Amber Archive Oct 2006 by author
472 messages
:
Starting
Wed Oct 04 2006 - 06:07:05 PDT,
Ending
Sun Nov 05 2006 - 06:07:31 PST
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AMBER: Parameters for Nickel
(Wed Oct 11 2006 - 02:05:15 PDT)
AMBER: Steered molecular dynamics with Amber 8.0
(Tue Oct 10 2006 - 02:44:56 PDT)
AMBER: Potential of Mean Force calculation or Steered molecular dynamics
(Sun Oct 08 2006 - 23:07:25 PDT)
Re: AMBER: RMSD: is it related to flexibility?
(Thu Oct 05 2006 - 19:50:43 PDT)
Re: AMBER: RMSD: is it related to flexibility?
(Wed Oct 04 2006 - 21:15:20 PDT)
AMBER: RMSD: is it related to flexibility?
(Wed Oct 04 2006 - 02:42:12 PDT)
Adrian Roitberg
Re: AMBER: Closest(closest water)
(Mon Oct 30 2006 - 05:12:13 PST)
Re: AMBER: md and implicit solvation
(Tue Oct 24 2006 - 17:19:34 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 23 2006 - 16:44:46 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 10:41:31 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:46:48 PDT)
Re: AMBER: generalized born model for organic solvent
(Wed Oct 11 2006 - 17:11:33 PDT)
Akshay Patny
RE: AMBER: LEAP error (Test Case)
(Mon Oct 09 2006 - 08:37:18 PDT)
Re: AMBER: LEAP error
(Fri Oct 06 2006 - 16:17:05 PDT)
AMBER: LEAP error
(Fri Oct 06 2006 - 09:49:42 PDT)
RE: AMBER: water prmtop/inpcrd problem
(Fri Oct 06 2006 - 07:49:22 PDT)
AMBER: water prmtop/inpcrd problem
(Thu Oct 05 2006 - 18:08:59 PDT)
AMBER: VMD PDB into LEAP Readable PDB
(Wed Oct 04 2006 - 18:07:11 PDT)
Amber admin
Re: AMBER: problem with calcpka.pl
(Tue Oct 31 2006 - 16:33:09 PST)
andrea carotti
AMBER: Re: Problems installing antechamber 1.27
(Tue Oct 31 2006 - 00:17:49 PST)
Andres Palencia
AMBER: error GRID command in ptraj
(Thu Oct 26 2006 - 10:39:19 PDT)
Re: AMBER: how to select the problematic residues(atoms) in VMD
(Thu Oct 26 2006 - 04:56:31 PDT)
AMBER: residence time& hydration density
(Wed Oct 25 2006 - 07:16:53 PDT)
Angelo
Re: AMBER: mm_pbsa: binding energy calculation
(Mon Oct 30 2006 - 01:36:25 PST)
AMBER: mm_pbsa reference
(Fri Oct 27 2006 - 05:47:07 PDT)
Re: AMBER: mm_pbsa: binding energy calculation
(Thu Oct 26 2006 - 06:04:18 PDT)
Anna Bowman
AMBER: Calculating native contacts for mdcrd files
(Thu Oct 26 2006 - 08:20:50 PDT)
anna.schrey.gmx.de
AMBER: Problems with carnal (Amber7)
(Tue Oct 31 2006 - 07:24:29 PST)
asli ertekin
Re: AMBER: force fiels for a-rna
(Fri Oct 13 2006 - 16:20:32 PDT)
AMBER: force fiels for a-rna
(Fri Oct 13 2006 - 15:28:58 PDT)
Atsutoshi Okabe
AMBER: To create methanol solvent box
(Tue Oct 17 2006 - 23:31:02 PDT)
RE: AMBER: Grid command of ptraj
(Tue Oct 17 2006 - 21:19:13 PDT)
RE: AMBER: Grid command of ptraj
(Mon Oct 16 2006 - 02:26:55 PDT)
AMBER: Grid command of ptraj
(Sat Oct 14 2006 - 00:31:01 PDT)
Austin B. Yongye
Re: AMBER: Interbox interactions
(Tue Oct 17 2006 - 09:03:18 PDT)
AMBER: Interbox interactions
(Mon Oct 16 2006 - 10:15:04 PDT)
b86203054.ntu.edu.tw
AMBER: Is GB/SANDER slower than TIP3P/PMEMD
(Wed Oct 04 2006 - 10:21:39 PDT)
bala
AMBER: splitting LES with ptraj in amber9
(Mon Oct 23 2006 - 22:18:16 PDT)
AMBER: Missing values for MM VDW
(Thu Oct 05 2006 - 04:33:14 PDT)
Barbault Florent
AMBER: MMPBSA entropy question
(Tue Oct 31 2006 - 01:08:55 PST)
Re: AMBER: ff for drug-dna complex and drug atom types assignment
(Mon Oct 23 2006 - 11:37:53 PDT)
Benjamin Juhl
Re: AMBER: problem with calcpka.pl
(Mon Oct 30 2006 - 05:57:42 PST)
AMBER: problem with calcpka.pl
(Tue Oct 24 2006 - 04:58:27 PDT)
Bill Ross
Re: AMBER: Problems with carnal (Amber7)
(Tue Oct 31 2006 - 09:09:57 PST)
Re: AMBER: HBON in frcmod file
(Sat Oct 21 2006 - 12:57:48 PDT)
Re: AMBER: HBON in frcmod file
(Sat Oct 21 2006 - 00:41:55 PDT)
Re: AMBER: problem of installing carnal on macosx
(Fri Oct 20 2006 - 11:50:19 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:26:18 PDT)
Re: AMBER: puzzles about solvatoct or solvatebox
(Tue Oct 17 2006 - 09:13:58 PDT)
Re: AMBER: General Coding Problem
(Mon Oct 16 2006 - 17:56:37 PDT)
Re: AMBER: puzzles about solvatoct or solvatebox
(Thu Oct 12 2006 - 10:43:38 PDT)
RE: AMBER: some puzzles in equilibration MD
(Mon Oct 09 2006 - 20:14:39 PDT)
Re: AMBER: on rst file
(Wed Oct 04 2006 - 10:17:10 PDT)
Re: AMBER: mdcrd file
(Mon Oct 02 2006 - 19:46:15 PDT)
Re: AMBER: mdcrd file
(Mon Oct 02 2006 - 17:23:18 PDT)
Biswa Ranjan Meher
Re: AMBER: Trouble with Leap
(Wed Oct 18 2006 - 22:28:46 PDT)
Re: AMBER: Trouble with Leap
(Tue Oct 17 2006 - 22:35:48 PDT)
AMBER: Trouble with Leap
(Mon Oct 09 2006 - 07:28:28 PDT)
Bonnet, Pascal [PRDBE]
RE: AMBER: problem to center solvateshell
(Mon Oct 02 2006 - 23:30:53 PDT)
caoch.cherry.bio.titech.ac.jp
AMBER: how to combine NEB method with QM/MM approach
(Mon Oct 09 2006 - 09:23:07 PDT)
Carlos Simmerling
Re: AMBER: CARNAL: carnal source code
(Wed Oct 25 2006 - 16:06:08 PDT)
Re: AMBER: Not getting proper structure after minimization
(Wed Oct 25 2006 - 06:45:38 PDT)
Re: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 14:06:14 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 23 2006 - 15:38:22 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:33:40 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:10:52 PDT)
Re: AMBER: force fiels for a-rna
(Fri Oct 13 2006 - 15:41:21 PDT)
Re: AMBER: amber force field
(Wed Oct 11 2006 - 11:33:36 PDT)
Re: AMBER: RMSD: is it related to flexibility?
