Amber Archive May 2004 by author
421 messages
:
Starting
Fri Apr 30 2004 - 21:53:01 PDT,
Ending
Tue Jun 01 2004 - 02:53:00 PDT
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A. Hungie
AMBER: Amber 8 compilation
(Wed May 26 2004 - 09:23:07 PDT)
AMBER: Installation AMber 8: "cannot find -lU77"
(Tue May 25 2004 - 06:21:09 PDT)
Adrian E. Roitberg
Re: AMBER: amber 8 under windows XP
(Thu May 27 2004 - 06:09:51 PDT)
AMBER: amber 8 under windows XP
(Wed May 26 2004 - 11:50:02 PDT)
ahmadis-bounces.imperial.ac.uk
Request to mailing list Ahmadis rejected
(Fri May 21 2004 - 05:31:19 PDT)
aini.UMDNJ.EDU
AMBER: question about mm-pbsa
(Mon May 10 2004 - 17:10:05 PDT)
Amber admin
AMBER: problems with mpich
(Fri May 28 2004 - 07:55:25 PDT)
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 10:25:03 PDT)
Re: AMBER: antechamber
(Wed May 05 2004 - 13:51:22 PDT)
Amber Administration
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 14:15:14 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Problem compiling amber7
(Tue May 25 2004 - 05:21:40 PDT)
Re: AMBER: CAP PROTOCOL SIMULATION
(Tue May 18 2004 - 05:13:56 PDT)
Re: AMBER: any program or tool
(Mon May 03 2004 - 05:11:50 PDT)
Annette Höglund
AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 06:23:27 PDT)
anshul.imtech.res.in
Re: AMBER: MD with NTR + NMROPT
(Wed May 12 2004 - 08:07:49 PDT)
AMBER: Charges and atom type
(Sat May 08 2004 - 14:06:25 PDT)
Re: AMBER: xleap don't recognize formaldehyde?
(Sat May 08 2004 - 12:44:33 PDT)
Re: AMBER: simulated anealing ...vlimit exceed
(Thu May 06 2004 - 16:14:53 PDT)
Re: AMBER: H Bonds
(Thu May 06 2004 - 16:01:33 PDT)
Re: AMBER: H Bonds
(Thu May 06 2004 - 15:51:32 PDT)
AMBER: simulated anealing ...vlimit exceed
(Thu May 06 2004 - 14:50:35 PDT)
AMBER: Implicit solvents
(Wed May 05 2004 - 13:10:20 PDT)
AMBER: H Bonds
(Wed May 05 2004 - 13:07:01 PDT)
AMBER: methane box
(Wed May 05 2004 - 11:57:16 PDT)
AMBER: instalation of RES
(Thu May 20 2004 - 11:22:08 PDT)
Re: AMBER: Simulated annealing ...vlimit problem
(Sun May 16 2004 - 13:01:55 PDT)
AMBER: antechamber
(Sat May 15 2004 - 09:43:48 PDT)
Arvind
Re: AMBER: Amber8 compilation error
(Fri Apr 30 2004 - 12:50:38 PDT)
atobak.eden.rutgers.edu
AMBER: ligand minimization
(Sat May 08 2004 - 14:13:21 PDT)
Beale, John
AMBER: dihedral driver
(Wed May 12 2004 - 06:58:35 PDT)
Ben Cossins
Re: AMBER: performance of periodic vs. non-periodic simulation
(Thu May 13 2004 - 02:22:21 PDT)
Bill Ross
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 15:16:56 PDT)
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 14:28:27 PDT)
Re: Re[4]: AMBER: rmsd over residues using ptraj
(Wed May 19 2004 - 14:15:01 PDT)
Re: Re[2]: AMBER: rmsd over residues using ptraj
(Wed May 19 2004 - 11:34:08 PDT)
Re: AMBER: rmsd over residues using ptraj
(Tue May 18 2004 - 17:57:54 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Tue May 18 2004 - 12:08:13 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 17:10:36 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 16:42:25 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 15:47:24 PDT)
Re: AMBER: reference with ptraj
(Thu May 06 2004 - 15:05:55 PDT)
Re: AMBER: H Bonds
(Thu May 06 2004 - 11:16:11 PDT)
Re: AMBER: H Bonds
(Wed May 05 2004 - 14:18:22 PDT)
Re: AMBER: reproduction of RESP charges for Gly
(Tue May 04 2004 - 13:35:49 PDT)
Re: AMBER: reproduction of RESP charges for Gly
(Tue May 04 2004 - 13:24:41 PDT)
Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded".
(Tue May 04 2004 - 09:44:16 PDT)
Re: AMBER: ptraj: radius of gyration
(Sun May 02 2004 - 13:12:23 PDT)
by way of riccardo nifosi
AMBER: SHAKE in thermodynamic integration
(Thu May 20 2004 - 03:38:21 PDT)
bybaker.itsa.ucsf.edu
Re: AMBER: Sander went through
(Sat May 29 2004 - 04:51:26 PDT)
AMBER: Sander went through
(Fri May 28 2004 - 17:19:02 PDT)
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 15:05:22 PDT)
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 14:22:00 PDT)
Re: AMBER: Cannot read in sander
(Thu May 27 2004 - 13:56:12 PDT)
Re: AMBER: Cannot read in sander
(Wed May 26 2004 - 17:47:30 PDT)
AMBER: Cannot read in sander
(Tue May 25 2004 - 15:51:48 PDT)
Carlos Simmerling
Re: AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 11:21:41 PDT)
Re: AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 10:56:24 PDT)
Re: AMBER: about amber8, replica exchange
(Fri May 28 2004 - 20:55:34 PDT)
Re: AMBER: Amber 7 (sander) use of PME
(Thu May 27 2004 - 12:47:50 PDT)
Re: AMBER: Reproducing the energy during restart in MD!
