Amber Archive Apr 2006 by author
288 messages
:
Starting
Sun Apr 02 2006 - 06:10:18 PDT,
Ending
Wed May 03 2006 - 06:07:07 PDT
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Adrian Roitberg
Re: AMBER: increase in computational time with LES
(Sun Apr 23 2006 - 15:26:20 PDT)
Alex Tzanov
Re: AMBER: compiling errors
(Mon Apr 24 2006 - 19:04:10 PDT)
AMBER: compiling errors
(Mon Apr 24 2006 - 17:17:50 PDT)
Alfredo Quevedo
AMBER: Installing Delphi to perform mm_pbsa analysis?
(Wed Apr 19 2006 - 10:39:13 PDT)
AMBER: How to evaluate the binding energy of a ligand?
(Tue Apr 11 2006 - 10:53:50 PDT)
AMBER: Obtaining an average structure from a trajectory
(Tue Apr 04 2006 - 16:11:02 PDT)
alfredoq.fcq.unc.edu.ar
AMBER: Performing Simulated Annealing?
(Fri Apr 28 2006 - 09:58:31 PDT)
amanda.mccook.gatech.edu
AMBER: DNA tutorial, in vacuo minimization
(Fri Apr 14 2006 - 12:15:31 PDT)
Amber admin
AMBER: separating LES copies in moil view
(Thu Apr 13 2006 - 10:28:02 PDT)
Ananda Rama Krishnan Selvaraj
AMBER: Error in the MD run
(Mon Apr 17 2006 - 23:13:04 PDT)
Re: AMBER: Calculation of g(r) from PTRAJ
(Mon Apr 17 2006 - 10:45:39 PDT)
AMBER: Calculation of g(r) from PTRAJ
(Sun Apr 16 2006 - 03:33:25 PDT)
andy ng
Re: AMBER: NGL error when creating snapshots for MM/PB(GB)SA
(Thu Apr 06 2006 - 23:20:16 PDT)
AMBER: NGL error when creating snapshots for MM/PB(GB)SA
(Thu Apr 06 2006 - 23:05:50 PDT)
Arjen-Joachim Jakobi
Re: AMBER: "average" command in ptraj
(Mon Apr 10 2006 - 11:50:34 PDT)
AMBER: "average" command in ptraj
(Mon Apr 10 2006 - 05:15:16 PDT)
Atro Tossavainen
Re: AMBER: compiling errors
(Wed Apr 26 2006 - 00:49:23 PDT)
Bill Ross
Re: AMBER: a question about "solvateoct" in AMBER 8
(Fri Apr 21 2006 - 11:48:01 PDT)
Re: AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 11:38:17 PDT)
Re: AMBER: saltcon with explicit water?
(Wed Apr 12 2006 - 16:26:05 PDT)
carlos
Re: AMBER: RMS
(Mon Apr 03 2006 - 14:18:24 PDT)
Re: AMBER: LES error
(Sat Apr 01 2006 - 10:04:46 PST)
Carlos Simmerling
Re: AMBER: about the execuation of REMD with sander of amber9
(Sat Apr 29 2006 - 06:43:46 PDT)
Re: AMBER: about the execuation of REMD with sander of amber9
(Sat Apr 29 2006 - 06:45:24 PDT)
Re: AMBER: Performing Simulated Annealing?
(Fri Apr 28 2006 - 10:16:43 PDT)
Re: AMBER: heating process
(Fri Apr 28 2006 - 04:06:03 PDT)
Re: AMBER: LES copies
(Mon Apr 24 2006 - 04:14:20 PDT)
Re: AMBER: increase in computational time with LES
(Sun Apr 23 2006 - 16:00:20 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 11:28:42 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 09:41:04 PDT)
Re: AMBER: separating LES copies in moil view
(Thu Apr 13 2006 - 16:45:35 PDT)
Cenk Andac
AMBER: Langevin mode error??
(Fri Apr 28 2006 - 04:52:02 PDT)
AMBER: Question about interpretation of sander.QMMM results
(Thu Apr 06 2006 - 12:10:09 PDT)
Chengwen Chen
Re: AMBER: a question about "solvateoct" in AMBER 8
(Sun Apr 23 2006 - 21:13:30 PDT)
AMBER: a question about "solvateoct" in AMBER 8
(Thu Apr 20 2006 - 23:48:14 PDT)
AMBER: Which one is the best force field for DNA?
