Amber Archive Jul 2005 by author
396 messages
:
Starting
Fri Jul 01 2005 - 01:53:01 PDT,
Ending
Mon Aug 01 2005 - 06:53:00 PDT
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Agata Jurkiewicz
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 15:06:49 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 12:12:10 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 10:01:16 PDT)
AMBER: SHAKE error
(Fri Jul 22 2005 - 07:09:34 PDT)
Alessio Coi
AMBER: problem with xleap
(Fri Jul 22 2005 - 06:47:23 PDT)
Alfonso Garcia-Sosa
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Mon Jul 18 2005 - 12:16:21 PDT)
Ananda Rama Krishnan Selvaraj
Re: AMBER: Atom type :Si
(Fri Jul 22 2005 - 12:45:30 PDT)
AMBER: Atom type :Si
(Thu Jul 21 2005 - 12:02:23 PDT)
AMBER: doubt on the value of Pressure on MD run
(Tue Jul 12 2005 - 01:21:07 PDT)
AMBER: how to see the box lines
(Sat Jul 09 2005 - 11:10:50 PDT)
AMBER: how to make cluster files?
(Fri Jul 01 2005 - 00:10:05 PDT)
Andreas Svrcek-Seiler
Re: AMBER: P4 EM64T Intel Fortran Compile Problem
(Fri Jul 15 2005 - 10:49:47 PDT)
Re: AMBER: Leap compilation issues
(Mon Jul 11 2005 - 03:43:39 PDT)
Andrew Box
AMBER: FW:
(Tue Jul 19 2005 - 19:07:44 PDT)
Angela Liu
Re: AMBER: Amber 8: heterogeneous multiple copy LES method
(Fri Jul 15 2005 - 07:16:23 PDT)
AMBER: Amber 8: heterogeneous multiple copy LES method
(Wed Jul 13 2005 - 11:47:08 PDT)
AMBER: Amber 8: create topology for solvent - PBC box size problem
(Wed Jul 13 2005 - 11:41:04 PDT)
Angelo Pugliese
AMBER: Energy decomposition parameters
(Fri Jul 15 2005 - 01:57:21 PDT)
Re: AMBER: DNA strands separate
(Wed Jul 06 2005 - 08:00:00 PDT)
Re: AMBER: how to average the structure along md trajectory
(Wed Jul 06 2005 - 08:02:48 PDT)
Re: AMBER: DNA strands separate
(Wed Jul 06 2005 - 07:04:36 PDT)
Re: AMBER: DNA strands separate
(Wed Jul 06 2005 - 05:46:05 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 07:38:37 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 03:42:28 PDT)
AMBER: Stacking energy
(Fri Jul 01 2005 - 01:32:34 PDT)
Anthony Cruz
Re: AMBER: sander problem
(Thu Jul 07 2005 - 08:25:29 PDT)
AMBER: Replica Exchange
(Thu Jul 07 2005 - 08:27:51 PDT)
AMBER: sander problem
(Wed Jul 06 2005 - 16:05:44 PDT)
AMBER: Replica exchange
(Fri Jul 01 2005 - 07:33:46 PDT)
AMBER: cavity volume
(Fri Jul 01 2005 - 05:46:24 PDT)
Arnoult, Eric [PRDFR]
RE: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Wed Jul 27 2005 - 08:59:43 PDT)
RE: AMBER: why not minimize snapshots before MM/PBSA calculations
(Wed Jul 27 2005 - 00:21:30 PDT)
RE: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Wed Jul 27 2005 - 00:20:27 PDT)
AMBER: An atom name with 4 characters is not compatible with Leap ?
(Fri Jul 22 2005 - 00:53:24 PDT)
ayongye.chem.uga.edu
AMBER: comparing md trajectories
(Mon Jul 18 2005 - 18:12:15 PDT)
Bill Ross
Re: AMBER: lib file for nonstandard residue
(Thu Jul 14 2005 - 15:20:25 PDT)
Re: AMBER: lib file for nonstandard residue
(Thu Jul 14 2005 - 12:37:01 PDT)
Re: AMBER: lib file for nonstandard residue
(Thu Jul 14 2005 - 12:08:03 PDT)
Re: AMBER: Leap compilation issues
(Mon Jul 11 2005 - 18:34:35 PDT)
Re: AMBER: Leap compilation issues
(Sun Jul 10 2005 - 19:11:43 PDT)
Re: AMBER: building nucleic acids
(Fri Jul 08 2005 - 12:05:15 PDT)
Re: AMBER: nucgen and nukit
(Tue Jul 05 2005 - 09:33:04 PDT)
blakrose.gazeta.pl
AMBER: [FWD] water minimalization problems
(Wed Jul 27 2005 - 08:46:47 PDT)
Caleb S Howe (cshowe.Princeton.EDU)
AMBER: Division by zero in sander
(Thu Jul 28 2005 - 07:57:00 PDT)
Carlos Simmerling
Re: AMBER: temperature keep increasing in high temp.
(Fri Jul 29 2005 - 17:28:42 PDT)
Re: AMBER: dihedral term in prmtop file
(Thu Jul 28 2005 - 07:59:36 PDT)
Re: AMBER: Minimized structure
(Thu Jul 28 2005 - 03:53:45 PDT)
Re: AMBER: Thermodynamic Integration for conformational changes?
