Amber Archive Oct 2007: by subject

about deoxy- and oxy- heme
- Yang, Lee-Wei (Sun Oct 28 2007 - 01:52:58 PDT)
Amber query !!
- Ross Walker (Mon Oct 08 2007 - 10:02:36 PDT)
AMBER: &dipole input and some questions on using polarizable force fields
- David A. Case (Wed Oct 31 2007 - 07:38:34 PDT)
- Seongeun Yang (Tue Oct 30 2007 - 20:52:45 PDT)
- David A. Case (Tue Oct 30 2007 - 08:58:20 PDT)
- Seongeun Yang (Tue Oct 30 2007 - 08:19:32 PDT)
- David A. Case (Tue Oct 30 2007 - 06:42:44 PDT)
- Seongeun Yang (Mon Oct 29 2007 - 23:14:13 PDT)
- Ross Walker (Mon Oct 29 2007 - 08:31:00 PDT)
- Seongeun Yang (Fri Oct 26 2007 - 22:03:36 PDT)
- Ross Walker (Fri Oct 26 2007 - 09:28:57 PDT)
- Seongeun Yang (Thu Oct 25 2007 - 06:11:48 PDT)
AMBER: 31 integers in the first section of a prmtop file
- David Cerutti (Wed Oct 03 2007 - 13:04:35 PDT)
- Carlos Simmerling (Wed Oct 03 2007 - 11:54:22 PDT)
- David Cerutti (Wed Oct 03 2007 - 11:47:42 PDT)
- Ross Walker (Wed Oct 03 2007 - 10:32:12 PDT)
- Carlos Simmerling (Wed Oct 03 2007 - 10:15:14 PDT)
- David Cerutti (Wed Oct 03 2007 - 09:58:03 PDT)
AMBER: Abnormality in MM-PBSA result
- Thomas Cheatham III (Fri Oct 19 2007 - 08:56:36 PDT)
- msubhamoy.ibab.ac.in (Fri Oct 19 2007 - 08:01:16 PDT)
AMBER: Addendum: Heat capacity calculations not coming out right
- David Cerutti (Sat Oct 20 2007 - 15:47:05 PDT)
- Robert Duke (Fri Oct 19 2007 - 21:24:30 PDT)
- David Cerutti (Fri Oct 19 2007 - 20:31:46 PDT)
AMBER: adding extra points to amber - how to?
- Jones de Andrade (Mon Oct 08 2007 - 09:44:42 PDT)
AMBER: AMBER 8: QMMM - molecule fluctuates wildly
- Ross Walker (Mon Oct 29 2007 - 14:06:45 PDT)
- Seth Lilavivat (Mon Oct 29 2007 - 13:40:06 PDT)
AMBER: AMBER 9 - Force Field Options - Question
- Yong Duan (Thu Oct 18 2007 - 12:18:01 PDT)
- Adrian Roitberg (Thu Oct 18 2007 - 11:56:23 PDT)
- Yong Duan (Thu Oct 18 2007 - 09:21:00 PDT)
- Carlos Simmerling (Thu Oct 18 2007 - 03:06:44 PDT)
- Yong Duan (Wed Oct 17 2007 - 13:47:55 PDT)
- WANG,YING (Wed Oct 17 2007 - 12:11:19 PDT)
- Adrian Roitberg (Wed Oct 17 2007 - 11:26:56 PDT)
- Yong Duan (Wed Oct 17 2007 - 09:25:16 PDT)
- WANG,YING (Wed Oct 17 2007 - 08:47:05 PDT)
- dpandit.brandeis.edu (Wed Oct 17 2007 - 08:27:12 PDT)
- Carlos Simmerling (Wed Oct 17 2007 - 06:54:51 PDT)
- dpandit.brandeis.edu (Tue Oct 16 2007 - 13:41:33 PDT)
AMBER: Amber 9 source code permissions (UNCLASSIFIED)
- Ross Walker (Mon Oct 29 2007 - 16:18:50 PDT)
- Monaghan, Martin (Cont, ARL/CISD) (Mon Oct 29 2007 - 14:30:30 PDT)
AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)
- David A. Case (Wed Oct 31 2007 - 14:52:18 PDT)
- sanket deshmukh (Wed Oct 31 2007 - 11:57:54 PDT)
AMBER: Amber FF parameters for the Zinc-hydroxammate interaction