(Wed Apr 12 2006 - 20:11:14 PDT)
AMBER: the best force field for DNA
(Mon Apr 10 2006 - 21:15:25 PDT)
Chris Moth
Re: AMBER: angle between planes
(Fri Apr 07 2006 - 14:19:26 PDT)
Claire Zerafa
AMBER:
(Wed Apr 05 2006 - 06:33:39 PDT)
Claudia Steinert
AMBER: LES copies
(Mon Apr 24 2006 - 01:28:06 PDT)
cristian obiol
AMBER: nmode different units
(Wed Apr 05 2006 - 03:47:04 PDT)
Daniel Oehme
AMBER: Mass wieghted Covariance Matrix
(Wed Apr 12 2006 - 00:16:32 PDT)
AMBER: Entropy calculations with Nmode and ptraj
(Tue Apr 04 2006 - 00:24:39 PDT)
darden
Re: AMBER: a quetion
(Mon Apr 24 2006 - 07:57:59 PDT)
Re: AMBER: Constant P for non-orthorhombic cells
(Wed Apr 12 2006 - 05:41:14 PDT)
David A. Case
Re: AMBER: Did these differences come from so-called "different machines" ?
(Sun Apr 30 2006 - 21:09:35 PDT)
Re: AMBER: Amber 9, sander imin = 5, -y flag
(Sun Apr 30 2006 - 21:08:24 PDT)
Re: AMBER: internal coordinates
(Sun Apr 30 2006 - 09:09:52 PDT)
Re: AMBER: Setting box dimensions in leap
(Sat Apr 29 2006 - 22:42:48 PDT)
Re: AMBER: Langevin mode error??
(Fri Apr 28 2006 - 13:13:31 PDT)
Re: AMBER: Antechamber & atom types
(Fri Apr 21 2006 - 08:22:45 PDT)
Re: AMBER: Problems compiling amber9
(Fri Apr 21 2006 - 08:03:37 PDT)
Re: AMBER: Error when compiling amber9 ptraj
(Fri Apr 21 2006 - 05:08:15 PDT)
Re: AMBER: RE: Respgen segemtation fault
(Thu Apr 20 2006 - 04:49:34 PDT)
Re: AMBER: Installing Delphi to perform mm_pbsa analysis?
(Wed Apr 19 2006 - 12:43:46 PDT)
Re: AMBER: Could not find atom type.
(Wed Apr 19 2006 - 12:37:33 PDT)
Re: AMBER: Could not find atom type.
(Tue Apr 18 2006 - 16:06:21 PDT)
Re: AMBER: probable bug in antechamber
(Mon Apr 17 2006 - 17:33:35 PDT)
Re: AMBER: Calculation of g(r) from PTRAJ
(Mon Apr 17 2006 - 09:45:27 PDT)
Re: AMBER: Could not find atom type.
(Mon Apr 17 2006 - 09:40:05 PDT)
Re: AMBER: amber memory usage
(Fri Apr 14 2006 - 17:30:44 PDT)
AMBER: How I wasted a rainy Friday in San Diego
(Fri Apr 14 2006 - 17:24:00 PDT)
Re: AMBER: compile error: can't locate file for: -lcrt1.o
(Fri Apr 14 2006 - 15:58:33 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 10:53:50 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 08:27:52 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Thu Apr 13 2006 - 14:41:03 PDT)
Re: AMBER: Respgen segemtation fault
(Thu Apr 13 2006 - 11:46:55 PDT)
Re: AMBER: saltcon with explicit water?
(Wed Apr 12 2006 - 12:25:38 PDT)
Re: AMBER: Nmode memory allocation error ?