(Tue Jul 26 2005 - 11:02:57 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 12:26:36 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 10:24:46 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 07:56:53 PDT)
Re: AMBER: comparing md trajectories
(Tue Jul 19 2005 - 05:58:44 PDT)
Re: AMBER: Amber 8: heterogeneous multiple copy LES method
(Thu Jul 14 2005 - 14:17:07 PDT)
Re: AMBER: pdb files from traj file
(Wed Jul 13 2005 - 14:16:52 PDT)
Re: AMBER: question replica exchange acceptance ratio
(Tue Jul 12 2005 - 16:43:01 PDT)
Re: AMBER: question replica exchange acceptance ratio
(Tue Jul 12 2005 - 14:42:55 PDT)
Re: AMBER: doubt on the value of Pressure on MD run
(Tue Jul 12 2005 - 04:07:08 PDT)
Re: AMBER: infinite DNA
(Fri Jul 08 2005 - 16:33:59 PDT)
Re: AMBER: Replica Exchange
(Thu Jul 07 2005 - 06:43:17 PDT)
Re: AMBER: restart file
(Tue Jul 05 2005 - 14:22:16 PDT)
Re: AMBER: restart file
(Tue Jul 05 2005 - 12:36:43 PDT)
Re: AMBER: estimation of interface size
(Mon Jul 04 2005 - 04:39:11 PDT)
Re: AMBER: MM-PBSA-big energies
(Sun Jul 03 2005 - 15:13:48 PDT)
cbala.igib.res.in
Re: AMBER: loading DNA-RNA hybrid in xleap
(Sat Jul 02 2005 - 12:57:33 PDT)
AMBER: loading DNA-RNA hybrid in xleap
(Sat Jul 02 2005 - 08:36:59 PDT)
Charles Karney
AMBER: Using Antechamber with Gamess and other molecular manipulations
(Mon Jul 18 2005 - 10:28:20 PDT)
Chris Moth
Re: AMBER: how is truncated octahedron box calculated
(Thu Jul 07 2005 - 14:50:24 PDT)
Claire Zerafa
AMBER: problem with protein ligand complex
(Sat Jul 16 2005 - 09:31:56 PDT)
Cordova, Luis E.
AMBER: question about spline in sander -- array size of eed_cub
(Thu Jun 30 2005 - 21:33:25 PDT)
Daniel Wetzler
Re: AMBER: Amber 7 Compiler Error
(Wed Jul 20 2005 - 02:38:25 PDT)
Re: AMBER: Problem with building AMBER7 on SUSE Linux 9.2
(Tue Jul 12 2005 - 00:53:40 PDT)
AMBER: Problem with building AMBER7 on SUSE Linux 9.2
(Fri Jul 08 2005 - 04:18:09 PDT)
AMBER: Re: AMBER: Problems with parameter lib and prep püarameter files
(Wed Jul 06 2005 - 03:40:53 PDT)
AMBER: Problems with parameter lib and prep püarameter files
(Mon Jul 04 2005 - 02:14:56 PDT)
David A. Case
Re: AMBER: Amber parameters for ADP
(Sat Jul 30 2005 - 10:08:08 PDT)
Re: AMBER: RESTARTED DUE TO LINMIN FAILURE
(Sat Jul 30 2005 - 09:59:19 PDT)
Re: AMBER: Failed sander runs for large systems
(Sat Jul 30 2005 - 09:57:14 PDT)
Re: AMBER: ambpdb core dump
(Fri Jul 29 2005 - 07:56:42 PDT)
Re: AMBER: ambpdb core dump
(Fri Jul 29 2005 - 07:40:03 PDT)
Re: AMBER: Fatal Error on loading a pdb in xLeap
(Thu Jul 28 2005 - 15:17:14 PDT)
Re: AMBER: cutoff in ANAL
(Thu Jul 28 2005 - 09:26:40 PDT)
Re: AMBER: Adding residues to a DNA sequence
(Wed Jul 27 2005 - 14:31:16 PDT)
Re: AMBER: new residue
(Wed Jul 27 2005 - 14:13:32 PDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Wed Jul 27 2005 - 10:39:08 PDT)
Re: AMBER: new residue
(Wed Jul 27 2005 - 10:20:42 PDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Wed Jul 27 2005 - 08:08:11 PDT)
Re: AMBER: prepi format and question about it
(Wed Jul 27 2005 - 07:57:30 PDT)
Re: AMBER: Thermodynamic Integration for conformational changes?