- snoze pa (Sun Oct 28 2007 - 17:59:26 PDT)
AMBER: amber with periodic condition
- Mattia Mori - CERM (Mon Oct 29 2007 - 10:16:14 PDT)
AMBER: Amber9 installation error on Mandriva 2007 linux
- Mark Williamson (Mon Oct 08 2007 - 10:31:39 PDT)
- Joe Nolan (Mon Oct 08 2007 - 10:07:58 PDT)
AMBER: amber9 installation problem
- Scott Brozell (Tue Oct 16 2007 - 10:15:04 PDT)
- Madjid Taghdir (Tue Oct 16 2007 - 01:46:05 PDT)
AMBER: amber9 parallel compile problem
- Ross Walker (Wed Oct 31 2007 - 10:36:00 PDT)
- Christopher Jones (Wed Oct 31 2007 - 10:09:32 PDT)
AMBER: Amber9 parallel installation error (retry)
- Joe Nolan (Tue Oct 30 2007 - 11:25:35 PDT)
AMBER: Amber9 parallel installation error (with openMPI)
- Joe Nolan (Mon Oct 29 2007 - 15:30:25 PDT)
- Wei Zhang (Mon Oct 29 2007 - 15:16:49 PDT)
- Joe Nolan (Mon Oct 29 2007 - 14:55:43 PDT)
- Wei Zhang (Mon Oct 29 2007 - 14:16:45 PDT)
- Joe Nolan (Mon Oct 29 2007 - 14:02:10 PDT)
AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690
- David Mobley (Wed Oct 24 2007 - 07:20:43 PDT)
- Catein Catherine (Wed Oct 24 2007 - 05:04:42 PDT)
AMBER: anal
- gurpreet singh (Wed Oct 17 2007 - 21:35:23 PDT)
AMBER: anal calculation error
- gurpreet singh (Tue Oct 16 2007 - 10:07:20 PDT)
AMBER: anal calculatons
- cgji (Mon Oct 15 2007 - 22:48:09 PDT)
- gurpreet singh (Mon Oct 15 2007 - 21:17:47 PDT)
- Eddie Men (Mon Oct 15 2007 - 00:43:02 PDT)
- gurpreet singh (Mon Oct 15 2007 - 00:19:33 PDT)
AMBER: anal error
- gurpreet singh (Wed Oct 17 2007 - 11:14:52 PDT)
AMBER: anal problem
- varsha rani (Tue Oct 30 2007 - 04:48:03 PDT)
AMBER: ANGVE/TORAVE
- Kyle Brown (Thu Oct 25 2007 - 11:33:52 PDT)
- Abi Ghanem josephine (Thu Oct 25 2007 - 08:58:11 PDT)
AMBER: antechamber fails with large molecules
- Junmei Wang (Wed Oct 31 2007 - 21:43:49 PDT)
- FyD (Wed Oct 31 2007 - 07:02:36 PDT)
- VANIA MARIA AMARO CALISTO (Wed Oct 31 2007 - 02:26:14 PDT)
AMBER: Applying bugfixes in Amber
- Ross Walker (Thu Oct 04 2007 - 14:53:31 PDT)
- Lili Peng (Thu Oct 04 2007 - 14:28:29 PDT)
AMBER: atomicfluct
- Andres Palencia (Mon Oct 01 2007 - 11:12:20 PDT)
AMBER: Average absolute value of cross velocity (Rate constant from PMF)
- David A. Case (Fri Oct 26 2007 - 08:22:40 PDT)
- Catein Catherine (Fri Oct 26 2007 - 00:26:58 PDT)
AMBER: Backbone flexibility/entropy
- Seth Lilavivat (Thu Oct 18 2007 - 14:47:37 PDT)
AMBER: Beowulf cluster from PSSC Labs
- Ross Walker (Tue Oct 23 2007 - 10:28:29 PDT)
- Aaron Greenwood (Tue Oct 23 2007 - 09:22:33 PDT)
AMBER: binary restart file
- Myunggi Yi (Sun Oct 07 2007 - 16:39:44 PDT)
- Gustavo Seabra (Fri Oct 05 2007 - 20:56:02 PDT)
- Myunggi Yi (Thu Oct 04 2007 - 07:49:28 PDT)
AMBER: BOMB!
