AMBER Archive (2002) - By Date

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Starting: Wed Jan 02 2002 - 16:22:14 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST

question Kang, Jonghoon (Wed Jan 02 2002 - 16:22:14 CST)
linux? Shixiang Yan (Thu Jan 03 2002 - 20:17:46 CST)
Re: linux? Carlos Simmerling (Fri Jan 04 2002 - 07:55:15 CST)
pairlist limit Laila Abou Zeid (Fri Jan 04 2002 - 08:32:57 CST)
xleap sara nunez (Fri Jan 04 2002 - 17:28:14 CST)
Re: pairlist limit Guanglei Cui (Fri Jan 04 2002 - 22:56:39 CST)
MPI (parallel) version of GIBBS Etienne ENGLER (Mon Jan 07 2002 - 06:13:45 CST)
Re: Not able to do parallel run (again) Stéphane Teletchéa (Mon Jan 07 2002 - 11:08:17 CST)
average position of water Hungie Hungie (Tue Jan 08 2002 - 06:28:00 CST)
Re: Not able to do parallel run (again) Stéphane Teletchéa (Tue Jan 08 2002 - 10:21:07 CST)
questions about resp X. Tan (Tue Jan 08 2002 - 10:31:55 CST)
Amber on Tru64 Sebastian Jayaraj (Tue Jan 08 2002 - 13:22:43 CST)
Re: Amber on Tru64 jim caldwell (Tue Jan 08 2002 - 13:51:06 CST)
Re: average position of water Elsa de Sousa Henriques (Tue Jan 08 2002 - 16:15:44 CST)
adiabatic map franck chevalier (Wed Jan 09 2002 - 06:41:57 CST)
SCEE parameter Sophia Kondratova (Wed Jan 09 2002 - 10:49:36 CST)
removing rotational motion in MD Michael G Cooney (Wed Jan 09 2002 - 11:41:26 CST)
question: velocity units Martina Roeselova (Wed Jan 09 2002 - 11:46:00 CST)
Re: question: velocity units Pascal Bonnet (Wed Jan 09 2002 - 11:57:58 CST)
Re: removing rotational motion in MD Stéphane Teletchéa (Wed Jan 09 2002 - 12:04:30 CST)
Re: removing rotational motion in MD Sanjeev B.S. (Wed Jan 09 2002 - 12:54:55 CST)
Amber 6 on IA64 Karen Haskell (Wed Jan 09 2002 - 15:35:02 CST)
Re: removing rotational motion in MD Stéphane Teletchéa (Thu Jan 10 2002 - 02:35:54 CST)
(no subject) amutha ramaswamy (Thu Jan 10 2002 - 04:11:15 CST)
inquiry regarding AMBER xz27 (Thu Jan 10 2002 - 15:24:08 CST)
Re: inquiry regarding AMBER David Case (Thu Jan 10 2002 - 16:51:54 CST)
seperate_solute_output Mirjam Lerch (Fri Jan 11 2002 - 03:02:31 CST)
Re: Re:ERROR TERMINATION DUE TO SHAKE OR TORCON sxzheng (Fri Jan 11 2002 - 21:21:30 CST)
multiple improper torsion terms Thijs Beuming (Fri Jan 11 2002 - 21:37:58 CST)
pukering of DNA bases? A.Madhumalar (Sat Jan 12 2002 - 23:03:50 CST)
ptraj cannot use compressed files? Michael G Cooney (Mon Jan 14 2002 - 10:17:03 CST)
ptraj and compressed files Michael G Cooney (Mon Jan 14 2002 - 10:48:40 CST)
(no subject) Sophia Kondratova (Mon Jan 14 2002 - 12:28:01 CST)
Re: your mail jim caldwell (Mon Jan 14 2002 - 13:01:44 CST)
how to neutralise the system? X. Tan (Mon Jan 14 2002 - 13:18:14 CST)
Re: how to neutralise the system? David Case (Mon Jan 14 2002 - 13:35:00 CST)
resizing and recompiling sander UMEMOTO kimiko (Mon Jan 14 2002 - 19:12:02 CST)
temperature control Jerry wu (Mon Jan 14 2002 - 21:55:16 CST)
azobenzene parameters Uwe Richter (Tue Jan 15 2002 - 04:18:03 CST)
minimising WATBOX216 sara nunez (Tue Jan 15 2002 - 13:11:04 CST)
Re: minimising WATBOX216 Michael G Cooney (Tue Jan 15 2002 - 15:38:58 CST)
I can not see text in xleap ! S. Jang (Wed Jan 16 2002 - 00:56:04 CST)
Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 02:14:48 CST)
Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 02:15:03 CST)
sander (Amber5) vs sander_classic (Amber6) Uwe Richter (Wed Jan 16 2002 - 05:33:32 CST)
unsuscribe Ivan Beà (Wed Jan 16 2002 - 09:25:38 CST)
Open position: Postdoctoral Scientist Joachim Reichelt (Wed Jan 16 2002 - 09:57:07 CST)
Parameters Marta Murcia (Wed Jan 16 2002 - 09:59:26 CST)
Stretching Constants Daniel Flint (Thu Jan 17 2002 - 05:21:52 CST)
Amino acid unit "NHE" problem ? S. Jang (Thu Jan 17 2002 - 06:27:19 CST)
Re: Amino acid unit "NHE" problem ? Michael Jakusch (Thu Jan 17 2002 - 08:32:28 CST)
Maxwell Boltzmann Distribution Stéphane Teletchéa (Thu Jan 17 2002 - 08:48:02 CST)
Re: Amino acid unit "NHE" problem ? Raik Grunberg (Thu Jan 17 2002 - 09:23:30 CST)
Re: Amino acid unit "NHE" problem ? David Case (Thu Jan 17 2002 - 10:37:55 CST)
NAD parameters Andy Purkiss (Thu Jan 17 2002 - 13:42:21 CST)
nmode memory requirements Michael Jakusch (Fri Jan 18 2002 - 10:15:52 CST)
Re: nmode memory requirements David Case (Fri Jan 18 2002 - 11:50:29 CST)
Amber6 + IBM SP3 Sanjeev B.S. (Sat Jan 19 2002 - 08:59:58 CST)
Latest parm + getting parm98 as default in LEaP Sanjeev B.S. (Mon Jan 21 2002 - 00:43:42 CST)
Re: Latest parm + getting parm98 as default in LEaP Andreas Svrcek-Seiler (Mon Jan 21 2002 - 04:01:49 CST)
nmode vectors Thijs Beuming (Mon Jan 21 2002 - 06:24:48 CST)
triNAG parameters?4 Andrea Bernini (Mon Jan 21 2002 - 09:13:26 CST)
Re: Latest parm + getting parm98 as default in LEaP Lepsa (Tue Jan 22 2002 - 00:39:59 CST)
Re:Latest parm + getting parm98 as default in LEaP Bill Ross (Tue Jan 22 2002 - 01:07:39 CST)
Re: Latest parm + getting parm98 as default in LEaP David Case (Tue Jan 22 2002 - 10:14:55 CST)
timescale of deoxyribose ring repuckering Jake Isaacs (Tue Jan 22 2002 - 10:43:40 CST)
Re: triNAG parameters?4 Michael Ford (Tue Jan 22 2002 - 11:19:21 CST)
"flags" in .lib files Sue Heavner (Wed Jan 23 2002 - 10:22:08 CST)
Re: "flags" in .lib files Bill Ross (Wed Jan 23 2002 - 13:39:45 CST)
DOCK Peter Gannett (Thu Jan 24 2002 - 08:48:52 CST)
MP_Lite Stéphane Teletchéa (Thu Jan 24 2002 - 11:44:40 CST)
torsional fit Fabrizio Giordanetto (Fri Jan 25 2002 - 04:34:55 CST)
group input in ANAL Elizabeth K. White (Fri Jan 25 2002 - 16:11:13 CST)
Re: group input in ANAL Mite51 (Sat Jan 26 2002 - 15:09:46 CST)
xleap and PDB file Prabal Maiti (Tue Jan 29 2002 - 01:28:23 CST)
restart md simulation Uwe Richter (Tue Jan 29 2002 - 03:35:50 CST)
box_size Susanna Monti (Tue Jan 29 2002 - 04:34:22 CST)
Re: box_size darden (Tue Jan 29 2002 - 09:38:55 CST)
Re: box_size jim caldwell (Tue Jan 29 2002 - 09:56:23 CST)
MacOS X David Bevan (Tue Jan 29 2002 - 10:15:12 CST)
Re: restart md simulation Michael G Cooney (Tue Jan 29 2002 - 10:44:03 CST)
B-factor Michal Otyepka (Thu Jan 31 2002 - 04:45:50 CST)
LIMIN Faliure/Energies per residue for B-DNA etc. Prabal Maiti (Thu Jan 31 2002 - 13:49:00 CST)
Re: LIMIN Faliure/Energies per residue for B-DNA etc. darden (Thu Jan 31 2002 - 15:11:19 CST)
question regarding ntwv. Margaret Cheung (Thu Jan 31 2002 - 19:55:58 CST)
Re: question regarding ntwv. David Case (Fri Feb 01 2002 - 00:43:51 CST)
help on parameters. X. Tan (Mon Feb 04 2002 - 19:40:52 CST)
Re: temperature control Michael G Cooney (Tue Feb 05 2002 - 13:15:58 CST)
quasih Sue Heavner (Wed Feb 06 2002 - 09:16:25 CST)
Re: quasih CUI, Guanglei (Wed Feb 06 2002 - 09:53:55 CST)
ImagingAtom eric ARNOULT (Wed Feb 06 2002 - 10:07:04 CST)
Re: ImagingAtom Bill Ross (Thu Feb 07 2002 - 04:41:57 CST)
compile AMBER on cygwin? quch quch (Thu Feb 07 2002 - 13:46:43 CST)
frcmod file format Sophia Kondratova (Mon Feb 11 2002 - 12:16:23 CST)
Re: frcmod file format CUI, Guanglei (Mon Feb 11 2002 - 12:38:37 CST)
Re: frcmod file format Lepsa (Tue Feb 12 2002 - 01:05:54 CST)
parm94.dat file x357l (Tue Feb 12 2002 - 12:21:44 CST)
IFTRES option in sander and gibbs Alexander Issanin (Tue Feb 12 2002 - 15:09:52 CST)
belly input Prabal Maiti (Tue Feb 12 2002 - 16:26:21 CST)
Lipid simulation, DMPC Samantha (Wed Feb 13 2002 - 10:24:20 CST)
Linking to its own image Miguel Angel Rodriguez Carvajal (Thu Feb 14 2002 - 08:15:52 CST)
RESP Crash Mike Keller (Thu Feb 14 2002 - 09:24:51 CST)
Re: problem in running MM-PBSA script David Case (Thu Feb 14 2002 - 10:42:52 CST)
residual dipolar coupling restraints Jake Isaacs (Thu Feb 14 2002 - 13:37:42 CST)
memory problem on gibbs X. Tan (Thu Feb 14 2002 - 18:24:55 CST)
flying monomers... Margaret Cheung (Fri Feb 15 2002 - 17:58:39 CST)
MPICH/LAM on sparc Sanjeev B.S. (Sat Feb 16 2002 - 06:23:26 CST)
Power Point slides Krishna Bisetty (Mon Feb 18 2002 - 01:11:22 CST)
.OFF file format Dr Jan Rosenzweig (Mon Feb 18 2002 - 12:14:27 CST)
Re: .OFF file format Bill Ross (Mon Feb 18 2002 - 14:26:16 CST)
Gibbs Question Bernd Wellenzohn (Mon Feb 18 2002 - 14:47:15 CST)
removing rotational motion John Finke (Tue Feb 19 2002 - 03:44:08 CST)
Re: removing rotational motion Andreas Svrcek-Seiler (Tue Feb 19 2002 - 06:27:18 CST)
Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
Re: removing rotational motion Stéphane Teletchéa (Tue Feb 19 2002 - 07:15:10 CST)
restrt problem Sanjeev B.S. (Tue Feb 19 2002 - 07:50:41 CST)
Xleap x357l (Tue Feb 19 2002 - 10:03:11 CST)
The link is out Stéphane Teletchéa (Tue Feb 19 2002 - 10:58:44 CST)
Re: The link is out Carlos Simmerling (Tue Feb 19 2002 - 14:53:45 CST)
ERROR from RESNBA X. Tan (Tue Feb 19 2002 - 19:39:21 CST)
AMBER logo citation FyD (Wed Feb 20 2002 - 01:53:18 CST)
Re: AMBER logo citation Pascal Bonnet (Wed Feb 20 2002 - 02:17:39 CST)
Re: AMBER logo citation Lepsa (Wed Feb 20 2002 - 03:02:15 CST)
Re: AMBER logo citation David Case (Wed Feb 20 2002 - 11:11:41 CST)
Re: The link is out David Case (Wed Feb 20 2002 - 11:20:00 CST)
rms and watershell (in ptraj) dkon_at_email.arizona.edu (Wed Feb 20 2002 - 18:54:58 CST)
MPI sander Uwe Richter (Thu Feb 21 2002 - 07:13:52 CST)
vlimit exceed Prabal Maiti (Thu Feb 21 2002 - 21:23:39 CST)
Re: vlimit exceed Yuguang Mu (Fri Feb 22 2002 - 01:44:53 CST)
MD with simulated annealing Giulio Rastelli (Fri Feb 22 2002 - 12:39:56 CST)
Re: removing rotational motion Jianxin Guo (Fri Feb 22 2002 - 16:32:48 CST)
anal input Prabal Maiti (Fri Feb 22 2002 - 18:31:58 CST)
Re: vlimit exceed David Case (Sun Feb 24 2002 - 00:03:24 CST)
recursively calling sander? Jeff Ames (Mon Feb 25 2002 - 10:32:54 CST)
redius of B-DNA duplex Hungie Hungie (Mon Feb 25 2002 - 10:49:26 CST)
Re: redius of B-DNA duplex A.Madhumalar (Mon Feb 25 2002 - 11:41:42 CST)
Carnal coordinate averaging Michael G Cooney (Mon Feb 25 2002 - 16:01:26 CST)
Re: Carnal coordinate averaging Bill Ross (Mon Feb 25 2002 - 16:44:17 CST)
Re: recursively calling sander? David Pearlman (Mon Feb 25 2002 - 21:10:22 CST)
(no subject) deepak rangaswamy (Tue Feb 26 2002 - 05:28:18 CST)
leap:segmentation fault Sanjeev B.S. (Tue Feb 26 2002 - 10:30:45 CST)
xleap and carbohydrates and stuff Amesh Patel (Wed Feb 27 2002 - 08:43:23 CST)
Cholesterol PREP file samantha hughes (Wed Feb 27 2002 - 09:28:46 CST)
(no subject) Ian Bates (Wed Feb 27 2002 - 15:23:17 CST)
visualizaion program for NMODE! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 16:48:30 CST)
correlated motions in a protein! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 17:52:55 CST)
Re: visualizaion program for NMODE! Yuguang Mu (Thu Feb 28 2002 - 02:56:44 CST)
Re: Cholesterol PREP file Stéphane Teletchéa (Thu Feb 28 2002 - 03:48:16 CST)
Persistence length Bernd Wellenzohn (Thu Feb 28 2002 - 09:39:11 CST)
AMBER 99 John Finke (Thu Feb 28 2002 - 18:22:55 CST)
Re: AMBER 99 Felipe Pineda (Fri Mar 01 2002 - 02:25:27 CST)
(no subject) deepak rangaswamy (Fri Mar 01 2002 - 05:00:51 CST)
Release of Amber, version 7 (fwd) amber mail account (Sun Mar 03 2002 - 17:13:26 CST)
concentrated system Jerry wu (Mon Mar 04 2002 - 02:36:21 CST)
carnal and union Pascal Bonnet (Mon Mar 04 2002 - 03:00:20 CST)
carnal and union: solution Pascal Bonnet (Mon Mar 04 2002 - 06:33:17 CST)
Re: GB simulation CUI, Guanglei (Mon Mar 04 2002 - 09:41:53 CST)
GB simulation Giulio Rastelli (Mon Mar 04 2002 - 10:32:28 CST)
amber 60 on Unicos Cray Cezary Czaplewski (Mon Mar 04 2002 - 11:56:36 CST)
(no subject) Campbell, Matthew P (Tue Mar 05 2002 - 11:21:07 CST)
Re: Release of Amber, version 7 (fwd) SPEROLEEM_at_aol.com (Tue Mar 05 2002 - 16:16:27 CST)
a question about .in files Vlad Cojocaru (Wed Mar 06 2002 - 09:00:02 CST)
leap calculation Itziar Maestre Asenjo (Wed Mar 06 2002 - 11:43:44 CST)
Re: a question about .in files Bill Ross (Wed Mar 06 2002 - 13:16:53 CST)
Re: leap calculation (loadamberprep) Bill Ross (Wed Mar 06 2002 - 13:22:33 CST)
Are the programs sander and gibbs in Amber 7 parallel? ramon kleber da rocha (Wed Mar 06 2002 - 13:28:01 CST)
converting some files Vlad Cojocaru (Thu Mar 07 2002 - 05:00:00 CST)
dG of wild type/mutant FyD (Thu Mar 07 2002 - 05:26:31 CST)
statistical analysis of MD trajectories Jake Isaacs (Thu Mar 07 2002 - 11:24:03 CST)
parameter estimation Vlad Cojocaru (Thu Mar 07 2002 - 12:32:25 CST)
choosing a forcefield nepenthes_at_vplaces.net (Thu Mar 07 2002 - 21:51:25 CST)
high electrostatic energy thenmalar rathinavelan (Thu Mar 07 2002 - 23:13:40 CST)
Fw: parameter estimation Lepsa (Fri Mar 08 2002 - 03:52:50 CST)
new units Vlad Cojocaru (Fri Mar 08 2002 - 08:35:46 CST)
rdparm error message Rukman Hertadi (Sun Mar 10 2002 - 02:46:53 CST)
Europium force field parms Peter Gannett (Sun Mar 10 2002 - 14:07:44 CST)
Re Europium force field parms Fabrice Yerly (Mon Mar 11 2002 - 01:32:59 CST)
scaleCharges Vojta Klusak (Mon Mar 11 2002 - 03:45:54 CST)
Re Europium force field parms Marc Baaden (Mon Mar 11 2002 - 05:52:40 CST)
Re: scaleCharges David Case (Mon Mar 11 2002 - 11:37:51 CST)
limit of written files with ptraj Carles Ferrer (Mon Mar 11 2002 - 14:54:16 CST)
combining trajectory file Rukman Hertadi (Tue Mar 12 2002 - 03:48:49 CST)
Re: combining trajectory file Natasja Brooijmans (Tue Mar 12 2002 - 10:00:38 CST)
Re: combining trajectory file CUI, Guanglei (Tue Mar 12 2002 - 10:24:44 CST)
Re: combining trajectory file Thomas Cheatham (Tue Mar 12 2002 - 12:30:51 CST)
Re: questions about resp X. Tan (Tue Mar 12 2002 - 15:02:22 CST)
question on Gibbs calculation X. Tan (Tue Mar 12 2002 - 15:50:24 CST)
help please :) Richard Kho (Fri Mar 15 2002 - 18:59:23 CST)
Post-doctoral position Wolfe, Jennifer (Mon Mar 18 2002 - 10:33:11 CST)
Dual AMD motherboards jim caldwell (Mon Mar 18 2002 - 17:47:12 CST)
RE: Dual AMD motherboards Demchuk, Eugene (Mon Mar 18 2002 - 18:52:55 CST)
RE: Dual AMD motherboards jim caldwell (Mon Mar 18 2002 - 20:04:24 CST)
Dual AMD ASUS A7M266-D Solved jim caldwell (Mon Mar 18 2002 - 20:37:19 CST)
Re: Amber shailendra singh (Mon Mar 18 2002 - 23:57:48 CST)
minimization problem Uwe Richter (Tue Mar 19 2002 - 06:22:06 CST)
Re: minimization problem Andreas Svrcek-Seiler (Tue Mar 19 2002 - 07:33:19 CST)
carnal RST output format Pascal Bonnet (Tue Mar 19 2002 - 08:12:31 CST)
Still no bench Stéphane Teletchéa (Tue Mar 19 2002 - 09:17:45 CST)
creating a unit wth xleap Marcela Madrid (Tue Mar 19 2002 - 13:07:30 CST)
Re: carnal RST output format Bill Ross (Tue Mar 19 2002 - 13:32:36 CST)
Re: creating a unit wth xleap Bill Ross (Tue Mar 19 2002 - 13:43:25 CST)
Re: carnal RST output format Andy Purkiss (Tue Mar 19 2002 - 14:45:00 CST)
Amber6 & ES40 incompatability Sanjeev B.S. (Wed Mar 20 2002 - 01:01:17 CST)
building bcyd with tleap Itziar Maestre Asenjo (Wed Mar 20 2002 - 04:51:47 CST)
MM-PBSA philosophy Michal Otyepka (Wed Mar 20 2002 - 06:34:24 CST)
atom connection, .off file problem Uwe Richter (Wed Mar 20 2002 - 07:48:07 CST)
Re: MM-PBSA philosophy Felipe Pineda (Wed Mar 20 2002 - 08:25:05 CST)
Re: MM-PBSA philosophy David Case (Wed Mar 20 2002 - 10:10:05 CST)
Question about obtaining amber! Peter Fojan (Thu Mar 21 2002 - 07:19:59 CST)
MS program ... A. Ababou (Sat Mar 23 2002 - 10:21:15 CST)
mdcrd to arc Ian R Bates (Sat Mar 23 2002 - 10:46:21 CST)
Re: MS program ... Samantha (Sat Mar 23 2002 - 11:09:14 CST)
nmropt problem in AMBER7 Rukman Hertadi (Mon Mar 25 2002 - 03:51:22 CST)
Resending: Medicinal and Computational Chemistry Job Market Computational Chemistry Job Market (Mon Mar 25 2002 - 14:05:03 CST)
Re: polarizabilities Lepsa (Tue Mar 26 2002 - 03:12:09 CST)
Hydrogen bond energy using Anal A.Madhumalar (Tue Mar 26 2002 - 04:23:34 CST)
One question about how to use the amber Zhe SUN (Tue Mar 26 2002 - 06:49:35 CST)
secondary structure Ian R Bates (Tue Mar 26 2002 - 13:49:48 CST)
problems using Link John Finke (Tue Mar 26 2002 - 14:39:59 CST)
GB model and belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 15:46:40 CST)
More GB/Belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 16:00:23 CST)
Re: GB model and belly David Case (Tue Mar 26 2002 - 17:07:33 CST)
Polarizabilities, charge scaling and ions Michal Otyepka (Wed Mar 27 2002 - 03:42:29 CST)
s-matrix format and ftnmr Shixiang Yan (Wed Mar 27 2002 - 15:49:50 CST)
What is the atoms limit for Amber 7? William Wei (Wed Mar 27 2002 - 16:19:34 CST)
Re: What is the atoms limit for Amber 7? David Case (Wed Mar 27 2002 - 17:45:44 CST)
sulfate and sulfamate parameters jeff dyason (Wed Mar 27 2002 - 22:28:55 CST)
AMBER 5 Monica (Wed Mar 27 2002 - 22:29:12 CST)
change topology Michal Otyepka (Thu Mar 28 2002 - 02:44:38 CST)
Re: change topology Bill Ross (Thu Mar 28 2002 - 03:45:49 CST)
Magnesium as a DNA counterion in AMBER 6.0 Mike Keller (Thu Mar 28 2002 - 09:31:29 CST)
Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) Wu, JianHui(IAF)(LAVAL) (Thu Mar 28 2002 - 11:56:04 CST)
Re: Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) David Case (Thu Mar 28 2002 - 12:40:16 CST)
a little bit confused with leap-frog algorithm... Margaret Cheung (Thu Mar 28 2002 - 15:08:40 CST)
Problem with atom type rhertadi_at_bio.titech.ac.jp (Thu Mar 28 2002 - 15:55:33 CST)
Re: Problem with atom type Bill Ross (Thu Mar 28 2002 - 18:14:16 CST)
Re: a little bit confused with leap-frog algorithm... David Case (Thu Mar 28 2002 - 19:52:38 CST)
convergence of MD simulations Sue Heavner (Sat Mar 30 2002 - 17:02:16 CST)
Re: a little bit confused with leap-frog algorithm... Margaret Cheung (Sat Mar 30 2002 - 21:35:36 CST)
compiling error. Margaret Cheung (Sun Mar 31 2002 - 01:26:53 CST)
Re: compiling error. Carlos Simmerling (Sun Mar 31 2002 - 09:24:19 CST)
Re: compiling error. Margaret Cheung (Sun Mar 31 2002 - 22:44:07 CST)
Re: compiling error. Bill Ross (Mon Apr 01 2002 - 01:30:24 CST)
does PME function without charge neutralization? Ian R Bates (Tue Apr 02 2002 - 12:30:41 CST)
Re: does PME function without charge neutralization? darden (Tue Apr 02 2002 - 16:23:02 CST)
(no subject) deepak rangaswamy (Tue Apr 02 2002 - 22:52:55 CST)
input files Monica (Wed Apr 03 2002 - 07:00:42 CST)
Re: input files Carlos Simmerling (Wed Apr 03 2002 - 07:40:30 CST)
Initial Amber 7 benchmark timings David Case (Wed Apr 03 2002 - 20:33:14 CST)
Re: Initial Amber 7 benchmark timings Stéphane Teletchéa (Thu Apr 04 2002 - 03:36:23 CST)
amber7, PME and anisotrop press. Arvid Soederhaell (Thu Apr 04 2002 - 03:46:58 CST)
new residues Vlad Cojocaru (Thu Apr 04 2002 - 07:03:37 CST)
About the sander_classic calculation Alan Leo (Thu Apr 04 2002 - 15:32:34 CST)
convergence of MD simulations Sue Heavner (Thu Apr 04 2002 - 16:24:05 CST)
Re: About the sander_classic calculation John Bushnell (Thu Apr 04 2002 - 16:31:11 CST)
Re: convergence of MD simulations Andreas Svrcek-Seiler (Fri Apr 05 2002 - 04:12:11 CST)
Sander-Gibbs Kidley N J (Mon Apr 08 2002 - 10:34:49 CDT)
PDB file with CONECT record Prabal Maiti (Mon Apr 08 2002 - 14:06:21 CDT)
Re:PDB file with CONECT record Bill Ross (Mon Apr 08 2002 - 15:02:21 CDT)
Re: convergence of MD simulations darden (Mon Apr 08 2002 - 15:08:10 CDT)
PDB file with CONECT record (fwd) Prabal Maiti (Tue Apr 09 2002 - 20:04:50 CDT)
Re: PDB file with CONECT record (fwd) David Case (Tue Apr 09 2002 - 22:30:38 CDT)
Roar 2.1 with Amber7 Soonmin Jang (Tue Apr 09 2002 - 22:39:07 CDT)
RE: Roar 2.1 with Amber7 Ross Walker (Wed Apr 10 2002 - 00:48:43 CDT)
Re: PDB file with CONECT record Bill Ross (Wed Apr 10 2002 - 01:09:36 CDT)
Amber7 and VMD Soonmin Jang (Wed Apr 10 2002 - 03:40:37 CDT)
Re: Amber7 and VMD Thomas Cheatham (Wed Apr 10 2002 - 08:55:46 CDT)
(no subject) Mark Hsieh (Wed Apr 10 2002 - 15:31:50 CDT)
Matching Patterns Tali (Wed Apr 10 2002 - 16:57:59 CDT)
DNA structure get distorted Monica (Thu Apr 11 2002 - 03:00:48 CDT)
noesy intensity input in DNA Monica (Thu Apr 11 2002 - 03:03:50 CDT)
Follow distances during MD Francois Dupradeau (Thu Apr 11 2002 - 05:19:02 CDT)
Re: Follow distances during MD Raik Grunberg (Thu Apr 11 2002 - 07:49:16 CDT)
(no subject) Mark Beardsell (Thu Apr 11 2002 - 08:36:29 CDT)
Re: your mail Andreas Svrcek-Seiler (Thu Apr 11 2002 - 09:33:22 CDT)
Save from LEaP to a PDBQ file ? jeff dyason (Thu Apr 11 2002 - 22:50:32 CDT)
