 2007 - 10:19:54 CST)
- Re: AMBER: coordinates ****** David A. Case (Thu Jan 25 2007 - 14:08:52 CST)
  - AMBER: about coordinates ****** and diffusion kepa koldo burusco (Sun Jan 28 2007 - 11:15:57 CST)
    - RE: AMBER: about coordinates ****** and diffusion Ross Walker (Sun Jan 28 2007 - 11:28:30 CST)
    - Re: AMBER: about coordinates ****** and diffusion Thomas Cheatham (Sun Jan 28 2007 - 15:09:00 CST)
Re: AMBER: nuc.in file Bill Ross (Tue Jan 23 2007 - 11:42:44 CST)
AMBER: dihedral angle by Ptraj Esther Brugger (Tue Jan 23 2007 - 12:24:42 CST)
- Re: AMBER: dihedral angle by Ptraj Thomas Cheatham III (Tue Jan 23 2007 - 12:41:22 CST)
  - Re: AMBER: dihedral angle by Ptraj Esther Brugger (Tue Jan 23 2007 - 17:02:00 CST)
Re: AMBER: coordinates ****** Bill Ross (Tue Jan 23 2007 - 15:20:10 CST)
AMBER: Does amber use water density around 1 at room temperature Li Su (Tue Jan 23 2007 - 16:07:20 CST)
- RE: AMBER: Does amber use water density around 1 at room temperature Ross Walker (Tue Jan 23 2007 - 17:11:41 CST)
  - Re: AMBER: Does amber use water density around 1 at room temperature Li Su (Wed Jan 24 2007 - 16:44:40 CST)
AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 19:26:45 CST)
AMBER: minimization using fcap Syed Tarique Moin (Wed Jan 24 2007 - 03:08:40 CST)
- Re: AMBER: minimization using fcap David A. Case (Wed Jan 24 2007 - 09:05:20 CST)
AMBER: MM-PSBA decoupling Sergey Samsonov (Wed Jan 24 2007 - 07:03:24 CST)
AMBER: Unable to compile amber9 Vinh To (Wed Jan 24 2007 - 08:41:06 CST)
- RE: AMBER: Unable to compile amber9 Ross Walker (Wed Jan 24 2007 - 09:48:41 CST)
AMBER: (no subject) Sophie Barbe (Wed Jan 24 2007 - 11:26:20 CST)
AMBER: organic solvent : hexan octan Sophie Barbe (Wed Jan 24 2007 - 11:38:50 CST)
- Re: AMBER: organic solvent : hexan octan Cenk Andac (Wed Jan 24 2007 - 12:18:19 CST)
  - Re: AMBER: organic solvent : hexan octan Sophie Barbe (Wed Jan 24 2007 - 12:28:38 CST)
    - Re: AMBER: organic solvent : hexan octan Gustavo Seabra (Wed Jan 24 2007 - 13:12:40 CST)
    - Re: AMBER: organic solvent : hexan octan Cenk Andac (Wed Jan 24 2007 - 13:37:12 CST)
- Re: AMBER: organic solvent : hexan octan FyD (Wed Jan 24 2007 - 22:50:33 CST)
AMBER: RE: a request Ross Walker (Wed Jan 24 2007 - 11:57:32 CST)
AMBER: LJ potential Steve Seibold (Wed Jan 24 2007 - 13:44:58 CST)
- Re: AMBER: LJ potential David A. Case (Sat Jan 27 2007 - 12:03:15 CST)
AMBER: evaluate expression Ji-Lai Li (Wed Jan 24 2007 - 22:14:11 CST)
AMBER: Drug Leads interaction with ds and Triplex DNA puneet kacker (Wed Jan 24 2007 - 23:28:41 CST)
AMBER: Fwd: a request santanu roy (Thu Jan 25 2007 - 02:55:32 CST)
- Re: AMBER: Fwd: a request Gustavo Seabra (Thu Jan 25 2007 - 06:44:58 CST)
  - Re: AMBER: Fwd: a request santanu roy (Thu Jan 25 2007 - 07:15:08 CST)
AMBER: error when compiling Moilview Kailee (Thu Jan 25 2007 - 05:31:24 CST)
- Re: AMBER: error when compiling Moilview Carlos Simmerling (Thu Jan 25 2007 - 06:24:53 CST)
  - Re: AMBER: error when compiling Moilview Kailee (Thu Jan 25 2007 - 07:03:07 CST)
AMBER: Gas-phase energies (and more) Jason K (Thu Jan 25 2007 - 17:04:16 CST)
- RE: AMBER: Gas-phase energies (and more) Yong Duan (Thu Jan 25 2007 - 17:58:48 CST)
  - Re: AMBER: Gas-phase energies (and more) Jason K (Fri Jan 26 2007 - 15:36:25 CST)
- RE: AMBER: Gas-phase energies (and more) Yong Duan (Tue Jan 30 2007 - 14:32:39 CST)
Re: AMBER: amber9 parralel compiling Seaclear Theory (Thu Jan 25 2007 - 20:15:05 CST)
- Re: AMBER: amber9 parralel compiling Seaclear Theory (Fri Jan 26 2007 - 12:55:43 CST)
- Re: AMBER: amber9 parralel compiling David A. Case (Fri Jan 26 2007 - 17:45:25 CST)
  - Re: AMBER: amber9 parralel compiling Seaclear Theory (Sat Jan 27 2007 - 12:59:23 CST)
    - Re: AMBER: amber9 parralel compiling David A. Case (Sat Jan 27 2007 - 13:28:27 CST)
    - Re: AMBER: amber9 parralel compiling Seaclear Theory (Sat Jan 27 2007 - 17:16:19 CST)
AMBER: sander bug? Nursultan Bogatov (Thu Jan 25 2007 - 20:28:53 CST)
- RE: AMBER: sander bug? Ross Walker (Fri Jan 26 2007 - 01:26:55 CST)
AMBER: another sander bug? Nursultan Bogatov (Fri Jan 26 2007 - 00:43:13 CST)
- RE: AMBER: another sander bug? Ross Walker (Fri Jan 26 2007 - 01:50:39 CST)
  - AMBER: improper dihedral lishan yao (Fri Jan 26 2007 - 08:42:15 CST)
    - Re: AMBER: improper dihedral David A. Case (Fri Jan 26 2007 - 10:09:55 CST)
AMBER: Regarding energy of decomposition tutorials zachary hartman (Fri Jan 26 2007 - 09:29:50 CST)
Fwd: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Fri Jan 26 2007 - 12:54:56 CST)
AMBER: amber parallel compile error with g95 Seaclear Theory (Fri Jan 26 2007 - 13:00:52 CST)
AMBER: radius of gyration Esther Brugger (Fri Jan 26 2007 - 14:17:37 CST)
AMBER: Is there a pmemd machine file for OSX Intel Kevin Kelliher (Fri Jan 26 2007 - 15:50:29 CST)
AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Akshay Patny (Fri Jan 26 2007 - 16:23:46 CST)
- RE: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Ross Walker (Fri Jan 26 2007 - 17:11:06 CST)
  - Re: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation David A. Case (Fri Jan 26 2007 - 19:45:51 CST)
  - AMBER: Amber/ANAL and psf files rebeca_at_mmb.pcb.ub.es (Wed Feb 21 2007 - 10:24:33 CST)
    - AMBER: contacts in ptraj (Amber 9) rebeca_at_mmb.pcb.ub.es (Wed Feb 21 2007 - 12:56:50 CST)
    - Re: AMBER: Amber/ANAL and psf files David A. Case (Wed Feb 21 2007 - 22:14:42 CST)
- RE: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Akshay Patny (Fri Jan 26 2007 - 17:27:56 CST)
AMBER: Ligand-Protein Distance Restraints during MD Simulation Akshay Patny (Fri Jan 26 2007 - 18:06:26 CST)
- Re: AMBER: Ligand-Protein Distance Restraints during MD Simulation David Mobley (Tue Jan 30 2007 - 11:16:19 CST)
AMBER: mm_pbsa Array reference error Syed Tarique Moin (Sat Jan 27 2007 - 02:02:16 CST)
- Re: AMBER: mm_pbsa Array reference error Scott Pendley (Wed Jan 31 2007 - 11:48:36 CST)
  - Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Wed Jan 31 2007 - 23:19:48 CST)
AMBER: yet another SANDER bug? Miyeegombo Enkhbold (Sat Jan 27 2007 - 21:11:22 CST)
- RE: AMBER: yet another SANDER bug? Ross Walker (Sat Jan 27 2007 - 22:18:24 CST)
AMBER: Improper angle by Antechamber Pavan G (Sun Jan 28 2007 - 11:28:29 CST)
- Re: AMBER: Improper angle by Antechamber David A. Case (Sun Jan 28 2007 - 20:20:26 CST)
Re: AMBER: radius of gyration Bill Ross (Sun Jan 28 2007 - 14:01:05 CST)
- Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 09:51:26 CST)
- Re: AMBER: radius of gyration Bill Ross (Mon Jan 29 2007 - 13:51:39 CST)
  - Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 15:06:00 CST)
    - Re: AMBER: radius of gyration Thomas Cheatham III (Mon Jan 29 2007 - 15:21:20 CST)
    - Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 16:27:34 CST)
AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Jiapu.Zhang_at_csiro.au (Mon Jan 29 2007 - 00:04:34 CST)
- RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Ross Walker (Mon Jan 29 2007 - 00:16:32 CST)
- RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Jiapu.Zhang_at_csiro.au (Mon Jan 29 2007 - 16:08:26 CST)
AMBER: gaussian output to prepin problem Rima Chaudhuri (Mon Jan 29 2007 - 11:14:31 CST)
- RE: AMBER: gaussian output to prepin problem Junmei Wang (Mon Jan 29 2007 - 20:43:56 CST)
AMBER: Antechamber Charge Calculation Method A Box (Mon Jan 29 2007 - 18:46:42 CST)
- RE: AMBER: Antechamber Charge Calculation Method Junmei Wang (Mon Jan 29 2007 - 20:48:17 CST)
AMBER: MM-PBSA doubt mathew k varghese (Mon Jan 29 2007 - 20:12:44 CST)
- RE: AMBER: MM-PBSA doubt Ray Luo (Mon Jan 29 2007 - 22:04:52 CST)
  - RE: AMBER: MM-PBSA doubt mathew k varghese (Mon Jan 29 2007 - 22:22:50 CST)
    - RE: AMBER: MM-PBSA doubt Ray Luo (Mon Jan 29 2007 - 23:29:01 CST)
AMBER: xleap deepti nayar (Tue Jan 30 2007 - 04:40:10 CST)
- Re: AMBER: xleap Chupakhin Vladimir (Tue Jan 30 2007 - 04:55:40 CST)
- Re: AMBER: xleap Navnit Kumar Mishra (Tue Jan 30 2007 - 05:53:11 CST)
- Re: AMBER: xleap Gustavo Seabra (Tue Jan 30 2007 - 09:57:11 CST)
AMBER: questions about analysing LES results Kailee (Tue Jan 30 2007 - 11:00:40 CST)
Fwd: AMBER: Improper angle by Antechamber Pavan G (Tue Jan 30 2007 - 12:46:34 CST)
AMBER: Charges in TI calculations and leap Austin B. Yongye (Tue Jan 30 2007 - 13:35:50 CST)
- Re: AMBER: Charges in TI calculations and leap Ilyas Yildirim (Tue Jan 30 2007 - 13:48:00 CST)
  - Re: AMBER: Charges in TI calculations and leap Austin B. Yongye (Tue Jan 30 2007 - 14:10:54 CST)
    - Re: AMBER: Charges in TI calculations and leap David A. Case (Tue Jan 30 2007 - 15:24:33 CST)
AMBER: Ptraj: watershell and distance Esther Brugger (Tue Jan 30 2007 - 15:26:17 CST)
- Re: AMBER: Ptraj: watershell and distance Pavan G (Tue Jan 30 2007 - 16:01:07 CST)
- Re: AMBER: Ptraj: watershell and distance Thomas Cheatham III (Thu Feb 01 2007 - 12:46:04 CST)
AMBER: I need some constant pressure MD help David Cerutti (Tue Jan 30 2007 - 22:39:06 CST)
- RE: AMBER: I need some constant pressure MD help Ross Walker (Tue Jan 30 2007 - 23:47:38 CST)
AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Wed Jan 31 2007 - 01:44:13 CST)
- RE: AMBER: some questions about minimization and MD of DNA duplex with sander Ross Walker (Wed Jan 31 2007 - 10:36:27 CST)
  - Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Thu Feb 01 2007 - 23:40:11 CST)
    - RE: AMBER: some questions about minimization and MD of DNA duplex with sander Ross Walker (Fri Feb 02 2007 - 11:23:02 CST)
    - Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Mon Feb 05 2007 - 23:43:29 CST)
AMBER: mm_pbsa error Syed Tarique Moin (Wed Jan 31 2007 - 03:19:46 CST)
AMBER: mm_pbsa error Syed Tarique Moin (Wed Jan 31 2007 - 03:19:02 CST)
AMBER: ptraj khn _ (Wed Jan 31 2007 - 10:26:00 CST)
- Re: AMBER: ptraj Thomas Cheatham III (Wed Jan 31 2007 - 18:03:00 CST)
AMBER: nonpolar solvation energy khn _ (Wed Jan 31 2007 - 10:33:55 CST)
- RE: AMBER: nonpolar solvation energy Ray Luo (Wed Jan 31 2007 - 13:37:34 CST)
  - Re: AMBER: nonpolar solvation energy Carlos Simmerling (Wed Jan 31 2007 - 13:54:14 CST)
AMBER: format of .xyz files and pdb Gobind Singh Bisht (Wed Jan 31 2007 - 16:05:24 CST)
- Re: AMBER: format of .xyz files and pdb Steven Winfield (Wed Jan 31 2007 - 16:20:43 CST)
AMBER: Still puzzled about this virial computation David Cerutti (Thu Feb 01 2007 - 02:00:10 CST)
- Re: AMBER: Still puzzled about this virial computation Robert Duke (Thu Feb 01 2007 - 09:35:25 CST)
  - Re: AMBER: Still puzzled about this virial computation Robert Duke (Thu Feb 01 2007 - 10:16:51 CST)
AMBER: xleap deepti nayar (Thu Feb 01 2007 - 02:04:09 CST)
- RE: AMBER: xleap Ross Walker (Thu Feb 01 2007 - 10:18:19 CST)
- Re: AMBER: xleap David A. Case (Thu Feb 01 2007 - 10:58:40 CST)
AMBER: subscribe amber Stéphane Téletchéa (Thu Feb 01 2007 - 09:11:25 CST)
AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 15:26:12 CST)
- Re: AMBER: Example needed for addAtomType command David A. Case (Thu Feb 01 2007 - 16:30:03 CST)
  - Re: AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 17:02:39 CST)
AMBER: ab initio modeling using Amber snoze pa (Thu Feb 01 2007 - 20:59:17 CST)
- Re: AMBER: ab initio modeling using Amber Gustavo Seabra (Thu Feb 01 2007 - 22:07:45 CST)
AMBER: Problem with paralell installation Martin Stennett (Fri Feb 02 2007 - 02:22:25 CST)
- RE: AMBER: Problem with paralell installation Ross Walker (Fri Feb 02 2007 - 09:21:16 CST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Feb 02 2007 - 10:05:35 CST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood (Fri Feb 02 2007 - 11:40:10 CST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood (Fri Feb 02 2007 - 11:41:50 CST)
AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 11:07:47 CST)
- Re: AMBER: iRED and corrired David A. Case (Fri Feb 02 2007 - 12:57:43 CST)
  - Re: AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 15:05:41 CST)
  - Re: AMBER: iRED and corrired Gohlke_at_bioinformatik.uni-frankfurt.de (Sun Feb 04 2007 - 07:01:17 CST)
    - Re: AMBER: iRED and corrired Holger Gohlke (Mon Feb 05 2007 - 10:09:15 CST)
AMBER: calculating distance between two atoms bertrand russell (Fri Feb 02 2007 - 11:49:07 CST)
- Re: AMBER: calculating distance between two atoms Carlos Simmerling (Fri Feb 02 2007 - 15:42:41 CST)
  - Re: AMBER: calculating distance between two atoms bertrand russell (Mon Feb 05 2007 - 06:22:16 CST)
    - Re: AMBER: calculating distance between two atoms Carlos Simmerling (Mon Feb 05 2007 - 06:55:19 CST)
AMBER: How do I make and enter new ff parameters into AMBER MARY O'CONNOR (Fri Feb 02 2007 - 13:35:20 CST)
AMBER: How do I make and enter new ff parameters into AMBER HL Eastwood (Fri Feb 02 2007 - 15:26:46 CST)
AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 18:20:34 CST)
- Re: AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 18:36:01 CST)
  - Re: AMBER: angle command in Ptraj Carlos Simmerling (Sat Feb 03 2007 - 07:17:26 CST)
AMBER: addions Amit Kumar (Sat Feb 03 2007 - 07:17:57 CST)
- Re: AMBER: addions David A. Case (Sun Feb 04 2007 - 11:33:37 CST)
AMBER: ptraj hbond jacopo.sgrignani_at_unifi.it (Sat Feb 03 2007 - 10:28:20 CST)
AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 11:40:12 CST)
- Re: AMBER: equilibration in explicit solvent David A. Case (Sun Feb 04 2007 - 12:21:18 CST)
  - Re: AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 12:32:05 CST)
- RE: AMBER: equilibration in explicit solvent Yong Duan (Sun Feb 04 2007 - 13:07:30 CST)
- Re: AMBER: equilibration in explicit solvent Ilyas Yildirim (Sun Feb 04 2007 - 23:13:48 CST)
AMBER: Calculate force constants Markus Weingarth (Sun Feb 04 2007 - 16:13:28 CST)
AMBER: force fields deepti nayar (Mon Feb 05 2007 - 01:05:09 CST)
- Re: AMBER: force fields Carlos Simmerling (Mon Feb 05 2007 - 06:49:29 CST)
- RE: AMBER: force fields Yong Duan (Mon Feb 05 2007 - 11:15:10 CST)
  - Re: AMBER: force fields deepti nayar (Mon Feb 05 2007 - 23:37:05 CST)
- RE: AMBER: force fields Yong Duan (Tue Feb 06 2007 - 10:13:58 CST)
AMBER: replacement of mutated atoms in protein structure bertrand russell (Mon Feb 05 2007 - 04:42:37 CST)
AMBER: MAXGRP error message Alexander Steudle (Mon Feb 05 2007 - 08:03:45 CST)
- Re: AMBER: MAXGRP error message David A. Case (Wed Feb 07 2007 - 11:43:33 CST)
AMBER: problem in xleap WANG,YING (Mon Feb 05 2007 - 09:45:14 CST)
- Re: AMBER: problem in xleap Steven Winfield (Mon Feb 05 2007 - 10:06:12 CST)
- Re: AMBER: problem in xleap WANG,YING (Tue Feb 06 2007 - 17:36:29 CST)
  - Re: AMBER: problem in xleap Carlos Simmerling (Tue Feb 06 2007 - 17:46:29 CST)
- Re: AMBER: problem in xleap WANG,YING (Tue Feb 06 2007 - 19:12:54 CST)
AMBER: Force fields for iron MARY O'CONNOR (Mon Feb 05 2007 - 10:19:52 CST)
- AMBER: positive binding energy saurabh agrawal (Mon Feb 05 2007 - 11:30:46 CST)
AMBER: Tutorial for chemical shift calculation? Mike Summers (Mon Feb 05 2007 - 19:04:48 CST)
- Re: AMBER: Tutorial for chemical shift calculation? David A. Case (Tue Feb 06 2007 - 10:25:40 CST)
  - Re: AMBER: Tutorial for chemical shift calculation? Mike Summers (Tue Feb 06 2007 - 12:36:05 CST)
  - AMBER: Pseudo-CSA in Amber? Mike Summers (Mon Feb 19 2007 - 08:30:13 CST)
    - Re: AMBER: Pseudo-CSA in Amber? David A. Case (Wed Feb 21 2007 - 18:04:32 CST)
AMBER: Link to Modified NA bases files Seth Lilavivat (Mon Feb 05 2007 - 16:22:50 CST)
- Re: AMBER: Link to Modified NA bases files Ilyas Yildirim (Mon Feb 05 2007 - 22:05:21 CST)
AMBER: Glycam Beale, John (Tue Feb 06 2007 - 07:07:22 CST)
- Re: AMBER: Glycam David A. Case (Tue Feb 06 2007 - 10:04:21 CST)
- Re: AMBER: Glycam kkirschn_at_hamilton.edu (Tue Feb 06 2007 - 08:44:52 CST)
AMBER: MM-PBSA questions/clarifications Rima Chaudhuri (Tue Feb 06 2007 - 12:51:08 CST)
- Re: AMBER: MM-PBSA questions/clarifications vanessa wai (Tue Feb 13 2007 - 04:36:27 CST)
AMBER: Compile Amber9 for MVAPICH Mike Hanby (Tue Feb 06 2007 - 13:51:18 CST)
- Re: AMBER: Compile Amber9 for MVAPICH David A. Case (Tue Feb 06 2007 - 14:23:07 CST)
AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 17:08:08 CST)
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) David A. Case (Tue Feb 06 2007 - 18:22:03 CST)
  - Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Z. Nevin Gerek (Wed Feb 07 2007 - 11:20:12 CST)
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Mike Summers (Tue Feb 06 2007 - 20:30:22 CST)
AMBER: Missing Value for MM ELE Rima Chaudhuri (Tue Feb 06 2007 - 17:26:08 CST)
AMBER: side chain orientation Esther Brugger (Tue Feb 06 2007 - 17:36:48 CST)
- Re: AMBER: side chain orientation Fenghui Fan (Tue Feb 06 2007 - 18:11:47 CST)
  - Re: AMBER: side chain orientation Esther Brugger (Wed Feb 07 2007 - 09:23:55 CST)
    - Re: AMBER: side chain orientation Ilyas Yildirim (Wed Feb 07 2007 - 12:00:37 CST)
AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 17:08:08 CST)
AMBER: trajectory problem Miguel Ferreira (Tue Feb 06 2007 - 22:52:25 CST)
- Re: AMBER: trajectory problem David A. Case (Wed Feb 07 2007 - 11:52:59 CST)
AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 04:42:51 CST)
- Re: AMBER: antechamber for topology file Carlos Simmerling (Wed Feb 07 2007 - 06:32:52 CST)
- Re: AMBER: antechamber for topology file FyD (Wed Feb 07 2007 - 07:28:58 CST)
  - Re: AMBER: antechamber for topology file deepti nayar (Thu Feb 08 2007 - 00:07:22 CST)
- RE: AMBER: antechamber for topology file Akshay Patny (Thu Feb 08 2007 - 00:28:50 CST)
  - Re: AMBER: antechamber for topology file deepti nayar (Thu Feb 08 2007 - 00:55:35 CST)
    - Re: AMBER: antechamber for topology file David A. Case (Thu Feb 08 2007 - 01:08:04 CST)
    - Re: AMBER: antechamber for topology file FyD (Thu Feb 08 2007 - 02:10:29 CST)
AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 08:03:07 CST)
- Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson (Wed Feb 07 2007 - 10:08:41 CST)
- RE: AMBER: Help!! I cannot perform the ambpdb Ross Walker (Wed Feb 07 2007 - 09:21:13 CST)
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 13:49:46 CST)
  - Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson (Wed Feb 07 2007 - 14:25:19 CST)
- RE: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 14:19:29 CST)
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 15:23:16 CST)
AMBER: Strange behavior on g95 compile. Martin Stennett (Wed Feb 07 2007 - 10:00:23 CST)
- Re: AMBER: Strange behavior on g95 compile. Seth Hayik (Wed Feb 07 2007 - 10:31:50 CST)
- Re: AMBER: Strange behavior on g95 compile. Mark Williamson (Wed Feb 07 2007 - 10:18:16 CST)
- RE: AMBER: Strange behavior on g95 compile. Ross Walker (Wed Feb 07 2007 - 10:17:37 CST)
AMBER: problem with AMBER8 installation Subhasish Chatterjee (Wed Feb 07 2007 - 11:50:48 CST)
- RE: AMBER: problem with AMBER8 installation Ross Walker (Wed Feb 07 2007 - 12:06:42 CST)
- Re: AMBER: problem with AMBER8 installation David A. Case (Wed Feb 07 2007 - 12:10:51 CST)
AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 13:50:12 CST)
AMBER: Membrane Simulation: NPT issues Akshay Patny (Wed Feb 07 2007 - 12:29:36 CST)
AMBER: Binding free energy calculation - MM-pbsa Rima Chaudhuri (Wed Feb 07 2007 - 14:55:26 CST)
AMBER: Membrane Simulation: NPT Issues Akshay Patny (Wed Feb 07 2007 - 11:28:05 CST)
- RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny (Mon Feb 12 2007 - 09:33:40 CST)
  - Re: AMBER: Membrane Simulation: NPT Issues David A. Case (Wed Feb 14 2007 - 17:04:47 CST)
    - RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny (Thu Feb 15 2007 - 10:54:02 CST)
AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 13:50:12 CST)
- Re: AMBER: Compiling Amber 8 on SuSE 10.2 Cenk Andac (Wed Feb 07 2007 - 14:02:17 CST)
  - Re: AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 16:35:27 CST)
AMBER: Missing values for MM ELE (MM-PBSA)..help!! Rima Chaudhuri (Wed Feb 07 2007 - 10:21:38 CST)
AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 09:13:00 CST)
- RE: AMBER: Compiling Amber 7 Ross Walker (Thu Feb 08 2007 - 10:30:30 CST)
  - RE: AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 13:27:41 CST)
  - RE: AMBER: Compiling Amber 7 David J. Powers (Sat Feb 10 2007 - 09:59:42 CST)
    - RE: AMBER: Compiling Amber 7 Ross Walker (Sat Feb 10 2007 - 11:11:54 CST)
AMBER: H-Bond Esther Brugger (Thu Feb 08 2007 - 11:06:57 CST)
AMBER: Protonation of Aspartate sai vikram (Thu Feb 08 2007 - 11:12:03 CST)
- Re: AMBER: Protonation of Aspartate Adrian Roitberg (Thu Feb 08 2007 - 11:17:11 CST)
AMBER: Calcium and peptides Beale, John (Thu Feb 08 2007 - 12:20:30 CST)
AMBER: Compiling AMBER 8 on RHEL4 AMD64 Seth Lilavivat (Thu Feb 08 2007 - 13:53:44 CST)
- Re: AMBER: Compiling AMBER 8 on RHEL4 AMD64 David A. Case (Fri Feb 09 2007 - 00:22:01 CST)
AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 14:11:16 CST)
AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 14:11:16 CST)
AMBER: phe-phe prep file deepti nayar (Fri Feb 09 2007 - 00:09:15 CST)
AMBER: assigning charges to a prepi file deepti nayar (Fri Feb 09 2007 - 00:38:27 CST)
- Re: AMBER: assigning charges to a prepi file David A. Case (Fri Feb 09 2007 - 00:58:08 CST)
AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) Chengwen Chen (Fri Feb 09 2007 - 02:25:00 CST)
- Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) David A. Case (Sun Feb 11 2007 - 00:57:27 CST)
AMBER: Umbrella sampling Franck Vendeix (Fri Feb 09 2007 - 08:37:35 CST)
- Re: AMBER: Umbrella sampling Jerome.GOLEBIOWSKI_at_unice.fr (Mon Feb 12 2007 - 03:33:18 CST)
  - Re: AMBER: Umbrella sampling Franck Vendeix (Wed Feb 14 2007 - 21:13:31 CST)
AMBER: amber9 possible failure tgtmd jlalonde (Fri Feb 09 2007 - 10:19:19 CST)
- Re: AMBER: amber9 possible failure tgtmd David A. Case (Mon Feb 12 2007 - 23:58:15 CST)
AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 11:43:14 CST)
- Re: AMBER: problem with sander David A. Case (Sat Feb 10 2007 - 04:08:01 CST)
  - Re: AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 13:35:34 CST)
AMBER: ptraj dipole calculation in QMMM simulation Evan Kelly (Fri Feb 09 2007 - 12:36:30 CST)
- Re: AMBER: ptraj dipole calculation in QMMM simulation Gustavo Seabra (Fri Feb 09 2007 - 12:54:04 CST)
- RE: AMBER: ptraj dipole calculation in QMMM simulation Ross Walker (Fri Feb 09 2007 - 12:53:30 CST)
AMBER: Heating the system prior to production run Ilyas Yildirim (Fri Feb 09 2007 - 15:28:08 CST)
AMBER: Umbrella sampling - Tutorial bertrand russell (Sat Feb 10 2007 - 01:35:31 CST)
AMBER: extracting coordinates from crd file gurpreet singh (Sat Feb 10 2007 - 02:40:44 CST)
- Re: AMBER: extracting coordinates from crd file Ilyas Yildirim (Sat Feb 10 2007 - 02:59:04 CST)
AMBER: extracting coordinate from crd file gurpreet singh (Sat Feb 10 2007 - 04:05:20 CST)
- Re: AMBER: extracting coordinate from crd file Amit Kumar (Sat Feb 10 2007 - 09:31:35 CST)
- Re: AMBER: extracting coordinate from crd file David A. Case (Sat Feb 10 2007 - 10:08:28 CST)
  - AMBER: atomicfluct Catein Catherine (Sun Feb 11 2007 - 23:45:40 CST)
AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Sat Feb 10 2007 - 18:00:11 CST)
- Re: AMBER: simulating part of a molecule with homology modeling Fenghui Fan (Sat Feb 10 2007 - 22:26:41 CST)
  - RE: AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Mon Feb 12 2007 - 10:50:36 CST)
AMBER: quasiharnomic analysis Hans Lee (Sun Feb 11 2007 - 15:12:52 CST)
- Re: AMBER: quasiharnomic analysis David A. Case (Mon Feb 12 2007 - 10:31:36 CST)
Re: AMBER: extracting coordinate from crd file Bill Ross (Sun Feb 11 2007 - 23:13:38 CST)
AMBER: connect atom deepti nayar (Mon Feb 12 2007 - 05:01:57 CST)
- Re: AMBER: connect atom David A. Case (Mon Feb 12 2007 - 10:28:57 CST)
AMBER: help me out... Anju Sharma (Mon Feb 12 2007 - 06:21:00 CST)
- AMBER: Fwd: help me out... Anju Sharma (Mon Feb 12 2007 - 06:22:57 CST)
  - Re: AMBER: Fwd: help me out... Chris Moth (Mon Feb 12 2007 - 09:08:24 CST)
- RE: AMBER: help me out... Ross Walker (Mon Feb 12 2007 - 09:11:03 CST)
AMBER: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 10:15:09 CST)
- AMBER: Re: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 10:16:45 CST)
- Re: AMBER: reporting EPtot and EKtot separately for two molecules David A. Case (Mon Feb 12 2007 - 10:25:55 CST)
AMBER: Lone Pairs Beale, John (Mon Feb 12 2007 - 12:52:48 CST)
- Re: AMBER: Lone Pairs David A. Case (Mon Feb 12 2007 - 15:24:48 CST)
  - RE: AMBER: Lone Pairs Beale, John (Tue Feb 13 2007 - 08:33:44 CST)
    - Re: AMBER: Lone Pairs David A. Case (Tue Feb 13 2007 - 10:00:21 CST)
AMBER: How to place torsion restraint Seth Lilavivat (Mon Feb 12 2007 - 19:24:40 CST)
- Re: AMBER: How to place torsion restraint Gustavo Seabra (Tue Feb 13 2007 - 10:48:08 CST)
AMBER: Modified nucleotides mathew k varghese (Mon Feb 12 2007 - 22:44:31 CST)
- Re: AMBER: Modified nucleotides Ilyas Yildirim (Mon Feb 12 2007 - 22:58:50 CST)
- RE: AMBER: Modified nucleotides Seth Lilavivat (Mon Feb 12 2007 - 22:59:37 CST)
- Re: AMBER: Modified nucleotides Thomas Cheatham (Mon Feb 12 2007 - 23:03:38 CST)
- Re: AMBER: Modified nucleotides Sean Rathlef (Mon Feb 12 2007 - 23:55:20 CST)
- Re: AMBER: Modified nucleotides Raviprasad Aduri (Tue Feb 13 2007 - 11:23:15 CST)
  - Re: AMBER: Modified nucleotides mathew k varghese (Tue Feb 13 2007 - 21:47:08 CST)
AMBER: hi Anju Sharma (Tue Feb 13 2007 - 04:08:01 CST)
- Re: AMBER: hi Steven Winfield (Tue Feb 13 2007 - 04:42:16 CST)
  - AMBER: Solvate box Sophie Barbe (Tue Feb 13 2007 - 07:21:28 CST)
    - RE: AMBER: Solvate box Ross Walker (Tue Feb 13 2007 - 10:26:51 CST)
    - Re: AMBER: Solvate box M. L. Dodson (Tue Feb 13 2007 - 21:33:49 CST)
  - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 22:44:45 CST)
    - Re: AMBER: hi Ilyas Yildirim (Wed Feb 14 2007 - 16:14:11 CST)
    - Re: AMBER: hi Steven Winfield (Wed Feb 14 2007 - 16:21:01 CST)
- RE: AMBER: hi Ross Walker (Tue Feb 13 2007 - 10:16:56 CST)
  - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 22:48:36 CST)
    - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 22:50:16 CST)
    - RE: AMBER: hi Ross Walker (Wed Feb 14 2007 - 10:15:50 CST)
AMBER: Constraint virial David Cerutti (Tue Feb 13 2007 - 04:22:20 CST)
AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 13:05:16 CST)
- Re: AMBER: Box problems in vacuum minimization with sander.serial 8 David A. Case (Tue Feb 13 2007 - 13:34:57 CST)
  - Re: AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 13:43:34 CST)
AMBER: How to parameterize frcmod for NA Seth Lilavivat (Tue Feb 13 2007 - 13:27:59 CST)
AMBER: Replica Exchange Christopher Gaughan (Tue Feb 13 2007 - 15:20:08 CST)
AMBER: Positive binding free energy! Rima Chaudhuri (Tue Feb 13 2007 - 16:53:05 CST)
- Re: AMBER: Positive binding free energy! David Cerutti (Tue Feb 13 2007 - 18:40:35 CST)
AMBER: SANDER bug Ichinkhorloo Erdenebaatar (Tue Feb 13 2007 - 19:19:21 CST)
- Re: AMBER: SANDER bug David A. Case (Wed Feb 14 2007 - 12:11:12 CST)
AMBER: LeaP: Mol2 files A Box (Tue Feb 13 2007 - 19:44:08 CST)
- Re: AMBER: LeaP: Mol2 files FyD (Wed Feb 14 2007 - 11:47:40 CST)
AMBER: Comparison of normal modes with ptraj? Harald Lanig (Wed Feb 14 2007 - 04:10:19 CST)
- Re: AMBER: Comparison of normal modes with ptraj? Gohlke_at_bioinformatik.uni-frankfurt.de (Wed Feb 14 2007 - 07:08:38 CST)
AMBER: NMR violations increase in explicite water Michel Becker (Wed Feb 14 2007 - 14:15:14 CST)
- Re: AMBER: NMR violations increase in explicite water David A. Case (Thu Feb 15 2007 - 10:40:12 CST)
AMBER: Deriving constraint forces on water molecules based on SETTLE moves David Cerutti (Wed Feb 14 2007 - 18:08:45 CST)
- Re: AMBER: Deriving constraint forces on water molecules based on SETTLE moves Steven Winfield (Thu Feb 15 2007 - 07:28:00 CST)
AMBER: Prepgen A Box (Wed Feb 14 2007 - 22:15:21 CST)
AMBER: units in hessian matrix Marie Brut (Thu Feb 15 2007 - 10:52:01 CST)
- Re: AMBER: units in hessian matrix David A. Case (Thu Feb 15 2007 - 11:31:01 CST)
  - Re: AMBER: units in hessian matrix Adrian Roitberg (Thu Feb 15 2007 - 11:35:07 CST)
    - Re: AMBER: units in hessian matrix David A. Case (Thu Feb 15 2007 - 12:07:03 CST)
AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 10:59:53 CST)
- Re: AMBER: Simulating a section of a molecule Carlos Simmerling (Thu Feb 15 2007 - 12:06:50 CST)
- Re: AMBER: Simulating a section of a molecule Thomas Cheatham III (Thu Feb 15 2007 - 15:33:40 CST)
  - RE: AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 17:10:06 CST)
AMBER: implicit solvent free energy calcs David Mobley (Thu Feb 15 2007 - 12:07:37 CST)
- Re: AMBER: implicit solvent free energy calcs David A. Case (Thu Feb 15 2007 - 14:19:53 CST)
AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 13:53:45 CST)
- Re: AMBER: read the data Florian Haberl (Thu Feb 15 2007 - 14:11:16 CST)
  - Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 11:43:39 CST)
- Re: AMBER: read the data David LeBard (Thu Feb 15 2007 - 15:18:08 CST)
  - Re: AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 17:00:39 CST)
  - Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 12:40:45 CST)
    - Re: AMBER: read the data David LeBard (Fri Feb 16 2007 - 13:00:10 CST)
- Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 10:54:06 CST)
AMBER: Density of a system in MD Akshay Patny (Thu Feb 15 2007 - 14:45:27 CST)
AMBER: How to modify the velocity of a water molecule? Ji-Lai Li (Thu Feb 15 2007 - 20:15:45 CST)
- Re: AMBER: How to modify the velocity of a water molecule? Carlos Simmerling (Thu Feb 15 2007 - 20:58:54 CST)
- Re: AMBER: How to modify the velocity of a water molecule? Thomas Cheatham (Thu Feb 15 2007 - 21:47:24 CST)
AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 09:13:45 CST)
- Re: AMBER: Box dimensions Gustavo Seabra (Fri Feb 16 2007 - 10:19:39 CST)
  - RE: AMBER: Box dimensions Akshay Patny (Fri Feb 16 2007 - 10:34:40 CST)
    - Re: AMBER: Box dimensions David A. Case (Fri Feb 16 2007 - 10:54:48 CST)
  - RE: AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 11:12:41 CST)
AMBER: H-bond ptraj dilemma Lorenzo Gontrani (Fri Feb 16 2007 - 09:46:54 CST)
AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 12:33:38 CST)
- Re: AMBER: Problem with dacdif when using cygwin Scott Brozell (Fri Feb 16 2007 - 13:32:06 CST)
- Re: AMBER: Problem with dacdif when using cygwin David A. Case (Fri Feb 16 2007 - 13:44:00 CST)
  - Re: AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 14:15:00 CST)
    - Re: AMBER: Problem with dacdif when using cygwin Scott Brozell (Fri Feb 16 2007 - 14:43:07 CST)
AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 14:57:40 CST)
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? Franck Vendeix (Fri Feb 16 2007 - 16:04:48 CST)
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 23:55:53 CST)
AMBER: Torsion Restraint on Glycosidic Bond Seth Lilavivat (Fri Feb 16 2007 - 15:13:52 CST)
- Re: AMBER: Torsion Restraint on Glycosidic Bond Thomas Cheatham III (Fri Feb 16 2007 - 15:32:30 CST)
- Re: AMBER: Torsion Restraint on Glycosidic Bond Carlos Simmerling (Fri Feb 16 2007 - 15:32:44 CST)
AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Fri Feb 16 2007 - 16:17:49 CST)
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case (Fri Feb 16 2007 - 19:22:05 CST)
  - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Sat Feb 17 2007 - 14:10:38 CST)
    - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case (Sat Feb 17 2007 - 15:22:38 CST)
    - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Wed Feb 28 2007 - 16:25:54 CST)
AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 10:12:28 CST)
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Sat Feb 17 2007 - 10:52:00 CST)
  - RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sun Feb 18 2007 - 23:51:55 CST)
AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 10:15:31 CST)
- Re: AMBER: Installing AMBER v9 in Linux Ilyas Yildirim (Sun Feb 18 2007 - 01:30:34 CST)
AMBER: REMD error on first exchange Daniel Oehme (Sun Feb 18 2007 - 20:31:57 CST)
- Re: AMBER: REMD error on first exchange Carlos Simmerling (Mon Feb 19 2007 - 08:21:16 CST)
AMBER: Water density calculation mathew k varghese (Mon Feb 19 2007 - 00:51:57 CST)
AMBER: Residence time of WATER gurpreet singh (Mon Feb 19 2007 - 02:33:59 CST)
AMBER: MDGRAPE and AMBER Craig Gough (Mon Feb 19 2007 - 02:34:43 CST)
- Re: AMBER: MDGRAPE and AMBER Carlos Simmerling (Mon Feb 19 2007 - 08:23:58 CST)
AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 07:27:34 CST)
- Re: AMBER: crd to pdb conversion Ilyas Yildirim (Mon Feb 19 2007 - 07:35:16 CST)
  - Re: Re: AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 09:04:58 CST)
    - Re: Re: AMBER: crd to pdb conversion Ilyas Yildirim (Mon Feb 19 2007 - 11:12:43 CST)
AMBER: carbohydrate-peptide Beale, John (Mon Feb 19 2007 - 10:09:54 CST)
- Re: AMBER: carbohydrate-peptide David A. Case (Wed Feb 21 2007 - 18:04:59 CST)
AMBER: DNA and RNA computations Jiri Sponer (Mon Feb 19 2007 - 12:16:53 CST)
AMBER: problems with bonding disulfide linkages Beale, John (Mon Feb 19 2007 - 14:39:10 CST)
- Re: AMBER: problems with bonding disulfide linkages Carlos Simmerling (Mon Feb 19 2007 - 14:45:28 CST)
- Re: AMBER: problems with bonding disulfide linkages Pankaj R. Daga (Mon Feb 19 2007 - 16:54:24 CST)
AMBER: Error in running replica exchange MD Seongeun Yang (Tue Feb 20 2007 - 05:45:38 CST)
- Re: AMBER: Error in running replica exchange MD Carlos Simmerling (Tue Feb 20 2007 - 08:17:56 CST)
  - Re: AMBER: Error in running replica exchange MD Carlos Simmerling (Tue Feb 20 2007 - 08:26:24 CST)
AMBER: Beale, John (Tue Feb 20 2007 - 07:02:24 CST)
AMBER: oops Beale, John (Tue Feb 20 2007 - 07:35:19 CST)
AMBER: RE: about ANTECHAMBER Ross Walker (Tue Feb 20 2007 - 10:22:21 CST)
- AMBER: interior dielectric constant Miguel Ferreira (Tue Feb 20 2007 - 11:22:31 CST)
AMBER: AMBER ff in CHARMM format!! Swarup Gupta (Tue Feb 20 2007 - 21:26:38 CST)
AMBER: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 22:02:56 CST)
AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Tue Feb 20 2007 - 22:17:41 CST)
- Re: AMBER: Is this system too large? Fenghui Fan (Tue Feb 20 2007 - 22:53:26 CST)
  - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Wed Feb 21 2007 - 11:02:21 CST)
    - RE: AMBER: Is this system too large? Fenghui Fan (Wed Feb 21 2007 - 16:55:57 CST)
- Re: AMBER: Is this system too large? David A. Case (Wed Feb 21 2007 - 18:05:39 CST)
  - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Thu Feb 22 2007 - 09:58:01 CST)
    - Re: AMBER: Is this system too large? David A. Case (Thu Feb 22 2007 - 20:01:52 CST)
    - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Fri Feb 23 2007 - 10:10:09 CST)
AMBER: LEaP Problem Beale, John (Wed Feb 21 2007 - 07:11:13 CST)
- Re: AMBER: LEaP Problem David A. Case (Thu Feb 22 2007 - 20:02:11 CST)
AMBER: native contact analysis! r. a. (Wed Feb 21 2007 - 20:52:37 CST)
AMBER: atom types deepti nayar (Wed Feb 21 2007 - 23:43:38 CST)
AMBER: Errors in amber9 parallel installation Seongeun Yang (Thu Feb 22 2007 - 07:34:23 CST)
- RE: AMBER: Errors in amber9 parallel installation Ross Walker (Thu Feb 22 2007 - 07:52:16 CST)
AMBER: applying restraints Seth Lilavivat (Thu Feb 22 2007 - 10:40:59 CST)
AMBER: Sander slower on 16 processors than 8 Sontum, Steve (Thu Feb 22 2007 - 14:32:42 CST)
- Re: AMBER: Sander slower on 16 processors than 8 Martin Stennett (Thu Feb 22 2007 - 15:10:40 CST)
- RE: AMBER: Sander slower on 16 processors than 8 Ross Walker (Thu Feb 22 2007 - 16:15:07 CST)
  - RE: AMBER: Sander slower on 16 processors than 8 Yong Duan (Thu Feb 22 2007 - 16:25:13 CST)
    - RE: AMBER: Sander slower on 16 processors than 8 Ross Walker (Thu Feb 22 2007 - 19:47:55 CST)
- Re: AMBER: Sander slower on 16 processors than 8 Robert Duke (Thu Feb 22 2007 - 21:27:12 CST)
AMBER: ptraj bug? -- doesn't like restart files from REMD Nicolas Lux Fawzi (Thu Feb 22 2007 - 15:33:58 CST)
AMBER: Problems with QMMM tests on Altix Jarrod Smith (Thu Feb 22 2007 - 16:03:14 CST)
- Re: AMBER: Problems with QMMM tests on Altix Luis Gracia (Thu Feb 22 2007 - 16:35:14 CST)
- RE: AMBER: Problems with QMMM tests on Altix Ross Walker (Thu Feb 22 2007 - 20:12:55 CST)
  - RE: AMBER: Problems with QMMM tests on Altix Jarrod Smith (Fri Feb 23 2007 - 13:34:53 CST)
    - RE: AMBER: Problems with QMMM tests on Altix Ross Walker (Sat Feb 24 2007 - 12:02:24 CST)
    - Re: AMBER: Problems with QMMM tests on Altix Roberto Gomperts (Thu Mar 08 2007 - 17:39:14 CST)
AMBER: units of mwcovar matrix befor conversion Chris Moth (Thu Feb 22 2007 - 17:01:57 CST)
AMBER: [rsachdeva@imtech.res.in: Pls help - REMD with torsional restraints] David A. Case (Thu Feb 22 2007 - 20:03:47 CST)
AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Craig Gough (Fri Feb 23 2007 - 02:47:36 CST)
- AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule Chris-Kriton Skylaris (Fri Feb 23 2007 - 03:54:00 CST)
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Andreas Svrcek-Seiler (Fri Feb 23 2007 - 05:02:52 CST)
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 David A. Case (Fri Feb 23 2007 - 10:35:34 CST)
AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 05:27:38 CST)
- RE: AMBER: SCF convergence issues Ross Walker (Fri Feb 23 2007 - 13:00:21 CST)
  - Re: AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 13:13:33 CST)
    - RE: AMBER: SCF convergence issues Ross Walker (Fri Feb 23 2007 - 17:35:47 CST)
    - Re: AMBER: SCF convergence issues Steven Winfield (Fri Mar 02 2007 - 07:43:58 CST)
AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Fri Feb 23 2007 - 08:15:48 CST)
- Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling (Fri Feb 23 2007 - 09:16:59 CST)
  - Re: AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Sat Feb 24 2007 - 02:49:49 CST)
    - Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling (Sat Feb 24 2007 - 14:27:01 CST)
AMBER: MD temperature and MM_pbsa temperature Rima Chaudhuri (Fri Feb 23 2007 - 15:22:30 CST)
AMBER: RESP calculation of modified nucleotides mathew k varghese (Sat Feb 24 2007 - 00:50:23 CST)
- Re: AMBER: RESP calculation of modified nucleotides rpaduri_at_chem.wayne.edu (Sat Feb 24 2007 - 15:49:10 CST)
  - Re: AMBER: RESP calculation of modified nucleotides FyD (Sun Feb 25 2007 - 11:49:55 CST)
  - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Sun Feb 25 2007 - 21:17:34 CST)
AMBER: Best way to apply WC basepair restraints during MD Seth Lilavivat (Sun Feb 25 2007 - 14:24:40 CST)
AMBER: problem with atom restraints Ed Pate (Sun Feb 25 2007 - 22:53:31 CST)
- Re: AMBER: problem with atom restraints David A. Case (Wed Feb 28 2007 - 12:54:58 CST)
AMBER: getting same box dimension bertrand russell (Sun Feb 25 2007 - 23:27:40 CST)