(Wed May 19 2004 - 06:41:17 PDT)
Re: AMBER: Removal of rotation: Flying ice cube
(Tue May 18 2004 - 17:39:59 PDT)
Re: AMBER: Simulated annealing ...vlimit problem
(Mon May 17 2004 - 10:08:56 PDT)
Re: AMBER: tmd questions
(Thu May 13 2004 - 04:41:31 PDT)
Re: AMBER: simulated anealing ...vlimit exceed
(Thu May 06 2004 - 06:24:02 PDT)
Re: AMBER: simulated anealing ...vlimit exceed
(Thu May 06 2004 - 04:47:48 PDT)
carlsonh.umich.edu
Re: AMBER: antechamber/Mopac: strange GTP charges
(Thu May 13 2004 - 11:40:03 PDT)
Carsten Detering
AMBER: address error
(Wed May 19 2004 - 10:09:12 PDT)
AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 13:37:42 PDT)
Re: AMBER: dummy atom other than H
(Wed May 12 2004 - 14:18:23 PDT)
AMBER: dummy atom other than H
(Tue May 11 2004 - 18:12:22 PDT)
Chen Yongzhi
Re: AMBER: problems with mpich
(Fri May 28 2004 - 11:23:48 PDT)
AMBER: A problem for compiling amber8 parallel version
(Tue May 25 2004 - 13:58:37 PDT)
Chutintorn Punwong
Re: AMBER: segmentation fault when running parmchk
(Fri May 28 2004 - 13:08:56 PDT)
Re: AMBER: segmentation fault when running parmchk
(Thu May 27 2004 - 11:37:09 PDT)
Re: AMBER: segmentation fault when running parmchk
(Thu May 27 2004 - 11:01:16 PDT)
Re: AMBER: segmentation fault when running parmchk
(Mon May 24 2004 - 15:34:11 PDT)
Craig TOEPFER
Re: AMBER: Computing psec/day using Amber 8
(Thu May 06 2004 - 12:19:01 PDT)
AMBER: Computing psec/day using Amber 8
(Thu May 06 2004 - 11:21:53 PDT)
Dalmaris, John
AMBER: MMPBSA problem
(Sun May 30 2004 - 06:22:55 PDT)
darden
Re: AMBER: Nonplanar ring systems in nucleic acid
(Wed May 19 2004 - 14:05:59 PDT)
Dave S Walker
AMBER: ntwprt feature in AMBER7
(Thu May 06 2004 - 19:26:51 PDT)
David A. Case
Re: AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 10:33:08 PDT)
Re: AMBER: program compatibility
(Sun May 30 2004 - 22:05:15 PDT)
Re: AMBER: question about NMODE for RNA
(Sun May 30 2004 - 16:14:33 PDT)
Re: AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file
(Fri May 28 2004 - 14:34:45 PDT)
Re: AMBER: problems with mpich
(Fri May 28 2004 - 11:43:23 PDT)
Re: AMBER: problems with mpich
(Fri May 28 2004 - 09:52:56 PDT)
Re: AMBER: segmentation fault when running parmchk
(Thu May 27 2004 - 16:47:49 PDT)
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 16:15:37 PDT)
Re: AMBER: types of water atom
(Thu May 27 2004 - 13:34:59 PDT)
Re: AMBER: segmentation fault when running parmchk
(Thu May 27 2004 - 11:24:27 PDT)
Re: AMBER: xleap solvatebox problem
(Thu May 27 2004 - 08:42:48 PDT)
Re: AMBER: amber 8 under windows XP
(Thu May 27 2004 - 08:34:50 PDT)
Re: AMBER: Cannot read in sander
(Thu May 27 2004 - 08:11:03 PDT)
Re: AMBER: amber 8 under windows XP
(Wed May 26 2004 - 13:07:05 PDT)
Re: AMBER: A problem for compiling amber8 parallel version
(Wed May 26 2004 - 10:08:43 PDT)
Re: AMBER: protein is out of the water box
(Wed May 26 2004 - 09:17:00 PDT)
Re: AMBER: Cannot read in sander
(Wed May 26 2004 - 09:14:52 PDT)
Re: AMBER: Scaling nb between groups
(Tue May 25 2004 - 13:52:30 PDT)
Re: AMBER: mm_pbsa energy decomposition error
(Tue May 25 2004 - 08:20:13 PDT)
Re: AMBER: IOUTFM and binary/unformatted files error
(Tue May 25 2004 - 08:01:28 PDT)
Re: AMBER: segmentation fault when running parmchk
(Mon May 24 2004 - 21:41:14 PDT)
Re: AMBER: Free energies using Sander in Amber8
(Mon May 24 2004 - 21:36:22 PDT)
Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz
(Mon May 24 2004 - 08:37:29 PDT)
Re: AMBER: NHE problem
(Sun May 23 2004 - 09:14:34 PDT)
Re: AMBER: IGR1/grnam1 problem
(Sat May 22 2004 - 21:03:16 PDT)
Re: AMBER: NHE problem
(Sat May 22 2004 - 16:55:52 PDT)
Re: AMBER: Problem compiling amber7
(Fri May 21 2004 - 08:23:09 PDT)
Re: AMBER: pbsa calculation on part of the molecule & nmode analysis
(Thu May 20 2004 - 18:40:10 PDT)
Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Thu May 20 2004 - 18:33:14 PDT)
Re: AMBER: SHAKE in thermodynamic integration
(Thu May 20 2004 - 11:01:17 PDT)
Re: AMBER: DEBUG and GB
(Thu May 20 2004 - 11:34:38 PDT)
Re: AMBER: instalation of RES
(Thu May 20 2004 - 10:15:35 PDT)
Re: AMBER:
(Thu May 20 2004 - 10:14:13 PDT)
Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Thu May 20 2004 - 08:22:26 PDT)
Re: AMBER: Does this warning matter? (about improper torsion parameters)
(Wed May 19 2004 - 08:00:59 PDT)
Re: AMBER: CAP PROTOCOL SIMULATION
(Tue May 18 2004 - 15:47:26 PDT)
Re: AMBER: NTT=4
(Tue May 18 2004 - 07:57:19 PDT)
Re: AMBER: Clean in RESP
(Tue May 18 2004 - 07:55:42 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 16:21:15 PDT)
Re: AMBER: sander_classic for cap simulations?