Re: Save from LEaP to a PDBQ file ? Bill Ross (Fri Apr 12 2002 - 01:16:28 CDT)
Re: PDB file with CONECT record Prabal Maiti (Fri Apr 12 2002 - 01:27:15 CDT)
Thanks FyD (Fri Apr 12 2002 - 02:04:53 CDT)
Re: PDB file with CONECT record Bill Ross (Fri Apr 12 2002 - 02:27:37 CDT)
Re: PDB file with CONECT record Miguel Angel (Fri Apr 12 2002 - 05:03:09 CDT)
order parameters? Arvid Soederhaell (Fri Apr 12 2002 - 07:55:33 CDT)
Re: DNA structure get distorted David Case (Fri Apr 12 2002 - 11:27:10 CDT)
Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Fri Apr 12 2002 - 18:59:38 CDT)
Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error David Case (Fri Apr 12 2002 - 19:37:01 CDT)
help ..problem about antechamber Yi ming Cheng (Sat Apr 13 2002 - 00:30:26 CDT)
Re: Carlos Simmerling (Sat Apr 13 2002 - 07:06:29 CDT)
Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Sat Apr 13 2002 - 08:59:29 CDT)
Vulgar Models Do Everything And Love It!!! telesales (Mon Apr 15 2002 - 19:03:45 CDT)
Re: Help! Sander run error: Bus error David Case (Tue Apr 16 2002 - 00:32:16 CDT)
Re: PDB file with CONECT record Prabal Maiti (Tue Apr 16 2002 - 00:48:00 CDT)
compiling amber 6.0 in a Sun starfire ENT10000 ramon kleber da rocha (Tue Apr 16 2002 - 14:08:54 CDT)
4 Medicinal and Computational Chemistry Candidates medicinal and Compuatational Chemistry Resumes and Jobs (Tue Apr 16 2002 - 16:55:48 CDT)
Recalculating energies John Finke (Tue Apr 16 2002 - 19:45:23 CDT)
RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 05:53:27 CDT)
Re: Recalculating energies Carlos Simmerling (Wed Apr 17 2002 - 06:39:27 CDT)
Amber in a distributed environment Peter Gannett (Wed Apr 17 2002 - 07:07:56 CDT)
Re: RESP charges Lepsa (Wed Apr 17 2002 - 07:26:27 CDT)
RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 07:36:43 CDT)
RE: RESP charges Ross Walker (Wed Apr 17 2002 - 08:21:37 CDT)
Re: Amber in a distributed environment Sudhakar Pamidighantam (Wed Apr 17 2002 - 08:55:34 CDT)
Re: RESP charges jim caldwell (Wed Apr 17 2002 - 09:22:04 CDT)
Re: Lepsa (Wed Apr 17 2002 - 09:38:47 CDT)
RE: RESP charges Ross Walker (Wed Apr 17 2002 - 10:28:58 CDT)
(no subject) Filip Ryjacek (Wed Apr 17 2002 - 11:01:48 CDT)
Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 12:32:28 CDT)
again...Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 13:03:23 CDT)
mm pbsa: generate snapshots Mark Hsieh (Wed Apr 17 2002 - 16:52:41 CDT)
Re: mm pbsa: generate snapshots Mathy Froeyen (Thu Apr 18 2002 - 02:19:35 CDT)
pentane minimization Hungie Hungie (Thu Apr 18 2002 - 04:15:33 CDT)
pentane minimization Hungie Hungie (Thu Apr 18 2002 - 04:16:46 CDT)
DNA shifts during MD; C.O.M. removing and ptraj doesn't help... Filip Ryjacek (Thu Apr 18 2002 - 10:17:12 CDT)
RESP cfrenz_at_aecom.yu.edu (Thu Apr 18 2002 - 10:55:55 CDT)
pentane minimization...again Hungie Hungie (Thu Apr 18 2002 - 11:30:15 CDT)
MPICH and AMBER 7 Mark Hsieh (Thu Apr 18 2002 - 18:12:58 CDT)
RESP-ivary Vlad Cojocaru (Fri Apr 19 2002 - 06:26:22 CDT)
To PROFEC users Salinthip Thipayang (Fri Apr 19 2002 - 09:13:11 CDT)
Re: RESP-ivary Qing Zhang (Fri Apr 19 2002 - 11:15:27 CDT)
RE: RESP-ivary John Bushnell (Fri Apr 19 2002 - 13:16:40 CDT)
amber7 compilation on a beowulf cluster Peter Gannett (Fri Apr 19 2002 - 14:59:56 CDT)
RE: amber7 compilation on a beowulf cluster John Bushnell (Fri Apr 19 2002 - 16:48:00 CDT)
RE: amber7 compilation on a beowulf cluster Bill Ross (Fri Apr 19 2002 - 17:26:19 CDT)
mm_pbsa for uhbd Mark Hsieh (Fri Apr 19 2002 - 20:56:18 CDT)
Re: amber7 compilation on a beowulf cluster David Case (Fri Apr 19 2002 - 20:56:50 CDT)
(no subject) deepak rangaswamy (Sat Apr 20 2002 - 00:22:54 CDT)
Re: amber7 compilation on a beowulf cluster Peter Gannett (Sat Apr 20 2002 - 07:14:01 CDT)
Re: your mail David Case (Sat Apr 20 2002 - 11:06:32 CDT)
dummy atoms. Yongjun Jiang (Sat Apr 20 2002 - 22:20:44 CDT)
leap bugfix Bill Ross (Sun Apr 21 2002 - 16:55:34 CDT)
RESP Vlad Cojocaru (Mon Apr 22 2002 - 05:17:17 CDT)
amber6 with parallel Khatcharin Siriwong (Mon Apr 22 2002 - 07:48:24 CDT)
Re: RESP jim caldwell (Mon Apr 22 2002 - 10:04:25 CDT)
a problem Vlad Cojocaru (Mon Apr 22 2002 - 10:56:48 CDT)
(no subject) SPEROLEEM_at_aol.com (Mon Apr 22 2002 - 13:47:28 CDT)
a more general question Vlad Cojocaru (Tue Apr 23 2002 - 09:20:34 CDT)
DME and Carnal with AMBER6 Katherine W. Abold (Tue Apr 23 2002 - 09:48:04 CDT)
RESP tutorial Michael G Cooney (Tue Apr 23 2002 - 12:15:51 CDT)
INTPRT and PMF Sophia Kondratova (Tue Apr 23 2002 - 13:23:36 CDT)
(no subject) Bill Ross (Tue Apr 23 2002 - 14:30:58 CDT)
parallel sander? Mark Hsieh (Tue Apr 23 2002 - 14:31:55 CDT)
RE: parallel sander? Mark Hsieh (Tue Apr 23 2002 - 14:35:44 CDT)
Re: INTPRT and PMF David Pearlman (Tue Apr 23 2002 - 15:05:12 CDT)
generating left-handed A-DNA Marcela Madrid (Tue Apr 23 2002 - 19:41:08 CDT)
Re: RESP tutorial David Case (Tue Apr 23 2002 - 19:41:49 CDT)
RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 20:34:23 CDT)
RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 20:34:23 CDT)
sander & prmtop file generated from antechamber input ? jeff dyason (Tue Apr 23 2002 - 22:33:58 CDT)
Re: sander & prmtop file generated from antechamber input ? David Case (Wed Apr 24 2002 - 10:59:14 CDT)
Re: generating left-handed A-DNA David Case (Wed Apr 24 2002 - 11:09:07 CDT)
RE: a problem John Bushnell (Wed Apr 24 2002 - 16:02:31 CDT)
Re: amber7 and tip5p David Case (Wed Apr 24 2002 - 16:04:05 CDT)
Number of WATBOX yuann (Thu Apr 25 2002 - 00:54:02 CDT)
Re: Number of WATBOX David Smith (Thu Apr 25 2002 - 08:25:40 CDT)
PMF calculations Sophia Kondratova (Thu Apr 25 2002 - 08:30:11 CDT)
Re: PMF calculations David Smith (Thu Apr 25 2002 - 10:13:23 CDT)
About Group in Carnal William Wei (Thu Apr 25 2002 - 10:50:08 CDT)
Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 13:30:24 CDT)
Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 13:36:41 CDT)
sander mpich hangs Mark Hsieh (Thu Apr 25 2002 - 17:01:26 CDT)
Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Fri Apr 26 2002 - 03:39:35 CDT)
Re: sander mpich hangs Stéphane Teletchéa (Fri Apr 26 2002 - 06:54:01 CDT)
Re: Problems with AMBER7 and Multiple Processors on SGI servers Carlos Simmerling (Fri Apr 26 2002 - 07:05:52 CDT)
Re: Problems with AMBER7 and Multiple Processors on SGI servers Ian bates (Fri Apr 26 2002 - 10:17:52 CDT)
RE: sander mpich hangs Mark Hsieh (Fri Apr 26 2002 - 14:08:48 CDT)
max_rstack requested Albert Codony (Sun Apr 28 2002 - 17:39:58 CDT)
parmjoin Vlad Cojocaru (Mon Apr 29 2002 - 11:53:01 CDT)
Re: parmjoin David Case (Mon Apr 29 2002 - 13:26:26 CDT)
Fail message:Segmantation fault and Bus error? William Wei (Mon Apr 29 2002 - 14:38:48 CDT)
NTT=5? Jung-Hsing Lin (Mon Apr 29 2002 - 18:10:30 CDT)
TIP4P parameters Ge Zhou (Mon Apr 29 2002 - 21:03:54 CDT)
Re: TIP4P parameters David Case (Tue Apr 30 2002 - 00:17:49 CDT)
Re: NTT=5? David Case (Tue Apr 30 2002 - 00:32:20 CDT)
install leap not working nepenthes_at_vplaces.net (Tue Apr 30 2002 - 02:52:07 CDT)
How to run the leap module param_at_ibab.ac.in (Tue Apr 30 2002 - 04:34:32 CDT)
RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Tue Apr 30 2002 - 04:59:11 CDT)
Re: How to run the leap module Sanjeev B.S. (Tue Apr 30 2002 - 05:37:11 CDT)
Re: your mail deepak rangaswamy (Tue Apr 30 2002 - 07:06:06 CDT)
valine to alanine example Sophia Kondratova (Tue Apr 30 2002 - 10:23:21 CDT)
heterochirical peptides ? Yuguang Mu (Tue Apr 30 2002 - 10:43:39 CDT)
Re: Problems with AMBER7 and Multiple Processors on SGI servers David Case (Tue Apr 30 2002 - 11:02:30 CDT)
Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 11:10:46 CDT)
Re: How to run the leap module John Bushnell (Tue Apr 30 2002 - 12:46:35 CDT)
Re: NTT=5? David Case (Tue Apr 30 2002 - 13:16:04 CDT)
Re: heterochirical peptides ? David Case (Tue Apr 30 2002 - 13:21:38 CDT)
Re: install leap not working Bill Ross (Tue Apr 30 2002 - 14:21:01 CDT)
NaCl concentration Peter Gannett (Tue Apr 30 2002 - 14:34:38 CDT)
Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 15:36:45 CDT)
about ew_legal.h X. Tan (Tue Apr 30 2002 - 19:12:01 CDT)
Amber7 compilation on IBM sp3 machine Soonmin Jang (Tue Apr 30 2002 - 23:33:05 CDT)
IFBOX=0 error in amber7 Eva Darian (Tue Apr 30 2002 - 23:43:31 CDT)
Re: IFBOX=0 error in amber7 Bill Ross (Wed May 01 2002 - 00:15:05 CDT)
AMBER 7 - more problems with leap Mark Beardsell (Wed May 01 2002 - 07:17:46 CDT)
Re: about ew_legal.h David Case (Wed May 01 2002 - 11:10:36 CDT)
Amber7 nmode Sue Heavner (Wed May 01 2002 - 12:23:19 CDT)
Re: Amber7 nmode David Case (Wed May 01 2002 - 12:55:07 CDT)
Re: NTT=5? Jake Isaacs (Wed May 01 2002 - 14:47:09 CDT)
Carnal BUG?? William Wei (Wed May 01 2002 - 22:19:03 CDT)
RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Thu May 02 2002 - 03:55:45 CDT)
RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 11:09:21 CDT)
Compilation on RedHat-7.2 with MPICH Vincent BOSQUIER (Thu May 02 2002 - 11:29:32 CDT)
RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 12:48:10 CDT)
new RNA residues Vlad Cojocaru (Thu May 02 2002 - 14:07:32 CDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 15:26:45 CDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 15:38:24 CDT)
Help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 09:40:41 CDT)
help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 10:03:47 CDT)
TI integration Joe Fernandez (Sat May 04 2002 - 08:59:57 CDT)
Thanks to all Albert Codony (Sat May 04 2002 - 10:38:12 CDT)
crdgrow Vlad Cojocaru (Sat May 04 2002 - 15:06:32 CDT)
missing residues Mark Hsieh (Sun May 05 2002 - 02:15:31 CDT)
topology file generation Sanjeev B.S. (Mon May 06 2002 - 00:36:36 CDT)
Re: topology file generation Andreas Svrcek-Seiler (Mon May 06 2002 - 07:11:54 CDT)
Re: topology file generation Sanjeev B.S. (Mon May 06 2002 - 07:24:30 CDT)
Re: topology file generation Carlos Simmerling (Mon May 06 2002 - 07:27:06 CDT)
(no subject) Sophia Kondratova (Mon May 06 2002 - 08:13:53 CDT)
TI using sander on cluster Joe Fernandez (Mon May 06 2002 - 09:52:50 CDT)
"Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 10:50:07 CDT)
Re: "Unit 5 Error" with a Linux/MPICH Amber7 David Case (Mon May 06 2002 - 11:18:24 CDT)
Re: "Unit 5 Error" with a Linux/MPICH Amber7 Stéphane Teletchéa (Mon May 06 2002 - 11:22:42 CDT)
RE: "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 11:44:09 CDT)
Problems with parallel computing in Amber7 Vincent BOSQUIER (Tue May 14 2002 - 09:28:10 CDT)
NMR refinement Jake Isaacs (Tue May 14 2002 - 14:16:37 CDT)
Topology file format in AMBER 7 Joffre Heredia (Tue May 14 2002 - 16:14:55 CDT)
RE: automated rescoring of ligands Vickie Tsui (Tue May 14 2002 - 16:23:29 CDT)
Re: Topology file format in AMBER 7 David Case (Tue May 14 2002 - 16:33:15 CDT)
question Masamichi Fujinami 4029 (Wed May 15 2002 - 00:49:03 CDT)
Energy problem during dynamics with amber 7 Florence CASSET (Wed May 15 2002 - 04:48:23 CDT)
Re: help: nmode compile question!!! Andreas Svrcek-Seiler (Wed May 15 2002 - 06:30:12 CDT)
Re: NMR refinement David Case (Wed May 15 2002 - 12:09:27 CDT)
Re: Energy problem during dynamics with amber 7 David Case (Wed May 15 2002 - 12:29:55 CDT)
Sander, Setup for Parallel SMP Linux Cluster Jianhui Wu (Wed May 15 2002 - 14:02:27 CDT)
Re: Sander, Setup for Parallel SMP Linux Cluster Tru (Wed May 15 2002 - 14:40:45 CDT)
Re: NMR refinement A. Hungie (Thu May 16 2002 - 10:02:17 CDT)
Re: Sander, Setup for Parallel SMP Linux Cluster Joffre Heredia (Thu May 16 2002 - 13:01:16 CDT)
Mutations - Molecular Dynamics William Wei (Thu May 16 2002 - 18:11:36 CDT)
igb=2,gbsa=1,antechamber,bad atom type Jianhui Wu (Fri May 17 2002 - 14:20:14 CDT)
Re: About the box info read error Bill Ross (Fri May 17 2002 - 15:33:51 CDT)
Re: Anal in AMBER7 David Case (Sun May 19 2002 - 20:44:38 CDT)
vanadium Natasja Brooijmans (Sun May 19 2002 - 21:35:27 CDT)
about sander_classic AMBER6.0 Nikolai Smolin (Mon May 20 2002 - 08:08:14 CDT)
helix analysis Prabal Maiti (Mon May 20 2002 - 14:20:45 CDT)
mm_pbsa X. Tan (Mon May 20 2002 - 18:04:52 CDT)
Energy conservation in NVE simulation ? Soonmin Jang (Tue May 21 2002 - 00:42:40 CDT)
Re: Anal in AMBER7 Ting Wang (Tue May 21 2002 - 07:48:48 CDT)
(no subject) Sophia Kondratova (Tue May 21 2002 - 13:37:24 CDT)
ptraj problem Jake Isaacs (Tue May 21 2002 - 16:20:02 CDT)
Re: ptraj problem Prabal Maiti (Tue May 21 2002 - 18:51:22 CDT)
Re: Junmei et al. 1999 Michal Otyepka (Wed May 22 2002 - 02:57:11 CDT)
Re: Junmei et al. 1999 Lepsa (Wed May 22 2002 - 03:58:41 CDT)
Re: Junmei et al. 1999 Yuguang Mu (Wed May 22 2002 - 04:30:29 CDT)
antechamber Giulio Rastelli (Wed May 22 2002 - 05:56:25 CDT)
Re: Protonate doesn-t recognize my pdb input file Stéphane Teletchéa (Wed May 22 2002 - 06:41:08 CDT)
again about sander_classic Amber 6.0 Nikolai Smolin (Wed May 22 2002 - 06:42:50 CDT)
this is a test of the amber reflector. Please ignore. Marcela Marcela Madrid (Wed May 22 2002 - 08:59:24 CDT)
Re: antechamber David Case (Wed May 22 2002 - 10:03:50 CDT)
Re: Junmei et al. 1999 David Case (Wed May 22 2002 - 10:05:23 CDT)
Re: again about sander_classic Amber 6.0 David Case (Wed May 22 2002 - 10:15:06 CDT)
still having ptraj problems Jake Isaacs (Wed May 22 2002 - 10:19:06 CDT)
Re: still having ptraj problems Jake Isaacs (Wed May 22 2002 - 10:50:11 CDT)
Protonate doesn-t recognize by pdb input file David Case (Wed May 22 2002 - 11:20:20 CDT)
TIP4P water with AMBER6 Noriaki Okimoto (Wed May 22 2002 - 13:01:35 CDT)
Re: TIP4P water with AMBER6 jim caldwell (Wed May 22 2002 - 15:25:00 CDT)
ambpdb in AMBER7 Matthew Lee (Wed May 22 2002 - 15:42:34 CDT)
Re: ambpdb in AMBER7 David Case (Wed May 22 2002 - 16:09:32 CDT)
this is a test for amber reflector - please ignore Asif Rahaman (Wed May 22 2002 - 17:17:29 CDT)
Problem with 2D Gibbs run Asif Rahaman (Wed May 22 2002 - 17:32:49 CDT)
This is a test for amber reflector - please ignore Lorenzo Gontrani (Thu May 23 2002 - 03:34:38 CDT)
CARNAL Vlad Cojocaru (Thu May 23 2002 - 05:35:29 CDT)
Re: Protonate doesn-t recognize by pdb input file Stéphane Teletchéa (Thu May 23 2002 - 07:23:31 CDT)
charges Marcela Madrid (Thu May 23 2002 - 15:25:43 CDT)
Re: charges David Case (Thu May 23 2002 - 15:54:38 CDT)
helix analysis (fwd) Prabal Maiti (Thu May 23 2002 - 16:30:33 CDT)
Re: helix analysis (fwd) David Case (Thu May 23 2002 - 16:41:00 CDT)
Fw: mm_pbsa Lepsa (Fri May 24 2002 - 09:27:21 CDT)
subdomain moving as a rigid unit during MD Marcela Madrid (Fri May 24 2002 - 10:59:40 CDT)
Re: compilation of sander on Alpha/Linux clusters jim caldwell (Fri May 24 2002 - 16:41:00 CDT)
PME & cutoff A. Hungie (Sat May 25 2002 - 08:12:48 CDT)
parallel sander on T3E Peter Gannett (Sat May 25 2002 - 09:46:37 CDT)
Re: parallel sander on T3E Natasja Brooijmans (Sat May 25 2002 - 10:44:34 CDT)
Re: PME & cutoff darden (Sun May 26 2002 - 12:03:30 CDT)
compilation for Hitachi SR8000 A. Hungie (Sun May 26 2002 - 12:25:17 CDT)
Charge export from Leap is rounded off jeff dyason (Sun May 26 2002 - 19:06:36 CDT)
Linux Parallel compilation Linux Mpich PGI Fabrice Yerly (Mon May 27 2002 - 07:31:09 CDT)
Re: Linux Parallel compilation Linux Mpich PGI Viktor Hornak (Mon May 27 2002 - 09:56:24 CDT)
RE: Mutations - Molecular Dynamics William Wei (Mon May 27 2002 - 10:21:04 CDT)
glucose Yuguang Mu (Tue May 28 2002 - 10:05:10 CDT)
Re: glucose Carlos Simmerling (Tue May 28 2002 - 10:50:59 CDT)
RESP charges for phosphorylated residues Uwe Richter (Tue May 28 2002 - 11:05:05 CDT)
xleap Marcela Madrid (Tue May 28 2002 - 16:21:39 CDT)
Cyclodextrin Toshikazu Matsuoka (Wed May 29 2002 - 01:48:19 CDT)
minimization to fix up hydrogen positions yuann (Wed May 29 2002 - 02:33:23 CDT)
SHAKE troubles Arvid Soederhaell (Wed May 29 2002 - 05:07:17 CDT)
Re: SHAKE troubles Stéphane Teletchéa (Wed May 29 2002 - 05:50:12 CDT)
Re: SHAKE troubles Yong Duan (Wed May 29 2002 - 07:33:14 CDT)
MPich error Fabrice Yerly (Wed May 29 2002 - 07:46:29 CDT)
Re: MPich error Stéphane Teletchéa (Wed May 29 2002 - 09:00:44 CDT)
Re: SHAKE troubles Lepsa (Wed May 29 2002 - 09:02:15 CDT)
xLeap problem Donald Thomas (Wed May 29 2002 - 23:42:04 CDT)
Re: xLeap problem John Bushnell (Thu May 30 2002 - 00:53:05 CDT)
sander_classic, erratic on IBM Giovanni Fossati (Thu May 30 2002 - 01:17:07 CDT)
GROUP Specification - Error decoding variable yuann (Thu May 30 2002 - 02:43:02 CDT)
Re: GROUP Specification - Error decoding variable Yongjun Jiang (Thu May 30 2002 - 03:23:57 CDT)
TIP4P SEKIJIMA Masakazu (Thu May 30 2002 - 03:43:14 CDT)
Intel ifc Compiler Joachim Reichelt (Thu May 30 2002 - 04:23:21 CDT)
AMBER7 Michael Sattler (Thu May 30 2002 - 07:59:11 CDT)
Re: Intel ifc Compiler Robert Duke (Thu May 30 2002 - 08:13:59 CDT)
Re: Intel ifc Compiler David Case (Thu May 30 2002 - 09:00:55 CDT)
Re: sander_classic, erratic on IBM David Case (Thu May 30 2002 - 09:13:44 CDT)
Comparing simulations using Amber 5 and Amber 6 Rebecca Perlow (Thu May 30 2002 - 09:18:36 CDT)
Re: sander_classic, erratic on IBM Giovanni Fossati (Thu May 30 2002 - 12:05:22 CDT)
(no subject) SPEROLEEM_at_aol.com (Thu May 30 2002 - 17:51:26 CDT)
Re: TIP4P SEKIJIMA Masakazu (Fri May 31 2002 - 02:32:08 CDT)
H-bond Dmitry Pavlov (Fri May 31 2002 - 03:01:42 CDT)
Re: SHAKE troubles Arvid Soederhaell (Fri May 31 2002 - 03:50:01 CDT)
Fwd: NPT-MD Antonio J. Díaz Quintana (Fri May 31 2002 - 04:17:55 CDT)
Re: SHAKE troubles Stéphane Teletchéa (Fri May 31 2002 - 04:45:48 CDT)
Re: TIP4P David Case (Fri May 31 2002 - 09:44:19 CDT)
Re: Intel ifc Compiler David Case (Fri May 31 2002 - 09:51:21 CDT)
Re: Fwd: NPT-MD David Case (Fri May 31 2002 - 09:56:43 CDT)
Problem with Gibbs 2D run Asif Rahaman (Sun Jun 02 2002 - 22:29:38 CDT)
Re: Intel ifc Compiler Joachim Reichelt (Mon Jun 03 2002 - 01:51:54 CDT)
(no subject) Ishita sharma (Mon Jun 03 2002 - 06:07:38 CDT)
Re: mm_pbsa in parallel system David Case (Mon Jun 03 2002 - 09:49:08 CDT)
Parallel Amber on Solaris 2.6 Thomas A. Spraggins (Mon Jun 03 2002 - 09:49:45 CDT)
Re: mm_pbsa in parallel system (fwd) Jianhui Wu (Mon Jun 03 2002 - 11:03:12 CDT)
Re: Parallel Amber on Solaris 2.6 William Gropp (Mon Jun 03 2002 - 14:20:26 CDT)
Clarification R.Sathyapriya (Tue Jun 04 2002 - 02:45:19 CDT)
Re: SHAKE troubles Arvid Soederhaell (Tue Jun 04 2002 - 03:22:40 CDT)
Amber PGF77 comilation error + MPICH problem Fabrice Yerly (Wed Jun 05 2002 - 03:31:26 CDT)
Parameters for hexachloroethane Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 04:13:54 CDT)
Machine_file for Hitachi SR8000 A. Hungie (Wed Jun 05 2002 - 06:09:03 CDT)
PME box ? Yi ming Cheng (Wed Jun 05 2002 - 07:11:15 CDT)
Re: PME box ? David Smith (Wed Jun 05 2002 - 09:15:44 CDT)
reference Marcela Madrid (Wed Jun 05 2002 - 10:48:55 CDT)
Question TL Poulos (Wed Jun 05 2002 - 10:49:10 CDT)
Re: PME box ? Long Hai (Wed Jun 05 2002 - 11:07:29 CDT)
Amber7, sander, restart, blast up Jianhui Wu (Wed Jun 05 2002 - 12:07:51 CDT)
Running amber7 and nab on FreeBSD bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 15:31:24 CDT)
cap water eric hu (Wed Jun 05 2002 - 19:14:10 CDT)
Re: Intel Kernel Math Library case (Thu Jun 06 2002 - 10:02:25 CDT)
Intel Kernel Math Library Joffre Heredia (Thu Jun 06 2002 - 14:46:32 CDT)
Mac OS X compiliation? Randy M. Wadkins (Thu Jun 06 2002 - 16:58:18 CDT)
amber on MAC OSX case (Thu Jun 06 2002 - 19:22:44 CDT)
analysis of Gibbs 2D run Asif Rahaman (Thu Jun 06 2002 - 23:46:34 CDT)
no mdcrd, no mden file Arvid Soederhaell (Fri Jun 07 2002 - 06:43:30 CDT)
benchmark for Amber7 A. Hungie (Fri Jun 07 2002 - 09:37:07 CDT)
charges for peptides Marcela Madrid (Fri Jun 07 2002 - 10:14:59 CDT)
Re: cap water eric hu (Fri Jun 07 2002 - 13:39:22 CDT)
Re: amber on MAC OSX Randy M. Wadkins (Fri Jun 07 2002 - 14:29:58 CDT)
Re: Suggestion to Bill and Case Bill Ross (Fri Jun 07 2002 - 15:16:30 CDT)
Suggestion to Bill and Case William Wei (Fri Jun 07 2002 - 15:49:10 CDT)
model molecules for getting charges of DNA Jiyoung Heo (Sat Jun 08 2002 - 19:20:10 CDT)
Re: model molecules for getting charges of DNA Qing Zhang (Sun Jun 09 2002 - 14:47:04 CDT)
C=C=C bending parameters Jones de Andrade (Sun Jun 09 2002 - 15:55:33 CDT)
cold belly run error eric hu (Sun Jun 09 2002 - 17:55:47 CDT)
