Amber Archive Jul 2004 by author
417 messages
:
Starting
Thu Jul 01 2004 - 05:53:01 PDT,
Ending
Sat Jul 31 2004 - 05:53:00 PDT
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Abd Ghani Bin Abd Aziz
AMBER: simulated annealing..
(Wed Jul 28 2004 - 06:45:55 PDT)
Re: AMBER: simulated annealing
(Wed Jul 28 2004 - 06:22:37 PDT)
ajakalian.lav.Boehringer-Ingelheim.com
RE: AMBER: RESP vs. AM1-BCC charges for isoprene
(Mon Jul 26 2004 - 08:09:31 PDT)
RE: AMBER: RESP vs. AM1-BCC charges for isoprene
(Thu Jul 22 2004 - 05:43:16 PDT)
aldo jongejan
Re: AMBER: animation?
(Wed Jul 28 2004 - 05:36:21 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Temperature Regulation
(Tue Jul 27 2004 - 07:09:51 PDT)
Re: AMBER: sander on multiprocessors
(Tue Jul 06 2004 - 04:15:48 PDT)
Re: AMBER: best PC laptop system to run Amber 8
(Sun Jul 04 2004 - 05:24:07 PDT)
Andy Purkiss
RE: AMBER: Molecular dynamic
(Tue Jul 13 2004 - 02:21:02 PDT)
anita pachaimuthu
AMBER: Co-ordination error while running tleap
(Wed Jul 21 2004 - 08:12:12 PDT)
AMBER: .lib file error in tleap
(Mon Jul 19 2004 - 10:19:19 PDT)
anshul.imtech.res.in
AMBER: erroe in installing amber8
(Sat Jul 24 2004 - 10:11:02 PDT)
AMBER: atoms not in residue templates
(Sat Jul 24 2004 - 08:19:42 PDT)
Re: AMBER: vdw energy in minimization
(Mon Jul 19 2004 - 20:44:30 PDT)
AMBER: vdw energy in minimization
(Mon Jul 19 2004 - 08:11:17 PDT)
AMBER: Parameter generation from RESP charges
(Tue Jul 13 2004 - 21:02:07 PDT)
AMBER: (no subject)
(Tue Jul 13 2004 - 20:40:08 PDT)
Re: AMBER: segmentation fault in leap
(Thu Jul 08 2004 - 18:17:40 PDT)
AMBER: segmentation fault in leap
(Thu Jul 08 2004 - 14:40:42 PDT)
Arvind
Re: AMBER: RNA sequence with DNA backbone?
(Wed Jul 14 2004 - 03:50:29 PDT)
AMBER: RNA sequence with DNA backbone?
(Mon Jul 12 2004 - 04:26:36 PDT)
Austin B. Yongye
Re: AMBER: tleap: automatically identify and connect disulfide bonds?
(Thu Jul 29 2004 - 06:13:46 PDT)
Bill Ross
Re: AMBER: user force
(Thu Jul 22 2004 - 14:57:24 PDT)
RE: AMBER: Xleap crash, problem with residue bonding
(Thu Jul 22 2004 - 14:55:58 PDT)
Re: AMBER: antechamber
(Fri Jul 16 2004 - 10:48:07 PDT)
RE: AMBER: How to apply OPLS force field?
(Thu Jul 15 2004 - 09:08:22 PDT)
Bimo Ario Tejo
Re: AMBER: pH effect on protein folding
(Thu Jul 15 2004 - 20:34:39 PDT)
AMBER: Correl in Amber8: Diagonal elements not 1?
(Thu Jul 15 2004 - 04:47:43 PDT)
AMBER: correlation in Amber 8
(Thu Jul 08 2004 - 01:14:34 PDT)
bybaker.itsa.ucsf.edu
Re: AMBER: Molecular dynamic & Acknowledgement
(Tue Jul 13 2004 - 11:20:50 PDT)
Re: AMBER: Molecular dynamic
(Fri Jul 09 2004 - 15:54:38 PDT)
Re: AMBER: Disulfide bond command
(Fri Jul 09 2004 - 11:51:46 PDT)
AMBER: Disulfide bond command
(Fri Jul 09 2004 - 11:16:13 PDT)
AMBER: Molecular dynamic
(Wed Jul 07 2004 - 14:12:33 PDT)
cailliez
AMBER: execution time
(Fri Jul 09 2004 - 02:50:25 PDT)
AMBER: sander on multiprocessors
(Tue Jul 06 2004 - 00:38:39 PDT)
carlos
Re: AMBER: vdw energy in minimization
(Mon Jul 19 2004 - 05:13:30 PDT)
Carlos Simmerling
Re: AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 12:03:31 PDT)
Re: AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 10:26:59 PDT)
Re: AMBER: simulated annealing..
