AMBER Archive (2003) - Aug 2003 By ThreadMost recent messages
286 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
Starting: Fri Aug 01 2003 - 01:12:33 CDT
Ending: Fri Aug 29 2003 - 16:32:55 CDT
- AMBER: about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 09:05:08 CDT)
- AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 09:58:31 CDT)
- Re: AMBER: one more line about the npscal, box size changes and rms Andy Purkiss (Thu Aug 07 2003 - 10:30:25 CDT)
- a bug? Re: AMBER: one more line about the npscal, box size changes and rms Dr. Yong Duan (Thu Aug 07 2003 - 10:49:10 CDT)
- Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 12:54:17 CDT)
- Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms David A. Case (Thu Aug 07 2003 - 13:35:46 CDT)
- AMBER: more than 100,000 atoms ? David Smith (Thu Aug 07 2003 - 14:44:23 CDT)
- Re: AMBER: more than 100,000 atoms ? Robert Duke (Thu Aug 07 2003 - 15:33:36 CDT)
- Re: AMBER: more than 100,000 atoms ? David Smith (Fri Aug 08 2003 - 10:17:39 CDT)
- Re: AMBER: more than 100,000 atoms ? darden (Thu Aug 07 2003 - 16:23:25 CDT)
- RE: AMBER: more than 100,000 atoms ? Kristina Furse (Fri Aug 08 2003 - 13:14:10 CDT)
- RE: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Yong Duan (Thu Aug 07 2003 - 13:49:39 CDT)
- AMBER: parallelisation gold gunaseelan (Fri Aug 01 2003 - 01:13:21 CDT)
- AMBER: parallelisation gold gunaseelan (Fri Aug 01 2003 - 01:12:33 CDT)
- AMBER: Amber parallelisation arun prasad (Fri Aug 01 2003 - 04:15:05 CDT)
- AMBER: Problem generating .tpp and .rst files for a complex Yogesh Sabnis (Fri Aug 01 2003 - 05:57:07 CDT)
- AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Fri Aug 01 2003 - 05:59:08 CDT)
- AMBER: AMBER7 & mpich takanori.kanazawa_at_pharma.novartis.com (Sat Aug 02 2003 - 07:17:52 CDT)
- AMBER: AMBER7 & mpich : (no-attachment version) takanori.kanazawa_at_pharma.novartis.com (Sat Aug 02 2003 - 08:03:06 CDT)
- AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 21:35:48 CDT)
- AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 21:34:24 CDT)
- AMBER: charge method of antechamber Helios Chen (Sun Aug 03 2003 - 23:00:35 CDT)
- AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 02:32:48 CDT)
- AMBER: separate thermostats for different molecules Arvid Soederhaell (Mon Aug 04 2003 - 08:13:11 CDT)
- AMBER: normal mode analysis Marcela Madrid (Mon Aug 04 2003 - 13:03:23 CDT)
- AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa_at_pharma.novartis.com (Mon Aug 04 2003 - 18:51:17 CDT)
- AMBER: (no subject) Narang Manpreet Kaur (Tue Aug 05 2003 - 08:55:57 CDT)
- AMBER: parallelisation gold gunaseelan (Tue Aug 05 2003 - 08:55:31 CDT)
- AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 09:03:59 CDT)
- AMBER: compile problem? Shuang Ding (Tue Aug 05 2003 - 15:51:25 CDT)
- AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 11:14:03 CDT)
- AMBER: problem regarding surface Vikas Varshney (Wed Aug 06 2003 - 12:00:09 CDT)
- AMBER: anal - memory problem sd233_at_georgetown.edu (Wed Aug 06 2003 - 12:02:44 CDT)
- AMBER: SHAKE Problem Richard Smith (Wed Aug 06 2003 - 15:02:30 CDT)
- AMBER: Re: dynamics of isolated system (fwd) David A. Case (Wed Aug 06 2003 - 16:43:29 CDT)
- AMBER: references about AMBER MD simulations sd233_at_georgetown.edu (Thu Aug 07 2003 - 00:23:35 CDT)
- AMBER: 2D periodic box Vikas Varshney (Thu Aug 07 2003 - 09:50:20 CDT)
- AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 12:57:03 CDT)