(Tue Apr 11 2006 - 12:09:26 PDT)
Re: AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3
(Tue Apr 11 2006 - 11:19:59 PDT)
Re: AMBER: protocols for NMR protein refinement with AMBER
(Mon Apr 10 2006 - 13:55:43 PDT)
Re: AMBER: mm-pbsa: distant-dependent dielectric constant
(Sat Apr 08 2006 - 23:11:49 PDT)
Re: AMBER: mm-pbsa: distant-dependent dielectric constant
(Sat Apr 08 2006 - 22:23:15 PDT)
Re: AMBER: Umbrella sampling
(Fri Apr 07 2006 - 13:56:48 PDT)
Re: AMBER: POPC parameters
(Fri Apr 07 2006 - 09:14:53 PDT)
Re: AMBER: Restarting constant pressure sims with restraints
(Wed Apr 05 2006 - 11:24:38 PDT)
Re: AMBER:
(Wed Apr 05 2006 - 07:46:18 PDT)
Re: AMBER: how to restrain the intramolecular hydrogen bond
(Tue Apr 04 2006 - 15:52:52 PDT)
Re: AMBER: Entropy calculations with Nmode and ptraj
(Tue Apr 04 2006 - 15:50:55 PDT)
AMBER: Using XML for Amber files
(Tue Apr 04 2006 - 15:42:35 PDT)
Re: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ?
(Tue Apr 04 2006 - 15:11:51 PDT)
Re: AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) !
(Mon Apr 03 2006 - 07:57:36 PDT)
Re: AMBER: Announcement: Amber 9 is now available
(Sat Apr 01 2006 - 09:21:52 PST)
Re: AMBER: what is the integration scheme for langevin dynamic used in amber8
(Sat Apr 01 2006 - 09:18:57 PST)
David Mobley
Re: AMBER: probable bug in antechamber
(Tue Apr 18 2006 - 06:52:13 PDT)
AMBER: probable bug in antechamber
(Mon Apr 17 2006 - 16:08:06 PDT)
Re: AMBER: How to evaluate the binding energy of a ligand?
(Tue Apr 11 2006 - 12:27:13 PDT)
Re: AMBER: Any difference about RESP or ESP with Chelpg or MK
(Tue Apr 04 2006 - 15:13:30 PDT)
Don.Bashford.stjude.org
AMBER: Restarting constant pressure sims with restraints
(Wed Apr 05 2006 - 11:08:41 PDT)
Ed Pate
AMBER: timing estimates
(Wed Apr 19 2006 - 16:10:30 PDT)
AMBER: amber memory usage
(Fri Apr 14 2006 - 15:45:59 PDT)
Evan Kelly
AMBER: Fujitsu frt compiler
(Fri Apr 21 2006 - 07:53:40 PDT)
AMBER: Semi-empirical parameterization -- van der Waals and H-bonding?
(Mon Apr 03 2006 - 15:28:27 PDT)
Feng X Zhou
Re: AMBER: Using XML for Amber files
(Tue Apr 25 2006 - 08:07:39 PDT)
Re: AMBER: Using XML for Amber files
(Fri Apr 07 2006 - 11:54:59 PDT)
RE: AMBER: Using XML for Amber files
(Wed Apr 05 2006 - 08:21:35 PDT)
Re: AMBER: Announcement: Amber 9 is now available
(Mon Apr 03 2006 - 08:28:48 PDT)
FyD
AMBER: Antechamber & atom types
(Thu Apr 20 2006 - 10:04:17 PDT)
Re: AMBER: An issue with the "multimolecule and multiconformational" resp fit
(Tue Apr 11 2006 - 12:39:40 PDT)
Re: AMBER: RESP problem
(Tue Apr 11 2006 - 09:31:12 PDT)
Re: AMBER: Any difference about RESP or ESP with Chelpg or MK
(Tue Apr 04 2006 - 10:01:40 PDT)
Re: AMBER: Announcement: Amber 9 is now available
(Mon Apr 03 2006 - 11:00:44 PDT)
german
AMBER: a quetion
(Mon Apr 24 2006 - 04:17:34 PDT)
AMBER: a question
(Fri Apr 21 2006 - 04:04:54 PDT)
Gert Kiss
Re: AMBER: AMBER9: MacG5 parallel sander.MPI
(Sat Apr 29 2006 - 15:29:51 PDT)
haixiao jin
AMBER: MM_PBSA: “Found unknown atflag DELPHI”
