Amber Archive Oct 2007 by author
331 messages
:
Starting
Wed Oct 03 2007 - 06:07:14 PDT,
Ending
Sun Nov 04 2007 - 06:07:19 PST
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Aaron Greenwood
Re: AMBER: mdfil: Error unknown flag: -p4pg
(Tue Oct 30 2007 - 05:03:29 PDT)
AMBER: mdfil: Error unknown flag: -p4pg
(Mon Oct 29 2007 - 12:38:44 PDT)
AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 10:03:43 PDT)
AMBER: Beowulf cluster from PSSC Labs
(Tue Oct 23 2007 - 09:22:33 PDT)
Abi Ghanem josephine
AMBER: ANGVE/TORAVE
(Thu Oct 25 2007 - 08:58:11 PDT)
Adrian Roitberg
Re: AMBER: Umbrella sampling
(Fri Oct 26 2007 - 07:11:14 PDT)
Re: AMBER: AMBER 9 - Force Field Options - Question
(Thu Oct 18 2007 - 11:56:23 PDT)
Re: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 11:26:56 PDT)
Re: AMBER: constant-pH MD with replica exchange
(Thu Oct 11 2007 - 11:55:18 PDT)
Re: AMBER: constant-pH MD with replica exchange
(Thu Oct 11 2007 - 08:33:30 PDT)
Age.Skjevik.student.uib.no
AMBER: RED III
(Mon Oct 15 2007 - 03:06:49 PDT)
Alexandar T Tzanov
Re: RE: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 11:35:25 PDT)
Re: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 10:11:46 PDT)
Anamika Awasthi
AMBER: Pre-requisites for AMBER software
(Thu Oct 25 2007 - 05:05:19 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 13:24:29 PDT)
Andres Palencia
AMBER: atomicfluct
(Mon Oct 01 2007 - 11:12:20 PDT)
Andy Purkiss
Re: AMBER: request for hardware recommendations
(Sat Oct 06 2007 - 10:53:23 PDT)
Anselm Horn
AMBER: Polarizable Force Field: Ligand Parameterization et al.
(Thu Oct 25 2007 - 02:00:03 PDT)
Anthony Cruz
Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!!
(Fri Oct 05 2007 - 05:44:50 PDT)
Anupam Nath Jha
AMBER: calculation of angle between helices
(Sun Oct 28 2007 - 23:06:37 PDT)
Bill Ross
Re: AMBER: Getting prmtop and inpcrd
(Mon Oct 29 2007 - 12:26:16 PDT)
Re: AMBER: Problems loading pdb file including Mg ions
(Wed Oct 24 2007 - 10:21:43 PDT)
Re: AMBER: Simulation died due to lack of disk space
(Fri Oct 19 2007 - 08:59:31 PDT)
RE: AMBER: Simulation died due to lack of disk space
(Thu Oct 18 2007 - 12:00:33 PDT)
caoch
AMBER: How to get sane package
(Tue Oct 02 2007 - 03:09:26 PDT)
Carlos Simmerling
Re: AMBER: Getting prmtop and inpcrd
(Mon Oct 29 2007 - 08:47:33 PDT)
Re: AMBER: replica exchange
(Sun Oct 28 2007 - 09:38:15 PDT)
Re: AMBER: HG atoms in CYX residues
(Fri Oct 26 2007 - 03:20:05 PDT)
Re: AMBER: AMBER 9 - Force Field Options - Question
(Thu Oct 18 2007 - 03:06:44 PDT)
Re: AMBER: error while Running TMD
(Thu Oct 18 2007 - 03:01:07 PDT)
Re: AMBER: error while Running TMD
(Wed Oct 17 2007 - 11:50:45 PDT)
Re: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 06:54:51 PDT)
Re: AMBER: constant-pH MD with replica exchange
(Thu Oct 11 2007 - 11:30:34 PDT)
Re: AMBER: ff99SB and the N- and C- charged terminal residues
(Wed Oct 10 2007 - 10:37:13 PDT)
Re: AMBER: neb for path between binding sites
(Tue Oct 09 2007 - 14:25:27 PDT)
Re: AMBER: request for hardware recommendations
(Sat Oct 06 2007 - 10:00:13 PDT)
Re: AMBER: multi chain simulations
(Thu Oct 04 2007 - 12:43:44 PDT)
Re: AMBER: multi chain simulations
(Thu Oct 04 2007 - 04:28:46 PDT)
Re: AMBER: multi chain simulations
(Thu Oct 04 2007 - 03:35:22 PDT)
Re: AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 11:54:22 PDT)
Re: AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 10:15:14 PDT)
Re: AMBER: dihedrals
(Tue Oct 02 2007 - 03:13:12 PDT)
Catein Catherine
AMBER: Question about ptraj matrix correl command
(Wed Oct 31 2007 - 00:18:55 PDT)
AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca
(Fri Oct 26 2007 - 00:28:57 PDT)
AMBER: Average absolute value of cross velocity (Rate constant from PMF)
(Fri Oct 26 2007 - 00:26:58 PDT)
RE: AMBER: Polarizable Force Field: Ligand Parameterization et al.