(Wed Jul 28 2004 - 07:06:01 PDT)
Re: AMBER: simulated annealing
(Wed Jul 28 2004 - 05:17:55 PDT)
Re: AMBER: question on simulated annealing
(Tue Jul 27 2004 - 11:28:27 PDT)
Re: AMBER: sander : constraints to conserve hydrogen bonds
(Fri Jul 23 2004 - 05:08:43 PDT)
Re: AMBER: user force
(Fri Jul 23 2004 - 04:47:17 PDT)
Re: AMBER: user force
(Thu Jul 22 2004 - 15:28:42 PDT)
Re: AMBER: sander tutorial
(Thu Jul 22 2004 - 05:33:08 PDT)
Re: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 14:32:18 PDT)
Re: AMBER: vdw energy in minimization
(Mon Jul 19 2004 - 11:47:21 PDT)
Re: AMBER: Implicit MD problem
(Wed Jul 14 2004 - 09:53:31 PDT)
Re: AMBER: Implicit MD problem
(Wed Jul 14 2004 - 06:42:18 PDT)
Re: AMBER: Angle restraint during MD
(Wed Jul 14 2004 - 06:39:38 PDT)
Re: AMBER: Angle restraint during MD
(Tue Jul 13 2004 - 10:47:16 PDT)
Re: AMBER: Angle restraint during MD
(Tue Jul 13 2004 - 05:00:42 PDT)
Re: AMBER:
(Tue Jul 13 2004 - 04:59:08 PDT)
Re: AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 13:37:13 PDT)
Re: AMBER: peptide-DNA crosslink modeling
(Thu Jul 01 2004 - 18:42:48 PDT)
Re: AMBER: MAXRMSPT error in MOIL-view
(Thu Jul 01 2004 - 15:26:53 PDT)
Re: AMBER: Implicit MD simulation
(Thu Jul 01 2004 - 05:07:52 PDT)
Carsten Detering
Re: AMBER: using ptraj
(Thu Jul 29 2004 - 15:11:11 PDT)
AMBER: using ptraj
(Tue Jul 27 2004 - 14:10:02 PDT)
Re: AMBER: parametrization problem
(Fri Jul 23 2004 - 13:33:01 PDT)
Re: AMBER: parametrization problem
(Fri Jul 23 2004 - 13:38:59 PDT)
AMBER: parametrization problem
(Fri Jul 23 2004 - 11:16:13 PDT)
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 14:37:22 PDT)
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 14:33:51 PDT)
AMBER: problems with mdcrd
(Thu Jul 08 2004 - 10:16:04 PDT)
Chen
Re: Re: AMBER:
(Fri Jul 30 2004 - 20:55:14 PDT)
Re: Re: AMBER: NB pairs exceeds?
(Fri Jul 16 2004 - 01:40:42 PDT)
AMBER: NB pairs exceeds?
(Fri Jul 16 2004 - 00:35:16 PDT)
Chen, Ya
AMBER: Question on Clustering Analysis
(Tue Jul 27 2004 - 11:26:30 PDT)
Chris Moth
Re: AMBER: average structure using ptraj
(Fri Jul 02 2004 - 10:11:42 PDT)
Chunhu Tan
AMBER: About the free energy difference in vacuum with GIBBS.
(Mon Jul 12 2004 - 15:34:35 PDT)
AMBER: My strange result of TI.
(Wed Jul 07 2004 - 16:35:19 PDT)
Re: AMBER: About TI with sander
(Sun Jul 04 2004 - 18:18:48 PDT)
csong.mail.sdu.edu.cn
AMBER:
(Fri Jul 30 2004 - 02:08:40 PDT)
Re: Re: AMBER: NB pairs exceeds?
(Sun Jul 18 2004 - 01:28:27 PDT)
Re: Re: AMBER: NB pairs exceeds?
(Sat Jul 17 2004 - 03:10:23 PDT)
David A. Case
Re: AMBER: lib file
(Fri Jul 30 2004 - 13:48:50 PDT)
Re: AMBER: (no subject)
(Fri Jul 30 2004 - 13:42:15 PDT)
Re: AMBER: WHAM program
(Fri Jul 30 2004 - 10:16:02 PDT)
Re: AMBER:
(Fri Jul 30 2004 - 08:06:56 PDT)
Re: AMBER: umbrella sampling
(Thu Jul 29 2004 - 11:19:13 PDT)
Re: AMBER: NSPSOL in parm file
(Thu Jul 29 2004 - 08:07:54 PDT)
Re: AMBER: question on simulated annealing
(Tue Jul 27 2004 - 12:26:06 PDT)
Re: AMBER: Temperature Regulation
(Tue Jul 27 2004 - 08:24:31 PDT)
Re: AMBER: erroe in installing amber8
(Sat Jul 24 2004 - 01:40:06 PDT)
Re: AMBER: Ewald parameter range
(Fri Jul 23 2004 - 01:53:50 PDT)
Re: AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in)
(Wed Jul 21 2004 - 06:32:44 PDT)
Re: AMBER: Is it a bug?(in prep file opls_unict.in)
(Wed Jul 21 2004 - 01:52:22 PDT)
Re: Re: AMBER: NB pairs exceeds?
(Sat Jul 17 2004 - 18:09:22 PDT)
Re: AMBER: Is it a bug?(in prep file opls_unict.in)
(Fri Jul 16 2004 - 09:27:41 PDT)
Re: AMBER: Amber8: Vlimit problem again
(Fri Jul 16 2004 - 09:26:06 PDT)
Re: Re: AMBER: NB pairs exceeds?
(Fri Jul 16 2004 - 09:23:22 PDT)
Re: AMBER: antechamber
(Fri Jul 16 2004 - 09:16:14 PDT)
Re: AMBER: antechamber
(Thu Jul 15 2004 - 16:30:26 PDT)
Re: AMBER: How to apply OPLS force field?
(Thu Jul 15 2004 - 10:04:22 PDT)
Re: AMBER: Normal mode calculation with periodic boundary condition
(Thu Jul 15 2004 - 10:04:07 PDT)
Re: AMBER: xleap solvatebox/oct problem
(Thu Jul 15 2004 - 10:02:11 PDT)
Re: AMBER: About the free energy difference in vacuum with GIBBS.
(Wed Jul 14 2004 - 13:51:38 PDT)
Re: AMBER: How to apply OPLS force field?
(Wed Jul 14 2004 - 09:29:59 PDT)
Re: AMBER: Implicit MD problem
(Wed Jul 14 2004 - 09:29:47 PDT)
Re: AMBER: torsion scan
(Tue Jul 13 2004 - 13:47:00 PDT)
Re: AMBER: anisotropic scaling
(Tue Jul 13 2004 - 13:43:02 PDT)
Re: AMBER: Use of ibelly with nmode analysis
(Tue Jul 13 2004 - 09:24:27 PDT)
Re: AMBER: RNA sequence with DNA backbone?
