Amber Archive Nov 2008 by thread
354 messages
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Starting
Sun Nov 02 2008 - 05:09:57 PST,
Ending
Fri Dec 05 2008 - 18:12:45 PST
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Re: AMBER: Optimal compiling of amber on XT3
Patrick McCarren
(Sat Nov 01 2008 - 00:13:08 PDT)
AMBER: Question on AMBER MD Implications
Campbell, Patrick
(Sat Nov 01 2008 - 03:01:17 PDT)
AMBER: Minimisation and heating under GB conditions
Francesco Pietra
(Mon Nov 03 2008 - 00:58:58 PST)
Re: AMBER: Minimisation and heating under GB conditions
Carlos Simmerling
(Mon Nov 03 2008 - 03:29:25 PST)
Re: AMBER: Minimisation and heating under GB conditions
David A. Case
(Mon Nov 03 2008 - 06:01:59 PST)
Re: AMBER: Minimisation and heating under GB conditions
Francesco Pietra
(Mon Nov 03 2008 - 06:17:34 PST)
Re: AMBER: Minimisation and heating under GB conditions
Francesco Pietra
(Mon Nov 03 2008 - 10:07:14 PST)
Re: AMBER: Minimisation and heating under GB conditions
Carlos Simmerling
(Mon Nov 03 2008 - 10:52:23 PST)
Re: AMBER: Minimisation and heating under GB conditions
Francesco Pietra
(Mon Nov 03 2008 - 23:27:55 PST)
Re: AMBER: Minimisation and heating under GB conditions
Francesco Pietra
(Mon Nov 03 2008 - 06:08:42 PST)
Re: AMBER: Minimisation and heating under GB conditions
Carlos Simmerling
(Mon Nov 03 2008 - 06:45:22 PST)
RE: AMBER: error message of xleap
Catein Catherine
(Mon Nov 03 2008 - 01:52:24 PST)
RE: AMBER: error message of xleap
Ross Walker
(Mon Nov 03 2008 - 09:05:54 PST)
AMBER: temperature error in md calculation
Catein Catherine
(Wed Nov 05 2008 - 00:11:41 PST)
Re: AMBER: temperature error in md calculation
David A. Case
(Wed Nov 05 2008 - 06:10:41 PST)
AMBER: Problems compiling leap on Altix Cluster
John Finke
(Mon Nov 03 2008 - 12:51:54 PST)
RE: AMBER: Problems compiling leap on Altix Cluster
Ross Walker
(Mon Nov 03 2008 - 13:47:06 PST)
Re: AMBER: Problems compiling leap on Altix Cluster
John Finke
(Mon Nov 03 2008 - 15:43:09 PST)
RE: AMBER: Problems compiling leap on Altix Cluster
Ross Walker
(Mon Nov 03 2008 - 16:06:07 PST)
AMBER:
Prem Prakash Pathak
(Mon Nov 03 2008 - 19:20:09 PST)
AMBER: process_mdout modify
Naser Alijabbari
(Mon Nov 03 2008 - 22:20:07 PST)
RE: AMBER: process_mdout modify
Ross Walker
(Tue Nov 04 2008 - 07:41:33 PST)
Re: AMBER: MM_PBSA binding error
Larry Layne
(Tue Nov 04 2008 - 05:51:22 PST)
RE: AMBER: MM_PBSA binding error
Ray Luo
(Tue Nov 04 2008 - 11:18:54 PST)
AMBER: problem with group input and NMR restaints
priya priya
(Tue Nov 04 2008 - 07:20:09 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Tue Nov 04 2008 - 07:35:46 PST)
RE: AMBER: problem with group input and NMR restaints
Ross Walker
(Tue Nov 04 2008 - 07:46:17 PST)
RE: AMBER: problem with group input and NMR restaints
priya priya
(Tue Nov 04 2008 - 08:16:34 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Tue Nov 04 2008 - 08:41:22 PST)
Re: AMBER: problem with group input and NMR restaints
priya priya
(Tue Nov 04 2008 - 09:38:37 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Tue Nov 04 2008 - 09:53:48 PST)
Re: AMBER: problem with group input and NMR restaints
priya priya
(Wed Nov 05 2008 - 08:05:05 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Wed Nov 05 2008 - 08:53:09 PST)
AMBER: Br - ion defined ?
Chih-Ying Lin
(Wed Nov 05 2008 - 09:20:36 PST)
Re: AMBER: problem with group input and NMR restaints
priya priya
(Wed Nov 05 2008 - 09:22:33 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Wed Nov 05 2008 - 10:13:29 PST)
Re: AMBER: problem with group input and NMR restaints
priya priya
(Wed Nov 05 2008 - 12:00:48 PST)
Re: AMBER: problem with group input and NMR restaints
Carlos Simmerling
(Wed Nov 05 2008 - 12:39:29 PST)
AMBER: AMBER10: QMMM parallel test error
Yang, Ping
(Wed Nov 05 2008 - 15:44:27 PST)
RE: AMBER: AMBER10: QMMM parallel test error
Ross Walker
(Wed Nov 05 2008 - 17:41:27 PST)
RE: AMBER: AMBER10: QMMM parallel test error
Yang, Ping
(Wed Nov 05 2008 - 19:57:29 PST)
AMBER: Steered MD and Jarzynski in pulling simulations
Samuel Genheden
(Wed Nov 05 2008 - 06:48:33 PST)
Re: AMBER: Steered MD and Jarzynski in pulling simulations
M. L. Dodson
(Wed Nov 05 2008 - 07:04:23 PST)
Re: AMBER: Steered MD and Jarzynski in pulling simulations
Gustavo Seabra
(Sun Nov 09 2008 - 18:36:38 PST)
Re: AMBER: ptraj and netcdf with AmberTools1.2 ?
