Amber Archive Mar 2008 by author
339 messages
:
Starting
Sun Mar 02 2008 - 06:07:56 PST,
Ending
Fri Apr 18 2008 - 21:15:44 PDT
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Alexander Metz
AMBER: Torsion potential in GAFF / "statistic value of parm94"
(Fri Mar 14 2008 - 05:53:10 PDT)
Andrew Borgert
Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Tue Mar 25 2008 - 08:11:20 PDT)
aneesh cna
AMBER: PF6 parameters
(Wed Mar 26 2008 - 21:43:58 PDT)
AMBER: OPLS force field
(Wed Mar 26 2008 - 08:48:19 PDT)
AMBER: problem with distance restraints
(Thu Mar 20 2008 - 03:13:31 PDT)
AMBER: problem with distance restrain
(Tue Mar 18 2008 - 03:16:09 PDT)
anna.schrey.gmx.de
Re: AMBER: Problems with neglected restaints
(Thu Mar 20 2008 - 12:43:20 PDT)
AMBER: Problems with neglected restaints
(Tue Mar 18 2008 - 09:40:20 PDT)
Re: AMBER: Atom types/parameters for chromene
(Thu Mar 06 2008 - 05:35:06 PST)
AMBER: Atom types/parameters for chromene
(Wed Mar 05 2008 - 01:34:24 PST)
Atro Tossavainen
AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER)
(Tue Mar 11 2008 - 07:33:33 PDT)
Re: AMBER: AMBER install problem
(Mon Mar 10 2008 - 23:51:18 PDT)
Re: AMBER: Compiler issues with Altix450
(Mon Mar 10 2008 - 16:13:45 PDT)
Re: AMBER: Benchmarks on Fujitsu PrimePower 2500?
(Mon Mar 10 2008 - 06:24:33 PDT)
Re: AMBER: Benchmarks on Fujitsu PrimePower 2500?
(Mon Mar 10 2008 - 01:04:20 PDT)
Re: AMBER: Compiler issues with Altix450
(Sat Mar 08 2008 - 14:19:36 PST)
Bertrand P. S. Russell
AMBER: Happy holi
(Thu Mar 20 2008 - 02:03:22 PDT)
Bill Ross
Re: AMBER: addions and addions2
(Tue Mar 25 2008 - 10:34:52 PDT)
Re: AMBER: XMGRACE on Linux 64 Bit
(Thu Mar 06 2008 - 16:12:51 PST)
Re: Fwd: Re: AMBER: xleap screen output
(Tue Mar 04 2008 - 09:59:58 PST)
Re: AMBER: xleap screen output
(Mon Mar 03 2008 - 14:08:17 PST)
Campbell, Patrick
FW: FW: AMBER: FW: MD run time inquiry
(Thu Mar 27 2008 - 06:55:28 PDT)
FW: AMBER: FW: MD run time inquiry
(Thu Mar 27 2008 - 05:14:16 PDT)
AMBER: FW: MD run time inquiry
(Thu Mar 27 2008 - 03:13:00 PDT)
RE: AMBER: cntrl namelist error
(Sat Mar 22 2008 - 09:22:18 PDT)
RE: AMBER: cntrl namelist error
(Sat Mar 22 2008 - 09:11:39 PDT)
AMBER: cntrl namelist error
(Sat Mar 22 2008 - 08:40:16 PDT)
RE: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 11:35:37 PDT)
RE: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 11:37:45 PDT)
RE: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 10:02:12 PDT)
AMBER: INPCRD error on open
(Thu Mar 20 2008 - 08:17:32 PDT)
RE: AMBER: Clarification on error message
(Sat Mar 08 2008 - 13:15:36 PST)
AMBER: Clarification on error message
(Sat Mar 08 2008 - 12:09:23 PST)
caoch
RE: AMBER: PF6 parameters
(Thu Mar 27 2008 - 21:28:03 PDT)
Carlos Simmerling
Re: FW: AMBER: FW: MD run time inquiry
(Thu Mar 27 2008 - 06:15:09 PDT)
Re: AMBER: FW: MD run time inquiry
(Thu Mar 27 2008 - 03:41:02 PDT)
Re: AMBER: hybrid remd imaging
(Mon Mar 24 2008 - 08:59:24 PDT)
Re: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 10:10:23 PDT)
Re: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 08:22:56 PDT)
Re: AMBER: replica exchange : problem with sander
(Thu Mar 20 2008 - 07:47:32 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 06:49:23 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 06:25:11 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 05:47:04 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 10:12:03 PDT)
Re: AMBER: Problems with neglected restaints