- Scott Brozell (Thu Oct 11 2007 - 16:59:50 PDT)
- Eddie Men (Thu Oct 11 2007 - 03:12:49 PDT)
AMBER: calculation of angle between helices
- Anupam Nath Jha (Sun Oct 28 2007 - 23:06:37 PDT)
AMBER: Constant pH
- Eddie Men (Tue Oct 02 2007 - 02:41:31 PDT)
- Eddie Men (Tue Oct 02 2007 - 02:45:34 PDT)
AMBER: constant-pH MD with replica exchange
- Adrian Roitberg (Thu Oct 11 2007 - 11:55:18 PDT)
- Carlos Simmerling (Thu Oct 11 2007 - 11:30:34 PDT)
- Adrian Roitberg (Thu Oct 11 2007 - 08:33:30 PDT)
- Maciej Dlugosz (Wed Oct 10 2007 - 23:38:49 PDT)
AMBER: cyclohexane and decalin on amber
- Jones de Andrade (Tue Oct 02 2007 - 20:12:48 PDT)
- FyD (Mon Oct 01 2007 - 00:20:29 PDT)
- Jones de Andrade (Sun Sep 30 2007 - 22:46:44 PDT)
AMBER: dihedral angles
- David A. Case (Wed Oct 31 2007 - 21:09:24 PDT)
- Jardas sucuriba (Tue Oct 30 2007 - 17:43:10 PDT)
AMBER: dihedrals
- Carlos Simmerling (Tue Oct 02 2007 - 03:13:12 PDT)
- FyD (Mon Oct 01 2007 - 23:36:30 PDT)
- Ed Pate (Mon Oct 01 2007 - 16:07:47 PDT)
AMBER: Energy calculations.
- Karen Callahan (Thu Oct 18 2007 - 12:15:29 PDT)
AMBER: entropy with ptraj
- David A. Case (Mon Oct 08 2007 - 06:47:57 PDT)
- Marius Retegan (Mon Oct 08 2007 - 05:24:36 PDT)
AMBER: error in modified PNA -DNA simulation..
- Scott Brozell (Thu Oct 11 2007 - 17:26:11 PDT)
- Sharad gupta (Wed Oct 10 2007 - 03:39:07 PDT)
AMBER: error in modified PNA DNA simulation
- Sharad gupta (Sun Oct 14 2007 - 22:35:13 PDT)
AMBER: error while Running TMD
- Carlos Simmerling (Thu Oct 18 2007 - 03:01:07 PDT)
- gurpreet singh (Wed Oct 17 2007 - 21:19:54 PDT)
- Carlos Simmerling (Wed Oct 17 2007 - 11:50:45 PDT)
- gurpreet singh (Wed Oct 17 2007 - 11:21:18 PDT)
AMBER: Error- MM_PBSA calculation
- Scott Pendley (Thu Oct 11 2007 - 14:56:43 PDT)
- vikky 99 (Thu Oct 11 2007 - 08:01:23 PDT)
- vikky 99 (Thu Oct 11 2007 - 00:28:25 PDT)
- vikky 99 (Wed Oct 10 2007 - 10:44:53 PDT)
AMBER: EVB Calculations
- Jimmy Heimdal (Sun Oct 21 2007 - 23:30:48 PDT)
AMBER: ff99SB and the N- and C- charged terminal residues
- Carlos Simmerling (Wed Oct 10 2007 - 10:37:13 PDT)
- Nicolas Lux Fawzi (Wed Oct 10 2007 - 09:03:09 PDT)
AMBER: follow-up
- Ross Walker (Tue Oct 09 2007 - 14:24:50 PDT)
- Wenyong Tong (Tue Oct 09 2007 - 13:56:04 PDT)
AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander
- Thomas Steinbrecher (Thu Oct 18 2007 - 16:43:47 PDT)
- Jiapu.Zhang.csiro.au (Thu Oct 18 2007 - 16:15:05 PDT)
AMBER: generating topology files for PBSA
- saccenti.cerm.unifi.it (Fri Oct 05 2007 - 02:46:14 PDT)
AMBER: Getting prmtop and inpcrd
- Bill Ross (Mon Oct 29 2007 - 12:26:16 PDT)
- Francesco Pietra (Mon Oct 29 2007 - 09:51:23 PDT)
- Carlos Simmerling (Mon Oct 29 2007 - 08:47:33 PDT)
- Francesco Pietra (Mon Oct 29 2007 - 08:43:44 PDT)
AMBER: gibbs problems
- David A. Case (Wed Oct 31 2007 - 21:09:35 PDT)
- JAVIER PEREZ (Wed Oct 31 2007 - 04:48:22 PDT)
AMBER: hbond analysis output
- Steve Spronk (Thu Oct 25 2007 - 06:10:05 PDT)
- Claire Zerafa (Wed Oct 24 2007 - 12:21:02 PDT)
AMBER: Heat capacity calculations not coming out right
- David Cerutti (Fri Oct 19 2007 - 19:37:38 PDT)
AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?