(Mon May 17 2004 - 13:18:41 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Mon May 17 2004 - 12:36:41 PDT)
Re: AMBER: antechamber/Mopac: strange GTP charges
(Mon May 17 2004 - 12:31:38 PDT)
Re: AMBER: Simulated annealing ...vlimit problem
(Mon May 17 2004 - 12:27:30 PDT)
Re: AMBER: Simulated annealing ...vlimit problem
(Sat May 15 2004 - 09:14:06 PDT)
Re: AMBER: install RESP
(Sat May 15 2004 - 09:03:57 PDT)
Re: AMBER: antechamber
(Sat May 15 2004 - 09:02:30 PDT)
Re: AMBER: solvents reference.
(Fri May 14 2004 - 13:16:06 PDT)
Re: AMBER: antechamber/Mopac: strange GTP charges
(Fri May 14 2004 - 12:20:24 PDT)
Re: AMBER: antechamber/Mopac: strange GTP charges
(Thu May 13 2004 - 11:41:18 PDT)
Re: AMBER: dummy atom other than H
(Wed May 12 2004 - 12:30:26 PDT)
Re: AMBER: shake option in sander
(Wed May 12 2004 - 12:11:53 PDT)
Re: AMBER: MD with NTR + NMROPT
(Wed May 12 2004 - 12:09:24 PDT)
Re: AMBER: ptraj and LES
(Wed May 12 2004 - 08:19:00 PDT)
Re: AMBER: what does EAMBER stand for?
(Tue May 11 2004 - 10:30:56 PDT)
Re: AMBER: some bugfixes
(Mon May 10 2004 - 16:10:08 PDT)
Re: AMBER: MD with NTR + NMROPT
(Mon May 10 2004 - 08:46:06 PDT)
Re: AMBER: Solvent accessible surface area(LCPO) computation
(Fri May 07 2004 - 08:23:33 PDT)
Re: AMBER: solvent cap and eedmeth
(Fri May 07 2004 - 08:20:18 PDT)
Re: AMBER: Opteron PMEMD
(Thu May 06 2004 - 15:09:47 PDT)
Re: AMBER: Computing psec/day using Amber 8
(Thu May 06 2004 - 12:27:10 PDT)
Re: AMBER: Computing psec/day using Amber 8
(Thu May 06 2004 - 11:42:37 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Thu May 06 2004 - 08:29:30 PDT)
Re: AMBER: Sander klambda question
(Wed May 05 2004 - 16:43:44 PDT)
Re: AMBER: How to choose force constant?
(Wed May 05 2004 - 15:00:14 PDT)
Re: AMBER: H Bonds
(Wed May 05 2004 - 09:20:26 PDT)
Re: AMBER: Implicit solvents
(Wed May 05 2004 - 08:54:56 PDT)
Re: AMBER: Normal Mode Analysis possibility
(Tue May 04 2004 - 11:25:27 PDT)
Re: AMBER: separate the longitudinal and transverse vibrations frequencies
(Tue May 04 2004 - 11:15:38 PDT)
Re: AMBER: PMF correction factor
(Tue May 04 2004 - 11:01:18 PDT)
Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded".
(Tue May 04 2004 - 08:10:36 PDT)
AMBER: some bugfixes
(Mon May 03 2004 - 11:10:47 PDT)
Re: AMBER: nmode analysis
(Mon May 03 2004 - 10:14:19 PDT)
Re: AMBER: nmode analysis
(Mon May 03 2004 - 08:50:44 PDT)
Re: Re: AMBER: xleap problem
(Mon May 03 2004 - 08:45:34 PDT)
Re: AMBER: xleap problem
(Sun May 02 2004 - 14:07:20 PDT)
david.evans.ulsop.ac.uk
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 09:32:18 PDT)
Deanna Yarbro
Extreme Privacy Violation 4896
(Wed May 19 2004 - 09:48:11 PDT)
Do Anh Tuan
AMBER: Program error in testing of Amber8
(Sat May 15 2004 - 21:16:44 PDT)
Dr. Yong Duan
Re: AMBER: energy conservation with GB !!
