AMBER Archive (2007) - Jan 2007 By Thread

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Starting: Mon Jan 01 2007 - 04:16:12 CST
Ending: Wed Jan 31 2007 - 23:19:48 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 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)
- 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)
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)
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)

Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:08 CST

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