(Mon Apr 24 2006 - 08:23:23 PDT)
harianto
AMBER: Born igb =2
(Mon Apr 24 2006 - 18:27:24 PDT)
Re: AMBER: VdW radii in the topology file
(Mon Apr 10 2006 - 09:51:55 PDT)
Re: AMBER: printing Amber VdW radii as separate column in pdb files
(Mon Apr 10 2006 - 08:12:39 PDT)
Hector A. Baldoni
Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product
(Sat Apr 29 2006 - 17:08:30 PDT)
Holger Gohlke
Re: AMBER: about the decomposition energies using mm/pbsa
(Fri Apr 21 2006 - 00:25:44 PDT)
Re: AMBER: Mass wieghted Covariance Matrix
(Wed Apr 12 2006 - 00:46:19 PDT)
Re: AMBER: PCA
(Tue Apr 11 2006 - 05:27:26 PDT)
Re: AMBER: MM-GBSA decomposition
(Sun Apr 09 2006 - 11:13:41 PDT)
Re: AMBER: PCA
(Sun Apr 09 2006 - 11:09:06 PDT)
Ilyas Yildirim
AMBER: Force Field Question
(Thu Apr 27 2006 - 14:57:58 PDT)
In Hee Park
AMBER: AMBER9: MacG5 parallel sander.MPI
(Sat Apr 29 2006 - 13:59:28 PDT)
Ioana Cozmuta
AMBER: internal coordinates
(Wed Apr 26 2006 - 14:56:20 PDT)
AMBER: two references- I got them, thank you!
(Wed Apr 26 2006 - 14:15:11 PDT)
AMBER: two references
(Wed Apr 26 2006 - 13:18:28 PDT)
Re: AMBER: DNA structure
(Wed Apr 26 2006 - 12:06:22 PDT)
AMBER: DNA structure
(Tue Apr 25 2006 - 13:17:12 PDT)
AMBER: reconstructing PMF
(Mon Apr 10 2006 - 11:15:20 PDT)
Jan Dohnalek
AMBER: passwordless ssh stopped working
(Thu Apr 13 2006 - 08:51:50 PDT)
Jan Kosinski
AMBER: modeling zinc binding site
(Mon Apr 24 2006 - 05:28:55 PDT)
Jason K
AMBER: An issue with the "multimolecule and multiconformational" resp fit
(Tue Apr 11 2006 - 11:16:57 PDT)
JAVIER PEREZ
AMBER: problems with saveamberprep command
(Fri Apr 21 2006 - 04:33:48 PDT)
Jennie Thomas
AMBER: Setting box dimensions in leap
(Fri Apr 28 2006 - 15:42:38 PDT)
Re: AMBER: Constant P for non-orthorhombic cells
(Wed Apr 12 2006 - 11:36:47 PDT)
AMBER: Constant P for non-orthorhombic cells
(Tue Apr 11 2006 - 21:40:00 PDT)
Jianyin Shao
Re: AMBER: error propagation in MM-PBSA binding free energy calculation
(Wed Apr 26 2006 - 17:13:48 PDT)
Jianzhong Liu
AMBER: Any difference about RESP or ESP with Chelpg or MK
(Tue Apr 04 2006 - 08:51:36 PDT)
Jiri Sponer
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 10:08:34 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 09:59:00 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 09:49:58 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 03:31:24 PDT)
John
AMBER: angle between planes
(Fri Apr 07 2006 - 09:55:59 PDT)
AMBER: angle between planes
(Fri Apr 07 2006 - 09:48:38 PDT)
John Mongan
Re: AMBER: Born igb =2
(Tue Apr 25 2006 - 10:30:22 PDT)
JunJun Liu
Re: AMBER: one question about mm_pbsa
(Thu Apr 06 2006 - 14:48:20 PDT)
Junmei Wang
AMBER: Nmode memory allocation error ?
(Tue Apr 11 2006 - 11:47:46 PDT)
Kenley Barrett
Re: AMBER: increase in computational time with LES
(Sun Apr 23 2006 - 15:46:56 PDT)
AMBER: increase in computational time with LES
(Sun Apr 23 2006 - 14:53:29 PDT)
Re: AMBER: saltcon with explicit water?
(Wed Apr 12 2006 - 16:07:44 PDT)
AMBER: saltcon with explicit water?
