Amber Archive Jul 2006 by author
383 messages
:
Starting
Sun Jul 02 2006 - 06:07:20 PDT,
Ending
Wed Aug 02 2006 - 06:07:09 PDT
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AMBER: FIX conformation of a ligand
(Wed Jul 05 2006 - 19:17:23 PDT)
RE: AMBER: fixing residues
(Mon Jul 03 2006 - 19:47:08 PDT)
AMBER: Tutorial 4-section 4 DIHE in frcmod file.
(Mon Jul 03 2006 - 19:13:04 PDT)
AMBER: Tutorial 4-section 4 - VDW parameters
(Mon Jul 03 2006 - 02:49:31 PDT)
AMBER: Tutorial 4-section 4 (plc.frcmod)
(Mon Jul 03 2006 - 02:41:44 PDT)
Re: AMBER: R.E.D II
(Mon Jul 03 2006 - 02:35:35 PDT)
Abhilash
AMBER: GB tutorials and disulphide bonds
(Mon Jul 31 2006 - 13:41:30 PDT)
Adam Pelzer
AMBER: Calculating energy for specific part of system
(Tue Jul 18 2006 - 15:32:34 PDT)
Adrian Roitberg
Re: AMBER: Replica Exchange
(Fri Jul 21 2006 - 06:37:26 PDT)
Re: AMBER: Replica exchange with Amber9
(Fri Jul 14 2006 - 06:00:14 PDT)
Alik Widge
AMBER: Re: Confusion re AMBER SMD output
(Mon Jul 31 2006 - 15:54:59 PDT)
Re: AMBER: process_mdout.perl's output is empty
(Tue Jul 25 2006 - 08:19:44 PDT)
AMBER: Confusion re AMBER SMD output
(Mon Jul 24 2006 - 13:31:34 PDT)
amere swathi
AMBER: problem with saving the parameters file
(Wed Jul 05 2006 - 01:50:40 PDT)
amit.mbu.iisc.ernet.in
AMBER: Having trouble with Nucgen for generating pdb more than 16 bps
(Sun Jul 30 2006 - 11:51:05 PDT)
AMBER: QMMM simulation
(Thu Jul 13 2006 - 11:38:48 PDT)
Re: AMBER: Problem with bcc flag of antechamber..continued
(Fri Jul 07 2006 - 03:09:32 PDT)
Andrea Bortolato
AMBER: dummy atoms in MMPBSA
(Thu Jul 27 2006 - 01:10:50 PDT)
AMBER: residue and atom number
(Mon Jul 10 2006 - 05:57:05 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Gb Na+ ions DNA
(Fri Jul 21 2006 - 02:22:21 PDT)
Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1
(Fri Jul 14 2006 - 03:38:10 PDT)
Re: AMBER: Namot on AMD 64 possible
(Wed Jul 05 2006 - 11:08:44 PDT)
Re: AMBER: Can you use VMD to measure bond angles/lengths
(Tue Jul 04 2006 - 09:09:21 PDT)
Re: AMBER: NAMOT
(Mon Jul 03 2006 - 04:02:57 PDT)
Andrew Box
AMBER: Dynamics and Restraint problem
(Mon Jul 17 2006 - 16:49:51 PDT)
AMBER: (no subject)
(Sun Jul 09 2006 - 15:49:02 PDT)
Re: AMBER: Sander NOE violations
(Thu Jul 06 2006 - 18:32:21 PDT)
AMBER: Sander NOE violations
(Thu Jul 06 2006 - 16:55:59 PDT)
Atro Tossavainen
Re: AMBER: combining different versions of AMBER
(Sun Jul 23 2006 - 22:44:10 PDT)
Atsutoshi Okabe
RE: AMBER: Replica exchange with Amber9
(Wed Jul 19 2006 - 09:22:49 PDT)
RE: AMBER: Replica exchange with Amber9
(Mon Jul 17 2006 - 01:20:25 PDT)
AMBER: Replica exchange with Amber9
(Thu Jul 13 2006 - 23:20:21 PDT)
RE: AMBER: Replica exchange
(Tue Jul 11 2006 - 21:13:38 PDT)
RE: AMBER: Replica exchange
(Mon Jul 10 2006 - 19:43:17 PDT)
AMBER: Replica exchange
(Mon Jul 10 2006 - 04:38:17 PDT)
AMBER: 2-D free energy surface using WHAM
(Mon Jul 03 2006 - 05:08:01 PDT)
Austin B. Yongye
Re: AMBER: Replica Exchange
(Fri Jul 21 2006 - 06:29:08 PDT)
AMBER: Replica Exchange
(Thu Jul 20 2006 - 19:07:46 PDT)
Re: AMBER: Replica exchange
(Wed Jul 19 2006 - 10:23:47 PDT)
AMBER: Replica exchange
(Wed Jul 19 2006 - 08:04:44 PDT)
Re: AMBER: Replica exchange
(Mon Jul 17 2006 - 15:22:51 PDT)
AMBER: Replica exchange
(Mon Jul 17 2006 - 05:31:09 PDT)
AYTUG TUNCEL
AMBER: leap error
(Wed Jul 26 2006 - 16:29:35 PDT)
Baker, Bo-Yang
AMBER: Distance between two regions
(Mon Jul 31 2006 - 17:16:02 PDT)