(Fri Oct 26 2007 - 00:17:16 PDT)
AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690
(Wed Oct 24 2007 - 05:04:42 PDT)
AMBER: How to intergrate the area under a curve.
(Sun Oct 21 2007 - 23:34:16 PDT)
cgji
AMBER: How can i calculate generalized order parameters using ptraj.
(Sun Oct 28 2007 - 07:59:37 PDT)
Re: Re: AMBER: anal calculatons
(Mon Oct 15 2007 - 22:48:09 PDT)
Re: AMBER: lipid bilayer
(Thu Oct 11 2007 - 07:38:45 PDT)
Christopher Jones
AMBER: amber9 parallel compile problem
(Wed Oct 31 2007 - 10:09:32 PDT)
Claire Zerafa
AMBER: hbond analysis output
(Wed Oct 24 2007 - 12:21:02 PDT)
David A. Case
Re: AMBER: gibbs problems
(Wed Oct 31 2007 - 21:09:35 PDT)
Re: AMBER: dihedral angles
(Wed Oct 31 2007 - 21:09:24 PDT)
Re: AMBER: How to get sane package
(Wed Oct 31 2007 - 21:09:08 PDT)
Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)
(Wed Oct 31 2007 - 14:52:18 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Wed Oct 31 2007 - 07:38:34 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Tue Oct 30 2007 - 08:58:20 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Tue Oct 30 2007 - 06:42:44 PDT)
Re: AMBER: mdfil: Error unknown flag: -p4pg
(Mon Oct 29 2007 - 19:46:01 PDT)
Re: AMBER: problems compiling amber on mac OSX
(Fri Oct 26 2007 - 08:48:35 PDT)
Re: AMBER: Average absolute value of cross velocity (Rate constant from PMF)
(Fri Oct 26 2007 - 08:22:40 PDT)
Re: AMBER: HG atoms in CYX residues
(Fri Oct 26 2007 - 08:28:36 PDT)
Re: AMBER: segmentation fault occured doing MD
(Fri Oct 26 2007 - 08:32:07 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 17:27:39 PDT)
Re: AMBER: Thermodynamic Integration with Explicit Solvent
(Tue Oct 09 2007 - 19:36:38 PDT)
Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?
(Tue Oct 09 2007 - 07:09:02 PDT)
Re: AMBER: entropy with ptraj
(Mon Oct 08 2007 - 06:47:57 PDT)
Re: AMBER: Problems with cpin file
(Tue Oct 02 2007 - 08:16:45 PDT)
Re: AMBER: regarding non bonded energy caculations
(Mon Oct 01 2007 - 07:46:00 PDT)
David Cerutti
AMBER: Solved: Heat capacity calculations not coming out right
(Mon Oct 22 2007 - 11:01:32 PDT)
Re: AMBER: Addendum: Heat capacity calculations not coming out right
(Sat Oct 20 2007 - 15:47:05 PDT)
AMBER: Addendum: Heat capacity calculations not coming out right
(Fri Oct 19 2007 - 20:31:46 PDT)
AMBER: Heat capacity calculations not coming out right
(Fri Oct 19 2007 - 19:37:38 PDT)
AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?
(Mon Oct 08 2007 - 22:25:43 PDT)
Re: AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 13:04:35 PDT)
RE: AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 11:47:42 PDT)
AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 09:58:03 PDT)
David Mobley
Re: AMBER: prepin file format description; pointers on parameterization
(Thu Oct 25 2007 - 13:39:08 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Thu Oct 25 2007 - 13:41:06 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 17:58:45 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 16:58:35 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 16:35:26 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 13:45:54 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 12:31:02 PDT)
AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 10:52:24 PDT)
Re: AMBER: results from TI
(Wed Oct 24 2007 - 07:18:50 PDT)
Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690
(Wed Oct 24 2007 - 07:20:43 PDT)
Re: AMBER: results from TI
(Tue Oct 23 2007 - 10:09:31 PDT)
Re: AMBER: results from TI
(Tue Oct 23 2007 - 06:40:26 PDT)
dpandit.brandeis.edu
Re: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 08:27:12 PDT)
AMBER: AMBER 9 - Force Field Options - Question
(Tue Oct 16 2007 - 13:41:33 PDT)
Ed Pate
AMBER: dihedrals
(Mon Oct 01 2007 - 16:07:47 PDT)
Eddie Men
Re: AMBER: anal calculatons
(Mon Oct 15 2007 - 00:43:02 PDT)
AMBER: BOMB!
