Amber Archive Jun 2008 by author
502 messages
:
Starting
Wed Jun 04 2008 - 06:07:04 PDT,
Ending
Wed Jul 02 2008 - 06:07:29 PDT
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Abhishek Singh
AMBER: Regarding force field ff02 and ion library
(Mon Jun 30 2008 - 13:54:52 PDT)
Adrian Roitberg
Re: AMBER: SMD RESTRAINTS
(Thu Jun 12 2008 - 12:23:26 PDT)
Re: AMBER: SMD RESTRAINTS
(Thu Jun 12 2008 - 09:51:56 PDT)
Re: AMBER: Problem of Ptraj analyze matrix
(Mon Jun 09 2008 - 06:51:42 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Sat Jun 07 2008 - 05:36:21 PDT)
Adrien Delmont
Re: AMBER: concerning force fields
(Sat Jun 28 2008 - 09:10:05 PDT)
Re: AMBER: concerning force fields
(Fri Jun 27 2008 - 05:22:08 PDT)
Re: AMBER: concerning force fields
(Thu Jun 26 2008 - 11:29:39 PDT)
AMBER: concerning force fields
(Thu Jun 26 2008 - 08:14:15 PDT)
Alan
AMBER: rdparm Segmentation fault
(Wed Jun 25 2008 - 14:24:34 PDT)
AMBER: rdparm Segmentation fault on Ubuntu
(Tue Jun 24 2008 - 08:50:12 PDT)
Re: AMBER: rdparm help
(Mon Jun 23 2008 - 08:23:50 PDT)
AMBER: amber10/dat/leap/cmd/README need update
(Mon Jun 23 2008 - 07:59:21 PDT)
AMBER: rdparm help
(Fri Jun 20 2008 - 04:12:17 PDT)
AMBER: about gaff.dat in ambeTools 1.0
(Wed Jun 18 2008 - 07:44:02 PDT)
AMBER: to understand GAFF: about A and B coefficients
(Tue Jun 17 2008 - 09:42:34 PDT)
AMBER: suggestion for next amberTools 1.1
(Tue Jun 17 2008 - 04:01:06 PDT)
Re: AMBER: problems with sleap
(Mon Jun 16 2008 - 09:07:24 PDT)
Re: AMBER: updating documentation
(Thu Jun 12 2008 - 16:09:24 PDT)
AMBER: updating documentation
(Thu Jun 12 2008 - 02:52:40 PDT)
Re: AMBER: problems with sleap
(Wed Jun 04 2008 - 23:48:03 PDT)
AMBER: problems with sleap
(Wed Jun 04 2008 - 08:40:04 PDT)
Re: AMBER: gasteiger is not working with ambertools 1.0
(Tue Jun 03 2008 - 07:44:07 PDT)
Alexander Metz
AW: AMBER: MM-PBSA
(Wed Jun 18 2008 - 03:43:18 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Thu Jun 12 2008 - 01:04:08 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Wed Jun 11 2008 - 22:59:18 PDT)
Alfredo Quevedo
Re: AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 08:29:24 PDT)
Re: AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 07:08:56 PDT)
AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 06:35:20 PDT)
Arturas Ziemys
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 11:19:36 PDT)
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 10:56:57 PDT)
AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 10:00:34 PDT)
AMBER: sander.MPI / openmpi on PBS
(Wed Jun 11 2008 - 11:59:52 PDT)
Atro Tossavainen
Re: AMBER: Installation Problem of AMBER10
(Tue Jun 24 2008 - 07:37:57 PDT)
Balazs JOJART
Re: AMBER: how to derive torsional angle parameters in gaff
(Thu Jun 26 2008 - 01:53:40 PDT)
Barbault Florent
Re: AMBER: trajout input
(Fri Jun 20 2008 - 02:43:28 PDT)
bhargav patel
Re: AMBER: Installation Problem of AMBER10
(Tue Jun 24 2008 - 03:06:45 PDT)
Re: AMBER: Installation Problem of AMBER10
(Fri Jun 20 2008 - 02:07:12 PDT)
AMBER: Installation Problem of AMBER10
(Thu Jun 19 2008 - 03:57:26 PDT)
Bill Ross
Re: AMBER: Installation Problem of AMBER10
(Fri Jun 20 2008 - 13:46:35 PDT)
Re: AMBER: Installation Problem of AMBER10
(Thu Jun 19 2008 - 10:31:42 PDT)
Re: AMBER: potassium ion
(Sat Jun 14 2008 - 13:04:31 PDT)
Biman Jana
AMBER: How to adjust the problem of "Vlimit exceeded"
(Mon Jun 23 2008 - 00:28:27 PDT)
Boutheina Kerkeni
Re: AMBER: hold atoms fixed
(Mon Jun 30 2008 - 06:12:33 PDT)
AMBER: hold atoms fixed
(Mon Jun 30 2008 - 05:51:17 PDT)
Campbell, Patrick
Re:AMBER:VMD Movie.mdcrd
(Fri Jun 06 2008 - 11:56:52 PDT)
AMBER: VMD Movie .mdcrd file ptraj
(Fri Jun 06 2008 - 06:22:50 PDT)
AMBER: VMD file generation 4 - mdcrd analysis
(Mon Jun 02 2008 - 13:21:00 PDT)
RE:AMBER: VMD file generation 4 - mdcrd ptraj analysis
(Mon Jun 02 2008 - 12:54:06 PDT)
AMBER: VMD file generation 4 - mdcrd ptraj analysis
(Mon Jun 02 2008 - 11:26:15 PDT)
caoch
AMBER: local coordinate system question
(Wed Jun 25 2008 - 02:33:15 PDT)
Carlos Simmerling
Re: AMBER: hold atoms fixed
(Mon Jun 30 2008 - 06:02:19 PDT)
Re: AMBER: question about the charge
(Fri Jun 27 2008 - 13:52:22 PDT)
Re: AMBER: ptraj - read in part of trajectory
(Fri Jun 27 2008 - 10:00:32 PDT)
Re: AMBER: REMD Amber10 : error in reading namelist cntrl
(Fri Jun 27 2008 - 07:47:42 PDT)
Re: AMBER: concerning force fields
(Fri Jun 27 2008 - 05:34:21 PDT)
Re: AMBER: Dihedral Angle Parameters
(Thu Jun 26 2008 - 15:20:41 PDT)
Re: AMBER: Dihedral Angle Parameters
(Thu Jun 26 2008 - 14:30:53 PDT)
Re: AMBER: concerning force fields
(Thu Jun 26 2008 - 12:25:04 PDT)
Re: AMBER: concerning force fields
(Thu Jun 26 2008 - 09:16:48 PDT)
Re: AMBER: A problem of dihedral angle
(Wed Jun 25 2008 - 08:53:16 PDT)
Re: AMBER: Installation Problem of AMBER10
(Thu Jun 19 2008 - 04:05:21 PDT)
Re: AMBER: How to create average structure?