AMBER: convert chemical structure to pdb file
(Fri Jul 07 2006 - 11:44:25 PDT)
Bill Ross
Re: AMBER: loading torsion parameters
(Mon Jul 31 2006 - 13:49:38 PDT)
Re: AMBER: Having trouble with Nucgen for generating pdb more than 16 bps
(Mon Jul 31 2006 - 11:53:11 PDT)
Re: AMBER: Can't open xleap
(Thu Jul 27 2006 - 10:21:39 PDT)
Re: AMBER: Creating an Intercalation site
(Mon Jul 17 2006 - 12:49:20 PDT)
Re: AMBER: Ring of dna
(Mon Jul 17 2006 - 12:19:49 PDT)
Re: AMBER: Ring of dna
(Mon Jul 17 2006 - 12:15:10 PDT)
Re: AMBER: Ring of dna
(Sat Jul 15 2006 - 10:55:07 PDT)
Re: AMBER: Ring of dna
(Fri Jul 14 2006 - 10:23:07 PDT)
Re: AMBER: working with large strained system
(Thu Jul 06 2006 - 10:06:57 PDT)
Re: AMBER: PTRAJ OUTPUT
(Wed Jul 05 2006 - 16:43:57 PDT)
Re: AMBER: problem with saving the parameters file
(Wed Jul 05 2006 - 11:23:05 PDT)
Bob Johnson
RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
(Fri Jul 07 2006 - 10:35:59 PDT)
AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
(Fri Jul 07 2006 - 07:55:32 PDT)
Brent Krueger
AMBER: pmemd9 issue
(Sat Jul 01 2006 - 20:45:11 PDT)
Carlos Simmerling
Re: AMBER: Harmonic restraint along z-axis
(Thu Jul 27 2006 - 09:15:18 PDT)
Re: AMBER: library for 8oxoguanine
(Mon Jul 24 2006 - 14:12:38 PDT)
Re: AMBER: converting from parm to parm7
(Sat Jul 22 2006 - 04:27:10 PDT)
Re: AMBER: Replica Exchange
(Thu Jul 20 2006 - 19:51:19 PDT)
Re: AMBER: Replica exchange
(Thu Jul 20 2006 - 05:32:07 PDT)
Re: AMBER: Replica exchange
(Wed Jul 19 2006 - 09:29:33 PDT)
Re: AMBER: temperature regulation
(Tue Jul 18 2006 - 04:41:18 PDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03
(Tue Jul 18 2006 - 04:28:20 PDT)
Re: AMBER: Replica exchange
(Mon Jul 17 2006 - 07:44:55 PDT)
Re: AMBER: center molecule using iwrap=1?
(Thu Jul 13 2006 - 12:43:37 PDT)
Re: AMBER: center molecule using iwrap=1?
(Thu Jul 13 2006 - 12:00:59 PDT)
Re: AMBER: Replica exchange
(Wed Jul 12 2006 - 07:25:14 PDT)
Re: AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 12:05:48 PDT)
Re: AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 08:09:21 PDT)
Re: AMBER: Replica exchange
(Tue Jul 11 2006 - 05:49:20 PDT)
Re: AMBER: Replica exchange
(Mon Jul 10 2006 - 05:13:48 PDT)
Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?
(Thu Jul 06 2006 - 18:51:58 PDT)
Re: AMBER: working with large strained system
(Thu Jul 06 2006 - 06:41:39 PDT)
Carra, Claudio \(JSC-SK\)[USRA]
AMBER: library for 8oxoguanine
(Mon Jul 24 2006 - 12:50:59 PDT)
RE: AMBER: change atom in a DNA double strand
(Mon Jul 10 2006 - 12:24:02 PDT)
AMBER: change atom in a DNA double strand
(Wed Jul 05 2006 - 14:09:23 PDT)
Changge Ji
AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ?
(Tue Jul 11 2006 - 23:03:30 PDT)
Chengwen Chen
AMBER: problems of running sander.MPI of amber9 on remote node
(Sun Jul 23 2006 - 23:29:20 PDT)
AMBER: error on running parallel sander on remote node- amber9
(Wed Jul 05 2006 - 00:46:11 PDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9
(Tue Jul 04 2006 - 21:29:38 PDT)
Chng Choon-Peng
Re: AMBER: Can't open xleap
(Thu Jul 27 2006 - 03:45:58 PDT)
Re: AMBER: xleap
(Thu Jul 27 2006 - 03:14:58 PDT)
Re: AMBER: process_mdout.perl's output is empty
(Mon Jul 24 2006 - 18:02:57 PDT)
Re: AMBER: Ptraj: Hbond time series
(Tue Jul 11 2006 - 16:56:20 PDT)
Christophe Guilbert
AMBER: program to calculate net charge of a ligand for Antechamber
(Mon Jul 10 2006 - 18:30:39 PDT)
AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?