(Wed Oct 04 2006 - 04:40:04 PDT)
Cenk Andac
Re: AMBER: DIST_RST
(Tue Oct 24 2006 - 03:51:01 PDT)
Re: AMBER: Amber 9 installation problem
(Thu Oct 19 2006 - 12:13:58 PDT)
Re: AMBER: Amber 9 installation problem
(Thu Oct 19 2006 - 10:55:54 PDT)
AMBER: Amber 9 installation problem
(Thu Oct 19 2006 - 08:43:02 PDT)
Re: AMBER: regarding PBCAL in MM-PBSA
(Mon Oct 16 2006 - 18:15:20 PDT)
AMBER: regarding PBCAL in MM-PBSA
(Mon Oct 16 2006 - 16:11:33 PDT)
Changge Ji
Re: Re: AMBER: PBSA calculation fail ....
(Thu Oct 05 2006 - 19:36:34 PDT)
AMBER: PBSA calculation fail ....
(Thu Oct 05 2006 - 06:42:39 PDT)
Charlisa Daniels
AMBER: Ptraj problems
(Thu Oct 12 2006 - 13:01:30 PDT)
Chris Moth
Re: AMBER: error estimate for free energy perturbation calculation
(Wed Oct 25 2006 - 09:58:14 PDT)
Re: AMBER: RESP charges of iron-porphyrin system
(Thu Oct 19 2006 - 09:39:24 PDT)
Christophe Deprez
Re: AMBER: problems for running sander.MPI
(Mon Oct 30 2006 - 10:27:12 PST)
Re: AMBER: problems for running sander.MPI
(Thu Oct 12 2006 - 06:54:41 PDT)
cristian obiol
Re: AMBER: parameters !!??
(Wed Oct 25 2006 - 03:29:42 PDT)
darden
Re: AMBER: PKDIV lone pair dihedrals
(Mon Oct 23 2006 - 14:05:37 PDT)
Dave, Sonya
RE: AMBER: How do we simulate deletion mutations
(Thu Oct 26 2006 - 11:05:01 PDT)
RE: AMBER: How do we simulate deletion mutations
(Wed Oct 25 2006 - 14:41:48 PDT)
AMBER: How do we simulate deletion mutations
(Wed Oct 25 2006 - 11:47:38 PDT)
RE: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 15:46:45 PDT)
AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 13:50:04 PDT)
RE: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 11:14:44 PDT)
RE: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 10:17:59 PDT)
RE: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 10:10:03 PDT)
AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:03:59 PDT)
David A. Case
Re: AMBER: MMPBSA entropy question
(Tue Oct 31 2006 - 17:04:29 PST)
Re: AMBER: solvation and His protonation
(Tue Oct 31 2006 - 07:57:53 PST)
Re: AMBER: ff99SB vs ff02 (ff02pol.rl)
(Mon Oct 30 2006 - 18:57:48 PST)
Re: AMBER: solvation and His protonation
(Mon Oct 30 2006 - 16:34:05 PST)
Re: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 08:32:56 PST)
Re: AMBER: ff02 force fields
(Sun Oct 29 2006 - 21:17:44 PST)
Re: AMBER: problem with calcpka.pl
(Sun Oct 29 2006 - 20:33:54 PST)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Fri Oct 27 2006 - 21:42:08 PDT)
Re: AMBER: where to set bondi radii for halogens
(Fri Oct 27 2006 - 17:24:12 PDT)
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 13:46:07 PDT)
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 12:12:35 PDT)
Re: AMBER: where to set bondi radii for halogens
(Fri Oct 27 2006 - 11:58:04 PDT)
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 09:45:36 PDT)
Re: AMBER: how to add hydrogen molecules in the protein
(Thu Oct 26 2006 - 17:57:22 PDT)
Re: AMBER: error estimate for free energy perturbation calculation
(Wed Oct 25 2006 - 11:40:47 PDT)
Re: AMBER: Shake&Lone Pairs
(Wed Oct 25 2006 - 11:21:02 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 24 2006 - 18:56:14 PDT)
Re: AMBER: md and implicit solvation
(Tue Oct 24 2006 - 18:47:18 PDT)
Re: AMBER: md and implicit solvation
(Tue Oct 24 2006 - 18:26:15 PDT)
Re: AMBER: load charges to antechamber calculations
(Tue Oct 24 2006 - 15:55:29 PDT)
Re: AMBER: PKDIV lone pair dihedrals
(Mon Oct 23 2006 - 13:26:58 PDT)
Re: AMBER: HBON in frcmod file
(Sun Oct 22 2006 - 22:11:58 PDT)
Re: Re: Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 15:55:05 PDT)
Re: Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 14:47:50 PDT)
Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 11:37:51 PDT)
Re: AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai
(Fri Oct 20 2006 - 10:27:50 PDT)
Re: AMBER: Probelm with running Amber 9 parallelly
(Fri Oct 20 2006 - 08:24:16 PDT)
Re: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Thu Oct 19 2006 - 12:22:47 PDT)
Re: AMBER: Amber 9 installation problem
(Thu Oct 19 2006 - 11:43:35 PDT)
Re: AMBER: sander/topology problem
(Tue Oct 17 2006 - 10:31:25 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 17 2006 - 09:41:24 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 17 2006 - 08:38:07 PDT)
Re: AMBER: How did the coordinates change in xleap?