(Thu Oct 11 2007 - 03:12:49 PDT)
Re: AMBER: Quick QUESTION
(Mon Oct 08 2007 - 22:02:10 PDT)
AMBER: Quick QUESTION
(Mon Oct 08 2007 - 21:23:49 PDT)
Re: AMBER: PB Bomb
(Sun Oct 07 2007 - 01:03:52 PDT)
AMBER: PB Bomb
(Sun Oct 07 2007 - 00:10:59 PDT)
Re: AMBER: Problems with cpin file
(Thu Oct 04 2007 - 13:46:22 PDT)
Re: AMBER: Problems with cpin file
(Wed Oct 03 2007 - 22:07:11 PDT)
AMBER: Problems with cpin file
(Tue Oct 02 2007 - 05:47:50 PDT)
AMBER: Constant pH
(Tue Oct 02 2007 - 02:41:31 PDT)
AMBER: constant pH
(Tue Oct 02 2007 - 02:45:34 PDT)
Eduardo Mendez
AMBER: hey
(Sat Oct 06 2007 - 22:19:36 PDT)
Re: AMBER: Problems with cpin file
(Thu Oct 04 2007 - 14:11:06 PDT)
Evan Kelly
AMBER: SASA per residue
(Mon Oct 22 2007 - 09:59:26 PDT)
Francesco Pietra
Re: AMBER: Getting prmtop and inpcrd
(Mon Oct 29 2007 - 09:51:23 PDT)
AMBER: Getting prmtop and inpcrd
(Mon Oct 29 2007 - 08:43:44 PDT)
francesco zonta
Re: AMBER: problems compiling amber on mac OSX
(Sat Oct 27 2007 - 05:03:51 PDT)
AMBER: HG atoms in CYX residues
(Fri Oct 26 2007 - 02:45:32 PDT)
AMBER: problems compiling amber on mac OSX
(Thu Oct 25 2007 - 06:50:04 PDT)
FyD
Re: AMBER: antechamber fails with large molecules
(Wed Oct 31 2007 - 07:02:36 PDT)
Re: AMBER: RED-vIII fails
(Tue Oct 30 2007 - 14:38:03 PDT)
Re: AMBER: RED-vIII fails
(Mon Oct 29 2007 - 09:25:09 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Fri Oct 26 2007 - 05:45:10 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Thu Oct 25 2007 - 23:40:46 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Thu Oct 25 2007 - 06:15:52 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 23:54:33 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 22:27:33 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 22:14:32 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 13:13:37 PDT)
Re: AMBER: prepin file format description; pointers on parameterization
(Wed Oct 24 2007 - 12:09:09 PDT)
Re: AMBER: how to simulate a ligand bound to a residue
(Thu Oct 18 2007 - 14:02:13 PDT)
Re: AMBER: using amber for cyclic peptides
(Mon Oct 15 2007 - 10:53:54 PDT)
Re: AMBER: RED III
(Mon Oct 15 2007 - 03:20:47 PDT)
Re: AMBER: Resp: "Statistics of the Fitting"
(Tue Oct 09 2007 - 21:53:05 PDT)
Re: AMBER: dihedrals
(Mon Oct 01 2007 - 23:36:30 PDT)
Re: AMBER: cyclohexane and decalin on amber
(Mon Oct 01 2007 - 00:20:29 PDT)
Geoff Wood
AMBER: replica exchange
(Sun Oct 28 2007 - 09:29:42 PDT)
gong wb
Re: AMBER: Test fails in Parallel version Amber9
(Tue Oct 23 2007 - 18:37:20 PDT)
Re: AMBER: Test fails in Parallel version Amber9
(Sun Oct 21 2007 - 23:52:48 PDT)
Re: AMBER: Test fails in Parallel version Amber9
(Thu Oct 18 2007 - 19:00:44 PDT)
Re: AMBER: Test fails in Parallel version Amber9
(Wed Oct 17 2007 - 01:04:13 PDT)
Re: AMBER: Test fails in Parallel version Amber9
(Wed Oct 17 2007 - 00:54:30 PDT)
AMBER: Test fails in Parallel version Amber9
(Mon Oct 15 2007 - 23:42:45 PDT)
gurpreet singh
AMBER: regarding anal calculations
(Wed Oct 24 2007 - 11:50:49 PDT)
AMBER: anal
(Wed Oct 17 2007 - 21:35:23 PDT)
Re: AMBER: error while Running TMD
(Wed Oct 17 2007 - 21:19:54 PDT)
AMBER: error while Running TMD
(Wed Oct 17 2007 - 11:21:18 PDT)
AMBER: anal error
(Wed Oct 17 2007 - 11:14:52 PDT)
AMBER: anal calculation error
(Tue Oct 16 2007 - 10:07:20 PDT)
Re: AMBER: anal calculatons
(Mon Oct 15 2007 - 21:17:47 PDT)
AMBER: anal calculatons
(Mon Oct 15 2007 - 00:19:33 PDT)
AMBER: interaction energy calculations
(Tue Oct 09 2007 - 10:06:24 PDT)
AMBER: regrading interaction energy calculations
(Sun Oct 07 2007 - 21:52:23 PDT)
AMBER: regarding non bonded energy caculations
(Sun Sep 30 2007 - 22:41:47 PDT)
Gustavo Seabra
Re: AMBER: binary restart file
(Fri Oct 05 2007 - 20:56:02 PDT)
Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!!
