Amber Archive Mar 2005 by author
381 messages
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Starting
Tue Mar 01 2005 - 07:53:00 PST,
Ending
Fri Apr 01 2005 - 03:53:01 PST
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aanzellotti.mail2.vcu.edu
RE: AMBER: Problem saving file in xleap
(Thu Mar 17 2005 - 08:45:07 PST)
AMBER: Problem saving file in xleap
(Tue Mar 15 2005 - 09:03:12 PST)
Adrian E. Roitberg
AMBER: protonated aspartic acid
(Tue Mar 29 2005 - 12:14:35 PST)
Re: AMBER: "personality" of Amber force field
(Fri Mar 18 2005 - 13:24:50 PST)
Akshay Patny
AMBER: X Windows for LEaP on SGI
(Tue Mar 08 2005 - 13:07:44 PST)
Alessio Coi
AMBER: MM-GBSA
(Wed Mar 02 2005 - 02:00:52 PST)
Amber
AMBER: Make test error
(Thu Mar 24 2005 - 13:10:53 PST)
Andreas Svrcek-Seiler
Re: AMBER: spherical boundary condition
(Mon Mar 14 2005 - 10:36:06 PST)
Andrew Box
AMBER: PTRAJ $ Antechamber
(Wed Mar 09 2005 - 22:47:29 PST)
Annette Höglund
AMBER: phosphorylated DNA not recognized
(Thu Mar 03 2005 - 06:55:18 PST)
Ashutosh Suhas Jogalekar
AMBER: Zn complex parametrization question
(Wed Mar 16 2005 - 13:27:38 PST)
Asim Okur
Re:AMBER: "personality" of Amber force field
(Fri Mar 18 2005 - 13:01:19 PST)
Re: AMBER: Trajectory problems
(Thu Mar 17 2005 - 15:14:28 PST)
Atro Tossavainen
AMBER: AMBER under MOSIX?
(Thu Mar 31 2005 - 03:47:47 PST)
Re: AMBER: Amber8 Parallel installation troubles
(Tue Mar 22 2005 - 23:43:18 PST)
Bill Ross
RE: AMBER: wierd behavior of addions
(Tue Mar 22 2005 - 13:23:52 PST)
Re: AMBER: periodicity problem
(Wed Mar 16 2005 - 14:23:03 PST)
Re: AMBER: Question about radial command in ptraj
(Mon Mar 14 2005 - 13:09:08 PST)
Re: AMBER: Question about radial command in ptraj
(Mon Mar 14 2005 - 11:48:17 PST)
Re: AMBER: gyration radius
(Sun Mar 13 2005 - 11:36:15 PST)
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 11:15:43 PST)
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 10:13:06 PST)
Re: Re :AMBER: Holes in water
(Fri Mar 11 2005 - 07:59:03 PST)
Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP
(Fri Mar 11 2005 - 07:46:40 PST)
Re: AMBER: PTRAJ $ Antechamber
(Thu Mar 10 2005 - 09:22:39 PST)
Re: AMBER: vlimit in heating
(Wed Mar 09 2005 - 07:44:06 PST)
Re: AMBER: amber on sgi
(Wed Mar 09 2005 - 07:35:21 PST)
Re: AMBER: heating
(Tue Mar 08 2005 - 14:55:47 PST)
Re: AMBER: radii "leap" from which file
(Tue Mar 08 2005 - 13:43:18 PST)
Bogos Agianian
AMBER: Sample more conformational space
(Wed Mar 02 2005 - 04:52:49 PST)
bybaker.itsa.ucsf.edu
AMBER: frcmod.mod_phipsi.2
(Tue Mar 15 2005 - 12:04:31 PST)
Re: AMBER: The pressure
(Tue Mar 08 2005 - 22:38:14 PST)
AMBER: The pressure
(Tue Mar 08 2005 - 17:54:44 PST)
Carlos Simmerling
Re: AMBER: What does this mean .. ?
(Thu Mar 31 2005 - 11:33:25 PST)
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 15:37:26 PST)
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 14:32:09 PST)
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 11:14:07 PST)
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 08:28:13 PST)
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 08:08:01 PST)
Re: AMBER: align snapshots to a reference
(Tue Mar 29 2005 - 14:15:29 PST)
Re: AMBER: TMD force constant
(Tue Mar 22 2005 - 05:57:01 PST)
Re: AMBER: question about periodicity of torsion parameter
(Fri Mar 18 2005 - 14:51:40 PST)
Re: AMBER: Problems with Iodine
(Fri Mar 18 2005 - 13:22:47 PST)
Re: AMBER: layer
(Fri Mar 18 2005 - 08:01:45 PST)
Re: AMBER: Replica Exchange crashing
(Fri Mar 18 2005 - 05:11:13 PST)
Re: AMBER: Separating solvent and solute energy in the microcanonical mode
(Thu Mar 17 2005 - 15:33:43 PST)
Re: AMBER: Separating solvent and solute energy in the microcanonical mode
(Thu Mar 17 2005 - 15:05:17 PST)
Re: AMBER: in vacuo parameters
(Tue Mar 15 2005 - 15:29:31 PST)
Re: AMBER: frcmod.mod_phipsi.2
(Tue Mar 15 2005 - 14:52:53 PST)
Re: AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 07:48:41 PST)
Re: AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 07:21:37 PST)
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 10:46:24 PST)
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 10:32:06 PST)
Re: AMBER: A problem about removing waters and counterions by ptraj
(Mon Mar 07 2005 - 05:29:14 PST)
Re: AMBER: Sample more conformational space
(Wed Mar 02 2005 - 08:35:18 PST)
Cenk Andac
AMBER: antechamber and multiplicity
(Mon Mar 14 2005 - 11:57:27 PST)
Re:Re: AMBER: Cu++ and RED
(Sat Mar 12 2005 - 10:39:10 PST)
Re: AMBER: Cu++ and RED
(Sat Mar 12 2005 - 04:28:34 PST)
AMBER: Citing Generalized Born Implicit solvent Model (igb=5)
(Sun Mar 06 2005 - 16:57:21 PST)
Claudio Morgado
AMBER: sander.QMMM and fcap
(Thu Mar 17 2005 - 05:56:34 PST)
David A. Case
Re: AMBER: how to cap regions
(Thu Mar 31 2005 - 07:45:26 PST)
Re: AMBER: All the tests passed except prmtop and prepin...