- David A. Case (Tue Oct 09 2007 - 07:09:02 PDT)
- Steven Winfield (Tue Oct 09 2007 - 03:06:53 PDT)
- David Cerutti (Mon Oct 08 2007 - 22:25:43 PDT)
AMBER: Heme and CYS !!
- Pradipta Bandyopadhyay (Fri Oct 26 2007 - 03:49:47 PDT)
AMBER: heme forcefield atom types
- Yang, Lee-Wei (Wed Oct 24 2007 - 11:41:29 PDT)
- L. W. Yang (Wed Oct 24 2007 - 09:18:31 PDT)
AMBER: hey
- Eduardo Mendez (Sat Oct 06 2007 - 22:19:36 PDT)
AMBER: HG atoms in CYX residues
- David A. Case (Fri Oct 26 2007 - 08:28:36 PDT)
- Carlos Simmerling (Fri Oct 26 2007 - 03:20:05 PDT)
- francesco zonta (Fri Oct 26 2007 - 02:45:32 PDT)
AMBER: How can i calculate generalized order parameters using ptraj.
- cgji (Sun Oct 28 2007 - 07:59:37 PDT)
AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca
- Catein Catherine (Fri Oct 26 2007 - 00:28:57 PDT)
AMBER: How to get sane package
- David A. Case (Wed Oct 31 2007 - 21:09:08 PDT)
- caoch (Tue Oct 02 2007 - 03:09:26 PDT)
AMBER: How to intergrate the area under a curve.
- Ilyas Yildirim (Mon Oct 22 2007 - 00:17:07 PDT)
- Catein Catherine (Sun Oct 21 2007 - 23:34:16 PDT)
AMBER: how to simulate a ligand bound to a residue
- FyD (Thu Oct 18 2007 - 14:02:13 PDT)
- Thomas Steinbrecher (Thu Oct 18 2007 - 11:29:25 PDT)
- Jena M (Thu Oct 18 2007 - 06:49:55 PDT)
AMBER: How to use loadpdbusingseq command to load branched structure?
- Siang Yip (Fri Oct 19 2007 - 10:21:36 PDT)
AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
- Ray Luo (Fri Oct 26 2007 - 10:31:03 PDT)
- Yang, Lee-Wei (Thu Oct 25 2007 - 22:52:56 PDT)
- Ray Luo (Thu Oct 25 2007 - 11:20:14 PDT)
- Yang, Lee-Wei (Thu Oct 25 2007 - 07:46:00 PDT)
AMBER: interaction energy calculations
- Scott Pendley (Tue Oct 09 2007 - 13:51:25 PDT)
- gurpreet singh (Tue Oct 09 2007 - 10:06:24 PDT)
AMBER: Interactive Molecular Dynamics with Amber?