(Fri Oct 05 2007 - 20:48:59 PDT)
Holly Freedman
Re: AMBER: results from TI
(Tue Oct 23 2007 - 13:29:00 PDT)
Re: AMBER: results from TI
(Tue Oct 23 2007 - 09:57:42 PDT)
Re: AMBER: results from TI
(Mon Oct 22 2007 - 12:03:20 PDT)
AMBER: results from TI
(Mon Oct 22 2007 - 09:42:26 PDT)
Re: AMBER: neb for path between binding sites
(Tue Oct 09 2007 - 16:35:19 PDT)
Re: AMBER: neb for path between binding sites
(Tue Oct 09 2007 - 16:37:20 PDT)
AMBER: neb for path between binding sites
(Tue Oct 09 2007 - 14:09:50 PDT)
Hopkins, Robert
AMBER: Please Disregard My Last E-mail: Missing 'yacc' command
(Sat Oct 13 2007 - 16:04:11 PDT)
AMBER: Missing 'yacc' command
(Sat Oct 13 2007 - 15:00:00 PDT)
RE: AMBER: Problems with 'make'
(Fri Oct 05 2007 - 11:32:24 PDT)
AMBER: Problems with 'make'
(Thu Oct 04 2007 - 12:07:42 PDT)
Idan Gabdank
Re: AMBER: Problems loading pdb file including Mg ions
(Wed Oct 24 2007 - 06:05:46 PDT)
AMBER: Problems loading pdb file including Mg ions
(Mon Oct 22 2007 - 08:53:12 PDT)
Ilyas Yildirim
Re: AMBER: How to intergrate the area under a curve.
(Mon Oct 22 2007 - 00:17:07 PDT)
Jardas sucuriba
AMBER: dihedral angles
(Tue Oct 30 2007 - 17:43:10 PDT)
JAVIER PEREZ
AMBER: gibbs problems
(Wed Oct 31 2007 - 04:48:22 PDT)
Jena M
AMBER: Umbrella sampling
(Fri Oct 26 2007 - 06:48:26 PDT)
AMBER: how to simulate a ligand bound to a residue
(Thu Oct 18 2007 - 06:49:55 PDT)
Jerome.GOLEBIOWSKI.unice.fr
Re: AMBER: Umbrella sampling
(Fri Oct 26 2007 - 10:08:09 PDT)
Jesper Soerensen
Re: AMBER: RED-vIII fails
(Tue Oct 30 2007 - 02:16:36 PDT)
AMBER: RED-vIII fails
(Mon Oct 29 2007 - 07:51:56 PDT)
Jiapu.Zhang.csiro.au
AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander
(Thu Oct 18 2007 - 16:15:05 PDT)
Jimmy Heimdal
AMBER: EVB Calculations
(Sun Oct 21 2007 - 23:30:48 PDT)
Joe Nolan
AMBER: Amber9 parallel installation error (retry)
(Tue Oct 30 2007 - 11:25:35 PDT)
Re: AMBER: Amber9 parallel installation error (with openMPI)
(Mon Oct 29 2007 - 15:30:25 PDT)
Re: AMBER: Amber9 parallel installation error (with openMPI)
(Mon Oct 29 2007 - 14:55:43 PDT)
AMBER: Amber9 parallel installation error (with openMPI)
(Mon Oct 29 2007 - 14:02:10 PDT)
AMBER: Amber9 installation error on Mandriva 2007 linux
(Mon Oct 08 2007 - 10:07:58 PDT)
Jones de Andrade
Re: AMBER: Resp: "Statistics of the Fitting"
(Wed Oct 10 2007 - 09:05:09 PDT)
AMBER: adding extra points to amber - how to?
