Amber Archive Aug 2003: By Thread

AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 23:13:21 PDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 23:12:33 PDT)
- RE: AMBER: parallelisation Yong Duan (Fri Aug 01 2003 - 05:21:36 PDT)
AMBER: Amber parallelisation arun prasad (Fri Aug 01 2003 - 02:15:05 PDT)
- RE: AMBER: Amber parallelisation Yong Duan (Fri Aug 01 2003 - 05:28:31 PDT)
- Re: AMBER: Amber parallelisation David A. Case (Fri Aug 01 2003 - 08:18:17 PDT)
AMBER: Problem generating .tpp and .rst files for a complex Yogesh Sabnis (Fri Aug 01 2003 - 03:57:07 PDT)
- Re: AMBER: Problem generating .tpp and .rst files for a complex David A. Case (Fri Aug 01 2003 - 08:32:24 PDT)
AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Fri Aug 01 2003 - 03:59:08 PDT)
- AMBER: RE: Restrain of dihedral angle! Yong Duan (Fri Aug 01 2003 - 06:27:04 PDT)
- Re: AMBER: Restrain of dihedral angle! Luis Gracia (Fri Aug 01 2003 - 09:14:21 PDT)
- RE: AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Mon Aug 04 2003 - 02:15:22 PDT)
AMBER: AMBER7 & mpich takanori.kanazawa.pharma.novartis.com (Sat Aug 02 2003 - 05:17:52 PDT)
- Re: AMBER: AMBER7 & mpich Carlos Simmerling (Sat Aug 02 2003 - 05:53:26 PDT)
AMBER: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Sat Aug 02 2003 - 06:03:06 PDT)
- Re: AMBER: AMBER7 & mpich : (no-attachment version) Natasja Brooijmans (Sat Aug 02 2003 - 11:24:59 PDT)
- Re: AMBER: AMBER7 & mpich : (no-attachment version) David A. Case (Sat Aug 02 2003 - 13:30:00 PDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 19:35:48 PDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 19:34:24 PDT)
AMBER: charge method of antechamber Helios Chen (Sun Aug 03 2003 - 21:00:35 PDT)
- Re: AMBER: charge method of antechamber Junmei Wang (Mon Aug 04 2003 - 07:39:58 PDT)
- Re: AMBER: charge method of antechamber David A. Case (Mon Aug 04 2003 - 22:24:00 PDT)
  - Re: AMBER: charge method of antechamber Helios Chen (Mon Aug 18 2003 - 05:39:18 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:32:48 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:34:25 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:32:43 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:33:14 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:40:10 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:39:29 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:13 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:03 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:40:29 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:42:22 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:35 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:44 PDT)
AMBER: separate thermostats for different molecules Arvid Soederhaell (Mon Aug 04 2003 - 06:13:11 PDT)
- Re: AMBER: separate thermostats for different molecules David A. Case (Mon Aug 04 2003 - 22:19:02 PDT)
AMBER: normal mode analysis Marcela Madrid (Mon Aug 04 2003 - 11:03:23 PDT)
- Re: AMBER: normal mode analysis David A. Case (Mon Aug 04 2003 - 22:12:36 PDT)
AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Mon Aug 04 2003 - 16:51:17 PDT)
- Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Wed Aug 06 2003 - 21:11:30 PDT)
  - Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) Scott Brozell (Thu Aug 07 2003 - 00:40:06 PDT)
AMBER: (no subject) Narang Manpreet Kaur (Tue Aug 05 2003 - 06:55:57 PDT)
- Re: AMBER: (no subject) David A. Case (Tue Aug 05 2003 - 12:32:56 PDT)
AMBER: parallelisation gold gunaseelan (Tue Aug 05 2003 - 06:55:31 PDT)