(no subject) Snyder, James (Sun Jun 09 2002 - 19:45:03 CDT)
Re: amber on MAC OSX Tru (Mon Jun 10 2002 - 04:18:03 CDT)
RE: xaLeap make fails on AIX Thomas A. Spraggins (Mon Jun 10 2002 - 11:13:01 CDT)
Re:xaLeap make fails on AIX Bill Ross (Mon Jun 10 2002 - 13:19:47 CDT)
entropy calculation X. Tan (Mon Jun 10 2002 - 18:42:59 CDT)
Re: cold belly run error Asim Okur (Mon Jun 10 2002 - 23:58:30 CDT)
Re: Floating Invalid Bill Ross (Tue Jun 11 2002 - 00:36:16 CDT)
Reorder water in amber7 Peter Varnai (Tue Jun 11 2002 - 03:38:32 CDT)
Re: Reorder water in amber7 Carlos Simmerling (Tue Jun 11 2002 - 06:36:04 CDT)
Amber protein-ion problem Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 06:41:29 CDT)
RE: Reorder water in amber7 case (Tue Jun 11 2002 - 08:53:59 CDT)
RE: entropy calculation case (Tue Jun 11 2002 - 08:56:37 CDT)
Re: Floating Invalid jim caldwell (Tue Jun 11 2002 - 09:43:49 CDT)
minimization probs Amesh Patel (Tue Jun 11 2002 - 10:57:12 CDT)
Re: Reorder water in amber7 Peter VARNAI (Tue Jun 11 2002 - 12:16:00 CDT)
RE: minimization probs case (Tue Jun 11 2002 - 12:36:57 CDT)
Re: cold belly run error eric hu (Tue Jun 11 2002 - 12:41:47 CDT)
Protonated database Andrew Petersen (Tue Jun 11 2002 - 14:12:28 CDT)
Re: cold belly run error eric hu (Tue Jun 11 2002 - 14:42:19 CDT)
sander input for a newbie Randy M. Wadkins (Tue Jun 11 2002 - 18:21:22 CDT)
test of mm_pbsa Yongjun Jiang (Tue Jun 11 2002 - 22:08:23 CDT)
igb problem in sander Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 04:11:20 CDT)
vlimit exceeded A. Hungie (Wed Jun 12 2002 - 04:49:44 CDT)
perturbed type DH not found Mao Xiang (Wed Jun 12 2002 - 05:47:19 CDT)
Re: vlimit exceeded Carlos Simmerling (Wed Jun 12 2002 - 06:42:14 CDT)
Re: sander input for a newbie Randy M. Wadkins (Wed Jun 12 2002 - 08:04:55 CDT)
Application of Amber Monica (Wed Jun 12 2002 - 10:24:49 CDT)
Re: vlimit exceeded Thomas Cheatham (Wed Jun 12 2002 - 14:35:53 CDT)
sander parallel eric hu (Wed Jun 12 2002 - 16:11:24 CDT)
RE: Floating Invalid lifang xu (Wed Jun 12 2002 - 22:02:21 CDT)
Re: sander parallel Joffre Heredia (Thu Jun 13 2002 - 12:39:55 CDT)
How to set the dielctric constant equals 1, when running MD simulations in real solvent water? Ling Zhang (Thu Jun 13 2002 - 15:54:53 CDT)
The atom number mismatch in coord and topology file. Ling Zhang (Thu Jun 13 2002 - 16:41:08 CDT)
Re: sander parallel eric hu (Thu Jun 13 2002 - 17:05:13 CDT)
Re: The atom number mismatch in coord and topology file. Carlos Simmerling (Thu Jun 13 2002 - 17:27:38 CDT)
Using TIP4P water S. Yamasaki (Thu Jun 13 2002 - 20:05:48 CDT)
(no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Fri Jun 14 2002 - 00:30:15 CDT)
Re: sander parallel Stéphane Teletchéa (Fri Jun 14 2002 - 03:58:53 CDT)
Periodic water box Rudesh Toofanny (Fri Jun 14 2002 - 07:41:01 CDT)
The atom number mismatch in coord and topology file in AMBER6. Ling Zhang (Fri Jun 14 2002 - 09:58:45 CDT)
Re: The atom number mismatch in coord and topology file in AMBER6. Robert Duke (Fri Jun 14 2002 - 11:27:00 CDT)
tleap error for systems with 64-bit pointers Karen Haskell (Fri Jun 14 2002 - 14:55:16 CDT)
free energy for binding Qing Zhang (Fri Jun 14 2002 - 17:50:54 CDT)
how to keep aromatic ring flat Qing Zhang (Fri Jun 14 2002 - 18:00:51 CDT)
Re: how to keep aromatic ring flat Bill Ross (Fri Jun 14 2002 - 18:34:42 CDT)
Amber tutorial rino ragno (Sat Jun 15 2002 - 04:53:53 CDT)
Mn parameters!!! navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 04:19:12 CDT)
(no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 05:09:11 CDT)
remove COM velocity in Amber7 Peter VARNAI (Mon Jun 17 2002 - 07:16:27 CDT)
WG: Christian.Pilger_at_bc.boehringer-ingelheim.com (Tue Jun 18 2002 - 00:48:01 CDT)
question Craig A Bayse (Tue Jun 18 2002 - 17:04:47 CDT)
Re: question jim caldwell (Tue Jun 18 2002 - 17:52:19 CDT)
propeller twist of ideal B-DNA A. Hungie (Wed Jun 19 2002 - 11:37:29 CDT)
solvated time-averaged restraint refinement of DNA Jake Isaacs (Wed Jun 19 2002 - 11:52:35 CDT)
parameters for Zn2+ bond to CYS- X. Tan (Wed Jun 19 2002 - 19:23:16 CDT)
Re: Periodic water box Thomas Cheatham (Wed Jun 19 2002 - 22:57:04 CDT)
Re: remove COM velocity in Amber7 Peter VARNAI (Thu Jun 20 2002 - 07:03:07 CDT)
re: parameters for zn2+ bond to cys- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:17:38 CDT)
turning PME off in AMBER7 lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:28:30 CDT)
Re: turning PME off in AMBER7 Arvid Soederhaell (Thu Jun 20 2002 - 08:45:25 CDT)
Re: turning PME off in AMBER7 David A. Case (Thu Jun 20 2002 - 08:49:33 CDT)
bug in .../sander/egb.f ? Thomas A. Spraggins (Thu Jun 20 2002 - 12:45:28 CDT)
RESP Multiconformer Fitting Miguel de Federico (Thu Jun 20 2002 - 18:05:11 CDT)
van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 03:54:05 CDT)
more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 04:00:59 CDT)
even more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 04:23:17 CDT)
j3 coupling Yuguang Mu (Fri Jun 21 2002 - 05:38:31 CDT)
Re: j3 coupling David A. Case (Fri Jun 21 2002 - 09:49:40 CDT)
Re: van der Waals explosion David A. Case (Fri Jun 21 2002 - 09:55:26 CDT)
Compilation ov Amber 7 Dov Barak (Fri Jun 21 2002 - 11:40:58 CDT)
taupt: time constant for heat bath coupling for the SOLUTE Qing Zhang (Fri Jun 21 2002 - 18:44:55 CDT)
Re: taupt: time constant for heat bath coupling for the SOLUTE David A. Case (Fri Jun 21 2002 - 19:28:38 CDT)
SHAKE... Arvid Soederhaell (Mon Jun 24 2002 - 06:25:05 CDT)
Passing arguments with SP2 LoadLeveler Thomas A. Spraggins (Mon Jun 24 2002 - 09:41:26 CDT)
New Residue Monica (Mon Jun 24 2002 - 10:01:42 CDT)
ptraj problem Vlad Cojocaru (Mon Jun 24 2002 - 10:54:32 CDT)
Re: ptraj problem Thomas Cheatham (Mon Jun 24 2002 - 12:24:30 CDT)
Re: SHAKE (actually: new atom types) Bill Ross (Mon Jun 24 2002 - 14:22:02 CDT)
antechamber charges don't sum up to zero Michael Jakusch (Mon Jun 24 2002 - 14:38:15 CDT)
partial charges Osvaldo Santos-Filho (Mon Jun 24 2002 - 19:33:15 CDT)
Re: partial charges Carlos Simmerling (Mon Jun 24 2002 - 20:38:35 CDT)
Re: partial charges David A. Case (Mon Jun 24 2002 - 20:52:47 CDT)
Query regarding Gamess Nitin Kumar Singh (Tue Jun 25 2002 - 10:23:09 CDT)
plep question FyD (Wed Jun 26 2002 - 02:28:23 CDT)
minimum image cut-off Nikolai Smolin (Wed Jun 26 2002 - 06:05:08 CDT)
transferring structures Matt Hartings (Wed Jun 26 2002 - 12:24:23 CDT)
Re: transferring structures Bill Ross (Wed Jun 26 2002 - 14:47:02 CDT)
Re: transferring structures Matt Hartings (Wed Jun 26 2002 - 15:58:11 CDT)
Using a trucated octahedral box in Amber6 Ling Zhang (Wed Jun 26 2002 - 20:28:46 CDT)
Problem in amber Monica (Thu Jun 27 2002 - 00:28:21 CDT)
xleap problem FyD (Thu Jun 27 2002 - 03:20:53 CDT)
a problem with AMBER7 Vlad Cojocaru (Thu Jun 27 2002 - 05:12:58 CDT)
dummy torsional parameters Giulio Rastelli (Thu Jun 27 2002 - 05:31:50 CDT)
Re: Problem in amber David Case (Thu Jun 27 2002 - 09:38:30 CDT)
Re: xleap problem David A. Case (Thu Jun 27 2002 - 10:33:16 CDT)
Re: dummy torsional parameters David A. Case (Thu Jun 27 2002 - 10:38:49 CDT)
problems compiling Amber 7 ramon kleber da rocha (Thu Jun 27 2002 - 12:18:50 CDT)
mopac David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 12:50:41 CDT)
Re: problems compiling Amber 7 David A. Case (Thu Jun 27 2002 - 13:27:09 CDT)
Re: mopac David A. Case (Thu Jun 27 2002 - 13:34:34 CDT)
iwrap set in sander of Amber6 Ling Zhang (Thu Jun 27 2002 - 15:43:41 CDT)
Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:59:35 CDT)
Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 17:23:29 CDT)
xmkmf: not found Bill Ross (Thu Jun 27 2002 - 17:29:08 CDT)
Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 17:47:41 CDT)
box size & 1st equilibrium yuann (Fri Jun 28 2002 - 01:16:51 CDT)
Re: mopac Pascal Bonnet (Fri Jun 28 2002 - 03:49:11 CDT)
EWALD BOMB (The system has extended beyond ...) Michael Jakusch (Fri Jun 28 2002 - 04:17:20 CDT)
Re: box size & 1st equilibrium Carlos Simmerling (Fri Jun 28 2002 - 06:56:09 CDT)
Re: error in rMD Guanglei Cui (Fri Jun 28 2002 - 08:22:35 CDT)
error in rMD Monica (Fri Jun 28 2002 - 08:35:34 CDT)
The crystal water is solute or solvent during solvation Ling Zhang (Fri Jun 28 2002 - 13:58:08 CDT)
Zn/Mg Counterion placement around DNA mdk7p_at_cms.mail.virginia.edu (Fri Jun 28 2002 - 14:46:11 CDT)
Interaction table from minimization kiyean.nam_at_pharma.novartis.com (Fri Jun 28 2002 - 16:40:59 CDT)
van der Waals, hydrogen bond energy Qing Zhang (Fri Jun 28 2002 - 17:57:10 CDT)
Re: van der Waals, hydrogen bond energy Carlos Simmerling (Fri Jun 28 2002 - 18:41:11 CDT)
Re: van der Waals, hydrogen bond energy jim caldwell (Fri Jun 28 2002 - 19:24:21 CDT)
Re: van der Waals, hydrogen bond energy Andreas Svrcek-Seiler (Sat Jun 29 2002 - 07:29:38 CDT)
Re: Compilation ov Amber 7 Sanjeev B.S. (Sun Jun 30 2002 - 12:42:28 CDT)
Analysis of LES simulation mer_at_chem.wayne.edu (Sun Jun 30 2002 - 17:40:39 CDT)
How to decrease the solvated system in Amber6? Ling Zhang (Mon Jul 01 2002 - 11:28:51 CDT)
Re: How to decrease the solvated system in Amber6? David A. Case (Tue Jul 02 2002 - 06:38:50 CDT)
Re: problems compiling Amber 7 ramon kleber da rocha (Tue Jul 02 2002 - 09:42:05 CDT)
Re: How to decrease the solvated system in Amber6? Ling Zhang (Tue Jul 02 2002 - 10:30:19 CDT)
torsion angle constrains Marcela Madrid (Tue Jul 02 2002 - 16:22:09 CDT)
parameter file for MgGTP Holger Sondermann (Tue Jul 02 2002 - 20:34:24 CDT)
BR parameters in AMBER Esther Kellenberger (Wed Jul 03 2002 - 09:24:26 CDT)
(no subject) Narang Manpreet Kaur (Wed Jul 03 2002 - 10:08:40 CDT)
Running TIP5P with PBC Sarah Tschampel (Wed Jul 03 2002 - 14:47:41 CDT)
Re: Running TIP5P with PBC David Case (Wed Jul 03 2002 - 14:49:28 CDT)
docking in xleap Bill Ross (Wed Jul 03 2002 - 23:25:50 CDT)
Origin300, Linux Cluster Jianhui Wu (Thu Jul 04 2002 - 11:04:07 CDT)
problem in compiling amber7 in IBMSP3 cluster A.Madhumalar (Thu Jul 04 2002 - 11:29:50 CDT)
Re: Origin300, Linux Cluster C. Klein (Thu Jul 04 2002 - 12:41:31 CDT)
create new atom problem on xleap yuann (Thu Jul 04 2002 - 15:04:01 CDT)
Re: create new atom problem on xleap Bill Ross (Thu Jul 04 2002 - 15:58:59 CDT)
Re: Origin300, Linux Cluster Stéphane Teletchéa (Fri Jul 05 2002 - 03:48:03 CDT)
TEST Sarangan Ravichandran (Fri Jul 05 2002 - 07:43:37 CDT)
Distance dependent vaccum energy minimization in AMBER7 Sarangan Ravichandran (Fri Jul 05 2002 - 10:29:40 CDT)
simulation management tools Tom Bishop (Fri Jul 05 2002 - 10:58:59 CDT)
problems compiling Amber 7 ramon kleber da rocha (Fri Jul 05 2002 - 12:52:45 CDT)
Re: problem in compiling amber7 in IBMSP3 cluster Michael Crowley (Fri Jul 05 2002 - 13:11:55 CDT)
RE: problems compiling Amber 7 Thomas A. Spraggins (Fri Jul 05 2002 - 13:42:32 CDT)
anal in AMBER7 gives inconsistent results with itself Prabal Maiti (Fri Jul 05 2002 - 18:00:55 CDT)
Re: anal in AMBER7 gives inconsistent results with itself Prabal Maiti (Mon Jul 08 2002 - 00:46:31 CDT)
installing MPICH for AMBER on Linux CLuster root (Mon Jul 08 2002 - 05:02:52 CDT)
Re: installing MPICH for AMBER on Linux CLuster Walter Langel (Mon Jul 08 2002 - 07:26:36 CDT)
Re: Origin300, Linux Cluster Stéphane Teletchéa (Mon Jul 08 2002 - 07:37:37 CDT)
RE: installing MPICH for AMBER on Linux CLuster Thomas A. Spraggins (Mon Jul 08 2002 - 08:15:23 CDT)
md equilibration in chloroform Sophia Kondratova (Mon Jul 08 2002 - 08:38:27 CDT)
Re: installing MPICH for AMBER on Linux CLuster update Thomas Steinbrecher (Mon Jul 08 2002 - 08:46:48 CDT)
Re: Origin300, Linux Cluster Dow Hurst (Mon Jul 08 2002 - 09:40:34 CDT)
RDC restraints Richard Stefl (Mon Jul 08 2002 - 10:01:39 CDT)
Re: md equilibration in chloroform David A. Case (Mon Jul 08 2002 - 10:42:24 CDT)
Re: bug in .../sander/egb.f ? Sanjeev B.S. (Mon Jul 08 2002 - 14:08:09 CDT)
heat up at constant pressure Qing Zhang (Mon Jul 08 2002 - 17:05:19 CDT)
Pictausch?? nicolescholiz1_at_web.de (Mon Jul 08 2002 - 18:14:10 CDT)
eedmeth variable in AMBER7 Sarangan Ravichandran (Tue Jul 09 2002 - 09:30:28 CDT)
Re: eedmeth variable in AMBER7 David A. Case (Tue Jul 09 2002 - 10:31:59 CDT)
Amber 7 Installation Rajesh Korde (Tue Jul 09 2002 - 11:45:36 CDT)
Re:Re: Running TIP5P with PBC Sarah Tschampel (Tue Jul 09 2002 - 12:32:32 CDT)
Re: Amber 7 Installation Sanjeev B.S. (Tue Jul 09 2002 - 12:38:16 CDT)
Net Charge is Different In The Sander Output!! Sarangan Ravichandran (Tue Jul 09 2002 - 20:19:00 CDT)
Re: Net Charge is Different In The Sander Output!! David A. Case (Tue Jul 09 2002 - 22:53:47 CDT)
Re: Amber 7 Installation Joffre Heredia (Wed Jul 10 2002 - 01:17:45 CDT)
MAX_RSTACK Jithesh (Wed Jul 10 2002 - 01:24:42 CDT)
Announcement: Optimally Partitioned Electric Properties - OPEP Chris Chipot (Wed Jul 10 2002 - 03:06:48 CDT)
Problem getting sander started Thomas Steinbrecher (Wed Jul 10 2002 - 07:24:00 CDT)
Re: Problem getting sander started Sanjeev B.S. (Wed Jul 10 2002 - 07:26:39 CDT)
new problems compiling amber 7 ramon kleber da rocha (Wed Jul 10 2002 - 08:11:52 CDT)
Re: new problems compiling amber 7 Sanjeev B.S. (Wed Jul 10 2002 - 09:57:40 CDT)
Not able to image a snapshot. Stéphane Teletchéa (Wed Jul 10 2002 - 10:28:12 CDT)
Re: MAX_RSTACK Joffre Heredia (Wed Jul 10 2002 - 12:12:15 CDT)
simulated annealing example Snyder, James (Wed Jul 10 2002 - 15:42:43 CDT)
Re: simulated annealing example Qing Zhang (Wed Jul 10 2002 - 21:59:20 CDT)
time scale to see the ion effect on DNA A.Madhumalar (Thu Jul 11 2002 - 01:40:52 CDT)
Re: Not able to image a snapshot. Stéphane Teletchéa (Thu Jul 11 2002 - 03:24:48 CDT)
compiling MPICH Thomas Steinbrecher (Thu Jul 11 2002 - 07:46:12 CDT)
counter-ions in FEP Christophe L M J Verlinde (Thu Jul 11 2002 - 11:37:41 CDT)
new problems compiling amber 7 ramon kleber da rocha (Thu Jul 11 2002 - 12:30:07 CDT)
RE: md equilibration in chloroform Thomas.Fox_at_bc.boehringer-ingelheim.com (Thu Jul 11 2002 - 12:51:47 CDT)
China International Biology Projects Fair Genefax (Fri Jul 12 2002 - 00:40:19 CDT)
looking for frcmod in AMBER Tutorials yuann (Fri Jul 12 2002 - 04:19:45 CDT)
Question about error message about "lastist" and "virtual box" Masaki Tomimoto (Fri Jul 12 2002 - 10:19:12 CDT)
RE: Dual AMD motherboards Greaves, Greg (Contractor-SIMTECH) (Fri Jul 12 2002 - 10:33:54 CDT)
Re: Question about error message about "lastist" and "virtual box" David A. Case (Fri Jul 12 2002 - 10:55:51 CDT)
Re: counter-ions in FEP David A. Case (Fri Jul 12 2002 - 11:00:11 CDT)
anal in AMBER7 gives inconsistent results with itself (fwd) Prabal Maiti (Fri Jul 12 2002 - 12:38:19 CDT)
This one with anal in amber6 Prabal Maiti (Fri Jul 12 2002 - 13:09:39 CDT)
are there inconsistencies in anal? David A. Case (Fri Jul 12 2002 - 13:58:02 CDT)
LEaP gives "no sp2 improper torsion term" warnings David A. Case (Fri Jul 12 2002 - 15:25:35 CDT)
Re: Dual AMD motherboards Pietro Amodeo (Mon Jul 15 2002 - 03:36:34 CDT)
Decrease the solvated system by removing the outside crystal water Ling Zhang (Mon Jul 15 2002 - 11:58:34 CDT)
RE: Dual AMD motherboards Ross Walker (Tue Jul 16 2002 - 02:31:56 CDT)
Problem with LEAP Miguel de Federico (Tue Jul 16 2002 - 05:53:37 CDT)
antechamber created prep file--Problem in xleap Sarangan Ravichandran (Tue Jul 16 2002 - 08:54:45 CDT)
antechamber created prep file--Problem in xleap--additional info Sarangan Ravichandran (Tue Jul 16 2002 - 09:06:31 CDT)
Minimization in GB-SA-E-Spikes, LINMIN Sarangan Ravichandran (Tue Jul 16 2002 - 10:02:58 CDT)
Re: Problem with LEAP David A. Case (Tue Jul 16 2002 - 10:19:24 CDT)
Re: Minimization in GB-SA-E-Spikes, LINMIN Andreas Svrcek-Seiler (Tue Jul 16 2002 - 11:00:55 CDT)
Re: Minimization in GB-SA-E-Spikes, LINMIN Sarangan Ravichandran (Tue Jul 16 2002 - 12:11:27 CDT)
PME in gibbs module X. Tan (Tue Jul 16 2002 - 15:29:27 CDT)
water molecules diffuse during equilibration Qing Zhang (Tue Jul 16 2002 - 18:56:53 CDT)
Re: water molecules diffuse during equilibration David A. Case (Tue Jul 16 2002 - 20:31:12 CDT)
PTRAJ: radial distribution function A. Hungie (Wed Jul 17 2002 - 10:58:14 CDT)
building general solvent boxes with leap Xavier Deupi (Wed Jul 17 2002 - 12:19:28 CDT)
Re: amber on sp3 David A. Case (Wed Jul 17 2002 - 14:14:44 CDT)
Re: building general solvent boxes with leap David A. Case (Wed Jul 17 2002 - 15:14:40 CDT)
prmtop file question. Carlos Andres Ramirez-Mondragon (Wed Jul 17 2002 - 16:15:59 CDT)
Re: PTRAJ: radial distribution function Thomas Cheatham (Wed Jul 17 2002 - 16:47:24 CDT)
Re: prmtop file question. David A. Case (Wed Jul 17 2002 - 19:08:28 CDT)
Re: Minimization in GB-SA-E-Spikes, LINMIN David A. Case (Wed Jul 17 2002 - 19:43:57 CDT)
GENERALIZED BORN model on a protein with Fe Mahadevan Seetharaman (Thu Jul 18 2002 - 09:55:01 CDT)
Re: GENERALIZED BORN model on a protein with Fe David A. Case (Thu Jul 18 2002 - 12:41:53 CDT)
Re: building general solvent boxes with leap Bill Ross (Thu Jul 18 2002 - 14:18:57 CDT)
Defining Restraints in Sander Asif Rahaman (Thu Jul 18 2002 - 15:21:59 CDT)
Re: Defining Restraints in Sander Carlos Simmerling (Thu Jul 18 2002 - 16:29:22 CDT)
Re: The 216 water box Mihaly Mezei (Thu Jul 18 2002 - 17:48:12 CDT)
Re: building general solvent boxes with leap Xavier Deupi (Thu Jul 18 2002 - 18:16:17 CDT)
Re: Defining Restraints in Sander John Bushnell (Thu Jul 18 2002 - 19:44:16 CDT)
Re: building general solvent boxes with leap Elsa de Sousa Henriques (Thu Jul 18 2002 - 22:41:25 CDT)
about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 03:22:20 CDT)
correction about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 04:09:58 CDT)
Re: correction about solvateOct Michael Jakusch (Fri Jul 19 2002 - 04:49:48 CDT)
electrostatics truncation in AMBER Therese Malliavin (Fri Jul 19 2002 - 08:21:59 CDT)
RE: correction about solvateOct William Wei (Fri Jul 19 2002 - 10:18:53 CDT)
Re: electrostatics truncation in AMBER David A. Case (Fri Jul 19 2002 - 10:26:20 CDT)
Re: correction about solvateOct Michael Crowley (Fri Jul 19 2002 - 11:37:10 CDT)
Questions about xleap and mm_pbsa] Salinthip Thipayang (Fri Jul 19 2002 - 12:49:08 CDT)
Re: Questions about xleap and mm_pbsa] David A. Case (Fri Jul 19 2002 - 13:59:24 CDT)
AMBER7 and Movie Y Fang (Fri Jul 19 2002 - 16:03:22 CDT)
water box size eric hu (Fri Jul 19 2002 - 17:09:25 CDT)
RE: AMBER7 and Movie Snyder, James (Fri Jul 19 2002 - 17:25:37 CDT)
Re: water box size Shixiang Yan (Fri Jul 19 2002 - 18:02:32 CDT)
Including explicit waters in GB dynamics Kristina Furse (Sat Jul 20 2002 - 19:30:43 CDT)
Re: AMBER7 and Movie Pascal Bonnet (Mon Jul 22 2002 - 03:36:50 CDT)
Re: Anal in AMBER7 Ting Wang (Mon Jul 22 2002 - 04:19:16 CDT)
Format in a trajectory files is suddenly changed Masaki Tomimoto (Mon Jul 22 2002 - 11:54:44 CDT)
Benchmark Stéphane Teletchéa (Mon Jul 22 2002 - 11:55:14 CDT)
Re: AMBER7 and Movie Carlos Simmerling (Mon Jul 22 2002 - 11:56:52 CDT)
C sp2 connected to OS Bimo Ario Tejo (Mon Jul 22 2002 - 12:37:27 CDT)
problem with make_crd_hg, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 13:28:29 CDT)
Re: AMBER7 and Movie Y Fang (Mon Jul 22 2002 - 15:58:23 CDT)
Summary: make_crd_hp, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 16:45:32 CDT)
(no subject) deepak rangaswamy (Tue Jul 23 2002 - 02:01:41 CDT)
Re: C sp2 connected to OS Bimo Ario Tejo (Tue Jul 23 2002 - 03:23:03 CDT)
Re: Carlos Simmerling (Tue Jul 23 2002 - 06:48:48 CDT)
Questions about xleap and mm_pbsa(cont.) Salinthip Thipayang (Tue Jul 23 2002 - 09:46:20 CDT)
Questions about xleap and mm_pbsa (cont.2) Salinthip Thipayang (Tue Jul 23 2002 - 10:21:23 CDT)
problem compiling roar (mop7mm) on alpha hagop demirdjian (Tue Jul 23 2002 - 10:35:11 CDT)
CA-OS parameter Bimo Ario Tejo (Tue Jul 23 2002 - 11:07:19 CDT)
"crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 11:23:56 CDT)
Re: problem compiling roar (mop7mm) on alpha Tru (Tue Jul 23 2002 - 12:05:08 CDT)
Re: problem compiling roar (mop7mm) on alpha Chuck Schneider (Tue Jul 23 2002 - 12:09:37 CDT)
Re: Questions about xleap and mm_pbsa(cont.) David A. Case (Tue Jul 23 2002 - 12:18:44 CDT)
Re: Questions about xleap ... Bill Ross (Tue Jul 23 2002 - 14:03:52 CDT)