(Tue Mar 18 2008 - 10:05:11 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 09:39:01 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 07:29:38 PDT)
Re: AMBER: Temperature Range For REMD
(Thu Mar 13 2008 - 08:26:44 PDT)
Re: AMBER: Problem running implicit minimization
(Tue Mar 04 2008 - 15:39:23 PST)
Re: AMBER: Problem running implicit minimization
(Tue Mar 04 2008 - 03:04:38 PST)
AMBER: ACS COMP Division awards- deadline this week
(Mon Mar 03 2008 - 16:14:03 PST)
Catein Catherine
AMBER: potential of mean force: Unit of PMF energies and min path
(Wed Mar 19 2008 - 22:26:43 PDT)
Cenk Andac
Re: AMBER: Amber9 Installation Problem
(Wed Mar 19 2008 - 13:55:23 PDT)
Re: AMBER: Amber9 Installation Problem
(Wed Mar 19 2008 - 13:43:50 PDT)
Re: AMBER: Amber9 Installation Problem
(Wed Mar 19 2008 - 13:25:25 PDT)
ChengZhong Zhang
AMBER: SMD using amber
(Mon Mar 10 2008 - 18:54:23 PDT)
Chih-Ying Lin
AMBER: Amber Workshop
(Mon Mar 31 2008 - 13:40:52 PDT)
AMBER: running minimisation on cis-azobenzene
(Mon Mar 31 2008 - 12:45:20 PDT)
AMBER: Amber Workshop
(Fri Mar 28 2008 - 22:58:14 PDT)
AMBER: Questions toward Azobenzene
(Thu Mar 27 2008 - 21:23:40 PDT)
Chris Moth
RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Wed Mar 26 2008 - 15:27:35 PDT)
Re: AMBER: mm-pbsa multiple trajectory approach?
(Wed Mar 26 2008 - 15:21:25 PDT)
cniu.ualberta.ca
AMBER: umbrella sampling for proton transfer
(Tue Mar 25 2008 - 17:30:33 PDT)
Craig Gough
AMBER: Benchmarks on Fujitsu PrimePower 2500?
(Sun Mar 09 2008 - 22:36:28 PDT)
Cyril Bauvais
Re: AMBER: INPCRD error on open
(Thu Mar 20 2008 - 09:04:31 PDT)
Da-Wei Li
Re: AMBER: RMSD of two different molecules
(Wed Mar 26 2008 - 13:39:19 PDT)
Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Tue Mar 25 2008 - 10:08:29 PDT)
Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Mon Mar 24 2008 - 13:12:42 PDT)
Daniel Cappel
AMBER: energy problems in simulation with restraints
(Mon Mar 31 2008 - 02:39:13 PDT)
Daniel Smith
AMBER: NTR Restraints
(Tue Mar 25 2008 - 18:17:27 PDT)
David A. Case
Re: AMBER: memory limitation of Amber 9
(Mon Mar 31 2008 - 22:50:41 PDT)
Re: AMBER: nmode
(Mon Mar 31 2008 - 12:25:52 PDT)
Re: AMBER: installation amber9
(Mon Mar 31 2008 - 10:51:45 PDT)
Re: AMBER: energy problems in simulation with restraints
(Mon Mar 31 2008 - 08:35:58 PDT)
Re: AMBER: AMBER 9 testing
(Sun Mar 30 2008 - 09:23:15 PDT)
Re: AMBER: problem with nmod
(Fri Mar 28 2008 - 17:19:40 PDT)
Re: AMBER: AMBER 9 testing
(Fri Mar 28 2008 - 17:10:02 PDT)
Re: AMBER: NTR Restraints
(Thu Mar 27 2008 - 13:17:31 PDT)
Re: AMBER: how to link two different atoms in xLeap
(Wed Mar 26 2008 - 21:52:18 PDT)
Re: AMBER: Error with a binary restart file
(Wed Mar 26 2008 - 18:11:58 PDT)
Re: AMBER: OPLS force field
(Wed Mar 26 2008 - 09:08:57 PDT)
Re: AMBER: help regarding warning message
(Tue Mar 25 2008 - 11:51:07 PDT)
Re: AMBER: Nmode segmentation fault
(Tue Mar 25 2008 - 11:44:51 PDT)
Re: AMBER: Nmode segmentation fault
(Tue Mar 25 2008 - 09:34:37 PDT)
Re: AMBER: RE: Force Field Parameterizing
(Tue Mar 25 2008 - 08:23:34 PDT)
Re: AMBER: equilibration of peptide
(Sat Mar 22 2008 - 10:51:47 PDT)
Re: AMBER: standard residues
(Sat Mar 22 2008 - 09:30:03 PDT)
Re: AMBER: cntrl namelist error
(Sat Mar 22 2008 - 09:11:52 PDT)
Re: AMBER: problem with distance restraints
(Fri Mar 21 2008 - 10:56:28 PDT)
Re: AMBER: Amber9 Installation Problem
(Thu Mar 20 2008 - 16:23:53 PDT)
Re: AMBER: What's making my system lose total energy?