(Sat May 15 2004 - 23:58:25 PDT)
Re: AMBER: why delete water molecule
(Tue May 04 2004 - 07:40:57 PDT)
Fang, Jianwen
AMBER: mm_pbsa energy decomposition error
(Tue May 25 2004 - 07:40:32 PDT)
AMBER: why EGB = nan
(Mon May 17 2004 - 07:54:44 PDT)
AMBER: questions on mm_pbsa
(Fri May 14 2004 - 11:49:54 PDT)
AMBER: ions in mm_pbsa
(Thu May 06 2004 - 08:30:12 PDT)
Feng, Hanqiao (NIH/NCI)
AMBER: protein is out of the water box
(Tue May 25 2004 - 15:35:01 PDT)
Fernandez-Carmona Juan
Re: AMBER: reference with ptraj
(Thu May 06 2004 - 23:27:53 PDT)
Fist Action
Five Fingered F'in amber Unreal Photos
(Fri May 14 2004 - 23:23:18 PDT)
Five Fingered F'in amber Unreal Photos
(Fri May 14 2004 - 23:23:15 PDT)
FyD
Re: AMBER: Use of RED
(Fri May 28 2004 - 13:20:42 PDT)
Re: AMBER: pdb in RED
(Thu May 27 2004 - 12:16:59 PDT)
Re: AMBER: Bug in babel conversion
(Tue May 25 2004 - 11:14:55 PDT)
Re: AMBER: parametrizacion partial charges
(Mon May 17 2004 - 08:37:02 PDT)
RE: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
(Wed May 12 2004 - 11:01:31 PDT)
Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
(Wed May 12 2004 - 09:42:31 PDT)
Re: AMBER: choosing 3 atoms for reorientaion in R.E.D
(Thu May 06 2004 - 15:00:44 PDT)
Re: AMBER: reorientation in R.E.D
(Wed May 05 2004 - 10:55:51 PDT)
Re: AMBER: methane box
(Wed May 05 2004 - 08:36:08 PDT)
Re: AMBER: reproduction of RESP charges for Gly
(Tue May 04 2004 - 13:48:43 PDT)
Re: AMBER: reproduction of RESP charges for Gly
(Tue May 04 2004 - 13:16:00 PDT)
Re: AMBER: resp demo files
(Mon May 03 2004 - 14:40:15 PDT)
Re: AMBER: esp or resp for all_amino94.lib
(Fri Apr 30 2004 - 16:28:57 PDT)
Gary Waters
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 13:08:49 PDT)
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 10:36:16 PDT)
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 09:55:14 PDT)
AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 09:00:33 PDT)
AMBER: Opteron PMEMD
(Thu May 06 2004 - 11:29:56 PDT)
Guanglei Cui
Re: AMBER: about amber8, replica exchange
(Fri May 28 2004 - 21:04:33 PDT)
Re: AMBER: Cannot read in sander-again
(Thu May 27 2004 - 14:28:39 PDT)
Re: AMBER: parallel installation problem
(Wed May 19 2004 - 18:54:21 PDT)
Re: AMBER: ptraj and LES
(Wed May 12 2004 - 12:34:31 PDT)
AMBER: ptraj and LES
(Tue May 11 2004 - 14:00:12 PDT)
AMBER: antechamber
(Tue May 04 2004 - 19:49:28 PDT)
Gustavo Pierdominici Sottile
AMBER: Use of RED
(Fri May 28 2004 - 11:44:26 PDT)
Re: AMBER: types of water atom
(Fri May 28 2004 - 11:25:45 PDT)
Re: AMBER: types of water atom
(Thu May 27 2004 - 12:28:27 PDT)
AMBER: pdb in RED
(Thu May 27 2004 - 10:29:44 PDT)
AMBER: types of water atom
(Wed May 26 2004 - 10:06:16 PDT)
AMBER: Clean in RESP
(Tue May 18 2004 - 04:46:38 PDT)
AMBER:
(Mon May 17 2004 - 11:38:53 PDT)
AMBER: parametrizacion partial charges
(Mon May 17 2004 - 06:45:58 PDT)
AMBER: installing RESP
(Sat May 15 2004 - 04:52:59 PDT)
AMBER: install RESP
(Sat May 15 2004 - 04:54:41 PDT)
Harvey, David Richard
AMBER: PMF correction factor
(Tue May 04 2004 - 06:35:13 PDT)
Helios Chen
AMBER: single amino acid energy
(Tue May 18 2004 - 01:15:02 PDT)
AMBER: why delete water molecule
(Mon May 03 2004 - 21:18:49 PDT)
AMBER: any program or tool
(Mon May 03 2004 - 03:16:15 PDT)
Herbert Georg
AMBER: solvents reference.
(Fri May 14 2004 - 12:56:38 PDT)
hj zou
AMBER: program compatibility
(Sun May 30 2004 - 19:07:39 PDT)
AMBER: tmd questions
(Wed May 12 2004 - 19:07:36 PDT)
Re: AMBER: xleap problem
(Tue May 04 2004 - 19:44:43 PDT)
Re: Re: AMBER: xleap problem
(Mon May 03 2004 - 01:02:34 PDT)
AMBER: xleap problem
(Sun May 02 2004 - 06:49:40 PDT)
Holger Gohlke
Re: AMBER: ptraj bug?
(Wed May 19 2004 - 08:31:12 PDT)
Re: AMBER: single amino acid energy
(Tue May 18 2004 - 08:23:26 PDT)
Re: AMBER: questions on mm_pbsa
(Tue May 18 2004 - 08:18:24 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Mon May 17 2004 - 11:05:57 PDT)
Re: AMBER: mm-pbsa:- atom charges and radii ?