(Tue Oct 17 2006 - 08:28:52 PDT)
Re: AMBER: Amber8: problem related to antechamber
(Tue Oct 17 2006 - 08:10:43 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 16 2006 - 17:33:54 PDT)
Re: AMBER: General Coding Problem
(Mon Oct 16 2006 - 17:27:56 PDT)
Re: AMBER: How to find equillibration time for my system in a generalised born solvation model
(Mon Oct 16 2006 - 15:33:14 PDT)
Re: AMBER: Density calculation
(Mon Oct 16 2006 - 15:26:49 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 16 2006 - 15:24:34 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Mon Oct 16 2006 - 09:41:31 PDT)
Re: AMBER: Amber8: problem related to antechamber
(Mon Oct 16 2006 - 08:29:19 PDT)
Re: AMBER: angle between two vectors
(Thu Oct 12 2006 - 11:14:14 PDT)
Re: AMBER: generalized born model for organic solvent
(Thu Oct 12 2006 - 11:00:00 PDT)
Re: AMBER: generalized born model for organic solvent
(Wed Oct 11 2006 - 16:53:49 PDT)
Re: AMBER: adding polar hydrogens
(Wed Oct 11 2006 - 11:28:11 PDT)
Re: AMBER: generalized born model for organic solvent
(Wed Oct 11 2006 - 09:16:23 PDT)
Re: AMBER: adding polar hydrogens
(Wed Oct 11 2006 - 09:14:29 PDT)
Re: AMBER: partial charges
(Wed Oct 11 2006 - 09:17:48 PDT)
Re: AMBER: LEAP error
(Sun Oct 08 2006 - 21:28:36 PDT)
Re: AMBER: question about building molecules
(Sun Oct 08 2006 - 09:31:27 PDT)
Re: AMBER: (no subject)
(Fri Oct 06 2006 - 09:20:03 PDT)
Re: AMBER: water prmtop/inpcrd problem
(Thu Oct 05 2006 - 19:01:22 PDT)
Re: AMBER: Building polymer with sequence command
(Thu Oct 05 2006 - 17:31:36 PDT)
Re: AMBER: VMD PDB into LEAP Readable PDB
(Thu Oct 05 2006 - 08:13:41 PDT)
Re: Re: AMBER: Pressure problem with restraint
(Wed Oct 04 2006 - 15:19:50 PDT)
Re: AMBER: Pressure problem with restraint
(Wed Oct 04 2006 - 11:03:45 PDT)
Re: AMBER: RMSD: is it related to flexibility?
(Wed Oct 04 2006 - 08:08:32 PDT)
Re: AMBER: Pressure problem with restraint
(Wed Oct 04 2006 - 08:06:38 PDT)
Re: AMBER: problem to center solvateshell
(Mon Oct 02 2006 - 09:01:44 PDT)
Re: AMBER: proposed patch for ptraj/evec.c (Amber 9.0)
(Mon Oct 02 2006 - 08:51:53 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Mon Oct 02 2006 - 08:28:25 PDT)
Re: AMBER: RE: Amber8: problem related to antechamber
(Sun Oct 01 2006 - 06:34:45 PDT)
Re: AMBER: Multiple Timestep MD
(Sun Oct 01 2006 - 06:35:25 PDT)
Re: AMBER: RE: Amber8: problem related to antechamber
(Sun Oct 01 2006 - 06:35:55 PDT)
Re: AMBER: chemical shift restrains
(Sun Oct 01 2006 - 06:35:01 PDT)
David LeBard
Re: AMBER: Two different HIS ligands
(Thu Oct 26 2006 - 16:16:42 PDT)
AMBER: Two different HIS ligands
(Thu Oct 26 2006 - 14:16:09 PDT)
David Mobley
Re: AMBER: single or dual topology for TI?
(Sat Oct 21 2006 - 13:58:41 PDT)
Re: AMBER: single or dual topology for TI?
(Sat Oct 21 2006 - 12:17:50 PDT)
Re: AMBER: charge models in antechamber
(Thu Oct 19 2006 - 10:48:14 PDT)
David Smith
AMBER: imaging issue
(Sun Oct 29 2006 - 08:26:07 PST)
dhruva chakravorty
AMBER: generating resp input files with antechamber
(Thu Oct 05 2006 - 12:53:03 PDT)
Elijah Gregory
Re: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 16:17:14 PDT)
Re: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 16:12:35 PDT)
Re: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 14:39:08 PDT)
AMBER: General Coding Problem
(Mon Oct 16 2006 - 16:53:27 PDT)
Eric Hu
AMBER: charge models in antechamber
(Wed Oct 18 2006 - 15:51:00 PDT)
Re: AMBER: generalized born model for organic solvent
(Thu Oct 12 2006 - 16:32:16 PDT)
Re: AMBER: generalized born model for organic solvent
(Thu Oct 12 2006 - 10:47:44 PDT)
Re: AMBER: generalized born model for organic solvent
(Wed Oct 11 2006 - 16:37:01 PDT)
AMBER: generalized born model for organic solvent
(Tue Oct 10 2006 - 18:29:12 PDT)
Esther Brugger
Re: AMBER: Compile AMBER 8
(Mon Oct 30 2006 - 10:14:05 PST)
Re: AMBER: Compile AMBER 8
(Mon Oct 30 2006 - 09:24:59 PST)
Re: AMBER: Compile AMBER 8
(Mon Oct 30 2006 - 07:28:08 PST)
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 13:18:00 PDT)
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 11:21:13 PDT)
AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 08:44:51 PDT)
Fabian Alejandro Rodriguez
Re: AMBER: Using modified NA bases
(Mon Oct 23 2006 - 16:17:41 PDT)
AMBER: partial charges
(Tue Oct 10 2006 - 09:35:53 PDT)
Feng X Zhou
Re: AMBER: RMSD: is it related to flexibility?
(Fri Oct 06 2006 - 09:28:36 PDT)
Fenghui Fan
RE: AMBER: How do we simulate deletion mutations
(Wed Oct 25 2006 - 15:43:49 PDT)
AMBER: Phosphorylated protein MD simulation
(Wed Oct 25 2006 - 14:16:50 PDT)
Re: AMBER: error estimate for free energy perturbation calculation
(Wed Oct 25 2006 - 13:34:42 PDT)
Re: AMBER: How do we simulate deletion mutations
(Wed Oct 25 2006 - 13:13:20 PDT)
Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms?