(Thu Mar 31 2005 - 07:40:18 PST)
Re: AMBER: "The system has extended beyond" error
(Wed Mar 30 2005 - 07:08:07 PST)
Re: AMBER: tleap,xleap bond order for triple bonds
(Tue Mar 29 2005 - 20:43:39 PST)
Re: AMBER: Are the constant pH simulations with explicit water possible?
(Tue Mar 29 2005 - 09:37:27 PST)
Re: AMBER: vlimit exceeded in thermalization
(Tue Mar 29 2005 - 09:22:20 PST)
Re: AMBER: antechamber availability
(Thu Mar 24 2005 - 10:42:49 PST)
Re: AMBER: nonbonded interaction
(Tue Mar 22 2005 - 21:38:08 PST)
Re: AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation
(Mon Mar 21 2005 - 10:27:40 PST)
Re: AMBER: Making prepin file for individual residues of huge molecule.
(Mon Mar 21 2005 - 08:27:23 PST)
Re: AMBER: lmanal input file problem
(Fri Mar 18 2005 - 12:10:00 PST)
Re: AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 10:54:18 PST)
Re: AMBER: Bus error - ambpdb
(Thu Mar 17 2005 - 08:54:28 PST)
Re: AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 08:51:59 PST)
Re: AMBER: sander.QMMM and fcap
(Thu Mar 17 2005 - 08:00:04 PST)
Re: AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 07:23:30 PST)
Re: AMBER: spherical boundary condition
(Sat Mar 12 2005 - 18:51:58 PST)
Re: AMBER: expected error in mean (Amber 8 TI tutorial)
(Sat Mar 12 2005 - 14:18:40 PST)
Re: AMBER: PTRAJ $ Antechamber
(Sat Mar 12 2005 - 14:17:49 PST)
Re: AMBER: IDIEL in sander
(Sat Mar 12 2005 - 14:10:09 PST)
Re: AMBER:
(Fri Mar 11 2005 - 11:02:40 PST)
Re: AMBER: radii "leap" from which file
(Wed Mar 09 2005 - 17:02:43 PST)
Re: AMBER: solvatebox problem in the antechamber tutorial
(Wed Mar 09 2005 - 16:18:19 PST)
Re: AMBER: vlimit in heating
(Wed Mar 09 2005 - 08:10:42 PST)
Re: AMBER: Dummy atoms: Changing the source code
(Tue Mar 08 2005 - 11:50:58 PST)
Re: AMBER: global pH variation in AMBER.
(Tue Mar 08 2005 - 11:38:30 PST)
Re: AMBER: Energy fluctuations
(Tue Mar 08 2005 - 11:36:14 PST)
Re: AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks
(Mon Mar 07 2005 - 10:36:40 PST)
Re: AMBER: AMBER8 Compile Error on Dual Opteron
(Sun Mar 06 2005 - 20:24:27 PST)
Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5)
(Sun Mar 06 2005 - 17:14:35 PST)
Re: AMBER: Amber 8 on cygwin install problem
(Sun Mar 06 2005 - 11:23:52 PST)
Re: AMBER: Antechamber/Divcon assigned charges
(Thu Mar 03 2005 - 21:17:13 PST)
Re: AMBER: A problem about Gaussian
(Thu Mar 03 2005 - 16:55:35 PST)
Re: AMBER: Installation problem
(Thu Mar 03 2005 - 08:18:47 PST)
Re: AMBER: Amber 8 on cygwin install problem
(Thu Mar 03 2005 - 08:07:52 PST)
Re: AMBER: bond type for a virtual bond in a biomolecular transition state
(Wed Mar 02 2005 - 15:08:38 PST)
Re: AMBER: MM-GBSA
(Wed Mar 02 2005 - 07:44:15 PST)
Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem
(Tue Mar 01 2005 - 08:41:08 PST)
Re: AMBER: Controlling number of water residues...