(Mon Jul 12 2004 - 13:35:43 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sat Jul 10 2004 - 20:46:57 PDT)
Re: AMBER: how to calculate E-pot from restart file?
(Thu Jul 08 2004 - 21:07:49 PDT)
Re: AMBER: name error
(Thu Jul 08 2004 - 13:54:48 PDT)
Re: AMBER: charge problem in minimization
(Thu Jul 08 2004 - 13:54:54 PDT)
Re: AMBER: running MD simulatons
(Tue Jul 06 2004 - 11:40:50 PDT)
Re: AMBER: Amber7 bugfix1
(Tue Jul 06 2004 - 11:37:04 PDT)
Re: AMBER: idecomp
(Tue Jul 06 2004 - 09:37:42 PDT)
Re: AMBER: combination rules
(Mon Jul 05 2004 - 10:29:04 PDT)
Re: AMBER: leap problem in AMBER7 (residue insertion)
(Mon Jul 05 2004 - 10:21:50 PDT)
Re: AMBER: Amber8 on Digital UNIX
(Mon Jul 05 2004 - 09:55:20 PDT)
Re: AMBER: About TI with sander
(Mon Jul 05 2004 - 08:31:23 PDT)
Re: AMBER: Problem to converge minimization
(Mon Jul 05 2004 - 08:22:01 PDT)
Re: AMBER: Namelist problem
(Mon Jul 05 2004 - 08:21:12 PDT)
Re: AMBER: question about antechamber program
(Fri Jul 02 2004 - 13:26:12 PDT)
Re: AMBER: mm_pbsa problem
(Fri Jul 02 2004 - 07:52:46 PDT)
Re: AMBER: peptide-DNA crosslink modeling
(Thu Jul 01 2004 - 22:01:40 PDT)
Re: AMBER: tleap input file error
(Thu Jul 01 2004 - 17:06:18 PDT)
Re: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 12:17:52 PDT)
David E. Konerding
Re: AMBER: Problems with CPU scaling on cluster
(Fri Jul 16 2004 - 08:46:01 PDT)
david.evans.ulsop.ac.uk
Re: AMBER: mm_pbsa problem
(Fri Jul 02 2004 - 03:53:23 PDT)
Dawsonzhu.aol.com
AMBER: Re: AMBER: Temperature Regulation
(Wed Jul 28 2004 - 17:44:56 PDT)
echanco.uci.edu
AMBER: Weird compiling problem in Amber 8
(Sun Jul 18 2004 - 22:51:29 PDT)
fangyu liang
Re: AMBER: Weird compiling problem in Amber 8
(Sun Jul 18 2004 - 23:30:22 PDT)
Re: AMBER: Setup for parallel computing
(Sat Jul 10 2004 - 16:10:19 PDT)
AMBER: Setup for parallel computing
(Fri Jul 09 2004 - 10:00:32 PDT)
Re: AMBER: best PC laptop system to run Amber 8
(Sun Jul 04 2004 - 22:04:41 PDT)
AMBER: best PC laptop system to run Amber 8
(Sat Jul 03 2004 - 14:05:35 PDT)
AMBER: tleap input file error
(Thu Jul 01 2004 - 16:26:18 PDT)
AMBER: no 'water.lib' in /amber8/dat/leap/
(Thu Jul 01 2004 - 13:21:50 PDT)
Re: AMBER: Amber 8 installation error
(Thu Jul 01 2004 - 00:53:21 PDT)
Furse, Kristina Elisabet
Re: AMBER: lib file
(Fri Jul 30 2004 - 14:38:37 PDT)
Re: AMBER: user force
(Thu Jul 22 2004 - 14:07:46 PDT)
Re: AMBER: torsion scan
(Tue Jul 13 2004 - 10:37:35 PDT)
FyD
AMBER: Re: Results from RED-II beta
(Sun Jul 18 2004 - 09:11:41 PDT)
AMBER: X-CA-CT-X dih. FF param ?
(Fri Jul 16 2004 - 10:08:26 PDT)
RE: AMBER: (no subject)
(Wed Jul 14 2004 - 12:30:04 PDT)
German Sciaini
Re: AMBER: antechamber - missing improper torsions
(Tue Jul 20 2004 - 06:04:17 PDT)
Re: AMBER: Amber8: Vlimit problem again
(Fri Jul 16 2004 - 06:12:59 PDT)
AMBER: combination rules
(Mon Jul 05 2004 - 05:31:43 PDT)
Grace Li
Re: AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 13:42:03 PDT)
RE: AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 11:52:15 PDT)
AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 10:17:39 PDT)
AMBER: about RDF calculation in action.c
(Fri Jul 23 2004 - 13:39:07 PDT)
RE: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 15:03:05 PDT)
RE: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 14:20:40 PDT)
AMBER: cut offs in amber?
(Wed Jul 21 2004 - 13:47:43 PDT)
AMBER: ptraj-closestwaters command
(Sat Jul 10 2004 - 09:14:34 PDT)
AMBER: "closestwater" algorithm
(Mon Jul 05 2004 - 15:42:08 PDT)
Guanglei Cui
Re: AMBER:
(Fri Jul 30 2004 - 06:39:51 PDT)
Re: AMBER: animation?
(Wed Jul 28 2004 - 06:20:12 PDT)
Re: AMBER: question about ptraj
(Wed Jul 21 2004 - 13:32:29 PDT)
Re: AMBER: X-CA-CT-X dih. FF param ?
(Fri Jul 16 2004 - 10:24:46 PDT)
Re: AMBER: torsion scan
(Tue Jul 13 2004 - 14:12:50 PDT)
AMBER: torsion scan
(Tue Jul 13 2004 - 08:18:32 PDT)
Re: AMBER: How to make leap recognise Zn2+?
