Amber Archive May 2006 by author
414 messages
:
Starting
Wed May 03 2006 - 06:07:06 PDT,
Ending
Sun Jun 04 2006 - 06:07:09 PDT
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3Dsig06
AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil
(Mon May 22 2006 - 15:03:45 PDT)
a a
AMBER: ESP calculations.
(Tue May 30 2006 - 03:10:41 PDT)
AMBER: Antechamber : +ve charge species
(Tue May 30 2006 - 03:04:05 PDT)
AMBER: Pt containing complex: antechamber
(Sun May 28 2006 - 20:42:31 PDT)
AMBER: Pt containing complex: xleap
(Sun May 28 2006 - 20:30:48 PDT)
RE: AMBER: trajin and rms
(Wed May 24 2006 - 03:49:05 PDT)
RE: AMBER: trajin and rms
(Mon May 22 2006 - 01:55:03 PDT)
AMBER: trajin and rms
(Sun May 21 2006 - 21:18:37 PDT)
AMBER: xmgr error
(Fri May 19 2006 - 02:50:25 PDT)
AMBER: process_mdout.perl error
(Fri May 19 2006 - 02:35:20 PDT)
AMBER: Tutorial one : xaLeap command not found.
(Wed May 17 2006 - 03:12:53 PDT)
AMBER: Tutorial one : libsvml.so error
(Tue May 16 2006 - 23:01:26 PDT)
RE: AMBER: Amber install on RedHat Linux
(Thu May 04 2006 - 00:37:34 PDT)
AMBER: Amber install on RedHat Linux
(Wed May 03 2006 - 19:17:14 PDT)
Adam Pelzer
AMBER: RE: trouble stripping waters with ptraj
(Mon May 29 2006 - 15:20:23 PDT)
AMBER: RE: trouble stripping waters with ptraj
(Thu May 25 2006 - 21:50:53 PDT)
AMBER: RE: trouble stripping waters with ptraj
(Sat May 20 2006 - 09:00:12 PDT)
AMBER: trouble stripping waters with ptraj
(Tue May 16 2006 - 13:09:30 PDT)
Adrian Roitberg
Re: AMBER: question about QM/MM in amber9
(Thu May 25 2006 - 03:57:25 PDT)
aixiaoli
AMBER: question about QM/MM in amber9
(Thu May 25 2006 - 01:37:10 PDT)
AMBER: vlimit exceeded
(Thu May 18 2006 - 01:14:29 PDT)
alfredoq.fcq.unc.edu.ar
Re: AMBER: strange mm_pbsa output
(Sun May 14 2006 - 07:22:14 PDT)
Re: AMBER: strange mm_pbsa output
(Sat May 13 2006 - 13:43:53 PDT)
AMBER: strange mm_pbsa output
(Sat May 13 2006 - 08:44:58 PDT)
AMBER: About mm_pbsa calculation setting up
(Thu May 11 2006 - 19:19:03 PDT)
AMBER: Compiler with AMD 64 bit support
(Tue May 09 2006 - 10:10:30 PDT)
amit.mbu.iisc.ernet.in
AMBER: AMBER9 compilation error on IBM Cluster
(Mon May 15 2006 - 04:11:50 PDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Wed May 10 2006 - 00:06:46 PDT)
AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Tue May 09 2006 - 11:32:52 PDT)
AMBER: Amber9 test error on SGI Altix
(Mon May 08 2006 - 10:14:19 PDT)
Ananda Rama Krishnan Selvaraj
Re: AMBER: Please reply
(Fri May 26 2006 - 12:36:26 PDT)
Andrea Bortolato
AMBER: different TI calculations starting from the same state
(Fri May 26 2006 - 03:12:12 PDT)
AMBER: different TI calculations starting from the same state
(Fri May 26 2006 - 06:56:47 PDT)
Andreas Svrcek-Seiler
RE: AMBER: SHAKE, TIP3P and 2fs Timesteps
(Wed May 31 2006 - 11:38:29 PDT)
Re: AMBER: Problems compiling amber9
(Mon May 22 2006 - 12:01:09 PDT)
Re: AMBER: amber8 compiled erro on opteron with 64 bit
(Tue May 16 2006 - 03:53:14 PDT)
Andrew Box
AMBER: Shared libraries error
(Tue May 02 2006 - 20:14:38 PDT)
Andy Purkiss
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names
(Tue May 30 2006 - 11:18:58 PDT)
Arvind Marathe
AMBER: amber9 serial compilation error
(Thu May 04 2006 - 09:55:39 PDT)
Asim Okur
Re: AMBER: RE: trouble stripping waters with ptraj
(Mon May 22 2006 - 09:49:46 PDT)
Re: AMBER: trouble stripping waters with ptraj
(Tue May 16 2006 - 13:17:32 PDT)
Atro Tossavainen
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system
(Mon May 08 2006 - 04:48:29 PDT)
Atsutoshi Okabe
AMBER: Replica exchage: about exchange interval
(Wed May 31 2006 - 05:36:27 PDT)
RE: AMBER: A dummy atom on the center of solute molecule
(Sun May 28 2006 - 22:51:49 PDT)
RE: AMBER: A dummy atom on the center of solute molecule
(Tue May 23 2006 - 18:46:35 PDT)
AMBER: A dummy atom on the center of solute molecule
(Mon May 22 2006 - 04:49:23 PDT)
AMBER: "The system has extended beyond" error message
(Wed May 17 2006 - 22:04:31 PDT)
bala
AMBER: question on distance calculation
(Mon May 08 2006 - 03:09:23 PDT)
AMBER: carnal prob
(Thu May 04 2006 - 00:44:53 PDT)
BAUVAIS.itodys.jussieu.fr
AMBER: "atom number exceeds the MAXATOM"
(Tue May 16 2006 - 22:54:24 PDT)
Bill Ross
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names
(Mon May 29 2006 - 13:26:56 PDT)
Re: AMBER: use_pme=0 problem
(Fri May 26 2006 - 13:32:35 PDT)
Re: AMBER: amber .off file format question
(Mon May 22 2006 - 11:17:26 PDT)
Re: AMBER: carnal prob
(Thu May 04 2006 - 10:31:22 PDT)
Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files]