(Tue May 11 2004 - 23:40:52 PDT)
Re: AMBER: ptraj read in matrix
(Tue May 11 2004 - 07:45:11 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Fri May 07 2004 - 05:48:51 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Wed May 05 2004 - 09:32:23 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Wed May 05 2004 - 03:28:57 PDT)
Re: AMBER: problem with MM/PBSA
(Wed May 05 2004 - 03:14:47 PDT)
Holly Freedman
Re: AMBER: ptraj
(Wed May 26 2004 - 10:30:07 PDT)
Re: AMBER: ptraj
(Tue May 25 2004 - 17:45:24 PDT)
AMBER: ptraj
(Tue May 25 2004 - 09:16:42 PDT)
AMBER: average structure from traj
(Tue May 18 2004 - 14:30:07 PDT)
Ian Withers
AMBER: ptraj bug?
(Wed May 19 2004 - 07:33:38 PDT)
Ilyas Yildirim
AMBER: Surface E&S Potential Mapping
(Tue May 25 2004 - 14:14:45 PDT)
AMBER: Bug in babel conversion (while following the RED manual in pp.15)
(Tue May 25 2004 - 11:00:39 PDT)
AMBER: Nonplanar ring systems in nucleic acid
(Wed May 19 2004 - 13:14:14 PDT)
Itziar Maestre Asenjo
AMBER: problem with MM/PBSA
(Tue May 04 2004 - 09:38:32 PDT)
J. Zhang, Dr
Re: Re: AMBER: about amber8, replica exchange
(Sun May 30 2004 - 17:09:24 PDT)
AMBER: about amber8, replica exchange
(Fri May 28 2004 - 20:45:49 PDT)
Re: Re: AMBER: Does this warning matter? (about improper torsion parameters)
(Wed May 19 2004 - 18:57:35 PDT)
AMBER: Does this warning matter? (about improper torsion parameters)
(Tue May 18 2004 - 20:04:32 PDT)
James W. Caldwell
Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Thu May 20 2004 - 20:02:01 PDT)
Jeffrey Dyason
AMBER: mm-pbsa:- atom charges and radii ?
(Tue May 11 2004 - 01:07:12 PDT)
Jiri Sponer
Re: Re: Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 07:42:27 PDT)
Re: Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 07:09:46 PDT)
Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 05:41:12 PDT)
Re: AMBER: Nonplanar ring systems in nucleic acid
(Thu May 20 2004 - 05:42:16 PDT)
Re: AMBER: Nonplanar ring systems in nucleic acid
(Thu May 20 2004 - 04:46:41 PDT)
Jiten
Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Mon May 24 2004 - 20:54:40 PDT)
AMBER: Free energies using Sander in Amber8
(Mon May 24 2004 - 19:52:52 PDT)
Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Thu May 20 2004 - 17:49:42 PDT)
AMBER: PF6- force field parameters
(Thu May 20 2004 - 17:32:29 PDT)
AMBER: Amber8 on Tru64 UNIX on Alpha systems
(Wed May 19 2004 - 18:28:50 PDT)
AMBER: Atom type with/without POL
(Thu May 13 2004 - 07:01:38 PDT)
Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded".
(Tue May 04 2004 - 03:58:20 PDT)
Joachim Reichelt
Re: AMBER: Problem compiling amber7
(Tue May 25 2004 - 05:27:59 PDT)
Re: AMBER: NTT=4
(Tue May 18 2004 - 10:01:50 PDT)
AMBER: NTT=4
(Tue May 18 2004 - 07:30:33 PDT)
John
AMBER: torsion angles
(Fri May 28 2004 - 16:02:04 PDT)
AMBER: time-averaged restraints
(Fri May 14 2004 - 10:04:49 PDT)
AMBER: reference with ptraj
(Thu May 06 2004 - 12:50:48 PDT)
Jones, Garth A
AMBER: DEBUG and GB
(Tue May 18 2004 - 05:02:32 PDT)
Junmei Wang
Re: AMBER: problem in antechamber
(Wed May 19 2004 - 15:21:43 PDT)
Re: AMBER: Problem : antechamber produces no output
(Wed May 12 2004 - 07:40:00 PDT)
AMBER: Possible amber8 antechamber PDB parsing bug
(Thu May 06 2004 - 10:09:30 PDT)
Re: AMBER: some bugfixes
(Tue May 04 2004 - 12:23:55 PDT)
Jyh-Shyong Ho
Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64
(Tue May 25 2004 - 17:07:34 PDT)
Kamp, Marc vander
AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file
(Thu May 27 2004 - 06:01:13 PDT)
Kazuo Koyano
Re: AMBER: mm_pbsa examples; delphi in mm_pbsa
(Fri May 14 2004 - 02:35:36 PDT)
Knut Langsetmo
Re: AMBER: amber7, namelist, xlf and osx
(Tue May 25 2004 - 06:17:26 PDT)
AMBER: amber7, namelist, xlf and osx
(Wed May 19 2004 - 15:47:26 PDT)
koby levy
AMBER: Removal of rotation: Flying ice cube
(Tue May 18 2004 - 17:23:54 PDT)
Kristy Mardis
AMBER: resp demo files
(Mon May 03 2004 - 12:29:45 PDT)
Linda Prengaman
AMBER: Amber 7 (sander) use of PME
(Thu May 27 2004 - 12:42:13 PDT)
AMBER: Sander klambda question
(Wed May 05 2004 - 15:14:22 PDT)
Lishan Yao
AMBER: Ammonia
(Thu May 20 2004 - 14:11:43 PDT)