Dave Rogers
(Wed Nov 05 2008 - 13:34:21 PST)
Re: AMBER: ptraj and netcdf with AmberTools1.2 ?
David A. Case
(Thu Nov 06 2008 - 04:08:00 PST)
AMBER: Glycam
Neha Gandhi
(Wed Nov 05 2008 - 20:02:01 PST)
Re: AMBER: Glycam
Lachele Foley (Lists)
(Thu Nov 06 2008 - 07:01:48 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query
Ross Walker
(Thu Nov 06 2008 - 00:18:22 PST)
AMBER: Force field for Gd (gadolinium)?
Lili Peng
(Thu Nov 06 2008 - 01:05:26 PST)
AMBER: gigabit ethernet cards and switches
Alessandro Nascimento
(Thu Nov 06 2008 - 08:51:43 PST)
RE: AMBER: gigabit ethernet cards and switches
Ross Walker
(Thu Nov 06 2008 - 10:37:04 PST)
Re: AMBER: gigabit ethernet cards and switches
Alessandro Nascimento
(Thu Nov 06 2008 - 11:28:46 PST)
Re: AMBER: gigabit ethernet cards and switches
Mengjuei Hsieh
(Thu Nov 06 2008 - 18:39:23 PST)
AMBER: ptraj new mask parser: differences from ambmask and core dumps
M. L. Dodson
(Thu Nov 06 2008 - 10:31:07 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
Jianyin Shao
(Thu Nov 06 2008 - 14:48:47 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
M. L. Dodson
(Thu Nov 06 2008 - 15:49:49 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
Jianyin Shao
(Fri Nov 07 2008 - 08:24:03 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
M. L. Dodson
(Fri Nov 07 2008 - 15:15:06 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
M. L. Dodson
(Mon Nov 10 2008 - 10:23:17 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query
Ross Walker
(Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: QUERRY?
Ross Walker
(Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: Problem with the NEB tutorial
Ross Walker
(Thu Nov 06 2008 - 11:24:30 PST)
AMBER: RE: problems about TMD in your tutorial
Ross Walker
(Thu Nov 06 2008 - 11:32:58 PST)
AMBER: coot mutation
Taufik Al-Sarraj
(Thu Nov 06 2008 - 12:19:00 PST)
AMBER: Extracting periodic box size deviation
CJ Dickson
(Thu Nov 06 2008 - 15:29:20 PST)
AMBER: using "EP" for dummy atom
Ashish Sangwai
(Thu Nov 06 2008 - 17:24:23 PST)
RE: AMBER: using "EP" for dummy atom
Ross Walker
(Thu Nov 06 2008 - 18:05:22 PST)
Re: AMBER: Extracting periodic box size deviation
Bill Ross
(Thu Nov 06 2008 - 17:42:35 PST)
AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
parul sharma
(Fri Nov 07 2008 - 01:52:07 PST)
Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
David A. Case
(Fri Nov 07 2008 - 21:33:48 PST)
AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
Francois Theillet
(Fri Nov 07 2008 - 07:24:36 PST)
Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
Lachele Foley (Lists)
(Fri Nov 07 2008 - 13:25:18 PST)
AMBER: AMBER question: perturbed charge twice the unperturbed
Edward M
(Sat Nov 08 2008 - 21:36:54 PST)
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
David A. Case
(Sun Nov 09 2008 - 09:16:52 PST)
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
E.M.
(Sun Nov 09 2008 - 15:08:05 PST)
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
David A. Case
(Thu Nov 13 2008 - 12:39:41 PST)
Re: AMBER: problem with zMatrix in tleap
David A. Case
(Sun Nov 09 2008 - 09:17:02 PST)
AMBER: looks like I have problem with "make clean" command
drugdesign
(Sun Nov 09 2008 - 23:27:22 PST)
Re: AMBER: looks like I have problem with "make clean" command
David A. Case
(Mon Nov 10 2008 - 04:39:26 PST)
AMBER: RE: problems about TMD in your tutorial
Ross Walker
(Mon Nov 10 2008 - 00:20:18 PST)
AMBER: ff02 in nmode gives error "too many dihedrals" ?
Jacob Kongsted
(Mon Nov 10 2008 - 01:16:36 PST)
Re: AMBER: ff02 in nmode gives error "too many dihedrals" ?