(Wed Jun 18 2008 - 21:52:35 PDT)
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 11:28:04 PDT)
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 10:43:39 PDT)
Re: AMBER: MM-GBSA with very positive GB value
(Fri Jun 13 2008 - 00:46:55 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Thu Jun 12 2008 - 01:05:15 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Tue Jun 10 2008 - 01:03:02 PDT)
Re: AMBER: problem in starting sander
(Sun Jun 08 2008 - 21:36:32 PDT)
Re: AMBER: problem in starting sander
(Sun Jun 08 2008 - 12:53:33 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Sun Jun 08 2008 - 12:33:47 PDT)
Re: AMBER: NAN errors still exist
(Fri Jun 06 2008 - 03:57:49 PDT)
Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC
(Thu Jun 05 2008 - 05:16:22 PDT)
Re: AMBER: syn and anti conformation
(Wed Jun 04 2008 - 12:34:31 PDT)
Re: AMBER: corrupted restart file
(Tue Jun 03 2008 - 03:15:21 PDT)
Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis
(Mon Jun 02 2008 - 13:06:39 PDT)
Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis
(Mon Jun 02 2008 - 12:11:24 PDT)
Catein Catherine
RE: AMBER: MM-GBSA with very positive GB value
(Fri Jun 13 2008 - 18:49:53 PDT)
AMBER: MM-GBSA with very positive GB value
(Fri Jun 13 2008 - 00:05:02 PDT)
Cenk \(Jenk\) Andac
Re: AMBER: corrupted restart file
(Tue Jun 03 2008 - 03:13:29 PDT)
Chih-Ying Lin
Re: AMBER: Error message: Install Amber9 on fedora 9
(Wed Jun 04 2008 - 20:54:29 PDT)
AMBER: Error message: Install Amber9 on fedora 9
(Mon Jun 02 2008 - 15:33:42 PDT)
Cyril Bauvais
AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2
(Wed Jun 25 2008 - 06:00:54 PDT)
Re: AMBER: problems form the pdb to the mol2
(Tue Jun 24 2008 - 07:05:36 PDT)
Daniel B. Kaplan
AMBER: (no subject)
(Wed Jun 25 2008 - 19:23:43 PDT)
AMBER: Antechamber Question
(Mon Jun 23 2008 - 09:51:28 PDT)
AMBER: (no subject)
(Sun Jun 22 2008 - 16:46:17 PDT)
Daniel Oehme
AMBER: MM-PBSA in AMBER 10
(Mon Jun 23 2008 - 18:32:24 PDT)
AMBER: MM-PBSA in AMBER 10
(Sun Jun 22 2008 - 22:07:34 PDT)
AMBER: MM-PBSA in AMBER 10
(Thu Jun 05 2008 - 20:52:12 PDT)
AMBER: MM-PBSA in AMBER 10
(Wed Jun 04 2008 - 22:27:39 PDT)
Daniel Smith
Re: AMBER: [Fwd: failure to load box parameters]
(Wed Jun 25 2008 - 11:30:18 PDT)
Re: AMBER: [Fwd: failure to load box parameters]
(Mon Jun 23 2008 - 14:26:22 PDT)
AMBER: [Fwd: failure to load box parameters]
(Wed Jun 18 2008 - 20:58:10 PDT)
AMBER: Calcium and Magnesium LJ parameters
(Mon Jun 09 2008 - 16:02:28 PDT)
David A. Case
Re: AMBER: Regarding force field ff02 and ion library
(Mon Jun 30 2008 - 14:14:37 PDT)
Re: AMBER: error in reading namelist cntrl
(Mon Jun 30 2008 - 13:28:36 PDT)
Re: AMBER: NMR refinement
(Mon Jun 30 2008 - 07:44:51 PDT)
Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?
(Sat Jun 28 2008 - 09:37:45 PDT)
Re: AMBER:
(Fri Jun 27 2008 - 11:55:04 PDT)
Re: AMBER: Test scripts
(Fri Jun 27 2008 - 09:44:25 PDT)
Re: AMBER: sleap - TER-card
(Thu Jun 26 2008 - 18:19:01 PDT)
Re: AMBER: rdparm Segmentation fault
(Wed Jun 25 2008 - 17:07:20 PDT)
Re: AMBER: sleap - TER-card
(Wed Jun 25 2008 - 15:05:59 PDT)
Re: AMBER: [Fwd: failure to load box parameters]
(Wed Jun 25 2008 - 12:09:28 PDT)
Re: AMBER: amber10 compile gfortran question
(Wed Jun 25 2008 - 12:03:54 PDT)
Re: AMBER: local coordinate system question
(Wed Jun 25 2008 - 07:32:16 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 15:06:15 PDT)
Re: AMBER: [Fwd: failure to load box parameters]
(Tue Jun 24 2008 - 08:14:51 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 07:55:10 PDT)
Re: AMBER: Installation Problem of AMBER10
(Tue Jun 24 2008 - 07:49:26 PDT)
Re: AMBER: problems form the pdb to the mol2
(Mon Jun 23 2008 - 18:51:46 PDT)
Re: AMBER: MM-PBSA in AMBER 10
(Mon Jun 23 2008 - 18:47:44 PDT)
Re: AMBER: How to adjust the problem of "Vlimit exceeded"
(Mon Jun 23 2008 - 08:16:05 PDT)
Re: AMBER: How to confirm atom types of small molecule perceived by antechamber
(Mon Jun 23 2008 - 07:56:17 PDT)
Re: AMBER: Installation Problem of AMBER10
(Fri Jun 20 2008 - 12:34:09 PDT)
Re: AMBER: AmberTools 1.0 installation error: x86_64
(Fri Jun 20 2008 - 09:17:35 PDT)
Re: AMBER: simple sander
(Thu Jun 19 2008 - 18:40:46 PDT)
Re: AMBER: [Fwd: segmentation fault in nmode]
(Thu Jun 19 2008 - 17:22:34 PDT)
Re: AMBER: Installation Problem of AMBER10
(Thu Jun 19 2008 - 07:53:03 PDT)
Re: AMBER: [Fwd: failure to load box parameters]
(Wed Jun 18 2008 - 22:35:53 PDT)
Re: AMBER: tip3p water and shake
(Wed Jun 18 2008 - 22:15:48 PDT)
Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1
(Wed Jun 18 2008 - 17:32:36 PDT)
Re: AMBER: sp carbon notation?
(Wed Jun 18 2008 - 17:22:14 PDT)
Re: AMBER: to understand GAFF: about A and B coefficients
(Tue Jun 17 2008 - 09:52:41 PDT)
Re: AMBER: suggestion for next amberTools 1.1
(Tue Jun 17 2008 - 08:42:14 PDT)
Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"?