(Tue Mar 01 2005 - 08:25:14 PST)
David C. Chan
AMBER: Bus error - ambpdb
(Thu Mar 17 2005 - 06:54:17 PST)
david.evans.ulsop.ac.uk
Re: AMBER: Compiling just sander
(Fri Mar 11 2005 - 01:24:24 PST)
David.LeBard.asu.edu
AMBER: Energy fluctuations
(Tue Mar 08 2005 - 09:40:46 PST)
David.Maxwell.di.mdacc.tmc.edu
AMBER: Problems with Iodine
(Fri Mar 18 2005 - 13:03:38 PST)
dmitri.mikhailov.novartis.com
AMBER: antechamber availability
(Wed Mar 23 2005 - 12:40:47 PST)
Eric Hu
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 16:23:32 PST)
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 14:50:03 PST)
Re: AMBER: OH- dynamics
(Wed Mar 30 2005 - 14:03:53 PST)
AMBER: OH- dynamics
(Wed Mar 30 2005 - 09:55:19 PST)
AMBER: mm-pbsa with multiple-processors
(Mon Mar 21 2005 - 14:21:16 PST)
AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation
(Fri Mar 18 2005 - 15:35:39 PST)
AMBER: expected error in mean (Amber 8 TI tutorial)
(Thu Mar 10 2005 - 15:38:13 PST)
Re: AMBER: bond connectivity among dummy atoms
(Thu Mar 03 2005 - 14:12:26 PST)
Re: AMBER: bond connectivity among dummy atoms
(Thu Mar 03 2005 - 13:25:19 PST)
AMBER: bond connectivity among dummy atoms
(Thu Mar 03 2005 - 10:56:32 PST)
AMBER: bond type for a virtual bond in a biomolecular transition state
(Wed Mar 02 2005 - 14:54:45 PST)
Fabien Cailliez
AMBER: warning in PBSA
(Wed Mar 23 2005 - 05:39:00 PST)
AMBER: add waters to a system + leap problem with solvateOct command
(Thu Mar 17 2005 - 10:30:24 PST)
Florian Barth
Re: AMBER: PMEMD with big systems
(Wed Mar 23 2005 - 12:48:10 PST)
AMBER: PMEMD with big systems
(Fri Mar 18 2005 - 15:25:41 PST)
FyD
AMBER: Re: ask for your help: parallel on mm_pbsa
(Sat Mar 26 2005 - 09:09:23 PST)
Re: AMBER: Methionine with both C-ter and N-ter
(Tue Mar 22 2005 - 16:26:35 PST)
Re: AMBER: mm-pbsa with multiple-processors
(Mon Mar 21 2005 - 14:39:54 PST)
Re: AMBER: Cu++ and RED
(Sat Mar 12 2005 - 14:00:56 PST)
Re: AMBER: Cu++ and RED
(Sat Mar 12 2005 - 09:35:53 PST)
RE: AMBER: capping?
(Wed Mar 09 2005 - 08:51:32 PST)
Re: AMBER: R.E.D
(Sun Mar 06 2005 - 17:42:20 PST)
Re: AMBER: A problem about Gaussian
(Thu Mar 03 2005 - 15:27:23 PST)
Re: AMBER: phosphorylated DNA not recognized
(Thu Mar 03 2005 - 10:59:27 PST)
Re: AMBER: An error during minimization using RED
(Tue Mar 01 2005 - 13:44:33 PST)
Giulio Rastelli
AMBER: surfen and surfoff
(Mon Mar 14 2005 - 08:21:22 PST)
Guanglei Cui
Re: AMBER: REM mdinfo file
(Tue Mar 29 2005 - 10:00:10 PST)
Re: AMBER: antechamber availability
(Wed Mar 23 2005 - 15:21:23 PST)
Re: AMBER: layer
(Fri Mar 18 2005 - 07:13:32 PST)
Re: AMBER: Velocity Info
(Wed Mar 16 2005 - 08:29:35 PST)
Re: AMBER: Velocity Info
(Wed Mar 16 2005 - 06:55:07 PST)
Re: AMBER: gyration radius
(Sun Mar 13 2005 - 10:18:18 PST)
Re: AMBER: mesure dihedral angle during MD
(Sun Mar 13 2005 - 10:10:46 PST)
Re: AMBER: Controlling number of water residues...
(Tue Mar 01 2005 - 07:49:57 PST)
Gustavo Pierdominici Sottile
AMBER: layer
(Fri Mar 18 2005 - 06:42:53 PST)
AMBER: vlimit
(Fri Mar 11 2005 - 04:33:36 PST)
AMBER: vlimit heat
(Wed Mar 09 2005 - 09:36:30 PST)
AMBER: vlimit in heating
(Wed Mar 09 2005 - 06:13:20 PST)
AMBER: heating
(Tue Mar 08 2005 - 14:20:34 PST)
Hayden Eastwood
AMBER: Replica Exchange crashing
(Fri Mar 18 2005 - 04:39:48 PST)
Heiko Meyer
Re: AMBER: capping?
(Wed Mar 09 2005 - 09:17:01 PST)
AMBER: solvatebox problem in the antechamber tutorial
(Wed Mar 09 2005 - 08:29:00 PST)
hj zou
AMBER: how can I deal with the puzzle?
(Tue Mar 08 2005 - 19:36:39 PST)
AMBER: What PRESS is?