(Tue Jul 26 2005 - 11:42:54 PDT)
Re: AMBER: nucgen H5T H3T
(Tue Jul 26 2005 - 07:54:32 PDT)
Re: AMBER: SHAKE error
(Mon Jul 25 2005 - 16:57:02 PDT)
Re: AMBER: NTWPRY problem
(Mon Jul 25 2005 - 16:54:25 PDT)
Re: AMBER: antechamber
(Mon Jul 25 2005 - 16:42:32 PDT)
Re: AMBER: Adding residues to a DNA sequence
(Mon Jul 25 2005 - 14:39:23 PDT)
Re: AMBER: [OT] A nab programming question
(Mon Jul 25 2005 - 14:35:49 PDT)
Re: AMBER: nucgen bdna types
(Sun Jul 24 2005 - 16:42:44 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 13:46:42 PDT)
Re: AMBER: Question about Prep file
(Fri Jul 22 2005 - 11:34:57 PDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Fri Jul 22 2005 - 10:27:31 PDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Fri Jul 22 2005 - 10:24:58 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 09:04:15 PDT)
Re: AMBER: problem with xleap
(Fri Jul 22 2005 - 08:59:24 PDT)
Re: AMBER: FW:
(Tue Jul 19 2005 - 19:46:48 PDT)
Re: AMBER: PMF calculations with TI using the sander
(Mon Jul 18 2005 - 09:03:47 PDT)
Re: AMBER: cap simulations questions
(Mon Jul 18 2005 - 09:01:34 PDT)
Re: AMBER: problem with protein ligand complex
(Sat Jul 16 2005 - 12:05:02 PDT)
Re: AMBER: lib file for nonstandard residue
(Thu Jul 14 2005 - 15:35:47 PDT)
Re: AMBER: Modeling of a radical
(Thu Jul 14 2005 - 08:48:54 PDT)
Re: AMBER: Leap question
(Thu Jul 14 2005 - 08:39:59 PDT)
Re: AMBER: MD simulation on a protein solvated by a combination of some water mod
(Thu Jul 14 2005 - 08:29:20 PDT)
Re: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 14:10:56 PDT)
Re: AMBER: molsurf error in MM/PBSA calculation
(Tue Jul 12 2005 - 18:23:50 PDT)
Re: AMBER: molsurf error in MM/PBSA calculation
(Tue Jul 12 2005 - 15:03:23 PDT)
Re: AMBER: Anal - problems with energy analysis
(Tue Jul 12 2005 - 15:00:45 PDT)
Re: AMBER: MM_PBSA help, please
(Tue Jul 12 2005 - 09:34:56 PDT)
Re: AMBER: Question about "nmanal"
(Tue Jul 12 2005 - 09:29:46 PDT)
Re: AMBER: Question about "nmanal"
(Mon Jul 11 2005 - 09:15:32 PDT)
Re: AMBER: Leap compilation issues
(Sun Jul 10 2005 - 22:13:04 PDT)
Re: AMBER: building nucleic acids
(Sun Jul 10 2005 - 21:51:46 PDT)
Re: AMBER: infinite DNA
(Fri Jul 08 2005 - 17:26:04 PDT)
Re: AMBER: Water simulation
(Fri Jul 08 2005 - 17:13:37 PDT)
Re: AMBER: problem with addIons
(Wed Jul 06 2005 - 15:41:21 PDT)
Re: AMBER: sander problem
(Wed Jul 06 2005 - 15:30:59 PDT)
Re: AMBER: box size in explicit water
(Wed Jul 06 2005 - 10:30:59 PDT)
Re: AMBER: AMBER on Mac OS X
(Wed Jul 06 2005 - 08:36:08 PDT)
Re: AMBER: 10-12 potential and create atom type
(Tue Jul 05 2005 - 15:03:09 PDT)
Re: AMBER: pmemd - bug report
(Tue Jul 05 2005 - 10:43:18 PDT)
Re: AMBER: pmemd - bug report
(Tue Jul 05 2005 - 10:38:09 PDT)
Re: AMBER: molecular dynamics simulation of protein containing Mg2+ cation
(Sun Jul 03 2005 - 16:34:14 PDT)
Re: AMBER: loading DNA-RNA hybrid in xleap
(Sat Jul 02 2005 - 10:30:58 PDT)
Re: AMBER: questions about topology file
(Fri Jul 01 2005 - 13:24:02 PDT)
Re: AMBER: least square fit of snapshots in md trajectory to a reference frame
(Fri Jul 01 2005 - 08:51:21 PDT)
David LeBard
Re: AMBER: pdb files from traj file
(Wed Jul 13 2005 - 14:30:07 PDT)
Re: AMBER: Water simulation
(Sat Jul 09 2005 - 17:30:55 PDT)
AMBER: Water simulation
(Fri Jul 08 2005 - 16:44:12 PDT)
Re: AMBER: problem with addIons
(Wed Jul 06 2005 - 15:08:35 PDT)
David.Maxwell.di.mdacc.tmc.edu
AMBER: LCPO SASA parameters for other elements when using gbsa=1 option
(Fri Jul 08 2005 - 13:10:00 PDT)
Dawei Zhang
Re: AMBER: P4 EM64T Intel Fortran Compile Problem
(Fri Jul 15 2005 - 13:54:39 PDT)
AMBER: P4 EM64T Intel Fortran Compile Problem
(Fri Jul 15 2005 - 10:04:49 PDT)
Devashish Kumar
AMBER: Comparison of AMBER against DL-POLY
(Tue Jul 12 2005 - 15:32:03 PDT)
Douali, Latifa
RE: AMBER: new residue
(Wed Jul 27 2005 - 14:36:27 PDT)
RE: AMBER: new residue
(Wed Jul 27 2005 - 13:45:17 PDT)
RE: AMBER: new residue
(Wed Jul 27 2005 - 09:09:01 PDT)
AMBER: new residue
(Tue Jul 26 2005 - 17:50:51 PDT)
FW: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 08:38:25 PDT)
drugdesign
AMBER: question about sander minimization error
(Thu Jul 07 2005 - 01:37:51 PDT)
dthomas.chem.uwa.edu.au
AMBER: nucgen and nukit
(Tue Jul 05 2005 - 07:55:44 PDT)
Dustin
AMBER: antechamber
(Mon Jul 25 2005 - 13:30:40 PDT)
AMBER: Trouble with Amber8
(Tue Jul 19 2005 - 13:16:10 PDT)
Eric Hu
Re: AMBER: lib file for nonstandard residue
(Thu Jul 14 2005 - 15:02:35 PDT)
AMBER: lib file for nonstandard residue
(Wed Jul 13 2005 - 16:52:19 PDT)
Fabien CAILLIEZ
AMBER: cap and ptraj
(Tue Jul 19 2005 - 15:14:50 PDT)
AMBER: cap simulations questions
(Mon Jul 18 2005 - 07:50:32 PDT)
AMBER: problems with bonds in sander
(Thu Jul 07 2005 - 11:18:19 PDT)
AMBER: questions about topology file
(Fri Jul 01 2005 - 08:49:20 PDT)
