Amber Archive Jun 2003 by thread
184 messages
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Starting
Mon Jun 02 2003 - 01:53:01 PDT,
Ending
Sun Jun 29 2003 - 16:53:01 PDT
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Re: information
David A. Case
(Sun Jun 01 2003 - 17:14:29 PDT)
Re: IR6 and makeDIST-RST
David A. Case
(Sun Jun 01 2003 - 17:14:04 PDT)
Re: antechamber read gaussian file
David A. Case
(Sun Jun 01 2003 - 17:18:54 PDT)
HGH, IGF-1 Supply
fsdjklfdsf.ddhdf.com
(Sun Jun 01 2003 - 18:09:08 PDT)
HGH, IGF-1 Supply
fsdjklfdsf.ddhdf.com
(Sun Jun 01 2003 - 23:20:52 PDT)
EGB problem in MMPBSA
Obdulia Rabal
(Mon Jun 02 2003 - 04:11:45 PDT)
Need help recompiling
Peter Anderson
(Mon Jun 02 2003 - 07:23:11 PDT)
Re: Need help recompiling
caldwell.heimdal.compchem.ucsf.edu
(Mon Jun 02 2003 - 08:14:06 PDT)
Install Amber7 in linux cluster
Wen Li
(Mon Jun 02 2003 - 07:20:51 PDT)
Re: Install Amber7 in linux cluster
Viktor Hornak
(Mon Jun 02 2003 - 08:11:10 PDT)
run sander?
quch quch
(Mon Jun 02 2003 - 09:22:35 PDT)
Re: run sander?
David A. Case
(Mon Jun 02 2003 - 10:52:00 PDT)
Re: run sander?
quch quch
(Mon Jun 02 2003 - 11:52:22 PDT)
Re: run sander?
Michael Crowley
(Tue Jun 03 2003 - 05:42:53 PDT)
pol_h
Giulio Rastelli
(Tue Jun 03 2003 - 09:34:23 PDT)
Re: pol_h
David A. Case
(Tue Jun 03 2003 - 09:26:41 PDT)
MGB RADII PARAMETRIZATION
Obdulia Rabal
(Tue Jun 03 2003 - 04:08:15 PDT)
Mg++ polarizability
Robert Duke
(Tue Jun 03 2003 - 04:39:25 PDT)
Nancy's leaving
caldwell.heimdal.compchem.ucsf.edu
(Tue Jun 03 2003 - 19:42:00 PDT)
solventbox at constant pressure
Petrodler.aol.com
(Wed Jun 04 2003 - 00:19:05 PDT)
Re: solventbox at constant pressure
David A. Case
(Wed Jun 04 2003 - 08:13:37 PDT)
angle violation in SANDER simulation
XU Xingfu
(Wed Jun 04 2003 - 02:11:24 PDT)
Re: angle violation in SANDER simulation
David A. Case
(Wed Jun 04 2003 - 08:17:32 PDT)
keeping pdb residues numbers ?
GUILBAUD Philippe 153683
(Wed Jun 04 2003 - 05:48:50 PDT)
Re: keeping pdb residues numbers ?
David A. Case
(Wed Jun 04 2003 - 10:40:08 PDT)
belly vs. position restraints
Peter Anderson
(Wed Jun 04 2003 - 07:17:05 PDT)
Re: belly vs. position restraints
David A. Case
(Wed Jun 04 2003 - 08:57:02 PDT)
RDPARM problems (ptraj)
Sophia Kondratova
(Thu Jun 05 2003 - 10:13:35 PDT)
PROBLEM WITH LIBRARY
Frederico.Miranda.ibmb.uib.no
(Thu Jun 05 2003 - 13:06:27 PDT)
constant volume
Shuang Ding
(Thu Jun 05 2003 - 15:26:39 PDT)
Re: constant volume
David A. Case
(Fri Jun 06 2003 - 15:48:16 PDT)
unit of output velocity
Yuguang Mu
(Fri Jun 06 2003 - 08:33:01 PDT)
Re: unit of output velocity
Holger Gohlke
(Fri Jun 06 2003 - 08:46:38 PDT)
Re: unit of output velocity
Satish Kumar
(Fri Jun 06 2003 - 09:25:58 PDT)
Re: unit of output velocity
Satish Mummadi
(Fri Jun 06 2003 - 09:39:45 PDT)
Re: unit of output velocity
Andreas Svrcek-Seiler
(Fri Jun 06 2003 - 09:49:32 PDT)
Q) vdw radii & GBSA error
Sukjoon Yoon
(Fri Jun 06 2003 - 09:58:03 PDT)
how to use profec???