(Tue Jun 17 2008 - 08:18:08 PDT)
Re: AMBER: [Fwd: segmentation fault in nmode]
(Mon Jun 16 2008 - 16:42:47 PDT)
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 11:33:35 PDT)
Re: AMBER: problems with sleap
(Mon Jun 16 2008 - 08:48:42 PDT)
Re: AMBER: Problem with running refinement of NMR structures with RDCs
(Sun Jun 15 2008 - 18:50:53 PDT)
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Sat Jun 14 2008 - 12:09:02 PDT)
Re: AMBER: Sander crashes >99999 atoms
(Fri Jun 13 2008 - 09:59:32 PDT)
Re: AMBER: updating documentation
(Fri Jun 13 2008 - 09:52:14 PDT)
Re: AMBER: Sander crashes >99999 atoms
(Thu Jun 12 2008 - 18:25:31 PDT)
Re: AMBER: using Velocity-Verlet algorithm
(Thu Jun 12 2008 - 09:09:49 PDT)
Re: AMBER: Antechamber and topology file
(Thu Jun 12 2008 - 09:03:50 PDT)
Re: AMBER: Coordinated Zinc
(Thu Jun 12 2008 - 08:59:42 PDT)
Re: AMBER: updating documentation
(Thu Jun 12 2008 - 08:10:36 PDT)
Re: AMBER: anisotropic pressure scaling ntp=2
(Thu Jun 12 2008 - 08:13:52 PDT)
Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating
(Wed Jun 11 2008 - 10:53:20 PDT)
Re: AMBER: box shape changed at NVT
(Wed Jun 11 2008 - 08:18:46 PDT)
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Wed Jun 11 2008 - 08:15:00 PDT)
Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating
(Tue Jun 10 2008 - 05:50:27 PDT)
Re: AMBER: NAB documentation
(Sun Jun 08 2008 - 18:38:05 PDT)
Re: AMBER: Problem of Ptraj analyze matrix
(Sun Jun 08 2008 - 18:38:13 PDT)
Re: AMBER: A problem of installing Amber10
(Fri Jun 06 2008 - 13:21:52 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 11:59:52 PDT)
Re: AMBER: Error message: Install Amber9 on fedora 9
(Thu Jun 05 2008 - 12:17:50 PDT)
Re: AMBER: A problem of installing Amber10
(Thu Jun 05 2008 - 12:13:16 PDT)
Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint?
(Thu Jun 05 2008 - 11:50:16 PDT)
Re: AMBER: NMODE units and hrmax value for Langevine modes
(Thu Jun 05 2008 - 11:12:24 PDT)
Re: AMBER: A problem of installing Amber10
(Thu Jun 05 2008 - 10:49:58 PDT)
Re: AMBER: problems with sleap
(Wed Jun 04 2008 - 16:52:00 PDT)
Re: AMBER: amber installation on cluster
(Wed Jun 04 2008 - 10:55:39 PDT)
Re: AMBER: NMODE units and hrmax value for Langevine modes
(Wed Jun 04 2008 - 10:30:36 PDT)
Re: AMBER: solvate box : buffer list
(Tue Jun 03 2008 - 11:22:16 PDT)
Re: AMBER: Temperature controlling method in AMBER
(Tue Jun 03 2008 - 07:56:51 PDT)
Re: AMBER: gasteiger is not working with ambertools 1.0
(Mon Jun 02 2008 - 17:12:55 PDT)
Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
(Mon Jun 02 2008 - 16:23:46 PDT)
Re: AMBER: MAXAT can not be changed for AMBERTool 1.0
(Mon Jun 02 2008 - 16:15:38 PDT)
Re: AMBER: Error message: Install Amber9 on fedora 9
(Mon Jun 02 2008 - 16:04:48 PDT)
Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1
(Mon Jun 02 2008 - 10:56:16 PDT)
David Case
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Fri Jun 06 2008 - 09:25:45 PDT)
AMBER: NAB documentation
(Fri Jun 06 2008 - 09:24:44 PDT)
Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Fri Jun 06 2008 - 09:27:06 PDT)
David LeBard
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 11:08:20 PDT)
Re: AMBER: sander.MPI / parallel
(Mon Jun 16 2008 - 11:07:21 PDT)
David Mobley
Re: AMBER: improving GAFF sulfonamide parameters
(Thu Jun 26 2008 - 13:50:03 PDT)
Re: AMBER: Free energy of dissociation
(Thu Jun 05 2008 - 09:22:24 PDT)
Re: AMBER: Jarzynski
(Mon Jun 02 2008 - 10:25:16 PDT)
David Watson
Re: AMBER: VMD Movie .mdcrd file ptraj
(Fri Jun 06 2008 - 07:57:16 PDT)
Dong Xu
AMBER: ligand partial charge and conformation question
(Thu Jun 26 2008 - 11:01:31 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Wed Jun 25 2008 - 23:21:03 PDT)
AMBER: Antechamber/mopac am1-bcc charge
(Wed Jun 25 2008 - 15:09:39 PDT)
dpandit.brandeis.edu
AMBER: Trajectory - Average Structure - Equilibration
(Wed Jun 11 2008 - 12:37:46 PDT)
Re: AMBER: PTRAJ - Segmentation Fault
(Wed Jun 11 2008 - 12:40:25 PDT)
RE: AMBER: Equilibration/Heating - Protein fixed -Problem
(Wed Jun 11 2008 - 11:17:56 PDT)
Re: AMBER: PTRAJ - Segmentation Fault
(Wed Jun 11 2008 - 10:48:54 PDT)
AMBER: Equilibration/Heating - Protein fixed -Problem
(Wed Jun 11 2008 - 08:31:40 PDT)
AMBER: PTRAJ - Segmentation Fault
(Tue Jun 10 2008 - 14:36:08 PDT)
Dr. Xiaofeng (Frank) Duan
AMBER: qmmm_DFTB problem
(Tue Jun 24 2008 - 06:58:46 PDT)
E.M.
Re: AMBER: Eigenmode dynamics - imaging traj
(Wed Jun 18 2008 - 04:16:49 PDT)
Ed Pate
AMBER: Amber 10 timing
(Fri Jun 20 2008 - 10:08:37 PDT)
AMBER: amber10 installation problem
(Tue Jun 10 2008 - 13:59:47 PDT)
fatima.chami.durham.ac.uk
AMBER: (no subject)
(Mon Jun 30 2008 - 09:26:23 PDT)
AMBER: wrapping a restart file
(Mon Jun 30 2008 - 07:40:58 PDT)
Re: AMBER: hold atoms fixed
(Mon Jun 30 2008 - 06:16:09 PDT)
AMBER: Constrained group
(Mon Jun 30 2008 - 02:54:02 PDT)
AMBER: Group specification problem
(Fri Jun 27 2008 - 05:59:09 PDT)
Re: SV: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 09:05:36 PDT)
Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?