- Re: AMBER: getting same box dimension David A. Case (Mon Feb 26 2007 - 20:10:30 CST)
AMBER: phe-phe molecule deepti nayar (Mon Feb 26 2007 - 00:01:26 CST)
- Re: AMBER: phe-phe molecule bertrand russell (Mon Feb 26 2007 - 00:08:42 CST)
  - Re: AMBER: phe-phe molecule deepti nayar (Mon Feb 26 2007 - 01:46:10 CST)
AMBER: Modified nucleotides-ATOM TYPES mathew k varghese (Mon Feb 26 2007 - 03:13:59 CST)
- Re: AMBER: Modified nucleotides-ATOM TYPES David A. Case (Mon Feb 26 2007 - 08:21:16 CST)
AMBER: PTRAJ problem Beale, John (Mon Feb 26 2007 - 12:26:21 CST)
AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring David A. Case (Mon Feb 26 2007 - 17:01:41 CST)
AMBER: IFVARI parameter Ed Pate (Tue Feb 27 2007 - 15:22:43 CST)
- Re: AMBER: IFVARI parameter Kristina Furse (Tue Feb 27 2007 - 15:50:45 CST)
AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Tue Feb 27 2007 - 17:13:29 CST)
- Re: AMBER: abnormal high temperature during NPT ensembles MD Carlos Simmerling (Tue Feb 27 2007 - 20:36:01 CST)
  - Re: AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Wed Feb 28 2007 - 10:29:41 CST)
AMBER: AM1-bcc Evan Kelly (Tue Feb 27 2007 - 18:26:22 CST)
- RE: AMBER: AM1-bcc Junmei Wang (Tue Feb 27 2007 - 20:57:23 CST)
AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 06:56:55 CST)
- Re: AMBER: Disulfide Bonds Jerome.GOLEBIOWSKI_at_unice.fr (Wed Feb 28 2007 - 07:27:23 CST)
  - RE: AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 07:37:48 CST)
AMBER: LEaP crashes Beale, John (Wed Feb 28 2007 - 10:29:16 CST)
- Re: AMBER: LEaP crashes David A. Case (Wed Feb 28 2007 - 12:03:29 CST)
AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 12:38:55 CST)
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Wed Feb 28 2007 - 16:50:20 CST)
  - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 17:54:51 CST)
AMBER: Difference in Equilibration & Production MD in Amber Akshay Patny (Wed Feb 28 2007 - 14:33:56 CST)
- Re: AMBER: Difference in Equilibration & Production MD in Amber Gustavo Seabra (Wed Feb 28 2007 - 14:54:13 CST)
AMBER: momentum and periodic boundary condition Wei Chen (Wed Feb 28 2007 - 19:59:49 CST)
- Re: AMBER: momentum and periodic boundary condition David A. Case (Thu Mar 01 2007 - 10:52:00 CST)
AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 07:49:22 CST)
- Re: AMBER: Disulfide Problem Carlos Simmerling (Thu Mar 01 2007 - 08:15:22 CST)
  - RE: AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 08:45:24 CST)
  - Re: AMBER: Disulfide Problem xiaoqin huang (Fri Mar 02 2007 - 08:48:14 CST)
    - Re: AMBER: Disulfide Problem Carlos Simmerling (Fri Mar 02 2007 - 08:54:42 CST)
AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 10:17:41 CST)
- Re: AMBER: Restart from restart file obtained from ptraj with added velocities Thomas Cheatham III (Thu Mar 01 2007 - 10:51:28 CST)
  - Re: AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 11:43:13 CST)
AMBER: [rsachdeva@imtech.res.in: A query] David A. Case (Thu Mar 01 2007 - 11:02:27 CST)
- Re: AMBER: [rsachdeva@imtech.res.in: A query] Viktor Hornak (Thu Mar 01 2007 - 12:56:40 CST)
AMBER: qm/mm ti Ben Sattelle (Fri Mar 02 2007 - 07:54:53 CST)
- Re: AMBER: qm/mm ti Adrian Roitberg (Fri Mar 02 2007 - 08:02:49 CST)
AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 09:26:03 CST)
- Re: AMBER: Restart Files Carlos Simmerling (Fri Mar 02 2007 - 09:32:46 CST)
  - RE: AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 11:01:19 CST)
AMBER: restraints during MD Seth Lilavivat (Fri Mar 02 2007 - 10:16:05 CST)
- Re: AMBER: restraints during MD Carlos Simmerling (Fri Mar 02 2007 - 10:27:50 CST)
AMBER: reproducibility between software Stern, Julie (Fri Mar 02 2007 - 10:34:32 CST)
- Re: AMBER: reproducibility between software Carlos Simmerling (Fri Mar 02 2007 - 10:43:04 CST)
- Re: AMBER: reproducibility between software Thomas Cheatham III (Fri Mar 02 2007 - 11:32:35 CST)
- Re: AMBER: reproducibility between software Robert Duke (Fri Mar 02 2007 - 11:49:01 CST)
AMBER: Amber 9 make parallel fails with mpich Rene Salmon (Fri Mar 02 2007 - 11:45:37 CST)
- Re: AMBER: Amber 9 make parallel fails with mpich David A. Case (Fri Mar 02 2007 - 11:59:50 CST)
AMBER: ptraj average structure strip water Youyi Peng (Fri Mar 02 2007 - 13:52:02 CST)
AMBER: Calcium parameters Lei Jia (Fri Mar 02 2007 - 13:58:27 CST)
- Re: AMBER: Calcium parameters Qing Zhang (Fri Mar 02 2007 - 17:10:24 CST)
AMBER: Restraints on modified NA's Seth Lilavivat (Fri Mar 02 2007 - 15:56:07 CST)
- Re: AMBER: Restraints on modified NA's David A. Case (Mon Mar 05 2007 - 10:44:56 CST)
AMBER: calculate RMSD of only chain C ÕÔÑÇÑ© (Fri Mar 02 2007 - 20:21:33 CST)
- Re: AMBER: calculate RMSD of only chain C Carlos Simmerling (Sat Mar 03 2007 - 08:51:34 CST)
AMBER: TI calculation: charge is not zero in the perturbed state brmeher_at_iitg.ernet.in (Sat Mar 03 2007 - 14:32:02 CST)
- Re: AMBER: TI calculation: charge is not zero in the perturbed state David A. Case (Sat Mar 03 2007 - 15:11:52 CST)
AMBER: denaturing salt conditions Sean Rathlef (Sat Mar 03 2007 - 16:35:45 CST)
- Re: AMBER: denaturing salt conditions Jiri Sponer (Sat Mar 03 2007 - 18:28:28 CST)
AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations Cenk Andac (Sun Mar 04 2007 - 06:06:22 CST)
AMBER: prep file limit exceeding gurpreet singh (Mon Mar 05 2007 - 01:52:49 CST)
- Re: AMBER: prep file limit exceeding David A. Case (Mon Mar 05 2007 - 23:25:20 CST)
AMBER: distance calculation! r. a. (Mon Mar 05 2007 - 02:43:45 CST)
AMBER: psi , phi angles deepti nayar (Mon Mar 05 2007 - 05:07:41 CST)
- Re: AMBER: psi , phi angles Carlos Simmerling (Mon Mar 05 2007 - 06:08:27 CST)
  - Re: AMBER: psi , phi angles Piotr Cieplak (Mon Mar 05 2007 - 11:29:30 CST)
AMBER: pbsa installation problem bala (Mon Mar 05 2007 - 06:34:32 CST)
- Re: AMBER: pbsa installation problem David A. Case (Mon Mar 05 2007 - 11:48:13 CST)
AMBER: Beale, John (Mon Mar 05 2007 - 11:50:26 CST)
AMBER: Beale, John (Mon Mar 05 2007 - 11:51:29 CST)
AMBER: constraint pdb file Stern, Julie (Mon Mar 05 2007 - 15:06:47 CST)
AMBER: mm_pbsa individual contributions of residues AYTUG TUNCEL (Mon Mar 05 2007 - 17:12:54 CST)
AMBER: how to incorporate ismem =1 into mm_pbsa AYTUG TUNCEL (Mon Mar 05 2007 - 17:32:19 CST)
AMBER: any general approach to create SiO2 wall Sisir Das (Mon Mar 05 2007 - 22:46:42 CST)
AMBER: Trimannoside Problem Sandeep Kaushik (Tue Mar 06 2007 - 06:44:20 CST)
- Re: AMBER: Trimannoside Problem kkirschn_at_hamilton.edu (Tue Mar 06 2007 - 12:13:43 CST)
  - Re: AMBER: Trimannoside Problem Sandeep Kaushik (Thu Mar 08 2007 - 01:02:02 CST)
AMBER: how is the standard deviations calculated in mm-pbsa? Magne Olufsen (Tue Mar 06 2007 - 06:58:17 CST)
- Re: AMBER: how is the standard deviations calculated in mm-pbsa? David A. Case (Tue Mar 06 2007 - 19:13:55 CST)
AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 08:31:28 CST)
- Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case (Tue Mar 06 2007 - 10:31:10 CST)
  - RE: AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 11:41:37 CST)
    - Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case (Wed Mar 07 2007 - 12:11:21 CST)
AMBER: how to modify map.DG-AMBER file? Seth Lilavivat (Tue Mar 06 2007 - 14:55:40 CST)
- Re: AMBER: how to modify map.DG-AMBER file? David A. Case (Tue Mar 06 2007 - 19:06:57 CST)
- Re: AMBER: how to modify map.DG-AMBER file? A Box (Tue Apr 10 2007 - 18:56:21 CDT)
AMBER: addles segmentation fault deepti nayar (Wed Mar 07 2007 - 01:18:39 CST)
- Re: AMBER: addles segmentation fault David A. Case (Wed Mar 07 2007 - 11:23:21 CST)
  - AMBER: simulation of the phosphorylated protein Fenghui Fan (Wed Mar 07 2007 - 19:20:09 CST)
  - Re: AMBER: addles segmentation fault deepti nayar (Thu Mar 08 2007 - 03:35:43 CST)
AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 05:08:39 CST)
- Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher (Wed Mar 07 2007 - 10:48:10 CST)
  - Re: AMBER: Topology file problem in TI ! Ilyas Yildirim (Wed Mar 07 2007 - 12:09:39 CST)
    - Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher (Wed Mar 07 2007 - 13:35:29 CST)
  - Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 23:55:26 CST)
    - Re: AMBER: Topology file problem in TI ! David A. Case (Thu Mar 08 2007 - 09:59:22 CST)
    - Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Thu Mar 08 2007 - 10:18:58 CST)
Re: AMBER: Amber 9, sander imin = 5, -y flag S.Sundar Raman (Wed Mar 07 2007 - 12:05:19 CST)
- Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling (Wed Mar 07 2007 - 13:15:22 CST)
  - AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) Chris Moth (Fri Apr 06 2007 - 13:50:29 CDT)
    - Re: AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) Geoff Wood (Mon Jul 23 2007 - 12:23:46 CDT)
AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Fri Mar 09 2007 - 02:04:00 CST)
- Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Carlos Simmerling (Fri Mar 09 2007 - 06:07:48 CST)
  - Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Sat Mar 10 2007 - 01:37:06 CST)
  - AMBER: Problem with PCSHIFT module Edoardo Saccenti (Fri Mar 30 2007 - 05:20:37 CST)
AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Fri Mar 09 2007 - 12:36:14 CST)
- Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case (Fri Mar 09 2007 - 19:01:44 CST)
  - Re: AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Sat Mar 10 2007 - 09:59:09 CST)
    - Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case (Sat Mar 10 2007 - 11:34:32 CST)
AMBER: abnormal termination of tleap Pankaj R. Daga (Fri Mar 09 2007 - 16:24:37 CST)
AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 07:24:50 CST)
AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 07:38:28 CST)
- Re: AMBER: rmsd calculation in ptraj Carlos Simmerling (Sat Mar 10 2007 - 08:26:34 CST)
AMBER: rmsd calculation in ptraj II gurpreet singh (Sat Mar 10 2007 - 22:37:10 CST)
- Re: AMBER: rmsd calculation in ptraj II David A. Case (Sat Mar 10 2007 - 23:55:32 CST)
AMBER: unable to run test Anju Sharma (Sun Mar 11 2007 - 23:14:03 CST)
- Re: AMBER: unable to run test David A. Case (Mon Mar 12 2007 - 00:54:34 CST)
AMBER: addles deepti nayar (Mon Mar 12 2007 - 00:29:37 CST)
- Re: AMBER: addles Carlos Simmerling (Mon Mar 12 2007 - 05:28:20 CST)
  - Re: AMBER: addles deepti nayar (Mon Mar 12 2007 - 05:37:27 CST)
AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 03:13:56 CST)
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Jiri Sponer (Mon Mar 12 2007 - 07:05:49 CST)
  - Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 08:03:03 CST)
AMBER: NEB tutorial deepti nayar (Mon Mar 12 2007 - 04:03:17 CST)
AMBER: The parallel test fails while sander.MPI seems to be installed correctly Mostafa Sadighi (Mon Mar 12 2007 - 05:43:14 CST)
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Carlos Simmerling (Mon Mar 12 2007 - 05:51:38 CST)
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Gustavo Seabra (Mon Mar 12 2007 - 07:23:50 CST)
AMBER: DNA Helicoïdal Plots over time Stéphane Téletchéa (Mon Mar 12 2007 - 06:31:02 CST)
- Re: AMBER: DNA Helicoïdal Plots over time Vitor Felix (Mon Mar 12 2007 - 06:51:12 CST)
- AMBER: dna forcefield: PARMBSC0 Alberto Perez (Wed Mar 14 2007 - 01:14:36 CST)
AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 10:21:55 CST)
- Re: AMBER: Can I measure improper torsion by ptarj? David A. Case (Mon Mar 12 2007 - 10:36:07 CST)
  - Re: AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 22:18:24 CST)
    - Re: AMBER: Can I measure improper torsion by ptarj? David A. Case (Tue Mar 13 2007 - 10:55:13 CST)
- Re: AMBER: Can I measure improper torsion by ptarj? Bill Ross (Tue Mar 13 2007 - 11:23:24 CST)
AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 05:59:24 CST)
- Re: AMBER: hi.. Carlos Simmerling (Tue Mar 13 2007 - 06:08:47 CST)
  - Re: AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 06:15:27 CST)
AMBER: problem with mm_pbsa Yves Boulard (Tue Mar 13 2007 - 08:21:22 CST)
AMBER: poor performance of sander on a quad-core linux machine Lillian chong (Tue Mar 13 2007 - 11:27:31 CST)
- Re: AMBER: poor performance of sander on a quad-core linux machine David A. Case (Tue Mar 13 2007 - 11:42:48 CST)
AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 22:10:15 CST)
- Re: AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 22:19:03 CST)
AMBER: Problem Solved Anju Sharma (Tue Mar 13 2007 - 22:19:57 CST)
AMBER: NEB tutorial and addles deepti nayar (Tue Mar 13 2007 - 22:28:20 CST)
- RE: AMBER: NEB tutorial and addles Ross Walker (Thu Mar 15 2007 - 10:21:29 CST)
AMBER: problem while analysing result Anju Sharma (Tue Mar 13 2007 - 23:38:37 CST)
- Re: AMBER: problem while analysing result puneet kacker (Tue Mar 13 2007 - 23:59:20 CST)
  - Re: AMBER: problem while analysing result Anju Sharma (Wed Mar 14 2007 - 00:27:20 CST)
    - Re: AMBER: problem while analysing result Syed Tarique Moin (Wed Mar 14 2007 - 00:43:59 CST)
    - Re: AMBER: problem while analysing result puneet kacker (Wed Mar 14 2007 - 00:46:22 CST)
AMBER: Need help in Analysis Anju Sharma (Wed Mar 14 2007 - 03:13:03 CST)
- Re: AMBER: Need help in Analysis Heike.Meiselbach_at_chemie.uni-erlangen.de (Wed Mar 14 2007 - 04:35:34 CST)
- Re: AMBER: Need help in Analysis Gustavo Seabra (Wed Mar 14 2007 - 04:39:51 CST)
- AMBER: AMBER hydrophobic Box : script Sophie Barbe (Wed Mar 14 2007 - 04:48:50 CST)
  - Re: AMBER: AMBER hydrophobic Box : script David A. Case (Wed Mar 14 2007 - 09:29:47 CST)
AMBER: torsion angle deepti nayar (Wed Mar 14 2007 - 06:03:08 CST)
- Re: AMBER: torsion angle Carlos Simmerling (Wed Mar 14 2007 - 06:27:02 CST)
  - Re: AMBER: torsion angle deepti nayar (Thu Mar 15 2007 - 00:13:43 CST)
    - AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais (Thu Mar 15 2007 - 03:27:57 CST)
    - AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais (Tue Mar 20 2007 - 05:15:29 CST)
AMBER: Question about Boron Kara Di Giorgio (Wed Mar 14 2007 - 11:15:22 CST)
AMBER: mmpbsa free energy pairwise decomposition Gianluca Degliesposti (Wed Mar 14 2007 - 12:54:32 CST)
AMBER: Regarding counter ions Rafi Ahmad (Wed Mar 14 2007 - 14:00:59 CST)
AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 19:12:49 CST)
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Carlos Simmerling (Wed Mar 14 2007 - 19:47:23 CST)
  - Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 20:18:55 CST)
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) David A. Case (Fri Mar 16 2007 - 14:51:14 CST)
AMBER: How to build organic compound in Amber Anju Sharma (Wed Mar 14 2007 - 22:24:09 CST)
AMBER: hii Anju Sharma (Thu Mar 15 2007 - 03:28:47 CST)
- Re: AMBER: hii Benjamin Juhl (Thu Mar 15 2007 - 03:44:18 CST)
AMBER: Problem related simulation of dimer priya priya (Thu Mar 15 2007 - 05:23:31 CST)
- Re: AMBER: Problem related simulation of dimer Carlos Simmerling (Thu Mar 15 2007 - 05:38:57 CST)
  - Re: AMBER: Problem related simulation of dimer Abhilash (Thu Mar 15 2007 - 10:03:06 CST)
- Re: AMBER: Problem related simulation of dimer Sandeep Kaushik (Fri Mar 16 2007 - 04:32:20 CST)
  - Re: AMBER: Problem related simulation of dimer priya priya (Sun Mar 18 2007 - 23:35:42 CST)
AMBER: Dipolar and Inertia Moments kepa koldo burusco (Thu Mar 15 2007 - 05:46:17 CST)
AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 10:33:13 CST)
- Re: AMBER: solvate shell Carlos Simmerling (Thu Mar 15 2007 - 10:36:52 CST)
  - Re: AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 11:27:42 CST)
  - AMBER: Problem with anisotropic pressure scaling Linda Prengaman (Fri Mar 16 2007 - 08:23:30 CST)
- Re: AMBER: solvate shell David A. Case (Thu Mar 15 2007 - 13:36:04 CST)
AMBER: van der waals parameters. Stefano Tonzani (Thu Mar 15 2007 - 11:52:09 CST)
- Re: AMBER: van der waals parameters. David A. Case (Thu Mar 15 2007 - 13:30:34 CST)
AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap Laura McDriscoll (Thu Mar 15 2007 - 23:59:33 CST)
- Re: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap David A. Case (Fri Mar 16 2007 - 09:24:16 CST)
AMBER: hi Anju Sharma (Fri Mar 16 2007 - 04:50:44 CST)
- Re: AMBER: hi Carlos Simmerling (Fri Mar 16 2007 - 05:14:15 CST)
AMBER: vlimit error Amit Kumar (Fri Mar 16 2007 - 17:10:06 CST)
- Re: AMBER: vlimit error David A. Case (Mon Mar 19 2007 - 17:11:57 CST)
AMBER: antechamber error Ilyas Yildirim (Sat Mar 17 2007 - 00:44:57 CST)
AMBER: targeted MD problem gurpreet singh (Sat Mar 17 2007 - 06:17:27 CST)
- Re: AMBER: targeted MD problem Carlos Simmerling (Sat Mar 17 2007 - 06:27:28 CST)
- AMBER: MMPBSA with water molecule in active site saurabh agrawal (Sun Mar 18 2007 - 11:25:44 CST)
  - Re: AMBER: MMPBSA with water molecule in active site Carlos Simmerling (Sun Mar 18 2007 - 11:43:44 CST)
AMBER: targetedMD problem gurpreet singh (Sun Mar 18 2007 - 07:32:40 CST)
AMBER: antechamber Ilyas Yildirim (Sun Mar 18 2007 - 11:56:00 CST)
- Re: AMBER: antechamber David A. Case (Sun Mar 18 2007 - 17:50:00 CST)
AMBER: hi Anju Sharma (Sun Mar 18 2007 - 21:56:22 CST)
- RE: AMBER: hi Ross Walker (Sun Mar 18 2007 - 23:09:56 CST)
AMBER: Problem while creating structure in xLeap Anju Sharma (Sun Mar 18 2007 - 22:30:03 CST)
- Re: AMBER: Problem while creating structure in xLeap Jin-Soo Kim (Sat Mar 24 2007 - 05:53:29 CST)
AMBER: Problem!! Anju Sharma (Mon Mar 19 2007 - 00:38:15 CST)
- RE: AMBER: Problem!! Ross Walker (Mon Mar 19 2007 - 09:23:40 CST)
AMBER: MM-GBSA residues decomposition comparison Sergey Samsonov (Tue Mar 20 2007 - 08:17:26 CST)
AMBER: basis set for RESP calculation Michel Becker (Tue Mar 20 2007 - 14:43:10 CST)
- Re: AMBER: basis set for RESP calculation FyD (Wed Mar 21 2007 - 02:03:15 CST)
- Re: AMBER: basis set for RESP calculation FyD (Wed Mar 21 2007 - 11:17:44 CST)
- Re: AMBER: basis set for RESP calculation Mark Williamson (Wed Mar 21 2007 - 11:36:40 CST)
AMBER: Problem while loading Pdb in xleap Anju Sharma (Tue Mar 20 2007 - 22:12:55 CST)
- Re: AMBER: Problem while loading Pdb in xleap David A. Case (Tue Mar 20 2007 - 23:31:42 CST)
- Re: AMBER: Problem while loading Pdb in xleap Sandeep Kaushik (Thu Mar 22 2007 - 04:07:13 CST)
AMBER: Problem while running Antechamber Anju Sharma (Wed Mar 21 2007 - 03:35:28 CST)
- Re:AMBER: Problem while running Antechamber Kateryna Miroshnychenko (Wed Mar 21 2007 - 05:06:15 CST)
AMBER: Modified Nucleic Acid Problem SHARAD gupta (Wed Mar 21 2007 - 07:22:10 CST)
- Re: AMBER: Modified Nucleic Acid Problem FyD (Wed Mar 21 2007 - 08:19:09 CST)
- Re: AMBER: Modified Nucleic Acid Problem FyD (Wed Mar 21 2007 - 08:20:34 CST)
AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 07:35:06 CST)
- Re: AMBER: How to reimage the trajectories of LES calculations? Carlos Simmerling (Wed Mar 21 2007 - 11:04:03 CST)
  - Re: AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 11:32:34 CST)
AMBER: ntt=1 or ntt= 3? Therese Malliavin (Wed Mar 21 2007 - 11:32:07 CST)
- Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling (Wed Mar 21 2007 - 11:40:20 CST)
- RE: AMBER: ntt=1 or ntt= 3? Yong Duan (Wed Mar 21 2007 - 12:00:56 CST)
- Re: AMBER: ntt=1 or ntt= 3? David A. Case (Wed Mar 21 2007 - 13:29:45 CST)
  - RE: AMBER: ntt=1 or ntt= 3? Yong Duan (Thu Mar 22 2007 - 04:42:37 CST)
  - RE: AMBER: ntt=1 or ntt= 3? Hu, Shaowen $JSC-SK$[USRA] (Thu Mar 22 2007 - 15:24:10 CST)
AMBER: xLeAP: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 13:17:12 CST)
- Re: AMBER: xLeAP: TI calculation: the perturbed charge is not integral David A. Case (Wed Mar 21 2007 - 13:33:33 CST)
  - AMBER: sander.MPI vs MPICH2 problem!!! Swarup Gupta (Fri Mar 23 2007 - 20:33:44 CST)
AMBER: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 13:21:52 CST)
AMBER: restraint in minimization deepti nayar (Thu Mar 22 2007 - 02:21:32 CST)
- Re: AMBER: restraint in minimization Carlos Simmerling (Thu Mar 22 2007 - 05:14:22 CST)
  - Re: AMBER: restraint in minimization Sandeep Kaushik (Mon Mar 26 2007 - 03:21:27 CST)
    - Re: AMBER: restraint in minimization Carlos Simmerling (Mon Mar 26 2007 - 06:19:13 CST)
    - Re: AMBER: restraint in minimization deepti nayar (Mon Mar 26 2007 - 23:10:50 CST)
AMBER: Holding NA Base syn during annealing Seth Lilavivat (Thu Mar 22 2007 - 09:23:20 CST)
- Re: AMBER: Holding NA Base syn during annealing David A. Case (Thu Mar 22 2007 - 09:41:30 CST)
AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 15:35:07 CST)
- Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD (Thu Mar 22 2007 - 16:11:07 CST)
  - Re: AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 16:17:22 CST)
    - Re: AMBER: Generating structure of polyethylene glycol in AMBER luckyang_at_gmail.com (Thu Mar 22 2007 - 16:38:02 CST)
    - Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD (Thu Mar 22 2007 - 16:57:55 CST)
Re: AMBER: sander/topology problem Jin-Soo Kim (Fri Mar 23 2007 - 08:31:00 CST)
- Re: AMBER: sander/topology problem Gustavo Seabra (Fri Mar 23 2007 - 09:15:21 CST)
  - Re: AMBER: sander/topology problem Jin-Soo Kim (Sat Mar 24 2007 - 05:17:51 CST)
AMBER: anneal algorthm Seth Lilavivat (Fri Mar 23 2007 - 13:33:42 CST)
AMBER: Error - must define AMBERHOME environment variable bertrand russell (Fri Mar 23 2007 - 14:05:47 CST)
- Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay (Fri Mar 23 2007 - 16:26:02 CST)
  - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Sat Mar 24 2007 - 14:18:55 CST)
    - Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay (Sat Mar 24 2007 - 18:32:40 CST)
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker (Sat Mar 24 2007 - 22:06:23 CST)
  - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 02:56:06 CST)
AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 15:41:04 CST)
- Re: AMBER: Combining RESP with AM1-BCC David Mobley (Fri Mar 23 2007 - 17:17:50 CST)
  - Re: AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 18:27:07 CST)
  - Re: AMBER: Combining RESP with AM1-BCC FyD (Sat Mar 24 2007 - 03:03:37 CST)
AMBER: water density Esther Brugger (Fri Mar 23 2007 - 16:47:33 CST)
- Re: AMBER: water density Cenk Andac (Fri Mar 23 2007 - 17:13:16 CST)
AMBER: amber 9 - output of forces Eric Shamay (Fri Mar 23 2007 - 17:00:39 CST)
- Re: AMBER: amber 9 - output of forces David A. Case (Fri Mar 23 2007 - 23:10:21 CST)
  - Re: AMBER: amber 9 - output of forces Eric Shamay (Sat Mar 24 2007 - 00:27:41 CST)
  - Re: AMBER: amber 9 - output of forces Eric Shamay (Mon Mar 26 2007 - 16:08:58 CST)
    - Re: AMBER: amber 9 - output of forces Eric Shamay (Tue Mar 27 2007 - 14:36:34 CST)
AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? Jin-Soo Kim (Sat Mar 24 2007 - 05:40:26 CST)
AMBER: Please check the total charge and your -nc flag snoze pa (Sun Mar 25 2007 - 22:54:52 CST)
- Re: AMBER: Please check the total charge and your -nc flag David A. Case (Tue Mar 27 2007 - 16:29:32 CST)
AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 01:25:19 CST)
- Re: AMBER: phe-phe simulation Carlos Simmerling (Mon Mar 26 2007 - 06:20:52 CST)
  - Re: AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 23:12:03 CST)
AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 03:14:50 CST)
- Re: AMBER: pmemd segmentation fault Robert Duke (Mon Mar 26 2007 - 07:25:36 CST)
  - Re: AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 08:29:12 CST)
AMBER: DNA Flat Angle Restraints Kyle L. Brown (Mon Mar 26 2007 - 11:04:09 CST)
AMBER: pdb file produced by vmd Rita Cassia (Mon Mar 26 2007 - 10:04:19 CST)
AMBER: distcovar in ptraj Zhenyu Lu (Mon Mar 26 2007 - 22:00:13 CST)
AMBER: Parameter file for Dipeptide Neelanjana Sengupta (Mon Mar 26 2007 - 23:23:32 CST)
- Re: AMBER: Parameter file for Dipeptide Carlos Simmerling (Tue Mar 27 2007 - 08:20:55 CST)
AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 08:04:48 CST)
- Re: AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 12:43:49 CST)
AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 12:31:56 CST)
- Re: AMBER: Question about loadMol2 Scott Brozell (Tue Mar 27 2007 - 13:49:25 CST)
- Re: AMBER: Question about loadMol2 David Mobley (Tue Mar 27 2007 - 14:15:26 CST)
  - Re: AMBER: Question about loadMol2 Thomas Steinbrecher (Tue Mar 27 2007 - 14:24:55 CST)
AMBER: amber 9 install: patch reject Stern, Julie (Tue Mar 27 2007 - 12:50:33 CST)
AMBER: amber 9: fortran/test failures Stern, Julie (Tue Mar 27 2007 - 12:55:43 CST)
- Re: AMBER: amber 9: fortran/test failures David A. Case (Tue Mar 27 2007 - 16:15:50 CST)
AMBER: residue types for GLY/high pH Stern, Julie (Tue Mar 27 2007 - 14:19:47 CST)
AMBER: Amber 9 TI Details Lachele Foley (Lists) (Tue Mar 27 2007 - 15:03:20 CST)
- Re: AMBER: Amber 9 TI Details Thomas Steinbrecher (Tue Mar 27 2007 - 15:58:55 CST)
- Re: AMBER: Amber 9 TI Details David A. Case (Tue Mar 27 2007 - 16:23:34 CST)
AMBER: specifying psi and phi for a dipeptide deepti nayar (Wed Mar 28 2007 - 05:50:28 CST)
AMBER: DISAVE value1 Kyle L. Brown (Wed Mar 28 2007 - 15:42:16 CST)
- Re: AMBER: DISAVE value1 David A. Case (Fri Mar 30 2007 - 09:24:27 CST)
AMBER: rms and rmsf in ptraj Mingfeng Yang (Wed Mar 28 2007 - 15:06:02 CST)
- Re: AMBER: rms and rmsf in ptraj Thomas Cheatham (Wed Mar 28 2007 - 18:01:13 CST)
  - Re: AMBER: rms and rmsf in ptraj Scott Brozell (Thu Mar 29 2007 - 09:57:43 CST)
AMBER: problem in implcit simulation gurpreet singh (Wed Mar 28 2007 - 22:25:53 CST)
- RE: AMBER: problem in implcit simulation Ross Walker (Wed Mar 28 2007 - 23:02:28 CST)
AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 03:50:29 CST)
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke (Thu Mar 29 2007 - 07:57:26 CST)
  - Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 09:25:59 CST)
    - Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke (Thu Mar 29 2007 - 09:53:56 CST)
AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 03:57:15 CST)
- Re: AMBER: minimization not running Vlad Cojocaru (Thu Mar 29 2007 - 04:15:36 CST)
  - Re: AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 04:51:26 CST)
AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 04:55:39 CST)
- Re: AMBER: minimization energy query Vlad Cojocaru (Thu Mar 29 2007 - 05:00:02 CST)
  - Re: AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 05:35:45 CST)
AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Thu Mar 29 2007 - 10:17:05 CST)
- Re: AMBER: is possible to compile pmemd using scali MPI? Robert Duke (Thu Mar 29 2007 - 10:36:01 CST)
  - Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Fri Mar 30 2007 - 13:48:12 CST)
    - Re: AMBER: is possible to compile pmemd using scali MPI? Gustavo Seabra (Fri Mar 30 2007 - 14:21:39 CST)
    - Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Mon Apr 23 2007 - 07:31:53 CDT)
AMBER: Amber9 Sander Error A Box (Thu Mar 29 2007 - 20:26:21 CST)
- Re: AMBER: Amber9 Sander Error David A. Case (Fri Mar 30 2007 - 08:04:40 CST)
AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Pankaj R. Daga (Thu Mar 29 2007 - 21:59:08 CST)
- RE: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Ross Walker (Thu Mar 29 2007 - 22:33:37 CST)
AMBER: minimization + simulation deepti nayar (Fri Mar 30 2007 - 01:54:03 CST)
- Re: AMBER: minimization + simulation Vlad Cojocaru (Fri Mar 30 2007 - 02:19:55 CST)
AMBER: RST can not be opened deepti nayar (Fri Mar 30 2007 - 03:21:58 CST)
- Re: AMBER: RST can not be opened Vlad Cojocaru (Fri Mar 30 2007 - 03:45:55 CST)
- RE: AMBER: RST can not be opened Ross Walker (Fri Mar 30 2007 - 09:42:45 CST)
  - AMBER: mm_pbsa error Wang, Xuelin (Fri Mar 30 2007 - 10:21:50 CST)
AMBER: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 03:35:49 CST)
- AMBER: Fwd: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 03:36:52 CST)
- Re: AMBER: problem regarding water handling in explicit simu Mingfeng Yang (Fri Mar 30 2007 - 13:50:00 CST)
AMBER: Some problems during the testing of Amber. Liang, Lei (Fri Mar 30 2007 - 12:12:50 CST)
- Re: AMBER: Some problems during the testing of Amber. David A. Case (Sat Mar 31 2007 - 22:13:38 CST)
AMBER: A question about biomineral simulation, help!! WANG,YING (Fri Mar 30 2007 - 15:36:02 CST)
AMBER: Distance restraint to centre of mass Evan Kelly (Fri Mar 30 2007 - 16:41:32 CST)
- Re: AMBER: Distance restraint to centre of mass David A. Case (Sat Mar 31 2007 - 22:13:48 CST)
AMBER: phosphorylated residues yxamber (Mon Apr 02 2007 - 00:13:17 CDT)
- Re: AMBER: phosphorylated residues David A. Case (Mon Apr 02 2007 - 17:13:37 CDT)
  - undefinedRe: AMBER: phosphorylated residues yxamber (Tue Apr 03 2007 - 08:12:35 CDT)
AMBER: Error at Equilibration.... Sandeep Kaushik (Mon Apr 02 2007 - 02:14:17 CDT)
- Re: AMBER: Error at Equilibration.... David A. Case (Mon Apr 02 2007 - 10:45:57 CDT)
AMBER: Problem with sander.MPI Sandeep Kaushik (Mon Apr 02 2007 - 08:06:21 CDT)
AMBER: RE: dihedral term charge dependence Williamson, Mark (Mon Apr 02 2007 - 11:07:29 CDT)
- Re: AMBER: RE: dihedral term charge dependence Carlos Simmerling (Mon Apr 02 2007 - 11:14:15 CDT)
AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 04:25:12 CDT)
- AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 05:21:51 CDT)
  - Re: AMBER: restraint command not taken Vlad Cojocaru (Mon Apr 02 2007 - 11:16:16 CDT)
- Re: AMBER: restraint command not taken Vlad Cojocaru (Mon Apr 02 2007 - 11:57:37 CDT)
- AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 04:54:44 CDT)
AMBER: Xleap errors Beale, John (Mon Apr 02 2007 - 12:20:43 CDT)
- Re: AMBER: Xleap errors David A. Case (Mon Apr 02 2007 - 12:32:47 CDT)
AMBER: Cut off for cavities Sangwai, Ashishvikas (Mon Apr 02 2007 - 13:47:30 CDT)
AMBER: Extra Points... How to Deal with Them David Cerutti (Tue Apr 03 2007 - 01:39:23 CDT)
AMBER: Sander.... Rita Cassia (Tue Apr 03 2007 - 03:23:06 CDT)
- RE: AMBER: Sander.... Ross Walker (Tue Apr 03 2007 - 10:28:51 CDT)
AMBER: nmode Marie Brut (Tue Apr 03 2007 - 05:17:39 CDT)
- Re: AMBER: nmode David A. Case (Tue Apr 03 2007 - 10:25:52 CDT)
- Re: AMBER: nmode Marie Brut (Tue Apr 03 2007 - 10:42:17 CDT)
  - Re: AMBER: nmode David A. Case (Tue Apr 03 2007 - 11:31:54 CDT)
AMBER: Regarding Simulated Annealing Anju Sharma (Tue Apr 03 2007 - 07:27:18 CDT)
- RE: AMBER: Regarding Simulated Annealing Ross Walker (Tue Apr 03 2007 - 10:43:55 CDT)
AMBER: RE: dihedral term charge dependence Kateryna Miroshnychenko (Tue Apr 03 2007 - 08:59:08 CDT)
AMBER: sander bomb janavi raghavan (Tue Apr 03 2007 - 09:28:39 CDT)
- RE: AMBER: sander bomb Ross Walker (Tue Apr 03 2007 - 10:35:40 CDT)
AMBER: principal axis calculation in Ptraj Esther Brugger (Tue Apr 03 2007 - 16:05:44 CDT)
AMBER: Energy minimization problem Bo Baker (Tue Apr 03 2007 - 20:24:05 CDT)
- Re: AMBER: Energy minimization problem David A. Case (Tue Apr 03 2007 - 20:39:37 CDT)
  - RE: AMBER: Energy minimization problem Bo Baker (Wed Apr 04 2007 - 19:02:42 CDT)
    - Re: AMBER: Energy minimization problem David A. Case (Wed Apr 04 2007 - 20:25:26 CDT)
    - RE: AMBER: Energy minimization problem Bo Baker (Thu Apr 05 2007 - 05:14:31 CDT)
AMBER: about define improper torsion in .frcmod file Chengwen Chen (Wed Apr 04 2007 - 04:02:57 CDT)
- Re: AMBER: about define improper torsion in .frcmod file David A. Case (Wed Apr 04 2007 - 10:25:11 CDT)
AMBER: parse radii AYTUG TUNCEL (Wed Apr 04 2007 - 04:10:10 CDT)
- Re: AMBER: parse radii Holger Gohlke (Wed Apr 04 2007 - 04:24:17 CDT)
  - Re: Re: AMBER: parse radii AYTUG TUNCEL (Mon Apr 09 2007 - 03:02:59 CDT)
    - Re: Re: AMBER: parse radii Gohlke_at_bioinformatik.uni-frankfurt.de (Mon Apr 09 2007 - 04:35:06 CDT)
AMBER: FW: parameter Ross Walker (Wed Apr 04 2007 - 10:18:07 CDT)
AMBER: choice of alpha carbons vs side chains Christopher Gaughan (Wed Apr 04 2007 - 17:34:31 CDT)
Re: AMBER: choice of alpha carbons vs side chains Bill Ross (Wed Apr 04 2007 - 18:28:34 CDT)
AMBER: Charges in antechamber Beale, John (Thu Apr 05 2007 - 10:46:34 CDT)
- Re: AMBER: Charges in antechamber Scott Brozell (Thu Apr 05 2007 - 15:43:59 CDT)
AMBER: Problems during compilation and test. Liang, Lei (Thu Apr 05 2007 - 15:43:23 CDT)
- Re: AMBER: Problems during compilation and test. Scott Brozell (Thu Apr 05 2007 - 21:11:30 CDT)
  - Re: AMBER: Problems during compilation and test. Liang, Lei (Mon Apr 09 2007 - 12:21:39 CDT)
    - Re: AMBER: Problems during compilation and test. David A. Case (Tue Apr 10 2007 - 20:27:39 CDT)
AMBER: principal mask dorotation Esther Brugger (Thu Apr 05 2007 - 16:46:51 CDT)
AMBER: amber 9 installation: broken pipe Stern, Julie (Thu Apr 05 2007 - 18:54:16 CDT)
- Re: AMBER: amber 9 installation: broken pipe Scott Brozell (Thu Apr 05 2007 - 20:46:09 CDT)
AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 09:10:18 CDT)
- Re: AMBER: MD at constan pH Scott Brozell (Fri Apr 06 2007 - 11:41:39 CDT)
  - Re: AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 22:53:52 CDT)
    - Re: AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 23:05:20 CDT)
AMBER: Blue Gene, compile Amber9? Mike Hanby (Fri Apr 06 2007 - 12:22:57 CDT)
- Re: AMBER: Blue Gene, compile Amber9? Carlos P. Sosa (Fri Apr 06 2007 - 13:55:28 CDT)
- RE: AMBER: Blue Gene, compile Amber9? Ross Walker (Fri Apr 06 2007 - 16:23:33 CDT)
  - RE: AMBER: Blue Gene, compile Amber9? Mike Hanby (Tue Apr 10 2007 - 09:04:13 CDT)
AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) Chris Moth (Fri Apr 06 2007 - 16:07:17 CDT)
- Re: AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) David A. Case (Fri Apr 06 2007 - 17:37:46 CDT)
  - AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) Chris Moth (Mon Apr 09 2007 - 12:32:35 CDT)
AMBER: PDB file format for AMBER Neelanjana Sengupta (Fri Apr 06 2007 - 21:41:43 CDT)
- Re: AMBER: PDB file format for AMBER David A. Case (Sat Apr 07 2007 - 10:56:18 CDT)
Re: AMBER: pH effect on protein folding tri nam Vo (Sat Apr 07 2007 - 01:27:40 CDT)
AMBER: Extra points... virial computation David Cerutti (Sun Apr 08 2007 - 01:48:11 CDT)
AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey_at_gmx.de (Sun Apr 08 2007 - 07:21:38 CDT)
- Re: AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) David A. Case (Mon Apr 09 2007 - 12:27:59 CDT)
AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey_at_gmx.de (Sun Apr 08 2007 - 09:15:22 CDT)
- Re: AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) David A. Case (Mon Apr 09 2007 - 09:56:56 CDT)
AMBER: ptraj hbond Evan Kelly (Sun Apr 08 2007 - 19:37:04 CDT)
- Re: AMBER: ptraj hbond Evan Kelly (Sun Apr 08 2007 - 21:00:29 CDT)
AMBER: Fails to load libraries present in /leap/lib/ Neelanjana Sengupta (Mon Apr 09 2007 - 04:33:29 CDT)
- Re: AMBER: Fails to load libraries present in /leap/lib/ David A. Case (Mon Apr 09 2007 - 12:25:41 CDT)
- RE: AMBER: Fails to load libraries present in /leap/lib/ Ross Walker (Tue Apr 10 2007 - 17:53:07 CDT)
AMBER: Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 05:06:37 CDT)
AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Sandeep Kaushik (Mon Apr 09 2007 - 05:35:54 CDT)
- Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? j j (Mon Apr 09 2007 - 09:18:58 CDT)
- Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? David A. Case (Mon Apr 09 2007 - 12:21:21 CDT)
- RE: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Ross Walker (Tue Apr 10 2007 - 17:53:19 CDT)
  - Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Sandeep Kaushik (Thu Apr 12 2007 - 01:11:40 CDT)
AMBER: I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 05:50:54 CDT)
AMBER: Question about MMPBSA v9 Cenk Andac (Mon Apr 09 2007 - 05:54:39 CDT)
- Re: AMBER: Question about MMPBSA v9 David A. Case (Tue Apr 10 2007 - 21:20:58 CDT)
  - Re: AMBER: Question about MMPBSA v9 Cenk Andac (Wed Apr 11 2007 - 05:38:12 CDT)
AMBER: Constant volume simulations Christopher Gaughan (Mon Apr 09 2007 - 13:59:26 CDT)
- Re: AMBER: Constant volume simulations David A. Case (Mon Apr 09 2007 - 15:24:09 CDT)
  - Re: AMBER: Constant volume simulations Christopher Gaughan (Tue Apr 10 2007 - 10:31:58 CDT)
AMBER: Sander Bomb in subroutine nonbond_list Jingyuan Luke (Mon Apr 09 2007 - 21:34:51 CDT)
AMBER: Problem while using antechamber Anju Sharma (Tue Apr 10 2007 - 01:15:47 CDT)
- Re: AMBER: Problem while using antechamber Benjamin Juhl (Tue Apr 10 2007 - 02:12:13 CDT)
  - Re: AMBER: Problem while using antechamber Anju Sharma (Tue Apr 10 2007 - 04:18:07 CDT)
AMBER: problem related to visualizing of structure deepti nayar (Tue Apr 10 2007 - 01:33:40 CDT)
- Re: AMBER: problem related to visualizing of structure Vlad Cojocaru (Tue Apr 10 2007 - 03:25:06 CDT)
  - Re: AMBER: problem related to visualizing of structure deepti nayar (Tue Apr 10 2007 - 04:18:38 CDT)
    - Re: AMBER: problem related to visualizing of structure Vlad Cojocaru (Tue Apr 10 2007 - 04:32:01 CDT)
    - Re: AMBER: problem related to visualizing of structure deepti nayar (Tue Apr 10 2007 - 04:42:58 CDT)
AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 13:22:39 CDT)
- Re: AMBER: sander (AMBER 9) and -y flag -- not working? Chris Moth (Tue Apr 10 2007 - 13:36:22 CDT)
  - Re: AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 13:52:29 CDT)
AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 11 2007 - 03:08:16 CDT)
- RE: AMBER: amber9: running parallel error Ross Walker (Wed Apr 11 2007 - 08:43:19 CDT)
  - RE: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 11 2007 - 22:40:27 CDT)
    - Re: AMBER: amber9: running parallel error Benjamin Juhl (Thu Apr 12 2007 - 03:33:48 CDT)
    - Re: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 18 2007 - 02:03:13 CDT)
  - RE: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 18 2007 - 02:00:29 CDT)
AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 05:06:08 CDT)
- Re: AMBER: Prblm rgrdng Simulated Annealing Carlos Simmerling (Wed Apr 11 2007 - 06:23:43 CDT)
  - Re: AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 06:33:03 CDT)
    - Re: AMBER: Prblm rgrdng Simulated Annealing Carlos Simmerling (Wed Apr 11 2007 - 06:39:30 CDT)
    - Re: AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 06:46:08 CDT)
AMBER: Problem with Sander restart file. Martin Stennett (Wed Apr 11 2007 - 05:56:37 CDT)
- Re: AMBER: Problem with Sander restart file. Navnit Kumar Mishra (Wed Apr 11 2007 - 06:19:20 CDT)
  - Re: AMBER: Problem with Sander restart file. Martin Stennett (Wed Apr 11 2007 - 06:45:03 CDT)
- Re: AMBER: Problem with Sander restart file. David A. Case (Wed Apr 11 2007 - 13:11:40 CDT)
AMBER: temperature artifacts with andersen and GB? David Mobley (Wed Apr 11 2007 - 11:50:17 CDT)
AMBER: working with Antechamber Atila Iamarino (Wed Apr 11 2007 - 12:45:20 CDT)
- Re: AMBER: working with Antechamber David Mobley (Wed Apr 11 2007 - 13:34:55 CDT)
  - Re: AMBER: working with Antechamber Atila Iamarino (Wed Apr 11 2007 - 13:59:03 CDT)