Furse, Kristina Elisabet
Re: AMBER: new residue
(Tue Jul 26 2005 - 18:40:51 PDT)
Re: AMBER: Leap problem
(Thu Jul 14 2005 - 17:31:40 PDT)
Re: AMBER: Ptraj and order of operations
(Wed Jul 13 2005 - 11:55:02 PDT)
Re: AMBER: Ptraj and order of operations
(Tue Jul 12 2005 - 18:07:04 PDT)
AMBER: Ptraj and order of operations
(Mon Jul 11 2005 - 17:26:09 PDT)
FyD
AMBER: Release of R.E.D-II
(Thu Jul 07 2005 - 10:58:54 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Thu Jul 07 2005 - 08:54:00 PDT)
Re: AMBER: please help us on partial charge calculation of PT complex using RESP
(Fri Jul 01 2005 - 09:07:40 PDT)
Re: AMBER: Create new Unit
(Thu Jun 30 2005 - 17:25:02 PDT)
Germán Sciaini
Re: AMBER: Question about Lennard-Jones Parameters in Topology file
(Mon Jul 04 2005 - 03:46:00 PDT)
Re: AMBER: cavity volume
(Mon Jul 04 2005 - 03:29:59 PDT)
glc0358.vip.sina.com
RE: Re: AMBER:
(Sat Jul 09 2005 - 03:37:54 PDT)
AMBER:
(Sat Jul 09 2005 - 00:03:23 PDT)
AMBER:
(Fri Jul 08 2005 - 23:22:45 PDT)
Grzegorz Jezierski
Re: AMBER: Periodic box imaging using ptraj
(Wed Jul 27 2005 - 04:28:29 PDT)
Re: AMBER: Periodic box imaging using ptraj
(Wed Jul 27 2005 - 02:27:24 PDT)
AMBER: Thermodynamic Integration for conformational changes?
(Tue Jul 26 2005 - 10:33:00 PDT)
AMBER: Periodic box imaging using ptraj
(Tue Jul 26 2005 - 06:25:53 PDT)
Guanglei Cui
Re: AMBER: Failed sander runs for large systems
(Fri Jul 29 2005 - 21:33:27 PDT)
Re: AMBER: Error in MD
(Thu Jul 21 2005 - 21:08:56 PDT)
Harianto Tjong
Re: AMBER: restart file
(Tue Jul 05 2005 - 13:49:16 PDT)
AMBER: restart file
(Tue Jul 05 2005 - 11:49:20 PDT)
hj zou
Re: Re: AMBER: how to reduce box size and delete excess solvent
(Wed Jul 27 2005 - 06:36:40 PDT)
Holger Gohlke
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Thu Jul 14 2005 - 22:39:21 PDT)
Hwankyu Lee
AMBER: temperature keep increasing in high temp.
(Fri Jul 29 2005 - 14:27:04 PDT)
Ilan Samish
Re: AMBER: molecular dynamics course
(Sat Jul 09 2005 - 23:23:05 PDT)
Ilyas Yildirim
Re: AMBER: Fatal Error on loading a pdb in xLeap
(Thu Jul 28 2005 - 20:56:32 PDT)
Re: AMBER: prepi format and question about it
(Wed Jul 27 2005 - 22:10:36 PDT)
AMBER: prepi format and question about it
(Wed Jul 27 2005 - 02:20:00 PDT)
Re: AMBER: SHAKE error
(Fri Jul 22 2005 - 12:23:06 PDT)
Re: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 14:32:41 PDT)
Re: FW: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 13:51:00 PDT)
Re: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 13:42:49 PDT)
Re: AMBER: TI - frcmod file
(Tue Jul 12 2005 - 15:06:53 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Mon Jul 11 2005 - 18:25:00 PDT)
Re: AMBER: tyrosyl charges
(Thu Jul 07 2005 - 15:30:20 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Thu Jul 07 2005 - 14:56:14 PDT)
Re: AMBER: question about sander minimization error
(Thu Jul 07 2005 - 01:59:13 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Wed Jul 06 2005 - 20:18:46 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Wed Jul 06 2005 - 15:24:45 PDT)
Re: AMBER: loading DNA-RNA hybrid in xleap
(Sun Jul 03 2005 - 04:23:56 PDT)
Istvan Kolossvary
AMBER: Apologies - LMOD website down
(Thu Jul 14 2005 - 07:39:54 PDT)
ivan.mmb.pcb.ub.es
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Fri Jul 22 2005 - 01:16:52 PDT)
Re: AMBER: DNA strands separate
(Wed Jul 06 2005 - 07:39:04 PDT)
Re: AMBER: DNA strands separate
(Wed Jul 06 2005 - 06:40:18 PDT)
AMBER: DNA strands separate
(Wed Jul 06 2005 - 03:39:24 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 01:44:57 PDT)
JIANING WANG
AMBER: questions about MG ions
(Sun Jul 31 2005 - 16:12:36 PDT)
Jiri Sponer
Re: AMBER: simulation with Mg2+ ions and counter ions
(Sat Jul 09 2005 - 01:50:10 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 08:00:03 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 07:01:24 PDT)
Re: AMBER: Stacking energy
(Fri Jul 01 2005 - 02:52:45 PDT)
John
AMBER: MM-PBSA-big energies
(Sun Jul 03 2005 - 14:31:56 PDT)
julien
Re: AMBER: AMBER-process_mdout.perl
(Mon Jul 18 2005 - 00:48:01 PDT)
JunJun Liu
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 19:22:20 PDT)
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 17:58:53 PDT)
AMBER: why not minimize snapshots before MM/PBSA calculations
(Tue Jul 26 2005 - 08:02:00 PDT)
AMBER: molsurf error in MM/PBSA calculation
(Tue Jul 12 2005 - 06:43:55 PDT)
AMBER: Temperature varible in MMPBSA script
(Fri Jul 01 2005 - 06:59:05 PDT)
justin litchfield
Re: AMBER: Leap compilation issues
(Mon Jul 11 2005 - 18:55:54 PDT)
Re: AMBER: Leap compilation issues
(Mon Jul 11 2005 - 18:25:10 PDT)
Re: AMBER: Leap compilation issues
(Sun Jul 10 2005 - 23:49:33 PDT)
AMBER: Leap compilation issues
(Sun Jul 10 2005 - 18:41:50 PDT)
Re: AMBER: Position Restraints!