(Wed Apr 12 2006 - 09:36:20 PDT)
lhsong
Re: AMBER: error propagation in MM-PBSA binding free energy calculation
(Fri Apr 28 2006 - 15:37:42 PDT)
AMBER: error propagation in MM-PBSA binding free energy calculation
(Tue Apr 25 2006 - 20:22:41 PDT)
AMBER: mm-pbsa: distant-dependent dielectric constant
(Sat Apr 08 2006 - 11:30:56 PDT)
Li Su
AMBER: what is the integration scheme for langevin dynamic used in amber8
(Sat Apr 01 2006 - 05:17:02 PST)
Lihua Wang
RE: AMBER: amber9 compilation error on SGI altix
(Sat Apr 22 2006 - 15:48:40 PDT)
AMBER: amber9 compilation error on SGI altix
(Sat Apr 22 2006 - 10:58:26 PDT)
linfu
AMBER: amber7 compiling error
(Sun Apr 16 2006 - 08:26:17 PDT)
Lishan Yao
AMBER: "vector" command in ptraj
(Mon Apr 10 2006 - 11:20:56 PDT)
litong
AMBER: about the decomposition energies using mm/pbsa
(Thu Apr 20 2006 - 06:34:11 PDT)
Maarit Hellman
AMBER: deviations from idealized geometry
(Wed Apr 12 2006 - 02:02:33 PDT)
Mark Williamson
Re: AMBER: RE: Respgen segemtation fault - debug attempt
(Thu Apr 20 2006 - 09:56:55 PDT)
Re: AMBER: RE: Respgen segemtation fault - debug attempt
(Thu Apr 20 2006 - 06:23:55 PDT)
martin peters
Re: AMBER: How to build 1,4-dimethyl benzene with amber9
(Fri Apr 28 2006 - 16:00:29 PDT)
AMBER: How to build 1,4-dimethyl benzene with amber9
(Fri Apr 28 2006 - 14:27:09 PDT)
Mathy Froeyen
AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3
(Tue Apr 11 2006 - 10:44:40 PDT)
Michael Crowley
Re: AMBER: a question about "solvateoct" in AMBER 8
(Fri Apr 21 2006 - 12:50:52 PDT)
Re: AMBER: Constant P for non-orthorhombic cells
(Wed Apr 12 2006 - 11:24:05 PDT)
Miguel Ferreira
Re: AMBER: MM-PBSA problem
(Mon Apr 17 2006 - 10:24:05 PDT)
Re: AMBER: MM-PBSA problem
(Fri Apr 14 2006 - 14:07:20 PDT)
AMBER: MM-PBSA problem
(Fri Apr 14 2006 - 08:27:43 PDT)
Mingfeng Yang
Re: AMBER: a quetion
(Mon Apr 24 2006 - 06:07:30 PDT)
Re: AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 13:05:43 PDT)
Re: AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 13:00:53 PDT)
mkseo
AMBER: distance restraints for umbrella sampling
(Thu Apr 27 2006 - 15:21:16 PDT)
ohucke.lav.boehringer-ingelheim.com
AMBER: protocols for NMR protein refinement with AMBER
(Mon Apr 10 2006 - 13:43:44 PDT)
Osmar Norberto de Souza
AMBER: Force field for DNA
(Mon Apr 17 2006 - 03:50:31 PDT)
pang zhao
Re: AMBER: about the execuation of REMD with sander of amber9
(Sun Apr 30 2006 - 01:58:06 PDT)
AMBER: about the shake with self-guide LD
(Sat Apr 29 2006 - 03:44:39 PDT)
Re: AMBER: about the execuation of REMD with sander of amber9
(Fri Apr 28 2006 - 22:12:22 PDT)
AMBER: about the execuation of REMD with sander of amber9
(Fri Apr 28 2006 - 20:08:41 PDT)
pascal.baillod.epfl.ch
AMBER: Non-periodic simulations: How is the system kept together?
(Thu Apr 20 2006 - 09:13:04 PDT)
Pradipta Bandyopadhyay
AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) !
(Sun Apr 02 2006 - 22:23:26 PDT)
r. a.