    - Re: AMBER: working with Antechamber David A. Case (Wed Apr 11 2007 - 14:56:00 CDT)
AMBER: CHARMM vs. AMBER ff literature Seth Lilavivat (Wed Apr 11 2007 - 10:21:07 CDT)
- Re: AMBER: CHARMM vs. AMBER ff literature Thomas Cheatham (Wed Apr 11 2007 - 16:21:14 CDT)
- Re: AMBER: CHARMM vs. AMBER ff literature Jiri Sponer (Thu Apr 12 2007 - 07:58:32 CDT)
  - AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 12 2007 - 09:38:09 CDT)
AMBER: Attaching capping groups Neelanjana Sengupta (Wed Apr 11 2007 - 20:28:33 CDT)
- Re: AMBER: Attaching capping groups Kristina Furse (Wed Apr 11 2007 - 21:30:30 CDT)
- RE: AMBER: Attaching capping groups Ross Walker (Wed Apr 11 2007 - 22:49:36 CDT)
  - Re: AMBER: Attaching capping groups Neelanjana Sengupta (Thu Apr 12 2007 - 21:54:30 CDT)
    - RE: AMBER: Attaching capping groups Ross Walker (Sun Apr 15 2007 - 22:49:26 CDT)
AMBER: Needed help regardng Simulated Annealing Anju Sharma (Thu Apr 12 2007 - 00:07:14 CDT)
AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine tonglei (Thu Apr 12 2007 - 02:13:34 CDT)
AMBER: topology for postprocessed files? anna.schrey_at_gmx.de (Thu Apr 12 2007 - 04:57:28 CDT)
- Re: AMBER: topology for postprocessed files? Vlad Cojocaru (Thu Apr 12 2007 - 05:07:08 CDT)
  - Re: AMBER: topology for postprocessed files? anna.schrey_at_gmx.de (Thu Apr 12 2007 - 05:42:41 CDT)
  - Re: AMBER: topology for postprocessed files? anna.schrey_at_gmx.de (Wed Apr 18 2007 - 12:40:51 CDT)
AMBER: bad atom type errors in GB for halides? David Mobley (Thu Apr 12 2007 - 12:19:51 CDT)
- Re: AMBER: bad atom type errors in GB for halides? Ilyas Yildirim (Thu Apr 12 2007 - 14:57:13 CDT)
- Re: AMBER: bad atom type errors in GB for halides? David A. Case (Thu Apr 12 2007 - 19:04:55 CDT)
AMBER: Multiple Bonds to one Atom crowfoot_at_unr.nevada.edu (Thu Apr 12 2007 - 15:41:36 CDT)
AMBER: polarization and water density Thérèse Malliavin (Fri Apr 13 2007 - 04:36:44 CDT)
- Re: AMBER: polarization and water density David A. Case (Fri Apr 13 2007 - 14:53:42 CDT)
AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Arvind Marathe (Fri Apr 13 2007 - 05:23:38 CDT)
- Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Mark Williamson (Fri Apr 13 2007 - 07:51:54 CDT)
  - Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Arvind Marathe (Fri Apr 13 2007 - 10:59:35 CDT)
AMBER: Amber:PBSA&Extract_coords problem (Needed help) odde (Fri Apr 13 2007 - 14:06:42 CDT)
- Re: AMBER: Amber:PBSA&Extract_coords problem (Needed help) Jiten (Sat Apr 14 2007 - 08:51:58 CDT)
AMBER: QMMM with printcharges Kijeong Kwac (Fri Apr 13 2007 - 19:37:45 CDT)
- RE: AMBER: QMMM with printcharges Ross Walker (Tue Apr 17 2007 - 16:37:27 CDT)
AMBER: mdfil.f Peljidiyn Genden (Sat Apr 14 2007 - 02:43:27 CDT)
- Re: AMBER: mdfil.f Robert Duke (Mon Apr 16 2007 - 12:02:28 CDT)
- Re: AMBER: mdfil.f David A. Case (Mon Apr 16 2007 - 12:25:02 CDT)
AMBER: Amber 8 support of CHARMM ff? Seth Lilavivat (Sat Apr 14 2007 - 13:36:35 CDT)
- Re: AMBER: Amber 8 support of CHARMM ff? David A. Case (Sat Apr 14 2007 - 14:21:23 CDT)
AMBER: Release of the R.E.D.-III tools FyD (Sun Apr 15 2007 - 05:10:25 CDT)
Re: AMBER: membrane simulation Florian Haberl (Mon Apr 16 2007 - 09:04:04 CDT)
- Re: AMBER: membrane simulation nag raj (Wed Apr 18 2007 - 21:53:27 CDT)
  - Re: AMBER: membrane simulation Vlad Cojocaru (Thu Apr 19 2007 - 04:07:52 CDT)
    - Re: AMBER: membrane simulation nag raj (Thu Apr 19 2007 - 07:51:56 CDT)
AMBER: Projecting trajectories onto normal modes Harald Lanig (Mon Apr 16 2007 - 09:50:38 CDT)
AMBER: ptraj and quasi harmonic analysis Hans Lee (Mon Apr 16 2007 - 16:19:34 CDT)
- Re: AMBER: ptraj and quasi harmonic analysis Hans Lee (Wed Apr 18 2007 - 09:47:11 CDT)
  - Re: AMBER: ptraj and quasi harmonic analysis Myunggi Yi (Wed Apr 18 2007 - 11:46:22 CDT)
  - AMBER: ptraj and quasi harmonic analysis Chris Moth (Thu Apr 19 2007 - 14:58:52 CDT)
AMBER: MM-PBSA_binding energy script error odde (Mon Apr 16 2007 - 18:33:14 CDT)
AMBER: Re: amber mm-pbsa problem Jiten (Mon Apr 16 2007 - 20:39:26 CDT)
- Re: AMBER: Re: amber mm-pbsa problem odde (Tue Apr 17 2007 - 08:57:37 CDT)
AMBER: problem with calculating RMSD tri nam Vo (Tue Apr 17 2007 - 02:01:35 CDT)
- Re: AMBER: problem with calculating RMSD Gustavo Seabra (Tue Apr 17 2007 - 07:41:26 CDT)
  - Re: AMBER: problem with calculating RMSD tri nam Vo (Wed Apr 18 2007 - 03:22:45 CDT)
    - Re: AMBER: problem with calculating RMSD Gustavo Seabra (Wed Apr 18 2007 - 09:50:21 CDT)
    - RE: AMBER: problem with calculating RMSD Ross Walker (Wed Apr 18 2007 - 11:03:37 CDT)
AMBER: vmd and amber deepti nayar (Tue Apr 17 2007 - 06:58:51 CDT)
- Re: AMBER: vmd and amber Gustavo Seabra (Tue Apr 17 2007 - 07:33:48 CDT)
AMBER: PDBs Beale, John (Tue Apr 17 2007 - 07:22:42 CDT)
- Re: AMBER: PDBs John E. Kerrigan (Tue Apr 17 2007 - 07:40:54 CDT)
AMBER: ptraj secstruct core dumped error vijayaraj_at_clri.info (Tue Apr 17 2007 - 08:45:04 CDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER Cenk Andac (Tue Apr 17 2007 - 12:18:30 CDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Cenk Andac (Tue Apr 17 2007 - 12:24:37 CDT)
- Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Melinda Layten (Mon Apr 23 2007 - 16:52:26 CDT)
  - Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Cenk Andac (Mon Apr 23 2007 - 17:35:36 CDT)
    - Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Vlad Cojocaru (Tue Apr 24 2007 - 03:30:40 CDT)
AMBER: Re: MM-PBSA amber script problem odde (Tue Apr 17 2007 - 13:45:06 CDT)
- Re: AMBER: Re: MM-PBSA amber script problem David A. Case (Tue Apr 17 2007 - 16:35:59 CDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? Nicolas Lux Fawzi (Tue Apr 17 2007 - 14:00:18 CDT)
AMBER: using glycam04 parameters Sara Alexandra Moura (Tue Apr 17 2007 - 14:17:44 CDT)
- Re: AMBER: using glycam04 parameters David A. Case (Tue Apr 17 2007 - 16:37:35 CDT)
  - Re: AMBER: using glycam04 parameters FyD (Wed Apr 18 2007 - 05:57:02 CDT)
  - Re: AMBER: using glycam04 parameters Sara Alexandra Moura (Wed Apr 18 2007 - 10:10:35 CDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try Nicolas Lux Fawzi (Tue Apr 17 2007 - 16:50:07 CDT)
- Re: AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try Pradipta Bandyopadhyay (Tue Apr 17 2007 - 23:33:52 CDT)
AMBER: frcmod file deepti nayar (Wed Apr 18 2007 - 01:31:52 CDT)
- Re: AMBER: frcmod file David A. Case (Wed Apr 18 2007 - 10:22:01 CDT)
- RE: AMBER: frcmod file Ross Walker (Wed Apr 18 2007 - 10:51:20 CDT)
AMBER: printcharges option when using QM/MM simulation ÇÑÀç¹ü (Wed Apr 18 2007 - 01:41:33 CDT)
- RE: AMBER: printcharges option when using QM/MM simulation Ross Walker (Wed Apr 18 2007 - 10:31:17 CDT)
AMBER: Protonation/deprotonation of terminal residues Jesper Soerensen (Wed Apr 18 2007 - 07:56:26 CDT)
- Re: AMBER: Protonation/deprotonation of terminal residues FyD (Wed Apr 18 2007 - 13:26:47 CDT)
AMBER: signal SIGSEGV(11) Pankaj R. Daga (Wed Apr 18 2007 - 10:25:55 CDT)
- Re: AMBER: signal SIGSEGV(11) David A. Case (Wed Apr 18 2007 - 10:49:24 CDT)
- RE: AMBER: signal SIGSEGV(11) Ross Walker (Wed Apr 18 2007 - 11:09:10 CDT)
  - Re: AMBER: signal SIGSEGV(11) Pankaj R. Daga (Wed Apr 18 2007 - 14:16:48 CDT)
AMBER: ff02 + POL3 - polar interactions !! Pradipta Bandyopadhyay (Wed Apr 18 2007 - 11:04:22 CDT)
AMBER: Antechamber Warning Beale, John (Wed Apr 18 2007 - 14:39:31 CDT)
AMBER: ptraj bug? Tamara Rogers (Wed Apr 18 2007 - 17:09:39 CDT)
AMBER: Sander BOMB.. simulation terminates by itself... Vijay Manickam Achari (Wed Apr 18 2007 - 20:24:28 CDT)
AMBER: Ewald BOMB....... what is this.. Vijay Manickam Achari (Wed Apr 18 2007 - 22:13:38 CDT)
- RE: AMBER: Ewald BOMB....... what is this.. Ross Walker (Sat Apr 21 2007 - 12:08:15 CDT)
AMBER: Antechamber Beale, John (Thu Apr 19 2007 - 08:51:03 CDT)
- RE: AMBER: Antechamber Junmei Wang (Thu Apr 19 2007 - 08:58:14 CDT)
AMBER: regarding frcmod file Santanu Roy (Thu Apr 19 2007 - 10:28:01 CDT)
- Re: AMBER: regarding frcmod file Gustavo Seabra (Thu Apr 19 2007 - 10:50:44 CDT)
- Re: AMBER: regarding frcmod file David A. Case (Thu Apr 19 2007 - 11:14:03 CDT)
AMBER: RE: RE: AMBER: QMMM with printcharges Kijeong Kwac (Thu Apr 19 2007 - 10:42:38 CDT)
- RE: AMBER: RE: RE: AMBER: QMMM with printcharges Ross Walker (Thu Apr 19 2007 - 11:42:15 CDT)
AMBER: Problems with Machine file for sander.MPI Terry Lang (Thu Apr 19 2007 - 15:15:45 CDT)
- RE: AMBER: Problems with Machine file for sander.MPI Ross Walker (Thu Apr 19 2007 - 16:02:24 CDT)
  - Re: AMBER: Problems with Machine file for sander.MPI Terry Lang (Tue Apr 24 2007 - 18:55:11 CDT)
AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Thu Apr 19 2007 - 18:30:35 CDT)
- Re: AMBER: AIX 5 test failures: -NaNQ Scott Brozell (Thu Apr 19 2007 - 19:13:54 CDT)
  - Re: AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Fri Apr 20 2007 - 18:01:53 CDT)
- Re: AMBER: AIX 5 test failures: -NaNQ David A. Case (Thu Apr 19 2007 - 20:13:46 CDT)
- RE: AMBER: AIX 5 test failures: -NaNQ Ross Walker (Thu Apr 19 2007 - 20:20:46 CDT)
AMBER: QM/MM NPT Simulation Daniel Oehme (Thu Apr 19 2007 - 23:46:14 CDT)
- RE: AMBER: QM/MM NPT Simulation Ross Walker (Fri Apr 20 2007 - 10:22:25 CDT)
AMBER: A test email Ruchi Sachdeva (Fri Apr 20 2007 - 01:54:55 CDT)
AMBER: process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 04:28:12 CDT)
- Re: AMBER: process and plot matrix data Patrick McCarren (Fri Apr 20 2007 - 05:02:15 CDT)
  - Re: AMBER: process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 08:18:46 CDT)
AMBER: rigid epoxide substrate Dr M. Blomberg (Fri Apr 20 2007 - 06:24:13 CDT)
- Re: AMBER: rigid epoxide substrate David A. Case (Fri Apr 20 2007 - 10:30:42 CDT)
AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 15:42:56 CDT)
- Re: AMBER: restraint value: written but none specified David A. Case (Fri Apr 20 2007 - 16:15:05 CDT)
  - Re: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 17:08:55 CDT)
- Re: AMBER: restraint value: written but none specified Chris Moth (Fri Apr 20 2007 - 16:16:52 CDT)
  - Re: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 16:51:30 CDT)
    - RE: AMBER: restraint value: written but none specified Ross Walker (Fri Apr 20 2007 - 17:37:01 CDT)
    - RE: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 18:05:47 CDT)
AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" Khatcharin Siriwong (Sat Apr 21 2007 - 02:42:14 CDT)
- Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" David A. Case (Sat Apr 21 2007 - 14:04:23 CDT)
  - Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" Khatcharin Siriwong (Sat Apr 21 2007 - 22:57:18 CDT)
  - AMBER: prep file new residue Dr M. Blomberg (Mon Apr 23 2007 - 03:48:27 CDT)
    - Re: AMBER: prep file new residue David A. Case (Tue Apr 24 2007 - 14:12:44 CDT)
AMBER: mol2 format Jardas sucuriba (Sun Apr 22 2007 - 17:57:12 CDT)
- Re: AMBER: mol2 format j j (Mon Apr 23 2007 - 04:04:53 CDT)
AMBER: .prmtop entries Neelanjana Sengupta (Mon Apr 23 2007 - 00:53:46 CDT)
- Re: AMBER: .prmtop entries Andy Purkiss-Trew (Mon Apr 23 2007 - 06:13:18 CDT)
AMBER: problem regarding implicit simulation gurpreet singh (Mon Apr 23 2007 - 01:16:35 CDT)
- Re: AMBER: problem regarding implicit simulation Carlos Simmerling (Mon Apr 23 2007 - 06:30:34 CDT)
  - Re: AMBER: problem regarding implicit simulation gurpreet singh (Tue Apr 24 2007 - 06:18:57 CDT)
    - Re: AMBER: problem regarding implicit simulation Carlos Simmerling (Tue Apr 24 2007 - 06:25:31 CDT)
AMBER: MM-PBSA: decompose energy error jitrayut jitonnom (Mon Apr 23 2007 - 06:31:43 CDT)
- Re: AMBER: MM-PBSA: decompose energy error Sergey Samsonov (Mon Apr 23 2007 - 06:56:30 CDT)
AMBER: MM-PBSA: decompose energy error jitrayut jitonnom (Mon Apr 23 2007 - 06:31:43 CDT)
AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom (Mon Apr 23 2007 - 07:34:48 CDT)
- Re: AMBER: MM-PBSA: Can't finish the binding energy process Navnit Kumar Mishra (Mon Apr 23 2007 - 09:04:12 CDT)
  - Fwd: AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom (Wed May 09 2007 - 23:12:55 CDT)
AMBER: Problem using Ptraj alfredoq_at_fcq.unc.edu.ar (Mon Apr 23 2007 - 10:41:56 CDT)
- Re: AMBER: Problem using Ptraj j j (Mon Apr 23 2007 - 11:47:50 CDT)
- Re: AMBER: Problem using Ptraj Thomas Cheatham III (Mon Apr 23 2007 - 12:02:17 CDT)
AMBER: Problems with AMBER8 on 32-bit FC6 David LeBard (Mon Apr 23 2007 - 13:51:02 CDT)
- Re: AMBER: Problems with AMBER8 on 32-bit FC6 David A. Case (Mon Apr 23 2007 - 16:17:09 CDT)
  - AMBER: Extracting Coords&MMPBSA&ambpdb Srinivas Odde (Tue Apr 24 2007 - 10:51:48 CDT)
AMBER: Error on compile amber8 tri nam Vo (Tue Apr 24 2007 - 00:04:34 CDT)
- Re: AMBER: Error on compile amber8 David LeBard (Tue Apr 24 2007 - 00:45:45 CDT)
  - Re: AMBER: Error on compile amber8 tri nam Vo (Tue Apr 24 2007 - 01:47:27 CDT)
AMBER: QM/MM simulation with SCC-DFTB ÇÑÀç¹ü (Tue Apr 24 2007 - 03:19:25 CDT)
- Re: AMBER: QM/MM simulation with SCC-DFTB Gustavo Seabra (Tue Apr 24 2007 - 05:48:11 CDT)
AMBER: amber equation of ff99 Chengwen Chen (Tue Apr 24 2007 - 11:13:54 CDT)
- Re: AMBER: amber equation of ff99 Carlos Simmerling (Tue Apr 24 2007 - 11:18:57 CDT)
  - Re: AMBER: amber equation of ff99 Chengwen Chen (Tue Apr 24 2007 - 21:19:15 CDT)
Re: AMBER:a question about RMSD Carlos Simmerling (Tue Apr 24 2007 - 08:06:40 CDT)
AMBER: NAD parameters Jardas sucuriba (Tue Apr 24 2007 - 13:02:56 CDT)
- RE: AMBER: NAD parameters Ross Walker (Tue Apr 24 2007 - 14:32:27 CDT)
  - RE: AMBER: NAD parameters Jardas sucuriba (Wed Apr 25 2007 - 17:46:17 CDT)
AMBER: mobile proton algorithm HL Eastwood (Tue Apr 24 2007 - 14:25:10 CDT)
AMBER: Error on compiling AMBER8 tri nam Vo (Tue Apr 24 2007 - 21:03:16 CDT)
- Re: AMBER: Error on compiling AMBER8 David A. Case (Tue Apr 24 2007 - 22:31:44 CDT)
  - Re: AMBER: Error on compiling AMBER8 tri nam Vo (Wed Apr 25 2007 - 11:35:31 CDT)
    - Re: AMBER: Error on compiling AMBER8 David A. Case (Wed Apr 25 2007 - 13:33:11 CDT)
AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Ruchi Sachdeva (Tue Apr 24 2007 - 22:54:14 CDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Scott Brozell (Fri Apr 27 2007 - 15:25:23 CDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Bill Ross (Fri Apr 27 2007 - 15:41:20 CDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Bill Ross (Fri Apr 27 2007 - 18:07:54 CDT)
AMBER: Work with constand pH tri nam Vo (Wed Apr 25 2007 - 03:13:05 CDT)
- Re: AMBER: Work with constand pH Myunggi Yi (Wed Apr 25 2007 - 08:49:59 CDT)
  - Re: AMBER: Work with constand pH tri nam Vo (Thu Apr 26 2007 - 22:37:53 CDT)
    - Re: AMBER: Work with constand pH Myunggi Yi (Fri Apr 27 2007 - 20:42:32 CDT)
AMBER: Employing SCC-DFTB with a periodic boundary condtion ÇÑÀç¹ü (Thu Apr 26 2007 - 01:48:58 CDT)
- Re: AMBER: Employing SCC-DFTB with a periodic boundary condtion Gustavo Seabra (Thu Apr 26 2007 - 08:18:32 CDT)
AMBER: protein-rna interaction & mmpbsa Antonio Morreale (Thu Apr 26 2007 - 03:28:19 CDT)
AMBER: Problems installing Amber9 Ângela dos Reis (Fri Apr 27 2007 - 06:14:05 CDT)
- Re: AMBER: Problems installing Amber9 Andreas Svrcek-Seiler (Fri Apr 27 2007 - 07:52:05 CDT)
- RE: AMBER: Problems installing Amber9 Ross Walker (Fri Apr 27 2007 - 10:56:41 CDT)
  - Re: AMBER: Problems installing Amber9 Ângela dos Reis (Fri Apr 27 2007 - 12:34:38 CDT)
AMBER: Error in protonating Neelanjana Sengupta (Fri Apr 27 2007 - 06:31:52 CDT)
- RE: AMBER: Error in protonating Ross Walker (Fri Apr 27 2007 - 10:46:50 CDT)
- Re: AMBER: Error in protonating David A. Case (Sat Apr 28 2007 - 16:26:08 CDT)
AMBER: Print individual free energies in MD trajectories using MM_PBSA Giulio Rastelli (Fri Apr 27 2007 - 11:05:39 CDT)
AMBER: QM/MM Umbrella sampling Jason DeChancie (Fri Apr 27 2007 - 15:53:08 CDT)
- RE: AMBER: QM/MM Umbrella sampling Ross Walker (Fri Apr 27 2007 - 17:01:46 CDT)
- Re: AMBER: QM/MM Umbrella sampling Jerome.GOLEBIOWSKI_at_unice.fr (Sat Apr 28 2007 - 02:55:49 CDT)
AMBER: thermodynamic integration Servaas Michielssens (Sat Apr 28 2007 - 12:48:10 CDT)
- Re: AMBER: thermodynamic integration David A. Case (Sat Apr 28 2007 - 16:26:28 CDT)
AMBER: Binding free energy errors: Grid setting fail jitrayut jitonnom (Sun Apr 29 2007 - 08:48:17 CDT)
AMBER: a problem of surface area calulated by MM/PBSA Chengwen Chen (Mon Apr 30 2007 - 02:34:38 CDT)
- Re: AMBER: a problem of surface area calulated by MM/PBSA David A. Case (Mon Apr 30 2007 - 10:20:43 CDT)
AMBER: Problem with MM-PBSA statistics Henar Martínez García (Mon Apr 30 2007 - 04:53:38 CDT)
- AMBER: AMBER MINIMIZATION Sophie Barbe (Mon Apr 30 2007 - 08:55:53 CDT)
  - Re: AMBER: AMBER MINIMIZATION David A. Case (Mon Apr 30 2007 - 10:24:34 CDT)
    - Re: AMBER: AMBER MINIMIZATION Sophie Barbe (Mon Apr 30 2007 - 11:23:41 CDT)
  - Re: AMBER: AMBER MINIMIZATION gsciaini_at_qi.fcen.uba.ar (Mon Apr 30 2007 - 16:08:47 CDT)
AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 06:35:23 CDT)
AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 08:04:11 CDT)
- Re: AMBER: Problem with calcpka.pl and constant pH David A. Case (Thu May 03 2007 - 12:13:50 CDT)
AMBER: PDB files Beale, John (Mon Apr 30 2007 - 11:16:59 CDT)
- RE: AMBER: PDB files Hayden Eastwood (Mon Apr 30 2007 - 12:12:01 CDT)
- RE: AMBER: PDB files Hayden Eastwood (Mon Apr 30 2007 - 12:20:14 CDT)
- Re: AMBER: PDB files David A. Case (Mon Apr 30 2007 - 15:00:33 CDT)
AMBER: pressure tensor in a slab configuration rdauria_at_uci.edu (Mon Apr 30 2007 - 21:16:08 CDT)
- AMBER: mm-pbsa error with nm = 1 Hayden Eastwood (Tue May 01 2007 - 12:21:22 CDT)
  - Re: AMBER: mm-pbsa error with nm = 1 Urszula Uciechowska (Tue May 01 2007 - 12:43:28 CDT)
  - Re: AMBER: mm-pbsa error with nm = 1 Cenk Andac (Tue May 01 2007 - 18:58:17 CDT)
AMBER: Problem with SCC-DFTB parameter files ÇÑÀç¹ü (Tue May 01 2007 - 23:55:03 CDT)
- Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra (Wed May 02 2007 - 06:46:58 CDT)
- RE: AMBER: Problem with SCC-DFTB parameter files Ross Walker (Wed May 02 2007 - 09:45:07 CDT)
- Re: AMBER: Problem with SCC-DFTB parameter files M. L. Dodson (Wed May 02 2007 - 09:59:02 CDT)
  - Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra (Wed May 02 2007 - 10:27:00 CDT)
AMBER: Steered MD & Jarzynski's equality James W (Wed May 02 2007 - 01:44:20 CDT)
- Re: AMBER: Steered MD & Jarzynski's equality Adrian Roitberg (Wed May 02 2007 - 02:26:30 CDT)
  - Re: AMBER: Steered MD & Jarzynski's equality James W (Wed May 02 2007 - 04:44:28 CDT)
AMBER: Group declaration question cristian obiol (Wed May 02 2007 - 04:28:19 CDT)
Re: AMBER: Group declaration question Bill Ross (Wed May 02 2007 - 14:10:23 CDT)
AMBER: command line alternatives for teLeap Neelanjana Sengupta (Wed May 02 2007 - 23:21:07 CDT)
- Re: AMBER: command line alternatives for teLeap David A. Case (Thu May 03 2007 - 09:30:00 CDT)
  - AMBER: DivCon calculation in Amber9 Wang, Xuelin (Thu May 03 2007 - 14:51:35 CDT)
AMBER: md output file deepti nayar (Thu May 03 2007 - 04:06:24 CDT)
- Re: AMBER: md output file Gustavo Seabra (Thu May 03 2007 - 06:32:56 CDT)
AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine (Thu May 03 2007 - 04:46:27 CDT)
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Jerome.GOLEBIOWSKI_at_unice.fr (Thu May 03 2007 - 08:57:32 CDT)
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley (Thu May 03 2007 - 17:17:31 CDT)
  - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine (Thu May 03 2007 - 21:13:55 CDT)
AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Thu May 03 2007 - 20:07:05 CDT)
- Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Fri May 04 2007 - 00:16:30 CDT)
  - Re: AMBER: Chemical shift: simulation vs. experiment Adrian Roitberg (Fri May 04 2007 - 01:42:55 CDT)
    - Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Fri May 04 2007 - 02:17:04 CDT)
    - Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Fri May 04 2007 - 02:52:48 CDT)
AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations? Catein Catherine (Fri May 04 2007 - 03:13:44 CDT)
AMBER: Rate of Dissociation Catein Catherine (Fri May 04 2007 - 04:37:46 CDT)
- Re: AMBER: Rate of Dissociation David Mobley (Fri May 04 2007 - 12:41:51 CDT)
  - Re: AMBER: Rate of Dissociation Sean Rathlef (Fri May 04 2007 - 14:15:03 CDT)
    - Re: AMBER: Rate of Dissociation Catein Catherine (Fri May 04 2007 - 21:10:02 CDT)
    - Re: AMBER: Rate of Dissociation wang (Sun May 06 2007 - 20:44:36 CDT)
AMBER: B or E Dihedral Labels in RDPARM output Mark Williamson (Fri May 04 2007 - 09:04:17 CDT)
- Re: AMBER: B or E Dihedral Labels in RDPARM output Thomas Cheatham III (Fri May 04 2007 - 10:24:07 CDT)
AMBER: Average PDB - Unusual Bonds Seth Lilavivat (Fri May 04 2007 - 09:12:25 CDT)
- RE: AMBER: Average PDB - Unusual Bonds Hayden Eastwood (Fri May 04 2007 - 09:45:01 CDT)
  - RE: AMBER: Average PDB - Unusual Bonds Ross Walker (Fri May 04 2007 - 10:29:36 CDT)
AMBER: Simulated Annealing - Best way to create randomness Seth Lilavivat (Fri May 04 2007 - 15:42:18 CDT)
AMBER: RE: RE: AMBER: Problem with SCC-DFTB parameter files ÇÑÀç¹ü (Fri May 04 2007 - 23:25:29 CDT)
- AMBER: polarizable water models. Karen Callahan (Sat May 05 2007 - 01:38:34 CDT)
  - Re: AMBER: polarizable water models. David A. Case (Sun May 06 2007 - 16:31:50 CDT)
AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker (Sun May 06 2007 - 20:31:24 CDT)
- Re: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Gustavo Seabra (Mon May 07 2007 - 07:36:15 CDT)
  - RE: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker (Mon May 07 2007 - 10:11:12 CDT)
AMBER: REF file problem deepti nayar (Mon May 07 2007 - 01:49:53 CDT)
- Re: AMBER: REF file problem Gustavo Seabra (Mon May 07 2007 - 07:20:10 CDT)
- RE: AMBER: REF file problem Ross Walker (Mon May 07 2007 - 10:13:58 CDT)
AMBER: Atoms closer to 2 angstroms to each other Christopher Gaughan (Mon May 07 2007 - 09:38:06 CDT)
- Re: AMBER: Atoms closer to 2 angstroms to each other David A. Case (Mon May 07 2007 - 09:55:30 CDT)
- RE: AMBER: Atoms closer to 2 angstroms to each other Ross Walker (Mon May 07 2007 - 10:30:29 CDT)
AMBER: GB Energy Spreads for MD Structures adelene_at_Stanford.EDU (Mon May 07 2007 - 14:19:47 CDT)
- Re: AMBER: GB Energy Spreads for MD Structures David A. Case (Mon May 07 2007 - 16:13:41 CDT)
AMBER: Keq computations Sean Rathlef (Mon May 07 2007 - 18:10:09 CDT)
- Re: AMBER: Keq computations Carlos Simmerling (Mon May 07 2007 - 17:43:53 CDT)
  - AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) wang (Thu May 17 2007 - 01:41:39 CDT)
    - Re: AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) Adrian Roitberg (Thu May 17 2007 - 10:06:49 CDT)
AMBER: NAB MD Output adelene_at_Stanford.EDU (Mon May 07 2007 - 17:30:51 CDT)
- Re: AMBER: NAB MD Output Russell Brown (Mon May 07 2007 - 18:06:27 CDT)
- Re: AMBER: NAB MD Output Andreas Svrcek-Seiler (Tue May 08 2007 - 05:09:18 CDT)
AMBER: PME memory requirement Russell Brown (Mon May 07 2007 - 17:36:45 CDT)
- Re: AMBER: PME memory requirement Robert Duke (Mon May 07 2007 - 21:05:48 CDT)
AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Catein Catherine (Tue May 08 2007 - 01:28:14 CDT)
- Re: AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Carlos Simmerling (Tue May 08 2007 - 06:11:42 CDT)
AMBER: query regarding parameter files for manganese and mercuric ions neetu_at_imtech.res.in (Tue May 08 2007 - 06:40:56 CDT)
- AMBER: query regarding parameter files for manganese neetu_at_imtech.res.in (Thu May 10 2007 - 07:43:44 CDT)
AMBER: Complexes Beale, John (Tue May 08 2007 - 13:54:34 CDT)
- Re: AMBER: Complexes M. L. Dodson (Tue May 08 2007 - 14:14:59 CDT)
  - Re: AMBER: Complexes M. L. Dodson (Tue May 08 2007 - 14:26:11 CDT)
AMBER: simulations stops in half way Vijay Manickam Achari (Wed May 09 2007 - 00:01:21 CDT)
- Re: AMBER: simulations stops in half way Robert Duke (Wed May 09 2007 - 07:51:17 CDT)
AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 05:15:16 CDT)
- AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 06:22:09 CDT)
  - Re: AMBER: hybrid remd Asim Okur (Wed May 09 2007 - 14:07:59 CDT)
AMBER: Compiling parallel Amber9 on Linux cluster Jesus Angulo (Wed May 09 2007 - 05:27:23 CDT)
- RE: AMBER: Compiling parallel Amber9 on Linux cluster Ross Walker (Wed May 09 2007 - 10:27:36 CDT)
AMBER: pmemd source issues Thomas Zeiser (Wed May 09 2007 - 06:33:11 CDT)
- Re: AMBER: pmemd source issues Robert Duke (Wed May 09 2007 - 08:37:59 CDT)
  - AMBER: Covert NOEs form Xplor to Amber saccenti_at_cerm.unifi.it (Wed May 09 2007 - 09:09:12 CDT)
  - Re: AMBER: pmemd source issues Thomas Zeiser (Wed May 09 2007 - 10:00:00 CDT)
    - Re: AMBER: pmemd source issues Robert Duke (Wed May 09 2007 - 10:43:36 CDT)
    - Re: AMBER: pmemd source issues Thomas Zeiser (Thu May 10 2007 - 06:55:16 CDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 07:03:51 CDT)
- Re: AMBER: leap problem David A. Case (Thu May 10 2007 - 15:51:13 CDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 07:28:01 CDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 07:48:33 CDT)
AMBER: Amber 9 compile on OS X Knut Langsetmo (Wed May 09 2007 - 16:29:44 CDT)
- Re: AMBER: Amber 9 compile on OS X David A. Case (Thu May 10 2007 - 18:48:49 CDT)
AMBER: (no subject) Dingguo Xu (Wed May 09 2007 - 16:29:58 CDT)
- Re: AMBER: (no subject) David A. Case (Thu May 10 2007 - 15:37:21 CDT)
AMBER: Missing BELE for MM in 1 (residue 47) AYTUG TUNCEL (Thu May 10 2007 - 02:32:26 CDT)
AMBER: umbrella sampling: distance restraint Catein Catherine (Thu May 10 2007 - 05:25:46 CDT)
- Re: AMBER: umbrella sampling: distance restraint Jerome.GOLEBIOWSKI_at_unice.fr (Thu May 10 2007 - 07:19:35 CDT)
AMBER: restraint_wt and fixing chi deepti nayar (Thu May 10 2007 - 05:44:40 CDT)
- Re: AMBER: restraint_wt and fixing chi Thomas Cheatham III (Thu May 10 2007 - 12:09:59 CDT)
AMBER: use of pucker function in ptraj Ben Tan (Thu May 10 2007 - 06:00:41 CDT)
- Re: AMBER: use of pucker function in ptraj Thomas Cheatham III (Thu May 10 2007 - 11:48:58 CDT)
AMBER: Electrostatic Energy in MD Simulation (GB) adelene_at_Stanford.EDU (Thu May 10 2007 - 12:20:32 CDT)
- Re: AMBER: Electrostatic Energy in MD Simulation (GB) David A. Case (Thu May 10 2007 - 12:45:45 CDT)
AMBER: need help to calculate IR spectra from amber trajectory S.Sundar Raman (Thu May 10 2007 - 12:53:16 CDT)
- Re: AMBER: need help to calculate IR spectra from amber trajectory Adrian Roitberg (Thu May 10 2007 - 14:16:59 CDT)
AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 13:08:10 CDT)
- Re: AMBER: bug in reprocessing with PB? Carlos Simmerling (Thu May 10 2007 - 13:14:08 CDT)
- Re: AMBER: bug in reprocessing with PB? David A. Case (Thu May 10 2007 - 13:24:20 CDT)
  - RE: AMBER: bug in reprocessing with PB? Ray Luo (Thu May 10 2007 - 13:52:37 CDT)
    - Re: AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 14:20:26 CDT)
    - RE: AMBER: bug in reprocessing with PB? Ray Luo (Thu May 10 2007 - 16:04:42 CDT)
  - Re: AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 14:18:23 CDT)
AMBER: Sander (Amber 9) crash on cortex Evan Kelly (Thu May 10 2007 - 13:57:20 CDT)
- Re: AMBER: Sander (Amber 9) crash on cortex David A. Case (Thu May 10 2007 - 14:55:16 CDT)
- RE: AMBER: Sander (Amber 9) crash on cortex Ross Walker (Thu May 10 2007 - 15:09:19 CDT)
  - Re: AMBER: Sander (Amber 9) crash on cortex Evan Kelly (Thu May 10 2007 - 20:10:46 CDT)
AMBER: single phospholipid molecule in vacuo Kliman, Michal (Thu May 10 2007 - 15:02:55 CDT)
- Re: AMBER: single phospholipid molecule in vacuo David A. Case (Thu May 10 2007 - 18:51:39 CDT)
AMBER: Rotations about center of mass of an isolated system Jennie Thomas (Thu May 10 2007 - 20:08:06 CDT)
- Re: AMBER: Rotations about center of mass of an isolated system David A. Case (Mon May 14 2007 - 11:19:20 CDT)
  - Re: AMBER: Rotations about center of mass of an isolated system Jennie Thomas (Mon May 14 2007 - 14:50:30 CDT)
AMBER: how to solvate the protein with different solvents Rachel (Fri May 11 2007 - 08:01:07 CDT)
AMBER: antechamber Santanu Roy (Fri May 11 2007 - 08:40:24 CDT)
- Re: AMBER: antechamber Scott Brozell (Fri May 11 2007 - 17:46:24 CDT)
AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Giulio Rastelli (Fri May 11 2007 - 09:47:39 CDT)
- RE: AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Ray Luo (Fri May 11 2007 - 11:54:21 CDT)
AMBER: missing impropers for nitros? David Mobley (Fri May 11 2007 - 19:03:55 CDT)
- AMBER: Re: missing impropers for nitros? David Mobley (Fri May 11 2007 - 19:15:11 CDT)
- Re: AMBER: missing impropers for nitros? David A. Case (Sat May 12 2007 - 12:37:27 CDT)
  - Re: AMBER: missing impropers for nitros? David Mobley (Mon May 14 2007 - 08:28:34 CDT)
- Fwd: AMBER: missing impropers for nitros? David Mobley (Mon May 21 2007 - 10:47:04 CDT)
  - RE: AMBER: missing impropers for nitros? Junmei Wang (Mon May 21 2007 - 12:48:58 CDT)
AMBER: distance.restraint for two groups of atoms (center of mass) Catein Catherine (Fri May 11 2007 - 21:30:36 CDT)
- Re: AMBER: distance.restraint for two groups of atoms (center of mass) David A. Case (Sat May 12 2007 - 12:18:59 CDT)
AMBER: PMF for DG calculation. Catein Catherine (Fri May 11 2007 - 21:45:30 CDT)
- Re: AMBER: PMF for DG calculation. David Mobley (Mon May 14 2007 - 09:06:46 CDT)
  - Re: AMBER: PMF for DG calculation. David A. Case (Mon May 14 2007 - 10:01:41 CDT)
AMBER: PMF along 1D axis or every axis Catein Catherine (Fri May 11 2007 - 22:05:57 CDT)
AMBER: PMF: WHAM result Catein Catherine (Fri May 11 2007 - 22:28:30 CDT)
AMBER: antechamber Santanu Roy (Sat May 12 2007 - 00:50:13 CDT)
- Re: AMBER: antechamber David A. Case (Sat May 12 2007 - 12:13:39 CDT)
AMBER: PMEMD and restart files Austin B. Yongye (Sat May 12 2007 - 13:21:30 CDT)
- Re: AMBER: PMEMD and restart files Robert Duke (Sat May 12 2007 - 17:01:38 CDT)
AMBER: Small scale compute environments M. L. Dodson (Sat May 12 2007 - 14:13:59 CDT)
- Re: AMBER: Small scale compute environments Robert Duke (Mon May 14 2007 - 10:59:50 CDT)
  - Re: AMBER: Small scale compute environments M. L. Dodson (Mon May 14 2007 - 13:32:36 CDT)
AMBER: problem about the coordinates out the box Shaoqing.Zhang_at_mail.uh.edu (Sat May 12 2007 - 22:26:45 CDT)
AMBER: restraining atoms deepti nayar (Sun May 13 2007 - 23:39:15 CDT)
- Re: AMBER: restraining atoms Thomas Cheatham III (Mon May 14 2007 - 12:27:01 CDT)
AMBER: polymer Achuth Prabhu (Mon May 14 2007 - 07:55:12 CDT)
AMBER: Energy Spread using GB & Langevin Dynamics (NAB) adelene_at_Stanford.EDU (Mon May 14 2007 - 15:17:28 CDT)
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case (Mon May 14 2007 - 16:40:50 CDT)
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) Andreas Svrcek-Seiler (Tue May 15 2007 - 04:20:16 CDT)
  - Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case (Tue May 15 2007 - 11:03:52 CDT)
AMBER: assigning of head atom as null. SHARAD gupta (Tue May 15 2007 - 02:26:23 CDT)
AMBER: Finding x-displacement Ben Tan (Tue May 15 2007 - 04:23:11 CDT)
AMBER: Heat of Vaporization Rita Cassia (Tue May 15 2007 - 07:35:49 CDT)
- Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 11:09:27 CDT)
  - Re: AMBER: Heat of Vaporization Thomas Cheatham III (Tue May 15 2007 - 11:37:01 CDT)
  - Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 11:51:36 CDT)
    - Re: AMBER: Heat of Vaporization Rita Cassia (Wed May 16 2007 - 06:55:49 CDT)
- RE: AMBER: Heat of Vaporization Falck da Silva Eirik (Tue May 15 2007 - 15:00:31 CDT)
  - Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 15:14:24 CDT)
    - AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA] (Tue May 15 2007 - 16:01:11 CDT)
    - AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA] (Wed May 16 2007 - 08:57:26 CDT)
AMBER: constant pH with 25 titrable sites tri nam Vo (Tue May 15 2007 - 12:44:22 CDT)
AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Tue May 15 2007 - 12:55:40 CDT)
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling (Tue May 15 2007 - 13:11:57 CDT)
  - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Tue May 15 2007 - 13:32:30 CDT)
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Gustavo Seabra (Tue May 15 2007 - 14:11:21 CDT)
AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Tue May 15 2007 - 20:37:22 CDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell (Wed May 16 2007 - 13:42:06 CDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Wed May 16 2007 - 15:37:53 CDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler Mark Williamson (Fri May 18 2007 - 07:19:37 CDT)
AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" S. Jamal Rahi (Wed May 16 2007 - 08:22:47 CDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Carlos Simmerling (Wed May 16 2007 - 08:29:35 CDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Thomas Steinbrecher (Wed May 16 2007 - 10:48:20 CDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" David A. Case (Wed May 16 2007 - 11:04:57 CDT)
AMBER: MM-PBSA calculation with GB dynamic Andrea - Tisacali (Wed May 16 2007 - 08:56:15 CDT)
- Re: AMBER: MM-PBSA calculation with GB dynamic Carlos Simmerling (Wed May 16 2007 - 09:03:01 CDT)
AMBER: protonate Christopher Gaughan (Wed May 16 2007 - 10:56:37 CDT)
- Re: AMBER: protonate saccenti_at_cerm.unifi.it (Wed May 16 2007 - 11:22:20 CDT)
  - AMBER: Minimization with heme group saccenti_at_cerm.unifi.it (Wed May 16 2007 - 11:25:23 CDT)
  - Re: AMBER: protonate David A. Case (Wed May 16 2007 - 11:33:20 CDT)
    - AMBER: Re: Minimization with heme group saccenti_at_cerm.unifi.it (Wed May 16 2007 - 12:11:43 CDT)
- AMBER: Ignore my reply to Amber protonate! saccenti_at_cerm.unifi.it (Wed May 16 2007 - 11:24:12 CDT)
- Re: AMBER: protonate David A. Case (Wed May 16 2007 - 11:32:37 CDT)
AMBER: work with constant pH on amber8 tri nam Vo (Wed May 16 2007 - 12:52:47 CDT)
- AMBER: work with constant pH on amber8 tri nam Vo (Wed May 16 2007 - 13:13:43 CDT)
- Re: AMBER: work with constant pH on amber8 David A. Case (Wed May 16 2007 - 13:40:42 CDT)
AMBER: NOC 3.0 is released mchen2_at_mailer.fsu.edu (Wed May 16 2007 - 15:03:30 CDT)
AMBER: hbond ptraj Catein Catherine (Wed May 16 2007 - 22:39:02 CDT)
- Re: AMBER: hbond ptraj Thomas Cheatham (Wed May 16 2007 - 22:57:46 CDT)
  - Re: AMBER: hbond ptraj Catein Catherine (Thu May 17 2007 - 01:33:31 CDT)
    - Re: AMBER: hbond ptraj Chris Moth (Thu May 17 2007 - 07:14:31 CDT)
    - Re: AMBER: hbond ptraj Thomas Cheatham (Thu May 17 2007 - 09:32:15 CDT)
AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL (Thu May 17 2007 - 04:53:07 CDT)
AMBER: deeper problem with the energetics Pankaj R. Daga (Thu May 17 2007 - 08:46:33 CDT)
- Re: AMBER: deeper problem with the energetics Carlos Simmerling (Thu May 17 2007 - 08:56:43 CDT)
  - Re: AMBER: deeper problem with the energetics Pankaj R. Daga (Thu May 17 2007 - 11:50:11 CDT)
    - Re: AMBER: deeper problem with the energetics Carlos Simmerling (Mon May 21 2007 - 09:11:58 CDT)
AMBER: Average structure Steve Seibold (Thu May 17 2007 - 09:33:41 CDT)
- Re: AMBER: Average structure Thomas Cheatham (Thu May 17 2007 - 09:57:12 CDT)
AMBER: multiple excecution of sander Achuth Prabhu (Thu May 17 2007 - 10:55:47 CDT)
- Re: AMBER: multiple excecution of sander Carlos Simmerling (Thu May 17 2007 - 11:03:23 CDT)
  - Re :Re: AMBER: multiple excecution of sander Achuth Prabhu (Fri May 18 2007 - 01:03:23 CDT)
    - Re: Re :Re: AMBER: multiple excecution of sander Carlos Simmerling (Mon May 21 2007 - 09:12:59 CDT)
AMBER: NAB Average Structure adelene_at_Stanford.EDU (Thu May 17 2007 - 11:12:47 CDT)
- Re: AMBER: NAB Average Structure David A. Case (Thu May 17 2007 - 11:32:59 CDT)
  - Re: AMBER: NAB Average Structure adelene_at_Stanford.EDU (Thu May 17 2007 - 13:59:42 CDT)
    - Re: AMBER: NAB Average Structure Andreas Svrcek-Seiler (Thu May 17 2007 - 14:40:26 CDT)
    - Re: AMBER: NAB Average Structure David A. Case (Thu May 17 2007 - 16:13:10 CDT)
AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL (Fri May 18 2007 - 01:39:43 CDT)
AMBER: Some questions on mm_pbsa Hu, Shaowen (JSC-SK)[USRA] (Fri May 18 2007 - 09:53:35 CDT)
AMBER: Temperature Drift in MD (NAB) adelene_at_Stanford.EDU (Fri May 18 2007 - 17:49:25 CDT)
- Re: AMBER: Temperature Drift in MD (NAB) David A. Case (Fri May 18 2007 - 18:07:09 CDT)
  - Re: AMBER: Temperature Drift in MD (NAB) adelene_at_Stanford.EDU (Fri May 18 2007 - 18:56:39 CDT)
    - Re: AMBER: Temperature Drift in MD (NAB) David A. Case (Sat May 19 2007 - 23:03:24 CDT)
AMBER: Statictical significance of differences in energy mean values between different simulations Mostafa Sadighi (Sat May 19 2007 - 10:54:40 CDT)
AMBER: antechamber question Francesco Pietra (Sun May 20 2007 - 02:05:59 CDT)
- Re: AMBER: antechamber question David A. Case (Sun May 20 2007 - 09:44:18 CDT)
  - Re: AMBER: antechamber question Francesco Pietra (Sun May 20 2007 - 10:36:28 CDT)
AMBER: Langevin dynamics in NAB David A. Case (Sun May 20 2007 - 20:39:42 CDT)
AMBER: [AMBER] QM/MM-DFTB ¹Ú¹ÎÈñ (Sun May 20 2007 - 20:55:42 CDT)
AMBER: QM/MM-DRFTB ¹Ú¹ÎÈñ (Sun May 20 2007 - 20:57:56 CDT)
- AMBER: Docking with AMber Urszula Uciechowska (Mon May 21 2007 - 02:13:01 CDT)
  - Re: AMBER: Docking with AMber David A. Case (Mon May 21 2007 - 23:26:07 CDT)
    - AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters. nag raj (Wed Jun 13 2007 - 22:58:22 CDT)
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra (Mon May 21 2007 - 10:43:43 CDT)
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra (Mon May 21 2007 - 14:18:10 CDT)
  - AMBER: dielectric constant in GB/SA Shuting Wei (Mon May 21 2007 - 15:25:12 CDT)
AMBER: ambpdb gives empty cpin Achuth Prabhu (Mon May 21 2007 - 03:27:16 CDT)
- Re: AMBER: ambpdb gives empty cpin tri nam Vo (Tue May 22 2007 - 09:01:42 CDT)
AMBER: Pi-pi interactions Roberto Veiga (Mon May 21 2007 - 07:33:32 CDT)
- Re: AMBER: Pi-pi interactions Jiri Sponer (Mon May 21 2007 - 08:09:08 CDT)
  - Re: AMBER: Pi-pi interactions Roberto Veiga (Mon May 21 2007 - 10:03:16 CDT)
- Re: AMBER: Pi-pi interactions David Cerutti (Mon May 21 2007 - 08:13:16 CDT)
  - Re: AMBER: Pi-pi interactions Jiri Sponer (Mon May 21 2007 - 08:28:22 CDT)
    - Re: AMBER: Pi-pi interactions Adrian Roitberg (Mon May 21 2007 - 08:56:51 CDT)
  - AMBER: LES problem Urszula Uciechowska (Mon Jun 04 2007 - 08:34:42 CDT)
    - Re: AMBER: LES problem Carlos Simmerling (Tue Jun 05 2007 - 07:14:15 CDT)
    - Re: AMBER: LES problem Vlad Cojocaru (Tue Jun 05 2007 - 07:41:19 CDT)
AMBER: REMD error Jason K (Mon May 21 2007 - 10:20:12 CDT)
- Re: AMBER: REMD error Carlos Simmerling (Mon May 21 2007 - 10:41:53 CDT)
  - Re: AMBER: REMD error Jason K (Tue May 22 2007 - 14:02:22 CDT)
- Re: AMBER: REMD error Carlos Simmerling (Tue May 22 2007 - 16:15:43 CDT)