(Mon Mar 07 2005 - 19:08:39 PST)
Holly Freedman
AMBER: vlimit exceeded in thermalization
(Mon Mar 28 2005 - 20:16:12 PST)
Hui-Hsu Tsai
Re: AMBER: "personality" of Amber force field
(Fri Mar 18 2005 - 15:05:07 PST)
Re:AMBER: "personality" of Amber force field
(Fri Mar 18 2005 - 13:22:11 PST)
AMBER: "personality" of Amber force field
(Wed Mar 16 2005 - 08:01:00 PST)
Re: AMBER: spherical boundary condition
(Mon Mar 14 2005 - 10:59:01 PST)
AMBER: spherical boundary condition
(Sat Mar 12 2005 - 11:05:52 PST)
AMBER: capping?
(Tue Mar 08 2005 - 13:34:59 PST)
Hwankyu Lee
AMBER: Making prepin file for individual residues of huge molecule.
(Mon Mar 21 2005 - 07:00:11 PST)
Re: AMBER: Making topology files of big moleucles in antechamber
(Fri Mar 18 2005 - 08:48:02 PST)
AMBER: Making topology files of big moleucles in antechamber
(Thu Mar 17 2005 - 08:09:06 PST)
ilaria massarelli
RE: AMBER: NaNQ
(Wed Mar 02 2005 - 07:01:33 PST)
AMBER: NaNQ
(Tue Mar 01 2005 - 00:45:10 PST)
Ilyas Yildirim
Re: AMBER: "The system has extended beyond" error
(Thu Mar 31 2005 - 04:26:21 PST)
AMBER: "The system has extended beyond" error
(Tue Mar 29 2005 - 14:28:35 PST)
Re: AMBER: periodicity problem
(Wed Mar 16 2005 - 13:25:39 PST)
AMBER: Compiling just sander
(Thu Mar 10 2005 - 19:07:31 PST)
Re: AMBER: heating
(Tue Mar 08 2005 - 15:02:17 PST)
Re: AMBER: Dummy atoms: Changing the source code
(Tue Mar 08 2005 - 12:56:48 PST)
Re: AMBER: Dummy atoms: Changing the source code
(Fri Mar 04 2005 - 18:56:34 PST)
AMBER: Dummy atoms: Changing the source code
(Thu Mar 03 2005 - 16:24:03 PST)
Re: AMBER: bond connectivity among dummy atoms
(Thu Mar 03 2005 - 13:58:38 PST)
Re: AMBER: bond connectivity among dummy atoms
(Thu Mar 03 2005 - 11:57:48 PST)
Jack Lei
Re: AMBER: Sander: idecomp
(Tue Mar 15 2005 - 15:57:21 PST)
Joe Nolan
AMBER: Amber8 Parallel installation troubles
(Tue Mar 22 2005 - 11:03:05 PST)
Re: AMBER: Sander questions on dual-processor Sun with MPICH
(Thu Mar 10 2005 - 08:46:23 PST)
AMBER: Sander questions on dual-processor Sun with MPICH
(Tue Mar 08 2005 - 12:37:50 PST)
AMBER: Xleap execution problems on Solaris
(Tue Mar 01 2005 - 12:51:26 PST)
Re: AMBER: Amber8 Solaris installation failure
(Tue Mar 01 2005 - 07:23:06 PST)
Joseph W.Toporowski
AMBER: ptraj: determining solvent/ion densities
(Thu Mar 17 2005 - 17:40:38 PST)
AMBER: determining solvent/ion densities
(Mon Mar 14 2005 - 15:35:25 PST)
julien
AMBER: gyration radius
(Sun Mar 13 2005 - 08:49:50 PST)
AMBER: mesure dihedral angle during MD
(Sun Mar 13 2005 - 08:52:01 PST)
Julien Michel
Re: AMBER: Dummy atoms: Changing the source code
(Fri Mar 04 2005 - 01:44:31 PST)
Junmei Wang
RE: AMBER: frcmod.mod_phipsi.2
(Tue Mar 15 2005 - 12:22:29 PST)
RE: AMBER: Antechamber/Divcon assigned charges
(Thu Mar 03 2005 - 21:20:38 PST)
RE: AMBER: Dihedral Energy calculation
(Tue Mar 01 2005 - 10:57:49 PST)
jz7.duke.edu
AMBER: Methionine with both C-ter and N-ter
(Tue Mar 22 2005 - 14:17:18 PST)
AMBER: wierd behavior of addions
(Tue Mar 22 2005 - 11:22:54 PST)
AMBER: question about periodicity of torsion parameter
(Fri Mar 18 2005 - 14:08:50 PST)
AMBER: question about amber parameter file format etc.
(Wed Mar 16 2005 - 09:37:29 PST)
Kara Di Giorgio
AMBER: question about placing a substrate in a protein pocket
(Thu Mar 24 2005 - 20:33:26 PST)
Karol Miaskiewicz
Re: AMBER: problem with running AMBER with lam-mpi though PBS script
(Wed Mar 09 2005 - 05:57:46 PST)
Re: AMBER: amber on sgi
(Wed Mar 09 2005 - 05:37:31 PST)
Kateryna Miroshnychenko
AMBER: Are the constant pH simulations with explicit water possible?