AMBER: heating process
(Thu Apr 27 2006 - 22:56:06 PDT)
Raffaella D'Auria
RE: AMBER: organic molecule - from newbie :)
(Mon Apr 10 2006 - 15:12:44 PDT)
AMBER: organic molecule - from newbie :)
(Thu Apr 06 2006 - 18:55:02 PDT)
Ray Luo
Re: AMBER: questions about mm_pbsa
(Wed Apr 26 2006 - 18:03:13 PDT)
Re: AMBER: Test Failure during amber9 serial compilation
(Wed Apr 26 2006 - 11:29:11 PDT)
Re: AMBER: Test Failure during amber9 serial compilation
(Tue Apr 25 2006 - 11:01:49 PDT)
Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI”
(Mon Apr 24 2006 - 11:40:28 PDT)
Re: AMBER: MM-PBSA problem
(Fri Apr 14 2006 - 14:40:45 PDT)
Re: AMBER: MM-PBSA problem
(Fri Apr 14 2006 - 09:57:52 PDT)
Re: AMBER: one question about mm_pbsa
(Thu Apr 13 2006 - 08:39:53 PDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short
(Sun Apr 09 2006 - 19:44:44 PDT)
rdauria.uci.edu
RE: AMBER: ibelly & fix atom
(Mon Apr 17 2006 - 21:22:16 PDT)
Re: AMBER: ibelly & fix atom
(Mon Apr 17 2006 - 20:59:56 PDT)
AMBER: ibelly & fix atom
(Mon Apr 17 2006 - 20:41:28 PDT)
Robert Duke
Re: AMBER: a question
(Mon Apr 24 2006 - 11:21:34 PDT)
Re: AMBER: timing estimates
(Wed Apr 19 2006 - 17:06:59 PDT)
Re: AMBER: amber memory usage
(Fri Apr 14 2006 - 15:56:12 PDT)
Re: AMBER: Restarting constant pressure sims with restraints
(Wed Apr 05 2006 - 11:30:05 PDT)
Ross Walker
RE: AMBER: How to build 1,4-dimethyl benzene with amber9
(Fri Apr 28 2006 - 16:46:23 PDT)
RE: AMBER: How to build 1,4-dimethyl benzene with amber9
(Fri Apr 28 2006 - 15:10:56 PDT)
RE: AMBER: Performing Simulated Annealing?
(Fri Apr 28 2006 - 10:13:56 PDT)
RE: AMBER: Test Failure during amber9 serial compilation
(Wed Apr 26 2006 - 11:49:06 PDT)
RE: AMBER: Test Failure during amber9 serial compilation
(Tue Apr 25 2006 - 12:30:19 PDT)
RE: AMBER: compiling errors
(Mon Apr 24 2006 - 17:58:52 PDT)
RE: AMBER: rmsd value for organic molecule
(Mon Apr 24 2006 - 12:25:23 PDT)
RE: AMBER: a quetion
(Mon Apr 24 2006 - 07:52:59 PDT)
RE: AMBER: amber9 compilation error on SGI altix
(Sat Apr 22 2006 - 12:21:24 PDT)
RE: AMBER: a question
(Fri Apr 21 2006 - 13:35:51 PDT)
RE: AMBER: Non-periodic simulations: How is the system kept together?
(Thu Apr 20 2006 - 09:35:26 PDT)
RE: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight
(Wed Apr 19 2006 - 08:16:51 PDT)
AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight
(Tue Apr 18 2006 - 08:42:41 PDT)
RE: AMBER: Error in the MD run
(Tue Apr 18 2006 - 08:35:41 PDT)
RE: AMBER: ibelly & fix atom
(Mon Apr 17 2006 - 21:08:42 PDT)
RE: AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 11:28:18 PDT)
RE: AMBER: amber memory usage
(Fri Apr 14 2006 - 17:28:31 PDT)
RE: AMBER: DNA tutorial, in vacuo minimization
(Fri Apr 14 2006 - 12:34:32 PDT)
RE: AMBER:a problem in parallel compiler
(Thu Apr 13 2006 - 08:54:43 PDT)
RE: AMBER: RESP problem
(Tue Apr 11 2006 - 08:08:25 PDT)
RE: AMBER: organic molecule - from newbie :)
(Mon Apr 10 2006 - 15:41:56 PDT)
RE: AMBER: printing Amber VdW radii as separate column in pdb files
(Mon Apr 10 2006 - 09:03:18 PDT)
RE: AMBER: organic molecule - from newbie :)
(Thu Apr 06 2006 - 19:13:46 PDT)
RE: AMBER: Obtaining an average structure from a trajectory
(Tue Apr 04 2006 - 17:07:18 PDT)
RE: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding?