(Sun Oct 15 2006 - 21:36:25 PDT)
AMBER: Re: atom nomination in the PDB file produced by Amber
(Wed Oct 04 2006 - 08:41:11 PDT)
AMBER: atom nomination in the PDB file produced by Amber
(Wed Oct 04 2006 - 08:37:45 PDT)
AMBER: on rst file
(Wed Oct 04 2006 - 07:02:40 PDT)
AMBER: Distance between 2 atoms
(Wed Oct 04 2006 - 06:52:16 PDT)
Re: AMBER: Re: Distance between two atoms
(Tue Oct 03 2006 - 23:41:27 PDT)
AMBER: Re: Distance between two atoms
(Tue Oct 03 2006 - 23:12:06 PDT)
AMBER: Distance between two atoms
(Tue Oct 03 2006 - 16:59:17 PDT)
Re: AMBER: mdcrd file
(Mon Oct 02 2006 - 19:17:12 PDT)
AMBER: mdcrd file
(Mon Oct 02 2006 - 17:09:37 PDT)
AMBER: Pressure in MD
(Mon Oct 02 2006 - 13:55:16 PDT)
ferranna.unimo.it
AMBER: SURFTEN/SURFOFF values in amber9
(Sat Oct 14 2006 - 00:27:42 PDT)
Franck_Vendeix.ncsu.edu
Re: AMBER: Using modified NA bases
(Tue Oct 24 2006 - 06:03:36 PDT)
FyD
Re: AMBER: RESP charge fitting
(Fri Oct 27 2006 - 23:37:59 PDT)
Re: AMBER: Using modified NA bases
(Tue Oct 24 2006 - 11:14:54 PDT)
Re: AMBER: RESP charges of iron-porphyrin system
(Thu Oct 19 2006 - 22:23:14 PDT)
Re: AMBER: AMBER minimization vs. Gaussian optimization
(Wed Oct 04 2006 - 22:14:07 PDT)
Giulio Rastelli
Re: AMBER: where to set bondi radii for halogens
(Fri Oct 27 2006 - 14:10:32 PDT)
AMBER: where to set bondi radii for halogens
(Fri Oct 27 2006 - 09:59:00 PDT)
AMBER: halogen bondi radii in mm_pbsa_calceneent.pm
(Fri Oct 27 2006 - 01:46:30 PDT)
Re: AMBER: amber9: SA Bomb in sa_arc
(Thu Oct 26 2006 - 08:58:50 PDT)
Re: AMBER: amber9: SA Bomb in sa_arc
(Thu Oct 26 2006 - 03:56:43 PDT)
Re: AMBER: Not getting proper structure after minimization
(Wed Oct 25 2006 - 06:52:48 PDT)
AMBER: amber9: SA Bomb in sa_arc
(Wed Oct 25 2006 - 04:03:54 PDT)
Gobind Singh Bisht
AMBER: how to simulate water flow inside a channel?
(Wed Oct 18 2006 - 07:33:51 PDT)
AMBER: How to find equillibration time for my system in a generalised born solvation model
(Mon Oct 16 2006 - 14:34:11 PDT)
gtg549i.mail.gatech.edu
AMBER: pmemd installation on linux_p3_athlon ifort
(Tue Oct 24 2006 - 09:20:30 PDT)
AMBER: problem of installing carnal on macosx
(Fri Oct 20 2006 - 11:37:39 PDT)
AMBER: Building polymer with sequence command
(Thu Oct 05 2006 - 09:46:11 PDT)
Gustavo Seabra
Re: AMBER: Not getting proper structure after minimization
(Tue Oct 24 2006 - 14:28:27 PDT)
Re: AMBER: RESP charges of iron-porphyrin system
(Thu Oct 19 2006 - 06:40:20 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 10:41:43 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:56:23 PDT)
Re: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:22:31 PDT)
Re: AMBER: RMSD: is it related to flexibility?
(Thu Oct 05 2006 - 09:08:05 PDT)
HL Eastwood
Re: AMBER: Compile AMBER 8
(Mon Oct 30 2006 - 09:37:22 PST)
Re: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 08:52:04 PST)
Re: AMBER: Compile AMBER 8
(Mon Oct 30 2006 - 08:43:51 PST)
Re: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 07:19:16 PST)
AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 06:42:53 PST)
Holger Gohlke
Re: AMBER: questions on mm_pbsa_statitistics.pl
(Wed Oct 18 2006 - 11:19:20 PDT)
Re: AMBER: questions on mm_pbsa_statitistics.pl
(Wed Oct 18 2006 - 00:42:52 PDT)
Holly Freedman
AMBER: mm_pbsa does not terminate
(Tue Oct 31 2006 - 16:51:19 PST)
Re: AMBER: single or dual topology for TI?
(Sat Oct 21 2006 - 13:32:42 PDT)
AMBER: single or dual topology for TI?
(Sat Oct 21 2006 - 11:20:51 PDT)
Ilyas Yildirim
Re: AMBER: error estimate for free energy perturbation calculation
(Wed Oct 25 2006 - 16:17:36 PDT)
Re: AMBER: HBON in frcmod file
(Sat Oct 21 2006 - 01:24:42 PDT)
AMBER: HBON in frcmod file
(Fri Oct 20 2006 - 22:46:31 PDT)
Re: AMBER: Trouble with Leap
(Thu Oct 19 2006 - 01:04:59 PDT)
Re: AMBER: LEAP error
(Fri Oct 06 2006 - 21:26:29 PDT)
Re: AMBER: water prmtop/inpcrd problem
(Fri Oct 06 2006 - 02:17:11 PDT)
Re: AMBER: AMBER minimization vs. Gaussian optimization
(Wed Oct 04 2006 - 15:17:51 PDT)
AMBER: AMBER minimization vs. Gaussian optimization
(Wed Oct 04 2006 - 13:27:48 PDT)
Ingvar Lagerstedt
AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai
(Fri Oct 20 2006 - 09:17:08 PDT)
Jardas sucuriba
Re: AMBER: solvation and His protonation
(Tue Oct 31 2006 - 05:07:24 PST)
AMBER: solvation and His protonation
(Sat Oct 28 2006 - 07:00:44 PDT)
Re: AMBER: md and implicit solvation
(Tue Oct 24 2006 - 18:29:35 PDT)
AMBER: md and implicit solvation
(Tue Oct 24 2006 - 16:57:24 PDT)
Jianhui
AMBER: Density calculation
(Mon Oct 16 2006 - 14:12:24 PDT)
Re: Re: AMBER: Pressure problem with restraint
(Wed Oct 04 2006 - 12:24:35 PDT)
Re: AMBER: Pressure problem with restraint
(Wed Oct 04 2006 - 10:49:29 PDT)
AMBER: Pressure problem with restraint
(Tue Oct 03 2006 - 07:41:46 PDT)
Jianhui Tian
AMBER: ptraj radial problem: Segmentation fault
(Mon Oct 23 2006 - 14:48:43 PDT)
Jiapu.Zhang.csiro.au
AMBER: How to get the VDW contacts' messages from the mdcrd files
(Mon Oct 02 2006 - 23:11:03 PDT)
Jiri Sponer
Re: AMBER: force fiels for a-rna
(Sat Oct 14 2006 - 00:59:13 PDT)
jitrayut jitonnom
AMBER: what is the RMS value in resp charge fitting ?