(Thu Jun 19 2008 - 09:00:32 PDT)
Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?
(Thu Jun 19 2008 - 07:47:50 PDT)
RE: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 06:46:22 PDT)
RE: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 06:43:39 PDT)
AMBER: how to extract x,y,z of a set of atoms from an MD trajectories
(Thu Jun 19 2008 - 02:16:52 PDT)
AMBER: cross correlation function using iRED matrix
(Wed Jun 18 2008 - 10:07:25 PDT)
AMBER: ptraj
(Wed Jun 18 2008 - 08:21:50 PDT)
AMBER: Eigenmode dynamics - imaging traj
(Wed Jun 18 2008 - 03:09:26 PDT)
Re: AMBER: multiple dihedral restraints using group (in Amber 10)
(Wed Jun 18 2008 - 03:05:40 PDT)
AMBER: IRED to time correlation
(Mon Jun 16 2008 - 13:25:22 PDT)
AMBER: Eigenmode dynamics in Ptraj
(Mon Jun 16 2008 - 05:59:42 PDT)
Re: AMBER: SMD RESTRAINTS
(Thu Jun 12 2008 - 10:07:49 PDT)
AMBER: SMD RESTRAINTS
(Thu Jun 12 2008 - 09:23:00 PDT)
AMBER: anisotropic pressure scaling ntp=2
(Thu Jun 12 2008 - 06:18:13 PDT)
AMBER: box shape changed at NVT
(Wed Jun 11 2008 - 07:25:09 PDT)
AMBER: SMD pulling velocity
(Tue Jun 10 2008 - 07:06:38 PDT)
Re: AMBER: Free energy of dissociation
(Thu Jun 05 2008 - 08:13:03 PDT)
AMBER: Free energy of dissociation
(Thu Jun 05 2008 - 05:02:43 PDT)
Re: AMBER: solvate box : buffer list
(Wed Jun 04 2008 - 03:07:06 PDT)
AMBER: solvate box : buffer list
(Tue Jun 03 2008 - 10:51:55 PDT)
Florian Haberl
Re: AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 06:41:31 PDT)
Floris Buelens
AMBER: improving GAFF sulfonamide parameters
(Tue Jun 17 2008 - 02:57:46 PDT)
Francesco Pietra
AMBER: Seed for random number generator
(Sun Jun 29 2008 - 01:22:12 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Sat Jun 28 2008 - 10:22:44 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Fri Jun 27 2008 - 15:02:21 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Thu Jun 26 2008 - 10:29:12 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Wed Jun 25 2008 - 01:17:59 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 14:52:09 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 09:28:18 PDT)
AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 07:32:54 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Thu Jun 12 2008 - 00:09:28 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Wed Jun 11 2008 - 07:57:59 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Tue Jun 10 2008 - 00:37:34 PDT)
AMBER: Combine mdcrd while stripping WAT problem
(Sun Jun 08 2008 - 08:40:07 PDT)
Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd'
(Mon Jun 02 2008 - 03:22:38 PDT)
RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
(Sun Jun 01 2008 - 00:12:12 PDT)
FyD
Re: AMBER: Antechamber/mopac am1-bcc charge
(Sun Jun 29 2008 - 06:18:15 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Sat Jun 28 2008 - 00:47:54 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Fri Jun 27 2008 - 02:07:45 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Thu Jun 26 2008 - 13:53:20 PDT)
Re: AMBER: about resp charges
(Tue Jun 17 2008 - 05:58:03 PDT)
Re: AMBER: Coordinated Zinc
(Fri Jun 13 2008 - 00:56:08 PDT)
Germain Vallverdu
AMBER: dihedral potential with odd periodicity
(Tue Jun 24 2008 - 07:43:26 PDT)
AMBER: source of AMBER9
(Mon Jun 23 2008 - 07:09:29 PDT)
Guillaume Renvez
Re: AMBER: [Fwd: segmentation fault in nmode]
(Mon Jun 23 2008 - 01:27:27 PDT)
Re: AMBER: [Fwd: segmentation fault in nmode]
(Tue Jun 17 2008 - 00:50:33 PDT)
Re: AMBER: [Fwd: segmentation fault in nmode]
(Tue Jun 17 2008 - 00:48:34 PDT)
AMBER: [Fwd: segmentation fault in nmode]
(Mon Jun 16 2008 - 07:31:12 PDT)
Gustavo Seabra
Re: AMBER: wrapping a restart file
(Mon Jun 30 2008 - 08:31:53 PDT)
Re: AMBER: hold atoms fixed
(Mon Jun 30 2008 - 07:10:53 PDT)
Re: AMBER: qmmm_DFTB problem
(Tue Jun 24 2008 - 07:31:15 PDT)
Re: AMBER: Compile amber10 parallel with suppied LAM
(Thu Jun 12 2008 - 11:20:24 PDT)
Re: AMBER: Compile amber10 parallel with suppied LAM
(Thu Jun 12 2008 - 10:39:34 PDT)
Re: AMBER: QM/MM
(Wed Jun 11 2008 - 08:22:16 PDT)
Re: AMBER: SMD pulling velocity
(Tue Jun 10 2008 - 07:22:48 PDT)
Re: AMBER: Combine mdcrd while stripping WAT problem
(Sun Jun 08 2008 - 11:58:34 PDT)
Re: AMBER: Free energy of dissociation
(Thu Jun 05 2008 - 06:41:03 PDT)
Hannes Kopitz
Re: AMBER: How to solve - Missing BELE for MM in 1 in amber.