(Tue Mar 29 2005 - 05:54:14 PST)
keiodai.shohoku.ac.jp
AMBER: Re: Amber 8 dual-Xeon compile problem
(Wed Mar 09 2005 - 20:14:33 PST)
lei jia
Re: AMBER: Sander: idecomp
(Tue Mar 15 2005 - 18:25:24 PST)
AMBER: Sander: idecomp
(Tue Mar 15 2005 - 11:45:47 PST)
Lihua Wang
AMBER: atom type designation
(Fri Mar 04 2005 - 16:05:10 PST)
luckyang.gmail.com
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Wed Mar 23 2005 - 15:01:49 PST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Wed Mar 23 2005 - 14:18:45 PST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Tue Mar 22 2005 - 16:46:26 PST)
AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Tue Mar 22 2005 - 15:34:05 PST)
Lukasz Bielecki
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 08:52:31 PST)
AMBER: Holes in water
(Fri Mar 11 2005 - 06:13:40 PST)
Maciej
AMBER: A few question about RDF input preparation
(Thu Mar 24 2005 - 03:13:10 PST)
AMBER: Could not open file (trajin) with mode (r)
(Wed Mar 23 2005 - 05:52:20 PST)
AMBER: RDF input preparation problem
(Sun Mar 13 2005 - 20:12:22 PST)
Re: AMBER: Amber 8 on cygwin install problem
(Thu Mar 03 2005 - 22:51:32 PST)
AMBER: Amber 8 on cygwin install problem
(Thu Mar 03 2005 - 02:49:17 PST)
Re: AMBER: Installation problem
(Thu Mar 03 2005 - 01:26:30 PST)
Marc Baaden
AMBER: Bio-Image summer school in Paris this year
(Wed Mar 16 2005 - 03:44:47 PST)
Re: AMBER: Sample more conformational space
(Wed Mar 02 2005 - 05:03:02 PST)
Marc Christensen
AMBER: Antechamber/Divcon assigned charges
(Thu Mar 03 2005 - 19:38:10 PST)
Marc Petitmermet
AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS
(Thu Mar 31 2005 - 07:32:31 PST)
Re: AMBER: compiler for amber8 on opteron
(Fri Mar 18 2005 - 00:22:42 PST)
AMBER: compiler for amber8 on opteron
(Thu Mar 17 2005 - 07:56:37 PST)
Markus W. Germann
AMBER: Xserve and amber
(Mon Mar 14 2005 - 08:55:53 PST)
mathew k varghese
AMBER: leap warnings
(Sun Mar 13 2005 - 22:34:32 PST)
AMBER: amber on sgi
(Wed Mar 09 2005 - 03:23:12 PST)
Melinda Layten
Re: AMBER: Making topology files of big moleucles in antechamber
(Thu Mar 17 2005 - 11:48:39 PST)
Re: AMBER: Trajectory problems
(Thu Mar 17 2005 - 11:34:50 PST)
Re: AMBER: amber on sgi
(Wed Mar 09 2005 - 08:52:28 PST)
Mengjuei Hsieh
Re: AMBER: Xserve and amber
(Mon Mar 14 2005 - 17:51:12 PST)
Mey Khalili
Re: AMBER: Separating solvent and solute energy in the microcanonical mode
(Thu Mar 17 2005 - 15:11:48 PST)
AMBER: Separating solvent and solute energy in the microcanonical mode
(Thu Mar 17 2005 - 14:50:09 PST)
Mingfeng Yang
AMBER: Target MD and nmode test hang
(Thu Mar 31 2005 - 18:08:13 PST)
Mingyue Zheng
Re: AMBER: What PRESS is?
(Mon Mar 07 2005 - 19:26:01 PST)
mmv.whu.edu.cn
AMBER: All the tests passed except prmtop and prepin...
(Thu Mar 31 2005 - 01:59:26 PST)
Nelson Fonseca
AMBER: Error limits of TI and MM_PBSA methods
(Tue Mar 08 2005 - 08:54:42 PST)
Nitin Bhardwaj
AMBER: Parameter files for general lipids
(Mon Mar 28 2005 - 16:57:46 PST)
Noriyuki Yamaotsu
Re: AMBER: compiler for amber8 on opteron
(Thu Mar 17 2005 - 17:50:24 PST)
opitz.che.udel.edu
Re: AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 07:34:53 PST)
AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 06:57:45 PST)
Re: AMBER: Question about radial command in ptraj
(Mon Mar 14 2005 - 12:04:55 PST)
AMBER: Question about radial command in ptraj
(Mon Mar 14 2005 - 11:19:11 PST)
Osman Gani
AMBER: global pH variation in AMBER.
(Tue Mar 08 2005 - 02:56:06 PST)
Pascal Auffinger
Re :AMBER: Holes in water
(Fri Mar 11 2005 - 07:26:31 PST)
Pavan Ghatty
AMBER: What does this mean .. ?
(Thu Mar 31 2005 - 11:14:53 PST)
peng79.email.unc.edu
AMBER: Geometrical distortion because of charge?