- Re: AMBER: parallelisation Jian Zhang (Wed Aug 06 2003 - 05:39:22 PDT)
AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 07:03:59 PDT)
- Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling David A. Case (Tue Aug 05 2003 - 12:39:22 PDT)
  - Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 14:12:10 PDT)
AMBER: compile problem? Shuang Ding (Tue Aug 05 2003 - 13:51:25 PDT)
AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 09:14:03 PDT)
- Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 09:33:42 PDT)
  - Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 09:40:16 PDT)
    - Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 09:45:53 PDT)
  - Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Thu Aug 07 2003 - 11:21:07 PDT)
    - Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Thu Aug 07 2003 - 12:57:11 PDT)
AMBER: problem regarding surface Vikas Varshney (Wed Aug 06 2003 - 10:00:09 PDT)
AMBER: anal - memory problem sd233.georgetown.edu (Wed Aug 06 2003 - 10:02:44 PDT)
- Re: AMBER: anal - memory problem David A. Case (Wed Aug 06 2003 - 12:00:32 PDT)
AMBER: SHAKE Problem Richard Smith (Wed Aug 06 2003 - 13:02:30 PDT)
- Re: AMBER: SHAKE Problem Xavier Periole (Wed Aug 06 2003 - 13:26:05 PDT)
- Re: AMBER: SHAKE Problem David A. Case (Wed Aug 06 2003 - 14:52:21 PDT)
  - RE: AMBER: SHAKE Problem Richard Smith (Thu Aug 07 2003 - 07:42:56 PDT)
AMBER: Re: dynamics of isolated system (fwd) David A. Case (Wed Aug 06 2003 - 14:43:29 PDT)
AMBER: references about AMBER MD simulations sd233.georgetown.edu (Wed Aug 06 2003 - 22:23:35 PDT)
- Re: AMBER: references about AMBER MD simulations David A. Case (Wed Aug 06 2003 - 23:21:05 PDT)
- Re: AMBER: references about AMBER MD simulations sd233.georgetown.edu (Thu Aug 07 2003 - 08:04:39 PDT)
AMBER: about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 07:05:08 PDT)
- AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 07:58:31 PDT)
  - Re: AMBER: one more line about the npscal, box size changes and rms Andy Purkiss (Thu Aug 07 2003 - 08:30:25 PDT)
  - a bug? Re: AMBER: one more line about the npscal, box size changes and rms Dr. Yong Duan (Thu Aug 07 2003 - 08:49:10 PDT)
    - Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 10:54:17 PDT)
    - Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms David A. Case (Thu Aug 07 2003 - 11:35:46 PDT)
    - AMBER: more than 100,000 atoms ? David Smith (Thu Aug 07 2003 - 12:44:23 PDT)
    - Re: AMBER: more than 100,000 atoms ? Robert Duke (Thu Aug 07 2003 - 13:33:36 PDT)
    - Re: AMBER: more than 100,000 atoms ? David Smith (Fri Aug 08 2003 - 08:17:39 PDT)
    - Re: AMBER: more than 100,000 atoms ? darden (Thu Aug 07 2003 - 14:23:25 PDT)
    - RE: AMBER: more than 100,000 atoms ? Kristina Furse (Fri Aug 08 2003 - 11:14:10 PDT)
    - RE: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Yong Duan (Thu Aug 07 2003 - 11:49:39 PDT)
AMBER: 2D periodic box Vikas Varshney (Thu Aug 07 2003 - 07:50:20 PDT)
- Re: AMBER: 2D periodic box David A. Case (Thu Aug 07 2003 - 09:28:09 PDT)
- Re: AMBER: 2D periodic box Teletchéa Stéphane (Thu Aug 07 2003 - 09:52:01 PDT)
- Re: AMBER: 2D periodic box Ioana Cozmuta (Thu Aug 07 2003 - 10:00:22 PDT)
Re: AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane (Thu Aug 07 2003 - 09:55:03 PDT)
- Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke (Thu Aug 07 2003 - 12:01:39 PDT)
AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 10:57:03 PDT)
- Re: AMBER: mpi in mm-pbsa Holger Gohlke (Thu Aug 07 2003 - 12:22:53 PDT)