AMBER: shake option in sander
(Wed May 12 2004 - 06:32:48 PDT)
M. L. Dodson
Re: AMBER: thermodynamic integration of ring opening
(Tue May 18 2004 - 05:33:28 PDT)
Re: AMBER: thermodynamic integration of ring opening
(Mon May 17 2004 - 16:46:29 PDT)
Majid moghaddam
AMBER: PCA prep file
(Tue May 18 2004 - 01:19:26 PDT)
Marc Perea
AMBER: Problem : antechamber produces no output
(Tue May 11 2004 - 03:19:52 PDT)
Marcin Krol
AMBER: Scaling nb between groups
(Tue May 25 2004 - 08:34:00 PDT)
AMBER: IGR1/grnam1 problem
(Tue May 18 2004 - 10:40:58 PDT)
AMBER: ptraj read in matrix
(Mon May 10 2004 - 04:57:25 PDT)
AMBER: ptraj analyze matrix entropy
(Fri May 07 2004 - 01:01:23 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Thu May 06 2004 - 06:48:02 PDT)
Re: AMBER: ptraj analyze matrix entropy
(Wed May 05 2004 - 08:07:05 PDT)
AMBER: ptraj analyze matrix entropy
(Wed May 05 2004 - 02:19:32 PDT)
Mark Williamson
AMBER: Possible amber8 antechamber PDB parsing bug
(Thu May 06 2004 - 08:16:19 PDT)
Martin Fabani
AMBER: MD with NTR + NMROPT
(Mon May 10 2004 - 01:56:28 PDT)
Martin Mucha
AMBER: IOUTFM and binary/unformatted files error
(Tue May 25 2004 - 00:18:44 PDT)
Mengjuei Hsieh
Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz
(Mon May 24 2004 - 12:12:39 PDT)
Re: AMBER: NHE problem
(Sat May 22 2004 - 17:30:07 PDT)
Re: AMBER: amber7, namelist, xlf and osx
(Wed May 19 2004 - 17:56:23 PDT)
Michele Porro
AMBER: simulated anealing ...vlimit exceed
(Tue May 11 2004 - 00:24:56 PDT)
Miguel
Re: AMBER: Problem compiling amber7
(Tue May 25 2004 - 02:54:55 PDT)
AMBER: Problem compiling amber7
(Fri May 21 2004 - 02:15:10 PDT)
Miguel de Federico
Re: AMBER: Gibbs and solvent caps
(Mon May 03 2004 - 03:28:47 PDT)
Mikyung Seo
AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
(Tue May 11 2004 - 15:51:01 PDT)
AMBER: choosing 3 atoms for reorientaion in R.E.D
(Thu May 06 2004 - 14:38:19 PDT)
AMBER: reorientation in R.E.D
(Wed May 05 2004 - 09:38:01 PDT)
AMBER: reproduction of RESP charges for Gly
(Tue May 04 2004 - 10:51:01 PDT)
Ming Lei
AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64
(Tue May 25 2004 - 08:27:49 PDT)
myang
AMBER: fit a 3D line to points
(Thu May 27 2004 - 14:11:08 PDT)
AMBER: Normal Mode Analysis possibility
(Tue May 04 2004 - 08:52:05 PDT)
Narang Manpreet Kaur
Re: AMBER: Simulated annealing ...vlimit problem
(Tue May 18 2004 - 07:09:31 PDT)
Obdulia Rabal
AMBER: CG maxitn exceeded
(Tue May 18 2004 - 09:29:53 PDT)
AMBER: CAP PROTOCOL SIMULATION
(Tue May 18 2004 - 02:32:29 PDT)
Oliver Hucke
Re: AMBER: parallel installation problem
(Mon May 24 2004 - 16:57:01 PDT)
AMBER: parallel installation problem
(Sat May 22 2004 - 17:40:17 PDT)
AMBER: parallel installation problem
(Wed May 19 2004 - 15:17:08 PDT)
Re: AMBER: CAP PROTOCOL SIMULATION
(Tue May 18 2004 - 14:07:45 PDT)
AMBER: sander_classic for cap simulations?
(Thu May 13 2004 - 15:43:36 PDT)
Re: AMBER: performance of periodic vs. non-periodic simulation
(Thu May 13 2004 - 09:14:08 PDT)
Re: AMBER: performance of periodic vs. non-periodic simulation
(Wed May 12 2004 - 13:42:50 PDT)
AMBER: performance of periodic vs. non-periodic simulation
(Wed May 12 2004 - 12:08:18 PDT)
AMBER: solvent cap and eedmeth
(Thu May 06 2004 - 16:31:42 PDT)
AMBER: cap waters always flexible?
(Thu May 06 2004 - 13:41:19 PDT)
Re: AMBER: antechamber gives GDP 0 charge
(Wed May 05 2004 - 13:46:06 PDT)
Re: AMBER: some bugfixes
(Tue May 04 2004 - 11:12:53 PDT)
Re: AMBER: why delete water molecule
(Tue May 04 2004 - 09:23:01 PDT)
Re: AMBER: xleap problem
(Sun May 02 2004 - 15:53:42 PDT)
Osman Gani
AMBER: FAD cofactor.
(Fri May 14 2004 - 02:34:28 PDT)
AMBER: Ligand from CCDC.
(Thu May 06 2004 - 08:38:16 PDT)
Peter Gannett
AMBER: Re: CCL:Helical parameters extraction from trajectory
(Fri May 28 2004 - 04:47:08 PDT)
Piotr Cieplak
Re: AMBER: amber 8 under windows XP
(Wed May 26 2004 - 15:08:38 PDT)
Re: AMBER: types of water atom
(Wed May 26 2004 - 10:28:17 PDT)
Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
(Wed May 12 2004 - 11:57:20 PDT)
Pradipta Bandyopadhyay
AMBER: Low frequency in quasi-harmonic analysis!!