(Thu Jul 06 2006 - 17:51:49 PDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
(Wed Jul 05 2006 - 19:50:24 PDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
(Wed Jul 05 2006 - 16:55:49 PDT)
Claire Zerafa
AMBER: hbond analysis2
(Tue Jul 04 2006 - 07:00:35 PDT)
AMBER: Dihedral analysis
(Mon Jul 03 2006 - 14:25:33 PDT)
AMBER: hbond analysis
(Mon Jul 03 2006 - 14:06:22 PDT)
Conn O'Rourke
AMBER: Gb Na+ ions DNA
(Thu Jul 20 2006 - 08:16:05 PDT)
Cporteli
AMBER: PTRAJ OUTPUT
(Wed Jul 05 2006 - 16:02:47 PDT)
darden
Re: AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 07:34:47 PDT)
David A. Case
Re: AMBER: Zinc-coordinating histidine protonation state
(Mon Jul 31 2006 - 08:50:16 PDT)
Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. .
(Fri Jul 28 2006 - 07:27:44 PDT)
Re: AMBER: Dynamics and Restraint problem
(Thu Jul 27 2006 - 16:08:16 PDT)
Re: AMBER: parallel installation of amber8 on HP cluster
(Thu Jul 27 2006 - 08:57:41 PDT)
Re: AMBER: leap error
(Thu Jul 27 2006 - 07:34:17 PDT)
Re: AMBER: Harmonic restraint along z-axis
(Thu Jul 27 2006 - 07:32:52 PDT)
Re: AMBER: Can't open xleap
(Thu Jul 27 2006 - 06:53:16 PDT)
Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap
(Wed Jul 26 2006 - 10:44:58 PDT)
Re: AMBER: parallel installation of amber8 on HP cluster
(Wed Jul 26 2006 - 08:00:53 PDT)
Re: AMBER: Hybridization in leap
(Tue Jul 25 2006 - 13:37:30 PDT)
Re: AMBER: Fwd: difficulties with antechamber: tests dont even run
(Tue Jul 25 2006 - 08:11:22 PDT)
Re: AMBER: Long line of input
(Mon Jul 24 2006 - 12:37:20 PDT)
Re: AMBER: Amber 8.0 MM_PBSA Stability : question about methodology
(Mon Jul 24 2006 - 12:36:30 PDT)
Re: AMBER: saltcon variable
(Mon Jul 24 2006 - 12:38:53 PDT)
Re: AMBER: converting from parm to parm7
(Sun Jul 23 2006 - 07:47:05 PDT)
Re: AMBER: Simulating an "average" DNA sequence
(Sun Jul 23 2006 - 07:47:15 PDT)
Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1
(Mon Jul 17 2006 - 20:00:36 PDT)
Re: AMBER: Compiling Leap problem
(Fri Jul 14 2006 - 15:57:31 PDT)
Re: AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1
(Fri Jul 14 2006 - 08:00:26 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Thu Jul 13 2006 - 11:14:20 PDT)
Re: AMBER: Ringof dna
(Thu Jul 13 2006 - 09:54:07 PDT)
Re: AMBER: problem about Distance Restraints.
(Wed Jul 12 2006 - 16:33:54 PDT)
Re: AMBER: iso command and a cubic box
(Wed Jul 12 2006 - 12:00:25 PDT)
Re: AMBER: applying restraints on pre-defined planes
(Tue Jul 11 2006 - 16:34:52 PDT)
Re: AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 11:55:16 PDT)
Re: AMBER: Question about NSCM
(Tue Jul 11 2006 - 08:02:11 PDT)
Re: AMBER: small bug in ambmask (amber9)
(Mon Jul 10 2006 - 08:39:38 PDT)
Re: AMBER: residue and atom number
(Mon Jul 10 2006 - 08:09:29 PDT)
Re: AMBER: about restraint format.
(Mon Jul 10 2006 - 08:10:11 PDT)
Re: AMBER: (no subject)
(Sun Jul 09 2006 - 16:20:30 PDT)
Re: AMBER: igb=2 and "bad atom type" conflict
(Fri Jul 07 2006 - 14:42:09 PDT)
Re: AMBER: AMBER 8: Problem with MPI_Finalize
(Fri Jul 07 2006 - 14:29:10 PDT)
Re: AMBER: Error in loading molecule in tleap
(Fri Jul 07 2006 - 14:11:15 PDT)
Re: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
(Fri Jul 07 2006 - 14:06:34 PDT)
Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?
(Thu Jul 06 2006 - 18:48:12 PDT)
Re: AMBER: Sander NOE violations
(Thu Jul 06 2006 - 18:41:28 PDT)
Re: AMBER: Sander NOE violations
(Thu Jul 06 2006 - 18:01:19 PDT)
Re: AMBER: change atom in a DNA double strand
(Thu Jul 06 2006 - 09:57:12 PDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Thu Jul 06 2006 - 09:43:36 PDT)
Re: AMBER: Units for Leonard-Jones potential parameters
(Thu Jul 06 2006 - 09:45:00 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Thu Jul 06 2006 - 08:16:11 PDT)
Re: AMBER: FIX conformation of a ligand
(Thu Jul 06 2006 - 07:30:01 PDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
(Wed Jul 05 2006 - 18:54:38 PDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Wed Jul 05 2006 - 15:22:42 PDT)
Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
(Wed Jul 05 2006 - 14:31:14 PDT)
Re: AMBER: problem with saving the parameters file
(Wed Jul 05 2006 - 11:09:12 PDT)
Re: AMBER: problems about compiling a parallel version of AMBER 9
(Wed Jul 05 2006 - 11:06:08 PDT)
Re: AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging
(Wed Jul 05 2006 - 10:50:52 PDT)
Re: AMBER: manual/prmtop/missing bonds section
(Wed Jul 05 2006 - 09:09:06 PDT)
David LeBard
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Mon Jul 03 2006 - 11:15:50 PDT)
David Mobley
Re: AMBER: For different ligand conformation
(Mon Jul 31 2006 - 15:29:40 PDT)
Re: AMBER: program to calculate net charge of a ligand for Antechamber
(Mon Jul 10 2006 - 21:18:36 PDT)
Re: AMBER: 2-D free energy surface using WHAM
(Mon Jul 03 2006 - 07:33:24 PDT)
Emilio Xavier Esposito
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 09:13:40 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Thu Jul 06 2006 - 09:08:34 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Thu Jul 06 2006 - 06:40:39 PDT)
Eric Hu
Re: AMBER: simulate a self-assemble process in vacuum
(Thu Jul 20 2006 - 14:43:35 PDT)
AMBER: simulate a self-assemble process in vacuum
(Wed Jul 12 2006 - 16:22:58 PDT)
Evan Kelly
AMBER: PDB from .rst?