(Tue Jul 06 2004 - 06:58:27 PDT)
Re: AMBER: Namelist problem
(Mon Jul 05 2004 - 05:56:10 PDT)
Guillaume Bollot
AMBER: Problem to converge minimization
(Mon Jul 05 2004 - 01:41:06 PDT)
Guillermo Mulliert Carlín
Re: AMBER: segmentation fault in leap
(Thu Jul 08 2004 - 05:02:05 PDT)
Re: AMBER: Amber8 on Digital UNIX
(Wed Jul 07 2004 - 02:41:53 PDT)
AMBER: Amber8 on Digital UNIX
(Mon Jul 05 2004 - 08:30:15 PDT)
Herbert Georg
Re: AMBER: weird box expansion
(Thu Jul 08 2004 - 10:38:01 PDT)
AMBER: weird box expansion
(Thu Jul 08 2004 - 09:57:57 PDT)
Herr/Señor/Monsieur/Mister Gregory
Re: AMBER: question about Ptraj - AND OR
(Mon Jul 12 2004 - 09:15:47 PDT)
hj zou
Re: Re: AMBER: xleap problem
(Mon Jul 12 2004 - 07:56:55 PDT)
AMBER: Fe parameter
(Mon Jul 12 2004 - 00:09:29 PDT)
AMBER: solvation free energy
(Fri Jul 09 2004 - 00:38:39 PDT)
AMBER:
(Sat Jul 10 2004 - 23:16:17 PDT)
Re: Re: AMBER: xleap problem
(Sat Jul 10 2004 - 23:16:19 PDT)
AMBER: solvation free energy
(Sat Jul 10 2004 - 23:16:19 PDT)
HL Eastwood
RE: AMBER: (no subject)
(Fri Jul 30 2004 - 11:12:34 PDT)
AMBER: (no subject)
(Fri Jul 30 2004 - 08:47:18 PDT)
Holger Gohlke
Re: AMBER: found unknown atflg PB
(Thu Jul 22 2004 - 07:56:38 PDT)
Holly Freedman
AMBER: average using ptraj
(Thu Jul 08 2004 - 12:13:58 PDT)
Ilyas Yildirim
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 15:36:22 PDT)
J. Zhang, Dr
AMBER: how to calculate E-pot from restart file?
(Thu Jul 08 2004 - 20:13:44 PDT)
james tomomi macdonald
AMBER: question about Ptraj - AND OR
(Mon Jul 12 2004 - 08:06:59 PDT)
Jean-Christophe Ducom
AMBER: Amber7 (8):FLUSH--FAILED:: Resource temporarily unavailable
(Sat Jul 17 2004 - 13:01:47 PDT)
Jiten
Re: AMBER: sander : constraints to conserve hydrogen bonds
(Thu Jul 22 2004 - 22:58:15 PDT)
Re: AMBER: xleap solvatebox/oct problem
(Fri Jul 16 2004 - 02:07:09 PDT)
Re: AMBER: xleap solvatebox/oct problem
(Thu Jul 15 2004 - 08:18:59 PDT)
Re: AMBER: Angle restraint during MD and namelist problem in amber8
(Wed Jul 14 2004 - 09:13:38 PDT)
Re: AMBER: Angle restraint during MD
(Tue Jul 13 2004 - 22:51:42 PDT)
Re: AMBER: Angle restraint during MD
(Tue Jul 13 2004 - 09:21:28 PDT)
AMBER: Angle restraint during MD
(Tue Jul 13 2004 - 02:28:14 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Tue Jul 13 2004 - 02:52:06 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Tue Jul 13 2004 - 02:46:57 PDT)
AMBER:
(Tue Jul 13 2004 - 02:25:53 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Mon Jul 12 2004 - 02:36:36 PDT)
Re: AMBER: Rigid counteranion during MD !!
(Sun Jul 11 2004 - 07:51:48 PDT)
AMBER: Rigid counteranion during MD !!
(Sun Jul 11 2004 - 01:26:35 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sat Jul 10 2004 - 22:24:27 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sat Jul 10 2004 - 22:04:35 PDT)
AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sat Jul 10 2004 - 08:30:15 PDT)
Re: AMBER: Problem to converge minimization
(Mon Jul 05 2004 - 05:38:26 PDT)
Joe Harriman
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Sat Jul 17 2004 - 05:44:47 PDT)
John
AMBER: mm_pbsa Abmer8 example
(Tue Jul 27 2004 - 03:38:50 PDT)
John Mongan
AMBER: Re: constant pH calculation in Amber8
(Thu Jul 29 2004 - 14:40:36 PDT)
Johnson Agbo
AMBER: Temperature Regulation
(Mon Jul 26 2004 - 21:40:44 PDT)
Re: AMBER: Ewald parameter range
(Fri Jul 23 2004 - 11:00:12 PDT)
AMBER: Ewald parameter range
(Thu Jul 22 2004 - 17:16:08 PDT)
AMBER: Cubic Ice
(Fri Jul 16 2004 - 18:08:14 PDT)
AMBER: Normal mode calculation with periodic boundary condition
(Wed Jul 14 2004 - 22:15:09 PDT)
Joseph Nachman
RE: AMBER: Molecular dynamic
(Tue Jul 13 2004 - 08:21:09 PDT)
Junmei Wang
RE: AMBER: antechamber - missing improper torsions
(Wed Jul 21 2004 - 09:11:04 PDT)
jz7.duke.edu
AMBER: about correlation calculation in ptraj
(Tue Jul 27 2004 - 14:20:53 PDT)
AMBER: about running ptraj in ambber8 (re-post)
(Mon Jul 26 2004 - 13:47:52 PDT)
RE: AMBER: about running ptraj in amber8
(Mon Jul 26 2004 - 09:30:42 PDT)
AMBER: about running ptraj in amber8
(Mon Jul 26 2004 - 07:04:33 PDT)
AMBER: question about ptraj
(Wed Jul 21 2004 - 13:00:01 PDT)
RE: AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 12:59:26 PDT)
AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 09:17:30 PDT)
AMBER: question about Ptraj
(Thu Jul 08 2004 - 09:32:07 PDT)
Karsten Suhre
AMBER: announcing normal mode analysis web server ElNemo
(Thu Jul 15 2004 - 01:21:07 PDT)
Kennie Merz
Re: AMBER: Problem with divcon - increasing MXATTS?