- Re: AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 13:14:53 PDT)
AMBER: import pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 12:07:17 PDT)
- Re: AMBER: import pdb file in xleap Vikas Varshney (Thu Aug 07 2003 - 12:21:32 PDT)
  - Re: AMBER: import pdb file in xleap Scott Brozell (Thu Aug 07 2003 - 16:25:18 PDT)
- Re: AMBER: import pdb file in xleap David A. Case (Thu Aug 07 2003 - 14:30:51 PDT)
AMBER: PMEMD and EAMBER Kristina Furse (Thu Aug 07 2003 - 13:32:45 PDT)
- Re: AMBER: PMEMD and EAMBER Robert Duke (Thu Aug 07 2003 - 14:06:11 PDT)
- RE: AMBER: PMEMD and EAMBER Kristina Furse (Fri Aug 08 2003 - 11:33:28 PDT)
- Re: Fw: AMBER: PMEMD and EAMBER Robert Duke (Mon Aug 11 2003 - 06:49:36 PDT)
AMBER: About the limitation of characters on one line in carnal input fi le Ming Lei (Thu Aug 07 2003 - 14:16:26 PDT)
Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 14:31:39 PDT)
- Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 15:01:40 PDT)
AMBER: Insight pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 16:09:47 PDT)
- Re: AMBER: Insight pdb file in xleap Rhonda Torres (Thu Aug 07 2003 - 16:29:47 PDT)
- RE: AMBER: Insight pdb file in xleap Yong Duan (Thu Aug 07 2003 - 16:35:03 PDT)
- AMBER: Insight pdb file in xleap Wayne Dawson (Thu Aug 07 2003 - 19:33:26 PDT)
- Re: AMBER: Insight pdb file in xleap Gaurav Sahni (Thu Aug 07 2003 - 23:25:42 PDT)
AMBER: saveamberprep in xLeap Mi-Kyung Seo (Thu Aug 07 2003 - 20:38:24 PDT)
- Re: AMBER: saveamberprep in xLeap David A. Case (Fri Aug 08 2003 - 09:38:34 PDT)
AMBER: derive corresponding torsional parameters yuann (Fri Aug 08 2003 - 03:25:31 PDT)
- Re: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 06:39:57 PDT)
  - Re[2]: AMBER: derive corresponding torsional parameters sychen (Fri Aug 08 2003 - 08:43:43 PDT)
    - Re: Re[2]: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 09:20:32 PDT)
AMBER: Reference for Amber7 heme parameters Ross Walker (Fri Aug 08 2003 - 04:41:30 PDT)
- Re: AMBER: Reference for Amber7 heme parameters David A. Case (Fri Aug 08 2003 - 08:23:46 PDT)
AMBER: water model tianxiao yang (Fri Aug 08 2003 - 08:10:04 PDT)
AMBER: saveamberprep and saveoff in xLeap Mi-Kyung Seo (Fri Aug 08 2003 - 10:39:37 PDT)
AMBER: PMEMD NMR Restraints fix Robert Duke (Fri Aug 08 2003 - 15:13:08 PDT)
AMBER: MD simulation with ATP and MG Thomas Steinbrecher (Mon Aug 11 2003 - 02:45:08 PDT)
- Re: AMBER: MD simulation with ATP and MG Heather A.Carlson (Mon Aug 11 2003 - 05:11:27 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 03:28:02 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 04:27:56 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 05:28:55 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 06:29:55 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 07:29:55 PDT)
AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 11:39:10 PDT)
- Re: AMBER: machine dependent? David A. Case (Mon Aug 11 2003 - 13:46:14 PDT)
- Re: AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 15:01:38 PDT)
  - Re: AMBER: machine dependent? Michael Crowley (Tue Aug 12 2003 - 07:24:58 PDT)
    - AMBER: secondary structure Yuguang Mu (Wed Aug 13 2003 - 05:37:08 PDT)
    - Re: AMBER: secondary structure Holger Gohlke (Wed Aug 13 2003 - 07:55:22 PDT)
- Re: AMBER: machine dependent? Shuang Ding (Tue Aug 12 2003 - 11:48:00 PDT)
AMBER: GLYCAM Herbert Georg (Mon Aug 11 2003 - 13:57:37 PDT)
AMBER: How to develop parameters for metallic atoms Gustavo A. Carri (Mon Aug 11 2003 - 14:11:19 PDT)
AMBER: "irstrnt=1"in input file for RESP Mi-Kyung Seo (Mon Aug 11 2003 - 15:26:30 PDT)