(Tue Jun 17 2008 - 01:32:31 PDT)
Re: AMBER: PCAL and polar contribution in the output file
(Sun Jun 15 2008 - 06:30:23 PDT)
Harry (Yicun) Ni
Re: AMBER: question about the charge
(Fri Jun 27 2008 - 16:57:37 PDT)
AMBER: question about the charge
(Fri Jun 27 2008 - 13:37:55 PDT)
Re: AMBER: A problem of dihedral angle
(Wed Jun 25 2008 - 12:42:09 PDT)
AMBER: A problem of dihedral angle
(Wed Jun 25 2008 - 08:31:24 PDT)
Harry Ni
Re: AMBER: A problem of installing Amber10
(Fri Jun 06 2008 - 14:36:48 PDT)
Re: AMBER: A problem of installing Amber10
(Fri Jun 06 2008 - 12:00:19 PDT)
Re: AMBER: A problem of installing Amber10
(Thu Jun 05 2008 - 11:27:23 PDT)
Hu, Shaowen (JSC-SK)[USRA]
AMBER: MAXAT can not be changed for AMBERTool 1.0
(Mon Jun 02 2008 - 12:41:54 PDT)
Ian
Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Wed Jun 11 2008 - 03:53:42 PDT)
AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Fri Jun 06 2008 - 02:19:58 PDT)
Ibrahim Moustafa
AMBER: PCA analysis
(Mon Jun 02 2008 - 14:09:17 PDT)
AMBER: PCA - analysis
(Sun Jun 01 2008 - 11:00:35 PDT)
Ilyas Yildirim
Re: AMBER: Dihedral Angle Parameters
(Thu Jun 26 2008 - 15:07:55 PDT)
AMBER: Dihedral Angle Parameters
(Thu Jun 26 2008 - 14:07:16 PDT)
In Hee Park
Re: AMBER: sleap - TER-card
(Thu Jun 26 2008 - 17:31:40 PDT)
AMBER: sleap - TER-card
(Wed Jun 25 2008 - 12:14:39 PDT)
JAMES W CALDWELL
Re: AMBER: simple sander
(Thu Jun 19 2008 - 18:47:32 PDT)
Re: AMBER: [Fwd: segmentation fault in nmode]
(Mon Jun 16 2008 - 17:53:03 PDT)
James W. Caldwell
RE: AMBER: Test scripts
(Fri Jun 27 2008 - 09:54:56 PDT)
AMBER: Test scripts
(Fri Jun 27 2008 - 09:35:26 PDT)
RE: AMBER: amber10 compile gfortran question
(Wed Jun 25 2008 - 12:11:58 PDT)
AMBER: amber10 compile gfortran question
(Wed Jun 25 2008 - 11:10:58 PDT)
AMBER: simple sander
(Thu Jun 19 2008 - 16:30:39 PDT)
AMBER: amber10 make fails for static/parallel
(Fri Jun 13 2008 - 15:50:19 PDT)
RE: AMBER: Compile amber10 parallel with suppied LAM
(Fri Jun 13 2008 - 10:17:57 PDT)
RE: AMBER: Compile amber10 parallel with suppied LAM
(Fri Jun 13 2008 - 10:06:19 PDT)
RE: AMBER: Compile amber10 parallel with suppied LAM
(Thu Jun 12 2008 - 11:08:54 PDT)
RE: AMBER: Compile amber10 parallel with suppied LAM
(Thu Jun 12 2008 - 10:32:13 PDT)
AMBER: Compile amber10 parallel with suppied LAM
(Thu Jun 12 2008 - 09:31:03 PDT)
Jarrod Smith
Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1
(Tue Jun 03 2008 - 12:29:31 PDT)
AMBER: Building ppc64 AMBER10 with xlf fortran 11.1
(Mon Jun 02 2008 - 09:43:24 PDT)
Jens Lattig
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Wed Jun 11 2008 - 01:59:12 PDT)
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Tue Jun 10 2008 - 01:00:08 PDT)
AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Fri Jun 06 2008 - 01:13:06 PDT)
AMBER: netcdf configure returned 1 - PROBLEM SOLVED
(Thu Jun 05 2008 - 07:42:03 PDT)
AMBER: netcdf configure returned 1
(Thu Jun 05 2008 - 06:46:45 PDT)
Jerome.GOLEBIOWSKI.unice.fr
Re: AMBER: dihedral energy calculation inconsistent with gaussian's result
(Tue Jun 24 2008 - 01:01:35 PDT)
Jianyin Shao
Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"?
(Tue Jun 17 2008 - 08:36:01 PDT)
Re: AMBER: 2D RMS plot
(Wed Jun 11 2008 - 15:17:43 PDT)
Re: AMBER: PTRAJ - Segmentation Fault
(Wed Jun 11 2008 - 09:01:07 PDT)
Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Wed Jun 11 2008 - 08:55:12 PDT)
Re: AMBER: ptraj imaging issue
(Thu Jun 05 2008 - 09:23:52 PDT)
Re: AMBER: ptraj imaging issue
(Wed Jun 04 2008 - 14:25:27 PDT)
Joachim Reichelt
Re: AMBER: nmode analysis
(Mon Jun 30 2008 - 05:36:32 PDT)
AMBER: nmode analysis
(Mon Jun 30 2008 - 04:53:21 PDT)
John Bennett
AMBER: missing torsion parameters
(Mon Jun 30 2008 - 14:06:07 PDT)
John Palmeri
AMBER: Debugf AMBER9
(Wed Jun 25 2008 - 00:38:53 PDT)
Jufang Shan
Re: AMBER: ptraj has trouble with x-plor psf file from VMD
(Mon Jun 02 2008 - 08:52:28 PDT)
Junmei Wang
Re: AMBER: Antechamber/mopac am1-bcc charge
(Fri Jun 27 2008 - 08:35:23 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Thu Jun 26 2008 - 15:25:32 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Thu Jun 26 2008 - 11:27:10 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Thu Jun 26 2008 - 07:33:44 PDT)
Re: AMBER: Antechamber/mopac am1-bcc charge
(Wed Jun 25 2008 - 15:44:07 PDT)
AMBER: Re: AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2
(Wed Jun 25 2008 - 09:29:44 PDT)
AMBER: how to derive torsional angle parameters in gaff
(Tue Jun 24 2008 - 18:45:42 PDT)
Re: AMBER: Further request answers from Dr. Junmei Wang
(Tue Jun 24 2008 - 09:58:49 PDT)
Re: AMBER: improving GAFF sulfonamide parameters
(Tue Jun 24 2008 - 07:34:28 PDT)
Re: AMBER: problems form the pdb to the mol2
(Tue Jun 24 2008 - 06:47:24 PDT)
Re: AMBER: about gaff.dat in ambeTools 1.0
(Tue Jun 24 2008 - 06:37:09 PDT)
Re: AMBER: Antechamber Question
(Tue Jun 24 2008 - 06:33:58 PDT)
Re: AMBER: GAFF for organic crystals
(Mon Jun 23 2008 - 08:16:50 PDT)
Re: AMBER: (no subject)
(Mon Jun 23 2008 - 08:01:39 PDT)
Re: AMBER: How to confirm atom types of small molecule perceived by antechamber
(Mon Jun 23 2008 - 07:57:18 PDT)
Re: AMBER: Missing gaff angle parameters for dimethyl esters
(Tue Jun 03 2008 - 06:19:25 PDT)
Karl Kirschner (kkirschn)
Re: AMBER: concerning force fields
(Fri Jun 27 2008 - 06:02:03 PDT)
Kateryna Miroshnychenko
Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
(Tue Jun 03 2008 - 00:05:51 PDT)
Khaled Barakat
AMBER: Coordinated Zinc
(Wed Jun 11 2008 - 12:29:18 PDT)
Lars Skjærven
Re: AMBER: potassium ion
(Thu Jun 12 2008 - 10:46:36 PDT)
Laura Benton
AMBER: sp carbon notation?