(Mon Apr 03 2006 - 16:53:06 PDT)
Sam
AMBER: mm_pbsa: "Missing values for MM ..."
(Fri Apr 21 2006 - 06:39:19 PDT)
Scott Brozell
Re: AMBER: amber7 compiling error
(Sun Apr 16 2006 - 12:30:23 PDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short
(Mon Apr 10 2006 - 07:59:46 PDT)
Scott Pendley
Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI”
(Wed Apr 26 2006 - 15:54:53 PDT)
Sergey Krishtal
Re[2]: AMBER: Could not find atom type.
(Tue Apr 18 2006 - 19:56:30 PDT)
Re[2]: AMBER: Could not find atom type.
(Tue Apr 18 2006 - 03:48:07 PDT)
AMBER: Could not find atom type.
(Mon Apr 17 2006 - 02:08:19 PDT)
AMBER: Saving single coordinate set from Amber trajectory file as a restrt file.
(Thu Apr 13 2006 - 20:05:45 PDT)
Shulin Zhuang
Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight
(Tue Apr 18 2006 - 22:58:06 PDT)
Simon Whitehead
RE: AMBER: RE: Respgen segemtation fault - debug attempt
(Thu Apr 20 2006 - 09:30:51 PDT)
RE: AMBER: RE: Respgen segemtation fault - debug attempt
(Thu Apr 20 2006 - 05:48:07 PDT)
Re: AMBER: RE: Respgen segemtation fault
(Thu Apr 20 2006 - 05:30:48 PDT)
AMBER: RE: Respgen segemtation fault
(Wed Apr 19 2006 - 10:10:11 PDT)
AMBER: Respgen segemtation fault
(Thu Apr 13 2006 - 09:38:41 PDT)
AMBER: dual xeon mpich compilation problem: sorted
(Thu Apr 13 2006 - 05:16:53 PDT)
AMBER: Dual Xeon mpich compilation error
(Thu Apr 13 2006 - 00:56:47 PDT)
AMBER: RESP problem
(Tue Apr 11 2006 - 06:44:00 PDT)
sishi.tang.utoronto.ca
Re: AMBER: MM-GBSA decomposition
(Sat Apr 15 2006 - 10:54:34 PDT)
AMBER: MM-GBSA decomposition
(Thu Apr 06 2006 - 13:20:36 PDT)
snowyowls
AMBER:a problem in parallel compiler
(Thu Apr 13 2006 - 01:15:09 PDT)
AMBER:a problem in parallel compiler
(Wed Apr 12 2006 - 21:27:10 PDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short
(Mon Apr 10 2006 - 20:07:40 PDT)
Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short
(Mon Apr 10 2006 - 20:09:35 PDT)
AMBER: PB bomb in pb_atmlist(): MAXNEI too short
(Mon Apr 10 2006 - 05:55:12 PDT)
snoze pa
Re: AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 11:48:55 PDT)
AMBER: ambpdb and original PDB
(Mon Apr 17 2006 - 11:20:05 PDT)
Supat Jiranusornkul
AMBER: 7-Methylguanine force field parameters
(Fri Apr 28 2006 - 07:13:55 PDT)
AMBER: 7-Methylguanine force field parameters
(Fri Apr 28 2006 - 07:03:22 PDT)
Thomas Cheatham
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 10:20:14 PDT)
Thomas E. Cheatham, III
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 09:01:50 PDT)
Re: AMBER: "average" command in ptraj
(Mon Apr 10 2006 - 11:06:20 PDT)
Thomas Patko (CSULB)
Re: AMBER: Announcement: Amber 9 is now available
(Sat Apr 01 2006 - 08:29:26 PST)
Thomas Steinbrecher
RE: AMBER: Test Failure during amber9 serial compilation
(Wed Apr 26 2006 - 02:23:24 PDT)
AMBER: Test Failure during amber9 serial compilation
(Tue Apr 25 2006 - 07:17:29 PDT)
AMBER: Problems compiling amber9
(Fri Apr 21 2006 - 07:27:51 PDT)
AMBER: Error when compiling amber9 ptraj
(Fri Apr 21 2006 - 01:19:54 PDT)
tonglei
AMBER: molsurf or LCPO method in MM_GB/SA?