- Marc Baaden (Sat Oct 20 2007 - 15:10:23 PDT)
AMBER: lipid bilayer
- cgji (Thu Oct 11 2007 - 07:38:45 PDT)
- Vlad Cojocaru (Thu Oct 11 2007 - 05:09:23 PDT)
- san_amber roy (Thu Oct 11 2007 - 04:52:42 PDT)
AMBER: MAXPR
- san_amber roy (Mon Oct 01 2007 - 23:58:03 PDT)
- Ross Walker (Mon Oct 01 2007 - 08:30:46 PDT)
- san_amber roy (Mon Oct 01 2007 - 01:10:35 PDT)
AMBER: mdfil: Error unknown flag: -p4pg
- Aaron Greenwood (Tue Oct 30 2007 - 05:03:29 PDT)
- David A. Case (Mon Oct 29 2007 - 19:46:01 PDT)
- Aaron Greenwood (Mon Oct 29 2007 - 12:38:44 PDT)
AMBER: Missing 'yacc' command
- Hopkins, Robert (Sat Oct 13 2007 - 15:00:00 PDT)
AMBER: MM_PBSA calcultion- help me
- varsha rani (Tue Oct 16 2007 - 22:40:48 PDT)
- Scott Pendley (Tue Oct 16 2007 - 10:24:34 PDT)
- S.Sundar Raman (Tue Oct 16 2007 - 06:58:50 PDT)
- varsha rani (Mon Oct 15 2007 - 22:53:14 PDT)
AMBER: mm_pbsa: missing values in ras-raf tutorials
- merc mertens (Fri Oct 19 2007 - 01:28:09 PDT)
AMBER: multi chain simulations
- Carlos Simmerling (Thu Oct 04 2007 - 12:43:44 PDT)
- priya priya (Thu Oct 04 2007 - 05:44:56 PDT)
- Carlos Simmerling (Thu Oct 04 2007 - 04:28:46 PDT)
- priya priya (Thu Oct 04 2007 - 04:07:44 PDT)
- Carlos Simmerling (Thu Oct 04 2007 - 03:35:22 PDT)
- priya priya (Thu Oct 04 2007 - 03:30:27 PDT)
AMBER: multichain simulations
- priya priya (Tue Oct 02 2007 - 02:31:26 PDT)
AMBER: neb for path between binding sites
- Holly Freedman (Tue Oct 09 2007 - 16:35:19 PDT)
- Holly Freedman (Tue Oct 09 2007 - 16:37:20 PDT)
- Carlos Simmerling (Tue Oct 09 2007 - 14:25:27 PDT)
- Holly Freedman (Tue Oct 09 2007 - 14:09:50 PDT)
AMBER: parameterization for copper
- Syed Tarique Moin (Wed Oct 03 2007 - 03:45:33 PDT)
AMBER: PB Bomb
- Eddie Men (Sun Oct 07 2007 - 01:03:52 PDT)
- Eddie Men (Sun Oct 07 2007 - 00:10:59 PDT)
AMBER: PBSA generate snapshots
- saccenti.cerm.unifi.it (Thu Oct 04 2007 - 02:17:04 PDT)
AMBER: Please Disregard My Last E-mail: Missing 'yacc' command
- Hopkins, Robert (Sat Oct 13 2007 - 16:04:11 PDT)
AMBER: PMEMD configuration and scaling
- Lars Skjærven (Tue Oct 09 2007 - 06:56:09 PDT)
- Robert Duke (Tue Oct 09 2007 - 06:15:34 PDT)
- Lars.Skjarven.biomed.uib.no (Tue Oct 09 2007 - 03:05:37 PDT)
- Robert Duke (Sun Oct 07 2007 - 08:04:03 PDT)
- Lars.Skjarven.biomed.uib.no (Sun Oct 07 2007 - 03:40:00 PDT)
- Ross Walker (Sat Oct 06 2007 - 09:27:16 PDT)
- Robert Duke (Sat Oct 06 2007 - 06:20:16 PDT)
- Lars.Skjarven.biomed.uib.no (Sat Oct 06 2007 - 04:35:03 PDT)
AMBER: Polarizable Force Field: Ligand Parameterization et al.
- Catein Catherine (Fri Oct 26 2007 - 00:17:16 PDT)
- Yong Duan (Thu Oct 25 2007 - 10:02:55 PDT)
- Anselm Horn (Thu Oct 25 2007 - 02:00:03 PDT)
AMBER: Portland Group vs. Intel Compilers.