David A. Case
(Wed Nov 12 2008 - 07:13:45 PST)
AMBER: test sander error in amber7
Saiful Islam
(Mon Nov 10 2008 - 05:43:45 PST)
Re: AMBER: test sander error in amber7
Saiful Islam
(Mon Nov 10 2008 - 23:36:30 PST)
Re: AMBER: test sander error in amber7
David A. Case
(Tue Nov 11 2008 - 04:15:51 PST)
AMBER: mm_pbsa.pl and Amber10
Stephan.Reiling.sanofi-aventis.com
(Mon Nov 10 2008 - 08:05:27 PST)
Re: AMBER: mm_pbsa.pl and Amber10
Holger Gohlke
(Mon Nov 10 2008 - 09:12:16 PST)
AMBER: Amber 9 installation problems
drugdesign
(Mon Nov 10 2008 - 03:27:39 PST)
Re: AMBER: Amber 9 installation problems
Shozeb Haider
(Mon Nov 10 2008 - 08:37:54 PST)
Re: AMBER: Amber 9 installation problems
David A. Case
(Mon Nov 10 2008 - 09:32:39 PST)
Re: AMBER: Amber 9 installation problems
drugdesign
(Tue Nov 11 2008 - 06:13:32 PST)
Re: AMBER: Amber 9 installation problems
David A. Case
(Tue Nov 11 2008 - 15:22:54 PST)
Re: AMBER: Amber 9 installation problems
drugdesign
(Tue Nov 11 2008 - 23:36:51 PST)
RE: AMBER: Amber 9 installation problems
Ross Walker
(Wed Nov 12 2008 - 07:21:59 PST)
Re: AMBER: Amber 9 installation problems
drugdesign
(Wed Nov 12 2008 - 11:09:47 PST)
RE: AMBER: Amber 9 installation problems
Ross Walker
(Wed Nov 12 2008 - 13:16:03 PST)
AMBER: Your "bellymask-patch"
Jochen Heil
(Thu Nov 13 2008 - 05:45:30 PST)
RE: AMBER: Your "bellymask-patch"
Ross Walker
(Thu Nov 13 2008 - 10:17:58 PST)
AMBER: Restraints
Joseph Nachman
(Thu Nov 13 2008 - 10:59:23 PST)
Re: AMBER: Restraints
Ashish Sangwai
(Thu Nov 13 2008 - 11:11:45 PST)
RE: AMBER: Restraints
Ross Walker
(Thu Nov 13 2008 - 11:11:53 PST)
Re: AMBER: Amber 9 installation problems
drugdesign
(Thu Nov 13 2008 - 08:25:34 PST)
Re: AMBER: changing pdb structure
Taufik Al-Sarraj
(Mon Nov 10 2008 - 12:31:39 PST)
Re: AMBER: changing pdb structure
Carlos Simmerling
(Mon Nov 10 2008 - 12:37:32 PST)
Re: AMBER: changing pdb structure
Taufik Al-Sarraj
(Mon Nov 10 2008 - 13:10:23 PST)
Re: AMBER: changing pdb structure
Carlos Simmerling
(Tue Nov 11 2008 - 03:35:42 PST)
Re: AMBER: changing pdb structure
Taufik Al-Sarraj
(Mon Nov 24 2008 - 15:37:24 PST)
AMBER: xLeap error
Lili Peng
(Mon Nov 10 2008 - 12:45:58 PST)
Re: AMBER: xLeap error
Lili Peng
(Mon Nov 10 2008 - 13:49:53 PST)
Re: AMBER: xLeap error
Mark Williamson
(Mon Nov 10 2008 - 13:58:27 PST)
AMBER: resp charges in parameterization
Mark M Huntress
(Wed Nov 12 2008 - 08:24:55 PST)
Re: AMBER: resp charges in parameterization
steinbrt.rci.rutgers.edu
(Wed Nov 12 2008 - 08:44:17 PST)
AMBER: Newbie question: partial minimization in implicit solvent
Jochen Heil
(Wed Nov 12 2008 - 09:48:38 PST)
Re: AMBER: Newbie question: partial minimization in implicit solvent
Carlos Simmerling
(Wed Nov 12 2008 - 12:47:56 PST)
RE: AMBER: Newbie question: partial minimization in implicit solvent
Ross Walker
(Wed Nov 12 2008 - 13:00:39 PST)
AMBER: Problem with evaporating water over longer simulation times
Sasha Buzko
(Wed Nov 12 2008 - 11:14:00 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
Gustavo Seabra
(Wed Nov 12 2008 - 11:48:01 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
steinbrt.rci.rutgers.edu
(Wed Nov 12 2008 - 11:57:33 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
Sasha Buzko
(Wed Nov 12 2008 - 12:56:16 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
Sasha Buzko
(Wed Nov 12 2008 - 16:53:06 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
Adrian Roitberg
(Wed Nov 12 2008 - 17:06:38 PST)
AMBER: question about ptraj
rai001.student.ucr.edu
(Wed Nov 12 2008 - 22:30:48 PST)
Re: AMBER: question about ptraj
Jianyin Shao
(Thu Nov 13 2008 - 15:38:44 PST)
Re: AMBER: question about ptraj
rai001.student.ucr.edu
(Thu Nov 13 2008 - 15:56:49 PST)
AMBER: PB Radii
Swarup Gupta
(Wed Nov 12 2008 - 23:06:34 PST)
Re: AMBER: PB Radii
David A. Case
(Thu Nov 13 2008 - 04:01:57 PST)
Re: AMBER: PB Radii
Swarup Gupta
(Sat Nov 15 2008 - 19:44:25 PST)
Re: AMBER: PB Radii
Swarup Gupta
(Mon Nov 17 2008 - 03:24:42 PST)
Re: AMBER: PB Radii
Carlos Simmerling
(Mon Nov 17 2008 - 03:30:41 PST)
AMBER: load opls force field
oguz gurbulak
(Thu Nov 13 2008 - 02:38:11 PST)
Re: AMBER: load opls force field
David A. Case
(Thu Nov 13 2008 - 04:06:40 PST)
Re: AMBER: load opls force field
Bill Ross
(Thu Nov 13 2008 - 12:32:19 PST)
AMBER: Chloride anion ligands leave the protein during MD
Francesco Pietra
(Thu Nov 13 2008 - 07:06:06 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
Gustavo Seabra
(Fri Nov 14 2008 - 05:40:45 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
Adrian Roitberg
(Fri Nov 14 2008 - 06:00:33 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
Jiri Sponer
(Fri Nov 14 2008 - 06:19:33 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
Francesco Pietra
(Sun Nov 16 2008 - 03:17:00 PST)
AMBER: MM-PBSA and trajectory input
Arturas Ziemys
(Thu Nov 13 2008 - 09:22:36 PST)
AMBER: segmentation fault when restarting periodic structure
Diddo Diddens
(Fri Nov 14 2008 - 04:47:23 PST)
AMBER: subroutine for torsional potential
CHAMI F.