Instantaneously Dig Up Free Money! Spomer Hooker (Tue Aug 12 2003 - 09:27:34 PDT)
AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 11:56:47 PDT)
- Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. David A. Case (Tue Aug 12 2003 - 12:23:55 PDT)
  - Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 12:46:24 PDT)
- Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Thomas E. Cheatham, III (Tue Aug 12 2003 - 12:32:36 PDT)
  - Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Ioana Cozmuta (Sun Aug 17 2003 - 20:08:00 PDT)
AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 12:38:49 PDT)
- Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 12:51:24 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 15:25:37 PDT)
    - Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 15:39:29 PDT)
    - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 06:00:20 PDT)
- Re: AMBER: constant energy simulation Andreas Svrcek-Seiler (Wed Aug 13 2003 - 06:50:32 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 08:07:29 PDT)
- Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 08:46:52 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 09:09:14 PDT)
    - Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 15:52:56 PDT)
    - Re: AMBER: constant energy simulation Lishan Yao (Thu Aug 14 2003 - 08:53:13 PDT)
AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Tue Aug 12 2003 - 19:50:40 PDT)
- Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 08:06:47 PDT)
  - Re: AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Wed Aug 13 2003 - 09:20:09 PDT)
    - Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 09:28:03 PDT)
AMBER: amber-on-cheetah-question Endres, Robert G. (Wed Aug 13 2003 - 12:20:10 PDT)
AMBER: ANAL component sd233.georgetown.edu (Wed Aug 13 2003 - 14:36:56 PDT)
- Re: AMBER: ANAL component David A. Case (Wed Aug 13 2003 - 15:45:36 PDT)
AMBER: Atom type in prepin file Yong-Liang Zhu (Wed Aug 13 2003 - 15:21:28 PDT)
Re: AMBER: Atom type in prepin file Rhonda Torres (Wed Aug 13 2003 - 15:38:26 PDT)
AMBER: complete pdb structure Mi-Kyung Seo (Wed Aug 13 2003 - 15:41:52 PDT)
- Re: AMBER: complete pdb structure David A. Case (Wed Aug 13 2003 - 22:30:08 PDT)
RE: AMBER: Atom type in prepin file - new problem Yong-Liang Zhu (Wed Aug 13 2003 - 16:05:01 PDT)
- RE: AMBER: Atom type in prepin file - new problem John Bushnell (Wed Aug 13 2003 - 17:01:21 PDT)
AMBER: modelling a Ca binding site Karsten Suhre (Thu Aug 14 2003 - 02:36:53 PDT)
- Re: AMBER: modelling a Ca binding site Xavier Periole (Thu Aug 14 2003 - 10:07:26 PDT)
  - Re: AMBER: modelling a Ca binding site Karsten Suhre (Fri Aug 15 2003 - 02:44:09 PDT)
AMBER: simulating a crystal using the unit cell Sarah Wittkopp (Thu Aug 14 2003 - 04:09:07 PDT)
- Re: AMBER: simulating a crystal using the unit cell David A. Case (Thu Aug 14 2003 - 08:40:42 PDT)
  - AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Fri Aug 15 2003 - 00:07:11 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Fri Aug 15 2003 - 09:17:15 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Mon Aug 18 2003 - 00:33:36 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Mon Aug 18 2003 - 08:08:57 PDT)
- Re: AMBER: simulating a crystal using the unit cell Joseph Nachman (Thu Aug 14 2003 - 09:01:34 PDT)
AMBER: minimization error Venkata S Koppuravuri (Thu Aug 14 2003 - 11:23:39 PDT)
- Re: AMBER: minimization error Xavier Periole (Thu Aug 14 2003 - 11:38:39 PDT)
- Re: AMBER: minimization error David A. Case (Thu Aug 14 2003 - 11:41:43 PDT)