(Thu Jul 20 2006 - 13:51:09 PDT)
Re: AMBER: igb=2 and "bad atom type" conflict
(Thu Jul 06 2006 - 15:01:39 PDT)
Re: AMBER: igb=2 and "bad atom type" conflict
(Thu Jul 06 2006 - 09:21:06 PDT)
Re: AMBER: igb=2 and "bad atom type" conflict
(Thu Jul 06 2006 - 08:45:10 PDT)
AMBER: Addendum: igb=2 and "bad atom type" conflict
(Wed Jul 05 2006 - 12:29:10 PDT)
AMBER: igb=2 and "bad atom type" conflict
(Wed Jul 05 2006 - 12:25:16 PDT)
f m
Re: AMBER: Ring of dna
(Tue Jul 18 2006 - 07:30:03 PDT)
Re: AMBER: Ring of dna
(Mon Jul 17 2006 - 06:48:33 PDT)
Re: AMBER: Ring of dna
(Mon Jul 17 2006 - 04:32:01 PDT)
Re: AMBER: Ring of dna
(Sat Jul 15 2006 - 09:37:59 PDT)
Re: AMBER: Ring of dna
(Fri Jul 14 2006 - 06:27:03 PDT)
Re: AMBER: Ringof dna
(Thu Jul 13 2006 - 10:00:48 PDT)
Fabian Boes
AMBER: AMBER9 netcdf trajectory with VMD 1.8.4
(Mon Jul 24 2006 - 01:01:46 PDT)
AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jul 06 2006 - 01:29:35 PDT)
Fabián Alejandro Rodríguez
AMBER: from traj to crd
(Mon Jul 31 2006 - 17:58:19 PDT)
fine wu
Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly...
(Thu Jul 20 2006 - 08:55:55 PDT)
Flora Mactavish
AMBER: Ringof dna
(Thu Jul 13 2006 - 06:14:22 PDT)
Franck Vendeix
Re: AMBER: R.E.D II
(Wed Jul 05 2006 - 07:56:24 PDT)
Franck_Vendeix.ncsu.edu
Re: AMBER: R.E.D II
(Tue Jul 04 2006 - 21:33:21 PDT)
Re: AMBER: R.E.D II
(Tue Jul 04 2006 - 07:29:59 PDT)
Re: AMBER: R.E.D II
(Mon Jul 03 2006 - 23:23:22 PDT)
AMBER: R.E.D II
(Sun Jul 02 2006 - 19:11:39 PDT)
frustrated modeller
AMBER: Fwd: difficulties with antechamber: tests dont even run
(Wed Jul 19 2006 - 16:30:07 PDT)
AMBER: difficulties with antechamber: tests dont even run
(Wed Jul 19 2006 - 16:06:36 PDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Wed Jul 05 2006 - 17:29:52 PDT)
Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Mon Jul 03 2006 - 11:40:50 PDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
(Mon Jul 03 2006 - 10:51:13 PDT)
FyD
Re: AMBER: library for 8oxoguanine
(Tue Jul 25 2006 - 05:39:27 PDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03
(Tue Jul 18 2006 - 00:57:24 PDT)
Re: AMBER: R.E.D II
(Tue Jul 04 2006 - 23:55:13 PDT)
Re: AMBER: R.E.D II
(Tue Jul 04 2006 - 09:33:46 PDT)
Re: AMBER: R.E.D II
(Tue Jul 04 2006 - 00:47:51 PDT)
Re: AMBER: R.E.D II
(Mon Jul 03 2006 - 03:03:19 PDT)
Re: AMBER: R.E.D II
(Sun Jul 02 2006 - 23:39:20 PDT)
Glass, Kevin A
AMBER: Amber 9 installation issues
(Fri Jul 14 2006 - 16:18:36 PDT)
Gobind Bisht
Re: AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 12:17:46 PDT)
Re: AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 10:13:36 PDT)
AMBER: Amber crashed due to power surge and giving problems..