(Fri Nov 14 2008 - 06:16:37 PST)
Re: AMBER: subroutine for torsional potential
steinbrt.rci.rutgers.edu
(Fri Nov 14 2008 - 06:49:25 PST)
Re: AMBER: segmentation fault when restarting periodic structure
David A. Case
(Tue Nov 18 2008 - 06:20:41 PST)
AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm?
Siddharth Rastogi
(Fri Nov 14 2008 - 06:02:34 PST)
AMBER: NMR optimization with group averages (IGR1 / IGR2)
Ryan Pavlovicz
(Fri Nov 14 2008 - 07:59:36 PST)
AMBER: Sander *.top and *.crd file from PDB file
Chin, Keith B
(Fri Nov 14 2008 - 11:43:41 PST)
Re: AMBER: Sander *.top and *.crd file from PDB file
Gustavo Seabra
(Fri Nov 14 2008 - 12:30:21 PST)
RE: AMBER: Sander *.top and *.crd file from PDB file
Chin, Keith B
(Fri Nov 14 2008 - 12:55:57 PST)
Re: AMBER: Sander *.top and *.crd file from PDB file
Carlos Simmerling
(Fri Nov 14 2008 - 13:00:30 PST)
AMBER: Ptraj Normal Mode Analysis
Jesse Jun
(Fri Nov 14 2008 - 13:19:31 PST)
AMBER: organic solvents
Marcelo Puiatti
(Fri Nov 14 2008 - 15:20:30 PST)
Re: AMBER: organic solvents
Mark Williamson
(Fri Nov 14 2008 - 15:28:10 PST)
Re: AMBER: organic solvents
FyD
(Fri Nov 14 2008 - 23:56:30 PST)
AMBER: Trajectory file ended and unit 24 error on open inptraj
Siddharth Rastogi
(Sat Nov 15 2008 - 07:33:10 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
Carlos Simmerling
(Sat Nov 15 2008 - 07:44:32 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
Siddharth Rastogi
(Sat Nov 15 2008 - 22:18:59 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
Carlos Simmerling
(Sun Nov 16 2008 - 04:42:22 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
Gustavo Seabra
(Sun Nov 16 2008 - 08:05:42 PST)
AMBER: How to create *.top & *.crd file with hexagonal lattice
Chin, Keith B
(Sun Nov 16 2008 - 17:02:05 PST)
Re: AMBER: How to create *.top & *.crd file with hexagonal lattice
David A. Case
(Tue Nov 18 2008 - 06:05:12 PST)
AMBER: problem
Arturas Ziemys
(Sun Nov 16 2008 - 21:07:38 PST)
Re: AMBER: problem
FyD
(Sun Nov 16 2008 - 23:40:33 PST)
RE: AMBER: problem
Arturas Ziemys
(Mon Nov 17 2008 - 20:36:25 PST)
Re: AMBER: problem
David A. Case
(Tue Nov 18 2008 - 04:15:57 PST)
Re: AMBER: problem
Arturas Ziemys
(Tue Nov 18 2008 - 07:07:19 PST)
AMBER: High ESURF
Siddharth Rastogi
(Mon Nov 17 2008 - 00:07:57 PST)
Re: AMBER: High ESURF
Andreas Svrcek-Seiler
(Mon Nov 17 2008 - 00:24:02 PST)
AMBER: velocity units?
Jose Borreguero
(Mon Nov 17 2008 - 08:14:35 PST)
Re: AMBER: velocity units?