(Wed Mar 19 2008 - 18:46:31 PDT)
Re: AMBER: Amber9 Installation Problem
(Wed Mar 19 2008 - 18:37:57 PDT)
Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Wed Mar 19 2008 - 15:54:24 PDT)
Re: AMBER: Inquiry on analyzing the amplitude from nmdout results
(Wed Mar 19 2008 - 15:49:21 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Wed Mar 19 2008 - 14:57:54 PDT)
Re: AMBER: Inquiry on analyzing the amplitude from nmdout results
(Wed Mar 19 2008 - 14:46:10 PDT)
Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Wed Mar 19 2008 - 08:42:13 PDT)
Re: AMBER: problem with distance restrain
(Tue Mar 18 2008 - 12:00:11 PDT)
Re: AMBER: Problems with neglected restaints
(Tue Mar 18 2008 - 10:15:56 PDT)
Re: Fwd: AMBER: lastrst problem
(Tue Mar 18 2008 - 08:37:48 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Mon Mar 17 2008 - 22:30:48 PDT)
Re: AMBER: compiling AMBER9 with bintraj option on AMD64
(Mon Mar 17 2008 - 16:48:00 PDT)
Re: AMBER: study of protein stability in different ion using AMBER
(Fri Mar 14 2008 - 22:48:13 PDT)
Re: AMBER: problem with antech amber
(Fri Mar 14 2008 - 22:09:00 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 21:41:09 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 20:40:35 PDT)
Re: AMBER: distance restraint
(Thu Mar 13 2008 - 13:40:07 PDT)
Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127
(Tue Mar 11 2008 - 22:43:26 PDT)
Re: AMBER: AMBER install problem
(Tue Mar 11 2008 - 17:47:58 PDT)
Re: AMBER: AMBER install problem
(Mon Mar 10 2008 - 17:50:30 PDT)
Re: AMBER: Fwd: positive potential energy and large 1-4 EEL
(Mon Mar 10 2008 - 17:19:51 PDT)
Re: AMBER: output effective Born radii
(Mon Mar 10 2008 - 17:07:39 PDT)
Re: AMBER: Compiler issues with Altix450
(Mon Mar 10 2008 - 16:29:50 PDT)
Re: AMBER: Microcannonical MD Reference
(Fri Mar 07 2008 - 14:47:02 PST)
Re: AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis
(Fri Mar 07 2008 - 13:36:33 PST)
Re: AMBER: NVE energy and temperature drift
(Fri Mar 07 2008 - 08:32:51 PST)
Re: AMBER: Atom types/parameters for chromene
(Wed Mar 05 2008 - 11:15:25 PST)
Re: AMBER: questions about run MD at different pH
(Tue Mar 04 2008 - 17:59:49 PST)
Re: AMBER: Problem running implicit minimization
(Mon Mar 03 2008 - 21:59:00 PST)
Re: AMBER: questions about run MD at different pH
(Mon Mar 03 2008 - 21:07:00 PST)
Re: AMBER: xleap screen output
(Mon Mar 03 2008 - 13:31:17 PST)
Re: AMBER: Writing pressure in md.out file in NVT simulation
(Mon Mar 03 2008 - 11:24:20 PST)
David Cerutti
Re: AMBER: What's making my system lose total energy?
(Tue Mar 18 2008 - 11:43:42 PDT)
Re: AMBER: What's making my system lose total energy?
(Mon Mar 17 2008 - 20:52:10 PDT)
AMBER: What's making my system lose total energy?
(Mon Mar 17 2008 - 17:20:30 PDT)
David LeBard
AMBER: Timing analysis on Ranger
(Sun Mar 09 2008 - 13:06:18 PDT)
Re: AMBER: XMGRACE on Linux 64 Bit
(Fri Mar 07 2008 - 10:53:47 PST)
David Rangel
Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127
(Wed Mar 12 2008 - 10:04:18 PDT)
AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127
(Tue Mar 11 2008 - 20:30:14 PDT)
Douglas Kojetin
AMBER: residual dipolar couplings - alignment tensor energy
(Wed Mar 26 2008 - 12:46:48 PDT)
dpandit.brandeis.edu
AMBER: addions and addions2
(Tue Mar 25 2008 - 07:38:22 PDT)
RE: AMBER: XMGRACE on Linux 64 Bit
(Fri Mar 07 2008 - 10:40:19 PST)
Re: AMBER: XMGRACE on Linux 64 Bit
(Thu Mar 06 2008 - 17:50:55 PST)
AMBER: XMGRACE on Linux 64 Bit
(Thu Mar 06 2008 - 15:15:00 PST)
E.M.