sxzheng
(Sun Jun 08 2003 - 01:04:09 PDT)
mm_pbsa error message
chernhoe
(Sun Jun 08 2003 - 02:48:02 PDT)
Re: mm_pbsa error message
Holger Gohlke
(Sun Jun 08 2003 - 09:19:24 PDT)
Amber Installation on Octane
Joseph Maxwell
(Sun Jun 08 2003 - 14:55:55 PDT)
VdW in FEP
ENikitina
(Mon Jun 09 2003 - 00:06:49 PDT)
Re: VdW in FEP
David A. Case
(Mon Jun 09 2003 - 08:05:58 PDT)
Re: VdW in FEP
ENikitina
(Tue Jun 10 2003 - 04:56:23 PDT)
VdW in FEP
ENikitina
(Wed Jun 18 2003 - 07:02:14 PDT)
May I get you help from new user of amber?
Wu Yingliang
(Mon Jun 09 2003 - 07:21:49 PDT)
Re: May I get you help from new user of amber?
Guanglei Cui
(Mon Jun 09 2003 - 07:41:07 PDT)
RE: May I get you help from new user of amber?
Yong Duan
(Mon Jun 09 2003 - 08:12:41 PDT)
Re: May I get you help from new user of amber?
Satish Mummadi
(Mon Jun 09 2003 - 08:28:54 PDT)
Re: May I get you help from new user of amber?(xmkmf)
Satish Kumar
(Mon Jun 09 2003 - 08:46:53 PDT)
saving trajectory of solute only
Peter Anderson
(Mon Jun 09 2003 - 09:01:53 PDT)
Re: saving trajectory of solute only
Carlos Simmerling
(Mon Jun 09 2003 - 09:06:01 PDT)
Re: saving trajectory of solute only
David A. Case
(Mon Jun 09 2003 - 09:24:03 PDT)
shake problem?
Shuang Ding
(Mon Jun 09 2003 - 11:33:50 PDT)
helix movement
Bimo Ario Tejo
(Tue Jun 10 2003 - 03:10:29 PDT)
Re: helix movement
Yuguang Mu
(Tue Jun 10 2003 - 03:47:42 PDT)
Re: helix movement
Bimo Ario Tejo
(Tue Jun 10 2003 - 04:19:05 PDT)
PME
Yuguang Mu
(Tue Jun 10 2003 - 05:04:08 PDT)
Re: PME
darden
(Wed Jun 11 2003 - 08:21:25 PDT)
Re: helix movement
Andreas Svrcek-Seiler
(Tue Jun 10 2003 - 05:07:49 PDT)
Re: helix movement
Bimo Ario Tejo
(Tue Jun 10 2003 - 05:18:14 PDT)
Re: helix movement
Yuguang Mu
(Wed Jun 11 2003 - 05:47:34 PDT)
helix axis for A-RNA
Vlad Cojocaru
(Tue Jun 10 2003 - 05:25:09 PDT)
Re: helix axis for A-RNA
M. L. Dodson
(Tue Jun 10 2003 - 06:36:44 PDT)
Superimposed trajectory
Filip Razga
(Tue Jun 10 2003 - 06:59:06 PDT)
Re: Superimposed trajectory
David A. Case
(Tue Jun 10 2003 - 07:53:42 PDT)
Problem in separating LES copies into different trajectory
Sameer P. Kawatkar
(Tue Jun 10 2003 - 08:15:18 PDT)
Re: Problem in separating LES copies into different trajectory
Viktor Hornak
(Tue Jun 10 2003 - 08:50:36 PDT)
A question of time
Darren Davies
(Tue Jun 10 2003 - 08:52:31 PDT)
Re: A question of time
David A. Case
(Tue Jun 10 2003 - 09:34:19 PDT)
restart MD
Shuang Ding
(Tue Jun 10 2003 - 11:12:08 PDT)
GB model
MF Yang
(Tue Jun 10 2003 - 12:54:33 PDT)
Minimization does not converge.
Javier Cuervo
(Tue Jun 10 2003 - 20:14:43 PDT)
Re: Minimization does not converge.