David A. Case
(Mon Nov 17 2008 - 08:53:19 PST)
AMBER: ptraj closest command
steinbrt.rci.rutgers.edu
(Mon Nov 17 2008 - 08:14:11 PST)
Re: AMBER: ptraj closest command
Gustavo Seabra
(Mon Nov 17 2008 - 08:51:42 PST)
AMBER: RESTRAINTS: no valid redirection found
Francesco Pietra
(Mon Nov 17 2008 - 09:15:17 PST)
Fwd: AMBER: RESTRAINTS: no valid redirection found
Francesco Pietra
(Mon Nov 17 2008 - 09:35:04 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
Robert Duke
(Mon Nov 17 2008 - 09:34:50 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
Francesco Pietra
(Mon Nov 17 2008 - 10:00:25 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
Francesco Pietra
(Mon Nov 17 2008 - 11:21:01 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
Robert Duke
(Mon Nov 17 2008 - 11:58:18 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
Francesco Pietra
(Mon Nov 17 2008 - 13:30:54 PST)
AMBER: AMBER10 installation question
Jeffrey
(Mon Nov 17 2008 - 19:20:14 PST)
Re: AMBER: AMBER10 installation question
David A. Case
(Tue Nov 18 2008 - 04:05:07 PST)
Re: Re: AMBER: AMBER10 installation question
Jeffrey
(Wed Nov 19 2008 - 05:27:13 PST)
AMBER: SPCFW temperature oscillations
Naser Alijabbari
(Mon Nov 17 2008 - 20:19:12 PST)
Re: AMBER: SPCFW temperature oscillations
David A. Case
(Tue Nov 18 2008 - 04:13:16 PST)
Re: AMBER: SPCFW temperature oscillations
Robert Duke
(Tue Nov 18 2008 - 05:16:27 PST)
AMBER: Equilibration protocol for large protein
Dmitri Nilov
(Tue Nov 18 2008 - 08:33:26 PST)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
John Chodera
(Tue Nov 18 2008 - 11:58:22 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
David A. Case
(Wed Nov 19 2008 - 06:35:45 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
Alan
(Thu Nov 20 2008 - 03:48:56 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
Alan
(Thu Nov 20 2008 - 04:13:09 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
David A. Case
(Thu Nov 20 2008 - 05:38:37 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
David A. Case
(Thu Nov 20 2008 - 05:36:48 PST)
AMBER: AMBER10 compiling SANDER parallel problem
Hazard, E. Starr
(Tue Nov 18 2008 - 12:48:31 PST)
Re: AMBER: AMBER10 compiling SANDER parallel problem
David A. Case
(Tue Nov 18 2008 - 13:25:23 PST)
AMBER:
Chin, Keith B
(Tue Nov 18 2008 - 15:39:26 PST)
AMBER: PMEMD with AMOEBA parms including a lone pair site
Margaret Johnson
(Tue Nov 18 2008 - 18:29:04 PST)
Re: AMBER: PMEMD with AMOEBA parms including a lone pair site
Robert Duke
(Tue Nov 18 2008 - 18:50:14 PST)
AMBER: question - gaff and leaprc.ff03ua
oguz gurbulak
(Wed Nov 19 2008 - 05:56:17 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
David A. Case
(Wed Nov 19 2008 - 07:08:02 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
oguz gurbulak
(Sun Nov 23 2008 - 08:43:48 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
David A. Case
(Sun Nov 23 2008 - 13:49:37 PST)
AMBER: MOLYBDENUM
Joachim Reichelt
(Wed Nov 19 2008 - 06:14:31 PST)
AMBER: problem with cartesian restraints with NTP simulations
Barbault Florent
(Wed Nov 19 2008 - 06:50:13 PST)
Re: AMBER: problem with cartesian restraints with NTP simulations
David A. Case
(Wed Nov 19 2008 - 07:02:56 PST)
AMBER: Amber on linux
Marudachalam S
(Wed Nov 19 2008 - 09:58:10 PST)
Re: AMBER: Amber on linux
steinbrt.rci.rutgers.edu
(Wed Nov 19 2008 - 11:47:45 PST)
AMBER: How to manually adjust periodic boundary conditions (PBC)
Chin, Keith B
(Wed Nov 19 2008 - 11:58:41 PST)
Re: AMBER: How to manually adjust periodic boundary conditions (PBC)
David A. Case
(Wed Nov 19 2008 - 15:35:33 PST)
RE: AMBER: How to manually adjust periodic boundary conditions (PBC)
Chin, Keith B
(Wed Nov 19 2008 - 17:15:17 PST)
Re: AMBER: How to manually adjust periodic boundary conditions (PBC)
David A. Case
(Thu Nov 20 2008 - 12:52:57 PST)
AMBER: compiling ambertools with intel compilers
Alan
(Thu Nov 20 2008 - 02:27:26 PST)
Re: AMBER: compiling ambertools with intel compilers
David A. Case
(Thu Nov 20 2008 - 04:04:22 PST)
Re: AMBER: compiling ambertools with intel compilers
Alan
(Thu Nov 20 2008 - 04:10:58 PST)
Re: AMBER: compiling ambertools with intel compilers
Francesco Pietra
(Thu Nov 20 2008 - 08:38:29 PST)
Re: AMBER: compiling ambertools with intel compilers
Francesco Pietra
(Thu Nov 20 2008 - 10:44:21 PST)
Re: AMBER: compiling ambertools with intel compilers
David A. Case
(Thu Nov 20 2008 - 12:50:27 PST)
Re: AMBER: compiling ambertools with intel compilers
Thomas Patko
(Thu Nov 20 2008 - 14:15:58 PST)
Re: AMBER: compiling ambertools with intel compilers
David A. Case
(Fri Nov 21 2008 - 09:44:58 PST)
AMBER: AMBER forfield choose
Wang,Ying
(Thu Nov 20 2008 - 06:32:24 PST)
Re: AMBER: AMBER forfield choose
Barbault Florent
(Thu Nov 20 2008 - 06:45:20 PST)
Re: AMBER: AMBER forfield choose
Carlos Simmerling
(Thu Nov 20 2008 - 07:51:18 PST)
Re: AMBER: AMBER forfield choose
Barbault Florent
(Thu Nov 20 2008 - 08:21:17 PST)
Re: AMBER: AMBER forfield choose
Carlos Simmerling
(Thu Nov 20 2008 - 08:21:51 PST)
Re: AMBER: AMBER forfield choose
Wang,Ying
(Thu Nov 20 2008 - 07:05:28 PST)
Re: AMBER: AMBER forfield choose
mori.cerm.unifi.it
(Thu Nov 20 2008 - 07:09:28 PST)
Re: AMBER: AMBER forfield choose
Wang,Ying
(Thu Nov 20 2008 - 07:17:45 PST)
AMBER: CG and HC atoms partial charges in AMBER
Stephane Abel
(Thu Nov 20 2008 - 07:40:17 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
David A. Case
(Thu Nov 20 2008 - 07:56:15 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
Stephane Abel
(Thu Nov 20 2008 - 08:26:10 PST)
RE: AMBER: CG and HC atoms partial charges in AMBER
Matthew Tessier
(Thu Nov 20 2008 - 08:40:43 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
Stephane Abel
(Thu Nov 20 2008 - 08:51:25 PST)
RE: AMBER: CG and HC atoms partial charges in AMBER
Matthew Tessier
(Thu Nov 20 2008 - 09:09:16 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
Stephane Abel
(Thu Nov 20 2008 - 09:07:07 PST)
RE: AMBER: CG and HC atoms partial charges in AMBER
Matthew Tessier
(Thu Nov 20 2008 - 08:15:56 PST)
AMBER: pmemd
Jeremy Harris
(Thu Nov 20 2008 - 08:27:14 PST)
RE: AMBER: pmemd
Ross Walker
(Thu Nov 20 2008 - 08:36:51 PST)
Re: AMBER: pmemd
Robert Duke
(Thu Nov 20 2008 - 08:40:36 PST)
Re: AMBER: Force field for Gd3+ (metal ion)?