  - RE: AMBER: minimization error Yong Duan (Thu Aug 14 2003 - 13:56:54 PDT)
AMBER: How to add new atom type. Yong-Liang Zhu (Thu Aug 14 2003 - 12:49:49 PDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Fri Aug 15 2003 - 03:16:02 PDT)
AMBER: Gibbs pmf calculation Lishan Yao (Fri Aug 15 2003 - 08:35:51 PDT)
- Re: AMBER: Gibbs pmf calculation David A. Case (Fri Aug 15 2003 - 09:51:07 PDT)
AMBER: protonation states of small molecules Lee, Matthew (Fri Aug 15 2003 - 11:33:40 PDT)
AMBER: NTX 5 or 7 after equilibration in constant pressure? Majid moghaddam (Sat Aug 16 2003 - 00:08:38 PDT)
- Re: AMBER: NTX 5 or 7 after equilibration in constant pressure? David A. Case (Sat Aug 16 2003 - 17:04:18 PDT)
AMBER: Is NTC=2 correct for minimization when hydrogens are added? Majid moghaddam (Sat Aug 16 2003 - 01:00:04 PDT)
- Re: AMBER: Is NTC=2 correct for minimization when hydrogens are added? Alexey Onufriev (Sat Aug 16 2003 - 09:37:35 PDT)
AMBER: minimum image convention mystery Martin Mucha (Sat Aug 16 2003 - 13:42:37 PDT)
- Re: AMBER: minimum image convention mystery David A. Case (Sat Aug 16 2003 - 17:02:03 PDT)
AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Sat Aug 16 2003 - 18:06:14 PDT)
- Re: AMBER: large changes in xyz coordinates David A. Case (Sat Aug 16 2003 - 21:07:25 PDT)
- RE: AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Mon Aug 18 2003 - 10:51:49 PDT)
- RE: AMBER: large changes in xyz coordinates Kristina Furse (Mon Aug 18 2003 - 11:26:27 PDT)
  - RE: AMBER: large changes in xyz coordinates james tomomi macdonald (Mon Aug 18 2003 - 11:35:18 PDT)
AMBER: AMBER 7_make install Krishna Bisetty (Mon Aug 18 2003 - 00:36:37 PDT)
- Re: AMBER: AMBER 7_make install David A. Case (Mon Aug 18 2003 - 08:16:20 PDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Mon Aug 18 2003 - 00:51:51 PDT)
AMBER: united atom weiner force field sohail qamar (Mon Aug 18 2003 - 03:46:18 PDT)
- Re: AMBER: united atom weiner force field David A. Case (Mon Aug 18 2003 - 08:21:03 PDT)
AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Martin Lepsik (Mon Aug 18 2003 - 06:12:51 PDT)
- Re: AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Holger Gohlke (Mon Aug 18 2003 - 08:50:49 PDT)
Re: AMBER: charge method of antechamber(it's ok) Helios Chen (Mon Aug 18 2003 - 06:15:28 PDT)
- Re: AMBER: charge method of antechamber(it's ok) Junmei Wang (Mon Aug 18 2003 - 07:26:41 PDT)
AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 08:18:47 PDT)
- Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 08:45:47 PDT)
  - Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 09:05:20 PDT)
    - Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 09:51:16 PDT)
    - Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 12:52:32 PDT)
Re: AMBER: united atom weiner force field Bill Ross (Mon Aug 18 2003 - 09:12:49 PDT)
AMBER: tleap under amber6 Qiang Lu (Mon Aug 18 2003 - 10:32:05 PDT)
- Re: AMBER: tleap under amber6 David A. Case (Mon Aug 18 2003 - 11:48:19 PDT)
AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 10:41:42 PDT)
- Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 11:44:20 PDT)
  - Re[2]: AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 12:17:30 PDT)
    - Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 12:54:04 PDT)
AMBER: ptraj problem Lishan Yao (Mon Aug 18 2003 - 11:22:43 PDT)
- Re: AMBER: ptraj problem Thomas E. Cheatham, III (Wed Aug 20 2003 - 12:00:57 PDT)
  - Re: AMBER: ptraj problem Lishan Yao (Mon Aug 25 2003 - 06:23:10 PDT)