- Andreas Svrcek-Seiler (Tue Oct 23 2007 - 13:24:29 PDT)
- Ross Walker (Tue Oct 23 2007 - 12:02:42 PDT)
- Alexandar T Tzanov (Tue Oct 23 2007 - 11:35:25 PDT)
- Robert Duke (Tue Oct 23 2007 - 10:46:52 PDT)
- Ross Walker (Tue Oct 23 2007 - 10:35:45 PDT)
- Alexandar T Tzanov (Tue Oct 23 2007 - 10:11:46 PDT)
- Aaron Greenwood (Tue Oct 23 2007 - 10:03:43 PDT)
AMBER: Pre-requisites for AMBER software
- Anamika Awasthi (Thu Oct 25 2007 - 05:05:19 PDT)
AMBER: prepin file format description; pointers on parameterization
- FyD (Fri Oct 26 2007 - 05:45:10 PDT)
- FyD (Thu Oct 25 2007 - 23:40:46 PDT)
- David Mobley (Thu Oct 25 2007 - 13:39:08 PDT)
- David Mobley (Thu Oct 25 2007 - 13:41:06 PDT)
- FyD (Thu Oct 25 2007 - 06:15:52 PDT)
- FyD (Wed Oct 24 2007 - 23:54:33 PDT)
- FyD (Wed Oct 24 2007 - 22:27:33 PDT)
- FyD (Wed Oct 24 2007 - 22:14:32 PDT)
- David Mobley (Wed Oct 24 2007 - 17:58:45 PDT)
- David A. Case (Wed Oct 24 2007 - 17:27:39 PDT)
- David Mobley (Wed Oct 24 2007 - 16:58:35 PDT)
- David Mobley (Wed Oct 24 2007 - 16:35:26 PDT)
- David Mobley (Wed Oct 24 2007 - 13:45:54 PDT)
- FyD (Wed Oct 24 2007 - 13:13:37 PDT)
- David Mobley (Wed Oct 24 2007 - 12:31:02 PDT)
- FyD (Wed Oct 24 2007 - 12:09:09 PDT)
- David Mobley (Wed Oct 24 2007 - 10:52:24 PDT)
AMBER: problems compiling amber on mac OSX
- Mengjuei Hsieh (Sat Oct 27 2007 - 12:41:26 PDT)
- francesco zonta (Sat Oct 27 2007 - 05:03:51 PDT)
- Mengjuei Hsieh (Sat Oct 27 2007 - 02:31:04 PDT)
- David A. Case (Fri Oct 26 2007 - 08:48:35 PDT)
- francesco zonta (Thu Oct 25 2007 - 06:50:04 PDT)
AMBER: Problems compiling Amber9 on IBM-AIX
- Ross Walker (Mon Oct 08 2007 - 07:39:08 PDT)
- Sampath Koppole (Mon Oct 08 2007 - 04:42:20 PDT)
AMBER: Problems loading pdb file including Mg ions
- Bill Ross (Wed Oct 24 2007 - 10:21:43 PDT)
- Idan Gabdank (Wed Oct 24 2007 - 06:05:46 PDT)
- Peter Varnai (Tue Oct 23 2007 - 03:38:53 PDT)
- Idan Gabdank (Mon Oct 22 2007 - 08:53:12 PDT)
AMBER: problems visualizing mdcrd in VMD
- Mattia Mori - CERM (Wed Oct 31 2007 - 05:59:24 PDT)
- Vlad Cojocaru (Wed Oct 31 2007 - 05:41:42 PDT)
- Vlad Cojocaru (Wed Oct 31 2007 - 04:33:37 PDT)
- Mattia Mori - CERM (Wed Oct 31 2007 - 04:17:21 PDT)
AMBER: Problems with 'make'
- Ross Walker (Fri Oct 05 2007 - 13:14:20 PDT)
- Hopkins, Robert (Fri Oct 05 2007 - 11:32:24 PDT)
- Ross Walker (Thu Oct 04 2007 - 13:55:25 PDT)
- Hopkins, Robert (Thu Oct 04 2007 - 12:07:42 PDT)
AMBER: Problems with cpin file
- Eduardo Mendez (Thu Oct 04 2007 - 14:11:06 PDT)
- Eddie Men (Thu Oct 04 2007 - 13:46:22 PDT)
- Eddie Men (Wed Oct 03 2007 - 22:07:11 PDT)
- David A. Case (Tue Oct 02 2007 - 08:16:45 PDT)
- Eddie Men (Tue Oct 02 2007 - 05:47:50 PDT)
AMBER: question about charge of prmtop file