Lili Peng
(Thu Nov 20 2008 - 16:00:29 PST)
AMBER: Problems for use manganese molecules
vallespardojl.chem.leidenuniv.nl
(Fri Nov 21 2008 - 01:06:37 PST)
Re: AMBER: Problems for use manganese molecules
David A. Case
(Fri Nov 21 2008 - 04:46:22 PST)
AMBER: ptraj center problem
robaldo.dna.uba.ar
(Fri Nov 21 2008 - 09:31:27 PST)
Re: AMBER: ptraj center problem
Carlos Simmerling
(Fri Nov 21 2008 - 10:42:17 PST)
Re: AMBER: ptraj center problem
robaldo.dna.uba.ar
(Fri Nov 21 2008 - 12:04:56 PST)
AMBER: Electrostatic Energy Components
guardiani.fi.infn.it
(Fri Nov 21 2008 - 11:29:08 PST)
RE: AMBER: Electrostatic Energy Components
Ross Walker
(Fri Nov 21 2008 - 13:36:20 PST)
RE: AMBER: Electrostatic Energy Components
Ilyas Yildirim
(Fri Nov 21 2008 - 14:11:14 PST)
RE: AMBER: Electrostatic Energy Components
Ross Walker
(Fri Nov 21 2008 - 14:33:30 PST)
Re: AMBER: Electrostatic Energy Components
Carlos Simmerling
(Fri Nov 21 2008 - 15:46:10 PST)
RE: AMBER: Electrostatic Energy Components
Ilyas Yildirim
(Fri Nov 21 2008 - 16:12:44 PST)
RE: AMBER: Electrostatic Energy Components
Ross Walker
(Fri Nov 21 2008 - 16:20:56 PST)
Re: AMBER: Electrostatic Energy Components
Jojart Balazs
(Fri Nov 21 2008 - 23:53:46 PST)
RE: AMBER: Electrostatic Energy Components
Ross Walker
(Sat Nov 22 2008 - 09:21:22 PST)
Re: AMBER: Electrostatic Energy Components
Carlos Simmerling
(Sat Nov 22 2008 - 09:42:53 PST)
Re: AMBER: Electrostatic Energy Components
David A. Case
(Sat Nov 22 2008 - 12:37:51 PST)
Re: AMBER: Electrostatic Energy Components
Jojart Balazs
(Sun Nov 23 2008 - 00:34:01 PST)
Re: AMBER: Electrostatic Energy Components
David A. Case
(Mon Nov 24 2008 - 04:14:13 PST)
Re: AMBER: Electrostatic Energy Components
Balazs JOJART
(Mon Nov 24 2008 - 04:19:42 PST)
AMBER: nonbonded parameters for titanium
saurabh agrawal
(Mon Nov 24 2008 - 08:57:56 PST)
Re: AMBER: Electrostatic Energy Components
Carlos Simmerling
(Sat Nov 22 2008 - 09:41:48 PST)
Re: AMBER: Electrostatic Energy Components
Junmei Wang
(Sun Nov 23 2008 - 19:36:38 PST)
AMBER: RE: About restart amber
Ross Walker
(Fri Nov 21 2008 - 13:45:16 PST)
Re: AMBER: RE: About restart amber
Francesco Pietra
(Sat Nov 22 2008 - 08:03:02 PST)
RE: AMBER: RE: About restart amber
Ross Walker
(Sat Nov 22 2008 - 09:18:57 PST)
Re: AMBER: RE: About restart amber
Francesco Pietra
(Mon Nov 24 2008 - 13:22:44 PST)
Re: AMBER: RE: About restart amber
Francesco Pietra
(Tue Nov 25 2008 - 00:00:38 PST)
Re: AMBER: RE: About restart amber
Robert Duke
(Tue Nov 25 2008 - 06:27:16 PST)
Re: AMBER: RE: About restart amber
Francesco Pietra
(Tue Nov 25 2008 - 12:59:35 PST)
Re: AMBER: RE: About restart amber
Robert Duke
(Tue Nov 25 2008 - 13:23:09 PST)
Re: AMBER: RE: About restart amber
Francesco Pietra
(Tue Nov 25 2008 - 13:47:35 PST)
Re: AMBER: RE: About restart amber
Robert Duke
(Tue Nov 25 2008 - 13:55:15 PST)
AMBER: compiling amber 10
Andrei Neamtu
(Fri Nov 21 2008 - 23:26:58 PST)
Re: AMBER: compiling amber 10
David A. Case
(Sat Nov 22 2008 - 12:33:54 PST)
AMBER: QM/MM simulation
Syed Tarique Moin
(Sat Nov 22 2008 - 00:00:36 PST)
Re: AMBER: QM/MM simulation
David A. Case
(Sat Nov 22 2008 - 06:53:50 PST)
Re: AMBER: QM/MM simulation