  - Re: AMBER: REMD error Jason K (Thu May 24 2007 - 10:31:17 CDT)
    - Re: AMBER: REMD error Carlos Simmerling (Thu May 24 2007 - 10:41:04 CDT)
- Re: AMBER: REMD error Carlos Simmerling (Thu May 24 2007 - 12:23:02 CDT)
AMBER: antechamber question Yao Xin (Tue May 22 2007 - 08:39:41 CDT)
- RE: AMBER: antechamber question Junmei Wang (Tue May 22 2007 - 10:08:18 CDT)
AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 09:59:01 CDT)
- Re: AMBER: Ionic strength in pbsa Qizhi Cui (Tue May 22 2007 - 15:21:27 CDT)
  - RE: AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 15:29:02 CDT)
AMBER: Simulated Annealing - Start with Poor Structure Seth Lilavivat (Tue May 22 2007 - 14:28:54 CDT)
- Re: AMBER: Simulated Annealing - Start with Poor Structure Carlos Simmerling (Tue May 22 2007 - 16:08:28 CDT)
AMBER: hbond ptraj pls help. Catein Catherine (Tue May 22 2007 - 23:56:50 CDT)
- Re: AMBER: hbond ptraj pls help. Kateryna Miroshnychenko (Wed May 23 2007 - 04:01:03 CDT)
  - Re: AMBER: hbond ptraj pls help. Catein Catherine (Wed May 23 2007 - 05:17:27 CDT)
AMBER: (no subject) Catein Catherine (Wed May 23 2007 - 00:00:36 CDT)
AMBER: MM/GBSA error message Catein Catherine (Wed May 23 2007 - 00:09:51 CDT)
AMBER: Minimization increases energy Hayden Eastwood (Wed May 23 2007 - 11:24:15 CDT)
AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL (Wed May 23 2007 - 08:26:32 CDT)
AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL (Wed May 23 2007 - 12:30:11 CDT)
Re: AMBER: adding polar hydrogens j j (Thu May 24 2007 - 06:09:04 CDT)
- Re: AMBER: adding polar hydrogens j j (Thu May 24 2007 - 08:00:12 CDT)
AMBER: thermodynamic integration Servaas Michielssens (Thu May 24 2007 - 10:50:48 CDT)
- Re: AMBER: thermodynamic integration David A. Case (Thu May 24 2007 - 23:14:43 CDT)
  - Re: AMBER: thermodynamic integration Servaas Michielssens (Fri May 25 2007 - 02:23:21 CDT)
AMBER: NAB normal mode output nadiav_at_soton.ac.uk (Thu May 24 2007 - 12:27:59 CDT)
- Re: AMBER: NAB normal mode output David A. Case (Thu May 24 2007 - 23:17:04 CDT)
  - Re: AMBER: NAB normal mode output Andreas Svrcek-Seiler (Fri May 25 2007 - 04:15:46 CDT)
    - AMBER: Less error Urszula Uciechowska (Fri May 25 2007 - 05:32:56 CDT)
    - Re: AMBER: Less error Carlos Simmerling (Fri May 25 2007 - 05:42:48 CDT)
AMBER: rfree: Error input file Steve Seibold (Thu May 24 2007 - 13:43:02 CDT)
- Re: AMBER: rfree: Error input file Carlos Simmerling (Thu May 24 2007 - 13:56:51 CDT)
  - RE: AMBER: rfree: Error input file Steve Seibold (Thu May 24 2007 - 14:22:39 CDT)
- AMBER: pi-pi interactions Sara Alexandra Moura (Fri May 25 2007 - 05:36:05 CDT)
AMBER: Steve Seibold (Thu May 24 2007 - 14:00:09 CDT)
AMBER: parameter file for Fe-S cluster devrani mitra (Thu May 24 2007 - 17:26:05 CDT)
AMBER: grid output: bulk water density mathew k varghese (Fri May 25 2007 - 05:19:30 CDT)
AMBER: software to extract data from the output file?? Avinash Kumar (Sat May 26 2007 - 03:49:37 CDT)
- Re: AMBER: software to extract data from the output file?? Steven Winfield (Sat May 26 2007 - 04:15:52 CDT)
- Re: AMBER: software to extract data from the output file?? Gustavo Seabra (Sat May 26 2007 - 09:09:08 CDT)
AMBER: inconsistency between PBSA and GBSA - help AYTUG TUNCEL (Sat May 26 2007 - 04:35:36 CDT)
AMBER: Question about determination of hydration points in binding sites Cenk Andac (Sun May 27 2007 - 03:51:27 CDT)
AMBER: Calculating RMS for each residue? tri nam Vo (Sun May 27 2007 - 11:01:38 CDT)
AMBER: Antechamber Catein Catherine (Sun May 27 2007 - 19:45:42 CDT)
- Re: AMBER: Antechamber Cenk Andac (Mon May 28 2007 - 01:56:57 CDT)
  - Re: AMBER: Antechamber Francesco Pietra (Mon May 28 2007 - 02:20:55 CDT)
AMBER: water count mathew k varghese (Mon May 28 2007 - 01:41:50 CDT)
- Re: AMBER: water count Carlos Simmerling (Mon May 28 2007 - 07:20:30 CDT)
AMBER: Amber 9 install on Debian Linux amd64 Francesco Pietra (Mon May 28 2007 - 02:14:49 CDT)
AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 19:54:18 CDT)
- AMBER: Re: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 19:56:55 CDT)
- Re: AMBER: divcon missing in Antechamber 1.27 David A. Case (Mon May 28 2007 - 20:33:52 CDT)
  - Re: AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 21:18:08 CDT)
    - Re: AMBER: divcon missing in Antechamber 1.27 David A. Case (Tue May 29 2007 - 09:24:20 CDT)
AMBER: 64-bit pgf90 revisited Ingvar Lagerstedt (Tue May 29 2007 - 03:39:07 CDT)
AMBER: error in running sander devrani mitra (Tue May 29 2007 - 15:22:35 CDT)
- Re: AMBER: error in running sander Carlos Simmerling (Tue May 29 2007 - 15:47:24 CDT)
  - Re: AMBER: error in running sander devrani mitra (Tue May 29 2007 - 16:27:09 CDT)
AMBER: Hydration points Cenk Andac (Tue May 29 2007 - 16:31:24 CDT)
- Re: AMBER: Hydration points Carlos Simmerling (Tue May 29 2007 - 16:34:54 CDT)
  - Re: AMBER: Hydration points Cenk Andac (Wed May 30 2007 - 16:23:33 CDT)
AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine (Wed May 30 2007 - 03:33:18 CDT)
- AMBER: electric field calculation lishan yao (Wed May 30 2007 - 07:25:16 CDT)
  - Re: AMBER: electric field calculation David A. Case (Wed May 30 2007 - 18:14:37 CDT)
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine (Wed May 30 2007 - 10:11:36 CDT)
AMBER: Atomic positional Fluctuations Sandeep Kaushik (Wed May 30 2007 - 08:08:09 CDT)
AMBER: (no subject) Catein Catherine (Wed May 30 2007 - 10:16:19 CDT)
- Re: AMBER: (no subject) M. L. Dodson (Wed May 30 2007 - 12:54:04 CDT)
AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Andrew Borgert (Wed May 30 2007 - 12:35:51 CDT)
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Carlos Simmerling (Wed May 30 2007 - 12:50:05 CDT)
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 kkirschn_at_hamilton.edu (Wed May 30 2007 - 15:28:55 CDT)
AMBER: cutoff & speed-up of GBSA Wei Chen (Wed May 30 2007 - 15:27:53 CDT)
- Re: AMBER: cutoff & speed-up of GBSA Carlos Simmerling (Wed May 30 2007 - 16:59:41 CDT)
  - Re: AMBER: cutoff & speed-up of GBSA Wei Chen (Thu May 31 2007 - 15:18:09 CDT)
AMBER: junk in `Noshake mask` output section Ben Sattelle (Wed May 30 2007 - 16:23:49 CDT)
- Re: AMBER: junk in `Noshake mask` output section David A. Case (Wed May 30 2007 - 16:47:51 CDT)
  - Re: AMBER: junk in `Noshake mask` output section Ben Sattelle (Wed May 30 2007 - 17:05:20 CDT)
AMBER: RESTRAINTMASK Roberto Veiga (Thu May 31 2007 - 09:29:26 CDT)
- Re: AMBER: RESTRAINTMASK David A. Case (Thu May 31 2007 - 10:59:42 CDT)
  - Re: AMBER: RESTRAINTMASK Sandeep Kaushik (Mon Jun 04 2007 - 00:38:21 CDT)
    - Re: AMBER: RESTRAINTMASK Roberto Veiga (Mon Jun 04 2007 - 15:09:23 CDT)
AMBER: Solvent models Francesco Pietra (Thu May 31 2007 - 10:23:56 CDT)
- Re: AMBER: Solvent models FyD (Thu May 31 2007 - 15:41:24 CDT)
  - Re: AMBER: Solvent models Francesco Pietra (Fri Jun 01 2007 - 02:00:36 CDT)
    - Re: AMBER: Solvent models FyD (Fri Jun 01 2007 - 03:14:20 CDT)
AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Thu May 31 2007 - 12:22:21 CDT)
- Re: AMBER: Reg restraint value obtained during umbrella sampling Jerome.GOLEBIOWSKI_at_unice.fr (Thu May 31 2007 - 13:02:45 CDT)
  - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Thu May 31 2007 - 13:28:50 CDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Thu May 31 2007 - 14:17:53 CDT)
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Thu May 31 2007 - 15:39:39 CDT)
  - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Fri Jun 01 2007 - 12:12:23 CDT)
AMBER: les/nudged elastic band Tamara Rogers (Thu May 31 2007 - 18:20:21 CDT)
- RE: AMBER: les/nudged elastic band Ross Walker (Thu May 31 2007 - 18:59:25 CDT)
AMBER: rms in nmode Marie Brut (Fri Jun 01 2007 - 02:22:22 CDT)
- Re: AMBER: rms in nmode cristian (Fri Jun 01 2007 - 02:59:18 CDT)
- Re: AMBER: rms in nmode David A. Case (Fri Jun 01 2007 - 10:50:27 CDT)
AMBER: problem in installing amber9 Syed Tarique Moin (Fri Jun 01 2007 - 02:10:44 CDT)
- Re: AMBER: problem in installing amber9 David A. Case (Fri Jun 01 2007 - 20:12:56 CDT)
  - Re: AMBER: problem in installing amber9 Syed Tarique Moin (Tue Jun 12 2007 - 03:04:57 CDT)
AMBER: Question about separating bonded force Shawn yy (Fri Jun 01 2007 - 10:31:04 CDT)
- Re: AMBER: Question about separating bonded force David A. Case (Fri Jun 01 2007 - 10:42:29 CDT)
AMBER: equilibrium constants via MMPBSA Sean Rathlef (Fri Jun 01 2007 - 11:57:46 CDT)
- Re: AMBER: equilibrium constants via MMPBSA Julien Michel (Fri Jun 01 2007 - 11:48:55 CDT)
- Re: AMBER: equilibrium constants via MMPBSA David Mobley (Mon Jun 04 2007 - 08:11:25 CDT)
  - AMBER: Installation Question Chrystal Bruce (Mon Jun 04 2007 - 09:53:46 CDT)
    - Re: AMBER: Installation Question Carlos Simmerling (Mon Jun 04 2007 - 09:16:30 CDT)
    - Re: AMBER: Installation Question Jianmin Feng (Mon Jun 04 2007 - 09:33:20 CDT)
AMBER: BUG? Does TLEAP understand SPC/E water? David Cerutti (Fri Jun 01 2007 - 12:35:02 CDT)
- RE: AMBER: BUG? Does TLEAP understand SPC/E water? Ross Walker (Fri Jun 01 2007 - 13:23:35 CDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? Thomas Steinbrecher (Fri Jun 01 2007 - 13:30:54 CDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case (Fri Jun 01 2007 - 13:37:10 CDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case (Fri Jun 01 2007 - 13:39:42 CDT)
AMBER: RE: process_mdout.perl Ross Walker (Fri Jun 01 2007 - 14:47:04 CDT)
AMBER: "distance" command in ptraj Roberto Veiga (Sat Jun 02 2007 - 06:19:42 CDT)
- Re: AMBER: "distance" command in ptraj Carlos Simmerling (Sat Jun 02 2007 - 06:56:15 CDT)
- Re: AMBER: "distance" command in ptraj Barbault Florent (Sat Jun 02 2007 - 10:28:44 CDT)
AMBER: pdb flie format Mr Defang Ouyang (Sun Jun 03 2007 - 07:53:08 CDT)
- Re: AMBER: pdb flie format Fenghui Fan (Sun Jun 03 2007 - 12:57:02 CDT)
- Re: AMBER: pdb flie format David A. Case (Sun Jun 03 2007 - 22:04:58 CDT)
  - Re: AMBER: pdb flie format j j (Mon Jun 04 2007 - 16:10:32 CDT)
AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out jitrayut jitonnom (Sun Jun 03 2007 - 11:08:16 CDT)
AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 09:06:19 CDT)
- Re: AMBER: Once again, "distance" command in ptraj Carlos Simmerling (Mon Jun 04 2007 - 09:15:22 CDT)
  - Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 09:20:34 CDT)
AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 11:47:01 CDT)
- Re: AMBER: Once again, "distance" command in ptraj Thomas Cheatham (Mon Jun 04 2007 - 23:22:45 CDT)
  - Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga (Tue Jun 05 2007 - 04:20:27 CDT)
AMBER: Amber9's sander.MPI on x86_64 kkirschn_at_hamilton.edu (Mon Jun 04 2007 - 12:13:51 CDT)
- Re: AMBER: Amber9's sander.MPI on x86_64 Thomas Steinbrecher (Mon Jun 04 2007 - 12:26:55 CDT)
- RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker (Mon Jun 04 2007 - 13:20:43 CDT)
- Re: AMBER: Amber9's sander.MPI on x86_64 Steve Young (Tue Jun 05 2007 - 12:23:43 CDT)
  - RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker (Wed Jun 06 2007 - 11:18:33 CDT)
AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 15:04:36 CDT)
- RE: AMBER: Problem about prepare the model when running antechamber Ross Walker (Mon Jun 04 2007 - 15:47:24 CDT)
  - Re: AMBER: Problem about prepare the model when running antechamber Carlos Simmerling (Mon Jun 04 2007 - 15:52:23 CDT)
    - Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 16:03:45 CDT)
  - Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 16:02:04 CDT)
AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Sophie Barbe (Mon Jun 04 2007 - 16:16:48 CDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Cenk Andac (Mon Jun 04 2007 - 17:00:25 CDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Thomas Cheatham (Tue Jun 05 2007 - 00:04:34 CDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Stéphane Téletchéa (Tue Jun 05 2007 - 03:01:10 CDT)
AMBER: problem with starting REM on amber9 priya priya (Tue Jun 05 2007 - 08:32:50 CDT)
- Re: AMBER: problem with starting REM on amber9 Carlos Simmerling (Tue Jun 05 2007 - 08:42:29 CDT)
  - Re: AMBER: problem with starting REM on amber9 priya priya (Tue Jun 05 2007 - 09:21:12 CDT)
    - RE: AMBER: problem with starting REM on amber9 Ross Walker (Tue Jun 05 2007 - 10:36:07 CDT)
    - RE: AMBER: problem with starting REM on amber9 priya priya (Wed Jun 06 2007 - 02:07:14 CDT)
AMBER: Ptraj hbond analysis Achuth Prabhu (Tue Jun 05 2007 - 09:51:54 CDT)
AMBER: problem running parallel jobs Nikola Trbovic (Tue Jun 05 2007 - 15:43:02 CDT)
- Re: AMBER: problem running parallel jobs Robert Konecny (Tue Jun 05 2007 - 16:34:44 CDT)
  - RE: AMBER: problem running parallel jobs Nikola Trbovic (Wed Jun 06 2007 - 12:31:16 CDT)
AMBER: REMD and mpiexec Steve Young (Tue Jun 05 2007 - 19:53:14 CDT)
- RE: AMBER: REMD and mpiexec Ross Walker (Wed Jun 06 2007 - 11:06:06 CDT)
  - RE: AMBER: REMD and mpiexec Steve Young (Thu Jun 07 2007 - 12:47:37 CDT)
AMBER: g(r) in mixtures? BJÖRN KARLSSON (Wed Jun 06 2007 - 02:56:05 CDT)
AMBER: Restraining valence angles Abi Ghanem josephine (Wed Jun 06 2007 - 03:35:12 CDT)
- Re: AMBER: Restraining valence angles David A. Case (Wed Jun 06 2007 - 09:49:08 CDT)
AMBER: Reg COM restraint to DNA D.Usharani (Wed Jun 06 2007 - 04:56:00 CDT)
AMBER: GB vs. Invacuo Energies Seth Lilavivat (Wed Jun 06 2007 - 09:38:32 CDT)
AMBER: Hardware recommendations please Jeremy Weedon (Wed Jun 06 2007 - 11:15:16 CDT)
- Re: AMBER: Hardware recommendations please Jeremy Weedon (Thu Jun 07 2007 - 10:24:54 CDT)
  - Re: AMBER: Hardware recommendations please David LeBard (Thu Jun 07 2007 - 13:31:21 CDT)
AMBER: Ptraj: reading PDB files Austin B. Yongye (Wed Jun 06 2007 - 16:37:31 CDT)
- Re: AMBER: Ptraj: reading PDB files Austin B. Yongye (Thu Jun 07 2007 - 09:16:10 CDT)
AMBER: How to fix two angle but do umberlla sampling for distance? Catein Catherine (Thu Jun 07 2007 - 10:14:30 CDT)
- Re: AMBER: How to fix two angle but do umberlla sampling for distance? Jerome.GOLEBIOWSKI_at_unice.fr (Thu Jun 07 2007 - 10:38:26 CDT)
  - AMBER: Potential of mean force. Catein Catherine (Fri Jun 08 2007 - 07:01:42 CDT)
    - Re: AMBER: Potential of mean force. Carlos Simmerling (Fri Jun 08 2007 - 07:08:06 CDT)
    - AMBER: Input files for the Potential of mean force. Catein Catherine (Sun Jun 10 2007 - 21:43:12 CDT)
AMBER: Should we just vary one parameter at a time only for PMF calculations? Catein Catherine (Thu Jun 07 2007 - 10:18:51 CDT)
- Re: AMBER: Should we just vary one parameter at a time only for PMF calculations? David A. Case (Fri Jun 08 2007 - 10:55:12 CDT)
  - AMBER: prepin for metal centre Mattias Blomberg (Mon Jun 25 2007 - 13:17:02 CDT)
    - Re: AMBER: prepin for metal centre David A. Case (Mon Jun 25 2007 - 19:43:26 CDT)
AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 13:06:15 CDT)
- Re: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim (Thu Jun 07 2007 - 13:14:18 CDT)
  - RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 14:33:35 CDT)
AMBER: Dihedral driver Beale, John (Thu Jun 07 2007 - 15:08:35 CDT)
- Re: AMBER: Dihedral driver Ilyas Yildirim (Thu Jun 07 2007 - 15:16:15 CDT)
AMBER: amber94 parameters for cholesterol paula lario (Thu Jun 07 2007 - 17:57:38 CDT)
AMBER: Trouble on wiki about GAFF j j (Thu Jun 07 2007 - 18:29:37 CDT)
- Re: AMBER: Trouble on wiki about GAFF David A. Case (Thu Jun 07 2007 - 22:31:12 CDT)
  - Re: AMBER: Trouble on wiki about GAFF j j (Fri Jun 08 2007 - 02:14:13 CDT)
    - Re: AMBER: Trouble on wiki about GAFF David A. Case (Fri Jun 08 2007 - 11:11:17 CDT)
AMBER: mmpbsa decomposition error cristian (Fri Jun 08 2007 - 10:34:21 CDT)
AMBER: Compiling openmpi/icc/icpc Francesco Pietra (Fri Jun 08 2007 - 12:27:20 CDT)
- RE: AMBER: Compiling openmpi/icc/icpc Ross Walker (Fri Jun 08 2007 - 16:30:02 CDT)
  - RE: AMBER: Compiling openmpi/icc/icpc Francesco Pietra (Sat Jun 09 2007 - 01:04:45 CDT)
AMBER: Taryn Hartley (Fri Jun 08 2007 - 13:39:15 CDT)
- Re: AMBER: Carlos Simmerling (Fri Jun 08 2007 - 13:47:43 CDT)
AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 16:24:47 CDT)
AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 16:18:23 CDT)
AMBER: antechamber/charges/conformation Francesco Pietra (Sun Jun 10 2007 - 02:02:15 CDT)
- Re: AMBER: antechamber/charges/conformation FyD (Mon Jun 11 2007 - 03:40:11 CDT)
  - Re: AMBER: antechamber/charges/conformation Francesco Pietra (Mon Jun 11 2007 - 04:44:21 CDT)
AMBER: amber9 compile problem hmeij_at_wesleyan.edu (Sun Jun 10 2007 - 08:58:54 CDT)
- Re: AMBER: amber9 compile problem Mark Williamson (Sun Jun 10 2007 - 11:03:28 CDT)
  - Re: AMBER: amber9 compile problem Henk Meij (Mon Jun 11 2007 - 08:20:17 CDT)
    - Re: AMBER: amber9 compile problem Mark Williamson (Mon Jun 11 2007 - 08:28:30 CDT)
- RE: AMBER: amber9 compile problem Ross Walker (Sun Jun 10 2007 - 12:15:18 CDT)
  - Re: AMBER: amber9 compile problem Henk Meij (Mon Jun 11 2007 - 08:51:12 CDT)
AMBER: problem installing amber7 Saiful Islam (Sun Jun 10 2007 - 09:55:19 CDT)
- Re: AMBER: problem installing amber7 Carlos Simmerling (Sun Jun 10 2007 - 10:23:10 CDT)
- Re: AMBER: problem installing amber7 David A. Case (Sun Jun 10 2007 - 21:59:17 CDT)
AMBER: Rdf question BJÖRN KARLSSON (Sun Jun 10 2007 - 14:51:16 CDT)
AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 18:42:25 CDT)
- Re: AMBER: Installing on windows Carlos Simmerling (Sun Jun 10 2007 - 18:54:04 CDT)
- Re: AMBER: Installing on windows Gustavo Seabra (Sun Jun 10 2007 - 19:28:01 CDT)
  - Re: AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 20:48:30 CDT)
- Re: AMBER: Installing on windows Bill Ross (Mon Jun 11 2007 - 14:01:06 CDT)
- Re: AMBER: Installing on windows Bill Ross (Mon Jun 11 2007 - 14:14:04 CDT)
AMBER: Steve Seibold (Mon Jun 11 2007 - 12:31:47 CDT)
AMBER: Question about MPI-IO David LeBard (Mon Jun 11 2007 - 15:58:54 CDT)
- Re: AMBER: Question about MPI-IO Thomas Cheatham III (Mon Jun 11 2007 - 16:40:08 CDT)
  - RE: AMBER: Question about MPI-IO Ross Walker (Mon Jun 11 2007 - 18:16:02 CDT)
    - Re: AMBER: Question about MPI-IO David LeBard (Mon Jun 11 2007 - 20:59:33 CDT)
- Re: AMBER: Question about MPI-IO Robert Duke (Mon Jun 11 2007 - 16:51:56 CDT)
AMBER: dihedral parameters Jardas sucuriba (Mon Jun 11 2007 - 17:13:36 CDT)
- Re: AMBER: dihedral parameters David A. Case (Tue Jun 12 2007 - 14:35:57 CDT)
- RE: AMBER: dihedral parameters Jardas sucuriba (Tue Jun 12 2007 - 21:18:12 CDT)
AMBER: xleap on cygwin Colby C (Mon Jun 11 2007 - 20:59:17 CDT)
- Re: AMBER: xleap on cygwin Wei Chen (Tue Jun 12 2007 - 08:06:45 CDT)
  - Re: AMBER: xleap on cygwin Colby C (Tue Jun 12 2007 - 11:34:21 CDT)
    - Re: AMBER: xleap on cygwin Steven Winfield (Tue Jun 12 2007 - 11:45:09 CDT)
    - Re: AMBER: xleap on cygwin Colby C (Tue Jun 12 2007 - 19:42:52 CDT)
AMBER: NMR vs. X-ray structures Sally Pias (Tue Jun 12 2007 - 00:22:19 CDT)
- Re: AMBER: NMR vs. X-ray structures Marc Baaden (Tue Jun 12 2007 - 00:51:21 CDT)
- Re: AMBER: NMR vs. X-ray structures Carlos Simmerling (Tue Jun 12 2007 - 05:57:12 CDT)
AMBER: Amber: Number density profile, pucker..reg Praveena Gopal (Tue Jun 12 2007 - 01:17:37 CDT)
AMBER: building water box with desired number of molecules Vijay Manickam Achari (Tue Jun 12 2007 - 02:33:21 CDT)
- Re: AMBER: building water box with desired number of molecules gurpreet singh (Tue Jun 12 2007 - 04:09:10 CDT)
AMBER: Internal dielectric and MMPBSA Ileana Stoica (Tue Jun 12 2007 - 06:32:17 CDT)
AMBER: Metal ions in GBSA Wei Chen (Tue Jun 12 2007 - 08:13:36 CDT)
AMBER: Using position restraints during constant pressure equilibration priya priya (Tue Jun 12 2007 - 08:17:44 CDT)
AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio saurabh agrawal (Tue Jun 12 2007 - 08:25:09 CDT)
AMBER: Steve Seibold (Tue Jun 12 2007 - 11:21:15 CDT)
- Re: AMBER: David A. Case (Tue Jun 12 2007 - 14:29:06 CDT)
RE: AMBER: Atom types Taryn Hartley (Tue Jun 12 2007 - 12:25:30 CDT)
- Re: AMBER: Atom types Melinda Layten (Tue Jun 12 2007 - 13:16:34 CDT)
AMBER: box size bomb in QMMM calculation M. L. Dodson (Tue Jun 12 2007 - 14:46:00 CDT)
- RE: AMBER: box size bomb in QMMM calculation Ross Walker (Tue Jun 12 2007 - 17:29:26 CDT)
  - Re: AMBER: box size bomb in QMMM calculation M. L. Dodson (Tue Jun 12 2007 - 18:23:50 CDT)
    - RE: AMBER: box size bomb in QMMM calculation Ross Walker (Tue Jun 12 2007 - 22:39:35 CDT)
    - Re: AMBER: box size bomb in QMMM calculation M. L. Dodson (Wed Jun 13 2007 - 04:43:52 CDT)
AMBER: frcmod Brooke Elizabeth Adams (Tue Jun 12 2007 - 15:38:50 CDT)
- Re: AMBER: frcmod David A. Case (Tue Jun 12 2007 - 16:34:35 CDT)
  - Re: AMBER: frcmod Brooke Elizabeth Adams (Fri Jun 15 2007 - 14:11:00 CDT)
AMBER: metal ions Wei Chen (Tue Jun 12 2007 - 16:20:26 CDT)
AMBER: Installing amber9 in IBM P5? Du, Shiyu (Tue Jun 12 2007 - 21:09:34 CDT)
- RE: AMBER: Installing amber9 in IBM P5? Ross Walker (Tue Jun 12 2007 - 22:34:33 CDT)
  - Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu (Wed Jun 13 2007 - 00:01:56 CDT)
AMBER: hydrogen bond Guillaume Renvez (Wed Jun 13 2007 - 03:49:22 CDT)
AMBER: problems using TIP4PBOX john chen (Wed Jun 13 2007 - 05:53:30 CDT)
- Re: AMBER: problems using TIP4PBOX David A. Case (Wed Jun 13 2007 - 07:26:11 CDT)
- Re: AMBER: problems using TIP4PBOX Andy Purkiss-Trew (Wed Jun 13 2007 - 07:36:14 CDT)
AMBER: [Fwd: Tr: H bonds] Guillaume Renvez (Wed Jun 13 2007 - 07:37:20 CDT)
AMBER: Hbonds mbrut_at_laas.fr (Wed Jun 13 2007 - 07:54:52 CDT)
- Re: AMBER: Hbonds David A. Case (Wed Jun 13 2007 - 15:50:11 CDT)
AMBER: S-nitrocysteine Anthony Cruz Balberdi (Wed Jun 13 2007 - 08:12:00 CDT)
- Re: AMBER: S-nitrocysteine FyD (Wed Jun 13 2007 - 16:44:59 CDT)
AMBER: g(r) khn _ (Wed Jun 13 2007 - 11:43:25 CDT)
AMBER: SANDER error: 'angles are not correct' Fred Baba (Wed Jun 13 2007 - 16:47:14 CDT)
THANKS -- Re: AMBER: NMR vs. X-ray structures Sally Pias (Wed Jun 13 2007 - 23:33:06 CDT)
AMBER: (no subject) Catein Catherine (Thu Jun 14 2007 - 00:54:28 CDT)
- AMBER: spring constant for restraint Catein Catherine (Thu Jun 14 2007 - 04:29:17 CDT)
- Re: AMBER: (no subject) Franck Vendeix (Thu Jun 14 2007 - 08:32:54 CDT)
- Re: AMBER: (no subject) Franck Vendeix (Thu Jun 14 2007 - 08:32:54 CDT)
AMBER: Hbonds mbrut_at_laas.fr (Thu Jun 14 2007 - 02:45:25 CDT)
- Re: AMBER: Hbonds David A. Case (Fri Jun 15 2007 - 13:06:26 CDT)
AMBER: ff99 vs ff99SB for RNA Brent Krueger (Thu Jun 14 2007 - 09:05:12 CDT)
- Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling (Thu Jun 14 2007 - 09:57:02 CDT)
  - Re: AMBER: ff99 vs ff99SB for RNA j j (Thu Jun 14 2007 - 10:30:21 CDT)
    - Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling (Thu Jun 14 2007 - 11:03:03 CDT)
- Re: AMBER: ff99 vs ff99SB for RNA Thomas Cheatham III (Thu Jun 14 2007 - 11:17:46 CDT)
AMBER: [ProblemSolved]Re: SANDER error: 'angles are not correct' Fred Baba (Thu Jun 14 2007 - 12:08:47 CDT)
AMBER: Compile openmpi Francesco Pietra (Thu Jun 14 2007 - 12:11:02 CDT)
AMBER: umbrella sampling dihedral restraint question Cen Gao (Thu Jun 14 2007 - 15:33:51 CDT)
- Re: AMBER: umbrella sampling dihedral restraint question David A. Case (Mon Jun 18 2007 - 00:46:16 CDT)
AMBER: pair distribution function khn _ (Thu Jun 14 2007 - 18:20:47 CDT)
- Re: AMBER: pair distribution function Thomas Cheatham III (Thu Jun 14 2007 - 18:41:51 CDT)
  - Re: AMBER: pair distribution function khn _ (Sun Jun 17 2007 - 03:25:56 CDT)
AMBER: isolated NTP Steve Seibold (Fri Jun 15 2007 - 09:07:16 CDT)
- Re: AMBER: isolated NTP David A. Case (Mon Jun 18 2007 - 00:40:29 CDT)
  - RE: AMBER: isolated NTP Steve Seibold (Mon Jun 18 2007 - 07:20:21 CDT)
    - Re: AMBER: isolated NTP David A. Case (Mon Jun 18 2007 - 10:39:06 CDT)
AMBER: Amber Installation Error Joe Nolan (Fri Jun 15 2007 - 10:58:00 CDT)
- Re: AMBER: Amber Installation Error David A. Case (Fri Jun 15 2007 - 13:56:29 CDT)
- RE: AMBER: Amber Installation Error Ross Walker (Fri Jun 15 2007 - 14:25:28 CDT)
  - RE: AMBER: Amber Installation Error Joe Nolan (Mon Jun 18 2007 - 09:34:12 CDT)
AMBER: Saving a structuring from trajectory Seth Lilavivat (Fri Jun 15 2007 - 13:42:12 CDT)
- Re: AMBER: Saving a structuring from trajectory Ilyas Yildirim (Fri Jun 15 2007 - 13:59:50 CDT)
AMBER: .lib files Taryn Hartley (Fri Jun 15 2007 - 14:42:16 CDT)
- Re: AMBER: .lib files Ilyas Yildirim (Fri Jun 15 2007 - 14:50:34 CDT)
AMBER: performance with implicit solvent Kijeong Kwac (Fri Jun 15 2007 - 15:02:49 CDT)
- Re: AMBER: performance with implicit solvent Carlos Simmerling (Fri Jun 15 2007 - 15:17:28 CDT)
- Re: AMBER: performance with implicit solvent David A. Case (Fri Jun 15 2007 - 15:18:31 CDT)
AMBER: PDB problems Taryn Hartley (Fri Jun 15 2007 - 15:17:13 CDT)
- Re: AMBER: PDB problems David A. Case (Fri Jun 15 2007 - 15:24:44 CDT)
- Re: AMBER: PDB problems Ilyas Yildirim (Fri Jun 15 2007 - 17:30:45 CDT)
Re: AMBER: Saving a structuring from trajectory Bill Ross (Fri Jun 15 2007 - 15:43:23 CDT)
AMBER: MMPBSA-nmode .top question Matthew Danielson (Fri Jun 15 2007 - 16:11:52 CDT)
- Re: AMBER: MMPBSA-nmode .top question David A. Case (Mon Jun 18 2007 - 00:35:39 CDT)
AMBER: Energy outputs in TI Approach Ilyas Yildirim (Sat Jun 16 2007 - 00:03:26 CDT)
- Re: AMBER: Energy outputs in TI Approach David A. Case (Sat Jun 16 2007 - 10:19:23 CDT)
AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 05:16:15 CDT)
- Re: AMBER: distance scan David A. Case (Sat Jun 16 2007 - 10:21:05 CDT)
AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 05:25:59 CDT)
AMBER: implementation of GB model in AMBER john chen (Sun Jun 17 2007 - 07:49:24 CDT)
- Re: AMBER: implementation of GB model in AMBER Carlos Simmerling (Sun Jun 17 2007 - 07:58:11 CDT)
  - AMBER: explanation to edit and use the script Syed Tarique Moin (Sun Jun 17 2007 - 23:26:38 CDT)
    - Re: AMBER: explanation to edit and use the script Syed Tarique Moin (Wed Jun 20 2007 - 04:33:15 CDT)
AMBER: error due to exceeding left-hand side digital numbers in restart output Cenk Andac (Mon Jun 18 2007 - 03:09:36 CDT)
- Re: AMBER: error due to exceeding left-hand side digital numbers in restart output David A. Case (Mon Jun 18 2007 - 13:06:16 CDT)
AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 07:41:02 CDT)
- Re: AMBER: problem with running rem on amber9 Carlos Simmerling (Mon Jun 18 2007 - 07:46:29 CDT)
  - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 07:59:38 CDT)
  - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 10:02:55 CDT)
    - Re: AMBER: problem with running rem on amber9 Carlos Simmerling (Mon Jun 18 2007 - 10:10:37 CDT)
    - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 10:25:37 CDT)
- Re: AMBER: problem with running rem on amber9 David A. Case (Mon Jun 18 2007 - 13:22:01 CDT)
AMBER: Charge not integral. Head-to-tail cyclic peptides Giacomo Bastianelli (Mon Jun 18 2007 - 08:55:46 CDT)
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Melinda Layten (Mon Jun 18 2007 - 09:28:57 CDT)
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Laurent Chiche (Mon Jun 18 2007 - 09:37:53 CDT)
Re: AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM) Carlos Simmerling (Mon Jun 18 2007 - 10:31:19 CDT)
AMBER: shell model MD Stern, Julie (Mon Jun 18 2007 - 11:48:54 CDT)
- Re: AMBER: shell model MD Carlos Simmerling (Mon Jun 18 2007 - 11:53:56 CDT)
AMBER: Questions about how ptraj calculates solvent shells Roberto Veiga (Mon Jun 18 2007 - 13:46:59 CDT)
AMBER: unres Carra, Claudio (JSC-SK)[USRA] (Mon Jun 18 2007 - 15:55:20 CDT)
- Re: AMBER: unres Piotr Cieplak (Mon Jun 18 2007 - 19:00:47 CDT)
AMBER: H bond Guillaume Renvez (Tue Jun 19 2007 - 03:18:45 CDT)
- Re: AMBER: H bond Carlos Simmerling (Tue Jun 19 2007 - 06:24:27 CDT)
AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 07:47:58 CDT)
- Re: AMBER: Re: Strange shape in my MD simulations Adrian Roitberg (Tue Jun 19 2007 - 07:57:07 CDT)
  - Re: AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 09:09:48 CDT)
- Re: AMBER: Re: Strange shape in my MD simulations gurpreet singh (Wed Jun 20 2007 - 02:58:03 CDT)
  - RE: AMBER: Re: Strange shape in my MD simulations Ross Walker (Wed Jun 20 2007 - 10:27:37 CDT)
AMBER: How to add semi-experience parameter in divcon? clarkzhy (Tue Jun 19 2007 - 09:23:04 CDT)
- RE: AMBER: How to add semi-experience parameter in divcon? Ross Walker (Tue Jun 19 2007 - 10:44:59 CDT)
- Re: AMBER: How to add semi-experience parameter in divcon? Seth Hayik (Tue Jun 19 2007 - 11:15:03 CDT)
AMBER: Reply regarding PCA with ptraj and IED Steve Spronk (Tue Jun 19 2007 - 16:00:37 CDT)
- Re: AMBER: Reply regarding PCA with ptraj and IED Hannes Loeffler (Tue Jun 19 2007 - 21:43:21 CDT)
AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 04:09:26 CDT)
- Re: AMBER: problems in adding ACE and NME group Carlos Simmerling (Wed Jun 20 2007 - 06:28:46 CDT)
  - Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 08:15:25 CDT)
- RE: AMBER: problems in adding ACE and NME group Gustavo Seabra (Wed Jun 20 2007 - 09:14:26 CDT)
AMBER: Re: Fwd: joshua j j (Wed Jun 20 2007 - 06:27:43 CDT)
- Re: AMBER: Re: Fwd: joshua j j (Wed Jun 20 2007 - 08:01:00 CDT)
AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 13:07:33 CDT)
- Re: AMBER: 5 Ligands and 1 Protein David A. Case (Wed Jun 20 2007 - 18:46:23 CDT)
  - Re: AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 19:10:22 CDT)
- Re: AMBER: 5 Ligands and 1 Protein Scott Brozell (Wed Jun 20 2007 - 19:25:05 CDT)
AMBER: Algorithm for integration of equations of motion Roberto Veiga (Wed Jun 20 2007 - 13:55:45 CDT)
- RE: AMBER: Algorithm for integration of equations of motion Ross Walker (Wed Jun 20 2007 - 14:38:36 CDT)
AMBER: sander core dumped during minimization zgleo (Wed Jun 20 2007 - 20:51:04 CDT)
- Re: AMBER: sander core dumped during minimization David A. Case (Thu Jun 21 2007 - 00:16:11 CDT)
AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi (Thu Jun 21 2007 - 10:56:57 CDT)
- Re: AMBER: set up system solution with 3 different components, each with multiple copies David A. Case (Tue Jun 26 2007 - 10:08:50 CDT)
  - Re: AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi (Tue Jun 26 2007 - 10:16:54 CDT)
    - Re: AMBER: set up system solution with 3 different components, each with multiple copies M. L. Dodson (Tue Jun 26 2007 - 10:27:41 CDT)
AMBER: ptray segfault: vector out Nicolas Lux Fawzi (Thu Jun 21 2007 - 14:19:49 CDT)
To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon? clarkzhy (Thu Jun 21 2007 - 20:19:23 CDT)
AMBER: testing protein stability Sally Pias (Fri Jun 22 2007 - 00:24:58 CDT)
- Re: AMBER: testing protein stability Carlos Simmerling (Fri Jun 22 2007 - 06:06:16 CDT)
  - Re: AMBER: testing protein stability Sally Pias (Fri Jun 22 2007 - 16:57:27 CDT)
AMBER: Limitation in number of atoms/residues Sascha Rehm (Fri Jun 22 2007 - 05:47:35 CDT)
- Re: AMBER: Limitation in number of atoms/residues Robert Duke (Fri Jun 22 2007 - 07:37:30 CDT)
  - Re: AMBER: Limitation in number of atoms/residues Sascha Rehm (Fri Jun 22 2007 - 08:46:05 CDT)
AMBER: radius of gyration priya priya (Fri Jun 22 2007 - 10:10:36 CDT)
- Re: AMBER: radius of gyration Carlos Simmerling (Fri Jun 22 2007 - 10:14:19 CDT)
  - Re: AMBER: radius of gyration priya priya (Fri Jun 22 2007 - 10:23:03 CDT)
AMBER: remd/rdc's McElheny, Dan (Fri Jun 22 2007 - 13:04:59 CDT)
- Re: AMBER: remd/rdc's Carlos Simmerling (Sat Jun 23 2007 - 07:43:21 CDT)
- Re: AMBER: remd/rdc's David A. Case (Sat Jun 23 2007 - 12:44:17 CDT)
  - Re: AMBER: remd/rdc's McElheny, Dan (Mon Jun 25 2007 - 11:12:20 CDT)
    - Re: AMBER: remd/rdc's David A. Case (Thu Jun 28 2007 - 10:37:44 CDT)
  - Re: AMBER: remd/rdc's McElheny, Dan (Mon Jun 25 2007 - 11:12:20 CDT)
AMBER: radial distribution function in ptraj khn _ (Fri Jun 22 2007 - 20:25:05 CDT)
AMBER: SPCFW water: angle problems in leap Thomas Hofer (Sat Jun 23 2007 - 11:02:32 CDT)
- RE: AMBER: SPCFW water: angle problems in leap Ross Walker (Sat Jun 23 2007 - 11:47:25 CDT)
AMBER: Antechamber--Boron Parameters brmeher_at_iitg.ernet.in (Mon Jun 25 2007 - 05:04:30 CDT)
- Re: AMBER: Antechamber--Boron Parameters David A. Case (Mon Jun 25 2007 - 20:08:48 CDT)
AMBER: how to calculate energy of the peptide priya priya (Mon Jun 25 2007 - 08:56:54 CDT)
AMBER: environment variables Francesco Pietra (Mon Jun 25 2007 - 10:51:05 CDT)
- RE: AMBER: environment variables Ross Walker (Mon Jun 25 2007 - 14:43:39 CDT)
AMBER: RDF of pure chloroform BJÖRN KARLSSON (Mon Jun 25 2007 - 10:56:19 CDT)
AMBER: sander MPI fails included tests Sergio Wong (Mon Jun 25 2007 - 12:20:55 CDT)
- RE: AMBER: sander MPI fails included tests Ross Walker (Mon Jun 25 2007 - 13:17:34 CDT)
  - RE: AMBER: sander MPI fails included tests Sergio Wong (Mon Jun 25 2007 - 14:06:21 CDT)
AMBER: Re: ff02 and ff03 parameters Pavan G (Mon Jun 25 2007 - 14:34:30 CDT)
- Re: AMBER: Re: ff02 and ff03 parameters Carlos Simmerling (Mon Jun 25 2007 - 18:28:02 CDT)
AMBER: PMF calculation Jena M (Mon Jun 25 2007 - 14:59:02 CDT)
- Re: AMBER: PMF calculation David A. Case (Mon Jun 25 2007 - 19:47:25 CDT)
AMBER: Simulated Annealing Joseph Maxwell (Mon Jun 25 2007 - 18:28:14 CDT)
- Re: AMBER: Simulated Annealing David A. Case (Mon Jun 25 2007 - 19:34:38 CDT)
- RE: AMBER: Simulated Annealing Hayden Eastwood (Tue Jun 26 2007 - 04:14:57 CDT)
  - Re: AMBER: Simulated Annealing Carlos Simmerling (Tue Jun 26 2007 - 06:16:25 CDT)
AMBER: PBSA Error Pankaj R. Daga (Tue Jun 26 2007 - 09:03:41 CDT)
AMBER: rst overflow for implicit REMD In Hee Park (Tue Jun 26 2007 - 09:37:45 CDT)
- Re: AMBER: rst overflow for implicit REMD David A. Case (Tue Jun 26 2007 - 10:28:28 CDT)
  - Re: AMBER: rst overflow for implicit REMD Carlos Simmerling (Tue Jun 26 2007 - 10:35:47 CDT)
AMBER: $AMBERHOME on PATH Francesco Pietra (Tue Jun 26 2007 - 12:38:35 CDT)
- Re: AMBER: $AMBERHOME on PATH David A. Case (Tue Jun 26 2007 - 13:01:02 CDT)
  - Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Tue Jun 26 2007 - 15:15:11 CDT)
AMBER: "FATAL: Atom xxx does not have a type." Fred Baba (Tue Jun 26 2007 - 12:59:51 CDT)
- Re: AMBER: "FATAL: Atom xxx does not have a type." David A. Case (Tue Jun 26 2007 - 17:20:21 CDT)
AMBER: Unexpected Failure in XLeap Jason Brown (Tue Jun 26 2007 - 13:45:14 CDT)
- Re: AMBER: Unexpected Failure in XLeap David A. Case (Tue Jun 26 2007 - 15:47:30 CDT)
AMBER: Does Chimera support AMBER file formats? Ilyas Yildirim (Tue Jun 26 2007 - 18:58:56 CDT)
- Re: AMBER: Does Chimera support AMBER file formats? Mingfeng Yang (Tue Jun 26 2007 - 19:12:53 CDT)
Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 09:30:09 CDT)
Fwd: Re: AMBER: $AMBERHOME on PATH & compilations Francesco Pietra (Wed Jun 27 2007 - 11:10:38 CDT)
- Re: Fwd: Re: AMBER: $AMBERHOME on PATH & compilations David A. Case (Wed Jun 27 2007 - 12:06:38 CDT)
Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 09:59:02 CDT)
- RE: Re: AMBER: $AMBERHOME on PATH Ross Walker (Wed Jun 27 2007 - 11:11:34 CDT)
  - RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 09:40:09 CDT)
AMBER: bugfix.all Francesco Pietra (Wed Jun 27 2007 - 15:26:15 CDT)
- Re: AMBER: bugfix.all Carlos Simmerling (Wed Jun 27 2007 - 15:52:15 CDT)
- Re: AMBER: bugfix.all M. L. Dodson (Wed Jun 27 2007 - 15:52:07 CDT)
  - Re: AMBER: bugfix.all Francesco Pietra (Thu Jun 28 2007 - 01:14:33 CDT)
- Re: AMBER: bugfix.all David A. Case (Wed Jun 27 2007 - 15:55:52 CDT)
- RE: AMBER: bugfix.all Ross Walker (Wed Jun 27 2007 - 16:19:32 CDT)
AMBER: how to stop ptraj atom renumbering Russell Green (Wed Jun 27 2007 - 15:25:53 CDT)
AMBER: Math libraries Francesco Pietra (Thu Jun 28 2007 - 04:56:45 CDT)
- Re: AMBER: Math libraries Robert Duke (Thu Jun 28 2007 - 07:15:07 CDT)
- Re: AMBER: Math libraries Andreas Svrcek-Seiler (Thu Jun 28 2007 - 11:27:28 CDT)
  - Re: AMBER: Math libraries Francesco Pietra (Thu Jun 28 2007 - 15:12:28 CDT)
AMBER: conversion of Macromodel substructure format to .frcmod file brmeher_at_iitg.ernet.in (Thu Jun 28 2007 - 05:24:24 CDT)
AMBER: Improving pmemd parallel scaling Alessandro Nascimento (Thu Jun 28 2007 - 11:07:15 CDT)
- Re: AMBER: Improving pmemd parallel scaling Mark Williamson (Thu Jun 28 2007 - 11:19:06 CDT)
- Re: AMBER: Improving pmemd parallel scaling Robert Duke (Thu Jun 28 2007 - 17:27:24 CDT)
AMBER: Problem with leaprc yen li (Thu Jun 28 2007 - 22:27:52 CDT)
- Re: AMBER: Problem with leaprc David A. Case (Fri Jun 29 2007 - 10:47:51 CDT)
  - Re: AMBER: Problem with leaprc yen li (Sat Jun 30 2007 - 09:11:47 CDT)
Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Fri Jun 29 2007 - 00:58:19 CDT)
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH M. L. Dodson (Fri Jun 29 2007 - 08:34:08 CDT)
  - Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Sun Jul 01 2007 - 09:38:03 CDT)
    - Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH M. L. Dodson (Sun Jul 01 2007 - 10:57:05 CDT)
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH David A. Case (Fri Jun 29 2007 - 11:05:09 CDT)
  - AMBER: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 12:17:39 CDT)
    - Re: AMBER: Serial "make" failure with xleap David A. Case (Fri Jun 29 2007 - 13:16:54 CDT)
    - Re: AMBER: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 15:53:52 CDT)
AMBER: Sander Error Colby C (Fri Jun 29 2007 - 09:47:05 CDT)
- RE: AMBER: Sander Error Ross Walker (Fri Jun 29 2007 - 10:40:08 CDT)
- Re: AMBER: Sander Error Phineus Markwick (Fri Jun 29 2007 - 10:45:18 CDT)
- Re: AMBER: Sander Error Phineus Markwick (Fri Jun 29 2007 - 10:48:04 CDT)
  - RE: AMBER: Sander Error Ross Walker (Fri Jun 29 2007 - 11:28:44 CDT)
AMBER: Fwd: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 12:26:54 CDT)
AMBER: Serial "make" failure Francesco Pietra (Fri Jun 29 2007 - 15:59:42 CDT)
AMBER: make serial failure for xleap Francesco Pietra (Fri Jun 29 2007 - 16:05:52 CDT)
- Re: AMBER: make serial failure for xleap M. L. Dodson (Fri Jun 29 2007 - 17:33:37 CDT)
  - Re: AMBER: make serial failure for xleap Francesco Pietra (Sat Jun 30 2007 - 03:39:32 CDT)
- Re: AMBER: make serial failure for xleap David A. Case (Fri Jun 29 2007 - 18:28:36 CDT)
Fwd: Re: AMBER: make serial failure for xleap Francesco Pietra (Sat Jun 30 2007 - 08:00:31 CDT)
AMBER: amber7 and xleap Saiful Islam (Sat Jun 30 2007 - 08:14:21 CDT)
- Re: AMBER: amber7 and xleap David A. Case (Sat Jun 30 2007 - 19:57:13 CDT)
  - Re: AMBER: amber7 and xleap Saiful Islam (Sat Jun 30 2007 - 22:37:00 CDT)
    - Re: AMBER: amber7 and xleap Saiful Islam (Sun Jul 01 2007 - 08:43:45 CDT)
    - RE: AMBER: amber7 and xleap Ross Walker (Sun Jul 01 2007 - 12:32:45 CDT)
Fwd: Re: AMBER: make test serial Francesco Pietra (Sat Jun 30 2007 - 08:42:56 CDT)
- Re: Fwd: Re: AMBER: make test serial David A. Case (Sat Jun 30 2007 - 10:28:01 CDT)
