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