Syed Tarique Moin
(Sat Nov 22 2008 - 07:11:12 PST)
RE: AMBER: QM/MM simulation
Ross Walker
(Sat Nov 22 2008 - 08:59:49 PST)
Re: AMBER: QM/MM simulation
Gustavo Seabra
(Sat Nov 22 2008 - 11:19:22 PST)
AMBER: AMBER10 failing to compile PMEMD
Hazard, E. Starr
(Sat Nov 22 2008 - 14:06:03 PST)
Re: AMBER: AMBER10 failing to compile PMEMD
Robert Duke
(Sat Nov 22 2008 - 14:42:50 PST)
AMBER: AdoMet parameterization with antechamber
Jeffrey
(Sun Nov 23 2008 - 07:55:30 PST)
Re: AMBER: AdoMet parameterization with antechamber
David A. Case
(Sun Nov 23 2008 - 13:13:23 PST)
Re: AMBER: AdoMet parameterization with antechamber
Alan
(Mon Nov 24 2008 - 02:46:52 PST)
Re: Re: AMBER: AdoMet parameterization with antechamber
Jeffrey
(Mon Nov 24 2008 - 08:19:41 PST)
Re: Re: AMBER: AdoMet parameterization with antechamber
Wei Huang
(Mon Nov 24 2008 - 08:41:12 PST)
Re: Re: AMBER: AdoMet parameterization with antechamber
David A. Case
(Mon Nov 24 2008 - 09:19:54 PST)
Re: Re: Re: AMBER: AdoMet parameterization with antechamber
Jeffrey
(Tue Nov 25 2008 - 08:14:44 PST)
Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
Jeffrey
(Wed Nov 26 2008 - 06:44:27 PST)
RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
Ross Walker
(Wed Nov 26 2008 - 09:28:51 PST)
Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
Jeffrey
(Thu Nov 27 2008 - 07:30:33 PST)
AMBER: Running Amber8 - Sander
tri nam Vo
(Sun Nov 23 2008 - 22:28:31 PST)
AMBER: GB versus explicit medium
Francesco Pietra
(Mon Nov 24 2008 - 01:39:58 PST)
Re: AMBER: GB versus explicit medium
Carlos Simmerling
(Mon Nov 24 2008 - 03:08:40 PST)
Re: AMBER: GB versus explicit medium
Francesco Pietra
(Mon Nov 24 2008 - 07:33:43 PST)
Re: AMBER: GB versus explicit medium
M. L. Dodson
(Mon Nov 24 2008 - 07:43:52 PST)
AMBER: Ewald troubles when running very big boxes
steinbrt.rci.rutgers.edu
(Mon Nov 24 2008 - 12:50:50 PST)
Re: AMBER: Ewald troubles when running very big boxes
Robert Duke
(Mon Nov 24 2008 - 18:09:23 PST)
RE: AMBER: Fully QM periodic runs
hfox1.nd.edu
(Mon Nov 24 2008 - 13:28:36 PST)
Re: AMBER: Fully QM periodic runs
David A. Case
(Tue Nov 25 2008 - 03:56:51 PST)
RE: AMBER: Fully QM periodic runs
Ross Walker
(Tue Nov 25 2008 - 08:54:24 PST)
AMBER: unsubscribe amber
Su Nwe
(Mon Nov 24 2008 - 23:12:02 PST)
AMBER: Gradual releasing of position restraints
Dmitri Nilov
(Tue Nov 25 2008 - 06:23:02 PST)
RE: AMBER: Gradual releasing of position restraints
Ross Walker
(Tue Nov 25 2008 - 08:48:13 PST)
Re: AMBER: Gradual releasing of position restraints
David A. Case
(Wed Nov 26 2008 - 09:00:41 PST)
AMBER: molsurf fails
Arturas Ziemys
(Tue Nov 25 2008 - 07:27:27 PST)
Re: AMBER: molsurf fails
David A. Case
(Tue Nov 25 2008 - 11:26:14 PST)
AMBER: using packmol file in Amber
oguz gurbulak
(Tue Nov 25 2008 - 07:49:19 PST)
Re: AMBER: using packmol file in Amber
David A. Case
(Tue Nov 25 2008 - 11:45:29 PST)
AMBER: Test failure with Amber 10
Kevin Parkes
(Wed Nov 26 2008 - 02:33:35 PST)
Re: AMBER: Test failure with Amber 10
David A. Case
(Wed Nov 26 2008 - 04:46:41 PST)
RE: AMBER: Test failure with Amber 10
Kevin Parkes
(Wed Nov 26 2008 - 06:36:36 PST)
AMBER: Choline chloride salt
CHAMI F.