(Tue Oct 31 2006 - 00:46:31 PST)
AMBER: mmpbsa: fail to run heat in tutorial A3
(Sun Oct 22 2006 - 10:31:53 PDT)
John Vieceli
AMBER: C -N -CT-CT torsion parameters
(Sun Oct 29 2006 - 17:10:49 PST)
Jones de Andrade
AMBER: parameters for fluoromolecules with more than one single carbon?
(Thu Oct 26 2006 - 14:51:27 PDT)
Joshua
Re: AMBER: restraints and constant pressure
(Fri Oct 13 2006 - 15:46:26 PDT)
JunJun Liu
Re: AMBER: change from .rst file to .mdcrd file
(Wed Oct 04 2006 - 13:14:22 PDT)
Re: AMBER: how to calculate rmsd for non hydrogen at oms?
(Tue Oct 03 2006 - 12:10:25 PDT)
Junmei Wang
RE: AMBER: Problem loading peptoid residues with antechamber
(Wed Oct 18 2006 - 09:05:24 PDT)
jz7.duke.edu
AMBER: error estimate for free energy perturbation calculation
(Tue Oct 24 2006 - 21:15:26 PDT)
Kateryna Miroshnychenko
AMBER: ff for drug-dna complex and drug atom types assignment
(Mon Oct 23 2006 - 09:08:59 PDT)
Keerthi Gottipati
Re: AMBER: CARNAL: carnal source code
(Thu Oct 26 2006 - 05:41:21 PDT)
AMBER: CARNAL: carnal source code
(Wed Oct 25 2006 - 15:14:41 PDT)
Kijeong Kwac
RE: RE: Re: Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 15:48:07 PDT)
RE: Re: Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 15:32:00 PDT)
RE: Re: AMBER: Question about sander code
(Fri Oct 20 2006 - 14:08:17 PDT)
AMBER: Question about sander code
(Fri Oct 20 2006 - 11:13:49 PDT)
Kristina Furse
Re: AMBER: imaging issue
(Mon Oct 30 2006 - 10:30:25 PST)
Re: AMBER: Two different HIS ligands
(Thu Oct 26 2006 - 14:41:49 PDT)
Lorenzo Gontrani
AMBER: Shake&Lone Pairs
(Wed Oct 25 2006 - 03:58:59 PDT)
AMBER: PKDIV lone pair dihedrals
(Mon Oct 23 2006 - 10:16:25 PDT)
AMBER: sander/topology problem
(Tue Oct 17 2006 - 09:51:39 PDT)
Lwin, ThuZar
RE: AMBER: angle between two vectors. .
(Mon Oct 16 2006 - 13:51:28 PDT)
AMBER: angle between two vectors
(Thu Oct 12 2006 - 09:51:15 PDT)
M. L. Dodson
Re: AMBER: angle between two vectors
(Thu Oct 12 2006 - 10:40:35 PDT)
Maniopoulou, A \(Mina\)
AMBER: Amber: Parallel Installation Problems
(Fri Oct 27 2006 - 10:13:56 PDT)
RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Tue Oct 24 2006 - 06:59:26 PDT)
RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Fri Oct 20 2006 - 03:27:29 PDT)
AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Thu Oct 19 2006 - 05:48:08 PDT)
Marcelo Puiatti
Re: AMBER: RESP charges of iron-porphyrin system
(Wed Oct 25 2006 - 10:42:07 PDT)
Mark Williamson
Re: AMBER: Compile AMBER 8
(Fri Oct 27 2006 - 09:03:07 PDT)
Re: AMBER: Amber 9 installation problem
(Thu Oct 19 2006 - 09:12:01 PDT)
mathew k varghese
AMBER: Free-energy using MM-PBSA
(Thu Oct 19 2006 - 01:05:45 PDT)
Michael F. Summers
AMBER: N1-protonated adenosine, N-terminal myristyl group
(Tue Oct 31 2006 - 12:54:49 PST)
Mingfeng Yang
Re: AMBER: Closest(closest water)
(Mon Oct 30 2006 - 12:29:00 PST)
AMBER: RESP charge fitting
(Fri Oct 27 2006 - 17:35:37 PDT)
AMBER: TFE parameters for Amber
(Thu Oct 12 2006 - 16:33:21 PDT)
Myunggi Yi
Re: AMBER: residence time& hydration density
(Thu Oct 26 2006 - 08:27:26 PDT)
Re: AMBER: Phosphorylated protein MD simulation
(Thu Oct 26 2006 - 08:13:17 PDT)
Re: AMBER: Phosphorylated protein MD simulation
(Thu Oct 26 2006 - 08:18:26 PDT)
Re: AMBER: ptraj atomicfluct
(Wed Oct 18 2006 - 12:13:36 PDT)
AMBER: ptraj atomicfluct
(Wed Oct 18 2006 - 11:59:22 PDT)
Re: AMBER: angle between two vectors
(Mon Oct 16 2006 - 09:15:59 PDT)
AMBER: How to merge two molecules to one
(Fri Oct 06 2006 - 11:51:19 PDT)
Nicolas Lux Fawzi
AMBER: ff99SB vs ff02 (ff02pol.rl)
(Mon Oct 30 2006 - 17:48:32 PST)
norberto.ualberta.ca
Re: AMBER: ff02 force fields
(Mon Oct 30 2006 - 10:37:57 PST)
AMBER: ff02 force fields
(Sun Oct 29 2006 - 12:18:25 PST)
AMBER: Help with polarization force field
(Fri Oct 27 2006 - 16:20:09 PDT)
Noriaki Okimoto
AMBER: amber force field
(Wed Oct 11 2006 - 11:21:03 PDT)
nur avneet
Re: AMBER:pls help load peptoid residues in antechamber
(Tue Oct 24 2006 - 22:29:55 PDT)
RE: AMBER: Problem loading peptoid residues with antechamber
(Wed Oct 18 2006 - 21:05:15 PDT)
AMBER: Problem loading peptoid residues with antechamber
(Tue Oct 17 2006 - 23:23:42 PDT)
AMBER: Problem working with Antechamber
(Tue Oct 17 2006 - 00:44:54 PDT)
Olayiwola Adekoya
AMBER: mmpbsa in parallell
(Thu Oct 19 2006 - 00:57:07 PDT)
Peter Gannett
AMBER: Virus?