(Wed May 03 2006 - 15:00:58 PDT)
Re: AMBER: Question bonds and angles in frcmod and lib files
(Wed May 03 2006 - 09:28:08 PDT)
Biswa Ranjan Meher
AMBER: Different results for TI calculation
(Wed May 31 2006 - 00:25:13 PDT)
brmeher.iitg.ernet.in
AMBER: Difference in results for TI calculation
(Mon May 29 2006 - 07:23:45 PDT)
AMBER: Difference in results for TI calculation
(Mon May 29 2006 - 06:53:41 PDT)
Carlos Simmerling
Re: AMBER: Replica exchage: about exchange interval
(Wed May 31 2006 - 06:02:32 PDT)
Re: AMBER: which time should I use to calculate the number of "ps/Day"
(Mon May 29 2006 - 02:50:31 PDT)
Re: AMBER: md error : sander
(Sun May 28 2006 - 13:06:21 PDT)
Re: AMBER: Saving RMSD values in VMD
(Fri May 26 2006 - 08:45:17 PDT)
Re: AMBER: RMSd error
(Fri May 26 2006 - 05:58:42 PDT)
Re: AMBER: RMSd error
(Fri May 26 2006 - 04:27:18 PDT)
Re: AMBER: RE: trouble stripping waters with ptraj
(Fri May 26 2006 - 04:28:35 PDT)
Re: AMBER: alpha helix preference problem
(Thu May 25 2006 - 18:35:10 PDT)
Re: AMBER: RMSd error
(Mon May 22 2006 - 05:02:02 PDT)
Re: AMBER: trajin and rms
(Mon May 22 2006 - 04:58:04 PDT)
Re: AMBER: RE: trouble stripping waters with ptraj
(Sat May 20 2006 - 10:10:24 PDT)
Re: AMBER: Fw: RMSd calculations
(Fri May 19 2006 - 06:00:50 PDT)
Re: AMBER: fail to execute addles
(Tue May 16 2006 - 06:47:37 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 09:59:29 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 05:43:31 PDT)
Re: AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 04:50:37 PDT)
Re: AMBER: proper restart procedure?
(Wed May 03 2006 - 04:48:25 PDT)
Re: AMBER: Amber 9, sander imin = 5, -y flag
(Mon May 01 2006 - 06:35:56 PDT)
Claire Zerafa
Re: AMBER: RMSd error
(Sun May 28 2006 - 09:26:14 PDT)
Re: AMBER: RMSd error
(Fri May 26 2006 - 06:30:57 PDT)
Re: AMBER: RMSd error
(Fri May 26 2006 - 05:26:06 PDT)
AMBER: RMSd error
(Thu May 25 2006 - 21:37:54 PDT)
AMBER: RMSd error
(Mon May 22 2006 - 01:52:34 PDT)
AMBER: Fw: RMSd calculations
(Fri May 19 2006 - 05:07:30 PDT)
AMBER: RMSd calculations
(Thu May 18 2006 - 12:25:57 PDT)
Craig Gough
AMBER: Correlation matrix used in quasih (Amber 7)
(Thu May 18 2006 - 00:06:03 PDT)
darden
Re: AMBER: Force units in forcedump.dat
(Wed May 31 2006 - 10:53:34 PDT)
David A. Case
Re: AMBER: Difference in results for TI calculation
(Tue May 30 2006 - 11:01:49 PDT)
Re: AMBER: Pt containing complex: antechamber
(Tue May 30 2006 - 10:39:20 PDT)
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names
(Tue May 30 2006 - 10:36:37 PDT)
Re: AMBER: Installing / Compiling Question
(Sat May 27 2006 - 21:50:54 PDT)
Re: AMBER: Please reply
(Fri May 26 2006 - 12:39:02 PDT)
Re: AMBER: use_pme=0 problem
(Fri May 26 2006 - 12:30:01 PDT)
Re: AMBER: use_pme=0 problem
(Fri May 26 2006 - 10:34:39 PDT)
Re: AMBER: different TI calculations starting from the same state
(Fri May 26 2006 - 08:16:19 PDT)
Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
(Thu May 25 2006 - 13:33:33 PDT)
Re: AMBER: use_pme=0 problem
(Thu May 25 2006 - 10:56:56 PDT)
Re: AMBER: use_pme=0 problem
(Wed May 24 2006 - 17:33:53 PDT)
Re: AMBER: use_pme=0 problem
(Wed May 24 2006 - 16:50:56 PDT)
Re: AMBER: problem with prepfile
(Wed May 24 2006 - 13:56:08 PDT)
Re: AMBER: freeze interval vibrations
(Wed May 24 2006 - 12:00:35 PDT)
Re: AMBER: amber8 bugfix effects
(Wed May 24 2006 - 07:38:39 PDT)
Re: AMBER: error in AMBER 9.0
(Tue May 23 2006 - 22:19:47 PDT)
Re: AMBER: amber .off file format question
(Mon May 22 2006 - 23:21:33 PDT)
Re: AMBER: Problems compiling amber9
(Mon May 22 2006 - 11:46:09 PDT)
Re: AMBER: problem loading forcefield leaprc.ff86
(Fri May 19 2006 - 08:45:33 PDT)
Re: AMBER: "The system has extended beyond" error message
(Thu May 18 2006 - 05:38:58 PDT)
Re: AMBER: Correlation matrix used in quasih (Amber 7)
(Thu May 18 2006 - 05:31:00 PDT)
Re: AMBER: vlimit exceeded
(Thu May 18 2006 - 05:24:49 PDT)
Re: AMBER: distance dependent dielectric constant
(Wed May 17 2006 - 04:59:41 PDT)
Re: AMBER: "atom number exceeds the MAXATOM"
(Wed May 17 2006 - 04:53:58 PDT)
Re: AMBER: amber compilation on Red Hat 8 with MPICH
(Wed May 17 2006 - 04:52:55 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 09:46:28 PDT)
Re: AMBER: strange mm_pbsa output
(Sat May 13 2006 - 15:44:14 PDT)
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
(Fri May 12 2006 - 10:01:05 PDT)
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
(Fri May 12 2006 - 08:39:37 PDT)
Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?