(Mon Mar 14 2005 - 10:21:28 PST)
Phineus Markwick
AMBER: TMD force constant
(Tue Mar 22 2005 - 05:14:53 PST)
AMBER: lmanal input file problem
(Fri Mar 18 2005 - 08:00:18 PST)
AMBER: problem with nmode using ntrun=5 (2)
(Fri Mar 11 2005 - 08:39:43 PST)
AMBER: problem with nmode using ntrun=5
(Fri Mar 11 2005 - 06:38:34 PST)
Piero Altoè
AMBER: restraintmask dimension
(Wed Mar 16 2005 - 03:42:12 PST)
Pieter Smith
AMBER: Problems Binding Protein to DNA
(Tue Mar 08 2005 - 21:21:30 PST)
Piotr Cieplak
Re: AMBER: mm-pbsa with multiple-processors
(Mon Mar 21 2005 - 16:17:30 PST)
Re: AMBER: R.E.D
(Sun Mar 06 2005 - 16:20:42 PST)
Pradipta Bandyopadhyay
Re: AMBER: how to excite a single residue ?
(Wed Mar 09 2005 - 21:24:34 PST)
Praveena Gopal
AMBER: Amber PBMD:Energy fluctuation
(Sat Mar 12 2005 - 01:48:03 PST)
Priti Hansia
AMBER: how to excite a single residue ?
(Wed Mar 09 2005 - 20:28:24 PST)
AMBER:
(Tue Mar 08 2005 - 23:38:59 PST)
protege.snu.ac.kr
Re: AMBER: spherical boundary condition
(Mon Mar 14 2005 - 09:43:14 PST)
Re: AMBER: spherical boundary condition
(Mon Mar 14 2005 - 09:43:14 PST)
putra abdullah
AMBER: amber with mpich-G2
(Sun Mar 06 2005 - 18:55:44 PST)
Ray Luo
Re: AMBER: igb10 vlimit exceeded
(Thu Mar 31 2005 - 08:52:50 PST)
Re: AMBER: warning in PBSA
(Wed Mar 23 2005 - 09:42:34 PST)
Re: AMBER: igb=10 some vdW terms disappear?
(Tue Mar 22 2005 - 14:59:00 PST)
Re: AMBER: igb=10 some vdW terms disappear?
(Tue Mar 22 2005 - 13:54:57 PST)
Re: AMBER: igb=10 some vdW terms disappear?
(Mon Mar 21 2005 - 09:15:24 PST)
Re: AMBER: "personality" of Amber force field
(Thu Mar 17 2005 - 14:17:03 PST)
Rhoad, Jonathan S.
AMBER: RESP of negatively charged molecule
(Tue Mar 01 2005 - 13:39:05 PST)
Robert Duke
Re: AMBER: PMEMD with big systems
(Fri Mar 18 2005 - 16:12:24 PST)
Re: AMBER: compiler for amber8 on opteron
(Fri Mar 18 2005 - 05:11:22 PST)
Re: AMBER: Sander questions on dual-processor Sun with MPICH
(Wed Mar 09 2005 - 05:41:08 PST)
Re: AMBER: amber on sgi
(Wed Mar 09 2005 - 05:32:29 PST)
AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks
(Mon Mar 07 2005 - 08:47:02 PST)
Re: AMBER: amber with mpich-G2
(Sun Mar 06 2005 - 20:07:21 PST)
AMBER: PMEMD on Opterons; building/benchmarks/recommendations
(Tue Mar 01 2005 - 11:14:56 PST)
Robert J. Woods
Re: AMBER: Amber Performance in Parallel on Itanium
(Wed Mar 30 2005 - 08:47:25 PST)
AMBER: Amber Performance in Parallel on Itanium
(Wed Mar 30 2005 - 07:32:10 PST)
Ross Walker
RE: AMBER: Amber Performance in Parallel on Itanium
(Wed Mar 30 2005 - 08:20:14 PST)
RE: AMBER: tleap,xleap bond order for triple bonds
(Tue Mar 29 2005 - 15:58:51 PST)
RE: AMBER: missing residue
(Mon Mar 28 2005 - 08:23:47 PST)
RE: AMBER: Could not open file (trajin) with mode (r)
(Wed Mar 23 2005 - 10:13:56 PST)
RE: AMBER: wierd behavior of addions
(Tue Mar 22 2005 - 11:45:32 PST)
RE: AMBER: Amber8 Parallel installation troubles
(Tue Mar 22 2005 - 11:20:22 PST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
(Tue Mar 22 2005 - 10:05:15 PST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
(Mon Mar 21 2005 - 16:54:52 PST)
RE: AMBER: Problem saving file in xleap
(Tue Mar 15 2005 - 10:02:32 PST)
RE: AMBER: leap warnings
(Sun Mar 13 2005 - 22:56:17 PST)
RE: AMBER:
(Sun Mar 13 2005 - 16:29:08 PST)
RE: AMBER: The pressure
(Tue Mar 08 2005 - 18:20:44 PST)
RE: AMBER: capping?
(Tue Mar 08 2005 - 18:09:44 PST)
RE: AMBER: X Windows for LEaP on SGI
(Tue Mar 08 2005 - 18:05:01 PST)
RE: AMBER: Sander questions on dual-processor Sun with MPICH
(Tue Mar 08 2005 - 17:50:55 PST)
RE: AMBER: What PRESS is?