(Mon Oct 23 2006 - 05:34:29 PDT)
Prashanth Athri
AMBER: Curve fitting during dihedral parameter calculation
(Thu Oct 19 2006 - 12:15:21 PDT)
AMBER: Calculation of Dihedral constants
(Thu Oct 05 2006 - 19:36:15 PDT)
AMBER: (no subject)
(Thu Oct 05 2006 - 19:34:47 PDT)
Pravin_Kumar.jubilantbiosys.com
AMBER: Issue with installation of Amber v9.0 parallel compilation
(Thu Oct 19 2006 - 21:17:51 PDT)
AMBER: Issue with installation of Amber v9.0 parallel compilation
(Thu Oct 19 2006 - 21:02:42 PDT)
Priti Hansia
RE: AMBER: Question regarding lastrst and taup
(Wed Oct 25 2006 - 21:58:10 PDT)
AMBER: Question regarding lastrst and taup
(Tue Oct 24 2006 - 23:37:09 PDT)
priya priya
Re: AMBER: Amber8: problem related to antechamber
(Mon Oct 16 2006 - 23:49:03 PDT)
RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration
(Mon Oct 16 2006 - 21:42:15 PDT)
AMBER: Amber8: how to do Simulated Annealing and Equilibration
(Mon Oct 16 2006 - 01:32:18 PDT)
AMBER: Amber8: problem related to antechamber
(Mon Oct 16 2006 - 00:00:38 PDT)
Qizhi Cui
Re: AMBER: Using modified NA bases
(Wed Oct 25 2006 - 08:51:32 PDT)
AMBER: problems for running sander.MPI
(Wed Oct 11 2006 - 13:39:36 PDT)
Rachel
AMBER: how to add hydrogen molecules in the protein
(Thu Oct 26 2006 - 09:28:16 PDT)
AMBER: how to select the problematic residues(atoms) in VMD
(Thu Oct 26 2006 - 04:00:21 PDT)
AMBER: reinstall amber8
(Wed Oct 25 2006 - 07:57:59 PDT)
Rafi Ahmad
AMBER: Probelm with running Amber 9 parallelly
(Fri Oct 20 2006 - 07:29:14 PDT)
Rajendra P. OJHA
AMBER: MM_PBSA
(Sat Oct 07 2006 - 09:21:49 PDT)
Raviprasad Aduri
AMBER: Announcement: Parameters for Modified Nucleosides in RNA
(Mon Oct 09 2006 - 14:13:56 PDT)
Ray Luo
Re: AMBER: amber9: SA Bomb in sa_arc
(Tue Oct 31 2006 - 00:29:27 PST)
Re: AMBER: amber9: SA Bomb in sa_arc
(Wed Oct 25 2006 - 02:14:08 PDT)
Re: AMBER: amber9: SA Bomb in sa_arc
(Tue Oct 24 2006 - 14:55:24 PDT)
Re: AMBER: regarding PBCAL in MM-PBSA
(Mon Oct 16 2006 - 17:35:42 PDT)
Re: AMBER: PBSA calculation fail ....
(Fri Oct 06 2006 - 09:22:11 PDT)
Re: AMBER: PBSA calculation fail ....
(Thu Oct 05 2006 - 09:36:32 PDT)
Reinhard Klement
Re: AMBER: ptraj hbond analysis troubles
(Wed Oct 11 2006 - 01:25:27 PDT)
Rita Cassia
Re: AMBER: question about building molecules
(Mon Oct 09 2006 - 08:49:10 PDT)
AMBER: question about building molecules
(Sun Oct 08 2006 - 04:05:59 PDT)
rob yang
AMBER: alanine scan (mm/pbsa)
(Wed Oct 18 2006 - 07:46:47 PDT)
Robert Duke
Re: AMBER: pmemd installation on linux_p3_athlon ifort
(Tue Oct 24 2006 - 10:08:58 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 18:55:42 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 11:35:20 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 06:58:50 PDT)
Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD
(Wed Oct 04 2006 - 10:45:06 PDT)
Re: AMBER: Multiple Timestep MD
(Sun Oct 01 2006 - 07:22:34 PDT)
Ross Walker
RE: AMBER: problems for running sander.MPI
(Mon Oct 30 2006 - 10:40:06 PST)
RE: AMBER: how to restrain some residues in a NPT MD?
(Mon Oct 30 2006 - 08:34:46 PST)
RE: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 08:24:26 PST)
RE: AMBER: Amber: Parallel Installation Problems
(Fri Oct 27 2006 - 10:53:10 PDT)
RE: AMBER: amber9: SA Bomb in sa_arc
(Thu Oct 26 2006 - 09:35:19 PDT)
RE: AMBER: amber9: SA Bomb in sa_arc
(Thu Oct 26 2006 - 08:38:05 PDT)
RE: AMBER: how to select the problematic residues(atoms) in VMD
(Thu Oct 26 2006 - 08:26:22 PDT)
RE: AMBER: parameters !!??