Segmentation fault Bimo Ario Tejo (Tue Jul 23 2002 - 14:44:58 CDT)
problemas running amber7 tests on a SP2 machine ramon kleber da rocha (Tue Jul 23 2002 - 15:33:28 CDT)
several questions David Keller (Tue Jul 23 2002 - 17:24:04 CDT)
Re: Segmentation fault David A. Case (Tue Jul 23 2002 - 17:44:02 CDT)
Re: several questions David A. Case (Tue Jul 23 2002 - 19:08:10 CDT)
"crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 19:47:04 CDT)
Re: "crd" file created with VMD Carlos Simmerling (Tue Jul 23 2002 - 20:42:15 CDT)
Re: "crd" file created with VMD Carlos Simmerling (Tue Jul 23 2002 - 22:02:50 CDT)
Re: several questions Heather A Carlson (Tue Jul 23 2002 - 22:17:35 CDT)
Re: "crd" file created with VMD David Case (Wed Jul 24 2002 - 02:04:02 CDT)
Re: "crd" file created with VMD Soonmin Jang (Wed Jul 24 2002 - 02:28:27 CDT)
Re: Segmentation fault Bimo Ario Tejo (Wed Jul 24 2002 - 04:42:26 CDT)
Trajectory files Miguel de Federico (Wed Jul 24 2002 - 07:10:51 CDT)
gaff and parm99 Pascal Bonnet (Wed Jul 24 2002 - 08:11:36 CDT)
Re: Trajectory files Natasja Brooijmans (Wed Jul 24 2002 - 09:34:28 CDT)
Re: gaff and parm99 David A. Case (Wed Jul 24 2002 - 10:13:48 CDT)
Re: Trajectory files David A. Case (Wed Jul 24 2002 - 10:15:55 CDT)
Re: Trajectory files Laurent Chiche (Wed Jul 24 2002 - 10:26:36 CDT)
Octane Box (equilibrated) samantha hughes (Wed Jul 24 2002 - 10:27:53 CDT)
CCL4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 10:40:10 CDT)
Re: gaff and parm99 Pascal Bonnet (Wed Jul 24 2002 - 10:51:30 CDT)
Re: Trajectory files Carlos Simmerling (Wed Jul 24 2002 - 10:52:29 CDT)
am1-bcc charges, antechamber Sophia Kondratova (Wed Jul 24 2002 - 14:02:02 CDT)
SS bond Masaki Tomimoto (Wed Jul 24 2002 - 14:04:21 CDT)
makeDIP_RST.dna McAteer, Kathleen (Wed Jul 24 2002 - 14:24:42 CDT)
CCl4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 14:55:04 CDT)
Re: am1-bcc charges, antechamber David A. Case (Wed Jul 24 2002 - 14:58:25 CDT)
Re: SS bond David A. Case (Wed Jul 24 2002 - 15:00:44 CDT)
Re: am1-bcc charges, antechamber M. L. Dodson (Wed Jul 24 2002 - 15:24:23 CDT)
increase lastist Marcela Madrid (Wed Jul 24 2002 - 15:41:45 CDT)
Umbrella sampling in AMBER Pratul Agarwal (Wed Jul 24 2002 - 15:53:54 CDT)
Re: increase lastist David A. Case (Wed Jul 24 2002 - 16:41:48 CDT)
Re: Umbrella sampling in AMBER David A. Case (Wed Jul 24 2002 - 16:44:35 CDT)
Re: increase lastist jim caldwell (Wed Jul 24 2002 - 17:45:43 CDT)
Re: makeDIP_RST.dna Vickie Tsui (Wed Jul 24 2002 - 18:49:57 CDT)
Gibbs tutorial problem yuann (Wed Jul 24 2002 - 19:40:50 CDT)
(no subject) deepak rangaswamy (Wed Jul 24 2002 - 22:57:14 CDT)
Re: trajectory problem? David Case (Thu Jul 25 2002 - 00:22:57 CDT)
Pressure probs in MD suvendu lomash (Thu Jul 25 2002 - 02:49:28 CDT)
Re: am1-bcc charges, antechamber Laurent Chiche (Thu Jul 25 2002 - 04:17:58 CDT)
Re: am1-bcc charges, antechamber Giulio Rastelli (Thu Jul 25 2002 - 05:53:46 CDT)
sulfonic group generated with antechamber Michael Jakusch (Thu Jul 25 2002 - 07:23:30 CDT)
Purine to Pyrimidine mutation Bernd Wellenzohn (Thu Jul 25 2002 - 07:29:27 CDT)
Re: am1-bcc charges, antechamber M. L. Dodson (Thu Jul 25 2002 - 07:32:05 CDT)
creating a solvent box Bimo Ario Tejo (Thu Jul 25 2002 - 07:32:17 CDT)
Re: your mail CUI, Guanglei (Thu Jul 25 2002 - 08:30:30 CDT)
Re: creating a solvent box CUI, Guanglei (Thu Jul 25 2002 - 08:33:01 CDT)
Re: creating a solvent box Laurent Chiche (Thu Jul 25 2002 - 09:46:47 CDT)
Re: Pressure probs in MD jim caldwell (Thu Jul 25 2002 - 10:55:57 CDT)
"amber mail" jim caldwell (Thu Jul 25 2002 - 11:11:01 CDT)
acetyl groups on protein fragments Elizabeth K. White (Thu Jul 25 2002 - 13:55:04 CDT)
Re: Gibbs tutorial problem David A. Case (Thu Jul 25 2002 - 14:03:17 CDT)
Re: water box size eric hu (Thu Jul 25 2002 - 14:21:24 CDT)
New Promotion Products at American Disc Corporation Service (Thu Jul 25 2002 - 14:56:47 CDT)
Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 17:28:25 CDT)
Re: Water molecule numbering Shixiang Yan (Thu Jul 25 2002 - 18:25:08 CDT)
RE: Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 19:04:01 CDT)
RE: Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 19:32:19 CDT)
RE: Water molecule numbering Shixiang Yan (Thu Jul 25 2002 - 21:28:02 CDT)
Re: acetyl groups on protein fragments Laurent Chiche (Fri Jul 26 2002 - 02:43:03 CDT)
mol2 with antechamber Giulio Rastelli (Fri Jul 26 2002 - 05:57:22 CDT)
Re: mol2 with antechamber David A. Case (Fri Jul 26 2002 - 10:54:08 CDT)
RE: ptraj Kristina Furse (Fri Jul 26 2002 - 13:32:38 CDT)
Re: ptraj David A. Case (Fri Jul 26 2002 - 14:08:54 CDT)
RE: ptraj Thomas Cheatham (Fri Jul 26 2002 - 14:15:04 CDT)
ptraj Joseph Nachman (Fri Jul 26 2002 - 14:43:36 CDT)
RE: ptraj Joseph Nachman (Fri Jul 26 2002 - 15:14:53 CDT)
periodic box Jiyoung Heo (Fri Jul 26 2002 - 17:00:28 CDT)
Re: periodic box Peter Gannett (Sat Jul 27 2002 - 09:41:50 CDT)
sander crash K.Seshadri (Mon Jul 29 2002 - 03:40:57 CDT)
parallel jobs die with no error message from sander lamon_at_lav.Boehringer-Ingelheim.com (Mon Jul 29 2002 - 12:48:20 CDT)
Re: amber-request@cgl.ucsf.edu Mihaly Mezei (Mon Jul 29 2002 - 13:42:22 CDT)
Re: parallel jobs die with no error message from sander jim caldwell (Mon Jul 29 2002 - 15:08:50 CDT)
Re: parallel jobs die with no error message from sander Scott Brozell (Mon Jul 29 2002 - 17:43:51 CDT)
Re: SANDER documentation for nmropt David A. Case (Mon Jul 29 2002 - 19:27:52 CDT)
a water jumps Masaki Tomimoto (Mon Jul 29 2002 - 22:47:21 CDT)
Re: parallel jobs die with no error message from sander Joffre Heredia (Mon Jul 29 2002 - 23:06:33 CDT)
Re: a water jumps David Case (Tue Jul 30 2002 - 00:13:16 CDT)
NON-BONDED INTERACTION Rosalia Pascual (Tue Jul 30 2002 - 09:41:49 CDT)
sander mpirun hangs with 4 CPU, but not with 2 Thomas Steinbrecher (Tue Jul 30 2002 - 10:09:03 CDT)
AMBER Machine Questions DTphonehome33_at_aol.com (Tue Jul 30 2002 - 12:00:33 CDT)
RE: sander mpirun hangs with 4 CPU, but not with 2 lamon_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 12:06:05 CDT)
AM1-BCC sensitivity to AM1 charges Matthew Lee (Tue Jul 30 2002 - 12:31:43 CDT)
Re: parallel jobs die with no error message from sander Joffre Heredia (Tue Jul 30 2002 - 12:46:37 CDT)
Energies/coordinate files from mm_pbsa problem Peter Gannett (Tue Jul 30 2002 - 13:25:29 CDT)
RE: AM1-BCC sensitivity to AM1 charges ajakalian_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 13:28:25 CDT)
'triangular' bond or angle Mahadevan Seetharaman (Tue Jul 30 2002 - 15:53:20 CDT)
building ss DNA/RNA Cozmuta (Tue Jul 30 2002 - 16:47:45 CDT)
Re: building ss DNA/RNA David A. Case (Tue Jul 30 2002 - 17:29:19 CDT)
tests for amber Cozmuta (Tue Jul 30 2002 - 18:47:18 CDT)
Re: tests for amber jim caldwell (Tue Jul 30 2002 - 19:57:49 CDT)
structure Cozmuta (Tue Jul 30 2002 - 22:34:44 CDT)
Re: structure David Case (Wed Jul 31 2002 - 00:43:50 CDT)
Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 05:52:02 CDT)
Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 07:37:46 CDT)
Re: periodic box Thomas E. Cheatham, III (Wed Jul 31 2002 - 09:26:49 CDT)
Re: Error decoding variable jim caldwell (Wed Jul 31 2002 - 09:43:56 CDT)
Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 10:41:04 CDT)
dielectric constant for partialy solvated MD Miyashita, Osamu (Wed Jul 31 2002 - 13:55:58 CDT)
Re: dielectric constant for partialy solvated MD Carlos Simmerling (Wed Jul 31 2002 - 15:54:12 CDT)
Re: Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 20:50:27 CDT)
problem with amber7 mpi Bimo Ario Tejo (Thu Aug 01 2002 - 05:50:32 CDT)
Re: problem with amber7 mpi Carlos Simmerling (Thu Aug 01 2002 - 07:34:43 CDT)
Re: problem with amber7 mpi Shixiang Yan (Thu Aug 01 2002 - 08:29:58 CDT)
Potential Energy and RMS-Deviation Issues mdk7p_at_cms.mail.virginia.edu (Thu Aug 01 2002 - 10:01:07 CDT)
distance restraint stuff Layi Adekoya (Thu Aug 01 2002 - 10:24:50 CDT)
Re: Potential Energy and RMS-Deviation Issues CUI, Guanglei (Thu Aug 01 2002 - 10:38:36 CDT)
Re: distance restraint stuff CUI, Guanglei (Thu Aug 01 2002 - 10:44:25 CDT)
Re: Potential Energy and RMS-Deviation Issues Thomas Cheatham (Thu Aug 01 2002 - 11:08:09 CDT)
Re: Potential Energy and RMS-Deviation Issues David A. Case (Thu Aug 01 2002 - 11:25:57 CDT)
file Cozmuta (Thu Aug 01 2002 - 12:24:13 CDT)
proton_info/PS Cozmuta (Thu Aug 01 2002 - 12:29:02 CDT)
Using the new2oldparm command dianah_at_unm.edu (Thu Aug 01 2002 - 15:18:32 CDT)
Re: file David A. Case (Thu Aug 01 2002 - 15:46:52 CDT)
Re: Using the new2oldparm command Holger Gohlke (Thu Aug 01 2002 - 15:52:23 CDT)
RE: Using the new2oldparm command Karen Haskell (Thu Aug 01 2002 - 15:55:28 CDT)
MD on cytochrome Mahadevan Seetharaman (Thu Aug 01 2002 - 16:15:52 CDT)
Solvated DNA using Amber 7 Nicholson, James D Mr ARO (Thu Aug 01 2002 - 16:32:13 CDT)
Re: Using the new2oldparm command Pascal Bonnet (Fri Aug 02 2002 - 03:17:54 CDT)
reorder water with nmropt Peter Varnai (Fri Aug 02 2002 - 07:24:59 CDT)
Re: reorder water with nmropt David A. Case (Fri Aug 02 2002 - 11:01:22 CDT)
look for benchmark with myrinet vs. 100-BT Jianhui Wu (Fri Aug 02 2002 - 12:15:29 CDT)
Re: look for benchmark with myrinet vs. 100-BT Margaret Cheung (Fri Aug 02 2002 - 13:20:22 CDT)
FWD: RE: Including explicit waters in GB dynamics Kristina Furse (Fri Aug 02 2002 - 15:32:52 CDT)
igb=2 in amber7 Randy M. Wadkins (Fri Aug 02 2002 - 17:28:48 CDT)
water box-nonperiodic Cozmuta (Fri Aug 02 2002 - 22:14:35 CDT)
PROTON_INFO Cozmuta (Fri Aug 02 2002 - 22:25:37 CDT)
Re: water box-nonperiodic David Case (Sat Aug 03 2002 - 00:16:18 CDT)
Benchmarks Sanjeev B.S. (Sat Aug 03 2002 - 00:48:09 CDT)
Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Sat Aug 03 2002 - 01:49:46 CDT)
Generalized Born and OPLS potential Soonmin Jang (Sat Aug 03 2002 - 03:05:27 CDT)
Re: Please give me a hand on understanding AMBER/MPI and locmem. David Case (Sat Aug 03 2002 - 15:02:42 CDT)
Re: Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Sat Aug 03 2002 - 17:23:50 CDT)
Re: PROTON_INFO Qing Zhang (Sat Aug 03 2002 - 20:12:24 CDT)
Re: look for benchmark with myrinet vs. 100-BT C. Klein (Sun Aug 04 2002 - 03:21:29 CDT)
problems with parallel sander on linux clusters? David Case (Sun Aug 04 2002 - 13:34:20 CDT)
(no subject) sepideh ameli (Sun Aug 04 2002 - 14:01:20 CDT)
Import of CHARMM force field and GB potential parameters into Amber7 Soonmin Jang (Sun Aug 04 2002 - 21:19:20 CDT)
MD in alcohol Marc DOBLER (Sun Aug 04 2002 - 21:33:52 CDT)
Re: Import of CHARMM force field and GB potential parameters into Amber7 David Case (Mon Aug 05 2002 - 00:25:28 CDT)
Re: MD in alcohol David Case (Mon Aug 05 2002 - 00:31:40 CDT)
Re: MD in alcohol Marc DOBLER (Mon Aug 05 2002 - 03:46:17 CDT)
Information request - where to buy software Claire Edmonds (Mon Aug 05 2002 - 08:23:59 CDT)
Amber 7 timings? Jim (Mon Aug 05 2002 - 09:53:25 CDT)
Re: Generalized Born and OPLS potential David A. Case (Mon Aug 05 2002 - 10:51:30 CDT)
"number of processors must be a power of two" Jim (Tue Aug 06 2002 - 09:50:53 CDT)
Amber trajectory movies in Powerpoint mdk7p_at_cms.mail.virginia.edu (Tue Aug 06 2002 - 10:53:39 CDT)
Re: "number of processors must be a power of two" Sanjeev B.S. (Tue Aug 06 2002 - 11:17:35 CDT)
Re: "number of processors must be a power of two" David A. Case (Tue Aug 06 2002 - 11:40:33 CDT)
creating a solvent box Bimo Ario Tejo (Tue Aug 06 2002 - 12:23:13 CDT)
Re: "number of processors must be a power of two" Jim (Tue Aug 06 2002 - 12:29:48 CDT)
Re: "number of processors must be a power of two" Michael Crowley (Tue Aug 06 2002 - 12:31:50 CDT)
Re: Amber trajectory movies in Powerpoint Cozmuta (Tue Aug 06 2002 - 13:25:31 CDT)
am1-bcc charges Sophia Kondratova (Tue Aug 06 2002 - 13:26:22 CDT)
Re: creating a solvent box David A. Case (Tue Aug 06 2002 - 13:53:50 CDT)
check-up question Cozmuta (Tue Aug 06 2002 - 14:13:31 CDT)
Re: am1-bcc charges David A. Case (Tue Aug 06 2002 - 14:32:12 CDT)
Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 14:50:04 CDT)
Re: Leap error: PDB file with more than 10000 residues David A. Case (Tue Aug 06 2002 - 16:13:30 CDT)
Re: check-up question David A. Case (Tue Aug 06 2002 - 16:14:56 CDT)
Re: Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 16:47:00 CDT)
Re: Leap error: PDB file with more than 10000 residues jim caldwell (Tue Aug 06 2002 - 16:57:34 CDT)
charges Cozmuta (Tue Aug 06 2002 - 18:24:14 CDT)
Re: Amber trajectory movies in Powerpoint Elsa de Sousa Henriques (Tue Aug 06 2002 - 20:58:15 CDT)
(no subject) Giulio Rastelli (Wed Aug 07 2002 - 04:07:21 CDT)
Re: your mail darden (Wed Aug 07 2002 - 06:58:17 CDT)
SHAKE problem Rosalia Pascual (Wed Aug 07 2002 - 10:13:12 CDT)
Amber+Mosix Jianhui Wu (Wed Aug 07 2002 - 15:40:15 CDT)
Re: charges David A. Case (Wed Aug 07 2002 - 20:35:07 CDT)
using belly with GB David A. Case (Wed Aug 07 2002 - 20:36:18 CDT)
Re: charges-again Cozmuta (Wed Aug 07 2002 - 20:47:14 CDT)
mpich, I/O, Master node, filesystem Jianhui Wu (Wed Aug 07 2002 - 23:24:13 CDT)
Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. jeff dyason (Wed Aug 07 2002 - 23:45:49 CDT)
Re: Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. Sanjeev B.S. (Wed Aug 07 2002 - 23:46:08 CDT)
Re: mpich, I/O, Master node, filesystem David Case (Thu Aug 08 2002 - 00:14:25 CDT)
nmode segmentation fault zhongh_at_umich.edu (Thu Aug 08 2002 - 08:56:08 CDT)
Re: nmode segmentation fault Holger Gohlke (Thu Aug 08 2002 - 13:16:11 CDT)
Re: nmode segmentation fault jim caldwell (Thu Aug 08 2002 - 13:21:03 CDT)
Gentoo vs. Redhat Linux, shared/distributed filesystem Jianhui Wu (Thu Aug 08 2002 - 14:44:53 CDT)
protonation pH dependent Cozmuta (Thu Aug 08 2002 - 16:14:46 CDT)
Re: protonation pH dependent David A. Case (Thu Aug 08 2002 - 17:05:25 CDT)
LINMIN failure during minimization Giulio Rastelli (Fri Aug 09 2002 - 03:46:18 CDT)
namelist error with sander Andreas Kerzmann (Fri Aug 09 2002 - 03:47:53 CDT)
Re: nmode segmentation fault Haizhen Zhong (Fri Aug 09 2002 - 08:46:19 CDT)
problems runing gibbs on a IBM SP2 machine ramon kleber da rocha (Fri Aug 09 2002 - 09:48:11 CDT)
Re: namelist error with sander David A. Case (Fri Aug 09 2002 - 10:50:27 CDT)
Re: LINMIN failure during minimization David A. Case (Fri Aug 09 2002 - 11:09:09 CDT)
FW: Compiling on HP-UX 11.00 Hagedorn, Dan N (Fri Aug 09 2002 - 13:45:00 CDT)
Amber/Gentoo linux Jianhui Wu (Fri Aug 09 2002 - 14:53:16 CDT)
RE: Amber/Gentoo linux Ross Walker (Sun Aug 11 2002 - 16:32:37 CDT)
RE: Amber+Mosix Ross Walker (Sun Aug 11 2002 - 16:33:04 CDT)
RE: Amber/Gentoo linux Margaret Cheung (Sun Aug 11 2002 - 18:31:02 CDT)
Nanotubes with AMBER Stefan Andreev Andreev (Sun Aug 11 2002 - 18:59:26 CDT)
Re: Nanotubes with AMBER David Case (Sun Aug 11 2002 - 23:13:23 CDT)
literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 04:07:05 CDT)
Re: namelist error with sander Andreas Kerzmann (Mon Aug 12 2002 - 07:40:12 CDT)
Constant pressure MD problems (sander) Pratul Agarwal (Mon Aug 12 2002 - 09:45:15 CDT)
Memory and swap in sander William Wei (Mon Aug 12 2002 - 10:11:35 CDT)
Re: literature for NVE David A. Case (Mon Aug 12 2002 - 10:38:45 CDT)
Re: Constant pressure MD problems (sander) David A. Case (Mon Aug 12 2002 - 10:47:10 CDT)
Re: Memory and swap in sander David A. Case (Mon Aug 12 2002 - 10:55:55 CDT)
Re: literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 11:19:03 CDT)
chesey@panther.gsu.edu Michael G Cooney (Mon Aug 12 2002 - 14:03:37 CDT)
misdirected message Michael G Cooney (Mon Aug 12 2002 - 14:35:35 CDT)
Format of prep input files dianah_at_unm.edu (Tue Aug 13 2002 - 12:42:11 CDT)
Re: Format of prep input files David A. Case (Tue Aug 13 2002 - 13:13:47 CDT)
sander minimizations failing John Bushnell (Tue Aug 13 2002 - 19:03:12 CDT)
minimization in amber7 for nonperiodic systems David Case (Wed Aug 14 2002 - 00:47:43 CDT)
dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Wed Aug 14 2002 - 03:37:50 CDT)
GB in Amber7 Jithesh (Wed Aug 14 2002 - 03:37:54 CDT)
problem reading rstrnt file with pgf77 compiled sander Michael Petersen (Wed Aug 14 2002 - 05:13:24 CDT)
Carnal stream problem Vlad Cojocaru (Wed Aug 14 2002 - 09:45:04 CDT)
Re: minimization in amber7 for nonperiodic systems Giulio Rastelli (Wed Aug 14 2002 - 10:03:11 CDT)
Re: minimization in amber7 for nonperiodic systems David A. Case (Wed Aug 14 2002 - 10:28:21 CDT)
Re: GB in Amber7 David A. Case (Wed Aug 14 2002 - 10:33:57 CDT)
Running amber7 on Param10000 Sanjeev B.S. (Wed Aug 14 2002 - 10:38:34 CDT)
Q: waters in NPT & periodic boundary condition Masaki Tomimoto (Wed Aug 14 2002 - 11:06:15 CDT)
a question about carnal Vlad Cojocaru (Wed Aug 14 2002 - 11:39:36 CDT)
Re: Q: waters in NPT & periodic boundary condition David A. Case (Wed Aug 14 2002 - 11:45:46 CDT)
E going up and down??? Jiyoung Heo (Wed Aug 14 2002 - 16:13:44 CDT)
Re: Can we get trajectories coordinates after FIT in Carnal? Holger Gohlke (Wed Aug 14 2002 - 16:29:41 CDT)
Can we get trajectories coordinates after FIT in Carnal? William Wei (Wed Aug 14 2002 - 16:52:34 CDT)
mpi version of sander in Amber 6.0 with constraints Stefan Andreev Andreev (Wed Aug 14 2002 - 17:13:26 CDT)
Re: E going up and down??? David A. Case (Wed Aug 14 2002 - 17:16:05 CDT)
PMF with sander module mer_at_gordon.chem.wayne.edu (Wed Aug 14 2002 - 18:23:25 CDT)
problem with amber7 compiling on SGI Chris Switzer (Wed Aug 14 2002 - 20:26:54 CDT)
Re: PMF with sander module Pratul Agarwal (Wed Aug 14 2002 - 22:49:34 CDT)
Re: Running amber7 on Param10000 Jithesh (Thu Aug 15 2002 - 02:35:46 CDT)
force field name A. Hungie (Thu Aug 15 2002 - 08:50:48 CDT)
RE: force field name Yong Duan (Thu Aug 15 2002 - 11:11:19 CDT)
sander on NEC-SX5 C. Klein (Thu Aug 15 2002 - 11:12:24 CDT)
RE: sander on NEC-SX5 Karen Haskell (Thu Aug 15 2002 - 11:38:57 CDT)
trajectory file limit??? Vlad Cojocaru (Thu Aug 15 2002 - 11:43:54 CDT)
Re: Help needed about mm_pbsa Holger Gohlke (Thu Aug 15 2002 - 12:04:03 CDT)
Re: trajectory file limit??? David A. Case (Thu Aug 15 2002 - 12:26:34 CDT)
Re: trajectory file limit??? jim caldwell (Thu Aug 15 2002 - 14:26:13 CDT)
Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 15:25:45 CDT)
Extra points Sarah Tschampel (Thu Aug 15 2002 - 15:25:45 CDT)
Re: trajectory file limit??? Pratul Agarwal (Thu Aug 15 2002 - 16:12:35 CDT)
RE: trajectory file limit??? Ross Walker (Thu Aug 15 2002 - 16:48:30 CDT)
Re: Extra points jim caldwell (Thu Aug 15 2002 - 16:54:21 CDT)
RE: Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 17:04:18 CDT)
Re: Extra points David A. Case (Thu Aug 15 2002 - 18:01:21 CDT)
RE: force field name Peter Gannett (Thu Aug 15 2002 - 18:03:52 CDT)
GB in amber6 Prabal Maiti (Thu Aug 15 2002 - 19:26:22 CDT)
Re: GB in amber6 CUI, Guanglei (Thu Aug 15 2002 - 21:33:27 CDT)
Re: GB in amber6 David Case (Fri Aug 16 2002 - 00:23:23 CDT)
add DUMMY atom into coordinate file yuann (Fri Aug 16 2002 - 04:12:04 CDT)
Re: problem reading rstrnt file with pgf77 Michael Petersen (Fri Aug 16 2002 - 08:23:48 CDT)
Re: GB in amber6 CUI, Guanglei (Fri Aug 16 2002 - 08:25:52 CDT)
dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Fri Aug 16 2002 - 11:37:03 CDT)
Etot drops after restarting MD in sander Pratul Agarwal (Fri Aug 16 2002 - 13:18:58 CDT)
antechamber's prepc option Matthew Lee (Fri Aug 16 2002 - 14:20:59 CDT)
Re: PMF with sander module David A. Case (Fri Aug 16 2002 - 14:23:16 CDT)
Re: add DUMMY atom into coordinate file Alan Leo (Fri Aug 16 2002 - 14:51:35 CDT)
Re: antechamber's prepc option David A. Case (Fri Aug 16 2002 - 15:10:55 CDT)
a couple missing gaff angle terms Matthew Lee (Fri Aug 16 2002 - 16:55:44 CDT)
mol2_to_off Matthew Randolph Lee, Ph.D. (Fri Aug 16 2002 - 17:15:41 CDT)
average of LES copies mer_at_chem.wayne.edu (Sun Aug 18 2002 - 20:00:22 CDT)
Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 15:56:00 CDT)
Re: Antibody residue numbering David A. Case (Mon Aug 19 2002 - 16:15:45 CDT)
mail host switchover jim caldwell (Mon Aug 19 2002 - 16:58:11 CDT)
RE: Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 20:00:03 CDT)
Im lost Sankha Subhra Som (Tue Aug 20 2002 - 00:16:00 CDT)