(Thu May 11 2006 - 07:43:28 PDT)
Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why
(Wed May 10 2006 - 13:12:52 PDT)
Re: AMBER: problem with prep file
(Wed May 10 2006 - 09:12:59 PDT)
Re: AMBER: Hexahydrated Counterions
(Wed May 10 2006 - 08:32:31 PDT)
Re: AMBER: bug in ambpdb (AMBER8)
(Wed May 10 2006 - 08:10:08 PDT)
Re: AMBER: xleap not recognizing residue
(Tue May 09 2006 - 15:42:14 PDT)
Re: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Tue May 09 2006 - 13:16:30 PDT)
Re: AMBER: Amber9 test error on SGI Altix
(Mon May 08 2006 - 11:45:30 PDT)
Re: AMBER: Amber9 test error on SGI Altix
(Mon May 08 2006 - 11:07:17 PDT)
Re: AMBER: xleap not recognizing residue
(Sun May 07 2006 - 18:50:06 PDT)
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system
(Sun May 07 2006 - 07:27:56 PDT)
Re: AMBER: Problem with shared libraries: libimf.so
(Sat May 06 2006 - 14:17:51 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 18:31:13 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 12:19:31 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 11:46:29 PDT)
Re: AMBER: molsurf.c error
(Fri May 05 2006 - 10:34:32 PDT)
Re: AMBER: molsurf.c error
(Thu May 04 2006 - 13:21:28 PDT)
Re: AMBER: amber9 serial compilation error
(Thu May 04 2006 - 10:36:53 PDT)
Re: AMBER: Amber install on RedHat Linux
(Thu May 04 2006 - 08:17:08 PDT)
Re: AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 23:13:06 PDT)
Re: AMBER: Question bonds and angles in frcmod and lib files
(Wed May 03 2006 - 08:23:12 PDT)
Re: AMBER: proper restart procedure?
(Wed May 03 2006 - 08:18:43 PDT)
Re: AMBER: How does amber calculate HB?
(Mon May 01 2006 - 23:20:31 PDT)
AMBER: some new tutorials
(Mon May 01 2006 - 16:55:19 PDT)
Re: AMBER: internal coordinates
(Mon May 01 2006 - 13:50:10 PDT)
David Mobley
Re: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7
(Fri May 12 2006 - 10:22:41 PDT)
DAVID P. RANGEL
AMBER: Installation of Amber8 on Fedora Core 5
(Wed May 31 2006 - 15:48:11 PDT)
Don Harden
Re: AMBER: Problems compiling amber9
(Tue May 23 2006 - 12:45:02 PDT)
Re: AMBER: Problems compiling amber9
(Mon May 22 2006 - 10:10:15 PDT)
Douali, Latifa
RE: AMBER: xmgr error
(Fri May 19 2006 - 10:07:01 PDT)
RE: AMBER: force field parameters
(Thu May 18 2006 - 11:40:53 PDT)
AMBER: force field parameters
(Thu May 18 2006 - 10:33:35 PDT)
Eric Hu
AMBER: freeze interval vibrations
(Wed May 24 2006 - 10:52:47 PDT)
Evan Kelly
AMBER: xleap on iMac G5
(Fri May 05 2006 - 21:01:53 PDT)
FyD
Re: AMBER: ESP calculations.
(Tue May 30 2006 - 04:15:31 PDT)
Re: AMBER: Qestion about input for RESP program
(Thu May 25 2006 - 08:53:28 PDT)
Re: AMBER: Fwd: RESP for deprotonated tyrosine and lysine
(Thu May 25 2006 - 01:26:15 PDT)
Re: AMBER: Qestion about input for RESP program
(Thu May 25 2006 - 01:22:13 PDT)
Re: AMBER: output of first stage RESP calculation
(Thu May 25 2006 - 01:12:12 PDT)
Re: AMBER: question about REDII
(Thu May 11 2006 - 23:34:48 PDT)
german
Re: AMBER: "The system has extended beyond" error message
(Thu May 18 2006 - 05:27:42 PDT)
Hall, Spencer
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
(Tue May 23 2006 - 14:15:12 PDT)
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
(Tue May 23 2006 - 14:15:08 PDT)
AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
(Thu May 18 2006 - 15:44:14 PDT)
Hannes Loeffler
AMBER: which patch for ioutfm = 1 in Amber8?