  - Re: Fwd: Re: AMBER: make test serial Francesco Pietra (Sat Jun 30 2007 - 11:18:38 CDT)
AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND Jojart Balazs (Sat Jun 30 2007 - 13:25:49 CDT)
AMBER: xleap and amber7 Saiful Islam (Sat Jun 30 2007 - 23:22:43 CDT)
- RE: AMBER: xleap and amber7 Ross Walker (Sun Jul 01 2007 - 12:33:15 CDT)
  - Re: AMBER: xleap and amber7 Saiful Islam (Mon Jul 02 2007 - 09:05:34 CDT)
AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Sun Jul 01 2007 - 14:13:17 CDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Sun Jul 01 2007 - 14:54:11 CDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Julien Michel (Sun Jul 01 2007 - 17:42:53 CDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David Mobley (Mon Jul 02 2007 - 15:03:17 CDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Mon Jul 02 2007 - 15:51:12 CDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David A. Case (Tue Jul 03 2007 - 01:34:13 CDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Tue Jul 03 2007 - 12:14:29 CDT)
Fwd: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Sun Jul 01 2007 - 15:50:39 CDT)
AMBER: Saving (.)prepin file Johnson Agbo (Mon Jul 02 2007 - 15:35:00 CDT)
- Re: AMBER: Saving (.)prepin file David A. Case (Mon Jul 02 2007 - 15:56:57 CDT)
Re: AMBER: Saving (.)prepin file Bill Ross (Mon Jul 02 2007 - 16:05:53 CDT)
AMBER: convergence criterion not reached Jena M (Mon Jul 02 2007 - 18:53:22 CDT)
- Re: AMBER: convergence criterion not reached David A. Case (Mon Jul 02 2007 - 20:14:53 CDT)
AMBER: Slow Processor Loads when Using PMEMD Jonathan Suever (Mon Jul 02 2007 - 19:28:48 CDT)
- Re: AMBER: Slow Processor Loads when Using PMEMD David A. Case (Mon Jul 02 2007 - 20:24:09 CDT)
- RE: AMBER: Slow Processor Loads when Using PMEMD Ross Walker (Mon Jul 02 2007 - 20:42:01 CDT)
AMBER: How to use antechamber properly? ÇÑÀç¹ü (Tue Jul 03 2007 - 00:57:33 CDT)
AMBER: O-acetylated sugar Toshifumi Yui (Tue Jul 03 2007 - 07:26:12 CDT)
AMBER: About amber7 Saiful Islam (Tue Jul 03 2007 - 08:49:28 CDT)
- Re: AMBER: About amber7 Carlos Simmerling (Tue Jul 03 2007 - 08:57:14 CDT)
AMBER: ptraj: RMS per residues and per time Sascha Rehm (Tue Jul 03 2007 - 09:03:04 CDT)
- Re: AMBER: ptraj: RMS per residues and per time Jianyin Shao (Fri Jul 06 2007 - 02:54:06 CDT)
AMBER: Nucleic acid : nonplanarity Sophie Barbe (Tue Jul 03 2007 - 10:48:07 CDT)
AMBER: antechamber save prmtop inpcrd Francesco Pietra (Tue Jul 03 2007 - 12:55:11 CDT)
AMBER: Who has the structure file of beta-chitin? WANG,YING (Tue Jul 03 2007 - 13:19:11 CDT)
AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Wed Jul 04 2007 - 01:14:23 CDT)
- Re: AMBER: Fwd: antechamber save prmtop inpcrd David A. Case (Wed Jul 04 2007 - 10:53:04 CDT)
  - Re: AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Wed Jul 04 2007 - 11:54:08 CDT)
    - Re: AMBER: Fwd: antechamber save prmtop inpcrd David A. Case (Wed Jul 04 2007 - 15:15:21 CDT)
    - Re: AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Wed Jul 04 2007 - 16:08:02 CDT)
AMBER: Simulated annealing - Nudget Elastic Band Francesco Pietra (Wed Jul 04 2007 - 02:01:58 CDT)
- Re: AMBER: Simulated annealing - Nudget Elastic Band Carlos Simmerling (Wed Jul 04 2007 - 05:39:10 CDT)
  - Re: AMBER: Simulated annealing - Nudget Elastic Band Francesco Pietra (Wed Jul 04 2007 - 08:13:41 CDT)
AMBER: Slight_error_on_Compiling_Replica_Exchange j j (Wed Jul 04 2007 - 03:57:28 CDT)
- Re: AMBER: Slight_error_on_Compiling_Replica_Exchange Ye Mei (Wed Jul 04 2007 - 04:30:09 CDT)
  - Re: AMBER: Slight_error_on_Compiling_Replica_Exchange j j (Wed Jul 04 2007 - 05:13:22 CDT)
AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field Anela Ivanova (Wed Jul 04 2007 - 07:26:02 CDT)
AMBER: Nucleic acid : nonplanarity Sophie Barbe (Wed Jul 04 2007 - 07:37:26 CDT)
- Re: AMBER: Nucleic acid : nonplanarity Mathy Froeyen (Wed Jul 04 2007 - 08:57:08 CDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Wed Jul 04 2007 - 14:53:01 CDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David Mobley (Thu Jul 05 2007 - 10:56:43 CDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Thomas Steinbrecher (Fri Jul 06 2007 - 12:55:32 CDT)
AMBER: antechamber: mopac charges Neelanjana Sengupta (Wed Jul 04 2007 - 18:21:02 CDT)
- Re: AMBER: antechamber: mopac charges David A. Case (Wed Jul 04 2007 - 18:27:02 CDT)
  - Re: AMBER: antechamber: mopac charges Neelanjana Sengupta (Thu Jul 05 2007 - 14:26:30 CDT)
    - Re: AMBER: antechamber: mopac charges David A. Case (Thu Jul 05 2007 - 15:24:09 CDT)
AMBER: testing amber9 for parallel use Sally Pias (Thu Jul 05 2007 - 01:47:22 CDT)
- Re: AMBER: testing amber9 for parallel use Carlos Simmerling (Thu Jul 05 2007 - 07:22:20 CDT)
AMBER: Convergence criteria in replica exchange simulations Seongeun Yang (Thu Jul 05 2007 - 06:18:17 CDT)
- Re: AMBER: Convergence criteria in replica exchange simulations Carlos Simmerling (Thu Jul 05 2007 - 07:26:26 CDT)
AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 09:31:03 CDT)
- Re: AMBER: How to extract energy of molecule from the system with explicit water molecules Carlos Simmerling (Thu Jul 05 2007 - 09:36:05 CDT)
  - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 10:10:23 CDT)
AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 12:43:43 CDT)
- Re: AMBER: Nudget Elastic Band query Carlos Simmerling (Thu Jul 05 2007 - 12:53:53 CDT)
  - Re: AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 14:02:19 CDT)
    - Re: AMBER: Nudget Elastic Band query Carlos Simmerling (Thu Jul 05 2007 - 14:08:31 CDT)
    - Re: AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 15:28:31 CDT)
AMBER: QM/MM LJ parameters Evan Kelly (Thu Jul 05 2007 - 18:31:35 CDT)
- RE: AMBER: QM/MM LJ parameters Ross Walker (Thu Jul 05 2007 - 19:58:49 CDT)
AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 07:33:11 CDT)
- Re: AMBER: Stirp command in ptraj Carlos Simmerling (Fri Jul 06 2007 - 07:35:33 CDT)
- Re: AMBER: Stirp command in ptraj Steven Winfield (Fri Jul 06 2007 - 07:36:06 CDT)
  - Re: AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 07:41:22 CDT)
AMBER: Substitute for GAFF Evan Kelly (Fri Jul 06 2007 - 12:32:50 CDT)
AMBER: Simulated Annealing - Best way to create randomness Francesco Pietra (Sat Jul 07 2007 - 09:56:41 CDT)
- Re: AMBER: Simulated Annealing - Best way to create randomness Seth Lilavivat (Mon Jul 09 2007 - 10:03:29 CDT)
AMBER: RESP charge generation Neelanjana Sengupta (Sat Jul 07 2007 - 18:08:07 CDT)
- Re: AMBER: RESP charge generation FyD (Sun Jul 08 2007 - 05:19:16 CDT)
AMBER: Problem with running Sander Lili Peng (Sat Jul 07 2007 - 18:10:06 CDT)
- Re: AMBER: Problem with running Sander David A. Case (Sat Jul 07 2007 - 23:59:05 CDT)
  - Re: AMBER: Problem with running Sander Carlos Simmerling (Sun Jul 08 2007 - 06:28:58 CDT)
  - Re: AMBER: Problem with running Sander Lili Peng (Tue Jul 10 2007 - 16:50:45 CDT)
AMBER: corrected reaction field energy and PBCAL AYTUG TUNCEL (Sun Jul 08 2007 - 19:40:53 CDT)
AMBER: program bug? M. Maeda (Sun Jul 08 2007 - 21:24:58 CDT)
- Re: AMBER: program bug? David A. Case (Mon Jul 09 2007 - 09:48:35 CDT)
- Re: AMBER: program bug? M. Maeda (Wed Jul 11 2007 - 23:47:19 CDT)
- Re: AMBER: program bug? M. Maeda (Wed Jul 11 2007 - 23:41:34 CDT)
  - Re: AMBER: program bug? Benjamin Juhl (Thu Jul 12 2007 - 02:17:31 CDT)
    - Re: AMBER: program bug? M. Maeda (Thu Jul 12 2007 - 06:29:03 CDT)
    - Re: AMBER: program bug? M. Maeda (Wed Aug 08 2007 - 21:37:13 CDT)
  - Re: AMBER: program bug? David A. Case (Thu Jul 12 2007 - 10:22:35 CDT)
    - Re: AMBER: program bug? Carlos Simmerling (Thu Jul 12 2007 - 10:32:54 CDT)
AMBER: adding water molecules in lipid bilayer model Vijay Manickam Achari (Sun Jul 08 2007 - 22:22:46 CDT)
- Re: AMBER: adding water molecules in lipid bilayer model M. L. Dodson (Mon Jul 09 2007 - 07:59:01 CDT)
  - Re: AMBER: adding water molecules in lipid bilayer model Vijay Manickam Achari (Tue Jul 10 2007 - 21:00:30 CDT)
- Re: AMBER: adding water molecules in lipid bilayer model Fenghui Fan (Mon Jul 09 2007 - 18:11:45 CDT)
  - AMBER: Question on TIP4P model Du, Shiyu (Mon Jul 09 2007 - 19:01:58 CDT)
AMBER: antechamber Marie Brut (Mon Jul 09 2007 - 06:56:19 CDT)
- Re: AMBER: antechamber David A. Case (Mon Jul 09 2007 - 09:41:23 CDT)
  - Re: AMBER: antechamber Francesco Pietra (Mon Jul 09 2007 - 16:57:45 CDT)
    - Re: AMBER: antechamber M. L. Dodson (Mon Jul 09 2007 - 19:08:27 CDT)
    - Re: AMBER: antechamber Francesco Pietra (Tue Jul 10 2007 - 02:04:39 CDT)
- Re: AMBER: antechamber Barbault Florent (Mon Jul 09 2007 - 09:59:03 CDT)
AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 09 2007 - 09:30:44 CDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber David A. Case (Mon Jul 09 2007 - 09:58:51 CDT)
  - Re: AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 09 2007 - 13:02:38 CDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber Bill Ross (Mon Jul 09 2007 - 13:48:28 CDT)
  - Re: AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 16 2007 - 16:35:53 CDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber Bill Ross (Mon Jul 16 2007 - 18:38:26 CDT)
AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 11:56:58 CDT)
- Re: AMBER: Could not find cntrl namelist M. L. Dodson (Mon Jul 09 2007 - 12:10:58 CDT)
  - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 15:53:43 CDT)
- RE: AMBER: Could not find cntrl namelist Ross Walker (Mon Jul 09 2007 - 12:26:29 CDT)
AMBER: TIP4P MD simulations Hashem Taha (Mon Jul 09 2007 - 12:53:28 CDT)
- Re: AMBER: TIP4P MD simulations Melinda Layten (Mon Jul 09 2007 - 13:05:39 CDT)
- Re: AMBER: TIP4P MD simulations David A. Case (Mon Jul 09 2007 - 13:31:15 CDT)
- Re: AMBER: TIP4P MD simulations Robert Duke (Mon Jul 09 2007 - 14:35:04 CDT)
AMBER: manganese ion Davide Moiani (Mon Jul 09 2007 - 16:02:31 CDT)
- Re: AMBER: manganese ion Guillermo Mulliert Carlín (Tue Jul 10 2007 - 03:39:40 CDT)
- Re: AMBER: manganese ion Davide Moiani (Tue Jul 10 2007 - 11:47:38 CDT)
  - Re: AMBER: manganese ion neetu_at_imtech.res.in (Tue Jul 10 2007 - 23:03:54 CDT)
- Re: AMBER: manganese ion Davide Moiani (Wed Jul 11 2007 - 16:47:18 CDT)
AMBER: surface area over the trajectory mkseo (Mon Jul 09 2007 - 16:52:32 CDT)
- Re: AMBER: surface area over the trajectory Carlos Simmerling (Mon Jul 09 2007 - 17:30:54 CDT)
  - Re: AMBER: surface area over the trajectory mkseo (Mon Jul 09 2007 - 17:55:18 CDT)
AMBER: tgtrmsmask and tgtfitmask Holly Freedman (Mon Jul 09 2007 - 21:03:39 CDT)
- Re: AMBER: tgtrmsmask and tgtfitmask Carlos Simmerling (Tue Jul 10 2007 - 06:26:08 CDT)
  - Re: AMBER: tgtrmsmask and tgtfitmask David A. Case (Tue Jul 10 2007 - 11:01:27 CDT)
AMBER: À´×Ôpig5678µÄÓÊ¼þ pig5678 (Tue Jul 10 2007 - 01:59:22 CDT)
- Re: AMBER: ????pig5678?????? David A. Case (Tue Jul 10 2007 - 10:14:45 CDT)
  - Re:Re: AMBER: ????pig5678?????? pig5678 (Tue Jul 10 2007 - 22:27:55 CDT)
  - Re:Re: AMBER: ????pig5678?????? pig5678 (Thu Jul 12 2007 - 20:36:10 CDT)
AMBER: Saving (.)prepin file Johnson Agbo (Mon Jul 09 2007 - 13:22:40 CDT)
- Re: AMBER: Saving (.)prepin file David A. Case (Tue Jul 10 2007 - 12:45:58 CDT)
AMBER: Input required for RESP Neelanjana Sengupta (Tue Jul 10 2007 - 13:03:54 CDT)
- Re: AMBER: Input required for RESP FyD (Wed Jul 11 2007 - 01:21:42 CDT)
AMBER: extract protein energy from MD trajectory Mikyung (Tue Jul 10 2007 - 16:47:53 CDT)
- Re: AMBER: extract protein energy from MD trajectory Carlos Simmerling (Tue Jul 10 2007 - 17:08:32 CDT)
  - Re: AMBER: extract protein energy from MD trajectory Mikyung (Wed Jul 11 2007 - 01:58:31 CDT)
    - Re: AMBER: extract protein energy from MD trajectory Carlos Simmerling (Wed Jul 11 2007 - 03:34:31 CDT)
AMBER: MPI Quiescence problem in REMD In Hee Park (Tue Jul 10 2007 - 23:03:08 CDT)
- Re: AMBER: MPI Quiescence problem in REMD Carlos Simmerling (Wed Jul 11 2007 - 04:28:56 CDT)
  - Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Wed Jul 11 2007 - 11:41:47 CDT)
    - Re: AMBER: MPI Quiescence problem in REMD Carlos Simmerling (Wed Jul 11 2007 - 12:08:23 CDT)
    - Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Thu Aug 16 2007 - 17:56:37 CDT)
AMBER: Question about NAB (Nucleic Acid Builder) Cenk Andac (Wed Jul 11 2007 - 03:30:18 CDT)
- Re: AMBER: Question about NAB (Nucleic Acid Builder) David A. Case (Wed Jul 11 2007 - 18:23:05 CDT)
AMBER: question about iwrap Kailee (Wed Jul 11 2007 - 08:17:29 CDT)
- Re: AMBER: question about iwrap David A. Case (Wed Jul 11 2007 - 18:24:11 CDT)
  - Re: AMBER: question about iwrap Kailee (Thu Jul 12 2007 - 05:55:28 CDT)
  - AMBER: dihedral angles Jardas sucuriba (Tue Oct 30 2007 - 18:43:10 CST)
    - Re: AMBER: dihedral angles David A. Case (Wed Oct 31 2007 - 22:09:24 CST)
AMBER: Belly Restraints and Distance Restraints Seth Lilavivat (Wed Jul 11 2007 - 14:13:04 CDT)
AMBER: Basic AMBER question Lili Peng (Wed Jul 11 2007 - 14:15:48 CDT)
- Re: AMBER: Basic AMBER question Melinda Layten (Wed Jul 11 2007 - 15:05:11 CDT)
- RE: AMBER: Basic AMBER question Ross Walker (Wed Jul 11 2007 - 15:07:42 CDT)
Fwd: Re: AMBER: Could not find cntrl namelist Francesco Pietra (Wed Jul 11 2007 - 16:52:25 CDT)
AMBER: computational Ala scan Sergio Wong (Wed Jul 11 2007 - 18:36:58 CDT)
AMBER: Amber9 analyze timecorr manual ambigous Nicolas Lux Fawzi (Thu Jul 12 2007 - 14:26:19 CDT)
- Re: AMBER: Amber9 analyze timecorr manual ambigous David A. Case (Thu Jul 12 2007 - 14:55:15 CDT)
  - Re: AMBER: Amber9 analyze timecorr manual ambigous Nicolas Lux Fawzi (Thu Jul 12 2007 - 17:11:30 CDT)
    - Re: AMBER: Amber9 analyze timecorr manual ambigous David A. Case (Thu Jul 12 2007 - 17:58:30 CDT)
AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Hashem Taha (Thu Jul 12 2007 - 15:31:59 CDT)
- Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Robert Duke (Thu Jul 12 2007 - 15:55:15 CDT)
  - Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Hashem Taha (Thu Jul 12 2007 - 16:45:50 CDT)
AMBER: related to new amber force field snoze pa (Fri Jul 13 2007 - 10:57:38 CDT)
- Re: AMBER: related to new amber force field Carlos Simmerling (Fri Jul 13 2007 - 11:33:12 CDT)
AMBER: Multiple residues position snoze pa (Fri Jul 13 2007 - 11:04:59 CDT)
- Re: AMBER: Multiple residues position Carlos Simmerling (Fri Jul 13 2007 - 11:20:19 CDT)
AMBER: Cutoff list exceeds largest sphere in unit cell Andrew Borgert (Fri Jul 13 2007 - 11:18:05 CDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Andrew Borgert (Fri Jul 13 2007 - 11:27:44 CDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Robert Duke (Fri Jul 13 2007 - 11:30:40 CDT)
  - Re: AMBER: Cutoff list exceeds largest sphere in unit cell neville forlemu (Sat Jul 14 2007 - 21:09:36 CDT)
    - Re: AMBER: Non bond list overflow David A. Case (Sun Jul 15 2007 - 18:50:11 CDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Barbault Florent (Fri Jul 13 2007 - 13:54:36 CDT)
AMBER: MPI script Taryn Hartley (Fri Jul 13 2007 - 17:06:45 CDT)
- Re: AMBER: MPI script Carlos Simmerling (Fri Jul 13 2007 - 17:15:36 CDT)
- Re: AMBER: MPI script Thomas Cheatham III (Fri Jul 13 2007 - 17:19:37 CDT)
  - Re: AMBER: MPI script Hashem Taha (Tue Jul 17 2007 - 15:10:46 CDT)
AMBER: can open PDB file in xleap Vijay Manickam Achari (Sun Jul 15 2007 - 20:44:17 CDT)
AMBER: Can't open PDB file in xleap Vijay Manickam Achari (Mon Jul 16 2007 - 04:43:16 CDT)
- Re: AMBER: Can t open PDB file in xleap Benjamin Juhl (Mon Jul 16 2007 - 05:53:16 CDT)
AMBER: convergence in classical MD Seongeun Yang (Mon Jul 16 2007 - 06:23:01 CDT)
- Re: AMBER: convergence in classical MD Carlos Simmerling (Mon Jul 16 2007 - 06:37:09 CDT)
AMBER: Atoms in conatct to a specific atoms during MD Rafi Ahmad (Mon Jul 16 2007 - 08:23:38 CDT)
- AMBER: modelling substrate binding Mattias Blomberg (Mon Jul 16 2007 - 08:53:15 CDT)
- Re: AMBER: Atoms in contact to a specific atoms during MD Mark Williamson (Mon Jul 16 2007 - 09:52:39 CDT)
  - SV: AMBER: Atoms in contact to a specific atoms during MD Rafi Ahmad (Mon Jul 16 2007 - 10:04:46 CDT)
    - Re: SV: AMBER: Atoms in contact to a specific atoms during MD Mark Williamson (Mon Jul 16 2007 - 10:18:00 CDT)
AMBER: Non-standard amino acid residue Sergey Samsonov (Mon Jul 16 2007 - 09:44:32 CDT)
- Re: AMBER: Non-standard amino acid residue FyD (Mon Jul 16 2007 - 11:45:07 CDT)
  - AMBER: Setting nonbonded cutoff to 1 Hayden Eastwood (Mon Jul 16 2007 - 12:27:45 CDT)
    - RE: AMBER: Setting nonbonded cutoff to 1 Ross Walker (Mon Jul 16 2007 - 12:43:28 CDT)
  - Re: AMBER: Non-standard amino acid residue Sergey Samsonov (Tue Jul 17 2007 - 07:30:14 CDT)
AMBER: help with phosphotyrosine Samantha Kaye (Mon Jul 16 2007 - 10:45:36 CDT)
- Re: AMBER: help with phosphotyrosine David A. Case (Mon Jul 16 2007 - 13:11:51 CDT)
  - Re: AMBER: help with phosphotyrosine Samantha Kaye (Tue Jul 17 2007 - 08:00:23 CDT)
AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Mon Jul 16 2007 - 14:19:07 CDT)
- Re: AMBER: Known residue, unknown error in teLeap David A. Case (Mon Jul 16 2007 - 20:32:16 CDT)
  - Re: AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Tue Jul 17 2007 - 11:33:39 CDT)
AMBER: RESP_compilation Karol Kaszuba (Mon Jul 16 2007 - 14:14:32 CDT)
- Re: AMBER: RESP_compilation FyD (Mon Jul 16 2007 - 17:55:20 CDT)
- Re: AMBER: RESP_compilation FyD (Mon Jul 16 2007 - 17:59:06 CDT)
  - Re: AMBER: RESP_compilation_IT_WORKS Karol Kaszuba (Tue Jul 17 2007 - 03:32:59 CDT)
  - AMBER: running_RED-III Karol Kaszuba (Wed Jul 18 2007 - 14:02:10 CDT)
    - Re: AMBER: running_RED-III FyD (Wed Jul 18 2007 - 20:33:20 CDT)
Re: SV: AMBER: Atoms in contact to a specific atoms during MD Bill Ross (Mon Jul 16 2007 - 14:49:45 CDT)
AMBER: refc error Lili Peng (Mon Jul 16 2007 - 18:56:11 CDT)
- Re: AMBER: refc error Davide Moiani (Mon Jul 16 2007 - 19:03:42 CDT)
  - Re: AMBER: refc error Lili Peng (Mon Jul 16 2007 - 19:08:18 CDT)
- Re: AMBER: refc error Davide Moiani (Mon Jul 16 2007 - 19:17:18 CDT)
  - Re: AMBER: refc error Lili Peng (Tue Jul 17 2007 - 13:35:06 CDT)
- Re: AMBER: refc error David A. Case (Mon Jul 16 2007 - 19:25:20 CDT)
- Re: AMBER: refc error Davide Moiani (Tue Jul 17 2007 - 16:00:20 CDT)
  - Re: AMBER: refc error Lili Peng (Tue Jul 17 2007 - 17:40:26 CDT)
AMBER: potential energy calculation Lili Peng (Mon Jul 16 2007 - 19:03:55 CDT)
- Re: AMBER: potential energy calculation Carlos Simmerling (Mon Jul 16 2007 - 20:34:01 CDT)
  - Re: AMBER: potential energy calculation Lili Peng (Tue Jul 17 2007 - 17:46:55 CDT)
AMBER: Gaff Charge Colby C (Mon Jul 16 2007 - 22:39:15 CDT)
- Re: AMBER: Gaff Charge David A. Case (Tue Jul 17 2007 - 00:18:17 CDT)
AMBER: how to create an O linked N-acetylglucosamine in a protein ming hui (Mon Jul 16 2007 - 22:41:40 CDT)
- AMBER: Re: how to create an O linked N-acetylglucosamine in a protein ming hui (Mon Jul 16 2007 - 22:44:08 CDT)
  - Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a Austin B. Yongye (Tue Jul 17 2007 - 01:22:12 CDT)
  - Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein Karl Kirschner (Tue Jul 17 2007 - 08:39:43 CDT)
AMBER: General AMBER questions Lili Peng (Tue Jul 17 2007 - 17:51:32 CDT)
- Re: AMBER: General AMBER questions David A. Case (Wed Jul 18 2007 - 18:12:34 CDT)
AMBER: incoherent intermediate scattering function Jason Whitte (Tue Jul 17 2007 - 17:59:21 CDT)
AMBER: Problems during compilation Sébastien Kozlowskyj (Wed Jul 18 2007 - 04:26:06 CDT)
AMBER: bound magnesium ions in proteins with GBSA Wei Chen (Wed Jul 18 2007 - 11:01:26 CDT)
AMBER: Error during compilation on a SGI Irix machine Ruchi Sachdeva (Wed Jul 18 2007 - 11:47:30 CDT)
- Re: AMBER: Error during compilation on a SGI Irix machine Carlos Simmerling (Wed Jul 18 2007 - 11:57:27 CDT)
  - Re: AMBER: Error during compilation on a SGI Irix machine Ruchi Sachdeva (Wed Jul 18 2007 - 23:18:30 CDT)
    - Re: AMBER: Error during compilation on a SGI Irix machine David A. Case (Wed Jul 18 2007 - 23:34:18 CDT)
AMBER: Verifying Bond Angles Seth Lilavivat (Wed Jul 18 2007 - 16:32:30 CDT)
AMBER: (no subject) n.buis_at_soton.ac.uk (Thu Jul 19 2007 - 03:58:06 CDT)
AMBER: Re: amber-developers: -y option in sander Geoff Wood (Thu Jul 19 2007 - 08:54:47 CDT)
AMBER: DNA RNA recognition problem Steve Seibold (Thu Jul 19 2007 - 08:51:43 CDT)
- Re: AMBER: DNA RNA recognition problem David A. Case (Thu Jul 19 2007 - 10:01:17 CDT)
AMBER: secstruct command Anna Díaz Cirac (Thu Jul 19 2007 - 12:35:42 CDT)
- Re: AMBER: secstruct command Carlos Simmerling (Thu Jul 19 2007 - 12:46:30 CDT)
- Re: AMBER: secstruct command Holger Gohlke (Thu Jul 19 2007 - 13:22:37 CDT)
  - AMBER: ptraj error FyD (Fri Jul 20 2007 - 16:21:17 CDT)
- Re: AMBER: secstruct command Tim Meyer (Fri Jul 20 2007 - 08:55:47 CDT)
AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 05:58:48 CDT)
- Re: AMBER: temperature fluctuation in REMD Carlos Simmerling (Fri Jul 20 2007 - 06:44:36 CDT)
  - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 07:11:17 CDT)
- Re: AMBER: temperature fluctuation in REMD David A. Case (Fri Jul 20 2007 - 11:16:46 CDT)
AMBER: problem in compiling amber9 and running amber9 Prem Prakash Pathak (Sat Jul 21 2007 - 07:27:18 CDT)
- Re: AMBER: problem in compiling amber9 and running amber9 Mark Williamson (Sat Jul 21 2007 - 09:21:18 CDT)
AMBER: RE Amber: Simulated Annealing Francesco Pietra (Sat Jul 21 2007 - 10:13:11 CDT)
AMBER: GDP UNKNOWN ATOM TYPE: O3 warning j j (Sat Jul 21 2007 - 12:21:32 CDT)
AMBER: offending restraint Jena M (Sat Jul 21 2007 - 19:15:42 CDT)
- Re: AMBER: offending restraint David A. Case (Sat Jul 21 2007 - 20:35:51 CDT)
- Re: AMBER: offending restraint Carlos Simmerling (Sun Jul 22 2007 - 06:32:51 CDT)
AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 11:47:45 CDT)
- Re: AMBER: question about formatted mdrcrd files... David A. Case (Sun Jul 22 2007 - 18:30:06 CDT)
  - Re: AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 19:51:02 CDT)
  - Re: AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 20:37:43 CDT)
AMBER: Truncated Octahedron box volume Ilyas Yildirim (Sun Jul 22 2007 - 21:52:16 CDT)
AMBER: using amber to minimize structure obatined from cyana Prem Prakash Pathak (Mon Jul 23 2007 - 02:27:26 CDT)
- Re: AMBER: using amber to minimize structure obatined from cyana David A. Case (Mon Jul 23 2007 - 09:52:00 CDT)
AMBER: parallel compilation Francesco Pietra (Mon Jul 23 2007 - 05:16:35 CDT)
- Re: AMBER: parallel compilation David A. Case (Mon Jul 23 2007 - 09:55:02 CDT)
  - Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 01:19:56 CDT)
    - Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 01:44:43 CDT)
    - Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 02:17:03 CDT)
AMBER: regarding distance restraints gurpreet singh (Mon Jul 23 2007 - 05:46:39 CDT)
- Re: AMBER: regarding distance restraints Carlos Simmerling (Mon Jul 23 2007 - 06:26:27 CDT)
- Re: AMBER: regarding distance restraints David A. Case (Mon Jul 23 2007 - 09:56:03 CDT)
AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water Ye Mei (Mon Jul 23 2007 - 08:00:34 CDT)
AMBER: RE: Query Ross Walker (Mon Jul 23 2007 - 10:13:13 CDT)
AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Mon Jul 23 2007 - 10:39:21 CDT)
- Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Steven Winfield (Mon Jul 23 2007 - 10:43:17 CDT)
- RE: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Ross Walker (Mon Jul 23 2007 - 10:52:00 CDT)
  - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Tue Jul 24 2007 - 07:30:31 CDT)
    - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap David A. Case (Tue Jul 24 2007 - 10:20:30 CDT)
    - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Tue Jul 24 2007 - 23:12:48 CDT)
AMBER: md potential energy Francesco Pietra (Mon Jul 23 2007 - 11:14:48 CDT)
AMBER: MPI error message Taryn Hartley (Mon Jul 23 2007 - 12:39:27 CDT)
- RE: AMBER: MPI error message Ross Walker (Mon Jul 23 2007 - 12:56:35 CDT)
AMBER: DNA denatures during MD simulation Prashanth Athri (Mon Jul 23 2007 - 14:38:12 CDT)
- Re: AMBER: DNA denatures during MD simulation Carlos Simmerling (Mon Jul 23 2007 - 14:44:35 CDT)
- Re: AMBER: DNA denatures during MD simulation Thomas Cheatham (Mon Jul 23 2007 - 14:49:49 CDT)
  - Re: AMBER: DNA denatures during MD simulation Prashanth Athri (Mon Jul 23 2007 - 17:51:32 CDT)
AMBER: Bug report: a bug of xleap associated with NumLock Ye Mei (Tue Jul 24 2007 - 01:15:27 CDT)
- Re: AMBER: Bug report: a bug of xleap associated with NumLock David A. Case (Tue Jul 24 2007 - 10:16:07 CDT)
Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 02:19:58 CDT)
- Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 05:07:31 CDT)
- Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 05:15:28 CDT)
  - Re: Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 09:07:10 CDT)
AMBER: not getting topology and restraint file Prem Prakash Pathak (Tue Jul 24 2007 - 09:09:40 CDT)
- Re: AMBER: not getting topology and restraint file Carlos Simmerling (Tue Jul 24 2007 - 09:46:49 CDT)
  - Re: AMBER: not getting topology and restraint file Prem Prakash Pathak (Tue Jul 24 2007 - 23:11:00 CDT)
    - Re: AMBER: not getting topology and restraint file Carlos Simmerling (Wed Jul 25 2007 - 05:16:02 CDT)
    - Re: AMBER: not getting topology and restraint file Prem Prakash Pathak (Wed Jul 25 2007 - 08:45:57 CDT)
AMBER: FW: MPI error message Taryn Hartley (Tue Jul 24 2007 - 14:00:25 CDT)
- RE: AMBER: FW: MPI error message Gustavo Seabra (Tue Jul 24 2007 - 14:32:52 CDT)
- RE: AMBER: FW: MPI error message Ross Walker (Tue Jul 24 2007 - 16:31:12 CDT)
AMBER: MD simulation error Lili Peng (Tue Jul 24 2007 - 18:53:59 CDT)
- Re: AMBER: MD simulation error David A. Case (Tue Jul 24 2007 - 19:55:09 CDT)
- RE: AMBER: MD simulation error Ross Walker (Tue Jul 24 2007 - 20:01:13 CDT)
  - Re: AMBER: MD simulation error Lili Peng (Wed Jul 25 2007 - 12:38:10 CDT)
AMBER: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 01:24:22 CDT)
- Re: AMBER: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 08:33:35 CDT)
  - Re: AMBER: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 09:00:58 CDT)
AMBER: Bad residue/molecule data in prmtop neva_at_mmb.pcb.ub.es (Wed Jul 25 2007 - 08:03:19 CDT)
- RE: AMBER: Bad residue/molecule data in prmtop Ross Walker (Wed Jul 25 2007 - 09:17:00 CDT)
AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 08:24:10 CDT)
- RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues Ross Walker (Wed Jul 25 2007 - 10:25:58 CDT)
  - RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 12:07:15 CDT)
- Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 12:36:43 CDT)
  - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 14:19:29 CDT)
AMBER: crg file umbrita itl (Wed Jul 25 2007 - 09:43:17 CDT)
- RE: AMBER: crg file Ross Walker (Wed Jul 25 2007 - 10:26:28 CDT)
AMBER: RE: Contact TSRI: Ross Walker Ross Walker (Wed Jul 25 2007 - 10:31:53 CDT)
RE: AMBER:charge file umbrita itl (Wed Jul 25 2007 - 10:36:11 CDT)
Fwd: Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 17:01:40 CDT)
AMBER: rmsd residue wise ravishk kumar (Thu Jul 26 2007 - 08:02:20 CDT)
AMBER: methods to approach two atoms Jena M (Thu Jul 26 2007 - 08:53:09 CDT)
AMBER: RE: A little question Ross Walker (Thu Jul 26 2007 - 09:51:55 CDT)
AMBER: about wrap the trajectory Rachel (Thu Jul 26 2007 - 11:18:32 CDT)
- Re: AMBER: about wrap the trajectory Carlos Simmerling (Thu Jul 26 2007 - 11:28:33 CDT)
  - Re: AMBER: about wrap the trajectory Rachel (Thu Jul 26 2007 - 11:43:48 CDT)
AMBER: adding organic molecule to polypeptide residue Lili Peng (Thu Jul 26 2007 - 17:36:29 CDT)
- Re: AMBER: adding organic molecule to polypeptide residue FyD (Sat Jul 28 2007 - 04:05:18 CDT)
AMBER: FLAG LENNARD_JONES_ACOEF NAN Greg Gannon (Fri Jul 27 2007 - 09:41:46 CDT)
- Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN David A. Case (Fri Jul 27 2007 - 10:19:49 CDT)
  - Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN Greg Gannon (Fri Jul 27 2007 - 10:55:52 CDT)
AMBER: RE: Query Ross Walker (Fri Jul 27 2007 - 10:24:56 CDT)
AMBER: errors in SHIFTS execution Tom Pochapsky (Sat Jul 28 2007 - 06:58:57 CDT)
- Re: AMBER: errors in SHIFTS execution David A. Case (Sun Jul 29 2007 - 10:44:05 CDT)
  - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 08:49:47 CDT)
  - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 09:06:19 CDT)
    - Re: AMBER: errors in SHIFTS execution David A. Case (Mon Jul 30 2007 - 10:37:26 CDT)
    - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 12:06:04 CDT)
AMBER: PCA with ptraj ravishk kumar (Sat Jul 28 2007 - 07:02:13 CDT)
- Re: AMBER: PCA with ptraj Chris Moth (Sun Jul 29 2007 - 07:27:32 CDT)
AMBER: thermodynamic data for conformers Francesco Pietra (Sun Jul 29 2007 - 12:11:11 CDT)
AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA? tonglei (Sun Jul 29 2007 - 22:45:24 CDT)
AMBER: heme force field hadi behzadi (Mon Jul 30 2007 - 06:55:07 CDT)
- Re: AMBER: heme force field Marcelo Puiatti (Mon Jul 30 2007 - 08:08:52 CDT)
AMBER: QM-MM output interpretation Francesco Pietra (Mon Jul 30 2007 - 09:08:36 CDT)
- RE: AMBER: QM-MM output interpretation Ross Walker (Mon Jul 30 2007 - 10:51:36 CDT)
  - RE: AMBER: QM-MM output interpretation Francesco Pietra (Mon Jul 30 2007 - 12:59:13 CDT)
    - RE: AMBER: QM-MM output interpretation Ross Walker (Mon Jul 30 2007 - 23:11:50 CDT)
    - RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Tue Jul 31 2007 - 00:09:02 CDT)
AMBER: RE: Problem with sander.MPI Ross Walker (Mon Jul 30 2007 - 09:12:58 CDT)
AMBER: RE: help:- regarding "perl" in analyzing the simulation Ross Walker (Mon Jul 30 2007 - 11:38:33 CDT)
AMBER: QMMM to follow reaction involving water M. L. Dodson (Mon Jul 30 2007 - 13:23:14 CDT)
- RE: AMBER: QMMM to follow reaction involving water Gustavo Seabra (Mon Jul 30 2007 - 14:41:17 CDT)
- RE: AMBER: QMMM to follow reaction involving water Ross Walker (Mon Jul 30 2007 - 23:49:23 CDT)
  - Re: AMBER: QMMM to follow reaction involving water M. L. Dodson (Tue Jul 31 2007 - 10:14:57 CDT)
AMBER: Problem while saving .top and .crd files. Anju Sharma (Mon Jul 30 2007 - 22:47:39 CDT)
- RE: AMBER: Problem while saving .top and .crd files. Ross Walker (Mon Jul 30 2007 - 23:28:42 CDT)
  - Re: AMBER: Problem while saving .top and .crd files. Anju Sharma (Thu Aug 02 2007 - 00:25:19 CDT)
    - RE: AMBER: Problem while saving .top and .crd files. Ross Walker (Thu Aug 02 2007 - 09:54:21 CDT)
AMBER: Problem while creating input files in antechamber Anju Sharma (Tue Jul 31 2007 - 00:33:12 CDT)
- Re: AMBER: Problem while creating input files in antechamber Benjamin Juhl (Tue Jul 31 2007 - 02:08:35 CDT)
AMBER: Linux install Beale, John (Tue Jul 31 2007 - 06:55:34 CDT)
- Re: AMBER: Linux install David A. Case (Tue Jul 31 2007 - 10:35:37 CDT)
AMBER: Resp hadi behzadi (Tue Jul 31 2007 - 09:15:15 CDT)
AMBER: resp hadi behzadi (Tue Jul 31 2007 - 12:15:37 CDT)
AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1) Alessandro Nascimento (Tue Jul 31 2007 - 16:34:12 CDT)
AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin (Wed Aug 01 2007 - 04:36:31 CDT)
AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 06:03:48 CDT)
- Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 09:50:30 CDT)
  - Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman (Wed Aug 01 2007 - 10:46:10 CDT)
  - Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 10:52:13 CDT)
    - Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 11:36:37 CDT)
Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Wed Aug 01 2007 - 08:58:02 CDT)
AMBER: Problem with Antechamber and point charges anna duraj (Wed Aug 01 2007 - 14:40:44 CDT)
- Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Wed Aug 01 2007 - 14:52:53 CDT)
  - Re: AMBER: Problem with Antechamber and point charges anna duraj (Fri Aug 03 2007 - 14:47:17 CDT)
    - Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Fri Aug 03 2007 - 14:55:43 CDT)
AMBER: neutral terminals Jena M (Wed Aug 01 2007 - 19:15:46 CDT)
- Re: AMBER: neutral terminals Carlos Simmerling (Thu Aug 02 2007 - 07:04:15 CDT)
Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 23:02:24 CDT)
- Re: AMBER: bugfix for impropers in parmchk David A. Case (Thu Aug 02 2007 - 00:04:20 CDT)
  - Re: AMBER: bugfix for impropers in parmchk Jiten (Thu Aug 02 2007 - 01:23:20 CDT)
AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 01:34:39 CDT)
- Re: AMBER: Problem with antechamber gurpreet singh (Thu Aug 02 2007 - 03:24:18 CDT)
  - Re: AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 04:03:36 CDT)
    - Re: AMBER: Problem with antechamber David A. Case (Thu Aug 02 2007 - 10:07:30 CDT)
    - RE: AMBER: Problem with antechamber Ross Walker (Thu Aug 02 2007 - 10:22:52 CDT)
- Re: AMBER: Problem with antechamber Bill Ross (Thu Aug 02 2007 - 15:14:37 CDT)
AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 01:50:59 CDT)
- Re: AMBER: (no subject) gurpreet singh (Thu Aug 02 2007 - 03:39:07 CDT)
  - Re: AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 07:36:21 CDT)
AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 08:12:18 CDT)
- Re: AMBER: planarity restraints for NA Carlos Simmerling (Thu Aug 02 2007 - 08:17:56 CDT)
  - Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 09:07:23 CDT)
AMBER: restrained md and mm pbsa Christopher Gaughan (Thu Aug 02 2007 - 09:15:17 CDT)
AMBER: vector corrplane Servaas Michielssens (Thu Aug 02 2007 - 10:25:45 CDT)
AMBER: Force Field Parameters Beale, John (Thu Aug 02 2007 - 11:46:16 CDT)
- Re: AMBER: Force Field Parameters Prashanth Athri (Thu Aug 02 2007 - 12:39:10 CDT)
- Re: AMBER: Force Field Parameters Raviprasad Aduri (Thu Aug 02 2007 - 14:49:37 CDT)
AMBER: Calculating cumulative average Francesco Pietra (Thu Aug 02 2007 - 12:00:10 CDT)
AMBER: edit.out amber version 9 Greg Gannon (Thu Aug 02 2007 - 13:21:31 CDT)
- Re: AMBER: edit.out amber version 9 David A. Case (Thu Aug 02 2007 - 14:00:22 CDT)
- Re: AMBER: edit.out amber version 9 WANG,YING (Thu Aug 02 2007 - 15:33:49 CDT)
AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 14:07:11 CDT)
- Re: AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 14:15:41 CDT)
- Re: AMBER: Problem generating .prepin file in Antechamber David A. Case (Thu Aug 02 2007 - 15:53:03 CDT)
AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 19:33:40 CDT)
- Re: AMBER: Any experience on Dell two quad core system? Ye Mei (Thu Aug 02 2007 - 22:57:00 CDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 23:23:17 CDT)
- Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Thu Aug 02 2007 - 23:18:42 CDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Fri Aug 03 2007 - 11:35:26 CDT)
- Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Mon Aug 13 2007 - 15:59:58 CDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Mon Aug 13 2007 - 19:39:01 CDT)
    - Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Tue Aug 14 2007 - 10:05:34 CDT)
    - Re: AMBER: Any experience on Dell two quad core system? Robert Duke (Tue Aug 14 2007 - 11:13:07 CDT)
Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Thu Aug 02 2007 - 20:44:28 CDT)
- Re: AMBER: Antechamber formal charges with Gasteiger method David A. Case (Fri Aug 03 2007 - 15:17:11 CDT)
  - Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Sat Aug 04 2007 - 14:42:43 CDT)
AMBER: Information about Amber 9 Lycourgos Chiniadis (Fri Aug 03 2007 - 00:11:17 CDT)
- Re: AMBER: Information about Amber 9 David A. Case (Fri Aug 03 2007 - 09:53:22 CDT)
AMBER: force field for hydrogels Prem Prakash Pathak (Fri Aug 03 2007 - 01:03:48 CDT)
AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 05:09:03 CDT)
- Re: AMBER: unable to save prmtop/inpcrd for chcl3box David A. Case (Fri Aug 03 2007 - 09:58:03 CDT)
AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 07:28:56 CDT)
- Re: AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 11:00:57 CDT)
AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 07:24:24 CDT)
AMBER: Binary file curiosities David LeBard (Fri Aug 03 2007 - 17:59:45 CDT)
- Re: AMBER: Binary file curiosities David A. Case (Fri Aug 03 2007 - 18:21:25 CDT)
- Re: AMBER: Binary file curiosities Thomas Cheatham III (Fri Aug 03 2007 - 18:32:55 CDT)
  - Re: AMBER: Binary file curiosities David LeBard (Sat Aug 04 2007 - 16:34:23 CDT)
    - Re: AMBER: Binary file curiosities David A. Case (Mon Aug 06 2007 - 10:03:07 CDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 03:32:40 CDT)
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 09:32:17 CDT)
  - Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 09:51:22 CDT)
    - Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 11:42:33 CDT)
- RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra (Sat Aug 04 2007 - 10:33:12 CDT)
  - RE: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Mon Aug 06 2007 - 01:28:13 CDT)
AMBER: nucleic acid electrostatic energy Tiago Sobreira (Sat Aug 04 2007 - 08:45:46 CDT)
- Re: AMBER: nucleic acid electrostatic energy David A. Case (Sat Aug 04 2007 - 10:28:36 CDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 09:33:35 CDT)
AMBER: GAFF atom typing for flavin Hans Martin Senn (Sat Aug 04 2007 - 11:15:30 CDT)
AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 13:20:42 CDT)
AMBER: setting dimensions of truncated octahedron Lillian chong (Sat Aug 04 2007 - 15:34:59 CDT)
- Re: AMBER: setting dimensions of truncated octahedron Thomas Cheatham (Sat Aug 04 2007 - 17:38:15 CDT)
  - Re: AMBER: setting dimensions of truncated octahedron Lillian chong (Sun Aug 05 2007 - 08:25:01 CDT)
AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker (Sun Aug 05 2007 - 22:09:46 CDT)
AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Sun Aug 05 2007 - 22:51:11 CDT)
- Re: AMBER: Problem while carrying out minimisation of drug molecule using sander David A. Case (Mon Aug 06 2007 - 09:35:25 CDT)
  - Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Tue Aug 07 2007 - 00:32:43 CDT)
    - Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Carlos Simmerling (Tue Aug 07 2007 - 05:57:53 CDT)
AMBER: Specific heat graph is a straight line priya priya (Mon Aug 06 2007 - 08:33:52 CDT)
AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert (Mon Aug 06 2007 - 14:18:58 CDT)
- Re: AMBER: Integrating the alpha-helix bias correction into ff94 Carlos Simmerling (Mon Aug 06 2007 - 14:42:17 CDT)
AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan (Mon Aug 06 2007 - 23:13:27 CDT)
- Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions David A. Case (Sat Aug 11 2007 - 15:35:15 CDT)
AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 02:58:12 CDT)
- Re: AMBER: heical content in simulations Chng Choon-Peng (Tue Aug 07 2007 - 03:19:26 CDT)
  - Re: AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 03:41:16 CDT)