(Wed Jul 14 2004 - 10:03:32 PDT)
Re: AMBER: Problem with divcon - increasing MXATTS?
(Wed Jul 14 2004 - 09:01:54 PDT)
Kuhn, Bernd {PRBD~Basel}
Re: AMBER: leap problem in AMBER7 (residue insertion)
(Wed Jul 14 2004 - 04:44:00 PDT)
AMBER: leap problem in AMBER7 (residue insertion)
(Mon Jul 05 2004 - 04:26:34 PDT)
Livadaru, Lucian
AMBER: amber compilation
(Mon Jul 26 2004 - 13:15:50 PDT)
M. L. Dodson
Re: AMBER: peptide-DNA crosslink modeling
(Fri Jul 02 2004 - 11:06:39 PDT)
AMBER: peptide-DNA crosslink modeling
(Thu Jul 01 2004 - 14:51:24 PDT)
Marc Perea
AMBER: Problems with amber8 and pgf90
(Thu Jul 15 2004 - 03:30:36 PDT)
Marcela Madrid
Re: AMBER: idecomp
(Thu Jul 08 2004 - 12:35:57 PDT)
AMBER: idecomp
(Tue Jul 06 2004 - 08:42:20 PDT)
Marcin Krol
AMBER: multiple heat bath GB+LES
(Mon Jul 05 2004 - 09:53:31 PDT)
Mark Williamson
RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sun Jul 11 2004 - 13:52:45 PDT)
Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sat Jul 10 2004 - 10:54:56 PDT)
mathew k varghese
AMBER: sander tutorial
(Thu Jul 22 2004 - 05:16:33 PDT)
mcpreto.fc.up.pt
Re: AMBER: How to apply OPLS force field?
(Wed Jul 14 2004 - 06:26:04 PDT)
Michael Dolan
Re: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 12:57:37 PDT)
Re: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 12:04:37 PDT)
Re: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 12:00:45 PDT)
Mike
RE: AMBER: Problem with sander - Error on Open
(Thu Jul 08 2004 - 18:57:43 PDT)
AMBER: Problem with sander - Error on Open
(Thu Jul 08 2004 - 14:38:37 PDT)
Myunggi Yi
AMBER: user force
(Thu Jul 22 2004 - 10:00:16 PDT)
myunggi.csit.fsu.edu
RE: AMBER: user force
(Thu Jul 22 2004 - 16:26:14 PDT)
RE: AMBER: user force
(Thu Jul 22 2004 - 15:25:50 PDT)
Re: AMBER: user force
(Thu Jul 22 2004 - 14:48:28 PDT)
AMBER: (no subject)
(Thu Jul 22 2004 - 10:10:09 PDT)
Nelson Fonseca
AMBER: mutation of atoms
(Thu Jul 22 2004 - 05:41:22 PDT)
NI AI
Re: AMBER: average structure using ptraj
(Fri Jul 02 2004 - 08:15:53 PDT)
AMBER: average structure using ptraj
(Thu Jul 01 2004 - 09:18:34 PDT)
O. Hucke
AMBER: antechamber - missing improper torsions
(Mon Jul 19 2004 - 11:58:39 PDT)
Oliver Hucke
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 23 2004 - 10:41:05 PDT)
AMBER: antechamber - improper torsions
(Tue Jul 20 2004 - 09:23:02 PDT)
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 15:49:00 PDT)
AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 14:00:57 PDT)
opitz.che.udel.edu
Re: AMBER: Xleap crash, problem with residue bonding
(Mon Jul 26 2004 - 08:39:51 PDT)
AMBER: Xleap crash, problem with residue bonding
(Thu Jul 22 2004 - 07:24:35 PDT)
AMBER: question about production runs
(Fri Jul 16 2004 - 12:42:06 PDT)
Osman Gani
AMBER: pmemd.
(Fri Jul 23 2004 - 10:09:55 PDT)
Ozlem Demir
AMBER: about GLYCAM prep files in AMBER
(Tue Jul 20 2004 - 10:34:07 PDT)
Prashansa Agrawal
AMBER: name error
(Wed Jul 07 2004 - 15:57:53 PDT)
Qizhi Cui
Re: AMBER: solvation free energy
(Mon Jul 19 2004 - 10:32:17 PDT)
Raik Grünberg
AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)
(Thu Jul 29 2004 - 03:34:44 PDT)
AMBER: tleap: automatically identify and connect disulfide bonds?
(Wed Jul 28 2004 - 10:27:31 PDT)
Ray Luo
Re: AMBER: PB Bomb in pb_reslist(): maxnbr too small
(Mon Jul 19 2004 - 05:22:26 PDT)
Re: AMBER: Weird compiling problem in Amber 8
(Sun Jul 18 2004 - 22:34:03 PDT)
Re: AMBER: solvation free energy
(Sun Jul 11 2004 - 19:25:44 PDT)
Rhonda Torres
Re: AMBER: Bondi radii for BR and F in mm_pbsa calculation
(Tue Jul 20 2004 - 17:23:10 PDT)
Re: AMBER: RESP vs. AM1-BCC charges for isoprene
(Fri Jul 16 2004 - 14:20:42 PDT)
Re: AMBER: no 'water.lib' in /amber8/dat/leap/
(Thu Jul 01 2004 - 13:25:15 PDT)
Robert Duke
Re: AMBER: pmemd.