(Wed May 10 2006 - 22:21:25 PDT)
harianto
Re: AMBER: alpha helix preference problem
(Fri May 26 2006 - 07:04:30 PDT)
AMBER: alpha helix preference problem
(Thu May 25 2006 - 14:16:23 PDT)
hayden
AMBER: 1st 2 lines of restart files
(Thu May 25 2006 - 04:40:03 PDT)
heaton.chem.utah.edu
RE: AMBER: Problem with running xleap remotely
(Sat May 20 2006 - 13:43:53 PDT)
AMBER: Problem with running xleap remotely
(Sat May 20 2006 - 12:20:27 PDT)
Holly Freedman
Re: AMBER: question about group format
(Thu May 04 2006 - 16:16:22 PDT)
AMBER: question about group format
(Wed May 03 2006 - 12:18:36 PDT)
homeira amirkhani
AMBER: San Fransisco Amber users
(Tue May 09 2006 - 04:38:06 PDT)
Hui Lei
AMBER: simulate proteins with non-standard residues
(Wed May 24 2006 - 10:10:08 PDT)
ian gould
Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 00:35:12 PDT)
Ilyas Yildirim
RE: AMBER: A dummy atom on the center of solute molecule
(Tue May 30 2006 - 16:06:54 PDT)
Re: AMBER: Thermodynamic integration using the amber 9
(Mon May 29 2006 - 07:25:21 PDT)
RE: AMBER: A dummy atom on the center of solute molecule
(Sun May 28 2006 - 21:26:33 PDT)
Re: AMBER: Pt containing complex: xleap
(Sun May 28 2006 - 21:00:08 PDT)
Re: AMBER: Question about .off file
(Fri May 26 2006 - 01:58:19 PDT)
Re: AMBER: Qestion about input for RESP program
(Wed May 24 2006 - 21:49:11 PDT)
RE: AMBER: A dummy atom on the center of solute molecule
(Tue May 23 2006 - 19:49:00 PDT)
Re: AMBER: amber .off file format question
(Mon May 22 2006 - 22:53:19 PDT)
Re: AMBER: A dummy atom on the center of solute molecule
(Mon May 22 2006 - 04:58:24 PDT)
Re: AMBER: amber .off file format question
(Mon May 22 2006 - 02:16:39 PDT)
AMBER: amber .off file format question
(Fri May 19 2006 - 19:30:55 PDT)
AMBER: AMBER 8 - dihedral angles when clambda=1
(Thu May 11 2006 - 21:57:37 PDT)
In Hee Park
AMBER: sequential execution of number of parallel jobs
(Mon May 01 2006 - 13:13:23 PDT)
Ioana Cozmuta
Re: AMBER: internal coordinates
(Tue May 02 2006 - 11:01:45 PDT)
JAVIER PEREZ
AMBER: energy terms
(Mon May 29 2006 - 08:25:31 PDT)
AMBER: problems with antechamber
(Mon May 29 2006 - 08:04:52 PDT)
Jennie Thomas
Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files]
(Thu May 04 2006 - 15:45:21 PDT)
[Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files]
(Wed May 03 2006 - 14:49:19 PDT)
Re: AMBER: Question bonds and angles in frcmod and lib files
(Wed May 03 2006 - 10:26:55 PDT)
Re: AMBER: Question bonds and angles in frcmod and lib files
(Wed May 03 2006 - 08:54:43 PDT)
AMBER: Question bonds and angles in frcmod and lib files
(Wed May 03 2006 - 01:02:55 PDT)
AMBER: Simulation of crystal - problem with excluded atom list
(Tue May 02 2006 - 10:07:20 PDT)
Jianyin Shao
Re: AMBER: error propagation in MM-PBSA binding free energy calculation
(Mon May 01 2006 - 10:17:04 PDT)
Jiayun Pang
AMBER: SAVEPDB in Xleap could not save 4 character atom names
(Mon May 29 2006 - 09:38:22 PDT)
Jim Paugh
AMBER: Opteron vs. Xeon performance
(Thu May 11 2006 - 11:47:42 PDT)
jitrayut jitonnom
AMBER: md error : sander
(Sun May 28 2006 - 11:11:45 PDT)
AMBER: check as error: load prepin in tleap
(Fri May 26 2006 - 10:13:41 PDT)
AMBER: How to build NH2 of amino acid in amber
(Wed May 24 2006 - 20:52:25 PDT)
AMBER: Fwd: RESP for deprotonated tyrosine and lysine
(Wed May 24 2006 - 19:57:45 PDT)
AMBER: How to built the deprotonated form of lysine and tyrosine
(Wed May 24 2006 - 19:49:04 PDT)
John J. Love
AMBER: proper restart procedure?