(Wed Jun 18 2008 - 16:16:35 PDT)
Lin, Pohan
RE: AMBER: Missing gaff angle parameters for dimethyl esters
(Tue Jun 03 2008 - 12:56:32 PDT)
AMBER: Missing gaff angle parameters for dimethyl esters
(Mon Jun 02 2008 - 14:20:24 PDT)
M. L. Dodson
libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1
(Wed Jun 18 2008 - 08:43:44 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Sat Jun 07 2008 - 07:53:57 PDT)
Maria Frushicheva
AMBER: error in reading namelist cntrl
(Mon Jun 30 2008 - 13:02:50 PDT)
Mark Williamson
Re: AMBER: nmode analysis
(Mon Jun 30 2008 - 05:12:09 PDT)
Re: AMBER: SIZE.h problems
(Sat Jun 21 2008 - 14:22:37 PDT)
Re: AMBER: questions about gaff
(Wed Jun 18 2008 - 19:35:42 PDT)
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Sat Jun 14 2008 - 08:13:18 PDT)
Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu
(Tue Jun 10 2008 - 04:31:48 PDT)
Matthew Danielson
AMBER: AmberTools 1.0 installation error: x86_64
(Fri Jun 20 2008 - 08:44:21 PDT)
Miguel Ortiz-Lombardía
Re: AMBER: MM-PBSA
(Wed Jun 18 2008 - 07:41:12 PDT)
mkseo
AMBER: multiple dihedral restraints using group (in Amber 10)
(Tue Jun 17 2008 - 14:00:50 PDT)
mori.cerm.unifi.it
Re: AMBER: ligand complexed simulation
(Tue Jun 17 2008 - 04:15:11 PDT)
Myunggi Yi
Re: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 09:06:36 PDT)
Re: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 06:14:51 PDT)
Re: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 05:52:55 PDT)
Re: AMBER: cross correlation function using iRED matrix
(Wed Jun 18 2008 - 11:07:03 PDT)
Re: AMBER: Eigenmode dynamics - imaging traj
(Wed Jun 18 2008 - 06:33:07 PDT)
Navnit Kumar Mishra
Re: AMBER: MM-PBSA and delphi
(Mon Jun 09 2008 - 02:05:38 PDT)
Neha Gandhi
AMBER: MM-PBSA
(Wed Jun 18 2008 - 00:37:33 PDT)
Re: AMBER: PCAL and polar contribution in the output file
(Sun Jun 15 2008 - 06:56:20 PDT)
AMBER: PCAL and polar contribution in the output file
(Thu Jun 12 2008 - 22:42:54 PDT)
Re: AMBER: MM-PBSA and delphi
(Mon Jun 09 2008 - 02:57:21 PDT)
Re: AMBER: MM-PBSA and delphi
(Sun Jun 08 2008 - 22:56:00 PDT)
AMBER: MM-PBSA and delphi
(Sun Jun 08 2008 - 22:49:54 PDT)
AMBER: Query on MM-PBSA
(Thu Jun 05 2008 - 22:46:32 PDT)
oguz gurbulak
AMBER: using Velocity-Verlet algorithm
(Thu Jun 12 2008 - 05:07:20 PDT)
Pankaj R. Daga
AMBER: amber installation on cluster
(Wed Jun 04 2008 - 10:27:57 PDT)
Panwang Zhou
Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?
(Thu Jun 19 2008 - 08:34:02 PDT)
AMBER: How to extract solvent box information from .rst or .mdcrd files?
(Thu Jun 19 2008 - 07:13:18 PDT)
Pavan G
AMBER: Ewald error estimate
(Sun Jun 15 2008 - 07:22:48 PDT)
Peseckis, Steven M.
AMBER: RE: AMBER 10 failure to run in UBUNTU
(Sun Jun 29 2008 - 17:13:38 PDT)
AMBER:
(Thu Jun 26 2008 - 08:54:05 PDT)
plmallip.mail.uh.edu
Re: AMBER: Sander crashes >99999 atoms
(Thu Jun 12 2008 - 21:47:47 PDT)
AMBER: Sander crashes >99999 atoms
(Thu Jun 12 2008 - 16:26:57 PDT)
Praveena Gopal
AMBER: NAN errors still exist
(Fri Jun 06 2008 - 02:56:58 PDT)
Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC
(Thu Jun 05 2008 - 23:16:40 PDT)
AMBER: NAN errors in Etot, EPtot, EKtot and EELEC
(Thu Jun 05 2008 - 05:04:00 PDT)
Purisima, Enrico
RE: AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 07:39:49 PDT)
RE: AMBER: Trajectory in "Sietraj"
(Tue Jun 03 2008 - 06:55:20 PDT)
Q733
AMBER: dihedral energy calculation inconsistent with gaussian's result
(Mon Jun 23 2008 - 19:43:36 PDT)
Qi Yan
AMBER: How to get all eigenvalues by "analyze matrix"
(Thu Jun 12 2008 - 10:39:52 PDT)
AMBER: Question for how to get all eigenvalues by "analyze matrix"
(Wed Jun 11 2008 - 14:34:40 PDT)
RE: AMBER: MM-PBSA and delphi
(Mon Jun 09 2008 - 12:58:28 PDT)
RE: AMBER: Problem of Ptraj analyze matrix
(Mon Jun 09 2008 - 07:47:16 PDT)
AMBER: Problem of Ptraj analyze matrix
(Mon Jun 09 2008 - 06:37:01 PDT)
AMBER: Problem of Ptraj analyze matrix
(Sat Jun 07 2008 - 11:24:55 PDT)
Qi Zhang
Re: AMBER: problems with sleap
(Mon Jun 16 2008 - 04:46:26 PDT)
AMBER: Problem with running refinement of NMR structures with RDCs
(Sun Jun 15 2008 - 13:20:21 PDT)
Qiuting Hong
Re: AMBER: problem in starting sander
(Sun Jun 08 2008 - 19:40:52 PDT)
Re: AMBER: problem in starting sander
(Sun Jun 08 2008 - 14:52:34 PDT)
AMBER: problem in starting sander
(Sun Jun 08 2008 - 11:25:43 PDT)
Rabin
AMBER: unsubscribe amber
(Wed Jun 25 2008 - 17:48:51 PDT)
AMBER: syn and anti conformation
(Wed Jun 04 2008 - 12:29:58 PDT)
Rabone, Jeremy
AMBER: GAFF for organic crystals
(Fri Jun 20 2008 - 01:05:18 PDT)
rams rams
AMBER: program to calculate rmsd
(Mon Jun 16 2008 - 19:28:24 PDT)
Ramu Anandakrishnan
Re: AMBER: NAB documentation
(Fri Jun 06 2008 - 21:08:51 PDT)
ramu.vt.edu
AMBER: NAB documentation for programmers
(Wed Jun 04 2008 - 11:59:27 PDT)
Ranga Swamy
AMBER: Problem While Installing Amber
(Fri Jun 06 2008 - 02:34:17 PDT)
rebeca
AMBER: watershell cero?