- WANG,YING (Wed Oct 24 2007 - 07:44:20 PDT)
- Steve Spronk (Wed Oct 24 2007 - 07:21:25 PDT)
- WANG,YING (Tue Oct 23 2007 - 09:08:15 PDT)
- Thomas Steinbrecher (Tue Oct 23 2007 - 08:41:09 PDT)
- WANG,YING (Tue Oct 23 2007 - 07:11:22 PDT)
AMBER: question about h bond
- WANG,YING (Fri Oct 19 2007 - 21:07:49 PDT)
- Yong Duan (Fri Oct 19 2007 - 17:41:19 PDT)
- WANG,YING (Fri Oct 19 2007 - 17:19:36 PDT)
AMBER: Question about ptraj matrix correl command
- Catein Catherine (Wed Oct 31 2007 - 00:18:55 PDT)
AMBER: Quick QUESTION
- Eddie Men (Mon Oct 08 2007 - 22:02:10 PDT)
- Eddie Men (Mon Oct 08 2007 - 21:23:49 PDT)
AMBER: RED III
- FyD (Mon Oct 15 2007 - 03:20:47 PDT)
- Age.Skjevik.student.uib.no (Mon Oct 15 2007 - 03:06:49 PDT)
AMBER: RED-vIII fails
- FyD (Tue Oct 30 2007 - 14:38:03 PDT)
- Jesper Soerensen (Tue Oct 30 2007 - 02:16:36 PDT)
- FyD (Mon Oct 29 2007 - 09:25:09 PDT)
- Jesper Soerensen (Mon Oct 29 2007 - 07:51:56 PDT)
AMBER: regarding anal calculations
- gurpreet singh (Wed Oct 24 2007 - 11:50:49 PDT)
AMBER: regarding non bonded energy caculations
- David A. Case (Mon Oct 01 2007 - 07:46:00 PDT)
- gurpreet singh (Sun Sep 30 2007 - 22:41:47 PDT)
AMBER: regrading interaction energy calculations
- gurpreet singh (Sun Oct 07 2007 - 21:52:23 PDT)
AMBER: replica exchange
- Robert Duke (Sun Oct 28 2007 - 09:38:04 PDT)
- Carlos Simmerling (Sun Oct 28 2007 - 09:38:15 PDT)
- Geoff Wood (Sun Oct 28 2007 - 09:29:42 PDT)
AMBER: request for hardware recommendations
- Ross Walker (Sat Oct 06 2007 - 18:45:14 PDT)
- Carlos Simmerling (Sat Oct 06 2007 - 10:00:13 PDT)
- Andy Purkiss (Sat Oct 06 2007 - 10:53:23 PDT)
- Parish, Carol (Sat Oct 06 2007 - 10:20:13 PDT)
- Parish, Carol (Sat Oct 06 2007 - 08:59:01 PDT)
AMBER: Resp: "Statistics of the Fitting"
- Jones de Andrade (Wed Oct 10 2007 - 09:05:09 PDT)
- FyD (Tue Oct 09 2007 - 21:53:05 PDT)
- Jones de Andrade (Sun Oct 07 2007 - 11:40:04 PDT)
AMBER: results from TI
- David Mobley (Wed Oct 24 2007 - 07:18:50 PDT)
- Thomas Steinbrecher (Tue Oct 23 2007 - 14:25:24 PDT)
- Holly Freedman (Tue Oct 23 2007 - 13:29:00 PDT)
- Thomas Steinbrecher (Tue Oct 23 2007 - 11:07:30 PDT)
- David Mobley (Tue Oct 23 2007 - 10:09:31 PDT)
- Holly Freedman (Tue Oct 23 2007 - 09:57:42 PDT)
- David Mobley (Tue Oct 23 2007 - 06:40:26 PDT)
- Holly Freedman (Mon Oct 22 2007 - 12:03:20 PDT)
- Thomas Steinbrecher (Mon Oct 22 2007 - 10:35:15 PDT)
- Holly Freedman (Mon Oct 22 2007 - 09:42:26 PDT)
AMBER: SASA per residue
- Evan Kelly (Mon Oct 22 2007 - 09:59:26 PDT)
AMBER: segmentation fault occured doing MD
- David A. Case (Fri Oct 26 2007 - 08:32:07 PDT)
- priya priya (Fri Oct 26 2007 - 04:51:31 PDT)
AMBER: Simulation continuation problem. Cant read restart file!!!!!!