AMBER: MNDO parameters for Mg+2
(Wed Mar 19 2008 - 10:28:09 PDT)
Edyta Malolepsza
Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Mon Mar 31 2008 - 06:05:42 PDT)
Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Wed Mar 19 2008 - 09:49:45 PDT)
AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Thu Mar 06 2008 - 04:23:06 PST)
Emilio Xavier Esposito
Re: AMBER: meet problem in adding ions and waterbox
(Sun Mar 30 2008 - 10:26:45 PDT)
Eric Germaneau
AMBER: GAFF
(Fri Mar 28 2008 - 05:38:41 PDT)
fatima.chami.durham.ac.uk
AMBER: TI: perturbation method
(Mon Mar 31 2008 - 01:40:40 PDT)
finke.oakland.edu
Re: AMBER: Compiler issues with Altix450
(Mon Mar 10 2008 - 13:45:37 PDT)
AMBER: Compiler issues with Altix450
(Sat Mar 08 2008 - 10:37:25 PST)
Francesco Pietra
Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
(Wed Mar 19 2008 - 10:26:24 PDT)
Re: AMBER: Atom types/parameters for chromene
(Wed Mar 05 2008 - 10:07:05 PST)
Fwd: Re: AMBER: xleap screen output SOLVED
(Tue Mar 04 2008 - 12:44:15 PST)
Fwd: Re: AMBER: xleap screen output
(Tue Mar 04 2008 - 09:33:34 PST)
Re: AMBER: xleap screen output
(Tue Mar 04 2008 - 09:27:00 PST)
Re: AMBER: xleap screen output
(Mon Mar 03 2008 - 13:48:59 PST)
AMBER: xleap screen output
(Mon Mar 03 2008 - 13:02:54 PST)
FyD
RE: AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 06:32:30 PDT)
RE: AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 04:19:49 PDT)
Re: AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 03:31:39 PDT)
Re: AMBER: FAD and NAD parameters
(Wed Mar 26 2008 - 03:57:27 PDT)
Re: AMBER: anion and cation simulaton
(Tue Mar 25 2008 - 12:54:56 PDT)
AMBER: RE: Force Field Parameterizing
(Tue Mar 25 2008 - 12:42:03 PDT)
Re: AMBER: Charge scheme for simulating protonated adenine
(Fri Mar 21 2008 - 00:43:51 PDT)
Geoff Wood
AMBER: installation amber9
(Mon Mar 31 2008 - 04:02:01 PDT)
Re: AMBER: hybrid remd imaging
(Thu Mar 27 2008 - 05:56:30 PDT)
Re: AMBER: hybrid remd imaging
(Mon Mar 24 2008 - 09:21:41 PDT)
Re: AMBER: hybrid remd imaging
(Mon Mar 24 2008 - 09:16:25 PDT)
AMBER: hybrid remd imaging
(Mon Mar 24 2008 - 08:51:51 PDT)
Gohlke.bioinformatik.uni-frankfurt.de
Re: AMBER: mmpbsa INSTRNG error?