PC (principal component) analysis Soonmin Jang (Tue Aug 20 2002 - 03:02:24 CDT)
Re: Im lost David A. Case (Tue Aug 20 2002 - 10:15:29 CDT)
RE: Antibody residue numbering Mark Hsieh (Tue Aug 20 2002 - 11:52:24 CDT)
follow-up post on missing gaff terms Matthew Randolph Lee, Ph.D. (Tue Aug 20 2002 - 12:21:50 CDT)
segmentation fault Vlad Cojocaru (Tue Aug 20 2002 - 16:21:30 CDT)
Nitro parameters Jerry Matthew Parks (Wed Aug 21 2002 - 16:28:48 CDT)
RMSD by residue (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:49:39 CDT)
Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:02 CDT)
adding_hydrogens_to_pdb (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:07 CDT)
ewald bomb in md equilibration (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:14 CDT)
why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:27 CDT)
ambpdb problem (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:32 CDT)
Gibbs (FEP) (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:36 CDT)
QUICK HELP! Parameters for neutral amino acids (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:43 CDT)
amber7, gaff and minimization (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:50 CDT)
regarding RESP run from gamess output (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:55 CDT)
why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:59 CDT)
Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:03 CDT)
How to make mpeg files from amber trajectories (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:07 CDT)
Carnal RMSDs (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:12 CDT)
Re: Etot drops after restarting MD in sander (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:16 CDT)
turning off ewald (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:21 CDT)
a more general question about ff (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:25 CDT)
leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:29 CDT)
Torsion restraint between center of mass groups Pratul Agarwal (Mon Aug 26 2002 - 16:51:33 CDT)
a more general question (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:41 CDT)
leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:44 CDT)
Re: Extra points (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:49 CDT)
Scaling of Sander on Linux Clusters (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:57 CDT)
Re: "number of processors must be a power of two" (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:01 CDT)
Using GBSA for a DNA-PROTEIN complex (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:06 CDT)
test James W. Caldwell (Mon Aug 26 2002 - 17:04:35 CDT)
mail reflector James W. Caldwell (Mon Aug 26 2002 - 17:35:53 CDT)
ewald bomb in md equilibration Sophia Kondratova (Mon Aug 26 2002 - 17:54:37 CDT)
Re: Can we get trajectories coordinates after FIT in Carnal? Bill Ross (Mon Aug 26 2002 - 18:54:25 CDT)
Re: Carnal RMSDs Bill Ross (Mon Aug 26 2002 - 18:56:50 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Pratul Agarwal (Mon Aug 26 2002 - 19:32:24 CDT)
Re: adding_hydrogens_to_pdb (fwd) David A. Case (Mon Aug 26 2002 - 19:34:36 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Peter Gannett (Mon Aug 26 2002 - 19:56:06 CDT)
Re: RMSD by residue (fwd) Holger Gohlke (Mon Aug 26 2002 - 20:08:35 CDT)
Re: leaprc file (fwd) David A. Case (Mon Aug 26 2002 - 20:09:22 CDT)
Re: RMSD by residue (fwd) Carlos Simmerling (Mon Aug 26 2002 - 20:10:41 CDT)
Re: turning off ewald (fwd) David A. Case (Mon Aug 26 2002 - 20:12:29 CDT)
Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) David A. Case (Mon Aug 26 2002 - 20:21:06 CDT)
Re: ewald bomb in md equilibration (fwd) David A. Case (Mon Aug 26 2002 - 20:23:52 CDT)
Re: ambpdb problem (fwd) David A. Case (Mon Aug 26 2002 - 20:27:08 CDT)
Re: Gibbs (FEP) (fwd) David A. Case (Mon Aug 26 2002 - 20:30:28 CDT)
Re: QUICK HELP! Parameters for neutral amino acids (fwd) David A. Case (Mon Aug 26 2002 - 20:32:50 CDT)
Re: amber7, gaff and minimization (fwd) David A. Case (Mon Aug 26 2002 - 20:35:26 CDT)
Interface and Amber 7.0 Nigel D Priestley (Mon Aug 26 2002 - 21:45:55 CDT)
question Sankha Subhra Som (Tue Aug 27 2002 - 01:24:32 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Stéphane Teletchéa (Tue Aug 27 2002 - 03:41:06 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S. (Tue Aug 27 2002 - 03:56:15 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Stéphane Teletchéa (Tue Aug 27 2002 - 04:31:16 CDT)
Re: Interface and Amber 7.0 David A. Case (Tue Aug 27 2002 - 06:53:45 CDT)
amber7: ES40s Sanjeev B.S. (Tue Aug 27 2002 - 08:08:49 CDT)
difference 94 99 force field Vlad Cojocaru (Tue Aug 27 2002 - 08:34:11 CDT)
Re: How to make mpeg files from amber trajectories (fwd) Jake Isaacs (Tue Aug 27 2002 - 08:48:24 CDT)
Re: difference 94 99 force field Carlos Simmerling (Tue Aug 27 2002 - 09:34:50 CDT)
Re: how to make mpeg files from amber trajectories Anke Eisenmann (Tue Aug 27 2002 - 09:41:01 CDT)
Re: Interface and Amber 7.0 David Pearlman (Tue Aug 27 2002 - 11:35:19 CDT)
Re: why is mm_pbsa broken ? (fwd) Holger Gohlke (Tue Aug 27 2002 - 12:12:17 CDT)
Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S. (Tue Aug 27 2002 - 12:59:51 CDT)
restraints in parm in amber7 Sarah Tschampel (Tue Aug 27 2002 - 16:57:33 CDT)
problem in MD Xiang Mao (Tue Aug 27 2002 - 19:05:11 CDT)
Re: restraints in parm in amber7 Carlos Simmerling (Tue Aug 27 2002 - 20:38:59 CDT)
Re: problem in MD Carlos Simmerling (Tue Aug 27 2002 - 20:40:06 CDT)
Re: How to make mpeg files from amber trajectories (fwd) Michal Otyepka (Wed Aug 28 2002 - 02:22:54 CDT)
What's this "interface" the tutorial talks about? Andreas Kerzmann (Wed Aug 28 2002 - 07:41:01 CDT)
iwrap and image Sophia Kondratova (Wed Aug 28 2002 - 07:55:36 CDT)
Re: iwrap and image James W. Caldwell (Wed Aug 28 2002 - 09:35:50 CDT)
Fw: amber problem Carlos Simmerling (Wed Aug 28 2002 - 12:10:26 CDT)
can carnal do the job as anal to break down the energy? Haizhen Zhong (Wed Aug 28 2002 - 13:02:48 CDT)
[Re: can carnal do the job as anal to break down the energy?] Holger Gohlke (Wed Aug 28 2002 - 13:36:51 CDT)
RE: What's this "interface" the tutorial talks about? priestle (Wed Aug 28 2002 - 14:02:52 CDT)
Re: What's this "interface" the tutorial talks about? David Pearlman (Wed Aug 28 2002 - 14:49:57 CDT)
gibbs sara nunez (Wed Aug 28 2002 - 14:52:56 CDT)
[Re: can carnal do the job as anal to break down the energy?] Bill Ross (Wed Aug 28 2002 - 15:35:40 CDT)
a missing variable Vlad Cojocaru (Wed Aug 28 2002 - 15:43:04 CDT)
Re: a missing variable Matthew Randolph Lee, Ph.D. (Wed Aug 28 2002 - 17:27:12 CDT)
sorry!!!!maybe another stupid question Vlad Cojocaru (Wed Aug 28 2002 - 17:48:03 CDT)
Tutorial Error Message Joel Konkle-Parker (Wed Aug 28 2002 - 18:19:48 CDT)
Re: sorry!!!!maybe another stupid question Pratul Agarwal (Wed Aug 28 2002 - 20:45:28 CDT)
IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch (Thu Aug 29 2002 - 02:36:57 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 05:14:06 CDT)
Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Carlos Simmerling (Thu Aug 29 2002 - 05:54:15 CDT)
Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch (Thu Aug 29 2002 - 06:56:12 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 07:20:52 CDT)
pbc in amber Xiang Mao (Thu Aug 29 2002 - 08:00:04 CDT)
Re: Tutorial Error Message Holger Gohlke (Thu Aug 29 2002 - 10:22:25 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 12:02:23 CDT)
image command Sophia Kondratova (Thu Aug 29 2002 - 12:46:01 CDT)
PyMOL + AMBER Trajectories DeLano, Warren (Thu Aug 29 2002 - 13:27:01 CDT)
ES40 hangs amber7 jobs. Sanjeev B.S. (Thu Aug 29 2002 - 22:09:13 CDT)
dump coordinate into mdcrd A. Hungie (Fri Aug 30 2002 - 03:03:17 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:08:15 CDT)
example gibbs file for the methane tutorial Andreas Kerzmann (Fri Aug 30 2002 - 05:18:06 CDT)
NTX value giudice (Fri Aug 30 2002 - 05:31:19 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:59:25 CDT)
sander7 on IBM 7040-681 under AIX 5.1 Peter Varnai (Fri Aug 30 2002 - 08:01:07 CDT)
ewald bomb Vlad Cojocaru (Fri Aug 30 2002 - 08:38:49 CDT)
Re: ES40 hangs amber7 jobs. James W. Caldwell (Fri Aug 30 2002 - 11:07:11 CDT)
Re: NTX value James W. Caldwell (Fri Aug 30 2002 - 11:10:10 CDT)
Vanderbilt Biomolecular Modeling Symposium Jarrod Smith (Fri Aug 30 2002 - 13:00:40 CDT)
Re: NTX value James W. Caldwell (Fri Aug 30 2002 - 13:35:30 CDT)
Re: NTX value David A. Case (Fri Aug 30 2002 - 14:07:44 CDT)
Re: ewald bomb David A. Case (Fri Aug 30 2002 - 14:13:14 CDT)
RE: Vanderbilt Biomolecular Modeling Symposium Douglas Kojetin (Fri Aug 30 2002 - 14:22:19 CDT)
Binding site volume/Sander MD Jianhui Wu (Fri Aug 30 2002 - 16:20:09 CDT)
GBSA with IGB=2, setting the PBradii bondi Sarangan Ravichandran (Fri Aug 30 2002 - 16:55:28 CDT)
Re: GBSA with IGB=2, setting the PBradii bondi David Case (Sat Aug 31 2002 - 12:58:35 CDT)
mpirun Ioana Cozmuta (Sun Sep 01 2002 - 13:32:08 CDT)
additional info Ioana Cozmuta (Sun Sep 01 2002 - 13:44:32 CDT)
RE: mpirun Ross Walker (Sun Sep 01 2002 - 17:36:24 CDT)
Re: NTX value giudice (Mon Sep 02 2002 - 02:05:45 CDT)
mm_pbsa positive binding energies Mathy Froeyen (Mon Sep 02 2002 - 04:11:34 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 05:12:42 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 06:25:18 CDT)
carnal averaging Vlad Cojocaru (Mon Sep 02 2002 - 06:43:33 CDT)
Re: mm_pbsa positive binding energies David A. Case (Mon Sep 02 2002 - 12:50:30 CDT)
Re: carnal averaging Holger Gohlke (Mon Sep 02 2002 - 15:43:52 CDT)
atoms coming too close during MD (with SHAKE on) Pratul Agarwal (Mon Sep 02 2002 - 20:01:18 CDT)
Re: ES40 hangs amber7 jobs. Sanjeev B.S. (Mon Sep 02 2002 - 21:29:45 CDT)
Re: protein minimization Lepsa (Tue Sep 03 2002 - 01:13:54 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 03 2002 - 06:57:12 CDT)
Re: protein minimization CUI, Guanglei (Tue Sep 03 2002 - 08:19:39 CDT)
compile Moil-View, GL header files Jianhui Wu (Tue Sep 03 2002 - 10:20:09 CDT)
protein minimization m.elizabeth sophia (Tue Sep 03 2002 - 11:01:35 CDT)
Re: compile Moil-View, GL header files Viktor Hornak (Tue Sep 03 2002 - 11:12:22 CDT)
Re: compile Moil-View, GL header files Renee olano (Tue Sep 03 2002 - 11:54:57 CDT)
question Ioana Cozmuta (Tue Sep 03 2002 - 12:46:04 CDT)
RE: PyMOL + AMBER Trajectories DeLano, Warren (Tue Sep 03 2002 - 12:51:57 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Wed Sep 04 2002 - 05:40:26 CDT)
Escaping Atoms ch cureton (Wed Sep 04 2002 - 05:43:03 CDT)
old prmtop Thomas Steinbrecher (Wed Sep 04 2002 - 10:56:47 CDT)
Re: old prmtop C. Klein (Wed Sep 04 2002 - 11:21:18 CDT)
Re: old prmtop Holger Gohlke (Wed Sep 04 2002 - 11:21:32 CDT)
Re: old prmtop Peter Gannett (Wed Sep 04 2002 - 13:10:56 CDT)
how to detect bad contact? X. Tan (Wed Sep 04 2002 - 14:14:40 CDT)
cut-off question Ioana Cozmuta (Wed Sep 04 2002 - 14:43:38 CDT)
DNA Tutorial Script Joel Konkle-Parker (Wed Sep 04 2002 - 18:18:16 CDT)
Re: DNA Tutorial Script Holger Gohlke (Wed Sep 04 2002 - 22:29:23 CDT)
average structure Raja Swaminathan (Thu Sep 05 2002 - 12:16:03 CDT)
RE: Escaping Atoms case (Thu Sep 05 2002 - 17:04:06 CDT)
bondbydistance eric hu (Thu Sep 05 2002 - 18:20:43 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 06 2002 - 06:13:47 CDT)
group selection for all heavy atoms ? Raik Grunberg (Fri Sep 06 2002 - 11:23:33 CDT)
compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 15:46:43 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 17:01:27 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC Florian Barth (Fri Sep 06 2002 - 17:13:31 CDT)
cut-off question Cozmuta (Fri Sep 06 2002 - 17:49:21 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 18:11:55 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC John Bushnell (Fri Sep 06 2002 - 18:43:12 CDT)
RE: cut-off question case (Fri Sep 06 2002 - 19:01:28 CDT)
RE: bondbydistance case (Fri Sep 06 2002 - 19:04:02 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 19:16:40 CDT)
Re: compiling amber on a linux box using DMEM-ALLOC James W. Caldwell (Fri Sep 06 2002 - 19:56:42 CDT)
RE: bondbydistance Nicholson, James D Mr ARO (Sat Sep 07 2002 - 19:16:28 CDT)
about amber and charmm, thanks Zhang Jian (Sun Sep 08 2002 - 04:10:57 CDT)
who to address this to?... Jessica Swanson (Sun Sep 08 2002 - 17:59:23 CDT)
Distace dependent dielectric constant Lorenzo Gontrani (Mon Sep 09 2002 - 03:33:43 CDT)
parameterization of a new class of compounds (nucleic acid base analogues) Vlad Cojocaru (Mon Sep 09 2002 - 04:40:05 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 09 2002 - 06:04:45 CDT)
Re: who to address this to?... Holger Gohlke (Mon Sep 09 2002 - 11:25:00 CDT)
Re: who to address this to?... Michael Crowley (Mon Sep 09 2002 - 12:41:16 CDT)
amber7 compilation on irix6.4 mp K.Seshadri (Mon Sep 09 2002 - 12:44:13 CDT)
How to check whether the trajectory file matches the coordinates file or not? Ling Zhang (Mon Sep 09 2002 - 13:31:13 CDT)
Re: How to check whether the trajectory file matches the coordinates file or not? Shixiang Yan (Mon Sep 09 2002 - 13:53:04 CDT)
RE: How to check whether the trajectory file matches the coordinates file or not? Kristina Furse (Mon Sep 09 2002 - 14:32:27 CDT)
why are the results so large difference calculating by mm_pbsa and mm_gbsa? Yongjun Jiang (Tue Sep 10 2002 - 02:18:46 CDT)
Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 05:09:06 CDT)
Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling (Tue Sep 10 2002 - 07:07:58 CDT)
nmode compile question? Yongjun Jiang (Tue Sep 10 2002 - 07:46:18 CDT)
GBSA and surface crystal waters Raik Grunberg (Tue Sep 10 2002 - 09:44:20 CDT)
Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 10:56:53 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 10 2002 - 10:57:00 CDT)
Re: nmode compile question? Holger Gohlke (Tue Sep 10 2002 - 11:17:24 CDT)
Re: why are the results so large difference calculating by mm_pbsa and mm_gbsa? Holger Gohlke (Tue Sep 10 2002 - 11:26:07 CDT)
Re: nmode compile question? James W. Caldwell (Tue Sep 10 2002 - 13:04:07 CDT)
rdparm Joffre Heredia (Tue Sep 10 2002 - 13:07:26 CDT)
loadpdb error messages Joel Konkle-Parker (Tue Sep 10 2002 - 17:58:07 CDT)
Re: loadpdb error messages James W. Caldwell (Tue Sep 10 2002 - 18:49:48 CDT)
Polarizability, a general question Michal Otyepka (Wed Sep 11 2002 - 03:56:32 CDT)
memory allocation in mm_pbsa Giulio Rastelli (Wed Sep 11 2002 - 05:41:04 CDT)
just a test Vlad Cojocaru (Wed Sep 11 2002 - 08:39:59 CDT)
Re: memory allocation in mm_pbsa James W. Caldwell (Wed Sep 11 2002 - 10:26:19 CDT)
Re: memory allocation in mm_pbsa Holger Gohlke (Wed Sep 11 2002 - 10:55:07 CDT)
Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 14:38:36 CDT)
Re: Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 15:14:05 CDT)
Dual Processor AMD vs. Single Processor DeLano, Warren (Wed Sep 11 2002 - 19:34:47 CDT)
Re: Strange MD simulation results with GB solvation at high temp. David A. Case (Wed Sep 11 2002 - 20:20:17 CDT)
Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling (Wed Sep 11 2002 - 21:04:44 CDT)
Re: Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 21:40:05 CDT)
why are the results so large difference calculating by mm_pbsaandmm_gbsa? Yongjun Jiang (Thu Sep 12 2002 - 02:25:32 CDT)
Re: Dual Processor AMD vs. Single Processor Stéphane Teletchéa (Thu Sep 12 2002 - 03:09:58 CDT)
Qustion about calculation of pressure Nikolai Smolin (Thu Sep 12 2002 - 05:01:44 CDT)
sorry this is just a test Vlad Cojocaru (Thu Sep 12 2002 - 10:23:24 CDT)
leap and topology file Marcela Madrid (Thu Sep 12 2002 - 11:12:20 CDT)
sander.LES questions Peter Varnai (Thu Sep 12 2002 - 11:27:12 CDT)
Re: Qustion about calculation of pressure James W. Caldwell (Thu Sep 12 2002 - 11:43:25 CDT)
Re: sander.LES questions Carlos Simmerling (Thu Sep 12 2002 - 12:24:25 CDT)
large energy fluctration eric hu (Thu Sep 12 2002 - 13:05:10 CDT)
the amino group of 2amino purine has strange behaviour Vlad Cojocaru (Thu Sep 12 2002 - 13:42:10 CDT)
Re: large energy fluctration Carlos Simmerling (Thu Sep 12 2002 - 13:50:09 CDT)
Re: Distace dependent dielectric constant David A. Case (Thu Sep 12 2002 - 17:39:35 CDT)
Changing MAXINT Joel Konkle-Parker (Thu Sep 12 2002 - 18:21:13 CDT)
binding site volume Shixiang Yan (Thu Sep 12 2002 - 18:38:41 CDT)
problems on IBM AIX Giovanni Fossati (Thu Sep 12 2002 - 20:43:52 CDT)
Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Fri Sep 13 2002 - 00:21:32 CDT)
Re: binding site volume Michal Otyepka (Fri Sep 13 2002 - 02:13:08 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:10:40 CDT)
MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:13:22 CDT)
Re: leap and topology file Lepsa (Fri Sep 13 2002 - 09:39:45 CDT)
Re: problems on IBM AIX David A. Case (Fri Sep 13 2002 - 09:42:14 CDT)
Re: problems on IBM AIX Carlos P. Sosa (Fri Sep 13 2002 - 10:47:31 CDT)
Beowulf killing jobs Peter Gannett (Fri Sep 13 2002 - 16:03:19 CDT)
Help using moilview to make animations of trajectories Nicholson, James D Mr ARO (Fri Sep 13 2002 - 17:15:33 CDT)
Re: Changing MAXINT John Bushnell (Fri Sep 13 2002 - 17:38:52 CDT)
D-tryptophan Perdita Barran (Sat Sep 14 2002 - 09:16:45 CDT)
Re: D-tryptophan James W. Caldwell (Sat Sep 14 2002 - 10:21:42 CDT)
amber K.Veluraja (Mon Sep 16 2002 - 00:14:04 CDT)
amber question yao yong (Mon Sep 16 2002 - 06:03:16 CDT)
RE: Changing MAXINT Ross Walker (Mon Sep 16 2002 - 09:39:36 CDT)
RE: Beowulf killing jobs Ross Walker (Mon Sep 16 2002 - 09:46:45 CDT)
example 1 problems Alicia Hopkins (Mon Sep 16 2002 - 10:57:23 CDT)
assistance required amit kumar (Mon Sep 16 2002 - 11:25:05 CDT)
Re: example 1 problems David A. Case (Mon Sep 16 2002 - 11:25:54 CDT)
Re: example 1 problems Natasja Brooijmans (Mon Sep 16 2002 - 11:40:38 CDT)
Re: amber question David A. Case (Mon Sep 16 2002 - 11:47:03 CDT)
Re: amber question James W. Caldwell (Mon Sep 16 2002 - 12:24:20 CDT)
SETVEL, incorrect number of arguments? Giovanni Fossati (Mon Sep 16 2002 - 17:43:30 CDT)
non-bonded metal ion in complex yuann (Tue Sep 17 2002 - 01:28:45 CDT)
question about nmode again. Yongjun Jiang (Tue Sep 17 2002 - 02:15:54 CDT)
Re: example 1 problems Alicia Hopkins (Tue Sep 17 2002 - 07:03:53 CDT)
Re: non-bonded metal ion in complex Pratul Agarwal (Tue Sep 17 2002 - 08:59:14 CDT)
Re: example 1 problems James W. Caldwell (Tue Sep 17 2002 - 09:24:30 CDT)
Re: question about nmode again. David A. Case (Tue Sep 17 2002 - 09:40:00 CDT)
Re: example 1 problems David A. Case (Tue Sep 17 2002 - 09:45:31 CDT)
mm_pbsa question. wentaofu (Tue Sep 17 2002 - 10:35:59 CDT)
Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 11:56:10 CDT)
Re: SETVEL, incorrect number of arguments? David A. Case (Tue Sep 17 2002 - 14:18:38 CDT)
Re: Density during equilibration (sander) David A. Case (Tue Sep 17 2002 - 14:21:49 CDT)
Z DNA Sue Heavner (Tue Sep 17 2002 - 14:55:04 CDT)
Re: Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 19:22:22 CDT)
Re: Density during equilibration (sander) Marc Dobler (Tue Sep 17 2002 - 19:29:22 CDT)
Re: Density during equilibration (sander) Carlos Simmerling (Tue Sep 17 2002 - 20:44:13 CDT)
Re: Density during equilibration (sander) Marc Dobler (Wed Sep 18 2002 - 02:11:21 CDT)
Carnal+HBond confusion Sanjeev B.S. (Wed Sep 18 2002 - 23:18:36 CDT)
bug in New2oldparm Pascal Bonnet (Thu Sep 19 2002 - 05:35:46 CDT)
new2oldparm format (2) Pascal Bonnet (Thu Sep 19 2002 - 05:43:39 CDT)
a freeware to display RMSD matrices Vlad Cojocaru (Thu Sep 19 2002 - 07:44:53 CDT)
Re: a freeware to display RMSD matrices CUI, Guanglei (Thu Sep 19 2002 - 08:42:29 CDT)
Re: bug in New2oldparm David A. Case (Thu Sep 19 2002 - 10:28:30 CDT)
offset of temperature when running MD with CAP and no periodic conditions Therese Malliavin (Thu Sep 19 2002 - 10:44:24 CDT)
Re: offset of temperature when running MD with CAP and no periodic conditions Andreas Svrcek-Seiler (Thu Sep 19 2002 - 12:11:31 CDT)
compiling without ISTAR2 Prem Raj (Thu Sep 19 2002 - 12:27:48 CDT)
image X. Tan (Thu Sep 19 2002 - 12:32:15 CDT)
Question about Counterions Markus Drumm (Thu Sep 19 2002 - 12:38:24 CDT)