(Tue Jul 11 2006 - 07:46:54 PDT)
AMBER: Error in running MD in sander
(Sat Jul 08 2006 - 10:20:10 PDT)
Re: AMBER: Error in loading molecule in tleap
(Fri Jul 07 2006 - 14:18:08 PDT)
AMBER: Error in loading molecule in tleap
(Fri Jul 07 2006 - 11:01:45 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 09:39:31 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 08:48:35 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 07:13:37 PDT)
AMBER: Problem with bcc flag of antechamber..continued
(Thu Jul 06 2006 - 10:08:45 PDT)
AMBER: Problem with bcc flag of antechamber
(Thu Jul 06 2006 - 10:00:49 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Thu Jul 06 2006 - 08:36:28 PDT)
AMBER: Compiling AMBER 9 on windows XP using cygwin
(Wed Jul 05 2006 - 22:17:54 PDT)
gtg549i.mail.gatech.edu
AMBER: Free energy calculated from mm_pbsa
(Thu Jul 13 2006 - 00:26:44 PDT)
Guanglei Cui
Re: AMBER: How to resume remaining simulation
(Mon Jul 24 2006 - 08:19:56 PDT)
Re: AMBER: Replica exchange
(Wed Jul 19 2006 - 11:24:55 PDT)
Re: AMBER: RMS & PCA
(Mon Jul 17 2006 - 11:22:56 PDT)
Re: AMBER: Replica exchange
(Mon Jul 17 2006 - 07:18:57 PDT)
Guillaume Bollot
AMBER: Amber 8.0 MM_PBSA Stability : question about methodology
(Mon Jul 17 2006 - 05:18:41 PDT)
AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!!
(Tue Jul 11 2006 - 04:19:29 PDT)
AMBER: Amber8.0 predictied pKa problem for a Lysine!
(Fri Jul 07 2006 - 02:38:08 PDT)
AMBER: Constant pH simulation : LYS residue
(Tue Jul 04 2006 - 04:13:00 PDT)
Gustavo Seabra
Re: AMBER: center molecule using iwrap=1?
(Thu Jul 13 2006 - 12:49:39 PDT)
Re: AMBER: center molecule using iwrap=1?
(Thu Jul 13 2006 - 12:07:40 PDT)
AMBER: center molecule using iwrap=1?
(Thu Jul 13 2006 - 11:21:17 PDT)
Re: AMBER: simulate a self-assemble process in vacuum
(Thu Jul 13 2006 - 06:22:15 PDT)
Re: AMBER: convert chemical structure to pdb file
(Fri Jul 07 2006 - 11:56:37 PDT)
Re: AMBER: script to extract data from minimization .out file
(Fri Jul 07 2006 - 10:35:32 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 09:00:36 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Fri Jul 07 2006 - 07:36:50 PDT)
Re: AMBER: Compiling AMBER 9 on windows XP using cygwin
(Thu Jul 06 2006 - 08:50:05 PDT)
hayden
RE: AMBER: Compiling / Installing Amber 8 on SUSE 10.1
(Fri Jul 14 2006 - 03:27:54 PDT)
RE: AMBER: amber9 compilation problems on EM64T xeon system
(Mon Jul 10 2006 - 09:57:44 PDT)
AMBER: amber9 compilation problems on EM64T xeon system
(Thu Jul 06 2006 - 11:11:04 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. .
(Thu Jul 06 2006 - 05:02:13 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .
(Mon Jul 03 2006 - 17:28:37 PDT)
hbluo
AMBER: Silicon related parameters
(Sat Jul 22 2006 - 10:52:17 PDT)
hornak.csb.sunysb.edu
Re: AMBER: Long line of input
(Wed Jul 19 2006 - 13:37:29 PDT)
Ilyas Yildirim
Re: AMBER: dummy atoms in MMPBSA
(Thu Jul 27 2006 - 05:18:01 PDT)
Re: AMBER: PDB from .rst?
(Thu Jul 20 2006 - 14:08:20 PDT)
Re: AMBER: Tutorial 4-section 4 DIHE in frcmod file.
(Mon Jul 03 2006 - 20:47:22 PDT)
j j
Re: AMBER: Ring of dna
(Fri Jul 14 2006 - 07:25:59 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Fri Jul 14 2006 - 01:48:33 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Fri Jul 14 2006 - 01:40:10 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Thu Jul 13 2006 - 10:59:00 PDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Thu Jul 13 2006 - 03:47:15 PDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Thu Jul 13 2006 - 03:50:55 PDT)
Jahidul Islam
AMBER: Xmgr in Windows
(Mon Jul 31 2006 - 20:24:19 PDT)
Re: AMBER: Can't open xleap
(Thu Jul 27 2006 - 04:57:30 PDT)
AMBER: Can't open xleap
(Thu Jul 27 2006 - 03:16:08 PDT)
jitrayut jitonnom
AMBER: Fwd: ADL: peptide simulation before docking
(Sun Jul 09 2006 - 02:26:59 PDT)
AMBER: peptide simulation before docking
(Sat Jul 08 2006 - 13:45:28 PDT)
John S. Zintsmaster
AMBER: Etot has downward drift in 'NVE' ensemble
(Wed Jul 12 2006 - 19:01:08 PDT)
jrd
AMBER: AMBER 8: Problem with MPI_Finalize
(Fri Jul 07 2006 - 11:24:08 PDT)
Junmei Wang
RE: AMBER: Fwd: difficulties with antechamber: tests dont even run
(Tue Jul 25 2006 - 16:00:04 PDT)
AMBER: Antechamber 1.26 is released
(Wed Jul 12 2006 - 16:42:32 PDT)
RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
(Fri Jul 07 2006 - 10:04:00 PDT)
RE: AMBER: Problem with bcc flag of antechamber
(Thu Jul 06 2006 - 10:53:37 PDT)
kanazta1.yahoo.co.jp
AMBER: multiple "restraint_wt" in sander
(Mon Jul 03 2006 - 07:12:21 PDT)
Kateryna Miroshnychenko
AMBER: small bug in ambmask (amber9)
(Mon Jul 10 2006 - 07:53:02 PDT)
Ken Merz
AMBER:
(Sat Jul 29 2006 - 08:28:53 PDT)
Lars Packschies
AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1
(Fri Jul 14 2006 - 03:18:08 PDT)
Lena Dolghih
AMBER: Modelling dsDNA less than 10bp
(Fri Jul 21 2006 - 06:15:16 PDT)
Lwin, ThuZar
RE: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. .