(Sun Mar 09 2008 - 09:13:05 PDT)
Guillaume Renvez
AMBER: REMD simulation error
(Fri Mar 28 2008 - 07:01:20 PDT)
Re: AMBER: replica exchange : problem with sander
(Thu Mar 20 2008 - 08:02:29 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 06:57:55 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 06:35:55 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 06:13:01 PDT)
Re: AMBER: replica exchange : problem with sander
(Wed Mar 19 2008 - 05:14:38 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 10:24:10 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 10:07:54 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 09:21:21 PDT)
Re: AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 08:29:39 PDT)
AMBER: replica exchange : problem with sander
(Tue Mar 18 2008 - 07:09:34 PDT)
gurpreet singh
AMBER: Regarding SHAKE
(Sun Mar 30 2008 - 03:38:48 PDT)
AMBER: anion and cation simulaton
(Tue Mar 25 2008 - 09:22:29 PDT)
AMBER: distance restraint
(Thu Mar 13 2008 - 04:28:28 PDT)
AMBER: Antechamber, net molecular charge
(Sun Mar 09 2008 - 21:51:58 PDT)
Re: AMBER: regarding:calculation of b factor using ptraj
(Sun Mar 02 2008 - 09:24:29 PST)
Holly Freedman
Re: AMBER: standard residues
(Sat Mar 22 2008 - 15:27:07 PDT)
AMBER: standard residues
(Wed Mar 19 2008 - 13:03:02 PDT)
Re: AMBER: output effective Born radii
(Mon Mar 10 2008 - 19:24:32 PDT)
AMBER: output effective Born radii
(Mon Mar 10 2008 - 15:57:06 PDT)
Ivelin Georgiev
Re: AMBER: Water Topology
(Thu Mar 20 2008 - 06:44:51 PDT)
AMBER: Water Topology
(Wed Mar 19 2008 - 21:12:28 PDT)
James Thomas
AMBER: nmode
(Mon Mar 31 2008 - 11:48:43 PDT)
Re: AMBER: Nmode segmentation fault
(Tue Mar 25 2008 - 12:00:44 PDT)
Re: AMBER: Nmode segmentation fault
(Tue Mar 25 2008 - 10:22:43 PDT)
AMBER: Nmode segmentation fault
(Tue Mar 25 2008 - 04:53:21 PDT)
Re: AMBER: Inquiry on analyzing the amplitude from nmdout results
(Wed Mar 19 2008 - 15:00:35 PDT)
AMBER: Inquiry on analyzing the amplitude from nmdout results
(Wed Mar 19 2008 - 09:09:05 PDT)
AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis
(Fri Mar 07 2008 - 09:30:58 PST)
jani sahil
AMBER: regarding:calculation of b factor using ptraj
(Sat Mar 01 2008 - 08:10:10 PST)
Jianyin Shao
Re: AMBER:
(Thu Mar 06 2008 - 13:24:03 PST)
Jojart Balazs
Re: AMBER: ptraj, hbond and non-bonded contacts
(Fri Mar 14 2008 - 01:19:37 PDT)
JunJun Liu
Re: AMBER: RMSD of two different molecules
(Wed Mar 26 2008 - 14:54:11 PDT)
AMBER: RMSD of two different molecules
(Wed Mar 26 2008 - 13:35:32 PDT)
Junmei Wang
Re: AMBER: can't make antechamber work for regular nucleotides
(Tue Mar 18 2008 - 14:08:46 PDT)
Re: AMBER: Torsion potential in GAFF / "statistic value of parm94"
(Fri Mar 14 2008 - 20:01:20 PDT)
Re: AMBER: can't make antechamber work for regular nucleotides
(Fri Mar 14 2008 - 19:10:41 PDT)
Re: AMBER: question on antechamber: jaguar ouput
(Tue Mar 11 2008 - 11:22:52 PDT)
Re: AMBER: Antechamber, net molecular charge
(Mon Mar 10 2008 - 07:39:08 PDT)
Re: AMBER: Atom types/parameters for chromene
(Wed Mar 05 2008 - 08:23:19 PST)
Re: AMBER: missing gaff parameters
(Tue Mar 04 2008 - 06:53:39 PST)
Kailee
Re: AMBER: questions about run MD at different pH
(Tue Mar 04 2008 - 03:40:30 PST)
AMBER: questions about run MD at different pH
(Mon Mar 03 2008 - 06:51:40 PST)
Kefa Lu
AMBER: convert AMBER format input files into DL_POLY format input files?
(Tue Mar 11 2008 - 01:27:23 PDT)
Kijeong Kwac
AMBER: Error with a binary restart file
(Wed Mar 26 2008 - 16:07:51 PDT)
AMBER: RE: Re: AMBER: AMBER install problem
(Thu Mar 13 2008 - 10:35:10 PDT)
Lars Skjærven
AMBER: Protein rotating out of box
(Thu Mar 27 2008 - 14:34:48 PDT)
Re: AMBER: NVE energy and temperature drift
(Fri Mar 07 2008 - 09:34:33 PST)
AMBER: NVE energy and temperature drift
(Fri Mar 07 2008 - 07:36:48 PST)
Li Dawei
AMBER: Energy calculation and replica exchange in Amber9
(Thu Mar 13 2008 - 06:50:49 PDT)
Lili Peng
Re: AMBER: Problem running implicit minimization
(Tue Mar 04 2008 - 17:29:36 PST)
Re: AMBER: Problem running implicit minimization
(Tue Mar 04 2008 - 15:25:32 PST)
Re: AMBER: Problem running implicit minimization
(Mon Mar 03 2008 - 22:17:27 PST)
AMBER: Problem running implicit minimization
(Mon Mar 03 2008 - 21:10:52 PST)
Lwin, ThuZar
RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . .
(Tue Mar 18 2008 - 09:45:49 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ).
(Fri Mar 14 2008 - 08:32:25 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib )
(Thu Mar 13 2008 - 17:13:57 PDT)
Madjid Taghdir
AMBER: problem with antech amber
(Mon Mar 10 2008 - 08:07:16 PDT)
Marcelo Puiatti
Re: AMBER: question on antechamber: jaguar ouput
(Tue Mar 11 2008 - 11:35:10 PDT)
Markus Kaukonen
AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water
(Sun Mar 30 2008 - 23:34:48 PDT)
Marta Rossini
RE: AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 05:57:04 PDT)
RE: AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 04:00:52 PDT)
AMBER: Select specific residues (leap)
(Mon Mar 31 2008 - 02:28:31 PDT)
Mey Khalili
Re: AMBER: can't make antechamber work for regular nucleotides
(Mon Mar 17 2008 - 06:59:01 PDT)
AMBER: can't make antechamber work for regular nucleotides
(Thu Mar 13 2008 - 07:03:45 PDT)
AMBER: Fwd: positive potential energy and large 1-4 EEL
(Fri Mar 07 2008 - 08:54:28 PST)
mkseo
AMBER: multiple dihedral restraints using group
(Mon Mar 31 2008 - 10:11:30 PDT)
Mohd Farid Ismail
RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program
(Tue Mar 04 2008 - 17:09:52 PST)
oguz gurbulak
AMBER: force field
(Thu Mar 13 2008 - 15:00:58 PDT)
Paul Johns
Re: AMBER: Heating POL3 Box Troubles
(Wed Mar 19 2008 - 12:22:50 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Mon Mar 17 2008 - 13:07:02 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 14:01:22 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 12:13:02 PDT)
AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 11:44:44 PDT)
prateeksha s
Re: AMBER: Charge scheme for simulating protonated adenine
(Fri Mar 21 2008 - 09:32:14 PDT)
Re: AMBER: Charge scheme for simulating protonated adenine
(Fri Mar 21 2008 - 09:32:06 PDT)
AMBER: Charge scheme for simulating protonated adenine
(Thu Mar 20 2008 - 23:58:19 PDT)
Prem Prakash Pathak
AMBER: study of protein stability in different ion using AMBER
(Wed Mar 12 2008 - 23:20:31 PDT)
priya priya
AMBER: Microcannonical MD Reference
(Fri Mar 07 2008 - 05:40:34 PST)
Qi Yan
RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Wed Mar 26 2008 - 07:42:54 PDT)
RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Tue Mar 25 2008 - 10:00:35 PDT)
RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Mon Mar 24 2008 - 13:50:40 PDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Mon Mar 24 2008 - 13:01:35 PDT)
RE: AMBER: mm_pbsa positive ELE
(Mon Mar 17 2008 - 12:23:52 PDT)
AMBER: mm_pbsa positive ELE
(Mon Mar 17 2008 - 11:20:21 PDT)
Qiang Li
AMBER: meet problem in adding ions and waterbox
(Sat Mar 29 2008 - 22:43:54 PDT)
Ray Luo
Re: AMBER: mm_pbsa positive ELE
(Mon Mar 17 2008 - 13:14:57 PDT)
Re: AMBER: mm_pbsa positive ELE
(Mon Mar 17 2008 - 11:33:11 PDT)
rebeca.mmb.pcb.ub.es
AMBER: measuring contacts: error "glibc detected"
(Fri Mar 28 2008 - 05:26:42 PDT)
AMBER: implicit energy calculations
(Thu Mar 13 2008 - 09:26:43 PDT)
Rita Cassia
Re: AMBER: solvate with methanol
(Tue Mar 11 2008 - 05:33:46 PDT)
Robert Duke
Re: AMBER: Benchmarks on Fujitsu PrimePower 2500?
(Mon Mar 10 2008 - 06:24:21 PDT)
Ross Walker
RE: AMBER: cntrl namelist error
(Sat Mar 22 2008 - 09:01:47 PDT)
RE: AMBER: Water Topology
(Thu Mar 20 2008 - 08:08:46 PDT)
RE: AMBER: Water Topology
(Wed Mar 19 2008 - 21:49:43 PDT)
RE: AMBER: MNDO parameters for Mg+2
(Wed Mar 19 2008 - 11:10:18 PDT)
RE: AMBER: What's making my system lose total energy?
(Mon Mar 17 2008 - 19:54:19 PDT)
RE: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ).