(Sat Jul 09 2005 - 17:08:15 PDT)
Kara Di Giorgio
Re: AMBER: questions about MG ions
(Sun Jul 31 2005 - 21:55:46 PDT)
Re: AMBER: Adding residues to a DNA sequence
(Fri Jul 29 2005 - 09:39:43 PDT)
AMBER: Fatal Error on loading a pdb in xLeap
(Thu Jul 28 2005 - 08:10:45 PDT)
Re: AMBER: Adding residues to a DNA sequence
(Mon Jul 25 2005 - 19:20:53 PDT)
AMBER: Adding residues to a DNA sequence
(Sun Jul 24 2005 - 18:50:45 PDT)
AMBER: Carbonane
(Thu Jul 21 2005 - 17:55:26 PDT)
Re: AMBER: Leap problem
(Fri Jul 15 2005 - 06:59:47 PDT)
Re: AMBER: Leap problem
(Thu Jul 14 2005 - 18:19:00 PDT)
AMBER: Leap problem
(Thu Jul 14 2005 - 17:06:50 PDT)
AMBER: Leap question
(Thu Jul 14 2005 - 08:10:12 PDT)
Re: AMBER: AMBER on Mac OS X
(Wed Jul 06 2005 - 09:46:11 PDT)
Karthikeyan Pasupathy
AMBER: Position Restraints!
(Sat Jul 09 2005 - 10:24:51 PDT)
Kateryna Miroshnychenko
Re: AMBER: fit
(Mon Jul 25 2005 - 03:11:11 PDT)
AMBER: segmentation fault in radial ptraj
(Mon Jul 18 2005 - 09:55:08 PDT)
AMBER: units of mwcovar matrix befor conversion
(Thu Jul 14 2005 - 01:18:28 PDT)
L Jin
AMBER: Modeling of a radical
(Thu Jul 14 2005 - 03:46:20 PDT)
Lihua Wang
Re: AMBER: simulation with Mg2+ ions and counter ions
(Sat Jul 09 2005 - 01:11:42 PDT)
Linchen Gong
RE: Re: AMBER: Minimized structure
(Wed Jul 27 2005 - 23:55:05 PDT)
Linda Prengaman
Re: AMBER: Question about Lennard-Jones Parameters in Topology file
(Tue Jul 05 2005 - 10:40:44 PDT)
AMBER: Question about Lennard-Jones Parameters in Topology file
(Sat Jul 02 2005 - 11:15:51 PDT)
Lwin, ThuZar
AMBER: how is truncated octahedron box calculated
(Thu Jul 07 2005 - 13:38:05 PDT)
AMBER: problem with addIons
(Wed Jul 06 2005 - 14:41:25 PDT)
AMBER: box size in explicit water
(Wed Jul 06 2005 - 09:39:47 PDT)
M. L. Dodson
Re: AMBER: [OT] A nab programming question
(Tue Jul 26 2005 - 07:32:47 PDT)
AMBER: [OT] A nab programming question
(Thu Jul 21 2005 - 13:07:09 PDT)
Madjid Taghdir
AMBER: cutoff in ANAL
(Wed Jul 27 2005 - 01:06:54 PDT)
Marc Baaden
Re: AMBER: Question about Prep file
(Thu Jul 21 2005 - 23:38:42 PDT)
mathew k varghese
AMBER: nucgen error (U not generated)
(Wed Jul 27 2005 - 20:28:51 PDT)
AMBER: Error in MD
(Thu Jul 21 2005 - 20:53:08 PDT)
Re: AMBER: AMBER-process_mdout.perl
(Mon Jul 18 2005 - 04:22:56 PDT)
Re: AMBER: building nucleic acids
(Fri Jul 08 2005 - 22:55:00 PDT)
AMBER: building nucleic acids
(Thu Jul 07 2005 - 21:07:03 PDT)
Matthew Davies
AMBER: mm_pbsa question
(Tue Jul 19 2005 - 03:07:51 PDT)
Melinda Layten
Re: AMBER: box size in explicit water
(Wed Jul 06 2005 - 09:52:55 PDT)
nag raj
AMBER: How to insert a protein in lipid bilayer
(Wed Jul 27 2005 - 09:56:07 PDT)
AMBER: Lipid parameters
(Tue Jul 26 2005 - 03:55:22 PDT)
AMBER: Lipid bilayer parameters and charmm force field parameters
(Fri Jul 22 2005 - 20:15:35 PDT)
AMBER: Lipid bilayer parameters
(Fri Jul 22 2005 - 00:18:24 PDT)
Oliver Hucke
Re: AMBER: Leap problem
(Thu Jul 14 2005 - 18:48:52 PDT)
Re: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 14:18:08 PDT)
Re: AMBER: TI - frcmod file
(Tue Jul 12 2005 - 16:54:11 PDT)
AMBER: TI - frcmod file
(Tue Jul 12 2005 - 12:21:44 PDT)