Returned mail Norton_AntiVirus_Gateways.cemi.rssi.ru (Mon Aug 18 2003 - 13:41:55 PDT)
AMBER: overlap problem Ioana Cozmuta (Mon Aug 18 2003 - 14:26:57 PDT)
- Re: AMBER: overlap problem Xavier Periole (Tue Aug 19 2003 - 09:23:45 PDT)
AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 15:23:20 PDT)
- Re: AMBER: nmanal's error message David Case (Mon Aug 18 2003 - 16:24:11 PDT)
  - Re[2]: AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 17:10:29 PDT)
AMBER: prepin file Helios Chen (Mon Aug 18 2003 - 23:53:27 PDT)
- Re: AMBER: prepin file David A. Case (Tue Aug 19 2003 - 08:45:30 PDT)
AMBER: temperature does not reach to temp0 Majid moghaddam (Tue Aug 19 2003 - 05:32:43 PDT)
- Re: AMBER: temperature does not reach to temp0 David A. Case (Tue Aug 19 2003 - 08:47:15 PDT)
AMBER: minimization termination sd233.georgetown.edu (Tue Aug 19 2003 - 10:40:53 PDT)
AMBER: ptraj problem Lishan Yao (Tue Aug 19 2003 - 14:08:02 PDT)
- Re: AMBER: ptraj problem Bill Ross (Mon Aug 25 2003 - 12:14:23 PDT)
AMBER: nmanal's rvec file Qiang Lu (Tue Aug 19 2003 - 16:19:27 PDT)
- Re: AMBER: nmanal's rvec file David A. Case (Tue Aug 19 2003 - 19:00:19 PDT)
AMBER: PARMSET problem Yichen Cao (Wed Aug 20 2003 - 10:07:29 PDT)
- Re: AMBER: PARMSET problem Junmei Wang (Wed Aug 20 2003 - 11:06:00 PDT)
AMBER: PMEMD 3.01 Update available Robert Duke (Wed Aug 20 2003 - 11:36:56 PDT)
AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 11:56:14 PDT)
- Re: AMBER: antechamber problem David A. Case (Wed Aug 20 2003 - 15:07:30 PDT)
  - Re[2]: AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 15:17:30 PDT)
    - Re[2]: AMBER: antechamber problem Natasja Brooijmans (Wed Aug 20 2003 - 15:26:58 PDT)
    - Re: Re[2]: AMBER: antechamber problem Junmei Wang (Thu Aug 21 2003 - 13:16:02 PDT)
    - Re: Re[2]: AMBER: antechamber problem David A. Case (Thu Aug 21 2003 - 16:34:17 PDT)
    - Re: Re[2]: AMBER: antechamber problem Junmei Wang (Fri Aug 22 2003 - 08:03:23 PDT)
    - AMBER: problems with pmemd james tomomi macdonald (Fri Aug 22 2003 - 08:37:34 PDT)
    - Re: AMBER: problems with pmemd Robert Duke (Fri Aug 22 2003 - 09:45:47 PDT)
AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 20 2003 - 12:24:29 PDT)
- Re: AMBER: gibbs pmf calculation David A. Case (Wed Aug 20 2003 - 15:13:23 PDT)
  - Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 06:16:03 PDT)
    - Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 08:25:27 PDT)
    - Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 14:06:29 PDT)
    - Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 16:07:16 PDT)
    - Re: AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 27 2003 - 08:34:02 PDT)
    - AMBER: RESP calculation Yuhui Cheng (Wed Aug 27 2003 - 19:04:57 PDT)
AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 09:31:06 PDT)
- Re: AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 12:48:17 PDT)
AMBER: The FCAP parameter in amber7 Thomas Steinbrecher (Fri Aug 22 2003 - 02:21:35 PDT)
- Re: AMBER: The FCAP parameter in amber7 David A. Case (Mon Aug 25 2003 - 16:59:45 PDT)
AMBER: PMEMD BUG ALERT!!! Robert Duke (Fri Aug 22 2003 - 13:50:02 PDT)
AMBER: Spartan and AMBER7 Peter Oelschlaeger (Fri Aug 22 2003 - 19:52:21 PDT)
AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Chen, Ya (Fri Aug 22 2003 - 21:47:21 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 05:41:49 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 07:41:42 PDT)
- Fw: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 20:44:06 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Mon Aug 25 2003 - 14:33:38 PDT)