David A. Case
(Tue Jun 10 2003 - 22:52:29 PDT)
Re: any tool to know what functions are being called while sander is being run??
Satish Mummadi
(Tue Jun 10 2003 - 22:32:11 PDT)
New location for the Amber web site
David A. Case
(Tue Jun 10 2003 - 23:04:54 PDT)
PME
Yuguang Mu
(Wed Jun 11 2003 - 01:33:29 PDT)
Re: PME
darden
(Wed Jun 11 2003 - 07:33:12 PDT)
delphi on linux
chernhoe
(Wed Jun 11 2003 - 02:03:13 PDT)
vlimit exceeded when sander calculate free energies using TI
zsx
(Wed Jun 11 2003 - 04:51:09 PDT)
Re: vlimit exceeded when sander calculate free energies using TI
David A. Case
(Wed Jun 11 2003 - 08:21:31 PDT)
any tool to know what functions are being called while sander is being run??
Satish Mummadi
(Wed Jun 11 2003 - 06:42:58 PDT)
Re: any tool to know what functions are being called while sander is being run??
Guanglei Cui
(Wed Jun 11 2003 - 06:53:45 PDT)
quasih problem
Yang, Mingfeng
(Wed Jun 11 2003 - 07:10:30 PDT)
Re: quasih problem
David A. Case
(Wed Jun 11 2003 - 08:12:54 PDT)
calculated b-factor higher than x-ray
Bimo Ario Tejo
(Wed Jun 11 2003 - 11:23:03 PDT)
which AMBER program to use to get the e-density output?
salinthip thipayang
(Wed Jun 11 2003 - 12:24:40 PDT)
bugfix ptraj-6.4 (need to confirm)
Bimo Ario Tejo
(Thu Jun 12 2003 - 05:51:27 PDT)
jarrod
Jarrod Wesley Barnes
(Thu Jun 12 2003 - 07:51:33 PDT)
Re: jarrod
Holger Gohlke
(Thu Jun 12 2003 - 08:18:43 PDT)
Re: jarrod
Matheus Froeyen
(Fri Jun 13 2003 - 00:36:14 PDT)
install problem
Dave S Walker
(Thu Jun 12 2003 - 14:18:02 PDT)
Re: install problem
David A. Case
(Thu Jun 12 2003 - 15:26:56 PDT)
Re: install problem
Dave S Walker
(Thu Jun 12 2003 - 17:03:21 PDT)
glycam force field with amber
PSR04996.mailstudenti.unimi.it
(Fri Jun 13 2003 - 04:28:07 PDT)
Re: glycam force field with amber
David A. Case
(Fri Jun 13 2003 - 09:42:31 PDT)
Problem with a library
Frederico.Miranda.ibmb.uib.no
(Fri Jun 13 2003 - 13:27:36 PDT)
Re: Problem with a library
David A. Case
(Fri Jun 13 2003 - 14:07:37 PDT)
parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator"
chris switzer
(Sat Jun 14 2003 - 19:00:51 PDT)
can you give me more advice about: vlimit exceeded when sander calculate free energies using TI
sxzheng
(Mon Jun 16 2003 - 05:47:53 PDT)
Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI
David A. Case
(Mon Jun 16 2003 - 08:12:05 PDT)
Medical Imaging Risk & Reward -- Medical Imaging Consultant
Radiation Aware
(Mon Jun 16 2003 - 20:17:03 PDT)
LEAP compiling problem
yuann
(Tue Jun 17 2003 - 03:14:23 PDT)
Re: LEAP compiling problem
David A. Case
(Tue Jun 17 2003 - 08:51:21 PDT)
Re: LEAP compiling problem
David A. Case
(Tue Jun 17 2003 - 09:09:26 PDT)
Re: LEAP compiling problem
yuann
(Tue Jun 17 2003 - 18:17:56 PDT)
CCL: Amber free energy equation
Daquan Gao
(Tue Jun 17 2003 - 09:33:39 PDT)
AMBER7 on linux cluster
Venkata S Koppuravuri
(Tue Jun 17 2003 - 09:49:06 PDT)
Re: AMBER7 on linux cluster
Carlos Simmerling
(Tue Jun 17 2003 - 09:54:28 PDT)
Re: AMBER7 on linux cluster
Venkata S Koppuravuri
(Fri Jun 20 2003 - 07:53:17 PDT)
Re: AMBER7 on linux cluster
Carlos Simmerling
(Fri Jun 20 2003 - 07:55:10 PDT)
RE: AMBER7 on linux cluster
Yong Duan
(Fri Jun 20 2003 - 18:35:04 PDT)
new tutorial available: introduction to ptraj
David A. Case
(Tue Jun 17 2003 - 11:03:54 PDT)
Sander error
Yuhui Cheng
(Tue Jun 17 2003 - 11:37:21 PDT)
Re: Sander error
Natasja Brooijmans
(Tue Jun 17 2003 - 11:44:53 PDT)
Error in minimization using sander_classic of AMBER6
dicksmit.umich.edu
(Tue Jun 17 2003 - 13:20:03 PDT)
Re: Error in minimization using sander_classic of AMBER6
David A. Case
(Tue Jun 17 2003 - 13:53:49 PDT)
web link for PLEP is not available.