    - Re: AMBER: heical content in simulations Scott Pendley (Fri Nov 09 2007 - 14:25:18 CST)
AMBER: Problem with minimization Syed Tarique Moin (Tue Aug 07 2007 - 08:11:32 CDT)
- RE: AMBER: Problem with minimization Ross Walker (Tue Aug 07 2007 - 08:57:18 CDT)
AMBER: compile amber8 with mpich2 Kailee (Tue Aug 07 2007 - 08:18:14 CDT)
- Re: AMBER: compile amber8 with mpich2 Scott Brozell (Wed Aug 08 2007 - 21:46:22 CDT)
AMBER: Positive EPtot in QM-MM Francesco Pietra (Tue Aug 07 2007 - 09:34:35 CDT)
AMBER: about shake linfu (Tue Aug 07 2007 - 20:36:59 CDT)
- Re: AMBER: about shake Steven Winfield (Wed Aug 08 2007 - 10:59:45 CDT)
  - Re: Re: AMBER: about shake linfu (Wed Aug 08 2007 - 20:10:05 CDT)
AMBER: msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:01:00 CDT)
AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:08:04 CDT)
- RE: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA Ross Walker (Wed Aug 08 2007 - 09:49:11 CDT)
- Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA linfu (Wed Aug 08 2007 - 08:33:58 CDT)
AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker (Wed Aug 08 2007 - 09:52:39 CDT)
AMBER: RE: Problem loading pdf into tleap Ross Walker (Wed Aug 08 2007 - 12:29:19 CDT)
AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:33:22 CDT)
- Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 17:29:24 CDT)
  - Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 18:04:31 CDT)
- Re: AMBER: Cygwin error Bill Ross (Thu Aug 09 2007 - 15:42:48 CDT)
  - Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 16:40:14 CDT)
Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 16:43:49 CDT)
- Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:56:00 CDT)
  - Re: AMBER: Cygwin error Mark Williamson (Wed Aug 08 2007 - 17:02:15 CDT)
    - Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 17:13:54 CDT)
    - Re: AMBER: Cygwin error Gustavo Seabra (Wed Aug 08 2007 - 17:21:01 CDT)
AMBER: how to combine two molecules Wenyong Tong (Thu Aug 09 2007 - 00:34:33 CDT)
- Re: AMBER: how to combine two molecules Benjamin Juhl (Fri Aug 10 2007 - 04:11:07 CDT)
  - Re: AMBER: how to combine two molecules Wenyong Tong (Sat Aug 11 2007 - 20:48:48 CDT)
    - Re: AMBER: how to combine two molecules David A. Case (Mon Aug 13 2007 - 11:43:57 CDT)
    - Re: AMBER: how to combine two molecules Wenyong Tong (Mon Aug 13 2007 - 18:14:49 CDT)
AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 15:24:11 CDT)
- Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 17:15:58 CDT)
  - Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 17:50:45 CDT)
- Re: AMBER: NVE energy and temperature drift Thomas Cheatham III (Thu Aug 09 2007 - 17:27:50 CDT)
- Re: AMBER: NVE energy and temperature drift David A. Case (Sat Aug 11 2007 - 15:28:30 CDT)
  - Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Sat Aug 11 2007 - 16:33:09 CDT)
AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 07:42:11 CDT)
- Re: AMBER: Implicit solvent simulation is too slow. Carlos Simmerling (Fri Aug 10 2007 - 08:07:50 CDT)
  - Re: AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 09:04:28 CDT)
- RE: AMBER: Implicit solvent simulation is too slow. Ross Walker (Fri Aug 10 2007 - 10:56:32 CDT)
AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 09:45:10 CDT)
- Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 10:55:02 CDT)
  - Re: AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 16:35:38 CDT)
    - Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 17:43:29 CDT)
AMBER: short 2'OH-OP contacts in RNA Jose Gallego (Fri Aug 10 2007 - 11:22:35 CDT)
AMBER: vlimit exceeded for the step Sudha Mani Karra (Fri Aug 10 2007 - 14:31:08 CDT)
- RE: AMBER: vlimit exceeded for the step Ross Walker (Fri Aug 10 2007 - 15:04:10 CDT)
AMBER: Steve Seibold (Fri Aug 10 2007 - 15:17:47 CDT)
- Re: AMBER: Thomas Pochapsky (Fri Aug 10 2007 - 15:34:32 CDT)
- Re: AMBER: David A. Case (Tue Aug 14 2007 - 10:27:48 CDT)
AMBER: Citation for Langevin thermostat? Marc Baaden (Sat Aug 11 2007 - 02:13:28 CDT)
- Re: AMBER: Citation for Langevin thermostat? David A. Case (Sat Aug 11 2007 - 14:47:59 CDT)
AMBER: Using charmm force field in amber Seongeun Yang (Sat Aug 11 2007 - 03:44:44 CDT)
AMBER: Failure to SCF convergence Francesco Pietra (Sat Aug 11 2007 - 11:56:53 CDT)
- RE: AMBER: Failure to SCF convergence Ross Walker (Sat Aug 11 2007 - 18:14:54 CDT)
  - RE: AMBER: Failure to SCF convergence & parallelization and memory Francesco Pietra (Sun Aug 12 2007 - 02:37:33 CDT)
AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 15:11:08 CDT)
- Re: AMBER: imin=5 and inptraj Carlos Simmerling (Sat Aug 11 2007 - 16:23:29 CDT)
  - Re: AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 16:31:40 CDT)
- Re: AMBER: imin=5 and inptraj Chris Moth (Sat Aug 11 2007 - 16:37:11 CDT)
AMBER: Neutralize charges for simulated annealing? Francesco Pietra (Sat Aug 11 2007 - 17:35:30 CDT)
AMBER: setbox command error priya priya (Mon Aug 13 2007 - 11:18:16 CDT)
- Re: AMBER: setbox command error David A. Case (Mon Aug 13 2007 - 15:38:30 CDT)
  - Re: AMBER: setbox command error priya priya (Tue Aug 14 2007 - 01:42:45 CDT)
AMBER: unsubscribe Pan, Yongmei (Mon Aug 13 2007 - 12:35:12 CDT)
AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti (Mon Aug 13 2007 - 16:09:51 CDT)
- Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? David A. Case (Mon Aug 13 2007 - 20:26:24 CDT)
  - Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? Thomas Cheatham (Mon Aug 13 2007 - 21:45:19 CDT)
AMBER: Normal Mode Analysis Kresimir Sikic (Mon Aug 13 2007 - 10:12:59 CDT)
- Re: AMBER: Normal Mode Analysis David A. Case (Wed Aug 15 2007 - 17:56:46 CDT)
AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 01:03:07 CDT)
- Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 03:28:09 CDT)
  - Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 03:54:03 CDT)
    - Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 04:10:16 CDT)
  - Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 04:19:37 CDT)
    - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 04:21:07 CDT)
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 04:45:53 CDT)
  - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 04:50:07 CDT)
  - Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 05:49:13 CDT)
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Wed Aug 15 2007 - 00:17:03 CDT)
  - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Wed Aug 15 2007 - 01:34:02 CDT)
AMBER: regarding implicit simulation gurpreet singh (Tue Aug 14 2007 - 01:21:35 CDT)
- Re: AMBER: regarding implicit simulation Carlos Simmerling (Tue Aug 14 2007 - 06:22:24 CDT)
AMBER: MMPBSA NOT Getting results msubhamoy_at_ibab.ac.in (Tue Aug 14 2007 - 03:26:57 CDT)
- RE: AMBER: MMPBSA NOT Getting results Rafi Ahmad (Tue Aug 14 2007 - 03:34:35 CDT)
AMBER: How to carry out drug-dna complex simulations Anju Sharma (Tue Aug 14 2007 - 03:50:04 CDT)
- Re: AMBER: How to carry out drug-dna complex simulations David A. Case (Tue Aug 14 2007 - 10:18:47 CDT)
  - Re: AMBER: How to carry out drug-dna complex simulations Scott Brozell (Sun Aug 19 2007 - 13:06:22 CDT)
AMBER: Tutorial about SMD? Qiang Zhong (Tue Aug 14 2007 - 05:19:09 CDT)
AMBER: Parallelizin antechamber? Francesco Pietra (Tue Aug 14 2007 - 08:29:11 CDT)
- Re: AMBER: Parallelizin antechamber? M. L. Dodson (Tue Aug 14 2007 - 09:29:16 CDT)
  - Re: AMBER: Parallelizin antechamber? Junmei Wang (Wed Aug 15 2007 - 08:41:45 CDT)
AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 15:31:34 CDT)
- Re: AMBER: torsional restraints in a solvated MD simulation. Carlos Simmerling (Tue Aug 14 2007 - 15:41:52 CDT)
  - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 18:11:27 CDT)
- Re: AMBER: torsional restraints in a solvated MD simulation. David A. Case (Tue Aug 14 2007 - 15:50:31 CDT)
  - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 18:15:06 CDT)
    - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 20:04:24 CDT)
AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 03:43:45 CDT)
- Re: AMBER: antechamber, how does it work Junmei Wang (Wed Aug 15 2007 - 08:33:36 CDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 09:25:12 CDT)
- Re: AMBER: antechamber, how does it work Gustavo Seabra (Wed Aug 15 2007 - 09:15:48 CDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 10:05:31 CDT)
- Re: AMBER: antechamber, how does it work Seth Hayik (Wed Aug 15 2007 - 10:10:22 CDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 11:08:37 CDT)
  - Re: AMBER: about parallelization in QM-MM Francesco Pietra (Fri Aug 17 2007 - 01:41:02 CDT)
    - RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 11:58:54 CDT)
    - RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 13:45:08 CDT)
AMBER: Building parallel Amber 9.0 Beale, John (Wed Aug 15 2007 - 07:21:56 CDT)
- Re: AMBER: Building parallel Amber 9.0 Gustavo Seabra (Wed Aug 15 2007 - 08:46:59 CDT)
- RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 09:26:36 CDT)
  - RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 10:41:25 CDT)
    - RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 22:53:44 CDT)
    - RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 23:02:38 CDT)
  - RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 10:44:10 CDT)
    - RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 12:43:28 CDT)
AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 09:38:06 CDT)
- Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 09:54:40 CDT)
  - Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 10:40:37 CDT)
  - Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 10:40:37 CDT)
AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 11:50:57 CDT)
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Wed Aug 15 2007 - 12:34:49 CDT)
  - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 23:39:37 CDT)
    - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Thu Aug 16 2007 - 11:33:52 CDT)
    - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Thu Aug 16 2007 - 11:52:56 CDT)
AMBER: docking ability anna duraj (Wed Aug 15 2007 - 12:34:37 CDT)
- Re: AMBER: docking ability Scott Brozell (Sun Aug 19 2007 - 13:19:08 CDT)
AMBER: Bug in ptraj mask processing? Steve Spronk (Wed Aug 15 2007 - 14:18:15 CDT)
AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 13:35:26 CDT)
- Re: AMBER: Missplaced TERs David A. Case (Thu Aug 16 2007 - 13:53:10 CDT)
  - RE: AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 14:47:38 CDT)
    - Re: AMBER: Missplaced TERs David A. Case (Mon Sep 10 2007 - 17:46:57 CDT)
AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 16:37:03 CDT)
- Re: AMBER: What is the best computer for running AMBER simulations? David LeBard (Thu Aug 16 2007 - 17:17:42 CDT)
- Re: AMBER: What is the best computer for running AMBER simulations? Andreas Svrcek-Seiler (Thu Aug 16 2007 - 17:51:06 CDT)
  - Re: AMBER: What is the best computer for running AMBER simulations? David A. Case (Thu Aug 16 2007 - 18:42:54 CDT)
AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik (Fri Aug 17 2007 - 00:44:17 CDT)
AMBER: Thermodynamic Integration for a CHARGED molecule ming hui (Fri Aug 17 2007 - 04:12:38 CDT)
- Re: AMBER: Thermodynamic Integration for a CHARGED molecule David Mobley (Fri Aug 17 2007 - 08:56:33 CDT)
  - Re: AMBER: Thermodynamic Integration for a CHARGED molecule David A. Case (Fri Aug 17 2007 - 10:46:38 CDT)
AMBER: MPI Beale, John (Fri Aug 17 2007 - 07:00:33 CDT)
- Re: AMBER: MPI Mark Williamson (Fri Aug 17 2007 - 07:58:00 CDT)
AMBER: Molsurf error Pankaj R. Daga (Fri Aug 17 2007 - 12:46:54 CDT)
AMBER: ptraj hydrogen bonding defaults Michael Lerner (Fri Aug 17 2007 - 17:26:09 CDT)
- Re: AMBER: ptraj hydrogen bonding defaults Thomas Cheatham (Fri Aug 17 2007 - 21:33:55 CDT)
AMBER: DFTB email address Francesco Pietra (Sat Aug 18 2007 - 02:14:53 CDT)
- Re: AMBER: DFTB email address tomas.kubar_at_marge.uochb.cas.cz (Sun Aug 19 2007 - 15:27:48 CDT)
AMBER: charges in PBSA calculation Neha Gandhi (Sat Aug 18 2007 - 21:20:16 CDT)
- Re: AMBER: charges in PBSA calculation Ray Luo (Sun Aug 19 2007 - 08:32:19 CDT)
  - Re: AMBER: charges in PBSA calculation Neha Gandhi (Sun Aug 19 2007 - 18:01:47 CDT)
  - Re: AMBER: charges in PBSA calculation David A. Case (Sun Aug 19 2007 - 19:57:14 CDT)
AMBER: CRESP charges in antechamber prepin Francesco Pietra (Mon Aug 20 2007 - 02:23:24 CDT)
AMBER: mmpbsa calculation msubhamoy_at_ibab.ac.in (Mon Aug 20 2007 - 04:53:42 CDT)
AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 07:59:28 CDT)
- Re: AMBER: TEST_FAILURES Martin Stennett (Mon Aug 20 2007 - 07:56:36 CDT)
- Re: AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 19:43:23 CDT)
AMBER: Entropy in MM_PBSA Sergey Samsonov (Mon Aug 20 2007 - 10:01:37 CDT)
- Re: AMBER: Entropy in MM_PBSA David Mobley (Fri Aug 24 2007 - 11:31:28 CDT)
AMBER: Beale, John (Mon Aug 20 2007 - 10:41:06 CDT)
- Re: AMBER: David A. Case (Mon Aug 20 2007 - 19:31:21 CDT)
AMBER: $tleap is not normal Qiang Zhong (Mon Aug 20 2007 - 20:34:00 CDT)
- RE: AMBER: $tleap is not normal Ross Walker (Mon Aug 20 2007 - 21:51:16 CDT)
AMBER: Regarding free energy calculation and covalent bond nag raj (Mon Aug 20 2007 - 23:07:04 CDT)
- Re: AMBER: Regarding free energy calculation and covalent bond David A. Case (Thu Aug 23 2007 - 11:52:17 CDT)
AMBER: Error in MMPBSA Calculation msubhamoy_at_ibab.ac.in (Tue Aug 21 2007 - 00:53:17 CDT)
- Re: AMBER: Error in MMPBSA Calculation jitrayut jitonnom (Tue Aug 21 2007 - 02:11:52 CDT)
AMBER: command tleap is not normal Qiang Zhong (Tue Aug 21 2007 - 03:12:44 CDT)
- Re: AMBER: command tleap is not normal Ilyas Yildirim (Tue Aug 21 2007 - 03:50:35 CDT)
AMBER: how to include mpirun in this script Syed Tarique Moin (Tue Aug 21 2007 - 05:50:12 CDT)
- RE: AMBER: how to include mpirun in this script Ross Walker (Tue Aug 21 2007 - 13:45:23 CDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Tue Aug 21 2007 - 07:36:46 CDT)
- Re: AMBER: How to use AMBER Parameter Database ? David A. Case (Thu Aug 23 2007 - 11:53:55 CDT)
AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 11:57:47 CDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 22:33:36 CDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 22:41:23 CDT)
  - Re: AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Wed Aug 22 2007 - 01:53:15 CDT)
AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 14:28:46 CDT)
- Re: AMBER: xLeap "Could not find type" error David A. Case (Tue Aug 21 2007 - 19:40:09 CDT)
  - Re: AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 20:17:44 CDT)
    - Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 10:15:25 CDT)
AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 08:08:38 CDT)
- Re: AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 19:07:32 CDT)
AMBER: Force field for RNA with U-turn motif Cenk Andac (Tue Aug 21 2007 - 08:52:48 CDT)
- Re: AMBER: Force field for RNA with U-turn motif Vlad Cojocaru (Wed Aug 22 2007 - 03:07:24 CDT)
  - Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 11:08:29 CDT)
    - Re: AMBER: Force field for RNA with U-turn motif Jiri Sponer (Wed Aug 22 2007 - 11:33:46 CDT)
    - Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 13:31:04 CDT)
AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong (Tue Aug 21 2007 - 09:06:53 CDT)
AMBER: a question about xleap WANG,YING (Tue Aug 21 2007 - 14:16:48 CDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Wed Aug 22 2007 - 03:53:04 CDT)
- AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal (Wed Aug 22 2007 - 04:48:52 CDT)
  - Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steven Winfield (Wed Aug 22 2007 - 05:12:16 CDT)
AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov (Wed Aug 22 2007 - 08:49:25 CDT)
AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 09:04:37 CDT)
- Re: AMBER: xLeap "Could not find type" error Wei Zhang (Wed Aug 22 2007 - 10:18:11 CDT)
- Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 10:45:02 CDT)
- Re: AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 10:46:58 CDT)
AMBER: Running Gaussian to get .out files Lili Peng (Wed Aug 22 2007 - 15:27:25 CDT)
- RE: AMBER: Running Gaussian to get .out files Steve Spronk (Thu Aug 23 2007 - 08:05:25 CDT)
AMBER: Performance of polarizable model simulations Jones de Andrade (Wed Aug 22 2007 - 23:17:52 CDT)
AMBER: Parse charges for small molecules Neha Gandhi (Wed Aug 22 2007 - 23:50:38 CDT)
AMBER: Ca(2+) parameter Qiang Zhong (Thu Aug 23 2007 - 06:01:24 CDT)
- Re: AMBER: Ca(2+) parameter David A. Case (Thu Aug 23 2007 - 10:04:01 CDT)
[Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield (Thu Aug 23 2007 - 08:31:49 CDT)
AMBER: Unable to open MDCRD file using vmd priya priya (Thu Aug 23 2007 - 10:04:19 CDT)
- RE: AMBER: Unable to open MDCRD file using vmd Ross Walker (Thu Aug 23 2007 - 15:40:27 CDT)
  - AMBER: ow to split MDCRD file using ptraj priya priya (Fri Aug 24 2007 - 02:34:27 CDT)
    - Re: AMBER: ow to split MDCRD file using ptraj Gustavo Seabra (Fri Aug 24 2007 - 21:17:27 CDT)
AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 11:13:51 CDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? Chris Moth (Thu Aug 23 2007 - 12:07:30 CDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 15:53:05 CDT)
  - Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Fri Aug 24 2007 - 21:21:59 CDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Wed Aug 29 2007 - 08:50:30 CDT)
  - Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Wed Aug 29 2007 - 09:53:11 CDT)
AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 23 2007 - 16:04:03 CDT)
- Re: AMBER: Prepin error (?) in xleap David A. Case (Thu Aug 23 2007 - 19:28:29 CDT)
  - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Aug 24 2007 - 14:19:07 CDT)
AMBER: protonation of His residue! Qiang Zhong (Thu Aug 23 2007 - 21:39:51 CDT)
- Re: AMBER: protonation of His residue! jitrayut jitonnom (Thu Aug 23 2007 - 22:52:51 CDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Fri Aug 24 2007 - 03:00:50 CDT)
AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 05:19:30 CDT)
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 08:11:06 CDT)
  - Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 11:01:31 CDT)
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 08:10:54 CDT)
AMBER: SMD simulation Qiang Zhong (Fri Aug 24 2007 - 05:33:41 CDT)
- Re: AMBER: SMD simulation Adrian Roitberg (Fri Aug 24 2007 - 07:43:35 CDT)
- RE: AMBER: SMD simulation Ross Walker (Fri Aug 24 2007 - 08:12:43 CDT)
- Re: AMBER: SMD simulation Qiang Zhong (Sat Aug 25 2007 - 04:49:09 CDT)
- Re: AMBER: SMD simulation Qiang Zhong (Sat Aug 25 2007 - 04:49:09 CDT)
AMBER: NETCDF Geoff Wood (Fri Aug 24 2007 - 05:43:11 CDT)
- Re: AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 07:58:34 CDT)
- AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 08:03:37 CDT)
  - Re: AMBER: NETCDF Geoff Wood (Mon Aug 27 2007 - 02:18:48 CDT)
AMBER: articles Beale, John (Fri Aug 24 2007 - 08:02:05 CDT)
- Re: AMBER: articles Lili Peng (Fri Aug 24 2007 - 14:10:12 CDT)
AMBER: PM6? Thomas Patko (CSULB) (Fri Aug 24 2007 - 08:46:16 CDT)
- RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 11:36:26 CDT)
  - Re: AMBER: PM6? Thomas Patko (Fri Aug 24 2007 - 12:43:35 CDT)
    - RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 15:19:22 CDT)
AMBER: Running Gaussian to get .out files Steve Spronk (Fri Aug 24 2007 - 09:08:13 CDT)
AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sat Aug 25 2007 - 12:54:12 CDT)
- Re: AMBER: SCC convergence failure in QM-MM DFTB Adrian Roitberg (Sat Aug 25 2007 - 13:10:35 CDT)
- Re: AMBER: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 12:20:37 CDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 02:26:42 CDT)
AMBER: personal computer configuration for parallel computing emine cebe (Sun Aug 26 2007 - 06:36:28 CDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 09:34:57 CDT)
- Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB M. L. Dodson (Sun Aug 26 2007 - 10:42:14 CDT)
  - Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 11:28:14 CDT)
Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Mon Aug 27 2007 - 01:24:33 CDT)
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 14:12:23 CDT)
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 15:50:40 CDT)
AMBER: metalloprotein dynamics Sally Pias (Mon Aug 27 2007 - 12:55:51 CDT)
AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky (Mon Aug 27 2007 - 13:41:56 CDT)
- Re: AMBER: generating a .rst file from an .mdcrd file Gustavo Seabra (Mon Aug 27 2007 - 14:15:23 CDT)
AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 14:06:44 CDT)
- Re: AMBER: Add hydrogen and charge calculation Chris Moth (Mon Aug 27 2007 - 15:33:25 CDT)
  - Re: AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 23:07:55 CDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 02:51:30 CDT)
- Re: AMBER: QM/MM in reaction pathways? Gustavo Seabra (Tue Aug 28 2007 - 09:55:20 CDT)
- RE: AMBER: QM/MM in reaction pathways? Ross Walker (Tue Aug 28 2007 - 10:21:40 CDT)
- RE: AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 19:52:21 CDT)
AMBER: protocols for high pressure simulation brmeher_at_iitg.ernet.in (Tue Aug 28 2007 - 10:23:00 CDT)
- Re: AMBER: protocols for high pressure simulation David A. Case (Tue Aug 28 2007 - 10:41:58 CDT)
AMBER: heating up system Francesco Pietra (Tue Aug 28 2007 - 11:16:57 CDT)
- Re: AMBER: heating up system Adrian Roitberg (Tue Aug 28 2007 - 13:45:26 CDT)
AMBER: energy minimization parameter Qiang Zhong (Wed Aug 29 2007 - 02:54:12 CDT)
- Re: AMBER: energy minimization parameter Lorenzo Gontrani (Wed Aug 29 2007 - 02:54:58 CDT)
AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Aug 29 2007 - 05:57:11 CDT)
- Re: AMBER: refinement of NMR struture using AMBER andy ng (Wed Sep 05 2007 - 04:59:00 CDT)
  - Re: AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Sep 05 2007 - 09:01:41 CDT)
AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:51:15 CDT)
- Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 12:11:29 CDT)
  - Re: AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 12:40:36 CDT)
    - Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 13:24:43 CDT)
    - RE: AMBER: Criteria for classical md being OK to move to QM-MM Ross Walker (Wed Aug 29 2007 - 13:40:30 CDT)
- Re: AMBER: Criteria for classical md being OK to move to QM-MM Gustavo Seabra (Wed Aug 29 2007 - 13:13:05 CDT)
AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 01:30:10 CDT)
- AMBER: Dihedrals in Sander Martin Stennett (Thu Aug 30 2007 - 03:36:17 CDT)
  - RE: AMBER: Dihedrals in Sander Steve Spronk (Thu Sep 06 2007 - 14:37:24 CDT)
- Re: AMBER: Schedule for QM-MM with Amber9/Amber10 Gustavo Seabra (Fri Aug 31 2007 - 12:41:18 CDT)
AMBER: RDF unit cell volume BJÖRN KARLSSON (Thu Aug 30 2007 - 03:14:20 CDT)
AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 06:49:07 CDT)
- Re: AMBER: AMBER at WESTGRID Gustavo Seabra (Thu Aug 30 2007 - 07:35:49 CDT)
AMBER: bad atom type:F Emilia Wu (Thu Aug 30 2007 - 07:36:14 CDT)
- Re: AMBER: bad atom type:F David A. Case (Thu Aug 30 2007 - 10:35:00 CDT)
AMBER: Beale, John (Thu Aug 30 2007 - 08:05:11 CDT)
- Re: AMBER: Melinda Layten (Fri Aug 31 2007 - 12:19:21 CDT)
AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 08:17:41 CDT)
AMBER: Connecting two ethanes in LEaP Kliman, Michal (Thu Aug 30 2007 - 15:53:46 CDT)
- Re: AMBER: Connecting two ethanes in LEaP David A. Case (Fri Aug 31 2007 - 11:18:18 CDT)
AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa (Thu Aug 30 2007 - 16:02:20 CDT)
AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 00:32:49 CDT)
- Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 07:40:48 CDT)
  - Re: AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 08:27:38 CDT)
    - Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 09:23:11 CDT)
AMBER: Confusion about Langevin dymamics Hayden Eastwood (Fri Aug 31 2007 - 08:46:28 CDT)
- Re: AMBER: Confusion about Langevin dymamics Carlos Simmerling (Fri Aug 31 2007 - 08:52:02 CDT)
- Re: AMBER: Confusion about Langevin dymamics David A. Case (Fri Aug 31 2007 - 09:53:47 CDT)
  - Re: AMBER: Confusion about Langevin dymamics David Mobley (Fri Aug 31 2007 - 11:05:13 CDT)
AMBER: antechamber question Beale, John (Fri Aug 31 2007 - 09:07:56 CDT)
- Re: AMBER: antechamber question Junmei Wang (Fri Aug 31 2007 - 15:07:09 CDT)
AMBER: Converting AMBER-format force fields for tinker Aaron Virshup (Fri Aug 31 2007 - 14:04:12 CDT)
AMBER: Measuring Bond Angle over simulation Seth Lilavivat (Fri Aug 31 2007 - 14:25:20 CDT)
- Re: AMBER: Measuring Bond Angle over simulation Carlos Simmerling (Fri Aug 31 2007 - 14:34:13 CDT)
AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 15:53:05 CDT)
- Re: AMBER: modified leaprc for glycoproteins David A. Case (Fri Aug 31 2007 - 16:42:03 CDT)
  - RE: AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 20:14:32 CDT)
AMBER: Using ntr=1 in xleap Lili Peng (Fri Aug 31 2007 - 16:27:44 CDT)
- Re: AMBER: Using ntr=1 in xleap David A. Case (Fri Aug 31 2007 - 17:52:13 CDT)
- Re: AMBER: Using ntr=1 in xleap Carlos Simmerling (Fri Aug 31 2007 - 16:49:14 CDT)
  - Re: AMBER: Using ntr=1 in xleap Lili Peng (Tue Sep 04 2007 - 17:23:59 CDT)
AMBER: Solvent in closest contact with solute Francesco Pietra (Sat Sep 01 2007 - 09:15:11 CDT)
AMBER: ntt parameter in vacuum Age.Skjevik_at_student.uib.no (Mon Sep 03 2007 - 08:40:15 CDT)
- Re: AMBER: ntt parameter in vacuum Carlos Simmerling (Mon Sep 03 2007 - 08:53:16 CDT)
- Re: AMBER: ntt parameter in vacuum David A. Case (Mon Sep 03 2007 - 10:51:53 CDT)
AMBER: creating topology files for RNA DNA hybrid.molecule msubhamoy_at_ibab.ac.in (Mon Sep 03 2007 - 18:00:25 CDT)
- Re: AMBER: creating topology files for RNA DNA hybrid.molecule saurabh agrawal (Mon Sep 03 2007 - 23:21:56 CDT)
AMBER: installing LMOD error Xioling Chuang (Tue Sep 04 2007 - 00:52:56 CDT)
- Re: AMBER: installing LMOD error David A. Case (Tue Sep 04 2007 - 10:01:06 CDT)
  - Re: AMBER: installing LMOD error Xioling Chuang (Tue Sep 04 2007 - 21:04:17 CDT)
    - Re: AMBER: installing LMOD error David A. Case (Wed Sep 05 2007 - 00:35:24 CDT)
    - Re: AMBER: installing LMOD error Xioling Chuang (Thu Sep 06 2007 - 22:54:48 CDT)
AMBER: Catein Catherine (Tue Sep 04 2007 - 00:56:20 CDT)
- AMBER: GBSA: NMODE ERROR Catein Catherine (Wed Sep 05 2007 - 05:49:32 CDT)
AMBER: Running mpirun -np 1 on different processors Francesco Pietra (Tue Sep 04 2007 - 08:37:27 CDT)
- Re: AMBER: Running mpirun -np 1 on different processors Adrian Roitberg (Tue Sep 04 2007 - 08:45:11 CDT)
- Re: AMBER: Running mpirun -np 1 on different processors Carlos Simmerling (Tue Sep 04 2007 - 08:47:27 CDT)
  - Re: AMBER: Running mpirun -np 1 on different processors Francesco Pietra (Tue Sep 04 2007 - 09:39:40 CDT)
AMBER: decomposition energy Pankaj R. Daga (Tue Sep 04 2007 - 09:31:25 CDT)
- AMBER: PMF calculation - minimum conformer Catein Catherine (Wed Sep 05 2007 - 05:48:04 CDT)
- RE: AMBER: decomposition energy Catein Catherine (Wed Sep 05 2007 - 05:42:42 CDT)
AMBER: Problem compiling AMBER 9 on ppc64 Eric Shamay (Tue Sep 04 2007 - 11:14:07 CDT)
- Re: AMBER: Problem compiling AMBER 9 on ppc64 David A. Case (Tue Sep 04 2007 - 15:56:06 CDT)
AMBER: Problem with modelling ammonium ion? David Cerutti (Tue Sep 04 2007 - 20:26:22 CDT)
- Re: AMBER: Problem with modelling ammonium ion? David Cerutti (Wed Sep 05 2007 - 00:22:50 CDT)
AMBER: Comparing explicit solvent/vacuum qmmm Francesco Pietra (Wed Sep 05 2007 - 02:31:32 CDT)
AMBER: Fwd: Comparing explicit solvent/vacuum qmmm Francesco Pietra (Wed Sep 05 2007 - 06:05:07 CDT)
AMBER: amber md movie using Chimera Wang, Xuelin (Wed Sep 05 2007 - 12:42:08 CDT)
- Re: AMBER: amber md movie using Chimera Mingfeng Yang (Wed Sep 05 2007 - 13:04:57 CDT)
- Re: AMBER: amber md movie using Chimera David A. Case (Wed Sep 05 2007 - 13:12:27 CDT)
  - RE: AMBER: amber md movie using Chimera. . Wang, Xuelin (Wed Sep 05 2007 - 13:42:02 CDT)
- Re: AMBER: amber md movie using Chimera Bill Ross (Wed Sep 05 2007 - 16:38:32 CDT)
AMBER: chiral surfaces Hector A. Baldoni (Wed Sep 05 2007 - 18:35:42 CDT)
- Re: AMBER: chiral surfaces Carlos Simmerling (Wed Sep 05 2007 - 19:21:51 CDT)
AMBER: RE: Tutorial5 -- sustiva and xleap Ross Walker (Thu Sep 06 2007 - 08:20:08 CDT)
AMBER: DelPhi Urszula Uciechowska (Thu Sep 06 2007 - 08:21:19 CDT)
AMBER: electron density difference Ozlem Demir (Thu Sep 06 2007 - 08:36:29 CDT)
AMBER: Harmonic constraints Johan Qvist (Fri Sep 07 2007 - 09:43:57 CDT)
- Re: AMBER: Harmonic constraints Carlos Simmerling (Fri Sep 07 2007 - 10:31:46 CDT)
  - Re: AMBER: Harmonic constraints Ilyas Yildirim (Fri Sep 07 2007 - 12:13:55 CDT)
- AMBER: for NMR restrains files Wenyong Tong (Fri Sep 07 2007 - 12:26:09 CDT)
  - Re: AMBER: for NMR restrains files Prem Prakash Pathak (Fri Sep 07 2007 - 23:36:11 CDT)
- RE: AMBER: Harmonic constraints Hu, Shaowen (JSC-SK)[USRA] (Mon Sep 10 2007 - 09:05:18 CDT)
  - Re: AMBER: Harmonic constraints Carlos Simmerling (Mon Sep 10 2007 - 09:14:27 CDT)
AMBER: System extending beyond of (non existent) virtual box Francesco Pietra (Fri Sep 07 2007 - 12:17:36 CDT)
AMBER: Fwd: System extending beyond of (non existent) virtual box Francesco Pietra (Sat Sep 08 2007 - 03:33:34 CDT)
AMBER: solvent box pyridine Francesco Pietra (Sat Sep 08 2007 - 09:46:37 CDT)
AMBER: rms and rms nofit Alana Canfield (Sat Sep 08 2007 - 16:23:39 CDT)
AMBER: Targeted MD Beale, John (Sat Sep 08 2007 - 17:29:08 CDT)
- Re: AMBER: Targeted MD Adrian Roitberg (Sat Sep 08 2007 - 17:35:22 CDT)
  - AMBER: Explicit water in implicit enviornment? Hayden Eastwood (Sun Sep 09 2007 - 14:57:26 CDT)
    - Re: AMBER: Explicit water in implicit enviornment? Carlos Simmerling (Mon Sep 17 2007 - 10:35:58 CDT)
AMBER: RE: Asking for help Ross Walker (Mon Sep 10 2007 - 18:31:24 CDT)
AMBER: AMBER parametrization (??) for OAA and Mg++ Eduardo Mendez (Mon Sep 10 2007 - 23:39:43 CDT)
- Re:AMBER: AMBER parametrization (??) for OAA and Mg++ Qiang Zhong (Tue Sep 11 2007 - 02:32:17 CDT)
- Re: AMBER: AMBER parametrization (??) for OAA and Mg++ FyD (Tue Sep 11 2007 - 02:28:46 CDT)
AMBER: heme forcefield atom types john chen (Tue Sep 11 2007 - 09:09:45 CDT)
- Re: AMBER: heme forcefield atom types Vlad Cojocaru (Tue Sep 11 2007 - 10:05:46 CDT)
- Re: AMBER: heme forcefield atom types L. W. Yang (Wed Oct 24 2007 - 11:18:31 CDT)
- RE: AMBER: heme forcefield atom types Yang, Lee-Wei (Wed Oct 24 2007 - 13:41:29 CDT)
AMBER: heme force-field (2) john chen (Tue Sep 11 2007 - 10:08:05 CDT)
- Re: AMBER: heme force-field (2) Vlad Cojocaru (Tue Sep 11 2007 - 10:43:53 CDT)
AMBER: Tutorial protein-small-molecule-associates Francesco Pietra (Tue Sep 11 2007 - 11:26:01 CDT)
- Re: AMBER: Tutorial protein-small-molecule-associates Scott Brozell (Fri Sep 14 2007 - 10:50:09 CDT)
AMBER: PBradii Steve Seibold (Tue Sep 11 2007 - 13:40:00 CDT)
- Re: AMBER: PBradii Carlos Simmerling (Tue Sep 11 2007 - 14:06:32 CDT)
  - RE: AMBER: PBradii Steve Seibold (Tue Sep 11 2007 - 14:21:21 CDT)
AMBER: TIP5P questions Prashanth Athri (Tue Sep 11 2007 - 16:26:56 CDT)
- Re: AMBER: TIP5P questions Thomas Cheatham III (Thu Sep 13 2007 - 14:14:25 CDT)
- Re: AMBER: TIP5P questions David A. Case (Thu Sep 13 2007 - 19:17:12 CDT)
AMBER: Problems with Carbohydrate Non-standard Residue Moruz Luminita (Wed Sep 12 2007 - 05:30:09 CDT)
- Re: AMBER: Problems with Carbohydrate Non-standard Residue David A. Case (Wed Sep 12 2007 - 09:47:48 CDT)
  - AMBER: Complexe Energy Analysis saccenti_at_cerm.unifi.it (Wed Sep 12 2007 - 10:16:07 CDT)
- RE: AMBER: Problems with Carbohydrate Non-standard Residue Irene Newhouse (Wed Sep 12 2007 - 11:58:17 CDT)
AMBER: LINMIN Failure vs Parallelization Sandeep Kaushik (Thu Sep 13 2007 - 02:04:19 CDT)
- Re: AMBER: LINMIN Failure vs Parallelization linfu (Thu Sep 13 2007 - 05:24:10 CDT)
  - Re: AMBER: LINMIN Failure vs Parallelization Gustavo Seabra (Thu Sep 13 2007 - 08:26:45 CDT)
AMBER: Too big EEL energy in energy minimization Wang, Xuelin (Thu Sep 13 2007 - 09:34:27 CDT)
- RE: AMBER: Too big EEL energy in energy minimization Ross Walker (Thu Sep 13 2007 - 09:52:11 CDT)
  - RE: AMBER: Too big EEL energy in energy minimization. . Wang, Xuelin (Thu Sep 13 2007 - 11:00:17 CDT)
    - RE: AMBER: Too big EEL energy in energy minimization. . Ross Walker (Thu Sep 13 2007 - 11:25:07 CDT)
AMBER: Problem with Sander anna duraj (Thu Sep 13 2007 - 17:42:29 CDT)
- Re: AMBER: Problem with Sander Carlos Simmerling (Thu Sep 13 2007 - 18:38:06 CDT)
AMBER: FF02: sander problem with irstdip=1 Anselm Horn (Fri Sep 14 2007 - 05:31:19 CDT)
- Re: AMBER: FF02: sander problem with irstdip=1 David A. Case (Fri Sep 14 2007 - 09:59:26 CDT)
- RE: AMBER: FF02: sander problem with irstdip=1 Yong Duan (Fri Sep 14 2007 - 16:30:17 CDT)
AMBER: parallel implementation of Amber 9 Beale, John (Fri Sep 14 2007 - 07:40:03 CDT)
- Re: AMBER: parallel implementation of Amber 9 David A. Case (Fri Sep 14 2007 - 10:04:16 CDT)
AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA] (Fri Sep 14 2007 - 10:29:46 CDT)
- Re: AMBER: DNA base planarity restraint Carlos Simmerling (Fri Sep 14 2007 - 11:00:22 CDT)
- RE: AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA] (Fri Sep 14 2007 - 13:29:13 CDT)
  - Re: AMBER: DNA base planarity restraint Carlos Simmerling (Fri Sep 14 2007 - 14:43:03 CDT)
AMBER: calcium ion force-fields john chen (Fri Sep 14 2007 - 10:35:29 CDT)
AMBER: xleap question Anna Díaz Cirac (Fri Sep 14 2007 - 11:26:33 CDT)
- Re: AMBER: xleap question Carlos Simmerling (Fri Sep 14 2007 - 11:32:20 CDT)
- Re: AMBER: xleap question Carlos Simmerling (Fri Sep 14 2007 - 11:32:20 CDT)
AMBER: Torsion terms in xleap Lili Peng (Fri Sep 14 2007 - 17:35:23 CDT)
- Re: AMBER: Torsion terms in xleap Carlos Simmerling (Fri Sep 14 2007 - 17:42:52 CDT)
- Re: AMBER: Torsion terms in xleap Wenyong Tong (Fri Sep 14 2007 - 18:00:20 CDT)
- Re: AMBER: Torsion terms in xleap Davide Moiani (Fri Sep 14 2007 - 18:55:37 CDT)
- Re: AMBER: Torsion terms in xleap David A. Case (Fri Sep 14 2007 - 19:44:17 CDT)
  - Re: AMBER: Torsion terms in xleap Lili Peng (Mon Sep 17 2007 - 18:42:12 CDT)
    - Re: AMBER: Torsion terms in xleap David A. Case (Mon Sep 17 2007 - 21:35:24 CDT)
    - Re: AMBER: Torsion terms in xleap Lili Peng (Wed Sep 19 2007 - 13:41:14 CDT)
AMBER: AMBER sander Eduardo Mendez (Fri Sep 14 2007 - 18:42:38 CDT)
- Re: AMBER: AMBER sander David A. Case (Fri Sep 14 2007 - 19:50:47 CDT)
AMBER: Can I set harmonic constraints in SMD simulations ? James W (Fri Sep 14 2007 - 21:50:35 CDT)
- Re: AMBER: Can I set harmonic constraints in SMD simulations ? David A. Case (Sat Sep 15 2007 - 11:59:33 CDT)
AMBER: Problem encountered during thermodynamic integration ming hui (Sat Sep 15 2007 - 03:18:59 CDT)
- Re: AMBER: Problem encountered during thermodynamic integration David A. Case (Sat Sep 15 2007 - 12:02:39 CDT)
  - Re: AMBER: Problem encountered during thermodynamic integration ming hui (Wed Sep 19 2007 - 12:30:14 CDT)
AMBER: Problem with Getting SHAKE to work David Cerutti (Sat Sep 15 2007 - 13:04:14 CDT)
- Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Sat Sep 15 2007 - 22:16:10 CDT)
- Re: AMBER: Problem with Getting SHAKE to work David A. Case (Sun Sep 16 2007 - 00:05:55 CDT)
  - Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Sun Sep 16 2007 - 11:29:38 CDT)
    - Re: AMBER: Problem with Getting SHAKE to work David A. Case (Mon Sep 17 2007 - 11:38:26 CDT)
    - Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Mon Sep 17 2007 - 15:36:59 CDT)
AMBER: replica exchange simulation Ji-Lai Li (Sat Sep 15 2007 - 19:58:06 CDT)
- Re: AMBER: replica exchange simulation Carlos Simmerling (Mon Sep 17 2007 - 09:04:46 CDT)
AMBER: Solvation net forces Tyler Luchko (Mon Sep 17 2007 - 11:23:03 CDT)
- Re: AMBER: Solvation net forces David A. Case (Tue Sep 18 2007 - 19:14:55 CDT)
  - Re: AMBER: Solvation net forces Tyler Luchko (Tue Sep 25 2007 - 14:21:24 CDT)
    - Re: AMBER: Solvation net forces Nicolas Lux Fawzi (Tue Sep 25 2007 - 16:24:05 CDT)
AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Mon Sep 17 2007 - 21:32:22 CDT)
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Mon Sep 17 2007 - 22:16:02 CDT)
  - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Ilyas Yildirim (Mon Sep 17 2007 - 23:38:58 CDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Jiri Sponer (Tue Sep 18 2007 - 03:11:19 CDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Tue Sep 18 2007 - 18:41:33 CDT)
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Tue Sep 18 2007 - 02:06:51 CDT)
AMBER: A question related with periodic boundary condition Jun Liu (Tue Sep 18 2007 - 20:48:22 CDT)
- Re: AMBER: A question related with periodic boundary condition Jun Liu (Wed Sep 19 2007 - 13:10:54 CDT)
AMBER: How to fix the distance between two atoms. nag raj (Tue Sep 18 2007 - 23:36:29 CDT)
AMBER: Targetted MD and ptraj analysis Ilyas Yildirim (Wed Sep 19 2007 - 00:47:19 CDT)
- RE: AMBER: Targetted MD and ptraj analysis Catein Catherine (Thu Sep 20 2007 - 21:11:30 CDT)
  - Re: AMBER: Targetted MD and ptraj analysis Carlos Simmerling (Fri Sep 21 2007 - 07:12:50 CDT)
    - Re: AMBER: Targetted MD and ptraj analysis Ilyas Yildirim (Fri Sep 21 2007 - 14:40:36 CDT)
AMBER: problem with Thermodynamic Integration Martin Stennett (Wed Sep 19 2007 - 06:46:30 CDT)
- Re: AMBER: problem with Thermodynamic Integration Ilyas Yildirim (Wed Sep 19 2007 - 11:45:47 CDT)
AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood (Wed Sep 19 2007 - 09:24:34 CDT)
- Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett (Wed Sep 19 2007 - 11:30:50 CDT)
  - RE: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood (Wed Sep 19 2007 - 12:25:21 CDT)
    - Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett (Wed Sep 19 2007 - 13:16:49 CDT)
AMBER: A question related with periodic boundary condition Jun Liu (Wed Sep 19 2007 - 13:42:25 CDT)
AMBER: RE: AMBER9 Installation Help Ross Walker (Thu Sep 20 2007 - 09:48:12 CDT)
AMBER: Problems loading parameter file in tleap Eduardo Mendez (Fri Sep 21 2007 - 05:58:48 CDT)
- Re: AMBER: Problems loading parameter file in tleap Eddie Men (Fri Sep 21 2007 - 06:27:35 CDT)
- Re: AMBER: Problems loading parameter file in tleap FyD (Fri Sep 21 2007 - 06:55:39 CDT)
AMBER: MM_PBSA with complex plus Ion saccenti_at_cerm.unifi.it (Fri Sep 21 2007 - 09:26:58 CDT)
- Re: AMBER: MM_PBSA with complex plus Ion Pankaj Daga (Sun Sep 23 2007 - 10:50:21 CDT)
AMBER: kanon gemini (Fri Sep 21 2007 - 10:35:11 CDT)
- Re: AMBER: David A. Case (Sun Sep 23 2007 - 20:31:19 CDT)
AMBER: about restraining atoms san_amber roy (Fri Sep 21 2007 - 23:52:59 CDT)