Re: image David A. Case (Thu Sep 19 2002 - 12:43:32 CDT)
RE: compiling without ISTAR2 Ross Walker (Thu Sep 19 2002 - 12:50:49 CDT)
BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 15:51:28 CDT)
Re: BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 16:39:48 CDT)
npairs Prem Raj (Thu Sep 19 2002 - 17:22:42 CDT)
Re: BLOWUP after 100 ns??? David A. Case (Thu Sep 19 2002 - 19:29:58 CDT)
Re: BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 20:41:16 CDT)
Dynamic Movement of Molecule Yuuki Komata (Fri Sep 20 2002 - 03:03:48 CDT)
Re: Parameters for AMBER David A. Case (Fri Sep 20 2002 - 08:53:18 CDT)
mol2 file format in the future of amber M. L. Dodson (Fri Sep 20 2002 - 09:41:02 CDT)
(no subject) Prem Raj (Fri Sep 20 2002 - 11:42:14 CDT)
vlimit and vmax Prem Raj (Fri Sep 20 2002 - 12:27:07 CDT)
Re: large energy fluctration eric hu (Fri Sep 20 2002 - 13:00:17 CDT)
Re: Dynamic Movement of Molecule Thomas Cheatham (Fri Sep 20 2002 - 14:01:39 CDT)
Re: vlimit and vmax Thomas Cheatham (Fri Sep 20 2002 - 14:14:11 CDT)
Re: vlimit and vmax darden (Fri Sep 20 2002 - 14:27:10 CDT)
mm_pbsa Sue Heavner (Fri Sep 20 2002 - 15:00:36 CDT)
ptraj rdf output Prabal Maiti (Fri Sep 20 2002 - 18:24:35 CDT)
Periodicity Question DeLano, Warren (Fri Sep 20 2002 - 19:29:49 CDT)
Re: mol2 file format in the future of amber David A. Case (Sun Sep 22 2002 - 10:10:42 CDT)
Re: mol2 file format in the future of amber M. L. Dodson (Sun Sep 22 2002 - 10:34:06 CDT)
Re: Do I have to rerun 1ns MD?? Holger Gohlke (Sun Sep 22 2002 - 14:30:40 CDT)
Re: betaP,SURFOFF inconsistency Holger Gohlke (Sun Sep 22 2002 - 15:20:03 CDT)
Re: mm_pbsa Holger Gohlke (Sun Sep 22 2002 - 16:01:22 CDT)
Re: mm_pbsa Mahadevan Seetharaman (Sun Sep 22 2002 - 21:07:27 CDT)
ptraj-6.4/LES Peter Varnai (Mon Sep 23 2002 - 04:18:25 CDT)
Re: mm_pbsa David A. Case (Mon Sep 23 2002 - 08:25:02 CDT)
Fw: Do I have to rerun 1ns MD?? Lepsa (Mon Sep 23 2002 - 10:50:26 CDT)
mm_pbsa output error Michael Murray (Mon Sep 23 2002 - 12:26:11 CDT)
antechamber best practices/charge equivalence w/ AM1-BCC Tom Bishop (Mon Sep 23 2002 - 16:28:57 CDT)
Re: mm_pbsa output error Holger Gohlke (Mon Sep 23 2002 - 23:21:30 CDT)
watershell in ptraj Michael Trieb (Tue Sep 24 2002 - 04:03:49 CDT)
Re: Carnal+HBond confusion Sanjeev B.S. (Tue Sep 24 2002 - 07:13:05 CDT)
expression of V(lambda) in GIBBS hagop demirdjian (Tue Sep 24 2002 - 07:44:02 CDT)
Re: expression of V(lambda) in GIBBS David A. Case (Tue Sep 24 2002 - 09:14:01 CDT)
RE: antechamber best practices/charge equivalence w/ AM1-BCC Bayly, Christopher (Tue Sep 24 2002 - 09:49:56 CDT)
Mopac509mn/linux James W. Caldwell (Tue Sep 24 2002 - 10:00:20 CDT)
Re: watershell in ptraj Thomas Cheatham (Tue Sep 24 2002 - 14:28:09 CDT)
ambpdb? Arvid Soederhaell (Wed Sep 25 2002 - 02:38:34 CDT)
Re: ambpdb? Lepsa (Wed Sep 25 2002 - 03:29:25 CDT)
ptraj - BONDS_WITHOUT_HYDROGEN Sophia Kondratova (Wed Sep 25 2002 - 11:54:48 CDT)
(no subject) Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 14:09:53 CDT)
compiling amber 7 with Intel Fortran Compiler 6.0 ramon kleber da rocha (Wed Sep 25 2002 - 14:23:21 CDT)
sander_classic: Recompile without ISTAR2 Mahadevan Seetharaman (Wed Sep 25 2002 - 14:53:59 CDT)
ISTAR2 - oops, just found the answer... Mahadevan Seetharaman (Wed Sep 25 2002 - 14:55:46 CDT)
Re: compiling amber 7 with Intel Fortran Compiler 6.0 Scott Brozell (Wed Sep 25 2002 - 15:05:45 CDT)
compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) John Bushnell (Wed Sep 25 2002 - 15:10:50 CDT)
Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell (Wed Sep 25 2002 - 15:16:48 CDT)
RMSD for heavy atoms only Pratul Agarwal (Wed Sep 25 2002 - 15:54:45 CDT)
Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell (Wed Sep 25 2002 - 15:58:04 CDT)
Question about Antechamber Masaki Tomimoto (Wed Sep 25 2002 - 16:37:55 CDT)
mm_pbsa and statistic program Pascal Bonnet (Thu Sep 26 2002 - 05:50:52 CDT)
different counterions for special type of DNA Vlad Cojocaru (Thu Sep 26 2002 - 07:59:31 CDT)
Re: Density during equilibration (sander) Pratul Agarwal (Thu Sep 26 2002 - 09:09:02 CDT)
Re: Question about Antechamber David A. Case (Thu Sep 26 2002 - 10:28:51 CDT)
Re: GB tutorial David A. Case (Thu Sep 26 2002 - 10:31:19 CDT)
Re: mm_pbsa and statistic program David A. Case (Thu Sep 26 2002 - 10:37:15 CDT)
Torsion driving ch cureton (Thu Sep 26 2002 - 11:00:34 CDT)
Question on Antechamber paper Nicholson, James D Mr ARO (Thu Sep 26 2002 - 12:18:17 CDT)
Amber Reflector James W. Caldwell (Thu Sep 26 2002 - 12:47:58 CDT)
Constant pressure equilibration in a system with a solvent cap dianah_at_unm.edu (Thu Sep 26 2002 - 20:04:38 CDT)
Re: Constant pressure equilibration in a system with a solvent cap James W. Caldwell (Fri Sep 27 2002 - 08:54:46 CDT)
nmanal help request Peter Fojan (Fri Sep 27 2002 - 08:59:11 CDT)
Re: Constant pressure equilibration in a system with a solvent cap David A. Case (Fri Sep 27 2002 - 10:26:09 CDT)
Re: nmanal help request David A. Case (Fri Sep 27 2002 - 10:38:23 CDT)
Re: Constant pressure equilibration in a system with a solvent cap David Smith (Fri Sep 27 2002 - 11:11:19 CDT)
MM-PBSA basics Michael Ford (Fri Sep 27 2002 - 14:53:01 CDT)
MD Primers Joel Konkle-Parker (Fri Sep 27 2002 - 14:54:03 CDT)
Is H-bonding really there? suvendu lomash (Fri Sep 27 2002 - 14:59:48 CDT)
Re: Is H-bonding really there? Thomas Cheatham (Fri Sep 27 2002 - 15:53:24 CDT)
Re: Is H-bonding really there? Pratul Agarwal (Fri Sep 27 2002 - 15:58:25 CDT)
Re: Is H-bonding really there? Ioana Cozmuta (Fri Sep 27 2002 - 17:04:37 CDT)
Anal Error : Group Lifeng Tian (Fri Sep 27 2002 - 17:35:23 CDT)
Re: MD Primers Peter Gannett (Fri Sep 27 2002 - 18:34:40 CDT)
Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:58:58 CDT)
Re: Request for help with Antechamber David A. Case (Fri Sep 27 2002 - 19:54:21 CDT)
RE: Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 20:00:37 CDT)
Re: Request for help with Antechamber James W. Caldwell (Sat Sep 28 2002 - 00:54:24 CDT)
question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 14:53:56 CDT)
Re: question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 15:35:48 CDT)
parameters for sugars A.Madhumalar (Sun Sep 29 2002 - 11:30:36 CDT)
Re: MM-PBSA basics Holger Gohlke (Sun Sep 29 2002 - 21:44:52 CDT)
Re: MM-PBSA basics Lepsa (Mon Sep 30 2002 - 02:13:16 CDT)
groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 08:15:10 CDT)
Re: groups in targeted md Carlos Simmerling (Mon Sep 30 2002 - 09:04:26 CDT)
Re: groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 09:48:16 CDT)
Amber 7 and 6 topology files. Miguel de Federico (Mon Sep 30 2002 - 10:08:36 CDT)
Re: Amber 7 and 6 topology files. James W. Caldwell (Mon Sep 30 2002 - 10:41:25 CDT)
BondEn shoots in solvent minimization suvendu lomash (Mon Sep 30 2002 - 10:50:39 CDT)
write problem on IBM-AIX Giovanni Fossati (Mon Sep 30 2002 - 10:51:54 CDT)
Image charges with the solvate cap command dkeller_at_unm.edu (Mon Sep 30 2002 - 10:52:11 CDT)
Re: your mail David A. Case (Mon Sep 30 2002 - 11:35:06 CDT)
Re: parameters for sugars Elsa de Sousa Henriques (Mon Sep 30 2002 - 11:42:24 CDT)
Problems with poly(A)-poly(T) tutorial... Andrei Leitão (Mon Sep 30 2002 - 14:55:53 CDT)
Partial charge generation RESP/antechamber James W. Caldwell (Mon Sep 30 2002 - 17:27:37 CDT)
divalent cations parameters Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 17:38:11 CDT)
Re: Image charges with the solvate cap command David A. Case (Mon Sep 30 2002 - 19:34:28 CDT)
Re: write problem on IBM-AIX Nicolas Grima (Tue Oct 01 2002 - 04:40:07 CDT)
Re: NON-BONDED INTERACTION David A. Case (Tue Oct 01 2002 - 10:28:00 CDT)
Re: Is H-bonding really there? Ioana Cozmuta (Tue Oct 01 2002 - 16:44:55 CDT)
Questions on crosslinking residues Nicholson, James D Mr ARO (Tue Oct 01 2002 - 16:59:19 CDT)
antechamber web page Ioana Cozmuta (Tue Oct 01 2002 - 17:33:36 CDT)
Re: antechamber web page David A. Case (Tue Oct 01 2002 - 18:00:33 CDT)
tutorial on plastocyanin Ioana Cozmuta (Wed Oct 02 2002 - 01:04:37 CDT)
restart without velocities Michal Otyepka (Wed Oct 02 2002 - 02:39:02 CDT)
Re: restart without velocities Sanjeev B.S. (Wed Oct 02 2002 - 02:44:57 CDT)
Re: tutorial on plastocyanin David A. Case (Wed Oct 02 2002 - 09:48:27 CDT)
RE: Sander multiprocessors running problem with MPI Ross Walker (Wed Oct 02 2002 - 12:52:27 CDT)
Sander multiprocessors running problem with MPI William Wei (Wed Oct 02 2002 - 13:09:49 CDT)
xleap XENVIRONMENT Mark C. Ballew (Wed Oct 02 2002 - 17:34:09 CDT)
Re: Questions on crosslinking residues David A. Case (Wed Oct 02 2002 - 18:34:47 CDT)
Re: xleap XENVIRONMENT David A. Case (Wed Oct 02 2002 - 18:55:31 CDT)
RE: Questions on crosslinking residues Nicholson, James D Mr ARO (Wed Oct 02 2002 - 20:03:47 CDT)
RESP gaussian job crashing Nicholson, James D Mr ARO (Wed Oct 02 2002 - 20:22:59 CDT)
Re: xleap XENVIRONMENT Lepsa (Thu Oct 03 2002 - 02:47:39 CDT)
regarding resp-doubts thenmalar rathinavelan (Thu Oct 03 2002 - 03:21:51 CDT)
about AMBER parallel edition Shimono Fumihiro (Thu Oct 03 2002 - 06:07:36 CDT)
atomicfluct Bimo Ario Tejo (Thu Oct 03 2002 - 06:40:47 CDT)
Re: about AMBER parallel edition Shimono Fumihiro (Thu Oct 03 2002 - 06:46:14 CDT)
Re: Questions on crosslinking residues M. L. Dodson (Thu Oct 03 2002 - 07:42:08 CDT)
Re: RESP gaussian job crashing James W. Caldwell (Thu Oct 03 2002 - 09:04:59 CDT)
Re: Questions on crosslinking residues David A. Case (Thu Oct 03 2002 - 10:04:18 CDT)
Re: regarding resp-doubts Wiktor Jurkowski (Thu Oct 03 2002 - 10:41:13 CDT)
Re: regarding resp-doubts Miguel de Federico (Thu Oct 03 2002 - 11:01:23 CDT)
Re: regarding resp-doubts David A. Case (Thu Oct 03 2002 - 11:10:48 CDT)
Re: regarding resp-doubts James W. Caldwell (Thu Oct 03 2002 - 11:35:26 CDT)
MM-GBSA and counterions Michael Ford (Thu Oct 03 2002 - 14:27:27 CDT)
Re: MM-GBSA and counterions David A. Case (Thu Oct 03 2002 - 15:43:35 CDT)
EGB = NaNQ Pratul Agarwal (Thu Oct 03 2002 - 16:05:55 CDT)
Re: xleap XENVIRONMENT Mark C. Ballew (Thu Oct 03 2002 - 16:09:25 CDT)
RE: RESP gaussian job crashing Nicholson, James D Mr ARO (Thu Oct 03 2002 - 16:57:46 CDT)
Re: RESP gaussian job crashing Carlos P. Sosa (Thu Oct 03 2002 - 17:39:59 CDT)
compiling SGI/mpi Ioana Cozmuta (Thu Oct 03 2002 - 20:16:38 CDT)
RE:SAMUEL METU sam_008_at_www.com (Thu Oct 03 2002 - 20:46:50 CDT)
RE:SAMUEL METU sam_008_at_www.com (Thu Oct 03 2002 - 20:46:51 CDT)
Re: compiling SGI/mpi David A. Case (Thu Oct 03 2002 - 20:50:11 CDT)
Re: compiling SGI/mpi Ioana Cozmuta (Thu Oct 03 2002 - 22:09:02 CDT)
RMSD calculation question Soonmin Jang (Fri Oct 04 2002 - 02:02:37 CDT)
Re: RESP gaussian job crashing David Smith (Fri Oct 04 2002 - 07:08:53 CDT)
Re: About the Memory allocation in MM_PBSA and SANDER Alan Leo (Fri Oct 04 2002 - 07:46:15 CDT)
Different numbers on different architectures. David Smith (Fri Oct 04 2002 - 08:33:24 CDT)
Re: compiling SGI/mpi David A. Case (Fri Oct 04 2002 - 10:07:23 CDT)
NTX / IREST inconsistency Bimo Ario Tejo (Fri Oct 04 2002 - 10:11:59 CDT)
Re: EGB = NaNQ Andreas Svrcek-Seiler (Fri Oct 04 2002 - 10:30:50 CDT)
Re: NTX / IREST inconsistency David A. Case (Fri Oct 04 2002 - 10:35:07 CDT)
Re: Different numbers on different architectures. David A. Case (Fri Oct 04 2002 - 11:26:07 CDT)
Re: EGB = NaNQ Pratul Agarwal (Fri Oct 04 2002 - 15:26:47 CDT)
(no subject) Ioana Cozmuta (Fri Oct 04 2002 - 19:12:44 CDT)
what are "end group interactions"? C. Klein (Mon Oct 07 2002 - 03:43:00 CDT)
How to generate PNA structure? A. Hungie (Mon Oct 07 2002 - 03:51:53 CDT)
xleap on a SGI Fuel Giulio Rastelli (Mon Oct 07 2002 - 09:50:39 CDT)
MACHINE file for Tru64 ES45 CUI, Guanglei (Mon Oct 07 2002 - 14:20:19 CDT)
geometry optimization/turning off Elec and Vdw terms Tom Bishop (Mon Oct 07 2002 - 15:17:52 CDT)
Re: geometry optimization/turning off Elec and Vdw terms Margaret Cheung (Mon Oct 07 2002 - 17:26:01 CDT)
AMBER6 on cluster Mako Furukawa (Mon Oct 07 2002 - 19:12:28 CDT)
Re: AMBER6 on cluster Mako Furukawa (Mon Oct 07 2002 - 19:43:31 CDT)
Re: xleap on a SGI Fuel David A. Case (Mon Oct 07 2002 - 21:50:33 CDT)
2D RMSd Luo Liu (Tue Oct 08 2002 - 03:32:34 CDT)
Re: MACHINE file for Tru64 ES45 Chuck Schneider (Tue Oct 08 2002 - 06:28:45 CDT)
Re: MACHINE file for Tru64 ES45 CUI, Guanglei (Tue Oct 08 2002 - 08:47:16 CDT)
do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ? hagop demirdjian (Tue Oct 08 2002 - 09:51:50 CDT)
crdgrow Ioana Cozmuta (Tue Oct 08 2002 - 12:19:23 CDT)
Re: crdgrow Sanjeev B.S. (Tue Oct 08 2002 - 12:24:09 CDT)
rdparm Ioana Cozmuta (Tue Oct 08 2002 - 12:33:41 CDT)
(no subject) kbyun_at_wesleyan.edu (Tue Oct 08 2002 - 13:10:53 CDT)
LINMIN FAILURE hung_at_atc.atccu.chula.ac.th (Tue Oct 08 2002 - 19:41:00 CDT)
Re: crdgrow David A. Case (Tue Oct 08 2002 - 20:17:45 CDT)
Re: LINMIN FAILURE David A. Case (Tue Oct 08 2002 - 20:33:07 CDT)
Re: rdparm Elsa de Sousa Henriques (Tue Oct 08 2002 - 21:40:58 CDT)
Re: reaction field energy of a ligand in MM-PBSA Lepsa (Wed Oct 09 2002 - 08:19:56 CDT)
Re: SHAKE problem Pratul Agarwal (Wed Oct 09 2002 - 08:39:55 CDT)
nmr and positional restraint in input Peter Varnai (Wed Oct 09 2002 - 12:44:03 CDT)
reaction field energy of a ligand in MM-PBSA Giulio Rastelli (Wed Oct 09 2002 - 13:04:10 CDT)
about dummy parameter of multiplicity sxzheng (Thu Oct 10 2002 - 02:55:15 CDT)
Re: nmr and positional restraint in input Christoph Brockmann (Thu Oct 10 2002 - 04:12:49 CDT)
MM-PBSA tutorial Giulio Rastelli (Thu Oct 10 2002 - 09:22:59 CDT)
trouble with snapshots GC option of MM_PBSA Michael Ford (Thu Oct 10 2002 - 09:23:24 CDT)
Re: trouble with snapshots GC option of MM_PBSA Michael Ford (Thu Oct 10 2002 - 09:31:05 CDT)
Re: trouble with snapshots GC option of MM_PBSA - Now no output for lig and rec Michael Ford (Thu Oct 10 2002 - 10:10:35 CDT)
solved: nmr and positional restraint in input Peter Varnai (Thu Oct 10 2002 - 10:26:27 CDT)
[Fwd: Re: trouble with snapshots GC option of MM_PBSA] Holger Gohlke (Thu Oct 10 2002 - 11:15:39 CDT)
IBELLY and NMROPT in sander Tom Bishop (Thu Oct 10 2002 - 11:54:43 CDT)
Dielectric constant for interior of proteins Pratul Agarwal (Thu Oct 10 2002 - 12:53:59 CDT)
Re: Dielectric constant for interior of proteins David A. Case (Thu Oct 10 2002 - 13:33:19 CDT)
Re: about dummy parameter of multiplicity David A. Case (Thu Oct 10 2002 - 13:37:40 CDT)
Re: MM-PBSA tutorial Holger Gohlke (Thu Oct 10 2002 - 13:57:41 CDT)
Re: Dielectric constant for interior of proteins Pratul Agarwal (Thu Oct 10 2002 - 14:25:51 CDT)
How to do 2dRMS in ptraj Ying Zhao (Thu Oct 10 2002 - 14:33:43 CDT)
question about antibodies Ioana Cozmuta (Thu Oct 10 2002 - 15:05:25 CDT)
Some error message on Leap Sichun Yang (Thu Oct 10 2002 - 15:15:43 CDT)
Re: Some error message on Leap Michael Ford (Thu Oct 10 2002 - 16:27:03 CDT)
Re: Some error message on Leap Ioana Cozmuta (Thu Oct 10 2002 - 17:22:51 CDT)
docking in amber? Sichun Yang (Thu Oct 10 2002 - 18:44:45 CDT)
problem in sander Ioana Cozmuta (Thu Oct 10 2002 - 21:11:06 CDT)
Re: problem in sander David A. Case (Fri Oct 11 2002 - 10:00:53 CDT)
volume of ucell too big!! sxzheng (Fri Oct 11 2002 - 10:06:52 CDT)
period boundary Shunzhou Wan (Fri Oct 11 2002 - 10:50:39 CDT)
DNA Tutorial: min_ntr.in Joel Konkle-Parker (Fri Oct 11 2002 - 17:28:47 CDT)
perturbation of gln to glu M. L. Dodson (Sun Oct 13 2002 - 19:02:00 CDT)
Re: MM-PBSA tutorial Lepsa (Mon Oct 14 2002 - 02:14:47 CDT)
MM-PBSA and Insight's version of Delphi Emma.Sigfridsson_at_astrazeneca.com (Mon Oct 14 2002 - 02:47:21 CDT)
pressure variation coupled with taup value Vlad Cojocaru (Mon Oct 14 2002 - 04:36:42 CDT)
loss of disulfide bonds Nicolas Le Novere (Mon Oct 14 2002 - 10:31:23 CDT)
Re: loss of disulfide bonds Holger Gohlke (Mon Oct 14 2002 - 10:51:01 CDT)
Re: loss of disulfide bonds David A. Case (Mon Oct 14 2002 - 11:04:30 CDT)
Re: loss of disulfide bonds Natasja Brooijmans (Mon Oct 14 2002 - 11:46:54 CDT)
Re: loss of disulfide bonds Carlos Simmerling (Mon Oct 14 2002 - 11:49:15 CDT)
Re: loss of disulfide bonds James W. Caldwell (Mon Oct 14 2002 - 12:28:15 CDT)
Re: loss of disulfide bonds Richard Henchman (Mon Oct 14 2002 - 12:44:30 CDT)
CH2Cl2 box Eric ARNOULT (Mon Oct 14 2002 - 12:51:21 CDT)
Re: loss of disulfide bonds David A. Case (Mon Oct 14 2002 - 13:10:50 CDT)
Potential bug in gbsa.h of sander-7 Vlad (Mon Oct 14 2002 - 19:35:58 CDT)
Compiler & Hardware requirement of AMBER7 ? yuann (Mon Oct 14 2002 - 23:08:12 CDT)
Re: Compiler & Hardware requirement of AMBER7 ? David Case (Tue Oct 15 2002 - 00:51:43 CDT)
Computational alchemy Aldo Jongejan (Tue Oct 15 2002 - 05:52:12 CDT)
new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 06:13:49 CDT)
new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 06:42:50 CDT)
Dummy torsions Aldo Jongejan (Tue Oct 15 2002 - 08:33:02 CDT)
Error in Antechamber program in ammber7 Narang Manpreet Kaur (Tue Oct 15 2002 - 09:49:52 CDT)
Re: Error in Antechamber program in ammber7 Lepsa (Tue Oct 15 2002 - 10:07:57 CDT)
Re: Dummy torsions David A. Case (Tue Oct 15 2002 - 10:25:41 CDT)
Re: Error in Antechamber program in ammber7 David A. Case (Tue Oct 15 2002 - 10:33:09 CDT)
Bug in reading binary restart file with BOX parameters Vlad (Tue Oct 15 2002 - 21:58:54 CDT)
Re: Error in Antechamber program in ammber7 Narang Manpreet Kaur (Wed Oct 16 2002 - 00:01:45 CDT)
dummy parameters Pierre Mignon (Wed Oct 16 2002 - 02:10:46 CDT)
How to specify the counterion positions using xleap? A.Madhumalar (Wed Oct 16 2002 - 07:54:41 CDT)
Re: Error in Antechamber program in ammber7 David A. Case (Wed Oct 16 2002 - 10:04:40 CDT)
Re: How to specify the counterion positions using xleap? David A. Case (Wed Oct 16 2002 - 10:09:21 CDT)
Can I use belly and ntr at the same time? sxzheng (Wed Oct 16 2002 - 10:21:10 CDT)
Re: Bug in reading binary restart file with BOX parameters David A. Case (Wed Oct 16 2002 - 10:27:51 CDT)
Re: How to specify the counterion positions using xleap? James W. Caldwell (Wed Oct 16 2002 - 10:28:06 CDT)
Re: Can I use belly and ntr at the same time? David A. Case (Wed Oct 16 2002 - 10:45:49 CDT)
Molecular Dynamic procedure... Andrei Leitão (Wed Oct 16 2002 - 10:48:10 CDT)
How to convert oldparmtop to newparmtop? A.Madhumalar (Wed Oct 16 2002 - 12:18:35 CDT)
error message Vlad Cojocaru (Wed Oct 16 2002 - 12:25:01 CDT)
more information about the previous email Vlad Cojocaru (Wed Oct 16 2002 - 12:26:43 CDT)
Re: error message Holger Gohlke (Wed Oct 16 2002 - 12:38:34 CDT)
Re: How to specify the counterion positions using xleap? Ioana Cozmuta (Wed Oct 16 2002 - 12:45:06 CDT)
Re: error message Natasja Brooijmans (Wed Oct 16 2002 - 12:48:41 CDT)
restraining atoms Ioana Cozmuta (Wed Oct 16 2002 - 12:56:10 CDT)
Re: error message Margaret Cheung (Wed Oct 16 2002 - 12:56:50 CDT)
Re: error message Andreas Svrcek-Seiler (Wed Oct 16 2002 - 12:58:18 CDT)
Re: How to convert oldparmtop to newparmtop? David A. Case (Wed Oct 16 2002 - 13:04:59 CDT)
IGB =4 with GAFF and bugfix24 incomplete? Tom Bishop (Wed Oct 16 2002 - 13:12:37 CDT)
syntax Ioana Cozmuta (Wed Oct 16 2002 - 13:14:54 CDT)
Re: confusing error messages David A. Case (Wed Oct 16 2002 - 13:42:15 CDT)
Re: IGB =4 with GAFF and bugfix24 incomplete? David A. Case (Wed Oct 16 2002 - 13:55:24 CDT)
Re: syntax David A. Case (Wed Oct 16 2002 - 13:57:44 CDT)
Re: error message Bill Ross (Wed Oct 16 2002 - 14:22:44 CDT)
Re: How to convert oldparmtop to newparmtop? Michael Ford (Wed Oct 16 2002 - 14:47:57 CDT)
Re: How to specify the counterion positions using xleap? M. L. Dodson (Wed Oct 16 2002 - 19:10:22 CDT)
Re: restraining atoms Lepsa (Thu Oct 17 2002 - 01:56:17 CDT)
Sir, Venkanna Belde (Thu Oct 17 2002 - 04:33:18 CDT)
Imaging & fitting in carnal Sanjeev B.S. (Thu Oct 17 2002 - 06:01:55 CDT)
Truncated Octahedron Box giudice (Thu Oct 17 2002 - 08:06:28 CDT)
a leap question Vlad Cojocaru (Thu Oct 17 2002 - 08:20:23 CDT)
Re: a leap question CUI, Guanglei (Thu Oct 17 2002 - 08:43:24 CDT)
Re: a leap question David A. Case (Thu Oct 17 2002 - 10:35:01 CDT)
dummy torsional parameters again. X. Tan (Thu Oct 17 2002 - 11:52:05 CDT)