(Tue May 02 2006 - 20:33:57 PDT)
Joseph Fernandez
RE: AMBER: Amber9/mpich2 performance
(Fri May 12 2006 - 18:09:20 PDT)
AMBER: Amber9/mpich2 performance
(Thu May 11 2006 - 15:30:03 PDT)
AMBER: PMEMD compilation error
(Mon May 08 2006 - 12:37:03 PDT)
AMBER: restraintmask
(Thu May 04 2006 - 11:22:21 PDT)
JunJun Liu
Re: AMBER: Qestion about input for RESP program
(Thu May 25 2006 - 07:01:41 PDT)
AMBER: Qestion about input for RESP program
(Wed May 24 2006 - 19:44:41 PDT)
AMBER: output of first stage RESP calculation
(Wed May 24 2006 - 15:23:55 PDT)
Junmei Wang
RE: AMBER: Antechamber : +ve charge species
(Tue May 30 2006 - 08:31:07 PDT)
RE: AMBER: problems with antechamber
(Tue May 30 2006 - 08:20:33 PDT)
RE: AMBER: problem with prepfile
(Thu May 25 2006 - 09:24:51 PDT)
RE: AMBER: problem with prep file
(Mon May 15 2006 - 14:10:53 PDT)
K. Yarem
AMBER: conflicting types for XawScrolledTableSetLocation
(Thu May 04 2006 - 08:43:57 PDT)
Kateryna Miroshnychenko
AMBER: cluster architecture for the best amber performance
(Wed May 03 2006 - 05:54:58 PDT)
kawamura_hiro.riken.jp
AMBER: amber8 bugfix effects
(Wed May 24 2006 - 01:17:32 PDT)
AMBER: amber compilation on Red Hat 8 with MPICH
(Tue May 16 2006 - 22:38:35 PDT)
Ken Merz
Re: AMBER: ESP calculations.
(Tue May 30 2006 - 04:59:38 PDT)
Re: AMBER: ESP calculations.
(Tue May 30 2006 - 04:55:24 PDT)
Kenley Barrett
AMBER: problem with installation, or bug?
(Thu May 18 2006 - 03:09:10 PDT)
AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed
(Wed May 10 2006 - 13:04:16 PDT)
Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why
(Wed May 10 2006 - 12:54:46 PDT)
Re: AMBER: xleap not recognizing residue
(Mon May 08 2006 - 10:04:37 PDT)
AMBER: xleap not recognizing residue
(Sun May 07 2006 - 17:13:13 PDT)
AMBER: concatenating .mdcrd files
(Wed May 03 2006 - 09:31:59 PDT)
Kerry P Donny-Clark
AMBER: Trouble with ptraj closestwater in Amber8
(Thu May 04 2006 - 10:29:23 PDT)
Li Su
AMBER: How does amber calculate HB?
(Mon May 01 2006 - 18:01:05 PDT)
linfu
Re: AMBER: problems with antechamber
(Tue May 30 2006 - 05:01:59 PDT)
lucas luquitas
AMBER: Again SASA
(Mon May 22 2006 - 12:51:22 PDT)
luckyang.gmail.com
Re: AMBER: use_pme=0 problem
(Fri May 26 2006 - 13:19:11 PDT)
Re: AMBER: use_pme=0 problem
(Fri May 26 2006 - 12:10:19 PDT)
Re: AMBER: use_pme=0 problem
(Thu May 25 2006 - 18:56:30 PDT)
Re: AMBER: use_pme=0 problem
(Thu May 25 2006 - 10:09:59 PDT)
Re: AMBER: use_pme=0 problem
(Wed May 24 2006 - 17:51:10 PDT)
Re: AMBER: use_pme=0 problem
(Wed May 24 2006 - 17:20:35 PDT)
AMBER: use_pme=0 problem
(Wed May 24 2006 - 16:18:47 PDT)
Lwin, ThuZar
AMBER: lipid bi-layer system
(Thu May 04 2006 - 10:41:11 PDT)
M. L. Dodson
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 19:34:07 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 15:00:10 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 11:59:48 PDT)
AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 11:37:19 PDT)
Magne Olufsen
AMBER: ptraj: calculating distances between atoms in charges residues
(Fri May 26 2006 - 00:13:48 PDT)
Mahalakshmi Sahasranaman
AMBER: problem loading forcefield leaprc.ff86
(Fri May 19 2006 - 07:27:38 PDT)
AMBER: distance dependent dielectric constant
(Wed May 17 2006 - 03:36:55 PDT)
AMBER: installation problem
(Mon May 15 2006 - 11:12:51 PDT)
AMBER: Hexahydrated Counterions
(Wed May 10 2006 - 06:22:02 PDT)
Mark Williamson
AMBER: SHAKE, TIP3P and 2fs Timesteps
(Wed May 31 2006 - 10:32:56 PDT)
Re: AMBER: Tutorial one : libsvml.so error
(Wed May 17 2006 - 00:27:05 PDT)
mathew k varghese
Re: AMBER: xmgr error
(Fri May 19 2006 - 03:54:00 PDT)
RE: AMBER: density
(Wed May 17 2006 - 20:24:07 PDT)
RE: AMBER: density
(Tue May 16 2006 - 21:09:17 PDT)
AMBER: density
(Mon May 15 2006 - 21:02:51 PDT)
Mengjuei Hsieh
Re: AMBER: AMBER9: MacG5 parallel sander.MPI
(Sun May 07 2006 - 07:33:01 PDT)
Re: AMBER: xleap on iMac G5
(Fri May 05 2006 - 22:44:00 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 19:05:41 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 17:30:16 PDT)
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 17:24:30 PDT)
Re: AMBER: AMBER9: MacG5 parallel sander.MPI
(Wed May 03 2006 - 17:32:14 PDT)
Michael Crowley
Re: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