opitz.che.udel.edu
AMBER: ptraj output missing
(Fri Jul 29 2005 - 08:05:19 PDT)
Re: AMBER: Question about Prep file
(Fri Jul 22 2005 - 12:21:20 PDT)
AMBER: Question about Prep file
(Thu Jul 21 2005 - 13:52:41 PDT)
Re: AMBER: MM_PBSA help, please
(Tue Jul 12 2005 - 15:18:50 PDT)
Re: AMBER: MM_PBSA help, please
(Tue Jul 12 2005 - 10:29:19 PDT)
Re: AMBER: MM_PBSA help, please
(Tue Jul 12 2005 - 07:19:05 PDT)
Re: AMBER: MM_PBSA help, please
(Mon Jul 11 2005 - 14:15:19 PDT)
AMBER: MM_PBSA help, please
(Mon Jul 11 2005 - 08:55:47 PDT)
Ozlem Demir
AMBER: tyrosyl charges
(Thu Jul 07 2005 - 10:07:24 PDT)
Paul Beroza
RE: AMBER: molsurf error in MM/PBSA calculation
(Thu Jul 14 2005 - 16:01:08 PDT)
peng79.email.unc.edu
AMBER: please help us on partial charge calculation of PT complex using RESP
(Fri Jul 01 2005 - 08:10:31 PDT)
Peter Gannett
AMBER: ambpdb core dump
(Fri Jul 29 2005 - 04:27:46 PDT)
Re: AMBER: ptraj-acceptor mask format
(Wed Jul 27 2005 - 13:54:50 PDT)
AMBER: ptraj-acceptor mask format
(Mon Jul 25 2005 - 12:10:47 PDT)
Re: AMBER: Modeling of a radical
(Sat Jul 23 2005 - 07:21:25 PDT)
Peter Varnai
Re: AMBER: parallel error
(Fri Jul 01 2005 - 08:51:18 PDT)
Petr Kulhanek
Re: AMBER: Ptraj and order of operations
(Wed Jul 13 2005 - 00:21:48 PDT)
Re: AMBER: pmemd - bug report
(Tue Jul 05 2005 - 09:29:54 PDT)
Re: AMBER: pmemd - bug report
(Tue Jul 05 2005 - 03:31:14 PDT)
AMBER: pmemd - bug report
(Mon Jul 04 2005 - 09:33:05 PDT)
Pratul K. Agarwal
AMBER: Failed sander runs for large systems
(Fri Jul 29 2005 - 19:41:44 PDT)
Praveena Gopal
AMBER: AMBER-process_mdout.perl
(Mon Jul 18 2005 - 00:26:19 PDT)
Qing Zhang
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Tue Jul 12 2005 - 12:59:01 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Thu Jul 07 2005 - 17:48:40 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Thu Jul 07 2005 - 01:30:14 PDT)
Rhoad, Jonathan S.
RE: AMBER: pdb files from traj file
(Wed Jul 13 2005 - 14:22:56 PDT)
RE: AMBER: TI - frcmod file
(Wed Jul 13 2005 - 14:03:17 PDT)
Robert Duke
AMBER: Critical PMEMD 8 Bugfix
(Mon Jul 11 2005 - 05:38:59 PDT)
Re: AMBER: pmemd - bug report
(Tue Jul 05 2005 - 09:47:19 PDT)
Re: AMBER: pmemd - bug report
(Mon Jul 04 2005 - 20:58:14 PDT)
Re: AMBER: pmemd - bug report
(Mon Jul 04 2005 - 14:40:18 PDT)
Re: AMBER: pmemd - bug report
(Mon Jul 04 2005 - 13:30:54 PDT)
Ross Walker
RE: AMBER: new residue
(Wed Jul 27 2005 - 09:54:14 PDT)
RE: AMBER: Periodic box imaging using ptraj
(Wed Jul 27 2005 - 09:28:05 PDT)
RE: AMBER: Tutoial 8 (Case Study)
(Tue Jul 26 2005 - 10:03:37 PDT)
RE: AMBER: Trouble with Amber8
(Tue Jul 19 2005 - 13:41:27 PDT)
RE: AMBER: pdb file and xleap
(Tue Jul 19 2005 - 08:33:44 PDT)
RE: AMBER: Amber 7 Compiler Error
(Tue Jul 19 2005 - 08:36:03 PDT)
RE: AMBER: AMBER-process_mdout.perl
(Mon Jul 18 2005 - 08:24:18 PDT)
RE: AMBER: P4 EM64T Intel Fortran Compile Problem
(Fri Jul 15 2005 - 10:26:36 PDT)
RE: AMBER: pdb files from traj file
(Wed Jul 13 2005 - 14:37:05 PDT)
RE: AMBER: Leap compilation issues
(Tue Jul 12 2005 - 09:47:05 PDT)
RE: AMBER: MD simulation on a protein solvated by a combination of some water models ?