Re: How to convert oldparmtop to newparmtop? A.Madhumalar (Thu Oct 17 2002 - 12:05:29 CDT)
sander6 running and crashing at PSC? CUI, Guanglei (Thu Oct 17 2002 - 12:17:40 CDT)
Re: restraining atoms Ioana Cozmuta (Thu Oct 17 2002 - 12:54:37 CDT)
Re: dummy torsional parameters again. David A. Case (Thu Oct 17 2002 - 12:58:38 CDT)
Solvent exposed surface area over a trajectory Rebecca Perlow (Thu Oct 17 2002 - 13:20:03 CDT)
Re: Solvent exposed surface area over a trajectory Michael Ford (Thu Oct 17 2002 - 14:09:17 CDT)
Re: Solvent exposed surface area over a trajectory Sanjeev B.S. (Thu Oct 17 2002 - 14:18:56 CDT)
Reference for GB model 2 Jianhui Wu (Thu Oct 17 2002 - 14:26:18 CDT)
Sander segmentation fault Joel Konkle-Parker (Thu Oct 17 2002 - 14:28:48 CDT)
Reference, GB 2, Amber7 Jianhui Wu (Thu Oct 17 2002 - 14:34:12 CDT)
Re: Solvent exposed surface area over a trajectory Natasja Brooijmans (Thu Oct 17 2002 - 14:35:34 CDT)
time averaged restraint parameters Jake Isaacs (Thu Oct 17 2002 - 15:09:59 CDT)
Re: Reference for GB model 2 Andreas Svrcek-Seiler (Thu Oct 17 2002 - 15:34:40 CDT)
cutoffs in GB David A. Case (Thu Oct 17 2002 - 16:08:16 CDT)
Carnal table output Christoph Brockmann (Fri Oct 18 2002 - 03:48:37 CDT)
targeted MD Giulio Rastelli (Fri Oct 18 2002 - 09:28:48 CDT)
Re: Carnal table output Holger Gohlke (Fri Oct 18 2002 - 10:20:57 CDT)
Re: targeted MD David A. Case (Fri Oct 18 2002 - 10:32:14 CDT)
Re: targeted MD Carlos Simmerling (Fri Oct 18 2002 - 10:45:33 CDT)
Not able to use xleap ... Stéphane Teletchéa (Fri Oct 18 2002 - 10:58:21 CDT)
Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 11:26:47 CDT)
Re: Not able to use xleap ... David A. Case (Fri Oct 18 2002 - 11:38:23 CDT)
Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 12:14:24 CDT)
Re: Not able to use xleap ... Stéphane Teletchéa (Fri Oct 18 2002 - 12:24:38 CDT)
allocation memory error Ioana Cozmuta (Fri Oct 18 2002 - 14:50:22 CDT)
Amber 4 question Tod Pascal (Fri Oct 18 2002 - 17:42:40 CDT)
RE: Not able to use xleap ... Ross Walker (Sat Oct 19 2002 - 04:51:30 CDT)
Re: targeted MD Peter VARNAI (Sat Oct 19 2002 - 09:26:30 CDT)
number of H-bonds Bimo Ario Tejo (Sat Oct 19 2002 - 23:54:44 CDT)
Re: number of H-bonds Sanjeev B.S. (Sun Oct 20 2002 - 00:14:32 CDT)
How to define a sphere to minimize? Guillermo Mulliert Carlín (Mon Oct 21 2002 - 01:46:57 CDT)
Re: Not able to use xleap ... Stéphane Teletchéa (Mon Oct 21 2002 - 02:08:12 CDT)
Re: How to define a sphere to minimize? David Smith (Mon Oct 21 2002 - 06:00:03 CDT)
Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 08:43:51 CDT)
Re: Not able to use xleap ... Stéphane Teletchéa (Mon Oct 21 2002 - 10:02:25 CDT)
Re: How to define a sphere to minimize? Bill Ross (Mon Oct 21 2002 - 10:11:19 CDT)
Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 10:33:23 CDT)
Re: reg: MAC OS David A. Case (Mon Oct 21 2002 - 11:11:56 CDT)
Re: reg: MAC OS Mengjuei Hsieh (Mon Oct 21 2002 - 13:13:35 CDT)
question on ouput of sander Sichun Yang (Mon Oct 21 2002 - 13:19:17 CDT)
Re: reg: MAC OS Prem Raj (Mon Oct 21 2002 - 13:19:40 CDT)
Re: question on ouput of sander CUI, Guanglei (Mon Oct 21 2002 - 13:43:40 CDT)
Re: question on ouput of sander Sichun Yang (Mon Oct 21 2002 - 13:45:29 CDT)
Re: question on ouput of sander David A. Case (Mon Oct 21 2002 - 13:59:27 CDT)
sander7: MPI_COMM_RANK problem Matteo Dal Peraro (Mon Oct 21 2002 - 14:17:14 CDT)
scaling of amber with number of atoms Marcela Madrid (Mon Oct 21 2002 - 14:23:59 CDT)
systems.Re: sander7: MPI_COMM_RANK problem Carlos P. Sosa (Mon Oct 21 2002 - 14:44:56 CDT)
problem with gibbs !!!! Asif Rahaman (Mon Oct 21 2002 - 21:18:10 CDT)
MM-PGBSA Question!! Bernd Wellenzohn (Tue Oct 22 2002 - 07:46:29 CDT)
Re: Compiler & Hardware requirement of AMBER7 ? yuann (Tue Oct 22 2002 - 09:30:34 CDT)
Re: problem with gibbs !!!! James W. Caldwell (Tue Oct 22 2002 - 09:34:23 CDT)
Re: MM-PGBSA Question!! David A. Case (Tue Oct 22 2002 - 09:45:20 CDT)
Amber Crd format Tod Pascal (Tue Oct 22 2002 - 13:21:05 CDT)
Re: Amber Crd format Natasja Brooijmans (Tue Oct 22 2002 - 14:04:43 CDT)
mm_pbsa-amber7 Sue Heavner (Tue Oct 22 2002 - 14:06:01 CDT)
replacing fft routines Florian Barth (Tue Oct 22 2002 - 15:08:14 CDT)
Re: allocation memory error Ioana Cozmuta (Tue Oct 22 2002 - 16:52:56 CDT)
Re: replacing fft routines David A. Case (Tue Oct 22 2002 - 17:58:34 CDT)
Dummy atoms... Miguel de Federico (Wed Oct 23 2002 - 02:44:34 CDT)
Re: Patching AMBER7 with #24 Lepsa (Wed Oct 23 2002 - 02:49:07 CDT)
Re: Patching AMBER7 with #24 Lepsa (Wed Oct 23 2002 - 10:23:14 CDT)
Re: Dummy atoms... David A. Case (Wed Oct 23 2002 - 11:35:31 CDT)
Amber6 and MPI Yu Chen (Wed Oct 23 2002 - 13:10:30 CDT)
Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 16:50:56 CDT)
Re: Antechamber generating bad charges w/ gaussian 98. James W. Caldwell (Wed Oct 23 2002 - 18:16:05 CDT)
min output Ioana Cozmuta (Wed Oct 23 2002 - 18:26:44 CDT)
Re: min output David A. Case (Wed Oct 23 2002 - 18:51:06 CDT)
RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:00:47 CDT)
RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:12:32 CDT)
SDS forcefield? Arvid Soederhaell (Thu Oct 24 2002 - 04:25:58 CDT)
Protein jump out, please help Lich Nguyen (Thu Oct 24 2002 - 04:45:45 CDT)
Re: min output James W. Caldwell (Thu Oct 24 2002 - 11:01:15 CDT)
Re: Protein jump out, please help Michael G Cooney (Thu Oct 24 2002 - 13:51:52 CDT)
carnal output trajectory Vlad Cojocaru (Thu Oct 24 2002 - 15:07:35 CDT)
Re: carnal output trajectory Margaret Cheung (Thu Oct 24 2002 - 15:57:50 CDT)
residue cross-correlation Bimo Ario Tejo (Thu Oct 24 2002 - 16:15:50 CDT)
Re: carnal output trajectory Bill Ross (Thu Oct 24 2002 - 16:26:15 CDT)
Re: HIS residues Ioana Cozmuta (Thu Oct 24 2002 - 16:51:40 CDT)
Re: HIS residues Natasja Brooijmans (Thu Oct 24 2002 - 18:09:55 CDT)
Re: Protein jump out, please help Lich Nguyen (Thu Oct 24 2002 - 22:21:40 CDT)
carnal output trajectory Vlad Cojocaru (Fri Oct 25 2002 - 04:50:55 CDT)
Re:SURFTEN for GB Lepsa (Fri Oct 25 2002 - 08:51:30 CDT)
Fw: Re:SURFTEN for GB Lepsa (Fri Oct 25 2002 - 08:55:12 CDT)
once again: residue cross-correlation Bimo Ario Tejo (Fri Oct 25 2002 - 09:39:40 CDT)
time correlation function Bimo Ario Tejo (Fri Oct 25 2002 - 09:47:28 CDT)
specification for memory requirement yuann (Fri Oct 25 2002 - 19:37:13 CDT)
Re: specification for memory requirement Carlos Simmerling (Fri Oct 25 2002 - 20:55:42 CDT)
2nd restart CUI, Guanglei (Sun Oct 27 2002 - 11:02:30 CST)
total energies during MM-PBSA Giulio Rastelli (Sun Oct 27 2002 - 12:20:19 CST)
Amber vijay dasa (Mon Oct 28 2002 - 00:51:02 CST)
Hello Amber, vijay dasa (Mon Oct 28 2002 - 04:20:24 CST)
leap - sander information flow Wiktor Jurkowski (Mon Oct 28 2002 - 06:34:51 CST)
Targeted MD Giulio Rastelli (Mon Oct 28 2002 - 15:44:05 CST)
Re: leap - sander information flow David A. Case (Mon Oct 28 2002 - 15:44:28 CST)
quasih Pratul Agarwal (Mon Oct 28 2002 - 16:25:02 CST)
Re: Targeted MD Carlos Simmerling (Mon Oct 28 2002 - 17:09:19 CST)
64-bit Compilation SUN's forte compiler Fernando Martin (Mon Oct 28 2002 - 17:15:52 CST)
Re: 64-bit Compilation SUN's forte compiler Ioana Cozmuta (Mon Oct 28 2002 - 17:33:49 CST)
Re: 64-bit Compilation SUN's forte compiler Scott Brozell (Mon Oct 28 2002 - 18:00:08 CST)
RE: 64-bit Compilation SUN's forte compiler Fernando Martin (Mon Oct 28 2002 - 18:24:21 CST)
Re: 64-bit Compilation SUN's forte compiler David A. Case (Mon Oct 28 2002 - 21:41:15 CST)
LEaP: The parm and coord files disagree on the number of atoms Miguel de Federico (Tue Oct 29 2002 - 02:24:58 CST)
FEP - ligand to nothing (or water)?? Aldo Jongejan (Tue Oct 29 2002 - 03:50:54 CST)
Re: FEP - ligand to nothing (or water)?? David A. Case (Tue Oct 29 2002 - 08:24:47 CST)
Re: LEaP: The parm and coord files disagree on the number of atoms James W. Caldwell (Tue Oct 29 2002 - 09:50:26 CST)
mm_pbsa curious output of coordinates and resulting errors... Michael Ford (Tue Oct 29 2002 - 16:01:43 CST)
mm_pbsa error message (warning?) Michael Ford (Tue Oct 29 2002 - 16:47:02 CST)
Problems with tes.antechamber Chen, Ya (Tue Oct 29 2002 - 19:21:59 CST)
Resp Multiconformational charge fitting! Marco Aurélio Correia Preto (Wed Oct 30 2002 - 05:50:52 CST)
carnal output trajectory Vlad Cojocaru (Wed Oct 30 2002 - 07:25:36 CST)
Re: carnal output trajectory Stéphane Teletchéa (Wed Oct 30 2002 - 07:50:19 CST)
Re: carnal output trajectory Sanjeev B.S. (Wed Oct 30 2002 - 07:50:45 CST)
Sander Recompilation for the Biotin-Streptavidin Tutorial? Thomas Steinbrecher (Wed Oct 30 2002 - 09:46:30 CST)
Re: carnal output trajectory Bill Ross (Wed Oct 30 2002 - 10:37:00 CST)
Charges derivation question! Marco Aurélio Correia Preto (Wed Oct 30 2002 - 10:39:24 CST)
Re: RESP-group constraint Marco Preto (Wed Oct 30 2002 - 10:50:21 CST)
IDECOMP Mark Hsieh (Wed Oct 30 2002 - 12:11:02 CST)
Re: IDECOMP Holger Gohlke (Wed Oct 30 2002 - 14:11:13 CST)
question on belly and restraint Sichun Yang (Wed Oct 30 2002 - 14:54:37 CST)
How to choose the box and cap size sxzheng (Thu Oct 31 2002 - 00:42:27 CST)
Re: time correlation function David A. Case (Thu Oct 31 2002 - 09:21:28 CST)
*.top file: "PARM-F-UHOSED, try again" david (Thu Oct 31 2002 - 11:17:18 CST)
Re: *.top file: "PARM-F-UHOSED, try again" David A. Case (Thu Oct 31 2002 - 11:19:06 CST)
Re: *.top file: "PARM-F-UHOSED, try again" Michael Ford (Thu Oct 31 2002 - 11:43:10 CST)
carnal Ioana Cozmuta (Thu Oct 31 2002 - 12:30:35 CST)
xleap and modified sugar residues Michael Ford (Thu Oct 31 2002 - 13:22:17 CST)
Re: xleap and modified sugar residues Holger Gohlke (Thu Oct 31 2002 - 13:54:23 CST)
NAV detected a virus in a document YOU sent to webmaster@nctimes.com. Mercury (Thu Oct 31 2002 - 21:12:51 CST)
flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 Pascal Bonnet (Fri Nov 01 2002 - 03:08:20 CST)
molsurf reference Giulio Rastelli (Fri Nov 01 2002 - 06:17:35 CST)
Re: molsurf reference David A. Case (Fri Nov 01 2002 - 07:46:21 CST)
Re: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 David A. Case (Fri Nov 01 2002 - 07:51:26 CST)
Re: carnal output trajectory Francesca Mocci (Fri Nov 01 2002 - 10:53:31 CST)
Re: total energies during MM-PBSA Lepsa (Fri Nov 01 2002 - 11:29:33 CST)
problem about cut and cap sxzheng (Sun Nov 03 2002 - 06:40:25 CST)
Re: carnal Stéphane Teletchéa (Mon Nov 04 2002 - 04:09:10 CST)
periodic box Craig A Bayse (Mon Nov 04 2002 - 10:49:53 CST)
P4_GLOBMEMSIZE problem Jean-Christophe Ducom (Mon Nov 04 2002 - 11:33:19 CST)
Re: periodic box David A. Case (Mon Nov 04 2002 - 12:32:11 CST)
Visualizing AMBER coordinates trajectory in VMD Pratul Agarwal (Mon Nov 04 2002 - 14:54:57 CST)
restart Ioana Cozmuta (Mon Nov 04 2002 - 14:57:16 CST)
Re: Visualizing AMBER coordinates trajectory in VMD David A. Case (Mon Nov 04 2002 - 15:57:10 CST)
Re: restart David A. Case (Mon Nov 04 2002 - 15:59:15 CST)
RUNMIN hung_at_atc.atccu.chula.ac.th (Mon Nov 04 2002 - 19:04:23 CST)
Re: RUNMIN Ioana Cozmuta (Mon Nov 04 2002 - 19:37:08 CST)
procheck hung_at_atc.atccu.chula.ac.th (Tue Nov 05 2002 - 00:53:56 CST)
pseudoatoms and NMR restraints david (Tue Nov 05 2002 - 03:46:42 CST)
Re: Visualizing AMBER coordinates trajectory in VMD Tom Bishop (Tue Nov 05 2002 - 05:36:41 CST)
CCl4 as solvent Aldo Jongejan (Tue Nov 05 2002 - 07:44:02 CST)
Snapshot stuff Layi Adekoya (Tue Nov 05 2002 - 08:32:11 CST)
Re: pseudoatoms and NMR restraints David A. Case (Tue Nov 05 2002 - 10:06:07 CST)
Re: equilibrium problem about cut and belly David A. Case (Tue Nov 05 2002 - 10:14:51 CST)
Re: torsion restraints in GIBBS David A. Case (Tue Nov 05 2002 - 10:20:57 CST)
Re: procheck David A. Case (Tue Nov 05 2002 - 10:31:31 CST)
RE: P4_GLOBMEMSIZE problem Ross Walker (Tue Nov 05 2002 - 11:16:55 CST)
Re: equilibrium problem about cut and belly Thomas Steinbrecher (Tue Nov 05 2002 - 11:24:54 CST)
Re: P4_GLOBMEMSIZE problem Jean-Christophe Ducom (Tue Nov 05 2002 - 11:53:11 CST)
entropy calcs in mm_pbsa giulio_at_unimo.it (Tue Nov 05 2002 - 14:21:00 CST)
Re: entropy calcs in mm_pbsa Holger Gohlke (Tue Nov 05 2002 - 15:27:39 CST)
RE: P4_GLOBMEMSIZE problem Ross Walker (Tue Nov 05 2002 - 17:04:03 CST)
torsion restraints in GIBBS Jose Ramon Blas (Tue Nov 05 2002 - 18:35:44 CST)
amber on RH8 chernhoe (Wed Nov 06 2002 - 01:23:18 CST)
Bugfixes William Wei (Wed Nov 06 2002 - 03:50:35 CST)
average and runningaverage in ptraj Vlad Cojocaru (Wed Nov 06 2002 - 09:40:51 CST)
Re: average and runningaverage in ptraj Holger Gohlke (Wed Nov 06 2002 - 10:56:23 CST)
Re: average and runningaverage in ptraj Thomas Cheatham (Wed Nov 06 2002 - 11:36:56 CST)
time-averaged restraint developer Jake Isaacs (Wed Nov 06 2002 - 16:20:11 CST)
restrt format problem Marcela Madrid (Wed Nov 06 2002 - 16:48:02 CST)
nbflag Ioana Cozmuta (Wed Nov 06 2002 - 21:19:26 CST)
nbflag Ioana Cozmuta (Wed Nov 06 2002 - 21:45:02 CST)
Re: amber on RH8 chernhoe (Wed Nov 06 2002 - 22:43:41 CST)
surface Ioana Cozmuta (Thu Nov 07 2002 - 15:03:56 CST)
Re: amber on RH8 Scott Brozell (Thu Nov 07 2002 - 15:13:14 CST)
averaging with ptraj and carnal Vlad Cojocaru (Fri Nov 08 2002 - 06:31:03 CST)
ramdomized start velocities Arvid Soederhaell (Fri Nov 08 2002 - 06:35:23 CST)
Sander: check COM velocity, temp: 0.000000 0.00(Removed) Miguel de Federico de la Rúa (Fri Nov 08 2002 - 08:08:38 CST)
more about averaging Vlad Cojocaru (Fri Nov 08 2002 - 08:12:00 CST)
residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 09:00:01 CST)
Roar capabilities M. L. Dodson (Fri Nov 08 2002 - 11:37:48 CST)
residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 12:57:48 CST)
Re: ramdomized start velocities David A. Case (Fri Nov 08 2002 - 13:20:54 CST)
Re: ramdomized start velocities Andy Purkiss (Fri Nov 08 2002 - 13:28:46 CST)
Re: residue cross-correlation Andreas Svrcek-Seiler (Fri Nov 08 2002 - 14:16:59 CST)
Re: ramdomized start velocities James W. Caldwell (Fri Nov 08 2002 - 14:35:39 CST)
Re: residue cross-correlation Thomas Cheatham (Fri Nov 08 2002 - 14:50:42 CST)
Re: more about averaging Bill Ross (Fri Nov 08 2002 - 15:21:39 CST)
Problem in run Monica (Fri Nov 08 2002 - 22:41:52 CST)
Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) Thomas Cheatham (Fri Nov 08 2002 - 23:49:21 CST)
MEP g98_option FyD (Sat Nov 09 2002 - 00:35:22 CST)
Re: Problem in run Monica Jain (Sat Nov 09 2002 - 00:52:46 CST)
Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) David Case (Sat Nov 09 2002 - 01:17:18 CST)
Re: Problem in run David Case (Sat Nov 09 2002 - 01:33:27 CST)
Forwarded mail.... Narang Manpreet Kaur (Sat Nov 09 2002 - 03:56:37 CST)
drifting from average structure Vlad Cojocaru (Sat Nov 09 2002 - 10:17:38 CST)
carnal7 produces memory fault and a core Giulio Rastelli (Sat Nov 09 2002 - 10:21:10 CST)
belly and EWALD in amber7 Zhang Jian (Sat Nov 09 2002 - 21:04:14 CST)
Re: belly and EWALD in amber7 darden (Sun Nov 10 2002 - 16:25:31 CST)
Re: belly and ivcap conflict in gibbs David A. Case (Sun Nov 10 2002 - 16:35:16 CST)
Re: Forwarded mail.... David A. Case (Sun Nov 10 2002 - 16:40:19 CST)
Re: belly and EWALD in amber7 Zhang Jian (Sun Nov 10 2002 - 19:36:25 CST)
.top files read into xLeap? Arvid Soederhaell (Mon Nov 11 2002 - 04:24:00 CST)
Re: MEP g98_option Pascal Bonnet (Mon Nov 11 2002 - 05:05:55 CST)
nonpeoridic boundary + mm/gbsa Yongjun Jiang (Mon Nov 11 2002 - 06:49:03 CST)
Re: nonpeoridic boundary + mm/gbsa Holger Gohlke (Mon Nov 11 2002 - 10:59:27 CST)
saveAmberParm of leap Sichun Yang (Mon Nov 11 2002 - 13:27:16 CST)
Re: saveAmberParm of leap David A. Case (Mon Nov 11 2002 - 18:05:15 CST)
Re: .top files read into xLeap? David A. Case (Mon Nov 11 2002 - 20:20:41 CST)
Re: residue cross-correlation Stéphane Teletchéa (Tue Nov 12 2002 - 04:57:10 CST)
problem in PME Monica (Tue Nov 12 2002 - 07:42:21 CST)
Re: problem in PME David A. Case (Tue Nov 12 2002 - 08:06:47 CST)
RE: problem in PME Kristina Furse (Tue Nov 12 2002 - 10:43:03 CST)
re: the removal of global motion Shixiang Yan (Tue Nov 12 2002 - 10:44:38 CST)
NMR restraints on a 10-mer DNA in Sander Jo.Vinje_at_kj.uib.no (Tue Nov 12 2002 - 11:34:55 CST)
Re: NMR restraints on a 10-mer DNA in Sander Michael G Cooney (Tue Nov 12 2002 - 14:16:32 CST)
Amber7/CYGWIN compiling James W. Caldwell (Tue Nov 12 2002 - 15:09:33 CST)
Re: problem in PME David A. Case (Tue Nov 12 2002 - 17:16:52 CST)
Re: the removal of global motion David A. Case (Tue Nov 12 2002 - 17:25:09 CST)
Re: NMR restraints on a 10-mer DNA in Sander David A. Case (Tue Nov 12 2002 - 17:30:52 CST)
Re: the removal of global motion Ioana Cozmuta (Tue Nov 12 2002 - 17:52:41 CST)
Re: the removal of global motion David A. Case (Tue Nov 12 2002 - 18:18:31 CST)
help! Non bond list overflow! Zhang Jian (Wed Nov 13 2002 - 04:56:39 CST)
help on VMD movie Zhang Jian (Wed Nov 13 2002 - 06:44:36 CST)
Re: help on VMD movie Stéphane Teletchéa (Wed Nov 13 2002 - 07:12:58 CST)
Re: help on VMD movie Francesca Mocci (Wed Nov 13 2002 - 08:28:06 CST)
Ewald Monica (Wed Nov 13 2002 - 09:20:23 CST)
Re: help on VMD movie Zhang Jian (Wed Nov 13 2002 - 09:21:30 CST)
Re: Ewald David A. Case (Wed Nov 13 2002 - 10:09:08 CST)
CMM method Ioana Cozmuta (Wed Nov 13 2002 - 16:57:10 CST)
Re: CMM method David A. Case (Wed Nov 13 2002 - 18:42:26 CST)
Re: help! Non bond list overflow! David A. Case (Wed Nov 13 2002 - 18:51:07 CST)
Re: help on VMD movie Zhang Jian (Wed Nov 13 2002 - 19:40:14 CST)
Re: input format for gibbs restraints David A. Case (Wed Nov 13 2002 - 19:53:27 CST)
Re: help! Non bond list overflow! Zhang Jian (Wed Nov 13 2002 - 20:10:02 CST)
Re: help! Non bond list overflow! Jian Zhang (Wed Nov 13 2002 - 20:32:01 CST)
input format for gibbs restraints Jose Ramon Blas (Wed Nov 13 2002 - 20:59:43 CST)
(no subject) Monica (Thu Nov 14 2002 - 00:26:57 CST)
restart mm_pbsa Layi Adekoya (Thu Nov 14 2002 - 07:02:51 CST)
Re: restart mm_pbsa Lepsa (Thu Nov 14 2002 - 07:52:22 CST)
Re: restart mm_pbsa Pascal Bonnet (Thu Nov 14 2002 - 09:13:06 CST)
Amber on PC-Linux Philippe Aplincourt (Thu Nov 14 2002 - 09:22:20 CST)
error in reading .crd file with GIBBS hagop demirdjian (Thu Nov 14 2002 - 09:40:32 CST)
Re: your mail David A. Case (Thu Nov 14 2002 - 10:00:48 CST)
Linmin question... Andrei Leitão (Thu Nov 14 2002 - 12:10:21 CST)
Linmin question... Andrei Leitão (Thu Nov 14 2002 - 12:13:01 CST)
Amber Perl module Tod Pascal (Thu Nov 14 2002 - 15:33:01 CST)
Re: Amber Perl module Luis Gracia (Thu Nov 14 2002 - 15:55:25 CST)
Re: Amber Perl module Michael Ford (Thu Nov 14 2002 - 17:26:24 CST)
non-zero 10-12 coefficient Anonymous (Thu Nov 14 2002 - 18:18:34 CST)
Re: Linmin question... David A. Case (Fri Nov 15 2002 - 02:12:20 CST)
simulating dna Tod Pascal (Fri Nov 15 2002 - 19:23:54 CST)
polarizabitlity X. Tan (Fri Nov 15 2002 - 19:41:37 CST)
Re: question David A. Case (Fri Nov 15 2002 - 20:45:34 CST)
Re: question Ioana Cozmuta (Fri Nov 15 2002 - 21:22:13 CST)
RE: question Yong Duan (Fri Nov 15 2002 - 22:40:56 CST)
Conterions Monica (Sat Nov 16 2002 - 02:10:15 CST)
(no subject) Narang Manpreet Kaur (Sat Nov 16 2002 - 04:17:02 CST)
Re: your mail David Case (Sat Nov 16 2002 - 09:43:29 CST)
Re: Conterions David Case (Sat Nov 16 2002 - 13:45:01 CST)
Are posters to the Amber list being spammed? Nicholson, James D Mr ARO (Sun Nov 17 2002 - 19:48:15 CST)
choose dt in gibbs sxzheng (Sun Nov 17 2002 - 21:06:34 CST)
NATOM mismatch in coord and topology files. Narang Manpreet Kaur (Mon Nov 18 2002 - 00:49:46 CST)
creating a pdb trajectory with carnal Vlad Cojocaru (Mon Nov 18 2002 - 09:29:21 CST)
makeDIST_RST? Sichun Yang (Mon Nov 18 2002 - 17:44:09 CST)
Re: makeDIST_RST? David A. Case (Mon Nov 18 2002 - 18:15:35 CST)
Re: EWALD crash David A. Case (Mon Nov 18 2002 - 18:27:37 CST)
Re: simulating dna David A. Case (Mon Nov 18 2002 - 18:29:22 CST)
Re: polarizabitlity David A. Case (Mon Nov 18 2002 - 18:44:10 CST)
defining groups on dif. sets in carnal Vlad Cojocaru (Tue Nov 19 2002 - 04:59:06 CST)
Re: question Stéphane Teletchéa (Tue Nov 19 2002 - 06:43:04 CST)
limit of RMSD value Bimo Ario Tejo (Tue Nov 19 2002 - 07:57:40 CST)
FEP/Gibbs question meiselba (Tue Nov 19 2002 - 09:29:07 CST)
GIBBS - Error message. Miguel de Federico (Tue Nov 19 2002 - 10:00:25 CST)