(Fri Jul 23 2004 - 10:46:48 PDT)
Robyn Ayscue
AMBER: MAXRMSPT error in MOIL-view
(Thu Jul 01 2004 - 15:19:23 PDT)
Ross Walker
RE: AMBER: (no subject)
(Fri Jul 30 2004 - 14:09:25 PDT)
RE: AMBER: AMBER 6 compilation problems!
(Fri Jul 30 2004 - 10:30:54 PDT)
RE: AMBER: (no subject)
(Fri Jul 30 2004 - 09:21:33 PDT)
RE: AMBER:
(Fri Jul 30 2004 - 08:46:52 PDT)
RE: AMBER: about running ptraj in amber8
(Mon Jul 26 2004 - 09:22:36 PDT)
RE: AMBER: atoms not in residue templates
(Sat Jul 24 2004 - 08:05:36 PDT)
RE: AMBER: parametrization problem
(Fri Jul 23 2004 - 12:32:15 PDT)
RE: AMBER: user force
(Thu Jul 22 2004 - 15:40:16 PDT)
RE: AMBER: user force
(Thu Jul 22 2004 - 15:08:04 PDT)
RE: AMBER: Xleap crash, problem with residue bonding
(Thu Jul 22 2004 - 14:31:22 PDT)
RE: AMBER: Problem with sander tutorial.
(Thu Jul 22 2004 - 13:57:20 PDT)
RE: AMBER: atom out of bounds (fwd)
(Thu Jul 22 2004 - 13:54:52 PDT)
RE: AMBER: Amber8: Vlimit problem again
(Wed Jul 21 2004 - 16:55:59 PDT)
RE: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 15:10:09 PDT)
RE: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 14:39:47 PDT)
RE: AMBER: amparm
(Wed Jul 21 2004 - 14:11:29 PDT)
RE: AMBER: cut offs in amber?
(Wed Jul 21 2004 - 14:05:02 PDT)
RE: AMBER: What happen when sander reads charge increments from cpin file?
(Wed Jul 21 2004 - 13:41:45 PDT)
RE: AMBER: Problem with sander tutorial.
(Tue Jul 20 2004 - 13:16:28 PDT)
RE: AMBER: Problems with CPU scaling on cluster
(Thu Jul 15 2004 - 11:48:15 PDT)
RE: AMBER: antechamber
(Thu Jul 15 2004 - 11:21:44 PDT)
RE: AMBER: How to apply OPLS force field?
(Wed Jul 14 2004 - 21:20:58 PDT)
RE: AMBER: (no subject)
(Wed Jul 14 2004 - 11:33:38 PDT)
RE: AMBER: Problem with divcon - increasing MXATTS?
(Wed Jul 14 2004 - 11:13:19 PDT)
RE: AMBER: anisotropic scaling
(Tue Jul 13 2004 - 12:39:05 PDT)
RE: AMBER: (no subject)
(Tue Jul 13 2004 - 10:32:22 PDT)
RE: AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 13:40:23 PDT)
RE: AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 11:51:47 PDT)
RE: AMBER: Problems with CPU scaling on cluster
(Mon Jul 12 2004 - 11:38:27 PDT)
RE: AMBER: Fe parameter
(Mon Jul 12 2004 - 11:19:23 PDT)
RE: AMBER: Molecular dynamic
(Mon Jul 12 2004 - 11:12:53 PDT)
RE: AMBER: MD simulation : problem
(Mon Jul 12 2004 - 10:55:33 PDT)
RE: AMBER: MD simulation : problem
(Sun Jul 11 2004 - 17:41:11 PDT)
RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Sun Jul 11 2004 - 11:38:49 PDT)
RE: AMBER: MD simulation : problem
(Fri Jul 09 2004 - 22:35:14 PDT)
RE: AMBER: execution time
(Fri Jul 09 2004 - 11:52:08 PDT)
RE: AMBER: Disulfide bond command
(Fri Jul 09 2004 - 11:27:13 PDT)
RE: AMBER: Problem with sander - Error on Open
(Thu Jul 08 2004 - 15:15:04 PDT)
RE: AMBER: average using ptraj
(Thu Jul 08 2004 - 13:18:58 PDT)
RE: AMBER: problems with mdcrd
(Thu Jul 08 2004 - 12:54:08 PDT)
RE: AMBER: parameter development for nucleotide analogues
(Thu Jul 08 2004 - 10:49:33 PDT)
RE: AMBER: charge problem in minimization
(Thu Jul 08 2004 - 10:40:56 PDT)
RE: AMBER: name error
(Thu Jul 08 2004 - 10:35:46 PDT)
RE: AMBER: problems with mdcrd
(Thu Jul 08 2004 - 10:32:04 PDT)
RE: AMBER: Molecular dynamic
(Thu Jul 08 2004 - 10:24:21 PDT)
RE: AMBER: segmentation fault in leap
(Thu Jul 08 2004 - 10:07:28 PDT)
RE: AMBER: ptraj
(Thu Jul 08 2004 - 10:01:43 PDT)
RE: AMBER: question about Ptraj
(Thu Jul 08 2004 - 09:47:28 PDT)
RE: AMBER: Amber7 bugfix1
(Tue Jul 06 2004 - 11:17:49 PDT)
RE: AMBER: no 'water.lib' in /amber8/dat/leap/
(Thu Jul 01 2004 - 13:30:25 PDT)
RE: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 13:13:00 PDT)
RE: AMBER: N-terminal Arg charges in ff99 not 1.00
(Thu Jul 01 2004 - 12:17:02 PDT)
Rukman Hertadi
AMBER: pH effect on protein folding
(Thu Jul 15 2004 - 19:00:54 PDT)
S. Frank Yan
AMBER: animation?