(Fri Mar 14 2008 - 09:30:13 PDT)
AMBER: RE: Request
(Fri Mar 07 2008 - 12:38:25 PST)
RE: AMBER: XMGRACE on Linux 64 Bit
(Thu Mar 06 2008 - 18:30:44 PST)
RE: AMBER:
(Thu Mar 06 2008 - 10:37:16 PST)
RE: AMBER: missing gaff parameters
(Tue Mar 04 2008 - 07:39:03 PST)
rpaduri.chem.wayne.edu
Re: AMBER: Charge scheme for simulating protonated adenine
(Fri Mar 21 2008 - 08:29:18 PDT)
Samuel Genheden (a03samge)
SV: SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 13:41:31 PDT)
SV: SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 05:00:52 PDT)
SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 04:02:59 PDT)
SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 03:43:21 PDT)
AMBER: ptraj, hbond and non-bonded contacts
(Thu Mar 13 2008 - 07:54:03 PDT)
AMBER: ptraj and non-bonded contacts
(Wed Mar 12 2008 - 09:34:44 PDT)
Samuele Giani
Re: AMBER: missing gaff parameters
(Tue Mar 04 2008 - 08:42:03 PST)
AMBER: missing gaff parameters
(Tue Mar 04 2008 - 00:46:38 PST)
san_amber roy
Re: Fwd: AMBER: lastrst problem
(Wed Mar 19 2008 - 09:07:26 PDT)
Fwd: AMBER: lastrst problem
(Wed Mar 12 2008 - 08:19:08 PDT)
AMBER: lastrst problem
(Wed Mar 12 2008 - 08:07:23 PDT)
AMBER: solvate with methanol
(Tue Mar 11 2008 - 02:23:40 PDT)
Scott Brozell
AMBER: Re: Amber: parameters for Silicon
(Mon Mar 10 2008 - 16:57:29 PDT)
Sergio Wong
AMBER: mmpbsa INSTRNG error?
(Sat Mar 08 2008 - 22:06:44 PST)
serhanyigen.mail.ege.edu.tr
AMBER: Adding New Parameters and Modifying Existing Parameters
(Tue Mar 11 2008 - 04:51:18 PDT)
Seth Lilavivat
Re: AMBER: mm-pbsa multiple trajectory approach?
(Fri Mar 28 2008 - 08:28:31 PDT)
AMBER: mm-pbsa multiple trajectory approach?
(Wed Mar 26 2008 - 10:32:54 PDT)
AMBER: Convert dcd to mdcrd
(Tue Mar 25 2008 - 11:13:22 PDT)
Shultz, Jack
AMBER: RE: Force Field Parameterizing
(Mon Mar 24 2008 - 08:31:32 PDT)
snoze pa
AMBER: how to link two different atoms in xLeap
(Wed Mar 26 2008 - 13:56:12 PDT)
Re: AMBER: help regarding warning message
(Tue Mar 25 2008 - 13:23:55 PDT)
AMBER: help regarding warning message
(Tue Mar 25 2008 - 09:17:43 PDT)
Steve Seibold
RE: AMBER:
(Thu Mar 06 2008 - 10:27:34 PST)
AMBER:
(Thu Mar 06 2008 - 10:04:01 PST)
Steven Winfield
Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
(Wed Mar 26 2008 - 08:22:26 PDT)
Sudha Mani Karra
Re: AMBER: Writing pressure in md.out file in NVT simulation
(Mon Mar 03 2008 - 12:56:13 PST)
AMBER: Writing pressure in md.out file in NVT simulation
(Mon Mar 03 2008 - 10:58:46 PST)
sychen
AMBER: How to calculate deformability by PTRAJ ?
(Thu Mar 13 2008 - 18:44:36 PDT)
Syed Tarique Moin
AMBER: Negative ligand
(Sat Mar 15 2008 - 02:12:09 PDT)
Fwd: AMBER: Negative ligand (Peroxide)
(Sun Mar 09 2008 - 22:59:43 PDT)
AMBER: Negative ligand (Peroxide)
(Sat Mar 08 2008 - 03:36:56 PST)
Taufik Al-Sarraj
Re: AMBER: AMBER 9 testing
(Fri Mar 28 2008 - 21:13:31 PDT)
AMBER: AMBER 9 testing
(Fri Mar 28 2008 - 17:18:30 PDT)
Thomas Cheatham
Re: AMBER: What's making my system lose total energy?