(Mon Jun 30 2008 - 09:22:11 PDT)
AMBER: REMD Amber10 : error in reading namelist cntrl
(Fri Jun 27 2008 - 02:01:26 PDT)
Rilei Yu
： Re: AMBER: problems form the pdb to the mol2
(Tue Jun 24 2008 - 09:14:15 PDT)
AMBER: Further request answers from Dr. Junmei Wang
(Tue Jun 24 2008 - 08:59:05 PDT)
AMBER: problems form the pdb to the mol2
(Mon Jun 23 2008 - 18:01:33 PDT)
Robert Duke
Re: AMBER: (no subject)
(Mon Jun 30 2008 - 09:43:11 PDT)
Re: AMBER: wrapping a restart file
(Mon Jun 30 2008 - 09:34:54 PDT)
Re: AMBER: Constrained group
(Mon Jun 30 2008 - 09:03:15 PDT)
Re: AMBER: Amber 10 timing
(Fri Jun 20 2008 - 14:29:00 PDT)
Re: AMBER: amber10 installation problem
(Tue Jun 10 2008 - 15:02:54 PDT)
Re: AMBER: Vaccum Simulations in PMEMD !!
(Thu Jun 05 2008 - 07:17:13 PDT)
Ross Walker
RE: AMBER: missing torsion parameters
(Mon Jun 30 2008 - 15:46:45 PDT)
RE: AMBER: error in reading namelist cntrl
(Mon Jun 30 2008 - 13:26:38 PDT)
RE: AMBER: pmemd 10 output
(Fri Jun 27 2008 - 09:40:48 PDT)
RE: AMBER: pmemd 10 output
(Fri Jun 27 2008 - 09:16:44 PDT)
RE: AMBER: Dihedral Angle Parameters
(Thu Jun 26 2008 - 15:18:52 PDT)
RE: AMBER: A problem of dihedral angle
(Wed Jun 25 2008 - 08:48:56 PDT)
RE: AMBER: drawing repeated units
(Tue Jun 24 2008 - 14:40:26 PDT)
RE: AMBER: Using AMBER forces
(Tue Jun 24 2008 - 11:19:13 PDT)
RE: AMBER: Using AMBER forces
(Tue Jun 24 2008 - 09:22:25 PDT)
RE: AMBER: tip3p water and shake
(Wed Jun 18 2008 - 14:35:30 PDT)
RE: AMBER: program to calculate rmsd
(Tue Jun 17 2008 - 01:26:53 PDT)
RE: AMBER: amber10 installation problem
(Tue Jun 10 2008 - 15:04:51 PDT)
RE: AMBER: problem in starting sander
(Sun Jun 08 2008 - 15:30:17 PDT)
RE: AMBER: 100 short MD runs within a single Sander script?
(Fri Jun 06 2008 - 22:22:36 PDT)
RE: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 22:15:32 PDT)
RE: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 16:34:39 PDT)
RE: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 15:55:37 PDT)
RE: AMBER: Problem While Installing Amber
(Fri Jun 06 2008 - 08:30:26 PDT)
AMBER: RE: solvating RNA in 8M urea box
(Thu Jun 05 2008 - 17:12:42 PDT)
RE: AMBER: amber installation on cluster
(Wed Jun 04 2008 - 10:54:36 PDT)
RE: AMBER: drawing repeated units
(Tue Jun 03 2008 - 16:49:54 PDT)
RE: AMBER: drawing repeated units
(Tue Jun 03 2008 - 14:50:23 PDT)
RE: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1
(Tue Jun 03 2008 - 13:43:43 PDT)
RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
(Mon Jun 02 2008 - 10:52:33 PDT)
Sampath Koppole
AMBER: Vaccum Simulations in PMEMD !!
(Thu Jun 05 2008 - 05:53:35 PDT)
Samuel Genheden (a03samge)
AMBER: TI calculations in Amber10
(Wed Jun 25 2008 - 04:58:28 PDT)
SV: SV: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 13:06:17 PDT)
SV: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 08:53:29 PDT)
RE: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 06:33:46 PDT)
RE: AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 06:10:51 PDT)
AMBER: Correlation functions from iRED analysis
(Thu Jun 19 2008 - 03:22:53 PDT)
sanket.deshmukh.ucd.ie
AMBER: Amber:unsubscribe amber
(Thu Jun 26 2008 - 04:53:22 PDT)
AMBER: unsubscribe amber
(Tue Jun 24 2008 - 04:07:42 PDT)
Sasha Buzko
AMBER: Simulating complexes with magnesium atoms
(Tue Jun 10 2008 - 14:32:13 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Mon Jun 09 2008 - 10:57:20 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 22:37:53 PDT)
RE: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 16:40:07 PDT)
RE: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 16:13:19 PDT)
Re: AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 15:16:29 PDT)
AMBER: Problems simulating a protein-ligand complex
(Fri Jun 06 2008 - 10:55:05 PDT)
Sebastian Stolzenberg
AMBER: 100 short MD runs within a single Sander script?
(Fri Jun 06 2008 - 21:55:37 PDT)
Seth Lilavivat
Re: AMBER: ptraj - read in part of trajectory
(Fri Jun 27 2008 - 10:01:03 PDT)
AMBER: ptraj - read in part of trajectory
(Fri Jun 27 2008 - 09:41:51 PDT)
AMBER: Nmode - entropy calculation of receptor - should I apply restraint?
(Thu Jun 05 2008 - 10:03:08 PDT)
Shen, Lingling
AMBER: How to create average structure?
(Wed Jun 18 2008 - 21:44:03 PDT)
Siddharth Rastogi
AMBER: ligand complexed simulation
(Fri Jun 20 2008 - 00:14:18 PDT)
AMBER: ligand complexed simulation
(Tue Jun 17 2008 - 03:56:15 PDT)
Steve Spronk
RE: AMBER: "Dumping RAW 2D RMS data is not yet implemented"?
(Tue Jun 17 2008 - 08:54:04 PDT)
AMBER: "Dumping RAW 2D RMS data is not yet implemented"?
(Tue Jun 17 2008 - 07:00:08 PDT)
RE: AMBER: 2D RMS plot
(Thu Jun 12 2008 - 05:42:41 PDT)
AMBER: 2D RMS plot
(Wed Jun 11 2008 - 12:18:32 PDT)
Steven
Re: Re: AMBER: questions about gaff
(Fri Jun 20 2008 - 07:11:08 PDT)
Steven Winfield
Re: AMBER: Using AMBER forces
(Tue Jun 24 2008 - 09:54:49 PDT)
AMBER: Using AMBER forces
(Tue Jun 24 2008 - 08:44:41 PDT)
Swarup Gupta
Re: AMBER: trajout input
(Sun Jun 22 2008 - 20:01:31 PDT)
sychen
AMBER: How to calculate RMSIP after PCA analysis by PTRAJ?