- Re: AMBER: about restraining atoms Carlos Simmerling (Sat Sep 22 2007 - 08:32:52 CDT)
AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sat Sep 22 2007 - 05:40:05 CDT)
- Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling (Sat Sep 22 2007 - 08:27:45 CDT)
  - Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sat Sep 22 2007 - 15:49:26 CDT)
AMBER: Water Question Eddie Men (Sun Sep 23 2007 - 03:09:21 CDT)
AMBER: about MD outputs saccenti_at_cerm.unifi.it (Sun Sep 23 2007 - 06:57:33 CDT)
- Re: AMBER: about MD outputs Carlos Simmerling (Sun Sep 23 2007 - 07:09:03 CDT)
  - Re: AMBER: about MD outputs saccenti_at_cerm.unifi.it (Sun Sep 23 2007 - 07:23:15 CDT)
AMBER: Water question Eddie Men (Sun Sep 23 2007 - 10:21:48 CDT)
- Re: AMBER: Water question David Cerutti (Sun Sep 23 2007 - 14:01:24 CDT)
AMBER: MAXPR san_amber roy (Sun Sep 23 2007 - 23:18:26 CDT)
- RE: AMBER: MAXPR Ross Walker (Mon Sep 24 2007 - 10:30:38 CDT)
  - Re: AMBER: MAXPR san_amber roy (Mon Oct 01 2007 - 03:10:35 CDT)
AMBER: Bertrand P. S. Russell (Mon Sep 24 2007 - 04:40:52 CDT)
AMBER: MacOSX installation help Quantum Mechanics (Mon Sep 24 2007 - 04:39:46 CDT)
- RE: AMBER: MacOSX installation help Ross Walker (Mon Sep 24 2007 - 09:26:35 CDT)
AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation.. cgji (Mon Sep 24 2007 - 08:13:36 CDT)
- AMBER: Help WARNING: The unperturbed charge of the unit saccenti_at_cerm.unifi.it (Mon Sep 24 2007 - 08:32:35 CDT)
  - Re: AMBER: Help WARNING: The unperturbed charge of the unit Ilyas Yildirim (Mon Sep 24 2007 - 16:53:40 CDT)
  - Re: AMBER: Help WARNING: The unperturbed charge of the unit saccenti_at_cerm.unifi.it (Tue Sep 25 2007 - 03:43:03 CDT)
AMBER: calcium parameters Mattia Mori - CERM (Mon Sep 24 2007 - 10:25:20 CDT)
- RE: AMBER: calcium parameters Ross Walker (Mon Sep 24 2007 - 11:04:08 CDT)
AMBER: RE: »Ø¸´£º RE: Asking for help about heating Ross Walker (Mon Sep 24 2007 - 10:52:41 CDT)
AMBER: effective step period for constant pH simulations Lillian chong (Mon Sep 24 2007 - 13:22:50 CDT)
- Re: AMBER: effective step period for constant pH simulations Adrian Roitberg (Mon Sep 24 2007 - 13:31:05 CDT)
AMBER: problem with ptraj Terry Lang (Mon Sep 24 2007 - 17:55:29 CDT)
- Re: AMBER: problem with ptraj Carlos Simmerling (Mon Sep 24 2007 - 19:45:44 CDT)
AMBER: energy calculation gurpreet singh (Tue Sep 25 2007 - 00:54:16 CDT)
- AMBER: Copper and Chlorine parameters Syed Tarique Moin (Tue Sep 25 2007 - 05:39:16 CDT)
- Re: AMBER: energy calculation David A. Case (Tue Sep 25 2007 - 09:51:40 CDT)
AMBER: total energy in sander and nmode mbrut_at_laas.fr (Tue Sep 25 2007 - 07:55:48 CDT)
- Re: AMBER: total energy in sander and nmode David A. Case (Tue Sep 25 2007 - 09:56:49 CDT)
AMBER: atomicfluct Andres Palencia (Tue Sep 25 2007 - 12:45:50 CDT)
AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 13:23:49 CDT)
- Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 13:30:17 CDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 13:55:07 CDT)
    - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 14:08:28 CDT)
    - RE: AMBER: Minimization and MD input files Ross Walker (Tue Sep 25 2007 - 14:23:53 CDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 16:28:32 CDT)
    - Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 17:08:20 CDT)
- Re: AMBER: Minimization and MD input files David A. Case (Tue Sep 25 2007 - 14:27:37 CDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 15:25:19 CDT)
AMBER: Re: using RESP Ilyas Yildirim (Tue Sep 25 2007 - 18:04:52 CDT)
- Re: AMBER: Re: using RESP FyD (Wed Sep 26 2007 - 01:14:58 CDT)
AMBER: regarding energy calculation gurpreet singh (Wed Sep 26 2007 - 00:16:41 CDT)
- Re: AMBER: regarding energy calculation Abi Ghanem josephine (Wed Sep 26 2007 - 04:13:38 CDT)
Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin (Wed Sep 26 2007 - 02:41:59 CDT)
AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Wed Sep 26 2007 - 09:55:45 CDT)
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Carlos Simmerling (Wed Sep 26 2007 - 10:44:29 CDT)
  - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Wed Sep 26 2007 - 11:03:41 CDT)
- RE: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Ross Walker (Wed Sep 26 2007 - 10:51:10 CDT)
  - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Fri Oct 05 2007 - 07:44:50 CDT)
    - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Gustavo Seabra (Fri Oct 05 2007 - 22:48:59 CDT)
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Harianto Tjong (Wed Sep 26 2007 - 11:23:14 CDT)
  - AMBER: NMR refinement Wenyong Tong (Wed Sep 26 2007 - 16:38:46 CDT)
AMBER: Solvation Issues Eddie Men (Wed Sep 26 2007 - 17:48:21 CDT)
- Re: AMBER: Solvation Issues David A. Case (Wed Sep 26 2007 - 18:16:58 CDT)
  - Re: AMBER: Solvation Issues David Cerutti (Wed Sep 26 2007 - 18:53:11 CDT)
    - Re: AMBER: Solvation Issues Eddie Men (Sat Sep 29 2007 - 01:31:26 CDT)
    - Re: AMBER: Solvation Issues David Cerutti (Sat Sep 29 2007 - 22:55:43 CDT)
AMBER: solvation issues Eddie Men (Wed Sep 26 2007 - 18:19:47 CDT)
Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin (Wed Sep 26 2007 - 22:21:31 CDT)
AMBER: Reproducing constant pH results !! Pradipta Bandyopadhyay (Thu Sep 27 2007 - 00:16:49 CDT)
AMBER: force field question Eddie Men (Thu Sep 27 2007 - 02:31:42 CDT)
- Re: AMBER: force field question David A. Case (Thu Sep 27 2007 - 10:45:38 CDT)
AMBER: needing more detailed knowledge of tautp than the manual ¹¬Î¬±ó (Thu Sep 27 2007 - 07:13:20 CDT)
- Re: AMBER: needing more detailed knowledge of tautp than the manual David A. Case (Thu Sep 27 2007 - 10:49:37 CDT)
AMBER: plotdat: Amber Data Plotting Program S. Ravichandran (Thu Sep 27 2007 - 09:33:37 CDT)
AMBER: restarting REMD simulations Austin B. Yongye (Thu Sep 27 2007 - 09:21:43 CDT)
- Re: AMBER: restarting REMD simulations Carlos Simmerling (Thu Sep 27 2007 - 11:48:45 CDT)
AMBER: step-by-ste weight changes of dwt -- patch? Douglas Kojetin (Thu Sep 27 2007 - 10:35:01 CDT)
- Re: AMBER: step-by-ste weight changes of dwt -- patch? David A. Case (Thu Sep 27 2007 - 14:04:20 CDT)
»Ø¸´:Re: AMBER: needing more detailed knowledge of tautp than the manual ¹¬Î¬±ó (Thu Sep 27 2007 - 21:07:09 CDT)
AMBER: implicit minimization Dr. Devanathan Raghunathan (Thu Sep 27 2007 - 21:21:14 CDT)
- Re: AMBER: implicit minimization David A. Case (Fri Sep 28 2007 - 10:17:16 CDT)
AMBER: the box vectors for a Leap generated truncated octahedron Vlad Cojocaru (Fri Sep 28 2007 - 03:48:33 CDT)
AMBER: cyclohexane and decalin on amber Jones de Andrade (Sat Sep 29 2007 - 10:26:02 CDT)
- Re: AMBER: cyclohexane and decalin on amber FyD (Sun Sep 30 2007 - 02:20:29 CDT)
  - Re: AMBER: cyclohexane and decalin on amber Jones de Andrade (Mon Oct 01 2007 - 00:46:44 CDT)
    - Re: AMBER: cyclohexane and decalin on amber FyD (Mon Oct 01 2007 - 02:20:29 CDT)
    - Re: AMBER: cyclohexane and decalin on amber Jones de Andrade (Tue Oct 02 2007 - 22:12:48 CDT)
AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía (Sat Sep 29 2007 - 13:53:05 CDT)
- Re: AMBER: fragment parametrization tutorial? Carlos Simmerling (Sat Sep 29 2007 - 16:48:30 CDT)
  - Re: AMBER: fragment parametrization tutorial? David A. Case (Sun Sep 30 2007 - 00:04:16 CDT)
    - Re: AMBER: fragment parametrization tutorial? FyD (Sun Sep 30 2007 - 02:12:41 CDT)
    - Re: AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía (Sun Sep 30 2007 - 05:37:56 CDT)
AMBER: regarding non bonded energy caculations gurpreet singh (Mon Oct 01 2007 - 00:41:47 CDT)
- Re: AMBER: regarding non bonded energy caculations David A. Case (Mon Oct 01 2007 - 09:46:00 CDT)
AMBER: atomicfluct Andres Palencia (Mon Oct 01 2007 - 13:12:20 CDT)
AMBER: dihedrals Ed Pate (Mon Oct 01 2007 - 18:07:47 CDT)
- Re: AMBER: dihedrals FyD (Tue Oct 02 2007 - 01:36:30 CDT)
- Re: AMBER: dihedrals Carlos Simmerling (Tue Oct 02 2007 - 05:13:12 CDT)
AMBER: Constant pH Eddie Men (Tue Oct 02 2007 - 04:41:31 CDT)
AMBER: constant pH Eddie Men (Tue Oct 02 2007 - 04:45:34 CDT)
AMBER: multichain simulations priya priya (Tue Oct 02 2007 - 04:31:26 CDT)
AMBER: multichain simulations priya priya (Tue Oct 02 2007 - 04:31:26 CDT)
AMBER: Problems with cpin file Eddie Men (Tue Oct 02 2007 - 07:47:50 CDT)
- Re: AMBER: Problems with cpin file David A. Case (Tue Oct 02 2007 - 10:16:45 CDT)
  - Re: AMBER: Problems with cpin file Eddie Men (Thu Oct 04 2007 - 00:07:11 CDT)
  - Re: AMBER: Problems with cpin file Eddie Men (Thu Oct 04 2007 - 15:46:22 CDT)
    - Re: AMBER: Problems with cpin file Eduardo Mendez (Thu Oct 04 2007 - 16:11:06 CDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Tue Oct 02 2007 - 21:00:07 CDT)
AMBER: parameterization for copper Syed Tarique Moin (Wed Oct 03 2007 - 05:45:33 CDT)
AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 11:58:03 CDT)
- Re: AMBER: 31 integers in the first section of a prmtop file Carlos Simmerling (Wed Oct 03 2007 - 12:15:14 CDT)
- RE: AMBER: 31 integers in the first section of a prmtop file Ross Walker (Wed Oct 03 2007 - 12:32:12 CDT)
  - RE: AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 13:47:42 CDT)
    - Re: AMBER: 31 integers in the first section of a prmtop file Carlos Simmerling (Wed Oct 03 2007 - 13:54:22 CDT)
    - Re: AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 15:04:35 CDT)
AMBER: PBSA generate snapshots saccenti_at_cerm.unifi.it (Thu Oct 04 2007 - 04:17:04 CDT)
AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 05:30:27 CDT)
- Re: AMBER: multi chain simulations Carlos Simmerling (Thu Oct 04 2007 - 05:35:22 CDT)
  - Re: AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 06:07:44 CDT)
AMBER: binary restart file Myunggi Yi (Thu Oct 04 2007 - 09:49:28 CDT)
- Re: AMBER: binary restart file Gustavo Seabra (Fri Oct 05 2007 - 22:56:02 CDT)
  - Re: AMBER: binary restart file Myunggi Yi (Sun Oct 07 2007 - 18:39:44 CDT)
AMBER: Problems with 'make' Hopkins, Robert (Thu Oct 04 2007 - 14:07:42 CDT)
- RE: AMBER: Problems with 'make' Ross Walker (Thu Oct 04 2007 - 15:55:25 CDT)
  - RE: AMBER: Problems with 'make' Hopkins, Robert (Fri Oct 05 2007 - 13:32:24 CDT)
    - RE: AMBER: Problems with 'make' Ross Walker (Fri Oct 05 2007 - 15:14:20 CDT)
AMBER: Applying bugfixes in Amber Lili Peng (Thu Oct 04 2007 - 16:28:29 CDT)
- RE: AMBER: Applying bugfixes in Amber Ross Walker (Thu Oct 04 2007 - 16:53:31 CDT)
AMBER: generating topology files for PBSA saccenti_at_cerm.unifi.it (Fri Oct 05 2007 - 04:46:14 CDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven_at_biomed.uib.no (Sat Oct 06 2007 - 06:35:03 CDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Sat Oct 06 2007 - 08:20:16 CDT)
- RE: AMBER: PMEMD configuration and scaling Ross Walker (Sat Oct 06 2007 - 11:27:16 CDT)
AMBER: request for hardware recommendations Parish, Carol (Sat Oct 06 2007 - 10:59:01 CDT)
- Re: AMBER: request for hardware recommendations Carlos Simmerling (Sat Oct 06 2007 - 12:00:13 CDT)
  - RE: AMBER: request for hardware recommendations Parish, Carol (Sat Oct 06 2007 - 12:20:13 CDT)
  - Re: AMBER: request for hardware recommendations Andy Purkiss (Sat Oct 06 2007 - 12:53:23 CDT)
AMBER: hey Eduardo Mendez (Sun Oct 07 2007 - 00:19:36 CDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven_at_biomed.uib.no (Sun Oct 07 2007 - 05:40:00 CDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Sun Oct 07 2007 - 10:04:03 CDT)
AMBER: Resp: "Statistics of the Fitting" Jones de Andrade (Sun Oct 07 2007 - 13:40:04 CDT)
- Re: AMBER: Resp: "Statistics of the Fitting" FyD (Tue Oct 09 2007 - 23:53:05 CDT)
  - Re: AMBER: Resp: "Statistics of the Fitting" Jones de Andrade (Wed Oct 10 2007 - 11:05:09 CDT)
AMBER: regrading interaction energy calculations gurpreet singh (Sun Oct 07 2007 - 23:52:23 CDT)
AMBER: Problems compiling Amber9 on IBM-AIX Sampath Koppole (Mon Oct 08 2007 - 06:42:20 CDT)
- RE: AMBER: Problems compiling Amber9 on IBM-AIX Ross Walker (Mon Oct 08 2007 - 09:39:08 CDT)
AMBER: entropy with ptraj Marius Retegan (Mon Oct 08 2007 - 07:24:36 CDT)
- Re: AMBER: entropy with ptraj David A. Case (Mon Oct 08 2007 - 08:47:57 CDT)
AMBER: adding extra points to amber - how to? Jones de Andrade (Mon Oct 08 2007 - 11:44:42 CDT)
AMBER: RE: Amber query !! Ross Walker (Mon Oct 08 2007 - 12:02:36 CDT)
AMBER: Amber9 installation error on Mandriva 2007 linux Joe Nolan (Mon Oct 08 2007 - 12:07:58 CDT)
- Re: AMBER: Amber9 installation error on Mandriva 2007 linux Mark Williamson (Mon Oct 08 2007 - 12:31:39 CDT)
AMBER: Quick QUESTION Eddie Men (Mon Oct 08 2007 - 23:23:49 CDT)
- Re: AMBER: Quick QUESTION Eddie Men (Tue Oct 09 2007 - 00:02:10 CDT)
AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? David Cerutti (Tue Oct 09 2007 - 00:25:43 CDT)
- Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? Steven Winfield (Tue Oct 09 2007 - 05:06:53 CDT)
- Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? David A. Case (Tue Oct 09 2007 - 09:09:02 CDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven_at_biomed.uib.no (Tue Oct 09 2007 - 05:05:37 CDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Tue Oct 09 2007 - 08:15:34 CDT)
  - Re: AMBER: PMEMD configuration and scaling Lars Skjærven (Tue Oct 09 2007 - 08:56:09 CDT)
AMBER: RE: antechamber Ross Walker (Tue Oct 09 2007 - 11:51:57 CDT)
AMBER: interaction energy calculations gurpreet singh (Tue Oct 09 2007 - 12:06:24 CDT)
- Re: AMBER: interaction energy calculations Scott Pendley (Tue Oct 09 2007 - 15:51:25 CDT)
AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 16:09:50 CDT)
- Re: AMBER: neb for path between binding sites Carlos Simmerling (Tue Oct 09 2007 - 16:25:27 CDT)
- Re: AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 18:35:19 CDT)
- Re: AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 18:37:20 CDT)
AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Tue Oct 09 2007 - 16:38:03 CDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent Thomas Steinbrecher (Tue Oct 09 2007 - 19:12:13 CDT)
  - Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Tue Oct 09 2007 - 20:09:14 CDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent David A. Case (Tue Oct 09 2007 - 21:36:38 CDT)
  - Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Wed Oct 10 2007 - 17:39:12 CDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Wed Oct 10 2007 - 17:38:20 CDT)
AMBER: error in modified PNA -DNA simulation.. Sharad gupta (Wed Oct 10 2007 - 05:39:07 CDT)
- Re: AMBER: error in modified PNA -DNA simulation.. Scott Brozell (Thu Oct 11 2007 - 19:26:11 CDT)
AMBER: ff99SB and the N- and C- charged terminal residues Nicolas Lux Fawzi (Wed Oct 10 2007 - 11:03:09 CDT)
- Re: AMBER: ff99SB and the N- and C- charged terminal residues Carlos Simmerling (Wed Oct 10 2007 - 12:37:13 CDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Wed Oct 10 2007 - 12:44:53 CDT)
AMBER: constant-pH MD with replica exchange Maciej Dlugosz (Thu Oct 11 2007 - 01:38:49 CDT)
- Re: AMBER: constant-pH MD with replica exchange Adrian Roitberg (Thu Oct 11 2007 - 10:33:30 CDT)
  - Re: AMBER: constant-pH MD with replica exchange Carlos Simmerling (Thu Oct 11 2007 - 13:30:34 CDT)
    - Re: AMBER: constant-pH MD with replica exchange Adrian Roitberg (Thu Oct 11 2007 - 13:55:18 CDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 02:28:25 CDT)
AMBER: BOMB! Eddie Men (Thu Oct 11 2007 - 05:12:49 CDT)
- Re: AMBER: BOMB! Scott Brozell (Thu Oct 11 2007 - 18:59:50 CDT)
AMBER: lipid bilayer san_amber roy (Thu Oct 11 2007 - 06:52:42 CDT)
- Re: AMBER: lipid bilayer Vlad Cojocaru (Thu Oct 11 2007 - 07:09:23 CDT)
- Re: AMBER: lipid bilayer cgji (Thu Oct 11 2007 - 09:38:45 CDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 10:01:23 CDT)
- Re: AMBER: Error- MM_PBSA calculation Scott Pendley (Thu Oct 11 2007 - 16:56:43 CDT)
AMBER: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 17:00:00 CDT)
AMBER: Please Disregard My Last E-mail: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 18:04:11 CDT)
AMBER: error in modified PNA DNA simulation Sharad gupta (Mon Oct 15 2007 - 00:35:13 CDT)
AMBER: anal calculatons gurpreet singh (Mon Oct 15 2007 - 02:19:33 CDT)
- Re: AMBER: anal calculatons Eddie Men (Mon Oct 15 2007 - 02:43:02 CDT)
  - Re: AMBER: anal calculatons gurpreet singh (Mon Oct 15 2007 - 23:17:47 CDT)
    - Re: Re: AMBER: anal calculatons cgji (Tue Oct 16 2007 - 00:48:09 CDT)
AMBER: RED III Age.Skjevik_at_student.uib.no (Mon Oct 15 2007 - 05:06:49 CDT)
- Re: AMBER: RED III FyD (Mon Oct 15 2007 - 05:20:47 CDT)
AMBER: using amber for cyclic peptides rebeca_at_mmb.pcb.ub.es (Mon Oct 15 2007 - 12:23:50 CDT)
- Re: AMBER: using amber for cyclic peptides FyD (Mon Oct 15 2007 - 12:53:54 CDT)
AMBER: Water cap MD error Rima Chaudhuri (Mon Oct 15 2007 - 17:17:07 CDT)
AMBER: MM_PBSA calcultion- help me varsha rani (Tue Oct 16 2007 - 00:53:14 CDT)
- Re: AMBER: MM_PBSA calcultion- help me S.Sundar Raman (Tue Oct 16 2007 - 08:58:50 CDT)
- Re: AMBER: MM_PBSA calcultion- help me Scott Pendley (Tue Oct 16 2007 - 12:24:34 CDT)
  - Re: AMBER: MM_PBSA calcultion- help me varsha rani (Wed Oct 17 2007 - 00:40:48 CDT)
    - AMBER: How to intergrate the area under a curve. Catein Catherine (Mon Oct 22 2007 - 01:34:16 CDT)
    - Re: AMBER: How to intergrate the area under a curve. Ilyas Yildirim (Mon Oct 22 2007 - 02:17:07 CDT)
AMBER: Test fails in Parallel version Amber9 gong wb (Tue Oct 16 2007 - 01:42:45 CDT)
- Re: AMBER: Test fails in Parallel version Amber9 Scott Brozell (Tue Oct 16 2007 - 13:35:24 CDT)
  - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Wed Oct 17 2007 - 02:54:30 CDT)
  - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Wed Oct 17 2007 - 03:04:13 CDT)
AMBER: amber9 installation problem Madjid Taghdir (Tue Oct 16 2007 - 03:46:05 CDT)
- Re: AMBER: amber9 installation problem Scott Brozell (Tue Oct 16 2007 - 12:15:04 CDT)
- Re: AMBER: amber9 installation problem Madjid Taghdir (Mon Nov 12 2007 - 02:38:57 CST)
AMBER: anal calculation error gurpreet singh (Tue Oct 16 2007 - 12:07:20 CDT)
AMBER: AMBER 9 - Force Field Options - Question dpandit_at_brandeis.edu (Tue Oct 16 2007 - 15:41:33 CDT)
- Re: AMBER: AMBER 9 - Force Field Options - Question Carlos Simmerling (Wed Oct 17 2007 - 08:54:51 CDT)
- Re: AMBER: AMBER 9 - Force Field Options - Question WANG,YING (Wed Oct 17 2007 - 10:47:05 CDT)
  - RE: AMBER: AMBER 9 - Force Field Options - Question Yong Duan (Wed Oct 17 2007 - 11:25:16 CDT)
- RE: AMBER: AMBER 9 - Force Field Options - Question WANG,YING (Wed Oct 17 2007 - 14:11:19 CDT)
AMBER: anal error gurpreet singh (Wed Oct 17 2007 - 13:14:52 CDT)
AMBER: error while Running TMD gurpreet singh (Wed Oct 17 2007 - 13:21:18 CDT)
- Re: AMBER: error while Running TMD Carlos Simmerling (Wed Oct 17 2007 - 13:50:45 CDT)
  - Re: AMBER: error while Running TMD gurpreet singh (Wed Oct 17 2007 - 23:19:54 CDT)
    - Re: AMBER: error while Running TMD Carlos Simmerling (Thu Oct 18 2007 - 05:01:07 CDT)
AMBER: Temperature fluctuation in NPT and NVE ensemble Lei Jia (Wed Oct 17 2007 - 18:46:29 CDT)
- Re: AMBER: Temperature fluctuation in NPT and NVE ensemble Robert Duke (Wed Oct 17 2007 - 20:44:47 CDT)
AMBER: anal gurpreet singh (Wed Oct 17 2007 - 23:35:23 CDT)
AMBER: how to simulate a ligand bound to a residue Jena M (Thu Oct 18 2007 - 08:49:55 CDT)
- Re: AMBER: how to simulate a ligand bound to a residue Thomas Steinbrecher (Thu Oct 18 2007 - 13:29:25 CDT)
- Re: AMBER: how to simulate a ligand bound to a residue FyD (Thu Oct 18 2007 - 16:02:13 CDT)
AMBER: Simulation died due to lack of disk space Samantha Kaye (Thu Oct 18 2007 - 08:57:57 CDT)
- RE: AMBER: Simulation died due to lack of disk space Ross Walker (Thu Oct 18 2007 - 09:53:50 CDT)
- RE: AMBER: Simulation died due to lack of disk space Bill Ross (Thu Oct 18 2007 - 14:00:33 CDT)
  - AMBER: Energy calculations. Karen Callahan (Thu Oct 18 2007 - 14:15:29 CDT)
  - Re: AMBER: Simulation died due to lack of disk space Samantha Kaye (Fri Oct 19 2007 - 04:23:33 CDT)
    - RE: AMBER: Simulation died due to lack of disk space Ross Walker (Fri Oct 19 2007 - 11:25:20 CDT)
    - Re: AMBER: Simulation died due to lack of disk space Robert Duke (Fri Oct 19 2007 - 12:25:21 CDT)
- Re: AMBER: Simulation died due to lack of disk space Bill Ross (Fri Oct 19 2007 - 10:59:31 CDT)
AMBER: Backbone flexibility/entropy Seth Lilavivat (Thu Oct 18 2007 - 16:47:37 CDT)
AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander Jiapu.Zhang_at_csiro.au (Thu Oct 18 2007 - 18:15:05 CDT)
- Re: AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander Thomas Steinbrecher (Thu Oct 18 2007 - 18:43:47 CDT)
AMBER: subroutine ephi !! Sampath Koppole (Fri Oct 19 2007 - 03:08:26 CDT)
- Re: AMBER: subroutine ephi !! Tom Darden (Fri Oct 19 2007 - 07:06:33 CDT)
AMBER: mm_pbsa: missing values in ras-raf tutorials merc mertens (Fri Oct 19 2007 - 03:28:09 CDT)
AMBER: Abnormality in MM-PBSA result msubhamoy_at_ibab.ac.in (Fri Oct 19 2007 - 10:01:16 CDT)
- Re: AMBER: Abnormality in MM-PBSA result Thomas Cheatham III (Fri Oct 19 2007 - 10:56:36 CDT)
AMBER: How to use loadpdbusingseq command to load branched structure? Siang Yip (Fri Oct 19 2007 - 12:21:36 CDT)
AMBER: question about h bond WANG,YING (Fri Oct 19 2007 - 19:19:36 CDT)
- RE: AMBER: question about h bond Yong Duan (Fri Oct 19 2007 - 19:41:19 CDT)
- RE: AMBER: question about h bond WANG,YING (Fri Oct 19 2007 - 23:07:49 CDT)
AMBER: Heat capacity calculations not coming out right David Cerutti (Fri Oct 19 2007 - 21:37:38 CDT)
- AMBER: Addendum: Heat capacity calculations not coming out right David Cerutti (Fri Oct 19 2007 - 22:31:46 CDT)
  - Re: AMBER: Addendum: Heat capacity calculations not coming out right Robert Duke (Fri Oct 19 2007 - 23:24:30 CDT)
    - AMBER: Interactive Molecular Dynamics with Amber? Marc Baaden (Sat Oct 20 2007 - 17:10:23 CDT)
    - Re: AMBER: Addendum: Heat capacity calculations not coming out right David Cerutti (Sat Oct 20 2007 - 17:47:05 CDT)
  - AMBER: Solved: Heat capacity calculations not coming out right David Cerutti (Mon Oct 22 2007 - 13:01:32 CDT)
AMBER: EVB Calculations Jimmy Heimdal (Mon Oct 22 2007 - 01:30:48 CDT)
AMBER: Problems loading pdb file including Mg ions Idan Gabdank (Mon Oct 22 2007 - 10:53:12 CDT)
- Re: AMBER: Problems loading pdb file including Mg ions Peter Varnai (Tue Oct 23 2007 - 05:38:53 CDT)
  - Re: AMBER: Problems loading pdb file including Mg ions Idan Gabdank (Wed Oct 24 2007 - 08:05:46 CDT)
- Re: AMBER: Problems loading pdb file including Mg ions Bill Ross (Wed Oct 24 2007 - 12:21:43 CDT)
AMBER: results from TI Holly Freedman (Mon Oct 22 2007 - 11:42:26 CDT)
- Re: AMBER: results from TI Thomas Steinbrecher (Mon Oct 22 2007 - 12:35:15 CDT)
- Re: AMBER: results from TI Holly Freedman (Mon Oct 22 2007 - 14:03:20 CDT)
  - Re: AMBER: results from TI David Mobley (Tue Oct 23 2007 - 08:40:26 CDT)
- Re: AMBER: results from TI Holly Freedman (Tue Oct 23 2007 - 11:57:42 CDT)
  - Re: AMBER: results from TI David Mobley (Tue Oct 23 2007 - 12:09:31 CDT)
    - Re: AMBER: results from TI Thomas Steinbrecher (Tue Oct 23 2007 - 13:07:30 CDT)
- Re: AMBER: results from TI Holly Freedman (Tue Oct 23 2007 - 15:29:00 CDT)
  - Re: AMBER: results from TI Thomas Steinbrecher (Tue Oct 23 2007 - 16:25:24 CDT)
    - Re: AMBER: results from TI David Mobley (Wed Oct 24 2007 - 09:18:50 CDT)
AMBER: SASA per residue Evan Kelly (Mon Oct 22 2007 - 11:59:26 CDT)
AMBER: question about charge of prmtop file WANG,YING (Tue Oct 23 2007 - 09:11:22 CDT)
- Re: AMBER: question about charge of prmtop file Thomas Steinbrecher (Tue Oct 23 2007 - 10:41:09 CDT)
- Re: AMBER: question about charge of prmtop file WANG,YING (Tue Oct 23 2007 - 11:08:15 CDT)
  - RE: AMBER: question about charge of prmtop file Steve Spronk (Wed Oct 24 2007 - 09:21:25 CDT)
- RE: AMBER: question about charge of prmtop file WANG,YING (Wed Oct 24 2007 - 09:44:20 CDT)
AMBER: Beowulf cluster from PSSC Labs Aaron Greenwood (Tue Oct 23 2007 - 11:22:33 CDT)
- RE: AMBER: Beowulf cluster from PSSC Labs Ross Walker (Tue Oct 23 2007 - 12:28:29 CDT)
AMBER: Portland Group vs. Intel Compilers. Aaron Greenwood (Tue Oct 23 2007 - 12:03:43 CDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Alexandar T Tzanov (Tue Oct 23 2007 - 12:11:46 CDT)
  - RE: AMBER: Portland Group vs. Intel Compilers. Ross Walker (Tue Oct 23 2007 - 12:35:45 CDT)
    - Re: RE: AMBER: Portland Group vs. Intel Compilers. Alexandar T Tzanov (Tue Oct 23 2007 - 13:35:25 CDT)
    - RE: RE: AMBER: Portland Group vs. Intel Compilers. Ross Walker (Tue Oct 23 2007 - 14:02:42 CDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Robert Duke (Tue Oct 23 2007 - 12:46:52 CDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Andreas Svrcek-Seiler (Tue Oct 23 2007 - 15:24:29 CDT)
AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 12:52:24 CDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 14:09:09 CDT)
  - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 14:31:02 CDT)
  - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 18:35:26 CDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Thu Oct 25 2007 - 08:15:52 CDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Fri Oct 26 2007 - 07:45:10 CDT)
  - AMBER: Umbrella sampling Jena M (Fri Oct 26 2007 - 08:48:26 CDT)
    - Re: AMBER: Umbrella sampling Adrian Roitberg (Fri Oct 26 2007 - 09:11:14 CDT)
    - Re: AMBER: Umbrella sampling Jerome.GOLEBIOWSKI_at_unice.fr (Fri Oct 26 2007 - 12:08:09 CDT)
AMBER: regarding anal calculations gurpreet singh (Wed Oct 24 2007 - 13:50:49 CDT)
AMBER: hbond analysis output Claire Zerafa (Wed Oct 24 2007 - 14:21:02 CDT)
- RE: AMBER: hbond analysis output Steve Spronk (Thu Oct 25 2007 - 08:10:05 CDT)
AMBER: Pre-requisites for AMBER software Anamika Awasthi (Thu Oct 25 2007 - 07:05:19 CDT)
AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Thu Oct 25 2007 - 08:11:48 CDT)
- RE: AMBER: &dipole input and some questions on using polarizable force fields Ross Walker (Fri Oct 26 2007 - 11:28:57 CDT)
  - Re: AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Sat Oct 27 2007 - 00:03:36 CDT)
AMBER: problems compiling amber on mac OSX francesco zonta (Thu Oct 25 2007 - 08:50:04 CDT)
- Re: AMBER: problems compiling amber on mac OSX David A. Case (Fri Oct 26 2007 - 10:48:35 CDT)
- Re: AMBER: problems compiling amber on mac OSX Mengjuei Hsieh (Sat Oct 27 2007 - 04:31:04 CDT)
  - Re: AMBER: problems compiling amber on mac OSX francesco zonta (Sat Oct 27 2007 - 07:03:51 CDT)
    - Re: AMBER: problems compiling amber on mac OSX Mengjuei Hsieh (Sat Oct 27 2007 - 14:41:26 CDT)
AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Yang, Lee-Wei (Thu Oct 25 2007 - 09:46:00 CDT)
- RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Ray Luo (Thu Oct 25 2007 - 13:20:14 CDT)
  - RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Yang, Lee-Wei (Fri Oct 26 2007 - 00:52:56 CDT)
    - Re: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Ray Luo (Fri Oct 26 2007 - 12:31:03 CDT)
AMBER: ANGVE/TORAVE Abi Ghanem josephine (Thu Oct 25 2007 - 10:58:11 CDT)
- Re: AMBER: ANGVE/TORAVE Kyle Brown (Thu Oct 25 2007 - 13:33:52 CDT)
AMBER: HG atoms in CYX residues francesco zonta (Fri Oct 26 2007 - 04:45:32 CDT)
- Re: AMBER: HG atoms in CYX residues Carlos Simmerling (Fri Oct 26 2007 - 05:20:05 CDT)
- Re: AMBER: HG atoms in CYX residues David A. Case (Fri Oct 26 2007 - 10:28:36 CDT)
AMBER: Heme and CYS !! Pradipta Bandyopadhyay (Fri Oct 26 2007 - 05:49:47 CDT)
AMBER: segmentation fault occured doing MD priya priya (Fri Oct 26 2007 - 06:51:31 CDT)
- Re: AMBER: segmentation fault occured doing MD David A. Case (Fri Oct 26 2007 - 10:32:07 CDT)
AMBER: RE: about deoxy- and oxy- heme Yang, Lee-Wei (Sun Oct 28 2007 - 02:52:58 CST)
AMBER: How can i calculate generalized order parameters using ptraj. cgji (Sun Oct 28 2007 - 08:59:37 CST)
- Re: AMBER: How can i calculate generalized order parameters using ptraj. David A. Case (Thu Nov 08 2007 - 20:23:34 CST)
AMBER: replica exchange Geoff Wood (Sun Oct 28 2007 - 10:29:42 CST)
- Re: AMBER: replica exchange Robert Duke (Sun Oct 28 2007 - 10:38:04 CST)
- Re: AMBER: replica exchange Carlos Simmerling (Sun Oct 28 2007 - 10:38:15 CST)
AMBER: Amber FF parameters for the Zinc-hydroxammate interaction snoze pa (Sun Oct 28 2007 - 18:59:26 CST)
AMBER: calculation of angle between helices Anupam Nath Jha (Mon Oct 29 2007 - 00:06:37 CST)
AMBER: The number of the path atoms exceeds MAXPATHATOMNUM VANIA MARIA AMARO CALISTO (Mon Oct 29 2007 - 06:13:01 CST)
AMBER: RED-vIII fails Jesper Soerensen (Mon Oct 29 2007 - 08:51:56 CST)
- Re: AMBER: RED-vIII fails FyD (Mon Oct 29 2007 - 10:25:09 CST)
  - Re: AMBER: RED-vIII fails Jesper Soerensen (Tue Oct 30 2007 - 03:16:36 CST)
AMBER: Getting prmtop and inpcrd Francesco Pietra (Mon Oct 29 2007 - 09:43:44 CST)
- Re: AMBER: Getting prmtop and inpcrd Carlos Simmerling (Mon Oct 29 2007 - 09:47:33 CST)
  - Re: AMBER: Getting prmtop and inpcrd Francesco Pietra (Mon Oct 29 2007 - 10:51:23 CST)
AMBER: amber with periodic condition Mattia Mori - CERM (Mon Oct 29 2007 - 11:16:14 CST)
Re: AMBER: Getting prmtop and inpcrd Bill Ross (Mon Oct 29 2007 - 13:26:16 CST)
AMBER: mdfil: Error unknown flag: -p4pg Aaron Greenwood (Mon Oct 29 2007 - 13:38:44 CST)
- Re: AMBER: mdfil: Error unknown flag: -p4pg David A. Case (Mon Oct 29 2007 - 20:46:01 CST)
  - Re: AMBER: mdfil: Error unknown flag: -p4pg Aaron Greenwood (Tue Oct 30 2007 - 06:03:29 CST)
AMBER: AMBER 8: QMMM - molecule fluctuates wildly Seth Lilavivat (Mon Oct 29 2007 - 14:40:06 CST)
- RE: AMBER: AMBER 8: QMMM - molecule fluctuates wildly Ross Walker (Mon Oct 29 2007 - 15:06:45 CST)
AMBER: AMBER 8: QMMM - molecule fluctuates wildly Seth Lilavivat (Mon Oct 29 2007 - 14:40:06 CST)
AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 15:02:10 CST)
- Re: AMBER: Amber9 parallel installation error (with openMPI) Wei Zhang (Mon Oct 29 2007 - 15:16:45 CST)
  - Re: AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 15:55:43 CST)
    - Re: AMBER: Amber9 parallel installation error (with openMPI) Wei Zhang (Mon Oct 29 2007 - 16:16:49 CST)
    - Re: AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 16:30:25 CST)
AMBER: Amber 9 source code permissions (UNCLASSIFIED) Monaghan, Martin (Cont, ARL/CISD) (Mon Oct 29 2007 - 15:30:30 CST)
- RE: AMBER: Amber 9 source code permissions (UNCLASSIFIED) Ross Walker (Mon Oct 29 2007 - 17:18:50 CST)
AMBER: anal problem varsha rani (Tue Oct 30 2007 - 05:48:03 CST)
AMBER: Amber9 parallel installation error (retry) Joe Nolan (Tue Oct 30 2007 - 12:25:35 CST)
AMBER: antechamber fails with large molecules VANIA MARIA AMARO CALISTO (Wed Oct 31 2007 - 03:26:14 CST)
- Re: AMBER: antechamber fails with large molecules FyD (Wed Oct 31 2007 - 08:02:36 CST)
- Re: AMBER: antechamber fails with large molecules Junmei Wang (Wed Oct 31 2007 - 22:43:49 CST)
  - Re: AMBER: antechamber fails with large molecules Francesco Pietra (Thu Nov 01 2007 - 02:29:26 CST)
- Re: AMBER: antechamber fails with large molecules Junmei Wang (Fri Nov 02 2007 - 00:16:41 CST)
  - Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Fri Nov 02 2007 - 02:24:26 CST)
AMBER: problems visualizing mdcrd in VMD Mattia Mori - CERM (Wed Oct 31 2007 - 05:17:21 CST)
- Re: AMBER: problems visualizing mdcrd in VMD Vlad Cojocaru (Wed Oct 31 2007 - 05:33:37 CST)
- Re: AMBER: problems visualizing mdcrd in VMD Vlad Cojocaru (Wed Oct 31 2007 - 06:41:42 CST)
  - Re: AMBER: problems visualizing mdcrd in VMD Mattia Mori - CERM (Wed Oct 31 2007 - 06:59:24 CST)
AMBER: gibbs problems JAVIER PEREZ (Wed Oct 31 2007 - 05:48:22 CST)
- Re: AMBER: gibbs problems David A. Case (Wed Oct 31 2007 - 22:09:35 CST)
AMBER: amber9 parallel compile problem Christopher Jones (Wed Oct 31 2007 - 11:09:32 CST)
- RE: AMBER: amber9 parallel compile problem Ross Walker (Wed Oct 31 2007 - 11:36:00 CST)
AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Wed Oct 31 2007 - 12:57:54 CST)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) David A. Case (Wed Oct 31 2007 - 15:52:18 CST)
  - Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Thu Nov 08 2007 - 13:29:35 CST)
AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Thu Nov 01 2007 - 04:43:54 CST)
- RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Thu Nov 01 2007 - 11:12:52 CST)
  - Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 03:07:04 CST)
    - RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Fri Nov 02 2007 - 12:42:54 CST)
  - Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 04:59:01 CST)
AMBER: Improper torsion terms Pavan G (Thu Nov 01 2007 - 18:24:46 CST)
Re: AMBER:antechamber fails with large molecules Junmei Wang (Fri Nov 02 2007 - 00:29:11 CST)
- AMBER: Failure to recompile antechamber Francesco Pietra (Fri Nov 02 2007 - 17:05:45 CST)
- Re: AMBER:antechamber fails with large molecules Francesco Pietra (Sun Nov 11 2007 - 05:13:56 CST)
- Re: AMBER:antechamber fails with large molecules Francesco Pietra (Sun Nov 11 2007 - 05:13:56 CST)
Re: AMBER: Improper torsion terms Bill Ross (Fri Nov 02 2007 - 10:41:00 CST)
AMBER: Compiling single programs Francesco Pietra (Fri Nov 02 2007 - 11:44:09 CST)
- Re: AMBER: Compiling single programs Mark Williamson (Fri Nov 02 2007 - 11:58:32 CST)
- Re: AMBER: Compiling single programs Adrian Roitberg (Fri Nov 02 2007 - 12:08:44 CST)
AMBER: error with amber9 production run. Vijay Singh (Sat Nov 03 2007 - 08:10:52 CST)
AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? sychen (Sun Nov 04 2007 - 06:46:09 CST)
- Re: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Jiri Sponer (Sun Nov 04 2007 - 07:01:02 CST)
  - RE: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Catein Catherine (Sun Nov 04 2007 - 23:20:48 CST)
AMBER: dihedral driver fatima.chami_at_durham.ac.uk (Sun Nov 04 2007 - 06:51:22 CST)
AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 03:01:08 CST)
- Re: AMBER: paper request FyD (Mon Nov 05 2007 - 03:13:38 CST)
- Re: AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 04:14:09 CST)
AMBER: "Atom valence violated" from LEaP Francesco Pietra (Mon Nov 05 2007 - 05:00:28 CST)
AMBER: Fe bonds in HEME ! Pradipta Bandyopadhyay (Mon Nov 05 2007 - 05:50:58 CST)
AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 08:19:25 CST)
- Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 09:34:20 CST)
  - Re: AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 10:07:00 CST)
    - Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 10:37:11 CST)
- Re: AMBER: ptraj frames maximum Thomas Cheatham (Mon Nov 05 2007 - 17:54:37 CST)
AMBER: DUMBFREQ Steve Seibold (Mon Nov 05 2007 - 09:52:19 CST)
AMBER: ptraj hbond mask Lars Skjærven (Mon Nov 05 2007 - 10:00:03 CST)
- Re: AMBER: ptraj hbond mask Thomas Cheatham III (Wed Nov 07 2007 - 15:00:40 CST)
AMBER: umbrella sampling and WHAM Allen, Thomas W., Ph.D. [RO BIOCHM] (Mon Nov 05 2007 - 14:03:31 CST)
AMBER: Parallel test error with shared libraries Joe Nolan (Mon Nov 05 2007 - 15:05:27 CST)
AMBER: Request reg parameter for vitamin e Rama krishnan (Tue Nov 06 2007 - 01:11:47 CST)
AMBER: Request reg parameter for vitamin e Rama krishnan (Tue Nov 06 2007 - 01:13:51 CST)
AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? ming hui (Tue Nov 06 2007 - 02:30:17 CST)
- Re: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? Carlos Simmerling (Tue Nov 06 2007 - 05:49:13 CST)
AMBER: Energy minimization problem of -SO3H group Takao Kobayashi (Tue Nov 06 2007 - 04:17:35 CST)
- Re: AMBER: Energy minimization problem of -SO3H group David A. Case (Tue Nov 06 2007 - 23:12:08 CST)
  - Re: AMBER: Energy minimization problem of -SO3H group Eddie Men (Tue Nov 06 2007 - 23:52:09 CST)
AMBER: Question dykyy (Tue Nov 06 2007 - 07:12:46 CST)
- Re: AMBER: Question David A. Case (Tue Nov 06 2007 - 23:18:33 CST)
AMBER: Minimum energy tolerance gradient setting for minimization Sandhya Tiwari (Tue Nov 06 2007 - 08:13:52 CST)
- Re: AMBER: Minimum energy tolerance gradient setting for minimization David A. Case (Tue Nov 06 2007 - 10:03:18 CST)
AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 10:02:39 CST)
- Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 11:15:33 CST)
- Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 11:36:35 CST)
  - Re: AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 13:04:05 CST)
    - Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 14:41:17 CST)
    - Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 15:03:13 CST)
AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 05:26:51 CST)
- Re: AMBER: calculating charges to modified 4GA unit FyD (Wed Nov 07 2007 - 07:21:03 CST)
- Re: AMBER: calculating charges to modified 4GA unit Karl Kirschner (Wed Nov 07 2007 - 07:37:42 CST)
AMBER: AMBER 9 - visualization of MD trajectory by MOE dinko.x.ziher_at_gsk.com (Wed Nov 07 2007 - 06:45:41 CST)
AMBER: LEaP bond problem Beale, John (Wed Nov 07 2007 - 06:57:30 CST)
- Re: AMBER: LEaP bond problem David A. Case (Wed Nov 07 2007 - 10:39:49 CST)
AMBER: divcon on AIX using xlf 10.1 Joachim Hein (Wed Nov 07 2007 - 10:23:14 CST)
- AMBER: Re: divcon on AIX using xlf 10.1 Joachim Hein (Mon Dec 03 2007 - 10:43:19 CST)
AMBER: (no subject) Biman Jana (Wed Nov 07 2007 - 11:09:00 CST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 07 2007 - 11:11:43 CST)
AMBER: TIP5P water Simulation Biman Jana (Wed Nov 07 2007 - 11:12:42 CST)
AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Wed Nov 07 2007 - 20:21:21 CST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? gsciaini_at_qi.fcen.uba.ar (Thu Nov 08 2007 - 10:09:31 CST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Thu Nov 08 2007 - 11:44:43 CST)
AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 02:33:21 CST)
- Re: AMBER: make test.parallel David A. Case (Thu Nov 08 2007 - 09:58:39 CST)
  - Re: AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 11:30:36 CST)
    - Re: AMBER: make test.parallel Gustavo Seabra (Fri Nov 09 2007 - 10:28:23 CST)
AMBER: divcon san_amber roy (Thu Nov 08 2007 - 11:19:41 CST)
- Re: AMBER: divcon Pablo Englebienne (Thu Nov 08 2007 - 11:50:25 CST)
- Re: AMBER: divcon David A. Case (Thu Nov 08 2007 - 20:06:55 CST)
AMBER: xleap patch for xorg-7.3 ?? M. L. Dodson (Thu Nov 08 2007 - 13:04:05 CST)
- Re: AMBER: xleap patch for xorg-7.3 ?? David A. Case (Thu Nov 08 2007 - 20:03:39 CST)
  - Re: AMBER: xleap patch for xorg-7.3 ?? Xuebin Qiao (Fri Nov 09 2007 - 08:26:38 CST)
AMBER: thermodynamic integration Cooper, Matthew (Thu Nov 08 2007 - 15:14:25 CST)
- Re: AMBER: thermodynamic integration Ilyas Yildirim (Thu Nov 08 2007 - 16:42:04 CST)
  - RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 08:32:52 CST)
- Re: AMBER: thermodynamic integration David A. Case (Thu Nov 08 2007 - 19:49:49 CST)
  - RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 08:03:32 CST)