(Mon Oct 08 2007 - 09:44:42 PDT)
AMBER: Resp: "Statistics of the Fitting"
(Sun Oct 07 2007 - 11:40:04 PDT)
Re: AMBER: cyclohexane and decalin on amber
(Tue Oct 02 2007 - 20:12:48 PDT)
Re: AMBER: cyclohexane and decalin on amber
(Sun Sep 30 2007 - 22:46:44 PDT)
Junmei Wang
Re: AMBER: antechamber fails with large molecules
(Wed Oct 31 2007 - 21:43:49 PDT)
Karen Callahan
AMBER: Energy calculations.
(Thu Oct 18 2007 - 12:15:29 PDT)
Kyle Brown
Re: AMBER: ANGVE/TORAVE
(Thu Oct 25 2007 - 11:33:52 PDT)
L. W. Yang
Re: AMBER: heme forcefield atom types
(Wed Oct 24 2007 - 09:18:31 PDT)
Lars Skjærven
Re: AMBER: PMEMD configuration and scaling
(Tue Oct 09 2007 - 06:56:09 PDT)
Lars.Skjarven.biomed.uib.no
AMBER: PMEMD configuration and scaling
(Tue Oct 09 2007 - 03:05:37 PDT)
AMBER: PMEMD configuration and scaling
(Sun Oct 07 2007 - 03:40:00 PDT)
AMBER: PMEMD configuration and scaling
(Sat Oct 06 2007 - 04:35:03 PDT)
Lei Jia
AMBER: Temperature fluctuation in NPT and NVE ensemble
(Wed Oct 17 2007 - 16:46:29 PDT)
Lili Peng
AMBER: Applying bugfixes in Amber
(Thu Oct 04 2007 - 14:28:29 PDT)
Maciej Dlugosz
AMBER: constant-pH MD with replica exchange
(Wed Oct 10 2007 - 23:38:49 PDT)
Madjid Taghdir
AMBER: amber9 installation problem
(Tue Oct 16 2007 - 01:46:05 PDT)
Marc Baaden
AMBER: Interactive Molecular Dynamics with Amber?
(Sat Oct 20 2007 - 15:10:23 PDT)
Marius Retegan
AMBER: entropy with ptraj
(Mon Oct 08 2007 - 05:24:36 PDT)
Mark Williamson
Re: AMBER: Amber9 installation error on Mandriva 2007 linux
(Mon Oct 08 2007 - 10:31:39 PDT)
Mattia Mori - CERM
Re: AMBER: problems visualizing mdcrd in VMD
(Wed Oct 31 2007 - 05:59:24 PDT)
AMBER: problems visualizing mdcrd in VMD
(Wed Oct 31 2007 - 04:17:21 PDT)
AMBER: amber with periodic condition
(Mon Oct 29 2007 - 10:16:14 PDT)
Mengjuei Hsieh
Re: AMBER: problems compiling amber on mac OSX
(Sat Oct 27 2007 - 12:41:26 PDT)
Re: AMBER: problems compiling amber on mac OSX
(Sat Oct 27 2007 - 02:31:04 PDT)
merc mertens
AMBER: mm_pbsa: missing values in ras-raf tutorials
(Fri Oct 19 2007 - 01:28:09 PDT)
Monaghan, Martin (Cont, ARL/CISD)
AMBER: Amber 9 source code permissions (UNCLASSIFIED)
(Mon Oct 29 2007 - 14:30:30 PDT)
msubhamoy.ibab.ac.in
AMBER: Abnormality in MM-PBSA result
(Fri Oct 19 2007 - 08:01:16 PDT)
Myunggi Yi
Re: AMBER: binary restart file
(Sun Oct 07 2007 - 16:39:44 PDT)
AMBER: binary restart file
(Thu Oct 04 2007 - 07:49:28 PDT)
Nicolas Lux Fawzi
AMBER: ff99SB and the N- and C- charged terminal residues
(Wed Oct 10 2007 - 09:03:09 PDT)
Parish, Carol
RE: AMBER: request for hardware recommendations
(Sat Oct 06 2007 - 10:20:13 PDT)
AMBER: request for hardware recommendations
(Sat Oct 06 2007 - 08:59:01 PDT)
Peter Varnai
Re: AMBER: Problems loading pdb file including Mg ions
(Tue Oct 23 2007 - 03:38:53 PDT)
Pradipta Bandyopadhyay
AMBER: Heme and CYS !!