Margaret Shun Cheung
(Tue Jun 17 2003 - 13:28:40 PDT)
Problem with LES topology file
Courtney Stanton
(Tue Jun 17 2003 - 15:28:10 PDT)
Re: Problem with LES topology file
Carlos Simmerling
(Tue Jun 17 2003 - 15:42:07 PDT)
Flag for antechamber
Nick Polfer
(Wed Jun 18 2003 - 01:59:01 PDT)
mpirun problem: no rsh
Peter Anderson
(Wed Jun 18 2003 - 10:50:26 PDT)
Re: mpirun problem: no rsh
Carlos Simmerling
(Wed Jun 18 2003 - 10:56:48 PDT)
Re: mpirun problem: no rsh
Michael Crowley
(Wed Jun 18 2003 - 12:04:52 PDT)
help on solvatecap
Mao Xiang
(Wed Jun 18 2003 - 18:47:36 PDT)
debug sander
Andrew Petersen
(Wed Jun 18 2003 - 23:40:04 PDT)
Re: debug sander
Satish Mummadi
(Thu Jun 19 2003 - 01:32:02 PDT)
RE: debug sander
Yong Duan
(Thu Jun 19 2003 - 02:21:27 PDT)
constraint + restraint
Jose Ramon Blas
(Thu Jun 19 2003 - 16:58:41 PDT)
Re: constraint + restraint
David A. Case
(Thu Jun 19 2003 - 08:39:44 PDT)
NOESY restraints
Teletchéa Stéphane
(Fri Jun 20 2003 - 04:28:03 PDT)
Re: NOESY restraints
David A. Case
(Fri Jun 20 2003 - 17:49:00 PDT)
Re: NOESY restraints
Steph
(Sat Jun 21 2003 - 03:27:35 PDT)
AMBER question
David
(Fri Jun 20 2003 - 09:31:55 PDT)
Re: AMBER question
David A. Case
(Fri Jun 20 2003 - 17:59:04 PDT)
perl question
Ioana Cozmuta
(Fri Jun 20 2003 - 15:28:57 PDT)
mm_pbsa problem
Peter Anderson
(Fri Jun 20 2003 - 15:31:17 PDT)
Re: mm_pbsa problem
Holger Gohlke
(Fri Jun 20 2003 - 18:47:21 PDT)
Question about defining force field
FUNG WAI KEUNG
(Fri Jun 20 2003 - 20:12:59 PDT)
Problem with XLEaP in Mandrake 9.1
Karthikeyan Pasupathy
(Sun Jun 22 2003 - 10:08:23 PDT)
RE: Problem with XLEaP in Mandrake 9.1
Ross Walker
(Sun Jun 22 2003 - 10:31:02 PDT)
Re: Problem with XLEaP in Mandrake 9.1
CUI, Guanglei
(Sun Jun 22 2003 - 10:44:51 PDT)
Re: Problem with XLEaP in Mandrake 9.1
John Bushnell
(Sun Jun 22 2003 - 18:04:43 PDT)
1-4 vdw term in Glycam2000
yuann
(Sun Jun 22 2003 - 21:24:16 PDT)
viewing movie with VMD
Layi Adekoya
(Mon Jun 23 2003 - 01:00:51 PDT)
Re: viewing movie with VMD
Lepsa
(Mon Jun 23 2003 - 01:09:29 PDT)
RE: viewing movie with VMD
Ross Walker
(Mon Jun 23 2003 - 15:36:30 PDT)
Running MD
Balvinder Singh
(Mon Jun 23 2003 - 10:33:56 PDT)
Re: Running MD
Carlos Simmerling
(Mon Jun 23 2003 - 05:10:23 PDT)
Re: Running MD
Balvinder Singh
(Mon Jun 23 2003 - 11:02:33 PDT)
Re: Running MD
Carlos Simmerling
(Mon Jun 23 2003 - 05:40:24 PDT)
how to restrain water
Mao Xiang
(Mon Jun 23 2003 - 07:59:23 PDT)