(Tue Jul 27 2004 - 23:29:51 PDT)
AMBER: Bondi radii for BR and F in mm_pbsa calculation
(Tue Jul 20 2004 - 16:01:03 PDT)
AMBER: FW: missing bondi radii of Br and F for surface area calculation
(Tue Jul 20 2004 - 10:30:13 PDT)
sachin patil
AMBER: sander : constraints to conserve hydrogen bonds
(Thu Jul 22 2004 - 21:15:04 PDT)
RE: AMBER: MD simulation : problem :THANK YOU
(Tue Jul 13 2004 - 07:51:28 PDT)
RE: AMBER: MD simulation : problem
(Sun Jul 11 2004 - 21:53:51 PDT)
RE: AMBER: MD simulation : problem
(Sun Jul 11 2004 - 08:08:13 PDT)
AMBER: MD simulation : problem
(Fri Jul 09 2004 - 22:08:15 PDT)
AMBER: Amber7 bugfix1
(Tue Jul 06 2004 - 10:47:38 PDT)
AMBER: running MD simulatons
(Tue Jul 06 2004 - 09:52:58 PDT)
scopio
Re: AMBER: xleap problem
(Mon Jul 12 2004 - 07:09:47 PDT)
Re: AMBER: Fe parameter
(Mon Jul 12 2004 - 07:18:52 PDT)
Scott
Re: AMBER: using ptraj
(Thu Jul 29 2004 - 15:48:19 PDT)
Re: AMBER: using ptraj
(Thu Jul 29 2004 - 14:15:17 PDT)
RE: AMBER: Problem with sander tutorial.
(Thu Jul 22 2004 - 19:08:19 PDT)
AMBER: found unknown atflg PB
(Thu Jul 22 2004 - 06:38:33 PDT)
AMBER: Enthalpy of solvent-solute vanderWaals
(Wed Jul 14 2004 - 12:56:45 PDT)
Scott Brozell
Re: AMBER: tleap: automatically identify and connect disulfide bonds?
(Wed Jul 28 2004 - 13:22:52 PDT)
Re: AMBER: erroe in installing amber8
(Sun Jul 25 2004 - 17:58:58 PDT)
Re: AMBER: Weird compiling problem in Amber 8
(Mon Jul 19 2004 - 10:08:54 PDT)
Re: AMBER: Problems with amber8 and pgf90
(Thu Jul 15 2004 - 09:23:44 PDT)
Re: AMBER: tleap - FATAL error
(Wed Jul 14 2004 - 14:44:41 PDT)
RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
(Mon Jul 12 2004 - 11:30:39 PDT)
Sichun Yang
AMBER: NSPSOL in parm file
(Wed Jul 28 2004 - 21:14:01 PDT)
Re: AMBER: How to apply OPLS force field?
(Wed Jul 14 2004 - 09:21:41 PDT)
Sivanesan Dakshanamurthy
AMBER: tleap - FATAL error
(Wed Jul 14 2004 - 14:28:41 PDT)
AMBER: question about antechamber program
(Fri Jul 02 2004 - 11:42:07 PDT)
Stef
Re: AMBER: Setup for parallel computing
(Sat Jul 10 2004 - 14:14:56 PDT)
Re: AMBER: sander on multiprocessors
(Tue Jul 06 2004 - 01:42:36 PDT)
Stefano.Pieraccini.unimi.it
AMBER: cys protecting groups parameters
(Fri Jul 09 2004 - 05:41:20 PDT)
AMBER: cys protecting group parameters
(Fri Jul 09 2004 - 06:48:36 PDT)
Steve Seibold
AMBER: Imaging problem
(Fri Jul 30 2004 - 12:05:12 PDT)
steven.j.enoch.gsk.com
Re: AMBER: PB bomb in pb_saarc
(Wed Jul 28 2004 - 01:49:20 PDT)
AMBER: PB bomb in pb_saarc
(Wed Jul 28 2004 - 01:26:38 PDT)
AMBER: PB Bomb in pb_reslist(): maxnbr too small
(Tue Jul 20 2004 - 06:00:59 PDT)
Re: AMBER: Problem with divcon - increasing MXATTS?
(Wed Jul 14 2004 - 09:45:54 PDT)
AMBER: Problem with divcon - increasing MXATTS?
(Wed Jul 14 2004 - 08:33:38 PDT)
AMBER: Use of ibelly with nmode analysis
(Tue Jul 13 2004 - 06:30:30 PDT)
AMBER: mm_pbsa problem
(Fri Jul 02 2004 - 03:29:57 PDT)
Sébastien Osborne
Re: AMBER: .lib file error in tleap
(Mon Jul 19 2004 - 11:15:11 PDT)
tang kwa
AMBER: WHAM program
(Fri Jul 30 2004 - 09:09:02 PDT)
AMBER: umbrella sampling
(Thu Jul 29 2004 - 10:25:00 PDT)
tarek mahfouz
RE: AMBER: Problem with sander tutorial.
(Thu Jul 22 2004 - 09:59:42 PDT)
AMBER: Problem with sander tutorial.
(Tue Jul 20 2004 - 12:09:44 PDT)
Thomas E. Cheatham, III
Re: AMBER: Imaging problem
(Fri Jul 30 2004 - 13:41:45 PDT)
Re: AMBER: about the parameter of the cystein pair in MD simulation
(Sun Jul 25 2004 - 20:07:44 PDT)
Re: AMBER: Angle restraint during MD and namelist problem in amber8
(Wed Jul 14 2004 - 09:22:26 PDT)
Re: AMBER: ptraj-closestwaters command
(Mon Jul 12 2004 - 13:38:41 PDT)
RE: AMBER: what is averaged RMS fluctuation?