(Fri Oct 26 2007 - 03:49:47 PDT)
priya priya
AMBER: segmentation fault occured doing MD
(Fri Oct 26 2007 - 04:51:31 PDT)
Re: AMBER: multi chain simulations
(Thu Oct 04 2007 - 05:44:56 PDT)
Re: AMBER: multi chain simulations
(Thu Oct 04 2007 - 04:07:44 PDT)
AMBER: multi chain simulations
(Thu Oct 04 2007 - 03:30:27 PDT)
AMBER: multichain simulations
(Tue Oct 02 2007 - 02:31:26 PDT)
Rajendra P. OJHA
AMBER: Transformation table
(Sun Oct 07 2007 - 03:12:37 PDT)
Ray Luo
Re: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
(Fri Oct 26 2007 - 10:31:03 PDT)
RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
(Thu Oct 25 2007 - 11:20:14 PDT)
rebeca.mmb.pcb.ub.es
AMBER: using amber for cyclic peptides
(Mon Oct 15 2007 - 10:23:50 PDT)
Rima Chaudhuri
AMBER: Water cap MD error
(Mon Oct 15 2007 - 15:17:07 PDT)
Robert Duke
Re: AMBER: replica exchange
(Sun Oct 28 2007 - 09:38:04 PDT)
Re: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 10:46:52 PDT)
Re: AMBER: Addendum: Heat capacity calculations not coming out right
(Fri Oct 19 2007 - 21:24:30 PDT)
Re: AMBER: Simulation died due to lack of disk space
(Fri Oct 19 2007 - 10:25:21 PDT)
Re: AMBER: Temperature fluctuation in NPT and NVE ensemble
(Wed Oct 17 2007 - 18:44:47 PDT)
Re: AMBER: PMEMD configuration and scaling
(Tue Oct 09 2007 - 06:15:34 PDT)
Re: AMBER: PMEMD configuration and scaling
(Sun Oct 07 2007 - 08:04:03 PDT)
Re: AMBER: PMEMD configuration and scaling
(Sat Oct 06 2007 - 06:20:16 PDT)
Ross Walker
RE: AMBER: amber9 parallel compile problem
(Wed Oct 31 2007 - 10:36:00 PDT)
RE: AMBER: Amber 9 source code permissions (UNCLASSIFIED)
(Mon Oct 29 2007 - 16:18:50 PDT)
RE: AMBER: AMBER 8: QMMM - molecule fluctuates wildly
(Mon Oct 29 2007 - 14:06:45 PDT)
RE: AMBER: &dipole input and some questions on using polarizable force fields
(Mon Oct 29 2007 - 08:31:00 PDT)
RE: AMBER: &dipole input and some questions on using polarizable force fields
(Fri Oct 26 2007 - 09:28:57 PDT)
RE: RE: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 12:02:42 PDT)
RE: AMBER: Portland Group vs. Intel Compilers.
(Tue Oct 23 2007 - 10:35:45 PDT)
RE: AMBER: Beowulf cluster from PSSC Labs
(Tue Oct 23 2007 - 10:28:29 PDT)
RE: AMBER: Simulation died due to lack of disk space
(Fri Oct 19 2007 - 09:25:20 PDT)
RE: AMBER: Test fails in Parallel version Amber9
(Fri Oct 19 2007 - 07:24:47 PDT)
RE: AMBER: Simulation died due to lack of disk space
(Thu Oct 18 2007 - 07:53:50 PDT)
RE: AMBER: follow-up
(Tue Oct 09 2007 - 14:24:50 PDT)
AMBER: RE: antechamber
(Tue Oct 09 2007 - 09:51:57 PDT)
AMBER: RE: Amber query !!
(Mon Oct 08 2007 - 10:02:36 PDT)
RE: AMBER: Problems compiling Amber9 on IBM-AIX
(Mon Oct 08 2007 - 07:39:08 PDT)
RE: AMBER: request for hardware recommendations
(Sat Oct 06 2007 - 18:45:14 PDT)
RE: AMBER: PMEMD configuration and scaling
(Sat Oct 06 2007 - 09:27:16 PDT)
RE: AMBER: Problems with 'make'
(Fri Oct 05 2007 - 13:14:20 PDT)
RE: AMBER: Applying bugfixes in Amber
(Thu Oct 04 2007 - 14:53:31 PDT)
RE: AMBER: Problems with 'make'
(Thu Oct 04 2007 - 13:55:25 PDT)
RE: AMBER: 31 integers in the first section of a prmtop file
(Wed Oct 03 2007 - 10:32:12 PDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Tue Oct 02 2007 - 19:00:07 PDT)
RE: AMBER: MAXPR
(Mon Oct 01 2007 - 08:30:46 PDT)
S.Sundar Raman
Re: AMBER: MM_PBSA calcultion- help me
(Tue Oct 16 2007 - 06:58:50 PDT)
saccenti.cerm.unifi.it
AMBER: generating topology files for PBSA
(Fri Oct 05 2007 - 02:46:14 PDT)
AMBER: PBSA generate snapshots
(Thu Oct 04 2007 - 02:17:04 PDT)
Samantha Kaye
Re: AMBER: Simulation died due to lack of disk space
(Fri Oct 19 2007 - 02:23:33 PDT)
AMBER: Simulation died due to lack of disk space
(Thu Oct 18 2007 - 06:57:57 PDT)
Sampath Koppole
AMBER: subroutine ephi !!
