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