(Mon Mar 07 2005 - 20:07:37 PST)
RE: AMBER: Dihedral Energy calculation
(Wed Mar 02 2005 - 14:37:20 PST)
RE: AMBER: Dihedral Energy calculation
(Wed Mar 02 2005 - 08:48:56 PST)
RE: AMBER: problem with MD simulation
(Tue Mar 01 2005 - 08:51:40 PST)
RE: AMBER: NaNQ
(Tue Mar 01 2005 - 08:46:08 PST)
Ru-Zhen Li
Re: AMBER: problem with running AMBER with lam-mpi though PBS script
(Wed Mar 09 2005 - 17:48:56 PST)
AMBER: problem with running AMBER with lam-mpi though PBS script
(Wed Mar 09 2005 - 06:01:24 PST)
S.Sundar Raman
AMBER: how to cap regions
(Tue Mar 29 2005 - 21:00:12 PST)
AMBER: Minimization failure
(Tue Mar 29 2005 - 20:47:22 PST)
AMBER: Installation problem
(Wed Mar 02 2005 - 22:28:29 PST)
Sanghyun Park
AMBER: Re: inconsistent ordering in an improper dihedral of TRP
(Thu Mar 10 2005 - 19:08:25 PST)
sanjeev.mbu.iisc.ernet.in
Re: AMBER: MD: Water network analysis + visualization
(Tue Mar 22 2005 - 05:58:24 PST)
scopio
Re: AMBER: ptraj
(Fri Mar 11 2005 - 21:44:04 PST)
Re: AMBER: A problem about removing waters and counterions by ptraj
(Mon Mar 07 2005 - 05:48:40 PST)
AMBER: A problem about removing waters and counterions by ptraj
(Mon Mar 07 2005 - 04:28:19 PST)
Scott Brozell
Re: AMBER: Xleap execution problems on Solaris
(Tue Mar 01 2005 - 19:36:56 PST)
sebnem
AMBER: IDIEL in sander
(Thu Mar 10 2005 - 23:14:50 PST)
Sergio E. Wong
AMBER: REM mdinfo file
(Mon Mar 28 2005 - 17:51:45 PST)
Shekter, Lee
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
(Wed Mar 23 2005 - 08:29:57 PST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
(Mon Mar 21 2005 - 19:39:42 PST)
AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
(Mon Mar 21 2005 - 16:12:26 PST)
Stern, Julie
AMBER: leap bond error
(Thu Mar 31 2005 - 17:11:29 PST)
AMBER: tleap,xleap bond order for triple bonds
(Tue Mar 29 2005 - 14:49:38 PST)
AMBER: periodicity problem
(Wed Mar 16 2005 - 13:02:28 PST)
AMBER: in vacuo parameters
(Tue Mar 15 2005 - 15:14:44 PST)
Steve Seibold
AMBER: Trajectory problems
(Thu Mar 17 2005 - 13:44:23 PST)
AMBER: Trajectory problems
(Thu Mar 17 2005 - 11:21:37 PST)
Svetlana Kirillova
Re: AMBER: nonbonded interactions
(Wed Mar 23 2005 - 01:23:47 PST)
AMBER: nonbonded interaction
(Tue Mar 22 2005 - 08:37:54 PST)
tanc.uci.edu
AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs
(Tue Mar 22 2005 - 21:11:41 PST)
Tatyana B Mamonova
AMBER: ptraj analysis
(Mon Mar 28 2005 - 09:24:55 PST)
Thomas E. Cheatham, III
Re: AMBER: PTRAJ:"hbond" analysis
(Wed Mar 30 2005 - 09:40:16 PST)
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 08:23:21 PST)
Re: AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 11:01:33 PST)
Re: AMBER: Hydrogen bonding question
(Tue Mar 15 2005 - 07:59:00 PST)
Re: Re :AMBER: Holes in water
(Sat Mar 12 2005 - 14:20:32 PST)
Re: AMBER: how can I deal with the puzzle?
(Tue Mar 08 2005 - 19:53:48 PST)
Thomas Patko
Re: AMBER: X Windows for LEaP on SGI
(Tue Mar 08 2005 - 21:44:26 PST)
AMBER: AMBER8 Compile Error on Dual Opteron
(Sun Mar 06 2005 - 17:53:46 PST)
tomjas.poczta.onet.pl
Re: Re: AMBER: An error during minimization using RED
(Wed Mar 02 2005 - 05:18:00 PST)
Re: Re: AMBER: An error during minimization using RED
(Wed Mar 02 2005 - 01:15:15 PST)
AMBER: An error during minimization using RED
(Mon Feb 28 2005 - 23:18:55 PST)
Vidana.Epa.csiro.au
AMBER: re Updating Tutorials
(Thu Mar 17 2005 - 19:17:50 PST)
Viktor Hornak
Re: AMBER: TMD force constant
(Tue Mar 22 2005 - 05:42:37 PST)
Re: AMBER: Replica Exchange crashing
(Fri Mar 18 2005 - 04:51:48 PST)
Re: AMBER: restraintmask dimension
(Wed Mar 16 2005 - 05:46:27 PST)
Re: AMBER: Sander error
(Fri Mar 11 2005 - 08:36:38 PST)
Vineet Pande
Re: AMBER: PTRAJ:"hbond" analysis
(Thu Mar 31 2005 - 01:17:57 PST)
AMBER: PTRAJ:"hbond" analysis
(Wed Mar 30 2005 - 09:15:30 PST)
RE: AMBER: Parameter files for general lipids
(Mon Mar 28 2005 - 23:28:48 PST)
AMBER: PTRAJ:"hbond" doubts
(Sun Mar 27 2005 - 05:55:24 PST)
RE: AMBER: question about placing a substrate in a protein pocket
(Fri Mar 25 2005 - 01:41:18 PST)
RE: AMBER: Could not open file (trajin) with mode (r)
(Wed Mar 23 2005 - 08:26:06 PST)
RE: AMBER: ANAL module/AMBER8
(Tue Mar 22 2005 - 10:11:22 PST)
AMBER: ANAL module/AMBER8
(Tue Mar 22 2005 - 09:32:06 PST)
Re: AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 12:11:10 PST)
Re: AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 10:45:01 PST)
AMBER: Minimization of avg structure-SANDER Bomb
(Thu Mar 17 2005 - 06:50:03 PST)
AMBER: van der Waals interactions (PTRAJ)
(Thu Mar 17 2005 - 06:07:12 PST)
RE: AMBER: question about amber parameter file format etc.