(Fri Oct 19 2007 - 01:08:26 PDT)
AMBER: Problems compiling Amber9 on IBM-AIX
(Mon Oct 08 2007 - 04:42:20 PDT)
san_amber roy
AMBER: lipid bilayer
(Thu Oct 11 2007 - 04:52:42 PDT)
Re: AMBER: MAXPR
(Mon Oct 01 2007 - 23:58:03 PDT)
Re: AMBER: MAXPR
(Mon Oct 01 2007 - 01:10:35 PDT)
sanket deshmukh
AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)
(Wed Oct 31 2007 - 11:57:54 PDT)
Scott Brozell
Re: AMBER: Test fails in Parallel version Amber9
(Tue Oct 16 2007 - 11:35:24 PDT)
Re: AMBER: amber9 installation problem
(Tue Oct 16 2007 - 10:15:04 PDT)
Re: AMBER: error in modified PNA -DNA simulation..
(Thu Oct 11 2007 - 17:26:11 PDT)
Re: AMBER: BOMB!
(Thu Oct 11 2007 - 16:59:50 PDT)
Scott Pendley
Re: AMBER: MM_PBSA calcultion- help me
(Tue Oct 16 2007 - 10:24:34 PDT)
Re: AMBER: Error- MM_PBSA calculation
(Thu Oct 11 2007 - 14:56:43 PDT)
Re: AMBER: Thermodynamic Integration with Explicit Solvent
(Wed Oct 10 2007 - 15:39:12 PDT)
Re: AMBER: Thermodynamic Integration with Explicit Solvent
(Wed Oct 10 2007 - 15:38:20 PDT)
Re: AMBER: Thermodynamic Integration with Explicit Solvent
(Tue Oct 09 2007 - 18:09:14 PDT)
AMBER: Thermodynamic Integration with Explicit Solvent
(Tue Oct 09 2007 - 14:38:03 PDT)
Re: AMBER: interaction energy calculations
(Tue Oct 09 2007 - 13:51:25 PDT)
Seongeun Yang
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Tue Oct 30 2007 - 20:52:45 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Tue Oct 30 2007 - 08:19:32 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Mon Oct 29 2007 - 23:14:13 PDT)
Re: AMBER: &dipole input and some questions on using polarizable force fields
(Fri Oct 26 2007 - 22:03:36 PDT)
AMBER: &dipole input and some questions on using polarizable force fields
(Thu Oct 25 2007 - 06:11:48 PDT)
Seth Lilavivat
AMBER: AMBER 8: QMMM - molecule fluctuates wildly
(Mon Oct 29 2007 - 13:40:06 PDT)
AMBER: Backbone flexibility/entropy
(Thu Oct 18 2007 - 14:47:37 PDT)
Sharad gupta
AMBER: error in modified PNA DNA simulation
(Sun Oct 14 2007 - 22:35:13 PDT)
AMBER: error in modified PNA -DNA simulation..
(Wed Oct 10 2007 - 03:39:07 PDT)
Siang Yip
AMBER: How to use loadpdbusingseq command to load branched structure?
(Fri Oct 19 2007 - 10:21:36 PDT)
snoze pa
AMBER: Amber FF parameters for the Zinc-hydroxammate interaction
(Sun Oct 28 2007 - 17:59:26 PDT)
Steve Spronk
RE: AMBER: hbond analysis output
(Thu Oct 25 2007 - 06:10:05 PDT)
RE: AMBER: question about charge of prmtop file
(Wed Oct 24 2007 - 07:21:25 PDT)
Steven Winfield
Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?