(Wed Nov 26 2008 - 06:49:45 PST)
AMBER: Referencing AMBER
Joseph Nachman
(Wed Nov 26 2008 - 08:01:57 PST)
Re: AMBER: Referencing AMBER
David A. Case
(Wed Nov 26 2008 - 08:25:20 PST)
RE: AMBER: Test failure with Amber 10
Ross Walker
(Wed Nov 26 2008 - 08:30:42 PST)
Re: AMBER: Test failure with Amber 10
Robert Duke
(Wed Nov 26 2008 - 09:28:14 PST)
AMBER: About antechamber and GAFF
Stephane Abel
(Wed Nov 26 2008 - 03:02:00 PST)
AMBER: About antechamber and GAFF [UPDATED]
Stephane Abel
(Wed Nov 26 2008 - 03:21:52 PST)
AMBER: subroutine Work : Jarynski work theorem
CHAMI F.
(Wed Nov 26 2008 - 04:21:07 PST)
Re: AMBER: About antechamber and GAFF [UPDATED]
Navnit Kumar Mishra
(Wed Nov 26 2008 - 05:04:20 PST)
RE: AMBER: About antechamber and GAFF [UPDATED]
Ross Walker
(Wed Nov 26 2008 - 08:39:30 PST)
Re: AMBER: About antechamber and GAFF [UPDATED]
Wenyong Tong
(Wed Nov 26 2008 - 09:13:34 PST)
Re: AMBER: About antechamber and GAFF [UPDATED]
Stephane Abel
(Thu Nov 27 2008 - 03:33:56 PST)
AMBER: Problem running NEB in AMBER10
Chris C.
(Wed Nov 26 2008 - 10:38:17 PST)
RE: AMBER: Problem running NEB in AMBER10
Ross Walker
(Wed Nov 26 2008 - 11:04:55 PST)
AMBER: problem with AMOEBA
j00323240.students.jsums.edu
(Wed Nov 26 2008 - 11:07:13 PST)
AMBER: Question fot Amber 10 Benchmarks
sychen
(Wed Nov 26 2008 - 23:50:11 PST)
Re: AMBER: Question fot Amber 10 Benchmarks
Robert Duke
(Thu Nov 27 2008 - 06:37:20 PST)
RE: AMBER: Question fot Amber 10 Benchmarks
Ross Walker
(Thu Nov 27 2008 - 08:57:06 PST)
Re[2]: AMBER: Question fot Amber 10 Benchmarks
sychen
(Thu Nov 27 2008 - 18:18:00 PST)
AMBER: Problems of MM/MM-GBSA calculations
Sergey Samsonov
(Thu Nov 27 2008 - 02:53:53 PST)
AMBER: antechamber and gaff for a homodimer
rebeca
(Thu Nov 27 2008 - 03:12:23 PST)
Re: AMBER: antechamber and gaff for a homodimer
Alan
(Thu Nov 27 2008 - 04:27:31 PST)
Re: AMBER: antechamber and gaff for a homodimer
rebeca
(Thu Nov 27 2008 - 05:33:19 PST)
Re: AMBER: antechamber and gaff for a homodimer
FyD
(Thu Nov 27 2008 - 08:02:55 PST)
AMBER: seeking help regrading Zinc protein GBSA minimization
S.Sundar Raman
(Thu Nov 27 2008 - 04:32:08 PST)
Re: AMBER: seeking help regrading Zinc protein GBSA minimization
Carlos Simmerling
(Fri Nov 28 2008 - 04:33:16 PST)
AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms
Ye Mei
(Thu Nov 27 2008 - 07:12:51 PST)
AMBER: cis - trans isomerization
Nina Fischer
(Thu Nov 27 2008 - 06:39:21 PST)
AMBER: Heating up
Francesco Pietra
(Thu Nov 27 2008 - 10:29:30 PST)
Re: AMBER: Heating up
Carlos Simmerling
(Fri Nov 28 2008 - 04:30:29 PST)
Re: AMBER: Heating up
Francesco Pietra
(Fri Nov 28 2008 - 07:57:49 PST)
AMBER: normal-vector of a plane with 'corrplane'
Gert Kiss
(Thu Nov 27 2008 - 12:28:46 PST)
AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
jitrayut jitonnom
(Thu Nov 27 2008 - 17:26:54 PST)
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
Guillermo Mulliert Carlín
(Thu Nov 27 2008 - 23:20:30 PST)
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
jitrayut jitonnom
(Fri Nov 28 2008 - 15:34:43 PST)
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
FyD
(Fri Nov 28 2008 - 23:30:19 PST)
RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
Ross Walker
(Fri Nov 28 2008 - 18:11:49 PST)
Re: AMBER: Setting GROUP for pmemd
Francesco Pietra
(Fri Nov 28 2008 - 02:12:07 PST)
AMBER: N(CN2)- ion
babak minoofar
(Fri Nov 28 2008 - 05:12:26 PST)
AMBER: Questions on TIP4P model?
Chin, Keith B
(Fri Nov 28 2008 - 11:20:38 PST)
Re: AMBER: Questions on TIP4P model?
Carlos Simmerling
(Fri Nov 28 2008 - 12:03:14 PST)
Re: AMBER: Questions on TIP4P model?
David A. Case
(Sat Nov 29 2008 - 11:21:01 PST)
RE: AMBER: Questions on TIP4P model?
Chin, Keith B
(Sat Nov 29 2008 - 15:43:21 PST)
AMBER: RED vIII-lack of charges in mol2
Neha Gandhi
(Sat Nov 29 2008 - 06:24:30 PST)
Re: AMBER: RED vIII-lack of charges in mol2
FyD
(Sat Nov 29 2008 - 08:23:34 PST)
Last message date
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Fri Dec 05 2008 - 18:12:45 PST
Archived on
: Mon Dec 23 2024 - 05:53:40 PST
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