AMBER Archive (2007) - By Thread

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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