(Thu Jul 27 2006 - 18:35:19 PDT)
AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap
(Tue Jul 25 2006 - 17:39:32 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. .
(Wed Jul 05 2006 - 16:01:25 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .
(Mon Jul 03 2006 - 12:02:31 PDT)
M. L. Dodson
Re: AMBER: library for 8oxoguanine
(Mon Jul 24 2006 - 13:07:17 PDT)
Re: AMBER: Ring of dna
(Mon Jul 17 2006 - 07:56:03 PDT)
madhumalar.bii-sg.org
Re: AMBER: Zinc coordinating CYS
(Fri Jul 28 2006 - 02:17:36 PDT)
Re: AMBER: Zinc coordinating CYS
(Thu Jul 27 2006 - 17:37:12 PDT)
AMBER: calculating dihedral angles, radius of gyration
(Fri Jul 07 2006 - 02:57:14 PDT)
Manish Datt
Re: AMBER: parallel installation of amber8 on HP cluster
(Wed Jul 26 2006 - 10:54:51 PDT)
AMBER: parallel installation of amber8 on HP cluster
(Wed Jul 26 2006 - 03:00:30 PDT)
Mark Williamson
Re: AMBER: Can you use VMD to measure bond angles/lengths
(Tue Jul 04 2006 - 09:06:59 PDT)
Re: AMBER: Tutorial 4-section 4 (plc.frcmod)
(Mon Jul 03 2006 - 05:46:08 PDT)
Md Jahidul Islam
AMBER: xleap
(Thu Jul 27 2006 - 02:49:36 PDT)
Melissa Foley
AMBER: combining different versions of AMBER
(Fri Jul 21 2006 - 12:25:35 PDT)
Michael Crowley
Re: AMBER: parallel installation of amber8 on HP cluster
(Wed Jul 26 2006 - 11:52:09 PDT)
Re: AMBER: parallel installation of amber8 on HP cluster
(Wed Jul 26 2006 - 07:42:19 PDT)
Mingfeng Yang
AMBER: Myrinet or Gigabit ethernet?
(Thu Jul 20 2006 - 06:35:08 PDT)
Myunggi Yi
AMBER: Harmonic restraint along z-axis
(Wed Jul 26 2006 - 17:26:02 PDT)
Re: [Fwd: AMBER: Long line of input]
(Tue Jul 25 2006 - 09:08:27 PDT)
Re: AMBER: Failure of iwrap in PMEMD
(Fri Jul 21 2006 - 06:57:03 PDT)
Re: AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 17:24:34 PDT)
Re: AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 08:04:31 PDT)
AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 07:01:07 PDT)
Re: AMBER: Long line of input
(Wed Jul 19 2006 - 19:03:11 PDT)
AMBER: Long line of input
(Wed Jul 19 2006 - 13:13:26 PDT)
Re: AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!!
(Tue Jul 11 2006 - 09:00:58 PDT)
Re: AMBER: Amber8.0 predictied pKa problem for a Lysine!
(Fri Jul 07 2006 - 09:14:42 PDT)
Re: AMBER: analysis of ATOMs in ´certain range distance during simulation
(Thu Jul 06 2006 - 15:03:12 PDT)
nadiav.soton.ac.uk
RE: AMBER: compiling amber9
(Tue Jul 04 2006 - 07:31:02 PDT)
AMBER: compiling amber9
(Mon Jul 03 2006 - 01:50:44 PDT)
Nitin Bhardwaj
Re: AMBER: loading torsion parameters
(Mon Jul 31 2006 - 13:35:18 PDT)
AMBER: loading torsion parameters
(Mon Jul 31 2006 - 12:47:19 PDT)
Re: AMBER: Zinc coordinating CYS
(Thu Jul 27 2006 - 21:00:45 PDT)
AMBER: Zinc coordinating CYS
(Thu Jul 27 2006 - 14:30:45 PDT)
AMBER: Zinc-coordinating histidine protonation state
(Thu Jul 27 2006 - 13:01:16 PDT)
AMBER: Correction on Zinc parameters
(Thu Jul 27 2006 - 09:38:00 PDT)
AMBER: Zinc parameters
(Thu Jul 27 2006 - 09:35:57 PDT)
opitz.che.udel.edu
AMBER: Hybridization in leap
(Tue Jul 25 2006 - 11:23:12 PDT)
Ozlem Demir
AMBER: "noimage" option for radial distribution functions
(Sun Jul 16 2006 - 14:14:31 PDT)
Patricia Hunt
AMBER: iso command and a cubic box
(Wed Jul 12 2006 - 00:03:03 PDT)
Petr Kulhanek
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Fri Jul 14 2006 - 02:24:26 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Fri Jul 14 2006 - 00:44:09 PDT)
Piotr Cieplak
RE: AMBER: amber9
(Fri Jul 14 2006 - 16:33:00 PDT)
AMBER: amber9
(Fri Jul 14 2006 - 15:02:36 PDT)
pkb bioinfo
AMBER: For different ligand conformation
(Mon Jul 31 2006 - 06:53:45 PDT)
AMBER: How to resume remaining simulation
(Mon Jul 24 2006 - 03:05:23 PDT)
AMBER: analysis of ATOMs in ´certain range distance during simulation
(Wed Jul 05 2006 - 20:37:46 PDT)
AMBER: analysis of atoms in a range during simulation
(Wed Jul 05 2006 - 05:41:58 PDT)
Prabhakar. G.