(Wed Oct 25 2006 - 08:53:01 PDT)
RE: AMBER: Question regarding lastrst and taup
(Wed Oct 25 2006 - 08:46:52 PDT)
RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Tue Oct 24 2006 - 08:33:45 PDT)
RE: AMBER: mmpbsa: fail to run heat in tutorial A3
(Mon Oct 23 2006 - 08:39:26 PDT)
RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Fri Oct 20 2006 - 09:06:49 PDT)
RE: AMBER: Issue with installation of Amber v9.0 parallel compilation
(Thu Oct 19 2006 - 21:55:00 PDT)
RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
(Thu Oct 19 2006 - 12:24:43 PDT)
RE: AMBER: Unstable RMS trajectory
(Tue Oct 17 2006 - 09:40:43 PDT)
RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration
(Mon Oct 16 2006 - 08:32:20 PDT)
RE: AMBER: Amber8: problem related to antechamber
(Mon Oct 16 2006 - 08:32:20 PDT)
AMBER: Updated Tutorials Page
(Fri Oct 13 2006 - 12:17:07 PDT)
RE: AMBER: problems for running sander.MPI
(Thu Oct 12 2006 - 10:41:19 PDT)
RE: AMBER: problems for running sander.MPI
(Wed Oct 11 2006 - 15:18:14 PDT)
RE: AMBER: some puzzles in equilibration MD
(Mon Oct 09 2006 - 15:41:54 PDT)
RE: AMBER: how to combine NEB method with QM/MM approach
(Mon Oct 09 2006 - 15:33:00 PDT)
RE: AMBER: some puzzles in equilibration MD
(Mon Oct 09 2006 - 07:53:20 PDT)
RE: AMBER: Is GB/SANDER slower than TIP3P/PMEMD
(Wed Oct 04 2006 - 10:51:24 PDT)
RE: AMBER: mdcrd file
(Mon Oct 02 2006 - 21:31:03 PDT)
Sayandeep Purkayasth
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Fri Oct 27 2006 - 18:25:37 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Sun Oct 15 2006 - 23:32:04 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Mon Oct 09 2006 - 01:59:18 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Mon Oct 09 2006 - 01:11:56 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 06:37:07 PDT)
AMBER: ptraj hbond analysis troubles
(Wed Oct 04 2006 - 14:14:10 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Tue Oct 03 2006 - 22:14:06 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Mon Oct 02 2006 - 17:30:40 PDT)
AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Sun Oct 01 2006 - 19:15:54 PDT)
Scott Brozell
Re: AMBER: Trouble with Leap
(Mon Oct 09 2006 - 18:42:38 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Mon Oct 09 2006 - 18:14:54 PDT)
Re: AMBER: LEAP error
(Fri Oct 06 2006 - 10:30:34 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Fri Oct 06 2006 - 10:13:15 PDT)
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Wed Oct 04 2006 - 01:16:09 PDT)
Sean Rathlef
Re: AMBER: modeling of ligand concentrations
(Tue Oct 24 2006 - 19:30:54 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 24 2006 - 19:29:43 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 24 2006 - 16:47:03 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 23 2006 - 15:19:18 PDT)
Re: AMBER: charge models in antechamber
(Wed Oct 18 2006 - 16:48:00 PDT)
Re: AMBER: charge models in antechamber
(Wed Oct 18 2006 - 16:29:02 PDT)
Re: AMBER: modeling of ligand concentrations
(Tue Oct 17 2006 - 09:07:18 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 16 2006 - 18:37:25 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 16 2006 - 15:48:16 PDT)
AMBER: modeling of ligand concentrations
(Mon Oct 16 2006 - 13:43:51 PDT)
Re: AMBER: Grid command of ptraj
(Sat Oct 14 2006 - 03:25:59 PDT)
AMBER: BioBlade
(Thu Oct 12 2006 - 20:12:41 PDT)
Re: AMBER: adding polar hydrogens
(Wed Oct 11 2006 - 11:35:47 PDT)
Re: AMBER: adding polar hydrogens
(Wed Oct 11 2006 - 11:02:28 PDT)
AMBER: adding polar hydrogens
(Tue Oct 10 2006 - 19:43:39 PDT)
Sergey Samsonov
Re: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 07:36:29 PST)
Re: AMBER: periodic boundary condition question...
(Mon Oct 30 2006 - 07:04:12 PST)
Re: AMBER: Closest(closest water)
(Mon Oct 30 2006 - 06:27:40 PST)
AMBER: Closest(closest water)
(Mon Oct 30 2006 - 04:58:11 PST)
AMBER: klambda
(Fri Oct 13 2006 - 07:49:05 PDT)
Re: AMBER: Reducing trajectory
(Wed Oct 11 2006 - 00:36:15 PDT)
AMBER: Reducind trajectory
(Wed Oct 11 2006 - 00:03:49 PDT)
Re: AMBER: hbond analysis
(Wed Oct 04 2006 - 23:40:59 PDT)
Re: AMBER: hbond analysis
(Wed Oct 04 2006 - 07:49:35 PDT)
sethl.gatech.edu
AMBER: Using modified NA bases
(Mon Oct 23 2006 - 12:59:15 PDT)
AMBER: atom type nh vs. n2
(Fri Oct 20 2006 - 14:31:09 PDT)
AMBER: Phenyl Ring atom types
(Thu Oct 12 2006 - 11:59:24 PDT)
Shin Tokumoto
Re: AMBER: RESP charges of iron-porphyrin system
(Thu Oct 19 2006 - 21:45:08 PDT)
AMBER: RESP charges of iron-porphyrin system
(Wed Oct 18 2006 - 19:50:26 PDT)
Shozeb Haider
AMBER: High Values in MMPBSA
(Thu Oct 12 2006 - 09:55:15 PDT)
AMBER: MMPBSA vDW error
(Mon Oct 09 2006 - 16:08:27 PDT)
AMBER: MM_PBSA error
(Tue Oct 03 2006 - 14:04:57 PDT)