(Sun May 30 2004 - 02:23:50 PDT)
AMBER: Reproducing the energy during restart in MD!
(Tue May 18 2004 - 23:33:27 PDT)
AMBER: energy conservation with GB !!
(Sat May 15 2004 - 23:27:01 PDT)
Qiang Lu
Re[4]: AMBER: rmsd over residues using ptraj
(Wed May 19 2004 - 12:19:33 PDT)
Re[2]: AMBER: rmsd over residues using ptraj
(Wed May 19 2004 - 10:19:38 PDT)
AMBER: rmsd over residues using ptraj
(Tue May 18 2004 - 17:41:16 PDT)
AMBER: A parm file suit for half beta and half alpha structure
(Mon May 10 2004 - 11:51:57 PDT)
AMBER: hbond in ptraj
(Fri May 07 2004 - 11:43:33 PDT)
Raik Grünberg
Re: AMBER: antechamber/Mopac: strange GTP charges
(Mon May 17 2004 - 08:38:17 PDT)
Re: AMBER: antechamber/Mopac: strange GTP charges
(Fri May 14 2004 - 03:35:13 PDT)
AMBER: antechamber/Mopac: strange GTP charges
(Thu May 13 2004 - 10:57:06 PDT)
AMBER: antechamber gives GDP 0 charge
(Wed May 05 2004 - 13:17:53 PDT)
Ray Luo
Re: AMBER: pbsa calculation on part of the molecule
(Wed May 19 2004 - 13:31:50 PDT)
Re: AMBER: PB bomb in pb_saarc
(Tue May 18 2004 - 17:54:21 PDT)
Re: AMBER: CAP PROTOCOL SIMULATION
(Mon May 17 2004 - 16:07:17 PDT)
Re: AMBER: PB bomb in pb_saarc
(Mon May 17 2004 - 15:58:21 PDT)
Re: AMBER: CAP PROTOCOL SIMULATION
(Mon May 17 2004 - 14:43:55 PDT)
Re: AMBER: CG maxitn exceeded
(Mon May 17 2004 - 12:10:29 PDT)
Re: AMBER: mm-pbsa:- atom charges and radii ?
(Mon May 10 2004 - 23:21:06 PDT)
Rhonda Torres
Re: AMBER: Sander went through
(Fri May 28 2004 - 17:49:44 PDT)
Robert Duke
Re: AMBER: Opteron PMEMD
(Thu May 06 2004 - 13:31:46 PDT)
Ross Walker
RE: AMBER: Cannot read in sander
(Thu May 27 2004 - 15:36:10 PDT)
RE: AMBER: Cannot read in sander
(Wed May 26 2004 - 18:08:48 PDT)
RE: AMBER: amber 8 under windows XP
(Wed May 26 2004 - 12:03:54 PDT)
RE: AMBER: ptraj
(Tue May 25 2004 - 10:35:39 PDT)
Ryan Ye
Re: AMBER: NHE problem
(Sun May 23 2004 - 08:19:56 PDT)
AMBER: NHE problem
(Fri May 21 2004 - 22:36:44 PDT)
S. Frank Yan
RE: AMBER: pbsa calculation on part of the molecule & nmode analysis
(Thu May 20 2004 - 18:06:11 PDT)
AMBER: pbsa calculation on part of the molecule
(Thu May 20 2004 - 13:25:46 PDT)
RE: AMBER: PB bomb in pb_saarc
(Tue May 18 2004 - 16:14:36 PDT)
AMBER: PB bomb in pb_saarc
(Tue May 18 2004 - 13:41:41 PDT)
FW: AMBER: ions in mm_pbsa
(Thu May 06 2004 - 10:23:55 PDT)
Sanjeev B.S.
Re: AMBER: H Bonds
(Fri May 07 2004 - 01:38:24 PDT)
Re: AMBER: H Bonds
(Wed May 05 2004 - 22:09:06 PDT)
Sarah Wittkopp
AMBER: Treating atom type LP the same as EP
(Mon May 17 2004 - 12:16:20 PDT)
scopio
Re: AMBER: ptraj
(Tue May 25 2004 - 16:49:47 PDT)
Re: AMBER: Problem compiling amber7
(Tue May 25 2004 - 05:15:28 PDT)
AMBER: Converting ORAC's topology file to AMBER's prepi file
(Fri May 14 2004 - 05:30:32 PDT)
AMBER: what does EAMBER stand for?
(Mon May 10 2004 - 18:08:35 PDT)
Re: AMBER: HIS protonation
(Mon May 10 2004 - 04:00:19 PDT)
AMBER: what is its file format ?
(Sat May 08 2004 - 07:13:21 PDT)
Re: AMBER: xleap problem
(Mon May 03 2004 - 01:51:03 PDT)
Re: AMBER: problem for compiling amber7 by ifc8
(Sun May 02 2004 - 21:18:31 PDT)
Re: AMBER: problem for compiling amber7 by ifc8
(Sun May 02 2004 - 17:15:58 PDT)
AMBER: problem for compiling amber7 by ifc8
(Sat May 01 2004 - 05:26:57 PDT)
Scott Brozell
Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64
(Tue May 25 2004 - 12:24:23 PDT)
Re: AMBER: Program error in testing of Amber8
(Sun May 16 2004 - 16:17:44 PDT)
Re: AMBER: PMEMD Built ? Wont run..
(Tue May 11 2004 - 12:41:15 PDT)
Re: AMBER: what does EAMBER stand for?