- AMBER: import pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 14:07:17 CDT)
- AMBER: PMEMD and EAMBER Kristina Furse (Thu Aug 07 2003 - 15:32:45 CDT)
- AMBER: About the limitation of characters on one line in carnal input fi le Ming Lei (Thu Aug 07 2003 - 16:16:26 CDT)
- Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 17:01:40 CDT)
- AMBER: Insight pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 18:09:47 CDT)
- AMBER: saveamberprep in xLeap Mi-Kyung Seo (Thu Aug 07 2003 - 22:38:24 CDT)
- AMBER: derive corresponding torsional parameters yuann (Fri Aug 08 2003 - 05:25:31 CDT)
- AMBER: Reference for Amber7 heme parameters Ross Walker (Fri Aug 08 2003 - 06:41:30 CDT)
- AMBER: water model tianxiao yang (Fri Aug 08 2003 - 10:10:04 CDT)
- AMBER: saveamberprep and saveoff in xLeap Mi-Kyung Seo (Fri Aug 08 2003 - 12:39:37 CDT)
- AMBER: PMEMD NMR Restraints fix Robert Duke (Fri Aug 08 2003 - 17:13:08 CDT)
- AMBER: MD simulation with ATP and MG Thomas Steinbrecher (Mon Aug 11 2003 - 04:45:08 CDT)
- AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 13:39:10 CDT)
- AMBER: GLYCAM Herbert Georg (Mon Aug 11 2003 - 15:57:37 CDT)
- AMBER: How to develop parameters for metallic atoms Gustavo A. Carri (Mon Aug 11 2003 - 16:11:19 CDT)
- AMBER: "irstrnt=1"in input file for RESP Mi-Kyung Seo (Mon Aug 11 2003 - 17:26:30 CDT)
- AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 13:56:47 CDT)
- AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 14:38:49 CDT)
- AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Tue Aug 12 2003 - 21:50:40 CDT)
- AMBER: amber-on-cheetah-question Endres, Robert G. (Wed Aug 13 2003 - 14:20:10 CDT)
- AMBER: ANAL component sd233_at_georgetown.edu (Wed Aug 13 2003 - 16:36:56 CDT)
- AMBER: Atom type in prepin file Yong-Liang Zhu (Wed Aug 13 2003 - 17:21:28 CDT)
- Re: AMBER: Atom type in prepin file Rhonda Torres (Wed Aug 13 2003 - 17:38:26 CDT)
- AMBER: complete pdb structure Mi-Kyung Seo (Wed Aug 13 2003 - 17:41:52 CDT)
- RE: AMBER: Atom type in prepin file - new problem Yong-Liang Zhu (Wed Aug 13 2003 - 18:05:01 CDT)
- AMBER: modelling a Ca binding site Karsten Suhre (Thu Aug 14 2003 - 04:36:53 CDT)
- AMBER: simulating a crystal using the unit cell Sarah Wittkopp (Thu Aug 14 2003 - 06:09:07 CDT)
- AMBER: minimization error Venkata S Koppuravuri (Thu Aug 14 2003 - 13:23:39 CDT)
- AMBER: How to add new atom type. Yong-Liang Zhu (Thu Aug 14 2003 - 14:49:49 CDT)
- AMBER: Hydrogen bond plot from carnal Layi Adekoya (Fri Aug 15 2003 - 05:16:02 CDT)
- AMBER: Gibbs pmf calculation Lishan Yao (Fri Aug 15 2003 - 10:35:51 CDT)
- AMBER: protonation states of small molecules Lee, Matthew (Fri Aug 15 2003 - 13:33:40 CDT)
- AMBER: NTX 5 or 7 after equilibration in constant pressure? Majid moghaddam (Sat Aug 16 2003 - 02:08:38 CDT)
- AMBER: Is NTC=2 correct for minimization when hydrogens are added? Majid moghaddam (Sat Aug 16 2003 - 03:00:04 CDT)
- AMBER: minimum image convention mystery Martin Mucha (Sat Aug 16 2003 - 15:42:37 CDT)
- AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Sat Aug 16 2003 - 20:06:14 CDT)
- AMBER: AMBER 7_make install Krishna Bisetty (Mon Aug 18 2003 - 02:36:37 CDT)
- AMBER: Hydrogen bond plot from carnal Layi Adekoya (Mon Aug 18 2003 - 02:51:51 CDT)
- AMBER: united atom weiner force field sohail qamar (Mon Aug 18 2003 - 05:46:18 CDT)
- AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Martin Lepsik (Mon Aug 18 2003 - 08:12:51 CDT)