(Mon May 22 2006 - 11:28:58 PDT)
Miguel Ferreira
Re: AMBER: molsurf.c error
(Fri May 05 2006 - 04:46:24 PDT)
RE: AMBER: molsurf.c error
(Thu May 04 2006 - 12:43:41 PDT)
AMBER: molsurf.c error
(Thu May 04 2006 - 09:00:31 PDT)
mkseo
AMBER: error in AMBER 9.0
(Tue May 23 2006 - 14:43:28 PDT)
Re: AMBER: MPI parallel problem in AMBER 8.0
(Tue May 02 2006 - 15:14:16 PDT)
AMBER: MPI parallel problem in AMBER 8.0
(Tue May 02 2006 - 14:21:50 PDT)
AMBER: distance restraints
(Mon May 01 2006 - 14:49:21 PDT)
nadiav.soton.ac.uk
Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
(Fri May 12 2006 - 09:00:21 PDT)
nag raj
AMBER: Saving RMSD values in VMD
(Fri May 26 2006 - 07:33:00 PDT)
Navnit Kumar Mishra
AMBER: Water density output
(Mon May 22 2006 - 04:02:48 PDT)
Re: AMBER: force field parameters
(Fri May 19 2006 - 04:01:59 PDT)
Re: AMBER: force field parameters
(Thu May 18 2006 - 11:21:59 PDT)
Re: AMBER: bond information in amber
(Thu May 11 2006 - 23:28:00 PDT)
Re: AMBER: bond information in amber
(Thu May 11 2006 - 10:25:10 PDT)
opitz.che.udel.edu
AMBER: Macromodel Amber* vs. Amber7
(Mon May 22 2006 - 05:56:54 PDT)
Osmar Norberto de Souza
AMBER: Problem with "impose" in leap
(Mon May 15 2006 - 04:27:13 PDT)
[Fwd: AMBER: Problem with impose in lep]
(Wed May 10 2006 - 10:09:48 PDT)
AMBER: Problem with impose in lep
(Mon May 08 2006 - 10:31:16 PDT)
Pan, Yongmei
AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
(Fri May 12 2006 - 08:22:00 PDT)
AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7
(Thu May 11 2006 - 11:50:36 PDT)
AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?
(Thu May 11 2006 - 07:13:02 PDT)
pang zhao
Re: AMBER: fail to execute addles
(Tue May 16 2006 - 07:42:36 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 23:39:28 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 23:17:05 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 23:13:21 PDT)
Re: AMBER: fail to execute addles
(Mon May 15 2006 - 07:31:19 PDT)
AMBER: fail to execute addles
(Mon May 15 2006 - 04:59:10 PDT)
Petr Kulhanek
AMBER: bug in ambpdb (AMBER8)
(Wed May 10 2006 - 03:54:55 PDT)
Re: AMBER: sequential execution of number of parallel jobs
(Tue May 02 2006 - 01:20:51 PDT)
pkb bioinfo
AMBER: antechamber help needed for FAD
(Mon May 29 2006 - 02:38:48 PDT)
Pradipta Bandyopadhyay
RE: AMBER: ff02 + POL3 problem !
(Tue May 16 2006 - 07:08:03 PDT)
AMBER: ff02 + POL3 problem !
(Mon May 15 2006 - 06:53:20 PDT)
AMBER: Compilers and libraries for AMBER in HPC!
(Sun May 14 2006 - 06:25:07 PDT)
Priti Hansia
RE: AMBER: RE: Intel Compiler.
(Wed May 10 2006 - 08:39:04 PDT)
AMBER: RE: Intel Compiler.
(Tue May 09 2006 - 10:12:18 PDT)
AMBER: Amber9 test error on SGI Altix
(Tue May 09 2006 - 08:18:02 PDT)
Re: AMBER: Intel compiler version 9.0.033
(Mon May 08 2006 - 12:55:37 PDT)
Re: AMBER: Problem with shared libraries: libimf.so
(Sat May 06 2006 - 22:40:49 PDT)
RE: AMBER: Problem with shared libraries: libimf.so
(Sat May 06 2006 - 00:01:51 PDT)
RE: AMBER: Problem with shared libraries: libimf.so
(Fri May 05 2006 - 11:39:50 PDT)
AMBER: Problem with shared libraries: libimf.so
(Fri May 05 2006 - 10:55:39 PDT)
Re: AMBER: Error while running test.serial in Amber9
(Thu May 04 2006 - 08:48:36 PDT)
RE: AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 22:08:02 PDT)
Re: AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 05:02:04 PDT)
AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 04:03:27 PDT)
Raffaella D'Auria
Re: AMBER: question about REDII
(Fri May 12 2006 - 12:12:41 PDT)
AMBER: question about REDII
(Thu May 11 2006 - 19:04:51 PDT)
Ray Luo
Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
(Wed May 24 2006 - 16:14:33 PDT)
Re: AMBER: strange mm_pbsa output
(Fri May 12 2006 - 17:22:57 PDT)
Re: AMBER: Amber9 test error on SGI Altix
(Tue May 09 2006 - 05:57:57 PDT)
renyanliang
AMBER: amber8 compiled erro on opteron with 64 bit
(Tue May 16 2006 - 02:15:24 PDT)
Robert Duke
Re: AMBER: which time should I use to calculate the number of "ps/Day"
(Mon May 29 2006 - 06:10:04 PDT)
AMBER: More Amber 9 Benchmarks available
(Mon May 22 2006 - 07:23:15 PDT)
Re: AMBER: RE: PMEMD compilation problems
(Fri May 19 2006 - 09:20:52 PDT)
Re: AMBER: Intel fortran compiler 7?