(Tue May 11 2004 - 10:45:09 PDT)
Re: AMBER: antechamber
(Wed May 05 2004 - 14:30:17 PDT)
Re: AMBER: ptraj: radius of gyration
(Sun May 02 2004 - 01:09:12 PDT)
sebnem
AMBER: nmode analysis
(Sun May 02 2004 - 17:52:12 PDT)
sebnem.mercury.chem.pitt.edu
Re: AMBER: nmode analysis
(Mon May 03 2004 - 09:31:18 PDT)
Seonah Kim
AMBER: Install Amber8 under cygwin
(Mon May 31 2004 - 18:35:16 PDT)
Sichun Yang
AMBER: ptraj: radius of gyration
(Sat May 01 2004 - 19:50:37 PDT)
Stefano.Pieraccini.unimi.it
AMBER: gaussian03 output in antechamber
(Wed May 12 2004 - 01:46:17 PDT)
AMBER: gaussian03 output in antechamber
(Tue May 11 2004 - 02:27:46 PDT)
AMBER: HIS protonation
(Mon May 10 2004 - 02:50:40 PDT)
Sunil_Koovakkat.berlex.com
AMBER: Solvent accessible surface area(LCPO) computation
(Wed May 05 2004 - 14:51:59 PDT)
Suwipa saen-oon
AMBER: problem in antechamber
(Wed May 19 2004 - 01:27:24 PDT)
Sébastien Osborne
Re: AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 11:12:54 PDT)
Re: AMBER: FEP error/early termination - why?
(Mon May 31 2004 - 10:51:15 PDT)
Re: AMBER: some bugfixes
(Mon May 03 2004 - 11:14:33 PDT)
AMBER: Gibbs and solvent caps
(Sat May 01 2004 - 11:59:07 PDT)
Thomas E. Cheatham, III
Re: AMBER: performance of periodic vs. non-periodic simulation
(Wed May 12 2004 - 13:17:33 PDT)
Re: AMBER: mm-pbsa:- atom charges and radii ?
(Tue May 11 2004 - 07:24:17 PDT)
Re: AMBER: hbond in ptraj
(Fri May 07 2004 - 12:15:15 PDT)
Re: AMBER: reference with ptraj
(Thu May 06 2004 - 15:12:18 PDT)
Re: AMBER: reference with ptraj
(Thu May 06 2004 - 13:11:58 PDT)
Re: AMBER: ions in mm_pbsa
(Thu May 06 2004 - 12:07:42 PDT)
Thomas Steinbrecher
AMBER: Decomposition in MMPBSA
(Thu May 13 2004 - 17:15:03 PDT)
Re: AMBER: question about mm-pbsa
(Mon May 10 2004 - 18:10:09 PDT)
Tomas Kubar
AMBER: xleap solvatebox problem
(Thu May 27 2004 - 05:33:44 PDT)
tomjas.poczta.onet.pl
AMBER: How to choose force constant?
(Tue May 04 2004 - 06:48:44 PDT)
Tru Huynh
Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz
(Tue May 25 2004 - 07:31:34 PDT)
AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz
(Mon May 24 2004 - 00:45:39 PDT)
Ty Curtis
RE: AMBER: rmsd over residues using ptraj
(Wed May 19 2004 - 09:23:50 PDT)
Venkata S Koppuravuri
Re: AMBER: Simulated annealing ...vlimit problem
(Mon May 17 2004 - 10:00:44 PDT)
AMBER: Simulated annealing ...vlimit problem
(Fri May 14 2004 - 07:22:44 PDT)
Viktor Hornak
Re: AMBER: problems with mpich
(Fri May 28 2004 - 12:00:15 PDT)
Re: AMBER: Amber 8 compilation
(Wed May 26 2004 - 10:08:08 PDT)
Re: AMBER: Problem compiling amber7
(Tue May 25 2004 - 05:20:40 PDT)
Re: AMBER: Problem compiling amber7
(Mon May 24 2004 - 08:19:04 PDT)
Re: AMBER: parallel installation problem
(Mon May 24 2004 - 07:38:50 PDT)
Re: AMBER: tmd questions
(Thu May 13 2004 - 05:16:36 PDT)
Re: AMBER: any program or tool
(Mon May 03 2004 - 05:18:56 PDT)
Re: AMBER: problem for compiling amber7 by ifc8
(Sat May 01 2004 - 07:11:49 PDT)
xhu1.memphis.edu
Re: AMBER: question about NMODE for RNA
(Sun May 30 2004 - 18:53:58 PDT)
AMBER: question about NMODE for RNA
(Sun May 30 2004 - 15:32:22 PDT)
AMBER: amber on AMD 64
(Fri May 28 2004 - 11:56:02 PDT)
Xiao He
Re: Re: Re: Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 08:01:28 PDT)
Re: Re: Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 07:29:56 PDT)
Re: Re: AMBER: a question about Van der waals radius
(Sat May 22 2004 - 06:55:05 PDT)
AMBER: a question about Van der waals radius
(Sat May 22 2004 - 05:07:05 PDT)
xiaowei li
AMBER: separate the longitudinal and transverse vibrations frequencies
(Mon May 03 2004 - 21:33:11 PDT)
Ye Mei
Re: Re: Re: Re: Re: AMBER: a question about Van der waals radius
(Sun May 23 2004 - 23:54:30 PDT)
AMBER: h bond
(Sun May 23 2004 - 23:27:37 PDT)
Ülo Lille
AMBER: Troubles in the NTP simulation: "vlimit exceeded".
(Tue May 04 2004 - 03:16:24 PDT)
Last message date
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Tue Jun 01 2004 - 02:53:00 PDT
Archived on
: Mon Dec 23 2024 - 05:53:17 PST
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