(Wed Jun 04 2008 - 05:27:45 PDT)
TAEJIN KIM
AMBER: Antechamber and topology file
(Wed Jun 11 2008 - 16:05:14 PDT)
Taufik Al-Sarraj
Re: AMBER: drawing repeated units
(Tue Jun 24 2008 - 15:15:39 PDT)
Re: AMBER: QM/MM
(Wed Jun 11 2008 - 09:28:34 PDT)
AMBER: QM/MM
(Wed Jun 11 2008 - 09:09:24 PDT)
Re: AMBER: drawing repeated units
(Wed Jun 04 2008 - 13:17:57 PDT)
Re: AMBER: drawing repeated units
(Tue Jun 03 2008 - 16:58:25 PDT)
Re: AMBER: drawing repeated units
(Tue Jun 03 2008 - 15:25:59 PDT)
AMBER: writing a script in amber
(Mon Jun 02 2008 - 17:28:39 PDT)
teresa.ierano.unina.it
AMBER: NMR refinement
(Mon Jun 30 2008 - 03:37:48 PDT)
Thomas Cheatham
Re: AMBER: rdparm help
(Fri Jun 20 2008 - 07:35:36 PDT)
Re: AMBER: PTRAJ - Segmentation Fault
(Wed Jun 11 2008 - 11:15:00 PDT)
Thomas Cheatham III
Re: AMBER: Regarding force field ff02 and ion library
(Mon Jun 30 2008 - 14:30:05 PDT)
Re: AMBER: trajout input
(Fri Jun 20 2008 - 10:57:43 PDT)
Thomas Leonard
Re: AMBER: trajout input
(Fri Jun 20 2008 - 03:05:55 PDT)
AMBER: trajout input
(Fri Jun 20 2008 - 02:23:55 PDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber.
(Mon Jun 16 2008 - 20:06:01 PDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber.
(Mon Jun 16 2008 - 20:05:59 PDT)
Thomas Steinbrecher
Re: AMBER: TI calculations in Amber10
(Wed Jun 25 2008 - 09:15:47 PDT)
Re: AMBER: how to calculate the interaction energy
(Tue Jun 10 2008 - 09:45:16 PDT)
tinni sona
AMBER: Temperature controlling method in AMBER
(Tue Jun 03 2008 - 02:43:11 PDT)
Vahdati N.
RE: AMBER: nmode analysis
(Mon Jun 30 2008 - 05:41:40 PDT)
RE: AMBER: Equilibration/Heating - Protein fixed -Problem
(Wed Jun 11 2008 - 10:38:50 PDT)
Vijay Manickam Achari
AMBER: output file AMBER9_MPI
(Thu Jun 26 2008 - 12:06:19 PDT)
Vlad Cojocaru
Re: AMBER: ptraj - read in part of trajectory
(Fri Jun 27 2008 - 09:59:14 PDT)
Re: AMBER: pmemd 10 output
(Fri Jun 27 2008 - 09:34:37 PDT)
Re: AMBER: pmemd 10 output
(Fri Jun 27 2008 - 09:24:58 PDT)
AMBER: pmemd 10 output
(Fri Jun 27 2008 - 08:48:35 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Wed Jun 25 2008 - 02:00:10 PDT)
Re: AMBER: Compilation of amber8 patched with ramd
(Tue Jun 24 2008 - 08:07:03 PDT)
Re: AMBER: amber10/dat/leap/cmd/README need update
(Mon Jun 23 2008 - 08:12:29 PDT)
AMBER: the SPCFW water model
(Mon Jun 16 2008 - 09:19:34 PDT)
Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Fri Jun 06 2008 - 11:50:55 PDT)
Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
(Fri Jun 06 2008 - 02:59:54 PDT)
Re: AMBER: ptraj imaging issue
(Thu Jun 05 2008 - 07:30:42 PDT)
Re: AMBER: ptraj imaging issue
(Thu Jun 05 2008 - 01:48:43 PDT)
AMBER: ptraj imaging issue
(Wed Jun 04 2008 - 12:07:44 PDT)
Wang,Ying
RE: AMBER: tip3p water and shake
(Wed Jun 18 2008 - 20:44:27 PDT)
RE: AMBER: tip3p water and shake
(Wed Jun 18 2008 - 18:03:55 PDT)
AMBER: tip3p water and shake
(Wed Jun 18 2008 - 13:07:13 PDT)
Re: AMBER: how to calculate the interaction energy
(Tue Jun 10 2008 - 12:12:17 PDT)
AMBER: how to calculate the interaction energy
(Tue Jun 10 2008 - 07:52:10 PDT)
WanJ Ding
AMBER: about resp charges
(Mon Jun 16 2008 - 12:44:55 PDT)
wanjian ding
Re: AMBER: about resp charges
(Wed Jun 18 2008 - 13:43:35 PDT)
Wei Huang
AMBER: MM-PBSA calculation problem
(Mon Jun 30 2008 - 09:41:16 PDT)
xiaonan zhang
AMBER: How to confirm atom types of small molecule perceived by antechamber
(Mon Jun 23 2008 - 01:39:30 PDT)
Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating
(Tue Jun 10 2008 - 07:23:15 PDT)
AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating
(Tue Jun 10 2008 - 05:24:02 PDT)
Xioling Chuang
RE: AMBER: problem of install amber9
(Thu Jun 05 2008 - 02:09:27 PDT)
AMBER: problem of install amber9
(Thu Jun 05 2008 - 01:37:27 PDT)
Yang, Lee-Wei
RE: AMBER: NMODE units and hrmax value for Langevine modes
(Wed Jun 04 2008 - 20:55:45 PDT)
AMBER: NMODE units and hrmax value for Langevine modes
(Wed Jun 04 2008 - 09:27:00 PDT)
yavuzturkm.prc.boun.edu.tr
AMBER: corrupted restart file
(Tue Jun 03 2008 - 02:18:25 PDT)
Yicun Ni
AMBER: A problem of installing Amber10
(Thu Jun 05 2008 - 08:55:53 PDT)
yzhao
AMBER: questions about gaff
(Wed Jun 18 2008 - 19:01:45 PDT)
欧阳德方
AMBER: A-prime RNA input file
(Tue Jun 24 2008 - 04:16:27 PDT)
AMBER: SIZE.h problems
(Sat Jun 21 2008 - 05:33:49 PDT)
Last message date
:
Wed Jul 02 2008 - 06:07:29 PDT
Archived on
: Sun Dec 22 2024 - 05:53:42 PST
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