- Gustavo Seabra (Fri Oct 05 2007 - 20:48:59 PDT)
- Anthony Cruz (Fri Oct 05 2007 - 05:44:50 PDT)
AMBER: Simulation died due to lack of disk space
- Robert Duke (Fri Oct 19 2007 - 10:25:21 PDT)
- Ross Walker (Fri Oct 19 2007 - 09:25:20 PDT)
- Bill Ross (Fri Oct 19 2007 - 08:59:31 PDT)
- Samantha Kaye (Fri Oct 19 2007 - 02:23:33 PDT)
- Bill Ross (Thu Oct 18 2007 - 12:00:33 PDT)
- Ross Walker (Thu Oct 18 2007 - 07:53:50 PDT)
- Samantha Kaye (Thu Oct 18 2007 - 06:57:57 PDT)
AMBER: Solved: Heat capacity calculations not coming out right
- David Cerutti (Mon Oct 22 2007 - 11:01:32 PDT)
AMBER: subroutine ephi !!
- Tom Darden (Fri Oct 19 2007 - 05:06:33 PDT)
- Sampath Koppole (Fri Oct 19 2007 - 01:08:26 PDT)
AMBER: Temperature fluctuation in NPT and NVE ensemble
- Robert Duke (Wed Oct 17 2007 - 18:44:47 PDT)
- Lei Jia (Wed Oct 17 2007 - 16:46:29 PDT)
AMBER: Test fails in Parallel version Amber9
- gong wb (Tue Oct 23 2007 - 18:37:20 PDT)
- gong wb (Sun Oct 21 2007 - 23:52:48 PDT)
- Ross Walker (Fri Oct 19 2007 - 07:24:47 PDT)
- gong wb (Thu Oct 18 2007 - 19:00:44 PDT)
- gong wb (Wed Oct 17 2007 - 01:04:13 PDT)
- gong wb (Wed Oct 17 2007 - 00:54:30 PDT)
- Scott Brozell (Tue Oct 16 2007 - 11:35:24 PDT)
- gong wb (Mon Oct 15 2007 - 23:42:45 PDT)
AMBER: The number of the path atoms exceeds MAXPATHATOMNUM
- VANIA MARIA AMARO CALISTO (Mon Oct 29 2007 - 05:13:01 PDT)
AMBER: Thermodynamic Integration with Explicit Solvent
- Scott Pendley (Wed Oct 10 2007 - 15:39:12 PDT)
- Scott Pendley (Wed Oct 10 2007 - 15:38:20 PDT)
- David A. Case (Tue Oct 09 2007 - 19:36:38 PDT)
- Thomas Steinbrecher (Tue Oct 09 2007 - 17:12:13 PDT)
- Scott Pendley (Tue Oct 09 2007 - 18:09:14 PDT)
- Scott Pendley (Tue Oct 09 2007 - 14:38:03 PDT)
AMBER: Transformation table
- Rajendra P. OJHA (Sun Oct 07 2007 - 03:12:37 PDT)
AMBER: Umbrella sampling
- Jerome.GOLEBIOWSKI.unice.fr (Fri Oct 26 2007 - 10:08:09 PDT)
- Adrian Roitberg (Fri Oct 26 2007 - 07:11:14 PDT)
- Jena M (Fri Oct 26 2007 - 06:48:26 PDT)
AMBER: using amber for cyclic peptides
- FyD (Mon Oct 15 2007 - 10:53:54 PDT)
- rebeca.mmb.pcb.ub.es (Mon Oct 15 2007 - 10:23:50 PDT)
AMBER: Water cap MD error
- Rima Chaudhuri (Mon Oct 15 2007 - 15:17:07 PDT)
antechamber
- Ross Walker (Tue Oct 09 2007 - 09:51:57 PDT)
IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- Ross Walker (Tue Oct 02 2007 - 19:00:07 PDT)

Amber Archive Oct 2007 by subject