(Mon Mar 17 2008 - 20:36:30 PDT)
Re: AMBER: Problem running implicit minimization
(Tue Mar 04 2008 - 15:47:50 PST)
Thomas Cheatham III
Re: SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 09:51:54 PDT)
Re: AMBER: ptraj, hbond and non-bonded contacts
(Thu Mar 13 2008 - 10:49:14 PDT)
Re: AMBER: implicit energy calculations
(Thu Mar 13 2008 - 10:47:04 PDT)
Thomas Leonard
AMBER: FAD and NAD parameters
(Wed Mar 26 2008 - 02:26:52 PDT)
Thomas Steinbrecher
Re: AMBER: running minimisation on cis-azobenzene
(Mon Mar 31 2008 - 13:14:17 PDT)
Re: AMBER: TI: perturbation method
(Mon Mar 31 2008 - 09:32:21 PDT)
Re: AMBER: umbrella sampling for proton transfer
(Tue Mar 25 2008 - 18:11:58 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 14:22:21 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 12:31:03 PDT)
Re: AMBER: Heating POL3 Box Troubles
(Fri Mar 14 2008 - 12:01:06 PDT)
Re: AMBER: Adding New Parameters and Modifying Existing Parameters
(Tue Mar 11 2008 - 09:46:33 PDT)
Re: AMBER: writing out a distance between two atoms in sander
(Mon Mar 10 2008 - 10:17:35 PDT)
Re: AMBER: Clarification on error message
(Sat Mar 08 2008 - 12:17:35 PST)
Re: AMBER:
(Thu Mar 06 2008 - 10:13:23 PST)
Re: AMBER: setBox command
(Thu Mar 06 2008 - 10:06:32 PST)
trudy.uoguelph.ca
Re: AMBER: Amber9 Installation Problem
(Thu Mar 20 2008 - 15:51:08 PDT)
Re: AMBER: Amber9 Installation Problem
(Thu Mar 20 2008 - 15:43:48 PDT)
AMBER: Amber9 Installation Problem
(Wed Mar 19 2008 - 09:28:35 PDT)
tushar garud
AMBER: equilibration of peptide
(Fri Mar 21 2008 - 21:02:25 PDT)
AMBER: Temperature Range For REMD
(Thu Mar 13 2008 - 08:20:02 PDT)
Uma R
AMBER: reg molecular dynamics
(Fri Mar 07 2008 - 19:17:32 PST)
Vijay Manickam Achari
AMBER: setBox command
(Wed Mar 05 2008 - 21:20:01 PST)
vikky 99
AMBER: Error- MM_PBSA calculation
(Thu Mar 27 2008 - 01:47:53 PDT)
Vlad Cojocaru
Re: AMBER: Convert dcd to mdcrd
(Wed Mar 26 2008 - 02:02:38 PDT)
Re: AMBER: compiling AMBER9 with bintraj option on AMD64
(Tue Mar 18 2008 - 02:32:13 PDT)
AMBER: compiling AMBER9 with bintraj option on AMD64
(Fri Mar 14 2008 - 10:44:56 PDT)
Re: SV: AMBER: ptraj, hbond and non-bonded contacts
(Mon Mar 17 2008 - 04:00:41 PDT)
Re: AMBER: writing out a distance between two atoms in sander
(Mon Mar 10 2008 - 10:35:58 PDT)
AMBER: writing out a distance between two atoms in sander
(Mon Mar 10 2008 - 06:33:55 PDT)
Re: AMBER: Writing pressure in md.out file in NVT simulation
(Mon Mar 03 2008 - 11:26:50 PST)
wei zhang
Re: AMBER: question on antechamber: jaguar ouput
(Wed Mar 12 2008 - 11:14:55 PDT)
AMBER: question on antechamber: jaguar ouput
(Tue Mar 11 2008 - 10:01:55 PDT)
Yannick Monclin
AMBER: [success] problem compiling Amber9 on Bull Linux
(Thu Mar 13 2008 - 04:56:48 PDT)
yavuzturkm.prc.boun.edu.tr
AMBER: memory limitation of Amber 9
(Mon Mar 31 2008 - 11:49:40 PDT)
Ye Mei
AMBER: a minor bug in RESP
(Tue Mar 18 2008 - 00:05:34 PDT)
AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit
(Wed Mar 05 2008 - 01:30:50 PST)
Yi-Ming Cheng
AMBER: Free energy landscape? HOWTO?
(Mon Mar 31 2008 - 01:12:05 PDT)
yuri pomè
AMBER: problem with nmod
(Fri Mar 28 2008 - 09:42:54 PDT)
Last message date
:
Fri Apr 18 2008 - 21:15:44 PDT
Archived on
: Mon Dec 23 2024 - 05:53:36 PST
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