(Wed Mar 16 2005 - 10:06:53 PST)
Re: AMBER: Velocity Info
(Wed Mar 16 2005 - 08:02:04 PST)
AMBER: Velocity Info
(Wed Mar 16 2005 - 06:08:42 PST)
RE: AMBER: Problems Binding Protein to DNA
(Wed Mar 09 2005 - 03:16:44 PST)
Vojtěch Klusák
AMBER: Sander error
(Thu Mar 10 2005 - 04:03:21 PST)
Wai Keat Yam
Re: AMBER: R.E.D
(Sun Mar 06 2005 - 18:31:57 PST)
AMBER: R.E.D
(Sat Mar 05 2005 - 21:14:49 PST)
Wei Wang
AMBER: parameter meaning
(Fri Mar 18 2005 - 10:33:15 PST)
Wei Zhang
Re: AMBER: A few question about RDF input preparation
(Thu Mar 24 2005 - 03:58:47 PST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Wed Mar 23 2005 - 16:49:14 PST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Tue Mar 22 2005 - 17:34:26 PST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
(Tue Mar 22 2005 - 16:29:26 PST)
Re: AMBER: Amber8 Parallel installation troubles
(Tue Mar 22 2005 - 15:39:06 PST)
Wells, David H
AMBER: igb10 vlimit exceeded
(Thu Mar 31 2005 - 01:08:55 PST)
Re: AMBER: igb=10 some vdW terms disappear?
(Wed Mar 23 2005 - 10:40:53 PST)
AMBER: igb=10 some vdW terms disappear?
(Sun Mar 20 2005 - 23:54:23 PST)
Wen Li
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 11:52:34 PST)
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 08:14:44 PST)
Re: AMBER: align snapshots to a reference
(Wed Mar 30 2005 - 07:43:21 PST)
AMBER: align snapshots to a reference
(Tue Mar 29 2005 - 13:38:36 PST)
xhu1.memphis.edu
Re: AMBER: radii "leap" from which file
(Tue Mar 08 2005 - 19:06:22 PST)
AMBER: radii "leap" from which file
(Tue Mar 08 2005 - 11:34:48 PST)
Xiao He
Re: Re: AMBER: Sander: idecomp
(Mon Mar 28 2005 - 05:44:53 PST)
Xin Hu
AMBER: across-correlation in ptraj
(Wed Mar 02 2005 - 08:20:09 PST)
xueping
AMBER: missing residue
(Sun Mar 27 2005 - 23:34:17 PST)
Re: AMBER: ptraj
(Fri Mar 11 2005 - 23:08:37 PST)
AMBER: ptraj
(Fri Mar 11 2005 - 20:56:29 PST)
Yanze Zhang
AMBER: building helix bundle
(Thu Mar 17 2005 - 13:30:54 PST)
AMBER: A problem about Gaussian
(Thu Mar 03 2005 - 14:38:59 PST)
Ye Mei
Re: RE: AMBER: problem with MD simulation
(Fri Mar 04 2005 - 17:46:24 PST)
AMBER: problem with MD simulation
(Tue Mar 01 2005 - 00:00:31 PST)
yen li
RE: AMBER: Dihedral Energy calculation
(Fri Mar 04 2005 - 13:29:08 PST)
RE: AMBER: Dihedral Energy calculation
(Wed Mar 02 2005 - 10:03:24 PST)
RE: AMBER: Dihedral Energy calculation
(Wed Mar 02 2005 - 04:37:01 PST)
AMBER: Dihedral Energy calculation
(Tue Mar 01 2005 - 10:12:56 PST)
YoungJin Cho
Re: AMBER: creating a new residue
(Tue Mar 01 2005 - 07:18:16 PST)
Yuuki Komata
Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5)
(Sun Mar 06 2005 - 17:14:18 PST)
ZhangJian
AMBER: For further question about Targeted MD
(Wed Mar 09 2005 - 04:48:44 PST)
Re: Re: AMBER: how can I deal with the puzzle?
(Tue Mar 08 2005 - 23:59:42 PST)
Last message date
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Fri Apr 01 2005 - 03:53:01 PST
Archived on
: Mon Dec 23 2024 - 05:53:21 PST
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