- Re: AMBER: charge method of antechamber(it's ok) Helios Chen (Mon Aug 18 2003 - 08:15:28 CDT)
- AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 10:18:47 CDT)
- Re: AMBER: united atom weiner force field Bill Ross (Mon Aug 18 2003 - 11:12:49 CDT)
- AMBER: tleap under amber6 Qiang Lu (Mon Aug 18 2003 - 12:32:05 CDT)
- AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 12:41:42 CDT)
- AMBER: ptraj problem Lishan Yao (Mon Aug 18 2003 - 13:22:43 CDT)
- AMBER: overlap problem Ioana Cozmuta (Mon Aug 18 2003 - 16:26:57 CDT)
- AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 17:23:20 CDT)
- AMBER: prepin file Helios Chen (Tue Aug 19 2003 - 01:53:27 CDT)
- AMBER: temperature does not reach to temp0 Majid moghaddam (Tue Aug 19 2003 - 07:32:43 CDT)
- AMBER: ptraj problem Lishan Yao (Tue Aug 19 2003 - 16:08:02 CDT)
- AMBER: nmanal's rvec file Qiang Lu (Tue Aug 19 2003 - 18:19:27 CDT)
- AMBER: minimization termination sd233_at_georgetown.edu (Tue Aug 19 2003 - 12:40:53 CDT)
- AMBER: PARMSET problem Yichen Cao (Wed Aug 20 2003 - 12:07:29 CDT)
- AMBER: PMEMD 3.01 Update available Robert Duke (Wed Aug 20 2003 - 13:36:56 CDT)
- AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 13:56:14 CDT)
- AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 20 2003 - 14:24:29 CDT)
- AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 11:31:06 CDT)
- AMBER: The FCAP parameter in amber7 Thomas Steinbrecher (Fri Aug 22 2003 - 04:21:35 CDT)
- AMBER: PMEMD BUG ALERT!!! Robert Duke (Fri Aug 22 2003 - 15:50:02 CDT)
- AMBER: Spartan and AMBER7 Peter Oelschlaeger (Fri Aug 22 2003 - 21:52:21 CDT)
- AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Chen, Ya (Fri Aug 22 2003 - 23:47:21 CDT)
- AMBER: temperature problem Lishan Yao (Mon Aug 25 2003 - 08:37:01 CDT)
- AMBER: CARNAL Wen Li (Mon Aug 25 2003 - 09:30:19 CDT)
- AMBER: Re: apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 14:20:48 CDT)
- AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 15:41:08 CDT)
- Re: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 14:04:56 CDT)
- AMBER: Antechamber formal charges with Gasteiger method Lee, Matthew (Tue Aug 26 2003 - 13:07:14 CDT)
- AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space zhaoxc_at_puccini.che.pitt.edu (Tue Aug 26 2003 - 18:17:00 CDT)
- AMBER: xleap memory issue Terry Downing (Tue Aug 26 2003 - 19:30:06 CDT)
- Re: AMBER: xleap memory issue Bill Ross (Tue Aug 26 2003 - 19:52:40 CDT)
- AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 09:50:01 CDT)
- AMBER: target MD simulation Lishan Yao (Wed Aug 27 2003 - 13:01:46 CDT)
- AMBER: PMF calculation with gibbs Xiao Jian Tan (Wed Aug 27 2003 - 17:34:16 CDT)
- AMBER: "ATTN, need revision" atobak_at_eden.rutgers.edu (Thu Aug 28 2003 - 11:31:05 CDT)
- AMBER: forces estimation Ioana Cozmuta (Thu Aug 28 2003 - 13:54:52 CDT)
- AMBER: what can't I use ibelly? nie beining (Thu Aug 28 2003 - 14:30:23 CDT)
- AMBER: Fxnal form of NMR-style restraints Kristina Furse (Thu Aug 28 2003 - 16:41:56 CDT)
- AMBER: usability of mm_pbsa with ligand - membrane protein - complex Frank Boeckler (Thu Aug 28 2003 - 17:20:09 CDT)
- AMBER: AmberFFC v1.3 released FyD (Fri Aug 29 2003 - 11:35:12 CDT)
- AMBER: sander minimization atobak_at_eden.rutgers.edu (Fri Aug 29 2003 - 15:39:58 CDT)
Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:44 CDT
286 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
|