(Tue Apr 04 2006 - 18:25:37 PDT)
AMBER: errors in mm_pbsa.in in AMBER 8 mannul ?
(Tue Apr 04 2006 - 06:10:59 PDT)
Varsha Goyal
RE: AMBER: rmsd value for organic molecule
(Mon Apr 24 2006 - 13:48:59 PDT)
AMBER: rmsd value for organic molecule
(Mon Apr 24 2006 - 12:00:20 PDT)
venditti2.unisi.it
Re: AMBER: PCA
(Mon Apr 10 2006 - 07:57:41 PDT)
AMBER: Umbrella sampling
(Fri Apr 07 2006 - 13:04:55 PDT)
AMBER: PCA
(Thu Apr 06 2006 - 13:27:20 PDT)
Vlad Cojocaru
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 10:01:27 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 09:30:23 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Fri Apr 14 2006 - 02:57:33 PDT)
Re: AMBER: Saving single coordinate set from Amber trajectory file as a restrt file.
(Fri Apr 14 2006 - 02:18:41 PDT)
Re: AMBER: Which one is the best force field for DNA?
(Thu Apr 13 2006 - 01:11:33 PDT)
Re: AMBER: VdW radii in the topology file
(Mon Apr 10 2006 - 10:01:33 PDT)
AMBER: VdW radii in the topology file
(Mon Apr 10 2006 - 09:14:16 PDT)
Re: AMBER: printing Amber VdW radii as separate column in pdb files
(Mon Apr 10 2006 - 08:43:18 PDT)
AMBER: printing Amber VdW radii as separate column in pdb files
(Mon Apr 10 2006 - 07:41:51 PDT)
Weihua Li
AMBER: questions about mm_pbsa
(Wed Apr 26 2006 - 20:09:45 PDT)
Wen Li
Re: AMBER: RMS (fwd)
(Tue Apr 04 2006 - 08:17:14 PDT)
Re: AMBER: RMS (fwd)
(Tue Apr 04 2006 - 08:02:02 PDT)
Re: AMBER: RMS
(Tue Apr 04 2006 - 06:59:04 PDT)
AMBER: RMS
(Mon Apr 03 2006 - 14:03:29 PDT)
xiaoqin huang
AMBER: POPC parameters
(Thu Apr 06 2006 - 20:18:10 PDT)
Xuebin Qiao
Re: AMBER: Using XML for Amber files
(Mon Apr 24 2006 - 20:57:47 PDT)
Re: AMBER: Using XML for Amber files
(Fri Apr 07 2006 - 10:52:08 PDT)
xyu3
AMBER: compile error: can't locate file for: -lcrt1.o
(Fri Apr 14 2006 - 15:37:50 PDT)
Ye Mei
AMBER: how to restrain the intramolecular hydrogen bond
(Tue Apr 04 2006 - 02:35:42 PDT)
Yong Duan
RE: AMBER: Could not find atom type.
(Mon Apr 17 2006 - 09:45:10 PDT)
Yu Zh.H.
AMBER: how to perform parallel MD on a linux cluster with Platform LSF product
(Fri Apr 28 2006 - 03:31:08 PDT)
Zhihong Yu
AMBER: Did these differences come from so-called "different machines" ?
(Sun Apr 30 2006 - 01:47:28 PDT)
杜永春
Re: AMBER: one question about mm_pbsa
(Thu Apr 13 2006 - 19:26:49 PDT)
AMBER: one question about mm_pbsa
(Thu Apr 13 2006 - 01:37:50 PDT)
AMBER: one question about mm_pbsa
(Tue Apr 04 2006 - 23:47:06 PDT)
Last message date
:
Wed May 03 2006 - 06:07:07 PDT
Archived on
: Sun Dec 01 2024 - 05:53:29 PST
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