Re: GIBBS - Error message. David A. Case (Tue Nov 19 2002 - 11:09:09 CST)
Re: limit of RMSD value Thomas Cheatham (Tue Nov 19 2002 - 11:51:53 CST)
Re: polarizabitlity X. Tan (Tue Nov 19 2002 - 12:08:31 CST)
Frictional forces in gB Kristina Furse (Tue Nov 19 2002 - 17:41:32 CST)
Nz-Acetyllysine parameters Luis Gracia (Tue Nov 19 2002 - 18:08:13 CST)
intdiel & extdiel Fredrick Robin Devadoss (Wed Nov 20 2002 - 05:23:59 CST)
Re: intdiel & extdiel David A. Case (Wed Nov 20 2002 - 09:51:44 CST)
Bulk Email Sending & Bullet Proof Web Hosting pposton (Wed Nov 20 2002 - 16:25:53 CST)
Re: intdiel & extdiel Fredrick Robin Devadoss (Wed Nov 20 2002 - 22:28:35 CST)
P.3 in antechamber Giulio Rastelli (Thu Nov 21 2002 - 05:02:16 CST)
PARMSET sara nunez (Thu Nov 21 2002 - 08:08:12 CST)
RE: PARMSET Ross Walker (Thu Nov 21 2002 - 08:30:36 CST)
Re: intdiel & extdiel Holger Gohlke (Thu Nov 21 2002 - 09:55:15 CST)
Re: PARMSET David A. Case (Thu Nov 21 2002 - 10:13:38 CST)
ion distances Marcela Madrid (Thu Nov 21 2002 - 14:59:12 CST)
targeted MD for more than 2 groups Sichun Yang (Thu Nov 21 2002 - 15:20:44 CST)
Re: PARMSET John Bushnell (Thu Nov 21 2002 - 16:32:25 CST)
Re: ion distances ë‚¨ê¸°ì—½ (Thu Nov 21 2002 - 16:52:55 CST)
Restraint Ambiguities Neema Salimi (Thu Nov 21 2002 - 16:56:44 CST)
Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu (Thu Nov 21 2002 - 17:10:39 CST)
Re: ion distances Thomas E. Cheatham, III (Thu Nov 21 2002 - 17:54:46 CST)
Re: targeted MD for more than 2 groups Carlos Simmerling (Thu Nov 21 2002 - 17:54:53 CST)
Re: Error running AMBER6 on Beowulf cluster David A. Case (Thu Nov 21 2002 - 19:31:47 CST)
Re: Restraint Ambiguities David A. Case (Thu Nov 21 2002 - 20:08:04 CST)
Re: Restraint Ambiguities Neema Salimi (Thu Nov 21 2002 - 22:37:13 CST)
Equilibration output Amber7 Fredrick Robin Devadoss (Fri Nov 22 2002 - 03:42:32 CST)
Re: Equilibration output Amber7 Guanglei Cui (Fri Nov 22 2002 - 08:42:02 CST)
Re: Restraint Ambiguities David A. Case (Fri Nov 22 2002 - 10:33:34 CST)
problem in restrt Marcela Madrid (Fri Nov 22 2002 - 10:37:53 CST)
Re: Equilibration output Amber7 Thomas Cheatham (Fri Nov 22 2002 - 11:49:55 CST)
Re: problem in restrt Thomas Cheatham (Fri Nov 22 2002 - 11:55:27 CST)
restarting simulation Marcela Madrid (Fri Nov 22 2002 - 14:06:42 CST)
Re: restarting simulation Guanglei Cui (Fri Nov 22 2002 - 14:50:05 CST)
Re: restarting simulation Carlos Simmerling (Fri Nov 22 2002 - 14:56:24 CST)
solvateOct Kristina Furse (Fri Nov 22 2002 - 15:36:33 CST)
Re: Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu (Fri Nov 22 2002 - 15:38:12 CST)
Re: restarting simulation Marcela Madrid (Fri Nov 22 2002 - 16:07:47 CST)
leap for peptide Sichun Yang (Fri Nov 22 2002 - 16:33:51 CST)
Re: Error running AMBER6 on Beowulf cluster Carlos Simmerling (Fri Nov 22 2002 - 17:33:49 CST)
ntx=7, irest=0 Marcela Madrid (Fri Nov 22 2002 - 17:56:00 CST)
pdb file Ioana Cozmuta (Fri Nov 22 2002 - 18:41:01 CST)
Re: pdb file Ioana Cozmuta (Fri Nov 22 2002 - 19:44:22 CST)
Re: solvateOct David A. Case (Fri Nov 22 2002 - 20:31:03 CST)
Re: ntx=7, irest=0 David A. Case (Fri Nov 22 2002 - 20:36:28 CST)
Re: ntx=7, irest=0, redux David Case (Sat Nov 23 2002 - 00:53:37 CST)
(no subject) Narang Manpreet Kaur (Sat Nov 23 2002 - 04:40:12 CST)
Calculating atomic charges for AMBER with Gaussian98W Thomas Steinbrecher (Sat Nov 23 2002 - 07:52:47 CST)
Re: Calculating atomic charges for AMBER with Gaussian98W M. L. Dodson (Sat Nov 23 2002 - 09:36:27 CST)
Re: your mail darden (Sun Nov 24 2002 - 16:46:35 CST)
Hydrophobic protein in water Luo Liu (Sun Nov 24 2002 - 16:52:20 CST)
atom type not recognized by GB eric hu (Sun Nov 24 2002 - 19:05:59 CST)
Re: atom type not recognized by GB David A. Case (Sun Nov 24 2002 - 19:50:01 CST)
Re: atom type not recognized by GB eric hu (Sun Nov 24 2002 - 20:30:17 CST)
Inquiry software_at_kagaku.com (Sun Nov 24 2002 - 21:44:51 CST)
(no subject) CHAUMONT Alain (Mon Nov 25 2002 - 09:32:50 CST)
using SHAKE for solvent only hagop demirdjian (Mon Nov 25 2002 - 09:42:57 CST)
Re: using SHAKE for solvent only David A. Case (Mon Nov 25 2002 - 12:17:54 CST)
external electric field Ioana Cozmuta (Mon Nov 25 2002 - 17:18:38 CST)
a second question Ioana Cozmuta (Mon Nov 25 2002 - 18:20:52 CST)
Re: ion distances Bill Ross (Mon Nov 25 2002 - 18:51:46 CST)
GIBBS - ERROR: Restraint read error from RSTIN; Check format: Miguel de Federico (Tue Nov 26 2002 - 03:14:19 CST)
Error in Equilibration Fredrick Robin Devadoss (Tue Nov 26 2002 - 04:14:12 CST)
RE: solvateOct Kristina Furse (Tue Nov 26 2002 - 16:51:52 CST)
Re: GIBBS - ERROR: Restraint read error from RSTIN; Check format: David A. Case (Tue Nov 26 2002 - 17:30:52 CST)
restrain a residue as center of mass eric hu (Tue Nov 26 2002 - 17:36:19 CST)
Re: solvateOct David A. Case (Tue Nov 26 2002 - 17:51:31 CST)
Re: restrain a residue as center of mass Carlos Simmerling (Tue Nov 26 2002 - 18:17:58 CST)
the tree name? Sichun Yang (Tue Nov 26 2002 - 21:29:27 CST)
Please help. Energy suddenly increase. Protein jump out Lich Nguyen (Wed Nov 27 2002 - 01:42:29 CST)
How Amber calculates electrostatic energy? Daniel Svozil (Wed Nov 27 2002 - 08:47:11 CST)
Re: Please help. Energy suddenly increase. Protein jump out David A. Case (Wed Nov 27 2002 - 10:26:55 CST)
esp.sh problem FyD (Wed Nov 27 2002 - 11:17:40 CST)
Re: esp.sh problem David Smith (Wed Nov 27 2002 - 12:13:09 CST)
Re: restrain a residue as center of mass eric hu (Wed Nov 27 2002 - 12:42:36 CST)
RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 12:42:39 CST)
Re: esp.sh problem David A. Case (Wed Nov 27 2002 - 13:12:54 CST)
Re: restrain a residue as center of mass Carlos Simmerling (Wed Nov 27 2002 - 15:34:00 CST)
Re: Please help. Energy suddenly increase. Protein jump out Carlos Simmerling (Wed Nov 27 2002 - 15:35:15 CST)
Re: restrain a residue as center of mass Carlos Simmerling (Wed Nov 27 2002 - 15:38:57 CST)
external electric field/another try Ioana Cozmuta (Wed Nov 27 2002 - 16:13:08 CST)
Re: the tree name? David A. Case (Wed Nov 27 2002 - 16:44:17 CST)
RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 16:52:54 CST)
Re: external electric field/another try darden (Wed Nov 27 2002 - 17:27:32 CST)
Re: external electric field/another try James W. Caldwell (Wed Nov 27 2002 - 17:31:24 CST)
Re: esp.sh problem FyD (Thu Nov 28 2002 - 02:03:33 CST)
C60 parameter vannajan_at_chiangmai.ac.th (Thu Nov 28 2002 - 02:47:47 CST)
Re: C60 parameter Pascal Bonnet (Thu Nov 28 2002 - 06:12:19 CST)
Problem Monica (Fri Nov 29 2002 - 00:35:19 CST)
parmchk -p option Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:09:09 CST)
parameters for cyclic nucleotides Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:11:43 CST)
(no subject) Narang Manpreet Kaur (Fri Nov 29 2002 - 04:54:03 CST)
Re: Problem David Case (Fri Nov 29 2002 - 13:49:20 CST)
Re: your mail David Case (Fri Nov 29 2002 - 14:07:19 CST)
Break down energy contributions Numan Oezguen (Fri Nov 29 2002 - 15:06:36 CST)
RE: solvateOct Kristina Furse (Sun Dec 01 2002 - 15:57:13 CST)
carnal amber 7.0 Vlad Cojocaru (Mon Dec 02 2002 - 02:35:34 CST)
combinig two trajectory files. Yongjun Jiang (Mon Dec 02 2002 - 06:18:29 CST)
Re: combinig two trajectory files. Carlos Simmerling (Mon Dec 02 2002 - 06:49:21 CST)
Re: combinig two trajectory files. Pascal Bonnet (Mon Dec 02 2002 - 06:50:26 CST)
Re: solvateOct David A. Case (Mon Dec 02 2002 - 09:40:02 CST)
err in specifying disulphide bridge using xleap! A.Madhumalar (Mon Dec 02 2002 - 10:25:30 CST)
LEAP - Introducing dummy atoms Miguel de Federico (Mon Dec 02 2002 - 10:42:49 CST)
Re: err in specifying disulphide bridge using xleap! David A. Case (Mon Dec 02 2002 - 11:05:01 CST)
penalty function in NMR refinement Mahadevan Seetharaman (Mon Dec 02 2002 - 11:09:05 CST)
Re: err in specifying disulphide bridge using xleap! James W. Caldwell (Mon Dec 02 2002 - 13:07:07 CST)
Re: LEAP - Introducing dummy atoms James W. Caldwell (Mon Dec 02 2002 - 13:11:27 CST)
Biphasic box (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:13:10 CST)
test mail Jim Caldwell (Tue Dec 03 2002 - 16:48:07 CST)
freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:10 CST)
Re: CCL:freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:21 CST)
Constraints in Amber (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:30 CST)
gB vs. explicit (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:53 CST)
Amber Trajectories + VMD (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:00 CST)
Energy decomposition with ANAL (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:05 CST)
Reflector problems amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 17:05:02 CST)
corrupted trajectory Guanglei Cui (Tue Dec 03 2002 - 17:07:46 CST)
Re: Biphasic box David A. Case (Tue Dec 03 2002 - 17:09:50 CST)
Re: freeware for RNA modeling on Linux (fwd) David A. Case (Tue Dec 03 2002 - 17:11:48 CST)
Re: Biphasic box (fwd) James W. Caldwell (Tue Dec 03 2002 - 17:15:50 CST)
Re: Constraints in Amber David A. Case (Tue Dec 03 2002 - 17:16:02 CST)
RE: Amber Trajectories + VMD (fwd) Nicholson, James D Mr ARO (Tue Dec 03 2002 - 17:35:09 CST)
Re: corrupted trajectory Shixiang Yan (Tue Dec 03 2002 - 17:36:37 CST)
increasing the number of processors Ioana Cozmuta (Tue Dec 03 2002 - 18:17:58 CST)
increasing the number of processors (fwd) Ioana Cozmuta (Tue Dec 03 2002 - 18:19:24 CST)
Re: corrupted trajectory CUI, Guanglei (Tue Dec 03 2002 - 20:04:13 CST)
Re: Biphasic box Gemma Kinsella (Wed Dec 04 2002 - 02:15:53 CST)
Re: gB vs. explicit David A. Case (Wed Dec 04 2002 - 10:28:43 CST)
Re: Energy decomposition with ANAL (fwd) David A. Case (Wed Dec 04 2002 - 10:31:52 CST)
restrained MD Vlad Cojocaru (Wed Dec 04 2002 - 12:18:54 CST)
DIANA like files Vlad Cojocaru (Wed Dec 04 2002 - 14:24:12 CST)
Amber 7 bugfix 27 !! urgent William Wei (Wed Dec 04 2002 - 14:45:13 CST)
Re: Amber 7 bugfix 27 !! urgent Holger Gohlke (Wed Dec 04 2002 - 15:18:48 CST)
MDaemon Warning - Virus Found postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 21:49:28 CST)
bug fixes Filip Lankas (Thu Dec 05 2002 - 08:48:00 CST)
not compiled with -DHAS_10_12!! William Wei (Thu Dec 05 2002 - 10:29:22 CST)
Re: bug fixes David A. Case (Thu Dec 05 2002 - 10:41:02 CST)
Re: not compiled with -DHAS_10_12!! Sarah Tschampel (Thu Dec 05 2002 - 10:43:40 CST)
Re: not compiled with -DHAS_10_12!! Carlos Simmerling (Thu Dec 05 2002 - 11:03:08 CST)
md failure: deep energetics problem eric hu (Thu Dec 05 2002 - 12:42:42 CST)
About counterions Andrei Leitão (Thu Dec 05 2002 - 13:10:30 CST)
Re: Cap-atom-pointer in GIBBS James W. Caldwell (Thu Dec 05 2002 - 13:23:45 CST)
Re: About counterions David A. Case (Thu Dec 05 2002 - 13:47:04 CST)
Cap-atom-pointer in GIBBS Jose Ramon Blas (Thu Dec 05 2002 - 13:50:45 CST)
Re: md failure: deep energetics problem David A. Case (Thu Dec 05 2002 - 13:55:40 CST)
ptraj rmsd calculation Thomas Steinbrecher (Thu Dec 05 2002 - 14:15:40 CST)
Overwrite files Joffre Heredia (Thu Dec 05 2002 - 14:25:33 CST)
Re: Overwrite files Long Hai (Thu Dec 05 2002 - 15:33:53 CST)
Re: Overwrite files Scott Brozell (Thu Dec 05 2002 - 15:39:23 CST)
RE: Overwrite files Yong Duan (Thu Dec 05 2002 - 20:41:37 CST)
timings? Arvid Soederhaell (Fri Dec 06 2002 - 02:51:10 CST)
positional restraints Vlad Cojocaru (Fri Dec 06 2002 - 06:55:05 CST)
Re: timings? David A. Case (Fri Dec 06 2002 - 09:46:27 CST)
Re: positional restraints David A. Case (Fri Dec 06 2002 - 10:05:02 CST)
Re: Energy decomposition with ANAL Numan Oezguen (Fri Dec 06 2002 - 11:08:20 CST)
Re: Energy decomposition with ANAL Natasja Brooijmans (Fri Dec 06 2002 - 11:24:21 CST)
default GB radii Robert G. Endres (Fri Dec 06 2002 - 15:00:31 CST)
Re: default GB radii David A. Case (Fri Dec 06 2002 - 15:11:13 CST)
carnal Ioana Cozmuta (Fri Dec 06 2002 - 17:47:56 CST)
Re: carnal Bill Ross (Fri Dec 06 2002 - 19:16:59 CST)
Re: default GB radii Andreas Svrcek-Seiler (Sat Dec 07 2002 - 06:02:09 CST)
(no subject) Jennifer Hawkings (Sat Dec 07 2002 - 16:48:46 CST)
CHARMm NPT input files Mahadevan Seetharaman (Sat Dec 07 2002 - 17:39:07 CST)
NMR restrains Marcela Madrid (Mon Dec 09 2002 - 14:33:31 CST)
running sander_classic for amber6 using different version of mpi Asif Rahaman (Mon Dec 09 2002 - 17:01:35 CST)
difference in energy in amber6 and amber7 Prabal Maiti (Mon Dec 09 2002 - 20:07:15 CST)
Question to perturbation charge meiselba (Tue Dec 10 2002 - 07:35:38 CST)
Re: FEP/Gibbs question Lepsa (Tue Dec 10 2002 - 09:59:39 CST)
dual H-bonding of bridging waters - CARNAL Michael Ford (Tue Dec 10 2002 - 18:16:24 CST)
bad protein structure eric hu (Tue Dec 10 2002 - 19:30:52 CST)
Re: bad protein structure Guanglei Cui (Tue Dec 10 2002 - 23:07:20 CST)
Re: difference in energy in amber6 and amber7 David A. Case (Wed Dec 11 2002 - 09:40:48 CST)
Fw: Charges derivation question! Lepsa (Wed Dec 11 2002 - 10:21:23 CST)
Re: CCL:Amber7 and partial charges David Case (Wed Dec 11 2002 - 12:07:10 CST)
MM-PBSA: .crg file for Delphi Thomas Steinbrecher (Wed Dec 11 2002 - 12:08:40 CST)
Re: MM-PBSA: .crg file for Delphi Holger Gohlke (Wed Dec 11 2002 - 12:31:07 CST)
Question on 2 stage RESP fit Ambarish Nag (Thu Dec 12 2002 - 00:39:08 CST)
Fw: Fw: Charges derivation question! Lepsa (Thu Dec 12 2002 - 03:55:17 CST)
Re: Question on 2 stage RESP fit M. L. Dodson (Thu Dec 12 2002 - 07:05:15 CST)
Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 CST)
MXVAR Guanglei Cui (Thu Dec 12 2002 - 10:34:17 CST)
Amber 7 MM-PBSA for Amber 6 trajectories Qing Zhang (Thu Dec 12 2002 - 13:52:23 CST)
ambpdb Vlad Cojocaru (Thu Dec 12 2002 - 16:01:23 CST)
Re: ambpdb Holger Gohlke (Thu Dec 12 2002 - 18:44:44 CST)
Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 CST)
GIBBS - end-of-file during read Miguel de Federico (Fri Dec 13 2002 - 04:12:48 CST)
plotting electrostatic potential surface Ioana Cozmuta (Fri Dec 13 2002 - 17:18:17 CST)
Re: ambpdb David A. Case (Fri Dec 13 2002 - 22:46:12 CST)
solvating a protein with large cavity Tom Bishop (Sat Dec 14 2002 - 09:42:38 CST)
Re: solvating a protein with large cavity M. L. Dodson (Sat Dec 14 2002 - 10:23:15 CST)
FEP/Gibbs question to valine alanine tutorial meiselba (Sat Dec 14 2002 - 10:58:12 CST)
Re: Amber 7 MM-PBSA for Amber 6 trajectories David A. Case (Sat Dec 14 2002 - 13:26:01 CST)
a question about force field in AMBER jzhou (Sat Dec 14 2002 - 19:55:15 CST)
Re: a question about force field in AMBER sychen (Sat Dec 14 2002 - 23:17:59 CST)
disulfide bond link between two chains pu xuemei (Mon Dec 16 2002 - 06:50:35 CST)
Fw: Valine to alanine Gibbs tutorial Lepsa (Mon Dec 16 2002 - 07:20:26 CST)
Re: disulfide bond link between two chains Natasja Brooijmans (Mon Dec 16 2002 - 07:49:46 CST)
Re: Energy decomposition with ANAL Numan Oezguen (Mon Dec 16 2002 - 09:49:08 CST)
Re: a question about force field in AMBER David A. Case (Mon Dec 16 2002 - 19:56:29 CST)
Re: freeware for RNA modeling on Linux (fwd) Joerg-Gerald Siebers (Mon Dec 16 2002 - 20:43:05 CST)
sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Tue Dec 17 2002 - 01:11:14 CST)
RST file for nonstandard residue vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 03:07:04 CST)
GIBBS - Routine TORCON (internal constraints) failed Miguel de Federico (Tue Dec 17 2002 - 09:29:04 CST)
Re: freeware for RNA modeling on Linux (fwd) James W. Caldwell (Tue Dec 17 2002 - 13:09:37 CST)
Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 13:47:59 CST)
Re: Chains, LEaP and ambpdb Ioana Cozmuta (Tue Dec 17 2002 - 15:07:24 CST)
Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 15:09:48 CST)
Re: Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 15:23:55 CST)
RE: sander (CAP) chokes on efc (Itanium2/Linux) Karen Haskell (Tue Dec 17 2002 - 16:05:31 CST)
water box, Ioana Cozmuta (Tue Dec 17 2002 - 17:18:31 CST)
solvatebox Luis Gracia (Tue Dec 17 2002 - 18:52:07 CST)
Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 21:28:21 CST)
Studying in Australia John Pritchard (Tue Dec 17 2002 - 22:36:07 CST)
amber trajectory Ioana Cozmuta (Tue Dec 17 2002 - 23:16:14 CST)
message during minimization Ioana Cozmuta (Tue Dec 17 2002 - 23:31:52 CST)
Re: sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Wed Dec 18 2002 - 03:38:25 CST)
Re: Resp Multiconformational charge fitting! Pascal Bonnet (Wed Dec 18 2002 - 04:21:46 CST)
Re: water box, Carlos Simmerling (Wed Dec 18 2002 - 07:18:18 CST)
Re: amber trajectory Guanglei Cui (Wed Dec 18 2002 - 09:02:05 CST)
SUMMARY: solvating a protein with large cavity Tom Bishop (Wed Dec 18 2002 - 09:03:27 CST)
MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 09:51:02 CST)
Re: solvatebox Luis Gracia (Wed Dec 18 2002 - 09:58:47 CST)
Re: message during minimization darden (Wed Dec 18 2002 - 10:24:48 CST)
Re: water box, darden (Wed Dec 18 2002 - 10:33:07 CST)
off-to-mol2 Anke Eisenmann (Wed Dec 18 2002 - 10:49:22 CST)
mm_pbsa error message! William Wei (Wed Dec 18 2002 - 11:17:16 CST)
Re: mm_pbsa error message! Michael Ford (Wed Dec 18 2002 - 11:37:57 CST)
Re: off-to-mol2 David A. Case (Wed Dec 18 2002 - 12:03:48 CST)
About heating... Andrei Leitão (Wed Dec 18 2002 - 12:23:43 CST)
antechamber Carsten Detering (Wed Dec 18 2002 - 13:38:16 CST)
Re: About heating... David A. Case (Wed Dec 18 2002 - 13:42:51 CST)
Re: SUMMARY: solvating a protein with large cavity Richard Henchman (Wed Dec 18 2002 - 13:56:20 CST)
roar-cp problems M. L. Dodson (Wed Dec 18 2002 - 15:00:37 CST)
Re: MPI_BCAST error Scott Brozell (Wed Dec 18 2002 - 15:24:55 CST)
antechamber Carsten Detering (Wed Dec 18 2002 - 16:32:44 CST)
Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 17:09:05 CST)
atomicfluct in ptraj Kristina Furse (Wed Dec 18 2002 - 17:16:29 CST)
Re: water box, Ioana Cozmuta (Wed Dec 18 2002 - 17:37:41 CST)
Re: water box, David A. Case (Wed Dec 18 2002 - 18:17:31 CST)
Re: message during minimization darden (Wed Dec 18 2002 - 18:32:21 CST)
Re: water box, darden (Wed Dec 18 2002 - 18:45:55 CST)
Re: SUMMARY: solvating a protein with large cavity Ioana Cozmuta (Wed Dec 18 2002 - 19:21:23 CST)
Re: MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 19:31:47 CST)
water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 19:33:23 CST)
Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 20:02:26 CST)
Re: water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 20:17:24 CST)
ntwv saves v(t) or v(t+dt/2) ? hagop demirdjian (Thu Dec 19 2002 - 10:04:55 CST)
Re: message during minimization David A. Case (Thu Dec 19 2002 - 10:05:00 CST)
Re: ntwv saves v(t) or v(t+dt/2) ? David A. Case (Thu Dec 19 2002 - 11:24:33 CST)
Re: atomicfluct in ptraj David A. Case (Thu Dec 19 2002 - 11:28:43 CST)
chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 12:07:07 CST)
RE: atomicfluct in ptraj Kristina Furse (Thu Dec 19 2002 - 13:28:16 CST)
RESTARTED DUE TO LINMIN FAILURE William Wei (Thu Dec 19 2002 - 13:33:07 CST)
Nmode Pratul Agarwal (Thu Dec 19 2002 - 15:07:47 CST)
Re: RESTARTED DUE TO LINMIN FAILURE Natasja Brooijmans (Thu Dec 19 2002 - 15:16:44 CST)
Re: Nmode James Caldwell (Thu Dec 19 2002 - 15:17:31 CST)
Re: chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 17:25:21 CST)
selection of residues Ioana Cozmuta (Fri Dec 20 2002 - 18:51:52 CST)
cap option Ioana Cozmuta (Sun Dec 22 2002 - 19:21:01 CST)
beginners question dynamic group (Sun Dec 22 2002 - 23:17:52 CST)
targeted MD sample eric hu (Thu Dec 26 2002 - 14:25:36 CST)
Molecular dynamic protocol... Andrei Leitão (Fri Dec 27 2002 - 12:40:26 CST)
Re: Molecular dynamic protocol... David A. Case (Fri Dec 27 2002 - 13:25:51 CST)
cannot deal with large trajectory? yuann (Sat Dec 28 2002 - 21:17:23 CST)
Trajectory file converted in pdb file Yongjun Jiang (Sun Dec 29 2002 - 19:13:38 CST)
Sander rfree error kxg2248_at_njit.edu (Mon Dec 30 2002 - 16:58:19 CST)
Re: Sander rfree error James Caldwell (Mon Dec 30 2002 - 18:36:45 CST)
Re: cannot deal with large trajectory? yuann (Mon Dec 30 2002 - 20:55:41 CST)
new on the Amber web pages... David A. Case (Tue Dec 31 2002 - 15:51:31 CST)

Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:25 CDT

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