Re: AMBER: fixing residues
(Wed Jul 05 2006 - 20:57:38 PDT)
AMBER: fixing residues
(Mon Jul 03 2006 - 05:16:46 PDT)
Prashanth Athri
AMBER: process_mdout.perl's output is empty
(Mon Jul 24 2006 - 13:53:04 PDT)
priya priya
Re: AMBER: PDB from .rst?
(Thu Jul 20 2006 - 20:24:08 PDT)
Qingning Shu
AMBER: problem about Distance Restraints.
(Tue Jul 11 2006 - 20:38:48 PDT)
AMBER: about restraint format.
(Mon Jul 10 2006 - 06:11:16 PDT)
Raffaella D'Auria
Re: AMBER: converting from parm to parm7
(Tue Jul 25 2006 - 09:00:50 PDT)
Re: AMBER: converting from parm to parm7 & L-J coeff A and B
(Sat Jul 22 2006 - 08:55:56 PDT)
AMBER: converting from parm to parm7
(Fri Jul 21 2006 - 18:26:55 PDT)
Ray Luo
Re: AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ?
(Thu Jul 13 2006 - 14:21:30 PDT)
Re: AMBER: MM/PBSA
(Fri Jul 07 2006 - 17:26:28 PDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
(Wed Jul 05 2006 - 10:45:49 PDT)
Robert Duke
Re: AMBER: Failure of iwrap in PMEMD
(Fri Jul 21 2006 - 06:34:02 PDT)
Re: AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 14:35:58 PDT)
Re: AMBER: Myrinet or Gigabit ethernet?
(Thu Jul 20 2006 - 07:45:45 PDT)
Re: AMBER: Failure of iwrap in PMEMD
(Thu Jul 20 2006 - 07:40:48 PDT)
Re: AMBER: PMEMD with NMR restraint and position restraint
(Tue Jul 18 2006 - 21:34:35 PDT)
Re: AMBER: PMEMD with NMR restraint and position restraint
(Tue Jul 18 2006 - 19:03:42 PDT)
Re: AMBER: PMEMD with NMR restraint and position restraint
(Tue Jul 18 2006 - 13:49:05 PDT)
Re: AMBER: PMEMD with NMR restraint and position restraint
(Mon Jul 17 2006 - 20:03:29 PDT)
Re: AMBER: working with large strained system
(Thu Jul 06 2006 - 07:06:48 PDT)
Re: AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jul 06 2006 - 05:43:24 PDT)
Re: AMBER: pmemd9 issue
(Sun Jul 02 2006 - 04:46:21 PDT)
Re: AMBER: pmemd9 issue
(Sun Jul 02 2006 - 04:12:11 PDT)
Ross Walker
RE: AMBER: loading torsion parameters
(Mon Jul 31 2006 - 13:25:08 PDT)
RE: AMBER: Zinc parameters
(Thu Jul 27 2006 - 10:26:29 PDT)
RE: AMBER: Tutorial 8, section 6: best fit before clustering
(Mon Jul 24 2006 - 07:45:59 PDT)
RE: AMBER: combining different versions of AMBER
(Fri Jul 21 2006 - 13:11:44 PDT)
RE: AMBER: Failure of iwrap in PMEMD
(Fri Jul 21 2006 - 08:33:53 PDT)
RE: AMBER: amber9
(Fri Jul 14 2006 - 15:37:19 PDT)
RE: AMBER: Error in running MD in sander
(Sat Jul 08 2006 - 10:38:15 PDT)
RE: AMBER: script to extract data from minimization .out file
(Sat Jul 08 2006 - 08:47:17 PDT)
RE: AMBER: amber9 compilation problems on EM64T xeon system
(Thu Jul 06 2006 - 20:06:15 PDT)
RE: AMBER: compiling amber9
(Mon Jul 03 2006 - 03:48:10 PDT)
S. Jamal Rahi
AMBER: Simulating an "average" DNA sequence
(Fri Jul 21 2006 - 20:20:36 PDT)
sangeeta
RE: AMBER: Tutorial 8, section 6: best fit before clustering
(Wed Jul 26 2006 - 06:42:47 PDT)
AMBER: Tutorial 8, section 6: best fit before clustering
(Mon Jul 24 2006 - 06:18:05 PDT)
sangeeta.bioinfo.ernet.in
Re: AMBER: script to extract data from minimization .out file
(Sat Jul 08 2006 - 03:41:44 PDT)
Re: AMBER: script to extract data from minimization .out file
(Sat Jul 08 2006 - 03:23:52 PDT)
Scott Pendley
Re: AMBER: analysis of ATOMs in ´certain range distance during simulation
(Thu Jul 06 2006 - 14:47:57 PDT)
Re: AMBER: igb=2 and "bad atom type" conflict