(Tue Jul 12 2005 - 09:41:44 PDT)
RE: AMBER: Leap compilation issues
(Mon Jul 11 2005 - 10:05:25 PDT)
RE: AMBER: molecular dynamics
(Sat Jul 09 2005 - 20:42:06 PDT)
RE: AMBER: sander problem
(Wed Jul 06 2005 - 14:19:34 PDT)
RE: AMBER: restart file
(Tue Jul 05 2005 - 14:15:49 PDT)
RE: AMBER: restart file
(Tue Jul 05 2005 - 12:29:27 PDT)
RE: AMBER: Loading a macmodel file complex
(Tue Jul 05 2005 - 08:54:57 PDT)
RE: AMBER: Problems with parameter lib and prep püarameter files
(Tue Jul 05 2005 - 08:47:22 PDT)
S.Sundar Raman
Re: AMBER: (no subject)
(Sat Jul 02 2005 - 05:58:59 PDT)
Scott Pendley
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Mon Jul 18 2005 - 10:31:29 PDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Fri Jul 15 2005 - 13:08:43 PDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Fri Jul 15 2005 - 10:46:46 PDT)
Re: AMBER: Ptraj and order of operations
(Tue Jul 12 2005 - 16:22:29 PDT)
Re: AMBER: MM_PBSA help, please
(Tue Jul 12 2005 - 14:57:08 PDT)
Re: AMBER: MM_PBSA help, please
(Mon Jul 11 2005 - 14:37:50 PDT)
Re: AMBER: MM_PBSA help, please
(Mon Jul 11 2005 - 11:30:34 PDT)
Shan Jufang
RE: Re: AMBER:
(Sat Jul 09 2005 - 12:37:54 PDT)
Stefano.Pieraccini.unimi.it
Re: AMBER: Atom type :Si
(Fri Jul 22 2005 - 01:37:50 PDT)
Stephen P. Molnar, Ph.D.
AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler
(Tue Jul 19 2005 - 13:14:30 PDT)
AMBER: Amber 7 Compiler Error
(Tue Jul 19 2005 - 05:26:14 PDT)
Stern, Julie
AMBER: nucgen H5T H3T
(Mon Jul 25 2005 - 18:55:52 PDT)
AMBER: nucgen bdna types
(Fri Jul 22 2005 - 18:01:20 PDT)
AMBER: infinite DNA
(Fri Jul 08 2005 - 14:44:25 PDT)
Sukjoon Yoon
AMBER: RESTARTED DUE TO LINMIN FAILURE
(Fri Jul 29 2005 - 23:00:24 PDT)
AMBER: Protein residue numbering
(Wed Jul 27 2005 - 04:52:42 PDT)
Suxin Zheng
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 17:39:15 PDT)
AMBER: pbsa problem
(Wed Jul 27 2005 - 12:47:29 PDT)
AMBER: mmpbsa test problem
(Fri Jul 22 2005 - 18:41:11 PDT)
Thomas E. Cheatham, III
Re: AMBER: Minimized structure
(Thu Jul 28 2005 - 20:09:55 PDT)
Re: AMBER: nucgen error (U not generated)
(Wed Jul 27 2005 - 20:49:33 PDT)
Re: AMBER: Minimized structure
(Wed Jul 27 2005 - 20:47:28 PDT)
Re: AMBER: convert_trajectory
(Wed Jul 27 2005 - 16:45:34 PDT)
Re: AMBER: convert_trajectory
(Wed Jul 27 2005 - 14:27:57 PDT)
Re: AMBER: Periodic box imaging using ptraj
(Tue Jul 26 2005 - 13:11:39 PDT)
Re: AMBER: ptraj-acceptor mask format
(Tue Jul 26 2005 - 13:06:08 PDT)
AMBER: Re: Problems with ptraj/rdparm
(Fri Jul 15 2005 - 12:22:28 PDT)
Re: AMBER: example script for hbond calculation
(Fri Jul 01 2005 - 09:10:07 PDT)
Tim Meyer
Re: AMBER: An atom name with 4 characters is not compatible with Leap ?