Shuting Wei
Re: AMBER: pmemd installation on linux_p3_athlon ifort
(Tue Oct 24 2006 - 12:19:31 PDT)
Re: AMBER: problem of installing carnal on macosx
(Fri Oct 20 2006 - 12:45:03 PDT)
Smriti Sharma
Re: AMBER: To create methanol solvent box
(Wed Oct 18 2006 - 01:14:38 PDT)
AMBER: simulation of protein in non-aq or organic solvent bath
(Sun Oct 15 2006 - 21:06:53 PDT)
Stefano Pieraccini
AMBER: MM-PBSA memory usage
(Thu Oct 26 2006 - 05:33:41 PDT)
Thomas Cheatham
Re: AMBER: ff99SB vs ff02 (ff02pol.rl)
(Mon Oct 30 2006 - 21:07:46 PST)
Re: AMBER: ff99SB vs ff02 (ff02pol.rl)
(Mon Oct 30 2006 - 18:15:18 PST)
Re: AMBER: imaging issue
(Mon Oct 30 2006 - 12:54:20 PST)
Re: AMBER: md and implicit solvation
(Tue Oct 24 2006 - 18:50:43 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 23 2006 - 15:51:28 PDT)
Re: AMBER: modeling of ligand concentrations
(Mon Oct 23 2006 - 09:38:55 PDT)
RE: AMBER: Grid command of ptraj
(Mon Oct 23 2006 - 09:24:20 PDT)
RE: AMBER: Grid command of ptraj
(Tue Oct 17 2006 - 08:40:22 PDT)
Re: AMBER: Interbox interactions
(Tue Oct 17 2006 - 08:34:50 PDT)
Re: AMBER: RDF calculation
(Tue Oct 17 2006 - 08:23:05 PDT)
Re: AMBER: puzzles about solvatoct or solvatebox
(Tue Oct 17 2006 - 08:05:08 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 12:43:37 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Thu Oct 05 2006 - 08:21:40 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Wed Oct 04 2006 - 15:41:55 PDT)
Re: AMBER: ptraj hbond analysis troubles
(Wed Oct 04 2006 - 14:36:49 PDT)
Re: AMBER: hbond analysis
(Wed Oct 04 2006 - 14:00:02 PDT)
Re: AMBER: AMBER minimization vs. Gaussian optimization
(Wed Oct 04 2006 - 13:45:59 PDT)
Re: AMBER: hbond analysis
(Tue Oct 03 2006 - 09:27:56 PDT)
Re: AMBER: hbond analysis
(Tue Oct 03 2006 - 09:05:00 PDT)
Thomas Steinbrecher
Re: AMBER: modeling of ligand concentrations
(Tue Oct 24 2006 - 18:11:05 PDT)
Re: AMBER: High Values in MMPBSA
(Thu Oct 12 2006 - 08:36:31 PDT)
Re: AMBER: Pressure in MD
(Mon Oct 02 2006 - 14:24:30 PDT)
Toshifumi Yui
AMBER: Re: AMBER: Ｆｅ complex (correction)
(Tue Oct 10 2006 - 18:41:05 PDT)
AMBER: Ｆｅ complex
(Tue Oct 10 2006 - 18:09:36 PDT)
Urszula Uciechowska
Re: AMBER: parameters !!??
(Wed Oct 25 2006 - 06:32:49 PDT)
AMBER: parameters !!??
(Wed Oct 25 2006 - 02:27:22 PDT)
AMBER: DIST_RST
(Tue Oct 24 2006 - 01:32:03 PDT)
Varsha Goyal
Re: AMBER: mm_pbsa: binding energy calculation
(Sat Oct 28 2006 - 14:41:02 PDT)
AMBER: mm_pbsa: binding energy calculation
(Wed Oct 25 2006 - 11:51:57 PDT)
Viktor Hornak
Re: AMBER: how to calculate rmsd for non hydrogen at oms?
(Tue Oct 03 2006 - 09:51:53 PDT)
Vitor Manuel Sousa F?x
AMBER: polarization effects
(Sun Oct 01 2006 - 07:08:55 PDT)
Vlad Cojocaru
Re: AMBER: hbond analysis
(Wed Oct 04 2006 - 08:26:32 PDT)
Re: AMBER: hbond analysis
(Tue Oct 03 2006 - 09:35:32 PDT)
Re: AMBER: hbond analysis
(Tue Oct 03 2006 - 09:18:28 PDT)
AMBER: hbond analysis
(Tue Oct 03 2006 - 08:45:23 PDT)
Wang, Xuelin
AMBER: load charges to antechamber calculations
(Tue Oct 24 2006 - 12:30:24 PDT)
AMBER: change from .rst file to .mdcrd file
(Wed Oct 04 2006 - 08:52:56 PDT)
AMBER: how to run a mm_pbsa on a minimized structure?
(Mon Oct 02 2006 - 14:50:02 PDT)
Wei Zhang
Re: AMBER: reinstall amber8
(Wed Oct 25 2006 - 08:13:01 PDT)
William Wei
AMBER: mm_pbsa PBCAL
(Tue Oct 03 2006 - 12:23:18 PDT)
Xioling Chuang
AMBER: RDF calculation
(Tue Oct 17 2006 - 03:54:02 PDT)
Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms?
(Mon Oct 16 2006 - 01:48:04 PDT)
AMBER: How to calculate RDF based on the center of mass of specific solute atoms?
(Sun Oct 15 2006 - 21:04:10 PDT)
Yongmei Pan
AMBER: question on molsurf
(Fri Oct 20 2006 - 15:38:38 PDT)
Re: AMBER: Free-energy using MM-PBSA
(Thu Oct 19 2006 - 06:20:07 PDT)
Re: Re: AMBER: questions on mm_pbsa_statitistics.pl
(Wed Oct 18 2006 - 08:12:58 PDT)
AMBER: questions on mm_pbsa_statitistics.pl
(Tue Oct 17 2006 - 15:57:59 PDT)
AMBER: question on mm_pbsa_statistics.pl
(Tue Oct 17 2006 - 15:36:23 PDT)
yxiong99
AMBER: how to calculate rmsd for non hydrogen at oms?
(Tue Oct 03 2006 - 09:43:49 PDT)
Zhihong Yu
AMBER: how to restrain some residues in a NPT MD?
(Mon Oct 30 2006 - 07:20:38 PST)
AMBER: How did the coordinates change in xleap?
(Tue Oct 17 2006 - 08:03:47 PDT)
Re: AMBER: puzzles about solvatoct or solvatebox
(Tue Oct 17 2006 - 07:42:54 PDT)
AMBER: puzzles about solvatoct or solvatebox
(Thu Oct 12 2006 - 03:00:08 PDT)
RE: AMBER: some puzzles in equilibration MD
(Mon Oct 09 2006 - 08:19:15 PDT)
AMBER: some puzzles in equilibration MD
(Mon Oct 09 2006 - 06:58:06 PDT)
Last message date
:
Sun Nov 05 2006 - 06:07:31 PST
Archived on
: Sun Nov 17 2024 - 05:53:31 PST
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