AMBER: temperature problem Lishan Yao (Mon Aug 25 2003 - 06:37:01 PDT)
AMBER: CARNAL Wen Li (Mon Aug 25 2003 - 07:30:19 PDT)
- RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 12:27:42 PDT)
- RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 12:40:29 PDT)
- RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 13:12:50 PDT)
- RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 13:45:13 PDT)
Re: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 12:04:56 PDT)
AMBER: Re: apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 12:20:48 PDT)
AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 13:41:08 PDT)
AMBER: Antechamber formal charges with Gasteiger method Lee, Matthew (Tue Aug 26 2003 - 11:07:14 PDT)
- Re: AMBER: Antechamber formal charges with Gasteiger method Junmei Wang (Tue Aug 26 2003 - 12:55:14 PDT)
AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space zhaoxc.puccini.che.pitt.edu (Tue Aug 26 2003 - 16:17:00 PDT)
- Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space David A. Case (Tue Aug 26 2003 - 18:32:20 PDT)
  - Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space Robert Duke (Tue Aug 26 2003 - 18:53:06 PDT)
  - AMBER: Antechamber Problem Yuhui Cheng (Wed Aug 27 2003 - 09:31:43 PDT)
    - Re: AMBER: Antechamber Problem Junmei Wang (Thu Aug 28 2003 - 10:16:24 PDT)
AMBER: xleap memory issue Terry Downing (Tue Aug 26 2003 - 17:30:06 PDT)
- Re: AMBER: xleap memory issue David A. Case (Tue Aug 26 2003 - 18:25:29 PDT)
Re: AMBER: xleap memory issue Bill Ross (Tue Aug 26 2003 - 17:52:40 PDT)
AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 07:50:01 PDT)
- Re: AMBER: LEaP not compiling David A. Case (Wed Aug 27 2003 - 08:42:49 PDT)
  - RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 08:58:52 PDT)
    - RE: AMBER: LEaP not compiling John Bushnell (Wed Aug 27 2003 - 14:56:32 PDT)
    - RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 21:58:24 PDT)
AMBER: target MD simulation Lishan Yao (Wed Aug 27 2003 - 11:01:46 PDT)
- Re: AMBER: target MD simulation Carlos Simmerling (Wed Aug 27 2003 - 12:59:09 PDT)
- Re: AMBER: target MD simulation David A. Case (Wed Aug 27 2003 - 13:39:31 PDT)
AMBER: PMF calculation with gibbs Xiao Jian Tan (Wed Aug 27 2003 - 15:34:16 PDT)
AMBER: "ATTN, need revision" atobak.eden.rutgers.edu (Thu Aug 28 2003 - 09:31:05 PDT)
- Re: AMBER: "ATTN, need revision" Junmei Wang (Thu Aug 28 2003 - 10:06:46 PDT)
AMBER: forces estimation Ioana Cozmuta (Thu Aug 28 2003 - 11:54:52 PDT)
AMBER: what can't I use ibelly? nie beining (Thu Aug 28 2003 - 12:30:23 PDT)
- Re: AMBER: what can't I use ibelly? David A. Case (Thu Aug 28 2003 - 12:40:55 PDT)
  - AMBER: Could you please give me an example? Thanks! nie beining (Thu Aug 28 2003 - 13:04:00 PDT)
AMBER: Fxnal form of NMR-style restraints Kristina Furse (Thu Aug 28 2003 - 14:41:56 PDT)
- Re: AMBER: Fxnal form of NMR-style restraints Holger Gohlke (Thu Aug 28 2003 - 15:41:04 PDT)
AMBER: usability of mm_pbsa with ligand - membrane protein - complex Frank Boeckler (Thu Aug 28 2003 - 15:20:09 PDT)
- Re: AMBER: usability of mm_pbsa with ligand - membrane protein - complex Holger Gohlke (Thu Aug 28 2003 - 16:01:11 PDT)
AMBER: AmberFFC v1.3 released FyD (Fri Aug 29 2003 - 09:35:12 PDT)
AMBER: sander minimization atobak.eden.rutgers.edu (Fri Aug 29 2003 - 13:39:58 PDT)
- Re: AMBER: sander minimization Qiang Lu (Fri Aug 29 2003 - 14:13:53 PDT)
- Re: AMBER: sander minimization David A. Case (Fri Aug 29 2003 - 14:32:55 PDT)

Amber Archive Aug 2003 By Thread