(Mon Jul 12 2004 - 13:28:21 PDT)
Re: AMBER: question about Ptraj - AND OR
(Mon Jul 12 2004 - 08:15:13 PDT)
RE: AMBER: Problem with sander - Error on Open
(Thu Jul 08 2004 - 19:18:10 PDT)
Re: AMBER: weird box expansion
(Thu Jul 08 2004 - 10:06:57 PDT)
Re: AMBER: question about Ptraj
(Thu Jul 08 2004 - 09:56:04 PDT)
Re: AMBER: average structure using ptraj
(Thu Jul 01 2004 - 10:40:25 PDT)
Ting Wang
Re: AMBER: solvate proteins in xleap/amber8
(Tue Jul 13 2004 - 05:23:51 PDT)
Venkata S Koppuravuri
AMBER: question on simulated annealing
(Tue Jul 27 2004 - 11:21:52 PDT)
AMBER: atom out of bounds (fwd)
(Thu Jul 22 2004 - 12:52:13 PDT)
AMBER: atom out of bounds
(Wed Jul 21 2004 - 06:25:25 PDT)
Viktor Hornak
Re: AMBER: amber compilation
(Mon Jul 26 2004 - 13:47:33 PDT)
Re: AMBER: Namelist problem
(Mon Jul 05 2004 - 07:07:36 PDT)
Vincent Bisetty
AMBER: amparm
(Wed Jul 21 2004 - 13:37:39 PDT)
Vlad Cojocaru
Re: AMBER: RNA sequence with DNA backbone?
(Wed Jul 14 2004 - 04:09:13 PDT)
AMBER: namelist problem solved
(Thu Jul 08 2004 - 10:50:10 PDT)
AMBER: parameter development for nucleotide analogues
(Thu Jul 08 2004 - 10:49:42 PDT)
AMBER: Namelist problem solved
(Wed Jul 07 2004 - 04:09:16 PDT)
AMBER: parameter development for nucleotide analogues
(Wed Jul 07 2004 - 03:37:50 PDT)
AMBER: details for Namelist problem
(Mon Jul 05 2004 - 06:22:33 PDT)
Re: AMBER: Namelist problem
(Mon Jul 05 2004 - 06:10:51 PDT)
AMBER: details for Namelist problem
(Mon Jul 05 2004 - 02:48:40 PDT)
AMBER: Namelist problem
(Mon Jul 05 2004 - 02:25:07 PDT)
Wen Li
AMBER: ptraj
(Wed Jul 14 2004 - 14:07:11 PDT)
AMBER: ptraj
(Thu Jul 08 2004 - 09:06:01 PDT)
Wen-Chi Tseng
Re: AMBER: problems in using glycam
(Thu Jul 01 2004 - 05:44:27 PDT)
Wu Lei
Re: AMBER: Is it a bug?(in prep file opls_unict.in)
(Fri Jul 16 2004 - 22:15:16 PDT)
Re: AMBER: NB pairs exceeds?
(Fri Jul 16 2004 - 01:07:56 PDT)
AMBER: Is it a bug?(in prep file opls_unict.in)
(Thu Jul 15 2004 - 20:44:09 PDT)
Re: AMBER: How to apply OPLS force field?
(Thu Jul 15 2004 - 00:45:31 PDT)
Re: AMBER: How to apply OPLS force field?
(Wed Jul 14 2004 - 21:12:50 PDT)
AMBER: How to apply OPLS force field?
(Tue Jul 13 2004 - 20:23:04 PDT)
Re: AMBER: Fe parameter
(Mon Jul 12 2004 - 00:51:18 PDT)
AMBER: About the calculation of non-bond list
(Sat Jul 10 2004 - 07:21:57 PDT)
Xiang, Tian-Xiang
AMBER: anisotropic scaling
(Tue Jul 13 2004 - 12:12:32 PDT)
Xin Hu
Re: AMBER: antechamber
(Thu Jul 15 2004 - 19:51:26 PDT)
Re: AMBER: antechamber
(Thu Jul 15 2004 - 13:57:09 PDT)
AMBER: antechamber
(Thu Jul 15 2004 - 11:03:44 PDT)
Yongzhi Chen
RE: AMBER: What happen when sander reads charge increments from cpin file?
(Wed Jul 21 2004 - 14:59:40 PDT)
AMBER: What happen when sander reads charge increments from cpin file?
(Wed Jul 21 2004 - 13:24:51 PDT)
AMBER: A problem regarding constant pH calculation in Amber 8
(Mon Jul 19 2004 - 18:54:43 PDT)
Re: AMBER: How to make leap recognise Zn2+?
(Tue Jul 06 2004 - 09:00:26 PDT)
AMBER: How to make leap recognise Zn2+?
(Mon Jul 05 2004 - 18:41:26 PDT)
Your Name
AMBER: Problems with CPU scaling on cluster
(Mon Jul 12 2004 - 01:12:48 PDT)
Yuhui Cheng
AMBER: about the parameter of the cystein pair in MD simulation
(Sun Jul 25 2004 - 19:01:13 PDT)
Re: AMBER: Amber8: Vlimit problem again
(Wed Jul 21 2004 - 16:44:09 PDT)
AMBER: Amber8: Vlimit problem again
(Thu Jul 15 2004 - 19:34:58 PDT)
吴磊
AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in)
(Wed Jul 21 2004 - 03:59:13 PDT)
AMBER: Leap could not find atom type CK
(Tue Jul 20 2004 - 21:35:54 PDT)
Last message date
:
Sat Jul 31 2004 - 05:53:00 PDT
Archived on
: Fri Nov 22 2024 - 05:53:20 PST
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