(Wed Jul 05 2006 - 13:22:43 PDT)
Sergei Smirnov
AMBER: water diffusion
(Mon Jul 17 2006 - 17:48:59 PDT)
sethl.gatech.edu
AMBER: Building an RNA - Proflavin Complex
(Mon Jul 24 2006 - 13:05:49 PDT)
AMBER: Compiling Leap problem
(Fri Jul 14 2006 - 14:36:38 PDT)
AMBER: Namot on AMD 64 possible
(Wed Jul 05 2006 - 10:05:26 PDT)
AMBER: Can you use VMD to measure bond angles/lengths
(Tue Jul 04 2006 - 08:24:49 PDT)
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
AMBER: saltcon variable
(Thu Jul 20 2006 - 12:00:01 PDT)
AMBER: temperature regulation
(Tue Jul 18 2006 - 01:31:04 PDT)
Tanya Johannsen
AMBER: script to extract data from minimization .out file
(Fri Jul 07 2006 - 09:55:44 PDT)
AMBER: working with large strained system
(Wed Jul 05 2006 - 19:29:58 PDT)
Thomas Cheatham
Re: AMBER: water diffusion
(Mon Jul 17 2006 - 23:36:36 PDT)
Re: AMBER: Creating an Intercalation site
(Mon Jul 17 2006 - 13:13:54 PDT)
Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent
(Thu Jul 13 2006 - 09:34:00 PDT)
Re: AMBER: Etot has downward drift in 'NVE' ensemble
(Wed Jul 12 2006 - 19:43:11 PDT)
Re: [UCE]AMBER: (no subject)
(Sun Jul 09 2006 - 16:18:49 PDT)
Re: AMBER: Dihedral analysis
(Mon Jul 03 2006 - 12:47:42 PDT)
Re: AMBER: hbond analysis
(Mon Jul 03 2006 - 12:19:57 PDT)
Thomas Steinbrecher
Re: AMBER: amber9
(Fri Jul 14 2006 - 15:12:13 PDT)
AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities
(Thu Jul 06 2006 - 16:02:19 PDT)
Ting Wang
Re: AMBER: PMEMD with NMR restraint and position restraint
(Tue Jul 18 2006 - 13:12:41 PDT)
AMBER: PMEMD with NMR restraint and position restraint
(Mon Jul 17 2006 - 16:18:31 PDT)
Vanessa Oklejas
AMBER: Units for Leonard-Jones potential parameters
(Wed Jul 05 2006 - 20:02:59 PDT)
Viktor Hornak
Re: AMBER: multiple "restraint_wt" in sander
(Mon Jul 03 2006 - 07:43:44 PDT)
Vlad Cojocaru
AMBER: applying restraints on pre-defined planes
(Tue Jul 11 2006 - 08:34:07 PDT)
Wei Chen
Re: AMBER: MM/PBSA
(Sat Jul 08 2006 - 11:29:06 PDT)
AMBER: MM/PBSA
(Fri Jul 07 2006 - 14:20:47 PDT)
Wei Zhang
Re: AMBER: loading torsion parameters
(Mon Jul 31 2006 - 13:13:57 PDT)
Re: AMBER: PDB from .rst?
(Thu Jul 20 2006 - 14:04:58 PDT)
Xiaowei (David) Li
AMBER: Question about NSCM
(Tue Jul 11 2006 - 01:25:48 PDT)
Xioling Chuang
Re: AMBER: How to calculate binding free energy using MM-PBSA
(Fri Jun 30 2006 - 21:39:09 PDT)
Yong Duan
RE: AMBER: amber9 compilation problems on EM64T xeon system
(Thu Jul 06 2006 - 12:38:05 PDT)
zachary hartman
AMBER: Obtaining LCPO parameters for F and Fe
(Mon Jul 17 2006 - 11:16:54 PDT)
Zu Thur Yew
AMBER: Using a trajectory and some PDB files as input for PCA
(Mon Jul 31 2006 - 03:20:42 PDT)
AMBER: Minimization problem: coordinates out of virtual box
(Mon Jul 24 2006 - 05:53:19 PDT)
Re: AMBER: RMS & PCA
(Mon Jul 17 2006 - 22:12:35 PDT)
AMBER: PhosphoThreonine Parms for use with ff03
(Mon Jul 17 2006 - 22:19:15 PDT)
AMBER: RMS & PCA
(Mon Jul 17 2006 - 07:55:12 PDT)
AMBER: Ptraj: Hbond time series
(Tue Jul 11 2006 - 08:19:34 PDT)
AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging
(Wed Jul 05 2006 - 10:03:13 PDT)
AMBER: MM-PBSA: Problem when Generating Snapshots
(Tue Jul 04 2006 - 00:20:39 PDT)
Last message date
:
Wed Aug 02 2006 - 06:07:09 PDT
Archived on
: Mon Dec 23 2024 - 05:53:27 PST
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