    - Re: AMBER: thermodynamic integration David A. Case (Fri Nov 09 2007 - 12:27:48 CST)
- Re: AMBER: thermodynamic integration Thomas Steinbrecher (Tue Nov 13 2007 - 10:36:15 CST)
AMBER: RESP question Eddie Men (Fri Nov 09 2007 - 18:33:16 CST)
- Re: AMBER: RESP question Gustavo Seabra (Fri Nov 09 2007 - 23:01:09 CST)
AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sat Nov 10 2007 - 08:57:20 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 Carlos Simmerling (Sat Nov 10 2007 - 09:00:36 CST)
  - Re: AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sun Nov 11 2007 - 08:21:56 CST)
AMBER: addles Peter Varnai (Sat Nov 10 2007 - 10:40:21 CST)
- Re: AMBER: addles David A. Case (Wed Nov 28 2007 - 11:46:57 CST)
AMBER: replica exchange problems with ifort >10.0.023 Peter Varnai (Sat Nov 10 2007 - 10:44:30 CST)
AMBER: invalid digit '*' in the input file rebeca_at_mmb.pcb.ub.es (Mon Nov 12 2007 - 08:06:16 CST)
- Re: AMBER: invalid digit '*' in the input file Martin Klefas-Stennett (Mon Nov 12 2007 - 08:31:08 CST)
  - Re: AMBER: invalid digit '*' in the input file rebeca_at_mmb.pcb.ub.es (Mon Nov 12 2007 - 08:56:26 CST)
    - Re: AMBER: invalid digit '*' in the input file Adrian Roitberg (Mon Nov 12 2007 - 09:17:43 CST)
    - RE: AMBER: invalid digit '*' in the input file Yong Duan (Mon Nov 12 2007 - 19:07:26 CST)
- Re: AMBER: invalid digit '*' in the input file Chris Moth (Mon Nov 12 2007 - 08:40:26 CST)
- RE: AMBER: invalid digit '*' in the input file Hayden Eastwood (Mon Nov 12 2007 - 09:10:03 CST)
AMBER: restrain center of mass of one domain Wei Chen (Mon Nov 12 2007 - 17:14:11 CST)
AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Mon Nov 12 2007 - 17:32:20 CST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 09:54:38 CST)
  - RE: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hu, Shaowen (JSC-SK)[USRA] (Tue Nov 13 2007 - 10:13:18 CST)
    - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 10:28:52 CST)
  - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Sun Dec 09 2007 - 15:44:34 CST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Tue Dec 11 2007 - 17:50:17 CST)
  - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Gustavo Seabra (Tue Dec 11 2007 - 18:23:49 CST)
AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 04:35:20 CST)
- Re: AMBER: Parallel scaling Carlos Simmerling (Tue Nov 13 2007 - 05:07:53 CST)
  - Re: AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 05:26:23 CST)
AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 05:06:13 CST)
- Re: AMBER: gb minimization using nab Andreas Svrcek-Seiler (Tue Nov 13 2007 - 05:58:05 CST)
  - Re: AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 08:49:48 CST)
AMBER: Protein containing iron. Syed Tarique Moin (Tue Nov 13 2007 - 05:16:48 CST)
- RE: AMBER: Protein containing iron. Ross Walker (Tue Nov 13 2007 - 12:37:40 CST)
AMBER: Parallel Amber compilation problems !! Sampath Koppole (Tue Nov 13 2007 - 08:05:28 CST)
- AMBER: Problem with xLeap alfredoq_at_mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 09:34:46 CST)
  - Re: AMBER: Problem with xLeap David A. Case (Tue Nov 13 2007 - 10:08:24 CST)
- RE: AMBER: Parallel Amber compilation problems !! Ross Walker (Tue Nov 13 2007 - 12:33:25 CST)
  - RE: AMBER: Parallel Amber compilation problems !! Sampath Koppole (Wed Nov 14 2007 - 03:22:15 CST)
AMBER: 2 double bond in AMBER ffield ABEL Stephane 984007 (Tue Nov 13 2007 - 11:00:08 CST)
AMBER: amber9 leap installation error on sgi_altix wei zhang (Tue Nov 13 2007 - 16:02:48 CST)
- RE: AMBER: amber9 leap installation error on sgi_altix Ross Walker (Tue Nov 13 2007 - 16:50:53 CST)
- Re: AMBER: amber9 leap installation error on sgi_altix David A. Case (Tue Nov 13 2007 - 17:27:55 CST)
  - Re: AMBER: amber9 leap installation error on sgi_altix wei zhang (Wed Nov 14 2007 - 10:05:26 CST)
[Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Wed Nov 14 2007 - 12:51:35 CST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Xuebin Qiao (Thu Nov 15 2007 - 00:59:58 CST)
  - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Thu Nov 15 2007 - 11:28:28 CST)
    - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Lili Peng (Thu Nov 15 2007 - 16:38:57 CST)
    - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] David A. Case (Fri Nov 16 2007 - 00:12:45 CST)
AMBER: Bug report: iwrap failure in PMEMD with netCDF Myunggi Yi (Wed Nov 14 2007 - 13:18:18 CST)
- Re: AMBER: Bug report: iwrap failure in PMEMD with netCDF Robert Duke (Wed Nov 14 2007 - 13:52:16 CST)
AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Wed Nov 14 2007 - 19:10:07 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 11:06:03 CST)
  - Re: AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Thu Nov 15 2007 - 18:48:05 CST)
AMBER: &shf setup McElheny, Dan (Thu Nov 15 2007 - 17:39:42 CST)
- Re: AMBER: &shf setup David A. Case (Fri Nov 16 2007 - 17:59:19 CST)
AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Thu Nov 15 2007 - 23:02:08 CST)
- Re: AMBER: Understading of mdcrd file and pdb file.. David A. Case (Fri Nov 16 2007 - 00:23:30 CST)
  - Re: AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Sun Nov 18 2007 - 23:27:19 CST)
AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 11:09:10 CST)
- Re: AMBER: [chirality.c] Atom did not match Jojart Balazs (Fri Nov 16 2007 - 11:48:51 CST)
  - Re: AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 13:38:20 CST)
AMBER: xleap heme iron coordination error Robyn Ayscue (Fri Nov 16 2007 - 13:33:35 CST)
- Re: AMBER: xleap heme iron coordination error David A. Case (Fri Nov 16 2007 - 13:47:53 CST)
AMBER: antechamber --> sander problem Yamada, Takahiro (Fri Nov 16 2007 - 14:18:18 CST)
- Re: AMBER: antechamber --> sander problem David A. Case (Fri Nov 16 2007 - 15:17:50 CST)
AMBER: chem shift format McElheny, Dan (Fri Nov 16 2007 - 15:46:57 CST)
- Re: AMBER: chem shift format David A. Case (Fri Nov 16 2007 - 18:00:27 CST)
AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 15:59:40 CST)
- Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Fri Nov 16 2007 - 18:03:33 CST)
  - Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 04:56:01 CST)
    - Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Sat Nov 17 2007 - 10:53:01 CST)
AMBER: five-coordinated phosphorus Smooth Cutie (Fri Nov 16 2007 - 17:48:40 CST)
AMBER: How to calculate S2 from P2 using ptraj ? brmeher_at_iitg.ernet.in (Sat Nov 17 2007 - 00:34:11 CST)
- Re: AMBER: How to calculate S2 from P2 using ptraj ? David A. Case (Mon Nov 19 2007 - 12:04:48 CST)
AMBER: How to calculate S2 from P2 using ptraj ? brmeher_at_iitg.ernet.in (Sat Nov 17 2007 - 00:40:31 CST)
AMBER: five-coordinated phosphorus Yubo Fan (Sat Nov 17 2007 - 08:19:06 CST)
AMBER: question with ptraj loop Vijay Singh (Sat Nov 17 2007 - 10:06:53 CST)
Fwd: Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 10:16:09 CST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 07:28:07 CST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 07:31:42 CST)
AMBER: Puzzle with WAT Francesco Pietra (Sat Nov 17 2007 - 12:14:38 CST)
AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Alessandro Nascimento (Sat Nov 17 2007 - 15:24:58 CST)
- Re: AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Carlos Simmerling (Sat Nov 17 2007 - 15:51:09 CST)
Re: AMBER: Puzzle with WAT Bill Ross (Sat Nov 17 2007 - 18:00:06 CST)
- Re: AMBER: Puzzle with WAT Francesco Pietra (Sun Nov 18 2007 - 02:09:27 CST)
- Re: AMBER: Puzzle with WAT Bill Ross (Sun Nov 18 2007 - 12:55:15 CST)
AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 11:14:14 CST)
- RE : AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 13:40:24 CST)
AMBER: R.E.D.-III bug fixes FyD (Sun Nov 18 2007 - 11:22:47 CST)
- Re: AMBER: R.E.D.-III bug fixes snoze pa (Sat Dec 22 2007 - 13:14:44 CST)
AMBER: Missing BELE for MM in 1 backy (Mon Nov 19 2007 - 06:19:09 CST)
AMBER: Solvation free energy Mike Wykes (Mon Nov 19 2007 - 12:08:23 CST)
- Re: AMBER: Solvation free energy Thomas Steinbrecher (Mon Nov 19 2007 - 12:21:23 CST)
AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 13:25:48 CST)
- Re: AMBER: pmemd with openmpi Francesco Pietra (Mon Nov 19 2007 - 14:31:56 CST)
  - Re: AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 15:40:41 CST)
AMBER: newby question on converting xyz format to pdb format after energy minimization Mehmet Serkan Apaydin (Tue Nov 20 2007 - 15:02:42 CST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization Eddie Men (Tue Nov 20 2007 - 15:24:56 CST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization David A. Case (Tue Nov 20 2007 - 15:33:08 CST)
AMBER: Implicit/Explicit solvation Eddie Men (Wed Nov 21 2007 - 01:03:12 CST)
- RE: AMBER: Implicit/Explicit solvation Ross Walker (Wed Nov 21 2007 - 10:10:58 CST)
- Re: AMBER: Implicit/Explicit solvation David A. Case (Wed Nov 21 2007 - 10:46:19 CST)
AMBER: Zinc-Histidine force field Mattia Mori - CERM (Wed Nov 21 2007 - 10:54:02 CST)
- RE: AMBER: Zinc-Histidine force field Ray Luo (Wed Nov 21 2007 - 11:30:21 CST)
  - Re: AMBER: Zinc-Histidine force field Mattia Mori - CERM (Thu Nov 22 2007 - 06:06:20 CST)
AMBER:How to calculate the free energy of a series of conformations huzehan19870731_at_126.com (Mon Nov 19 2007 - 21:18:41 CST)
- Re: AMBER:How to calculate the free energy of a series of conformations David A. Case (Wed Nov 21 2007 - 13:42:09 CST)
  - Re: AMBER:How to calculate the free energy of a series of conformations Carlos Simmerling (Wed Nov 21 2007 - 17:04:03 CST)
AMBER: Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 21 2007 - 14:45:17 CST)
- Re: AMBER: Problem with LEaP generating topology and coord files after double bond creation David A. Case (Wed Nov 21 2007 - 19:08:08 CST)
AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 21 2007 - 15:41:45 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Wed Nov 21 2007 - 16:30:30 CST)
  - Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 28 2007 - 09:36:38 CST)
AMBER: McElheny, Dan (Wed Nov 21 2007 - 16:04:26 CST)
AMBER: Atom type definition Xioling Chuang (Thu Nov 22 2007 - 03:03:29 CST)
AMBER: BELLY issues Eddie Men (Thu Nov 22 2007 - 04:03:52 CST)
AMBER: RE: FF94 or FF99? Patel, Bhavesh H (Thu Nov 22 2007 - 08:34:55 CST)
- Re: AMBER: RE: FF94 or FF99? Adrian Roitberg (Thu Nov 22 2007 - 09:20:22 CST)
  - Re: AMBER: RE: FF94 or FF99? Jerome.GOLEBIOWSKI_at_unice.fr (Thu Nov 22 2007 - 09:57:33 CST)
- Re: AMBER: RE: FF94 or FF99? Carlos Simmerling (Thu Nov 22 2007 - 18:13:16 CST)
  - Re: AMBER: RE: FF94 or FF99? Ilyas Yildirim (Thu Nov 22 2007 - 18:29:08 CST)
AMBER: Pressure Variation for NPT simulation of TIP5P water Biman Jana (Thu Nov 22 2007 - 08:50:16 CST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water David A. Case (Thu Nov 22 2007 - 11:34:34 CST)
AMBER: Pre-ABMER Installation Prob w/ MPICH2 Joseph Maxwell (Thu Nov 22 2007 - 13:55:18 CST)
- Re: AMBER: Pre-ABMER Installation Prob w/ MPICH2 jantonioms J. A. Mondragon S (Fri Nov 23 2007 - 11:36:12 CST)
AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Thu Nov 22 2007 - 18:48:31 CST)
- Re: AMBER: frcmod file and NONB for dummy atoms David A. Case (Fri Nov 23 2007 - 12:58:46 CST)
  - Re: AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Fri Nov 23 2007 - 20:26:37 CST)
AMBER: About TER records Francesco Pietra (Fri Nov 23 2007 - 02:15:05 CST)
- Re: AMBER: About TER records David A. Case (Fri Nov 23 2007 - 12:35:46 CST)
  - Re: AMBER: About TER records Francesco Pietra (Sat Nov 24 2007 - 15:34:59 CST)
AMBER: connecting a non standard residue to the rest of an enzyme Boutheïna Kerkeni (Fri Nov 23 2007 - 07:43:36 CST)
- Re: AMBER: connecting a non standard residue to the rest of an enzyme David A. Case (Fri Nov 23 2007 - 12:39:13 CST)
AMBER: Fwd: About TER records Francesco Pietra (Fri Nov 23 2007 - 09:23:41 CST)
- Re: AMBER: Fwd: About TER records Ilyas Yildirim (Fri Nov 23 2007 - 09:41:47 CST)
  - Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 12:29:15 CST)
- Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 15:27:11 CST)
AMBER: Hello Eddie Men (Fri Nov 23 2007 - 20:44:05 CST)
- Re: AMBER: Hello Carlos Simmerling (Fri Nov 23 2007 - 21:01:13 CST)
  - Re: AMBER: Hello Eddie Men (Sat Nov 24 2007 - 12:47:11 CST)
    - Re: AMBER: Hello Carlos Simmerling (Sat Nov 24 2007 - 12:55:46 CST)
    - Re: AMBER: Hello David A. Case (Sun Nov 25 2007 - 00:14:23 CST)
AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) Biman Jana (Sat Nov 24 2007 - 07:22:39 CST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) David A. Case (Sat Nov 24 2007 - 11:36:44 CST)
AMBER: solvatebox vs solvateoct Francesco Pietra (Sun Nov 25 2007 - 12:27:06 CST)
AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 13:21:44 CST)
- RE: AMBER: umbrella sampling Jardas sucuriba (Sun Nov 25 2007 - 13:32:28 CST)
  - Re: AMBER: umbrella sampling Carlos Simmerling (Sun Nov 25 2007 - 13:52:57 CST)
- Re: AMBER: question about ntx=5 David A. Case (Sun Nov 25 2007 - 18:27:30 CST)
  - Re: AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 19:21:52 CST)
    - Re: AMBER: question about ntx=5 David A. Case (Tue Nov 27 2007 - 10:49:33 CST)
AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 Hai Long (Mon Nov 26 2007 - 11:41:18 CST)
- Re: AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 David A. Case (Wed Nov 28 2007 - 13:27:52 CST)
AMBER: LJ parameters for alkynes David Mobley (Mon Nov 26 2007 - 12:07:37 CST)
AMBER: Polarizable potentials Denis Courtier (Mon Nov 26 2007 - 12:49:33 CST)
- Re: AMBER: Polarizable potentials David A. Case (Mon Nov 26 2007 - 20:23:05 CST)
AMBER: Value of taup for bulk TIP5P water simulation(amber7) Biman Jana (Mon Nov 26 2007 - 13:25:37 CST)
AMBER: Restrained MD (amber9) Vincent Bisetty (Mon Nov 26 2007 - 16:52:28 CST)
- Re: AMBER: Restrained MD (amber9) David A. Case (Mon Nov 26 2007 - 17:49:43 CST)
AMBER: restraints to individual atoms Eddie Men (Mon Nov 26 2007 - 21:02:11 CST)
- Re: AMBER: restraints to individual atoms Gustavo Seabra (Tue Nov 27 2007 - 10:34:14 CST)
- RE: AMBER: restraints to individual atoms Ross Walker (Tue Nov 27 2007 - 11:05:44 CST)
  - Re: AMBER: restraints to individual atoms Eddie Men (Tue Nov 27 2007 - 21:54:30 CST)
AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 02:57:54 CST)
- Re: AMBER: Extra-term to the Energy function !! Carlos Simmerling (Tue Nov 27 2007 - 05:12:13 CST)
  - Re: AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 05:31:22 CST)
AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 05:26:22 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 09:02:21 CST)
  - Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 09:23:39 CST)
    - Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 13:29:58 CST)
    - Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Tue Nov 27 2007 - 15:10:40 CST)
AMBER: Xleap and Hydrogens Shozeb Haider (Tue Nov 27 2007 - 08:38:56 CST)
- Re: AMBER: Xleap and Hydrogens Ilyas Yildirim (Tue Nov 27 2007 - 09:08:29 CST)
  - Re: AMBER: Xleap and Hydrogens Marius Retegan (Tue Nov 27 2007 - 09:43:36 CST)
- Re: AMBER: Xleap and Hydrogens David A. Case (Tue Nov 27 2007 - 10:40:05 CST)
- Re: AMBER: Xleap and Hydrogens Bill Ross (Tue Nov 27 2007 - 11:11:35 CST)
AMBER: antechamber: read in charges fatima.chami_at_durham.ac.uk (Tue Nov 27 2007 - 09:40:13 CST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Tue Nov 27 2007 - 11:50:11 CST)
  - Re: AMBER: antechamber: read in charges fatima.chami_at_durham.ac.uk (Wed Nov 28 2007 - 12:52:41 CST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Wed Nov 28 2007 - 14:58:36 CST)
AMBER: predictive NOE generation Seth Lilavivat (Tue Nov 27 2007 - 11:41:08 CST)
- Re: AMBER: predictive NOE generation Nicolas Lux Fawzi (Tue Nov 27 2007 - 12:26:48 CST)
AMBER: Polarizable Potential Denis Courtier (Tue Nov 27 2007 - 11:40:34 CST)
AMBER: Re: antechamber problem Junmei Wang (Tue Nov 27 2007 - 11:38:17 CST)
- Re: AMBER: Re: antechamber problem sanket deshmukh (Wed Nov 28 2007 - 08:05:37 CST)
AMBER: RE: Amber9 compile problem Ross Walker (Tue Nov 27 2007 - 11:24:22 CST)
Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Tue Nov 27 2007 - 15:45:44 CST)
- Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 28 2007 - 12:33:38 CST)
AMBER: Would amber work with Linspire 6.0? Campbell, Patrick (Tue Nov 27 2007 - 17:01:02 CST)
- RE: AMBER: Would amber work with Linspire 6.0? Ross Walker (Tue Nov 27 2007 - 18:36:02 CST)
- Re: AMBER: Would amber work with Linspire 6.0? Peter Gannett (Tue Nov 27 2007 - 21:20:19 CST)
- Re: AMBER: Would amber work with Linspire 6.0? Christophe Guilbert (Tue Nov 27 2007 - 21:35:35 CST)
AMBER: QMMM simulations Pankaj R. Daga (Tue Nov 27 2007 - 17:20:51 CST)
- RE: AMBER: QMMM simulations Ross Walker (Tue Nov 27 2007 - 18:41:11 CST)
AMBER: bondi radii problems Eddie Men (Tue Nov 27 2007 - 21:31:19 CST)
- Re: AMBER: bondi radii problems David A. Case (Wed Nov 28 2007 - 10:32:21 CST)
  - Re: AMBER: bondi radii problems Eddie Men (Wed Nov 28 2007 - 12:45:34 CST)
AMBER: PB warning in pb_miccg(): CG maxitn exceeded! Eddie Men (Tue Nov 27 2007 - 22:35:17 CST)
AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Wed Nov 28 2007 - 05:27:53 CST)
- Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Wed Nov 28 2007 - 06:19:35 CST)
  - Re: AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Thu Nov 29 2007 - 00:26:39 CST)
    - Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Thu Nov 29 2007 - 02:07:07 CST)
AMBER: Polarizable potential Denis Courtier (Wed Nov 28 2007 - 08:32:49 CST)
- Re: AMBER: Polarizable potential David A. Case (Wed Nov 28 2007 - 10:19:06 CST)
AMBER: radial distribution by Ptraj Esther Brugger (Wed Nov 28 2007 - 08:35:49 CST)
AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Wed Nov 28 2007 - 09:01:37 CST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated M. L. Dodson (Wed Nov 28 2007 - 11:31:04 CST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Gustavo Seabra (Wed Nov 28 2007 - 15:04:32 CST)
- RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Steve Spronk (Thu Nov 29 2007 - 08:44:33 CST)
  - RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Thu Nov 29 2007 - 09:44:33 CST)
AMBER: (no subject) Gabriele Viliani (Wed Nov 28 2007 - 10:56:32 CST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 28 2007 - 11:09:04 CST)
AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Wed Nov 28 2007 - 11:44:21 CST)
- Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Wed Nov 28 2007 - 12:58:30 CST)
  - Re: AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Thu Nov 29 2007 - 05:01:38 CST)
    - Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Thu Nov 29 2007 - 09:40:04 CST)
    - RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Thu Nov 29 2007 - 09:54:13 CST)
- RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Wed Nov 28 2007 - 12:38:47 CST)
AMBER: [Fwd: Re: BOUNCE amber@scripps.edu: Non-member submission from [Taufik Al-Sarraj <taufik.alsarraj@utoronto.ca>]] Taufik Al-Sarraj (Wed Nov 28 2007 - 12:23:27 CST)
- AMBER: DNA on Si surface Taufik Al-Sarraj (Thu Nov 29 2007 - 17:20:12 CST)
AMBER: Calculating dipole moments Austin B. Yongye (Wed Nov 28 2007 - 13:33:41 CST)
- RE: AMBER: Calculating dipole moments Ross Walker (Wed Nov 28 2007 - 15:57:12 CST)
  - RE: AMBER: Calculating dipole moments Austin B. Yongye (Thu Nov 29 2007 - 09:40:51 CST)
    - RE: AMBER: Calculating dipole moments Ross Walker (Thu Nov 29 2007 - 10:08:50 CST)
AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 15:29:41 CST)
- Re: AMBER: questions about smd of amber 9 Wei Chen (Wed Nov 28 2007 - 16:35:10 CST)
- Re: AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 20:14:21 CST)
  - Re: AMBER: questions about smd of amber 9 Wei Chen (Thu Nov 29 2007 - 10:28:34 CST)
    - Re: AMBER: questions about smd of amber 9 Adrian Roitberg (Thu Nov 29 2007 - 10:56:15 CST)
- Re: AMBER: questions about smd of amber 9 Gustavo Seabra (Thu Nov 29 2007 - 08:53:24 CST)
AMBER: Error in installing amber8 on Ubuntu tri nam Vo (Wed Nov 28 2007 - 22:24:24 CST)
- RE: AMBER: Error in installing amber8 on Ubuntu Ross Walker (Thu Nov 29 2007 - 09:44:10 CST)
AMBER: About RAMD Francesco Pietra (Thu Nov 29 2007 - 01:26:45 CST)
- Re: AMBER: About RAMD Alessandro Nascimento (Thu Nov 29 2007 - 04:54:02 CST)
AMBER: ele vs van der Waals backy (Thu Nov 29 2007 - 03:14:19 CST)
AMBER: Error in reading number of frame in PTRAJ Vijay Manickam Achari (Thu Nov 29 2007 - 03:20:12 CST)
AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 05:43:45 CST)
- Re: AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 07:33:22 CST)
  - RE: AMBER: vlimit exceeded, polarizable force field Ross Walker (Thu Nov 29 2007 - 10:02:24 CST)
AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1 Wei Chen (Thu Nov 29 2007 - 11:15:51 CST)
AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 06:24:18 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Carlos Simmerling (Fri Nov 30 2007 - 06:32:04 CST)
  - Re: AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 06:55:14 CST)
AMBER: angle between vectors Mag. rer. nat. Hannes WallnÃ¶fer (Fri Nov 30 2007 - 06:45:02 CST)
- Re: AMBER: angle between vectors Ilyas Yildirim (Fri Nov 30 2007 - 11:28:59 CST)
  - Re: AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Mon Dec 03 2007 - 01:55:51 CST)
    - Re: AMBER: angle between vectors Prem (Tue Dec 04 2007 - 15:59:29 CST)
AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 10:28:50 CST)
- Re: AMBER: Group input for restrained atoms Pavan G (Fri Nov 30 2007 - 10:43:23 CST)
  - Re: AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 15:12:42 CST)
AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sat Dec 01 2007 - 09:46:23 CST)
- Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg (Sat Dec 01 2007 - 10:17:15 CST)
  - Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sat Dec 01 2007 - 12:48:01 CST)
    - Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg (Sat Dec 01 2007 - 13:44:16 CST)
    - Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sun Dec 02 2007 - 03:51:42 CST)
AMBER: mm_pbsa continue run Christopher Gaughan (Sun Dec 02 2007 - 12:46:42 CST)
AMBER: I need some help in PTRAJ Vijay Manickam Achari (Mon Dec 03 2007 - 00:49:29 CST)
- Re: AMBER: I need some help in PTRAJ Chris Moth (Mon Dec 03 2007 - 19:29:21 CST)
AMBER: sander and pmemd Nadia Vahdati (Mon Dec 03 2007 - 07:20:17 CST)
- Re: AMBER: sander and pmemd Robert Duke (Mon Dec 03 2007 - 08:19:24 CST)
Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 10:30:11 CST)
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault David A. Case (Mon Dec 03 2007 - 11:08:48 CST)
  - Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 15:45:14 CST)
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 16:18:01 CST)
  - Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Ilyas Yildirim (Mon Dec 03 2007 - 16:42:54 CST)
AMBER: Free energy for part of the system jialei (Mon Dec 03 2007 - 13:12:47 CST)
- Re: AMBER: Free energy for part of the system David A. Case (Mon Dec 03 2007 - 20:35:50 CST)
  - RE: AMBER: Free energy for part of the system jialei (Tue Dec 04 2007 - 12:21:03 CST)
    - Re: AMBER: Free energy for part of the system David A. Case (Tue Dec 04 2007 - 12:37:16 CST)
    - RE: AMBER: Free energy for part of the system jialei (Tue Dec 04 2007 - 19:10:18 CST)
AMBER: During the Sander process, does the pH of the solution change orr not Fenghui Fan (Mon Dec 03 2007 - 19:58:44 CST)
AMBER: Restraintmask syntax Francesco Pietra (Tue Dec 04 2007 - 09:30:50 CST)
- RE: AMBER: Restraintmask syntax Steve Spronk (Tue Dec 04 2007 - 10:49:36 CST)
  - RE: AMBER: Restraintmask syntax Francesco Pietra (Tue Dec 04 2007 - 11:44:01 CST)
    - RE: AMBER: Restraintmask syntax Andrew Purkiss-Trew (Wed Dec 05 2007 - 04:39:08 CST)
    - RE: AMBER: Restraintmask syntax Francesco Pietra (Wed Dec 05 2007 - 12:00:49 CST)
AMBER: Solution Structure Determination Protocols - Simulated Annealing Seth Lilavivat (Tue Dec 04 2007 - 11:23:16 CST)
AMBER: correlation time Tuncel, Aytug (Tue Dec 04 2007 - 12:22:55 CST)
- Re: AMBER: correlation time David A. Case (Tue Dec 04 2007 - 12:40:20 CST)
  - RE: AMBER: correlation time Tuncel, Aytug (Thu Dec 06 2007 - 03:44:29 CST)
    - Re: AMBER: correlation time David A. Case (Thu Dec 06 2007 - 11:09:07 CST)
AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey (Tue Dec 04 2007 - 18:39:29 CST)
- Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File David A. Case (Tue Dec 04 2007 - 19:11:53 CST)
  - Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey (Fri Dec 07 2007 - 00:45:59 CST)
AMBER: phosphorylation bosco (Tue Dec 04 2007 - 19:36:27 CST)
- Re: AMBER: phosphorylation FyD (Thu Dec 06 2007 - 14:07:57 CST)
AMBER: (no subject) Madjid Taghdir (Wed Dec 05 2007 - 03:18:11 CST)
AMBER: nmode ntrun=2 JM Beames (Wed Dec 05 2007 - 04:03:24 CST)
- Re: AMBER: nmode ntrun=2 David A. Case (Wed Dec 05 2007 - 11:58:34 CST)
  - Re: AMBER: nmode ntrun=2 JM Beames (Thu Dec 06 2007 - 05:48:43 CST)
AMBER: leap restrainTorsion fatima.chami_at_durham.ac.uk (Wed Dec 05 2007 - 04:24:30 CST)
- Re: AMBER: leap restrainTorsion David A. Case (Wed Dec 05 2007 - 10:50:12 CST)
AMBER: calcium and zinc parameter Madjid Taghdir (Wed Dec 05 2007 - 05:07:17 CST)
- Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Wed Dec 05 2007 - 05:15:08 CST)
  - Re: AMBER: calcium and zinc parameter Taufik Al-Sarraj (Wed Dec 05 2007 - 12:43:45 CST)
    - Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Thu Dec 06 2007 - 07:21:10 CST)
- Re: AMBER: calcium and zinc parameter Madjid Taghdir (Tue Dec 11 2007 - 01:21:37 CST)
  - Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Tue Dec 11 2007 - 07:07:31 CST)
AMBER: THF parameters Yves Boulard (Wed Dec 05 2007 - 04:21:04 CST)
- Re: AMBER: THF parameters FyD (Wed Dec 05 2007 - 08:32:27 CST)
  - Re: AMBER: THF parameters David A. Case (Wed Dec 05 2007 - 11:56:18 CST)
    - Re: AMBER: THF parameters Piotr Cieplak (Wed Dec 05 2007 - 13:33:42 CST)
    - Re: AMBER: THF parameters FyD (Wed Dec 05 2007 - 14:42:29 CST)
AMBER: Amber 9 - bugfix.40 fails Kevin Davies (Wed Dec 05 2007 - 11:27:27 CST)
- Re: AMBER: Amber 9 - bugfix.40 fails Holger Gohlke (Wed Dec 05 2007 - 11:56:23 CST)
AMBER: Bulk water simulation with centre of mass position restrain Biman Jana (Wed Dec 05 2007 - 12:08:56 CST)
Fwd: Re: AMBER: leap restrainTorsion fatima.chami_at_durham.ac.uk (Wed Dec 05 2007 - 12:45:24 CST)
- Re: Fwd: Re: AMBER: leap restrainTorsion David A. Case (Wed Dec 05 2007 - 20:15:36 CST)
  - AMBER: Surface Taufik Al-Sarraj (Thu Dec 06 2007 - 13:11:21 CST)
    - Re: AMBER: Surface David A. Case (Thu Dec 06 2007 - 15:34:04 CST)
AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat (Wed Dec 05 2007 - 13:28:37 CST)
- Re: AMBER: How to apply psuedo-bonds for restraints David A. Case (Wed Dec 05 2007 - 20:16:43 CST)
  - Re: AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat (Thu Dec 06 2007 - 10:08:55 CST)
    - Re: AMBER: How to apply psuedo-bonds for restraints David A. Case (Thu Dec 06 2007 - 10:56:59 CST)
AMBER: amber on AMD opteron-250 servaas michielssens (Wed Dec 05 2007 - 14:10:22 CST)
- Re: AMBER: amber on AMD opteron-250 Robert Duke (Wed Dec 05 2007 - 14:35:04 CST)
- Re: AMBER: amber on AMD opteron-250 David LeBard (Wed Dec 05 2007 - 14:29:22 CST)
  - Re: AMBER: amber on AMD opteron-250 Robert Duke (Wed Dec 05 2007 - 15:31:28 CST)
AMBER: MD_model Urszula Uciechowska (Wed Dec 05 2007 - 17:05:45 CST)
- Re: AMBER: MD_model Thomas Steinbrecher (Wed Dec 05 2007 - 17:26:04 CST)
- Re: AMBER: MD_model Ilyas Yildirim (Wed Dec 05 2007 - 17:54:50 CST)
AMBER: Making movies in VMD Lili Peng (Wed Dec 05 2007 - 18:57:08 CST)
- Re: AMBER: Making movies in VMD Vijay Singh (Wed Dec 05 2007 - 19:25:26 CST)
- Re: AMBER: Making movies in VMD rdauria_at_uci.edu (Wed Dec 05 2007 - 23:20:12 CST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 02:44:09 CST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 02:45:35 CST)
AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Ye Mei (Thu Dec 06 2007 - 06:20:56 CST)
- Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Andreas Svrcek-Seiler (Thu Dec 06 2007 - 09:49:34 CST)
  - Re: Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran10.1.008 and IMKL 10.0.1.014 Ye Mei (Thu Dec 06 2007 - 21:23:11 CST)
AMBER: pmend vs sander.MPI Francesco Pietra (Thu Dec 06 2007 - 09:13:39 CST)
- Re: AMBER: pmend vs sander.MPI Robert Duke (Thu Dec 06 2007 - 09:18:20 CST)
  - Re: AMBER: pmend vs sander.MPI Francesco Pietra (Sun Dec 09 2007 - 11:35:48 CST)
Re: AMBER: Problem in running CARNAL Bill Ross (Thu Dec 06 2007 - 13:37:07 CST)
- Re: AMBER: Problem in running CARNAL Bill Ross (Fri Dec 07 2007 - 11:48:15 CST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 23:52:26 CST)
AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 13:47:26 CST)
- Re: AMBER: Troubles installing amber Wei Zhang (Fri Dec 07 2007 - 13:54:47 CST)
  - Re: AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 15:36:36 CST)
    - Re: AMBER: Troubles installing amber David A. Case (Fri Dec 07 2007 - 16:15:36 CST)
    - Re: AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 16:22:22 CST)
- Re: AMBER: Troubles installing amber Alessandro Nascimento (Fri Dec 07 2007 - 13:55:54 CST)
AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni (Fri Dec 07 2007 - 16:13:19 CST)
- Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT David A. Case (Fri Dec 07 2007 - 19:24:30 CST)
AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni (Fri Dec 07 2007 - 16:17:07 CST)
Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT Bill Ross (Fri Dec 07 2007 - 16:20:49 CST)
AMBER: running equilibration Boutheina Kerkeni (Fri Dec 07 2007 - 18:29:59 CST)
- RE: AMBER: running equilibration Ross Walker (Fri Dec 07 2007 - 19:00:15 CST)
Re: AMBER: running equilibration Bill Ross (Fri Dec 07 2007 - 19:11:02 CST)
AMBER: Continuing an amber 8 simulation with amber 9 ming hui (Sat Dec 08 2007 - 01:03:55 CST)
- Re: AMBER: Continuing an amber 8 simulation with amber 9 David A. Case (Sat Dec 08 2007 - 12:40:09 CST)
AMBER: protein_model Urszula Uciechowska (Sat Dec 08 2007 - 10:11:16 CST)
- Re: AMBER: protein_model steinbrt_at_scripps.edu (Sat Dec 08 2007 - 12:51:35 CST)
  - AMBER: AMBER7 Si atom type Taufik Al-Sarraj (Wed Dec 12 2007 - 11:30:49 CST)
AMBER: Backbone atoms Boutheina Kerkeni (Sat Dec 08 2007 - 16:42:20 CST)
- Re: AMBER: Backbone atoms David A. Case (Sat Dec 08 2007 - 16:58:30 CST)
AMBER: website problems Sally Pias (Sat Dec 08 2007 - 23:06:16 CST)
- Re: AMBER: website problems David A. Case (Sun Dec 09 2007 - 11:03:47 CST)
  - Re: AMBER: website problems Andreas Svrcek-Seiler (Sun Dec 09 2007 - 11:25:12 CST)
- RE: AMBER: website problems Ross Walker (Sun Dec 09 2007 - 11:52:42 CST)
  - Re: AMBER: website problems Sally Pias (Sun Dec 09 2007 - 12:45:51 CST)
  - RE: AMBER: website problems Ross Walker (Sun Dec 09 2007 - 13:06:00 CST)
AMBER: ptraj with protein-ligand Francesco Pietra (Sun Dec 09 2007 - 04:11:30 CST)
AMBER: Fwd: ptraj with protein-ligand Francesco Pietra (Sun Dec 09 2007 - 04:18:24 CST)
AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI# (Sun Dec 09 2007 - 06:06:18 CST)
- Re: AMBER: Troubling with installing Amber8 David A. Case (Sun Dec 09 2007 - 11:18:29 CST)
- RE: AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI# (Thu Dec 13 2007 - 08:19:47 CST)
  - Re: AMBER: Troubling with installing Amber8 David A. Case (Fri Dec 14 2007 - 10:39:58 CST)
AMBER: some input problem Urszula Uciechowska (Sun Dec 09 2007 - 09:25:52 CST)
- Re: AMBER: some input problem David A. Case (Sun Dec 09 2007 - 11:09:51 CST)
AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 10:46:32 CST)
- Re: AMBER: Re: Amber_ifort_x86_64 test error David A. Case (Sun Dec 09 2007 - 11:13:00 CST)
  - Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 11:22:17 CST)
AMBER: TI Approach - mass perturbation Ilyas Yildirim (Mon Dec 10 2007 - 12:20:49 CST)
- Re: AMBER: TI Approach - mass perturbation David A. Case (Tue Dec 11 2007 - 01:13:08 CST)
  - Re: AMBER: TI Approach - mass perturbation Ilyas Yildirim (Tue Dec 11 2007 - 01:47:52 CST)
AMBER: Ligand-Residue interaction tracking Evan Kelly (Mon Dec 10 2007 - 12:20:29 CST)
AMBER: implicit solvent simulations with calcium ion Akansha Saxena (Mon Dec 10 2007 - 15:19:01 CST)
AMBER: implicit solvent simulations WANG,YING (Tue Dec 11 2007 - 13:21:11 CST)
- Re: AMBER: implicit solvent simulations liu junjun (Tue Dec 11 2007 - 21:49:57 CST)
  - RE: AMBER: implicit solvent simulations Steve Spronk (Wed Dec 12 2007 - 07:00:01 CST)
- Re: AMBER: implicit solvent simulations WANG,YING (Tue Dec 11 2007 - 22:00:59 CST)
AMBER: tleap crashing Ranjib Dey (Tue Dec 11 2007 - 13:12:20 CST)
- Re: AMBER: tleap crashing David A. Case (Tue Dec 11 2007 - 17:04:25 CST)
  - Re: AMBER: tleap crashing Ranjib Dey (Wed Dec 12 2007 - 01:04:55 CST)
AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang (Tue Dec 11 2007 - 15:07:25 CST)
- RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker (Tue Dec 11 2007 - 15:32:43 CST)
  - Re: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang (Mon Dec 17 2007 - 16:49:57 CST)
    - RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker (Mon Dec 17 2007 - 17:20:23 CST)
AMBER: equilibration Urszula Uciechowska (Wed Dec 12 2007 - 11:08:00 CST)
AMBER: Free Energy Calculations Mike Wykes (Wed Dec 12 2007 - 12:08:20 CST)
- Re: AMBER: Free Energy Calculations Thomas Steinbrecher (Wed Dec 12 2007 - 13:19:55 CST)
AMBER: New 2 the board Campbell, Patrick (Wed Dec 12 2007 - 15:12:30 CST)
- Re: AMBER: New 2 the board David A. Case (Wed Dec 12 2007 - 18:03:46 CST)
  - AMBER: loading a crystal PDB file Taufik Al-Sarraj (Wed Dec 12 2007 - 19:33:36 CST)
AMBER: make test.parallel not complete Prem Prakash Pathak (Thu Dec 13 2007 - 02:10:16 CST)
- RE: AMBER: make test.parallel not complete Ross Walker (Thu Dec 13 2007 - 08:19:42 CST)
  - Re: AMBER: make test.parallel not complete Prem Prakash Pathak (Thu Dec 20 2007 - 03:59:03 CST)
AMBER: MMPBSA Syed Tarique Moin (Thu Dec 13 2007 - 06:34:21 CST)
AMBER: protein-ligand binding affinity Francesco Pietra (Thu Dec 13 2007 - 08:00:17 CST)
AMBER: help in QM/MM simulation Pankaj R. Daga (Thu Dec 13 2007 - 15:02:17 CST)
- Re: AMBER: help in QM/MM simulation Gustavo Seabra (Wed Dec 19 2007 - 08:42:19 CST)
AMBER: PMEMD internals !! Sampath Koppole (Fri Dec 14 2007 - 03:13:49 CST)
- Re: AMBER: PMEMD internals !! Robert Duke (Fri Dec 14 2007 - 07:41:43 CST)
AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 11:02:41 CST)
- Re: AMBER: replica exchange out files continually overwritten David A. Case (Fri Dec 14 2007 - 11:17:09 CST)
  - Re: AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 12:47:27 CST)
- Re: AMBER: replica exchange out files continually overwritten Adrian Roitberg (Fri Dec 14 2007 - 12:33:23 CST)
AMBER: Time step & non-bonded interactions updating Francesco Pietra (Sat Dec 15 2007 - 12:39:48 CST)
- RE: AMBER: Time step & non-bonded interactions updating Ross Walker (Sat Dec 15 2007 - 19:32:08 CST)
  - RE: AMBER: Time step & non-bonded interactions updating Francesco Pietra (Sun Dec 16 2007 - 10:36:46 CST)
AMBER: MMTSB Toolset Urszula Uciechowska (Mon Dec 17 2007 - 06:19:34 CST)
- Re: AMBER: MMTSB Toolset Carlos Simmerling (Mon Dec 17 2007 - 06:26:27 CST)
AMBER: amber9/mmtsb Francesco Pietra (Tue Dec 18 2007 - 04:21:31 CST)
- Re: AMBER: amber9/mmtsb David A. Case (Tue Dec 18 2007 - 09:59:11 CST)
  - Re: AMBER: amber9/mmtsb Francesco Pietra (Tue Dec 18 2007 - 11:15:55 CST)
    - Re: AMBER: amber9/mmtsb David A. Case (Wed Dec 19 2007 - 10:19:47 CST)
AMBER: Scripts for md analysis Francesco Pietra (Tue Dec 18 2007 - 05:05:24 CST)
AMBER: PME and counter ions Lars Skjærven (Tue Dec 18 2007 - 10:04:12 CST)
Re: AMBER: PME and counter ions Bill Ross (Tue Dec 18 2007 - 12:36:38 CST)
- Re: AMBER: PME and counter ions Lars Skjærven (Tue Dec 18 2007 - 20:34:26 CST)
  - Re: AMBER: PME and counter ions Pablo Englebienne (Wed Dec 19 2007 - 13:05:30 CST)
    - Re: AMBER: PME and counter ions David A. Case (Wed Dec 19 2007 - 14:01:55 CST)
AMBER: closest water molecules with 8 angstroms nag raj (Wed Dec 19 2007 - 00:52:45 CST)
- Re: AMBER: closest water molecules with 8 angstroms Alessandro Nascimento (Wed Dec 19 2007 - 04:49:56 CST)
AMBER: Electron density profile Age.Skjevik_at_student.uib.no (Thu Dec 20 2007 - 06:13:56 CST)
AMBER: Use of Counter Ions in binding energy calculations Jonathan Suever (Thu Dec 20 2007 - 12:42:15 CST)
AMBER: Steered MD M kutty (Fri Dec 21 2007 - 00:03:29 CST)
- Re: AMBER: Steered MD M. L. Dodson (Fri Dec 21 2007 - 09:52:30 CST)
  - Re: AMBER: Steered MD M. L. Dodson (Fri Dec 21 2007 - 10:00:58 CST)
    - RE: AMBER: Steered MD M kutty (Sun Dec 23 2007 - 23:04:41 CST)
AMBER: No radius found for K+ (MM_PBSA) saurabh agrawal (Fri Dec 21 2007 - 08:45:01 CST)
- Re: AMBER: No radius found for K+ (MM_PBSA) Thomas Cheatham III (Fri Dec 21 2007 - 12:53:55 CST)
AMBER: About protein-ligand binding Francesco Pietra (Fri Dec 21 2007 - 08:52:00 CST)
AMBER: RESP using antechamber snoze pa (Sat Dec 22 2007 - 13:21:07 CST)
- Re: AMBER: RESP using antechamber Barbault Florent (Sat Dec 22 2007 - 14:13:31 CST)
AMBER: installation of amber9 on suse linux 10.3 s lal badshah (Sun Dec 23 2007 - 23:47:21 CST)
- Re: AMBER: installation of amber9 on suse linux 10.3 David A. Case (Mon Dec 24 2007 - 00:03:38 CST)
  - Re: AMBER: installation of amber9 on suse linux 10.3 s lal badshah (Wed Dec 26 2007 - 23:02:24 CST)
    - RE: AMBER: installation of amber9 on suse linux 10.3 Ross Walker (Thu Dec 27 2007 - 00:18:51 CST)
AMBER: installation s lal badshah (Wed Dec 26 2007 - 23:11:29 CST)
- Re: AMBER: installation Mark Williamson (Sat Dec 29 2007 - 11:23:15 CST)
AMBER: RESP charge fitting using antechamber Wei Chen (Sat Dec 29 2007 - 13:22:16 CST)
- Re: AMBER: RESP charge fitting using antechamber David A. Case (Sat Dec 29 2007 - 20:05:25 CST)
- Re: AMBER: RESP charge fitting using antechamber FyD (Sun Dec 30 2007 - 08:54:59 CST)
  - Re: AMBER: RESP charge fitting using antechamber Francesco Pietra (Mon Dec 31 2007 - 01:19:42 CST)
    - Re: AMBER: RESP charge fitting using antechamber FyD (Mon Dec 31 2007 - 09:40:11 CST)
- Re: AMBER: RESP charge fitting using antechamber FyD (Mon Dec 31 2007 - 08:06:34 CST)
AMBER: About RAMD Francesco Pietra (Mon Dec 31 2007 - 09:27:36 CST)
AMBER: a question of ptraj WANG,YING (Mon Dec 31 2007 - 13:39:03 CST)
- Re: AMBER: a question of ptraj Chris Moth (Mon Dec 31 2007 - 14:38:21 CST)

Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:07 CST

4765 messages sorted by: [ author ] [ date ] [ subject ]
About this archive