(Fri May 19 2006 - 04:59:43 PDT)
Re: AMBER: installation problem
(Mon May 15 2006 - 11:25:53 PDT)
Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 08:24:43 PDT)
Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 05:46:08 PDT)
Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 05:29:14 PDT)
Re: AMBER: Opteron vs. Xeon performance
(Thu May 11 2006 - 19:02:10 PDT)
Re: AMBER: Amber9 test error on SGI Altix
(Tue May 09 2006 - 09:06:19 PDT)
Re: AMBER: PMEMD compilation error
(Mon May 08 2006 - 13:18:05 PDT)
Re: AMBER: cluster architecture for the best amber performance
(Wed May 03 2006 - 10:05:57 PDT)
Ross Walker
RE: AMBER: SHAKE, TIP3P and 2fs Timesteps
(Wed May 31 2006 - 10:56:31 PDT)
RE: AMBER: Installing / Compiling Question
(Sat May 27 2006 - 22:12:46 PDT)
RE: AMBER: Saving RMSD values in VMD
(Fri May 26 2006 - 08:27:08 PDT)
RE: AMBER: alpha helix preference problem
(Fri May 26 2006 - 08:23:27 PDT)
RE: AMBER: question about QM/MM in amber9
(Thu May 25 2006 - 08:33:17 PDT)
RE: AMBER: trajin and rms
(Sun May 21 2006 - 21:43:09 PDT)
RE: AMBER: Problem with running xleap remotely
(Sat May 20 2006 - 12:37:35 PDT)
RE: AMBER: process_mdout.perl error
(Fri May 19 2006 - 07:43:25 PDT)
RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
(Thu May 18 2006 - 16:37:30 PDT)
RE: AMBER: AMBER9 installation error on Compaq machine.
(Thu May 18 2006 - 15:32:57 PDT)
RE: AMBER: density
(Wed May 17 2006 - 21:11:11 PDT)
RE: AMBER: Tutorial one : xaLeap command not found.
(Wed May 17 2006 - 08:40:12 PDT)
RE: AMBER: amber compilation on Red Hat 8 with MPICH
(Wed May 17 2006 - 08:35:00 PDT)
RE: AMBER: density
(Wed May 17 2006 - 08:31:20 PDT)
RE: AMBER: AMBER9 compilation error on IBM Cluster
(Mon May 15 2006 - 20:28:12 PDT)
RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs
(Sun May 14 2006 - 22:13:01 PDT)
RE: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 08:13:48 PDT)
RE: AMBER: Opteron vs. Xeon performance
(Thu May 11 2006 - 16:17:12 PDT)
RE: AMBER: Amber9/mpich2 performance
(Thu May 11 2006 - 16:07:21 PDT)
RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Tue May 09 2006 - 12:12:09 PDT)
RE: AMBER: RE: Intel Compiler.
(Tue May 09 2006 - 10:21:43 PDT)
RE: AMBER: Compiler with AMD 64 bit support
(Tue May 09 2006 - 10:19:18 PDT)
AMBER: RE: Intel Compiler.
(Tue May 09 2006 - 09:05:28 PDT)
AMBER: Intel compiler version 9.0.033
(Mon May 08 2006 - 12:40:23 PDT)
AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
(Mon May 08 2006 - 11:13:11 PDT)
RE: AMBER: AMBER9 INSTALLATION problem on O2 sgi system
(Mon May 08 2006 - 08:17:55 PDT)
RE: AMBER: Problem with shared libraries: libimf.so
(Sun May 07 2006 - 09:10:54 PDT)
RE: AMBER: Problem with shared libraries: libimf.so
(Fri May 05 2006 - 14:08:31 PDT)
RE: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 14:10:51 PDT)
RE: AMBER: Problem with shared libraries: libimf.so
(Fri May 05 2006 - 11:04:10 PDT)
RE: AMBER: molsurf.c error
(Thu May 04 2006 - 09:28:49 PDT)
RE: AMBER: Amber install on RedHat Linux
(Thu May 04 2006 - 08:31:56 PDT)
RE: AMBER: Amber install on RedHat Linux
(Wed May 03 2006 - 19:36:45 PDT)
RE: AMBER: concatenating .mdcrd files
(Wed May 03 2006 - 09:39:11 PDT)
RE: AMBER: cluster architecture for the best amber performance
(Wed May 03 2006 - 08:42:19 PDT)
RE: AMBER: Error while running test.serial in Amber9
(Wed May 03 2006 - 08:21:42 PDT)
RE: AMBER: Shared libraries error
(Wed May 03 2006 - 08:13:32 PDT)
RE: AMBER: MPI parallel problem in AMBER 8.0
(Tue May 02 2006 - 15:40:37 PDT)
RE: AMBER: MPI parallel problem in AMBER 8.0
(Tue May 02 2006 - 14:42:33 PDT)
AMBER: AMBER Workshops, London UK 26th - 30th June 2006
(Tue May 02 2006 - 08:45:33 PDT)
S.Sundar Raman
Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system
(Mon May 08 2006 - 04:33:58 PDT)
AMBER: AMBER9 INSTALLATION problem on O2 sgi system
(Sun May 07 2006 - 00:10:15 PDT)
Sergey Krishtal
AMBER: Question about .off file
(Fri May 26 2006 - 01:15:06 PDT)
Sergio Dall'Angelo
Re: AMBER: Xleap compilation problem
(Fri May 12 2006 - 08:21:02 PDT)
AMBER: Xleap compilation problem
(Fri May 12 2006 - 03:19:48 PDT)
AMBER: Xleap compilation problem
(Fri May 12 2006 - 02:49:16 PDT)
Seth Lilavivat
AMBER: Installing / Compiling Question
(Fri May 26 2006 - 20:29:06 PDT)
Shafinaz
AMBER: Please reply
(Fri May 26 2006 - 12:19:42 PDT)
AMBER: problem with prepfile
(Wed May 24 2006 - 12:50:21 PDT)
Simon Whitehead
AMBER: RE: PMEMD compilation problems
(Fri May 19 2006 - 08:37:46 PDT)
AMBER: Intel fortran compiler 7?