Re: how to restrain water
Alfonso Garcia Sosa
(Mon Jun 23 2003 - 08:14:02 PDT)
Re: how to restrain water
Alfonso Garcia Sosa
(Mon Jun 23 2003 - 08:42:42 PDT)
AMBER parameters
D Fernandez
(Mon Jun 23 2003 - 22:26:09 PDT)
Re: AMBER parameters
David A. Case
(Tue Jun 24 2003 - 08:25:35 PDT)
ptraj question
Ioana Cozmuta
(Tue Jun 24 2003 - 00:59:48 PDT)
Re: ptraj question
Thomas Cheatham
(Tue Jun 24 2003 - 13:56:51 PDT)
Another mm_pbsa problem
Peter Anderson
(Tue Jun 24 2003 - 09:47:58 PDT)
Re: Another mm_pbsa problem
Holger Gohlke
(Tue Jun 24 2003 - 10:08:25 PDT)
GAFF in GUI MD apps
Thomas
(Tue Jun 24 2003 - 12:07:54 PDT)
Re: GAFF in GUI MD apps
FyD
(Tue Jun 24 2003 - 22:50:58 PDT)
electrostatic interaction energ. /delphi
Tommi Kajander
(Tue Jun 24 2003 - 12:39:51 PDT)
Re: electrostatic interaction energ. /delphi
Natasja Brooijmans
(Tue Jun 24 2003 - 12:45:22 PDT)
RE: Software Sales
Pete Koladich
(Tue Jun 24 2003 - 13:41:53 PDT)
Memory problem
Frederico.Miranda.ibmb.uib.no
(Tue Jun 24 2003 - 17:17:40 PDT)
T in MD vs. T in wet experiments
Jianhui Wu
(Tue Jun 24 2003 - 18:34:31 PDT)
Sander problem
Yuhui Cheng
(Tue Jun 24 2003 - 19:31:28 PDT)
Re: Sander problem
David A. Case
(Wed Jun 25 2003 - 15:30:21 PDT)
Question about defining force field (followup)
FUNG WAI KEUNG
(Tue Jun 24 2003 - 21:14:10 PDT)
unifying trajectory files
Peter Anderson
(Wed Jun 25 2003 - 08:57:42 PDT)
Re: unifying trajectory files
Carlos Simmerling
(Wed Jun 25 2003 - 09:05:57 PDT)
Re: unifying trajectory files
Natasja Brooijmans
(Wed Jun 25 2003 - 09:25:41 PDT)
Re: unifying trajectory files
Ioana Cozmuta
(Wed Jun 25 2003 - 12:58:39 PDT)
Antechamber
Shweta Sikri
(Wed Jun 25 2003 - 09:47:52 PDT)
Re: Antechamber
David A. Case
(Wed Jun 25 2003 - 10:31:31 PDT)
Re: Antechamber
Shweta Sikri
(Wed Jun 25 2003 - 12:26:31 PDT)
pyroglutamic acid (PCA)
Javier Cuervo
(Wed Jun 25 2003 - 18:16:44 PDT)
Re: pyroglutamic acid (PCA)
David A. Case
(Thu Jun 26 2003 - 10:34:25 PDT)
Amber6 on RH 9
Yichen Cao
(Thu Jun 26 2003 - 08:37:09 PDT)
Re: Amber6 on RH 9
David A. Case
(Thu Jun 26 2003 - 10:31:56 PDT)
Problem with Snader
Frederico.Miranda.ibmb.uib.no
(Sat Jun 28 2003 - 06:17:12 PDT)
Re: Problem with Snader
Guanglei Cui
(Sat Jun 28 2003 - 07:53:59 PDT)
protonate
Giulio Rastelli
(Sun Jun 29 2003 - 14:31:20 PDT)
Last message date
:
Sun Jun 29 2003 - 16:53:01 PDT
Archived on
: Fri Dec 20 2024 - 05:53:20 PST
184 messages
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