(Fri Jul 22 2005 - 08:06:52 PDT)
Varsha Goyal
AMBER: random-coil polymer
(Sat Jul 16 2005 - 15:35:19 PDT)
AMBER: AMBER on Mac OS X
(Wed Jul 06 2005 - 07:55:12 PDT)
Re: AMBER: (no subject)
(Sat Jul 02 2005 - 09:10:49 PDT)
AMBER: (no subject)
(Fri Jul 01 2005 - 14:46:55 PDT)
Vijay Manickam Achari
AMBER: molecular dynamics
(Sat Jul 09 2005 - 19:55:55 PDT)
AMBER: question about leaprc.gaff and xxx.top
(Thu Jun 30 2005 - 22:52:15 PDT)
Vitor Manuel Sousa F?x
Re: AMBER: Minimized structure
(Thu Jul 28 2005 - 04:07:09 PDT)
AMBER: PMF calculations with TI using the sander
(Mon Jul 18 2005 - 00:30:59 PDT)
Wai Keat Yam
RE: AMBER: pdb file and xleap
(Wed Jul 20 2005 - 23:01:07 PDT)
AMBER: pdb file and xleap
(Tue Jul 19 2005 - 03:06:50 PDT)
Wei Chen
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 20:53:36 PDT)
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 18:09:13 PDT)
Re: AMBER: mm_pbsa
(Fri Jul 29 2005 - 17:55:07 PDT)
AMBER: mm_pbsa
(Fri Jul 29 2005 - 17:10:46 PDT)
Re: AMBER: convert_trajectory
(Wed Jul 27 2005 - 19:06:28 PDT)
Re: AMBER: convert_trajectory
(Wed Jul 27 2005 - 16:07:55 PDT)
AMBER: convert_trajectory
(Wed Jul 27 2005 - 13:58:36 PDT)
wenfei Li
Re: AMBER: NTWPRY problem
(Mon Jul 25 2005 - 18:51:09 PDT)
Re: AMBER: NTWPRY problem
(Mon Jul 25 2005 - 18:42:16 PDT)
Re: AMBER: NTWPRY problem
(Mon Jul 25 2005 - 18:39:21 PDT)
AMBER: NTWPRY problem
(Mon Jul 25 2005 - 08:44:31 PDT)
Yam
Re: AMBER: Minimized structure
(Thu Jul 28 2005 - 21:03:40 PDT)
Re: AMBER: Minimized structure
(Thu Jul 28 2005 - 19:25:29 PDT)
AMBER: Minimized structure
(Wed Jul 27 2005 - 20:02:03 PDT)
Ye Mei
AMBER: dihedral term in prmtop file
(Thu Jul 28 2005 - 07:38:55 PDT)
AMBER: potential of mean force calculation along reaction coordinates
(Tue Jul 26 2005 - 00:04:00 PDT)
AMBER: simulation with Mg2+ ions and counter ions
(Fri Jul 08 2005 - 23:54:16 PDT)
AMBER: how to average the structure along md trajectory
(Wed Jul 06 2005 - 06:51:56 PDT)
AMBER: estimation of interface size
(Sun Jul 03 2005 - 19:19:55 PDT)
AMBER: molecular dynamics simulation of protein containing Mg2+ cation
(Fri Jul 01 2005 - 02:33:31 PDT)
AMBER: least square fit of snapshots in md trajectory to a reference frame
(Thu Jun 30 2005 - 19:56:08 PDT)
Yen-Ting Lai
Re: AMBER: Question about "nmanal"
(Tue Jul 12 2005 - 06:36:25 PDT)
Re: AMBER: Question about "nmanal"
(Tue Jul 12 2005 - 03:09:24 PDT)
AMBER: Question about "nmanal"
(Mon Jul 11 2005 - 07:11:25 PDT)
Yogesh Sabnis
AMBER: Anal - problems with energy analysis
(Tue Jul 12 2005 - 01:33:30 PDT)
AMBER: Loading a macmodel file complex
(Mon Jul 04 2005 - 08:02:49 PDT)
Yong Xu
Re: AMBER: How to insert a protein in lipid bilayer
(Wed Jul 27 2005 - 18:47:22 PDT)
AMBER: fit
(Mon Jul 25 2005 - 02:04:57 PDT)
Yong Duan
RE: AMBER: temperature keep increasing in high temp.
(Fri Jul 29 2005 - 20:43:52 PDT)
RE: AMBER: a bimolecular reaction
(Fri Jul 22 2005 - 12:25:09 PDT)
Re: AMBER: a bimolecular reaction
(Fri Jul 22 2005 - 10:44:23 PDT)
YoungJin Cho
AMBER: pdb files from traj file
(Wed Jul 13 2005 - 14:06:30 PDT)
zgleo
Re: Re: AMBER: mm_pbsa
(Sun Jul 31 2005 - 08:26:02 PDT)
AMBER: Amber parameters for ADP
(Fri Jul 29 2005 - 22:22:19 PDT)
Zhang Bing
AMBER: P4 EM64T Intel Fortran Compile Problem
(Wed Jul 20 2005 - 19:24:20 PDT)
Zhiguo Liu
Re: RE: Re: AMBER:
(Sun Jul 10 2005 - 00:37:36 PDT)
Re: AMBER:
(Sat Jul 09 2005 - 01:39:43 PDT)
zhli_2000.126.com
AMBER: Re: (瑞星提示-此邮件可能是垃圾邮件)Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Mon Jul 18 2005 - 18:09:23 PDT)
AMBER: Re: (瑞星提示-此邮件可能是垃圾邮件)Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Mon Jul 18 2005 - 18:23:39 PDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Sat Jul 16 2005 - 20:30:47 PDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa?
(Fri Jul 15 2005 - 00:10:41 PDT)
AMBER: Can GB and MS work correctly together in mmpbsa?
(Thu Jul 14 2005 - 19:38:08 PDT)
Zhuang
Re: AMBER: question replica exchange acceptance ratio
(Tue Jul 12 2005 - 15:39:47 PDT)
AMBER: question replica exchange acceptance ratio
(Tue Jul 12 2005 - 14:01:19 PDT)
荒牧 武志
Re:AMBER: MD simulation on a protein solvated by a combination of some water mod
(Thu Jul 14 2005 - 02:56:39 PDT)
AMBER: MD simulation on a protein solvated by a combination of some water models ?
(Mon Jul 11 2005 - 21:10:12 PDT)
Last message date
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Mon Aug 01 2005 - 06:53:00 PDT
Archived on
: Wed Dec 25 2024 - 05:53:29 PST
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