(Fri May 19 2006 - 02:47:55 PDT)
AMBER: problem with prep file
(Wed May 10 2006 - 03:52:32 PDT)
snoze pa
Re: AMBER: AMBER mdcrd file bigger than 2GB
(Wed May 31 2006 - 16:04:53 PDT)
AMBER: AMBER mdcrd file bigger than 2GB
(Wed May 31 2006 - 14:57:22 PDT)
Re: AMBER: bond information in amber
(Thu May 11 2006 - 12:16:56 PDT)
Re: AMBER: bond information in amber
(Thu May 11 2006 - 11:41:00 PDT)
Re: AMBER: bond information in amber
(Thu May 11 2006 - 11:36:18 PDT)
AMBER: bond information in amber
(Thu May 11 2006 - 09:48:58 PDT)
Soonmin Jang
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
(Thu May 25 2006 - 03:51:02 PDT)
AMBER: AMBER9 installation error on Compaq machine.
(Thu May 18 2006 - 00:11:46 PDT)
Stefan Henrich
AMBER: RMSD calculation between ligands
(Fri May 12 2006 - 05:09:15 PDT)
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
Re: AMBER: carnal prob
(Thu May 04 2006 - 00:58:18 PDT)
Stern, Julie
AMBER: PBS script for lemieux
(Sun May 14 2006 - 16:09:30 PDT)
Steve Gwaltney
AMBER: OT: software to support AMBER?
(Thu May 18 2006 - 11:37:06 PDT)
Steven Winfield
AMBER: Namelists in input files
(Wed May 31 2006 - 09:42:05 PDT)
AMBER: Force units in forcedump.dat
(Wed May 31 2006 - 06:41:43 PDT)
Re: AMBER: 1st 2 lines of restart files
(Thu May 25 2006 - 04:50:18 PDT)
Thomas Cheatham
Re: AMBER: AMBER mdcrd file bigger than 2GB
(Wed May 31 2006 - 16:27:16 PDT)
Re: [UCE]AMBER: RE: trouble stripping waters with ptraj
(Tue May 30 2006 - 10:17:31 PDT)
Re: AMBER: ptraj: calculating distances between atoms in charges residues
(Fri May 26 2006 - 09:12:40 PDT)
Re: [UCE]AMBER: RE: trouble stripping waters with ptraj
(Fri May 26 2006 - 09:04:22 PDT)
Re: AMBER: RMSd error
(Fri May 26 2006 - 08:59:34 PDT)
Thomas Pochapsky
AMBER: xleap problem and answer
(Wed May 31 2006 - 11:32:32 PDT)
Varsha Goyal
AMBER: binpos file
(Fri May 12 2006 - 13:46:24 PDT)
Viktor Hornak
Re: AMBER: Shared libraries error
(Thu May 04 2006 - 11:54:26 PDT)
Re: AMBER: question about group format
(Thu May 04 2006 - 11:49:20 PDT)
Re: AMBER: restraintmask
(Thu May 04 2006 - 11:41:37 PDT)
Vitor Manuel Sousa F?x
AMBER: Thermodynamic integration using the amber 9
(Mon May 29 2006 - 06:41:14 PDT)
wang
AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format
(Mon May 08 2006 - 23:25:47 PDT)
Wei Zhang
Re: AMBER: amber .off file format question
(Mon May 22 2006 - 11:13:12 PDT)
Re: AMBER: conflicting types for XawScrolledTableSetLocation
(Thu May 04 2006 - 10:17:40 PDT)
Xuebin Qiao
Re: AMBER: experiences with compiling amber9 for FreeBSD
(Fri May 05 2006 - 23:31:06 PDT)
Ye Mei
Re: Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 06:23:00 PDT)
Re: AMBER: Opteron vs. Xeon performance
(Fri May 12 2006 - 01:04:45 PDT)
Yong Duan
RE: AMBER: ff02 + POL3 problem !
(Tue May 16 2006 - 13:06:54 PDT)
RE: AMBER: density
(Mon May 15 2006 - 22:37:28 PDT)
RE: AMBER: ff02 + POL3 problem !
(Mon May 15 2006 - 09:15:02 PDT)
RE: AMBER: Opteron vs. Xeon performance
(Sun May 14 2006 - 17:53:55 PDT)
z3020110.student.unsw.edu.au
AMBER: Amber 9, sander imin = 5, -y flag
(Sun Apr 30 2006 - 18:08:44 PDT)
Zhihong Yu
Re: AMBER: which time should I use to calculate the number of "ps/Day"
(Mon May 29 2006 - 17:42:01 PDT)
AMBER: which time should I use to calculate the number of "ps/Day"
(Mon May 29 2006 - 02:32:26 PDT)
RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs
(Mon May 15 2006 - 02:00:03 PDT)
AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs
(Sun May 14 2006 - 20:55:51 PDT)
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Sun Jun 04 2006 - 06:07:09 PDT
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