(Tue Oct 09 2007 - 03:06:53 PDT)
Syed Tarique Moin
AMBER: parameterization for copper
(Wed Oct 03 2007 - 03:45:33 PDT)
Thomas Cheatham III
Re: AMBER: Abnormality in MM-PBSA result
(Fri Oct 19 2007 - 08:56:36 PDT)
Thomas Steinbrecher
Re: AMBER: results from TI
(Tue Oct 23 2007 - 14:25:24 PDT)
Re: AMBER: results from TI
(Tue Oct 23 2007 - 11:07:30 PDT)
Re: AMBER: question about charge of prmtop file
(Tue Oct 23 2007 - 08:41:09 PDT)
Re: AMBER: results from TI
(Mon Oct 22 2007 - 10:35:15 PDT)
Re: AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander
(Thu Oct 18 2007 - 16:43:47 PDT)
Re: AMBER: how to simulate a ligand bound to a residue
(Thu Oct 18 2007 - 11:29:25 PDT)
Re: AMBER: Thermodynamic Integration with Explicit Solvent
(Tue Oct 09 2007 - 17:12:13 PDT)
Tom Darden
Re: AMBER: subroutine ephi !!
(Fri Oct 19 2007 - 05:06:33 PDT)
VANIA MARIA AMARO CALISTO
AMBER: antechamber fails with large molecules
(Wed Oct 31 2007 - 02:26:14 PDT)
AMBER: The number of the path atoms exceeds MAXPATHATOMNUM
(Mon Oct 29 2007 - 05:13:01 PDT)
varsha rani
AMBER: anal problem
(Tue Oct 30 2007 - 04:48:03 PDT)
Re: AMBER: MM_PBSA calcultion- help me
(Tue Oct 16 2007 - 22:40:48 PDT)
AMBER: MM_PBSA calcultion- help me
(Mon Oct 15 2007 - 22:53:14 PDT)
vikky 99
AMBER: Error- MM_PBSA calculation
(Thu Oct 11 2007 - 08:01:23 PDT)
AMBER: Error- MM_PBSA calculation
(Thu Oct 11 2007 - 00:28:25 PDT)
AMBER: Error- MM_PBSA calculation
(Wed Oct 10 2007 - 10:44:53 PDT)
Vlad Cojocaru
Re: AMBER: problems visualizing mdcrd in VMD
(Wed Oct 31 2007 - 05:41:42 PDT)
Re: AMBER: problems visualizing mdcrd in VMD
(Wed Oct 31 2007 - 04:33:37 PDT)
Re: AMBER: lipid bilayer
(Thu Oct 11 2007 - 05:09:23 PDT)
WANG,YING
RE: AMBER: question about charge of prmtop file
(Wed Oct 24 2007 - 07:44:20 PDT)
Re: AMBER: question about charge of prmtop file
(Tue Oct 23 2007 - 09:08:15 PDT)
AMBER: question about charge of prmtop file
(Tue Oct 23 2007 - 07:11:22 PDT)
RE: AMBER: question about h bond
(Fri Oct 19 2007 - 21:07:49 PDT)
AMBER: question about h bond
(Fri Oct 19 2007 - 17:19:36 PDT)
RE: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 12:11:19 PDT)
Re: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 08:47:05 PDT)
Wei Zhang
Re: AMBER: Amber9 parallel installation error (with openMPI)
(Mon Oct 29 2007 - 15:16:49 PDT)
Re: AMBER: Amber9 parallel installation error (with openMPI)
(Mon Oct 29 2007 - 14:16:45 PDT)
Wenyong Tong
Re: AMBER: follow-up
(Tue Oct 09 2007 - 13:56:04 PDT)
Yang, Lee-Wei
AMBER: RE: about deoxy- and oxy- heme
(Sun Oct 28 2007 - 01:52:58 PDT)
RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
(Thu Oct 25 2007 - 22:52:56 PDT)
AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
(Thu Oct 25 2007 - 07:46:00 PDT)
RE: AMBER: heme forcefield atom types
(Wed Oct 24 2007 - 11:41:29 PDT)
Yong Duan
RE: AMBER: Polarizable Force Field: Ligand Parameterization et al.
(Thu Oct 25 2007 - 10:02:55 PDT)
RE: AMBER: question about h bond
(Fri Oct 19 2007 - 17:41:19 PDT)
RE: AMBER: AMBER 9 - Force Field Options - Question
(Thu Oct 18 2007 - 12:18:01 PDT)
RE: AMBER: AMBER 9 - Force Field Options - Question
(Thu Oct 18 2007 - 09:21:00 PDT)
RE: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 13:47:55 PDT)
RE: AMBER: AMBER 9 - Force Field Options - Question
(Wed Oct 17 2007 - 09:25:16 PDT)
Last message date
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Sun Nov 04 2007 - 06:07:19 PST
Archived on
: Fri Dec 20 2024 - 05:53:40 PST
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