Amber Archive Aug 2002 by thread
272 messages
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Starting
Wed Jul 31 2002 - 18:50:27 PDT,
Ending
Sat Aug 31 2002 - 10:58:35 PDT
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Re: Error decoding variable
Rukman Hertadi
(Wed Jul 31 2002 - 18:50:27 PDT)
problem with amber7 mpi
Bimo Ario Tejo
(Thu Aug 01 2002 - 03:50:32 PDT)
Re: problem with amber7 mpi
Carlos Simmerling
(Thu Aug 01 2002 - 05:34:43 PDT)
Re: problem with amber7 mpi
Shixiang Yan
(Thu Aug 01 2002 - 06:29:58 PDT)
Potential Energy and RMS-Deviation Issues
mdk7p_at_cms.mail.virginia.edu
(Thu Aug 01 2002 - 08:01:07 PDT)
Re: Potential Energy and RMS-Deviation Issues
CUI, Guanglei
(Thu Aug 01 2002 - 08:38:36 PDT)
Re: Potential Energy and RMS-Deviation Issues
Thomas Cheatham
(Thu Aug 01 2002 - 09:08:09 PDT)
Re: Potential Energy and RMS-Deviation Issues
David A. Case
(Thu Aug 01 2002 - 09:25:57 PDT)
file
Cozmuta
(Thu Aug 01 2002 - 10:24:13 PDT)
Re: file
David A. Case
(Thu Aug 01 2002 - 13:46:52 PDT)
proton_info/PS
Cozmuta
(Thu Aug 01 2002 - 10:29:02 PDT)
Using the new2oldparm command
dianah_at_unm.edu
(Thu Aug 01 2002 - 13:18:32 PDT)
Re: Using the new2oldparm command
Holger Gohlke
(Thu Aug 01 2002 - 13:52:23 PDT)
RE: Using the new2oldparm command
Karen Haskell
(Thu Aug 01 2002 - 13:55:28 PDT)
MD on cytochrome
Mahadevan Seetharaman
(Thu Aug 01 2002 - 14:15:52 PDT)
Solvated DNA using Amber 7
Nicholson, James D Mr ARO
(Thu Aug 01 2002 - 14:32:13 PDT)
Re: Using the new2oldparm command
Pascal Bonnet
(Fri Aug 02 2002 - 01:17:54 PDT)
reorder water with nmropt
Peter Varnai
(Fri Aug 02 2002 - 05:24:59 PDT)
Re: reorder water with nmropt
David A. Case
(Fri Aug 02 2002 - 09:01:22 PDT)
look for benchmark with myrinet vs. 100-BT
Jianhui Wu
(Fri Aug 02 2002 - 10:15:29 PDT)
Re: look for benchmark with myrinet vs. 100-BT
Margaret Cheung
(Fri Aug 02 2002 - 11:20:22 PDT)
FWD: RE: Including explicit waters in GB dynamics
Kristina Furse
(Fri Aug 02 2002 - 13:32:52 PDT)
igb=2 in amber7
Randy M. Wadkins
(Fri Aug 02 2002 - 15:28:48 PDT)
water box-nonperiodic
Cozmuta
(Fri Aug 02 2002 - 20:14:35 PDT)
Re: water box-nonperiodic
David Case
(Fri Aug 02 2002 - 22:16:18 PDT)
Benchmarks
Sanjeev B.S.
(Fri Aug 02 2002 - 22:48:09 PDT)
Please give me a hand on understanding AMBER/MPI and locmem.
Margaret Cheung
(Fri Aug 02 2002 - 23:49:46 PDT)
Re: Please give me a hand on understanding AMBER/MPI and locmem.
David Case
(Sat Aug 03 2002 - 13:02:42 PDT)
Re: Please give me a hand on understanding AMBER/MPI and locmem.
Margaret Cheung
(Sat Aug 03 2002 - 15:23:50 PDT)
Generalized Born and OPLS potential
Soonmin Jang
(Sat Aug 03 2002 - 01:05:27 PDT)
Re: Generalized Born and OPLS potential
David A. Case
(Mon Aug 05 2002 - 08:51:30 PDT)
Amber trajectory movies in Powerpoint
mdk7p_at_cms.mail.virginia.edu
(Tue Aug 06 2002 - 08:53:39 PDT)
Re: Amber trajectory movies in Powerpoint
Cozmuta
(Tue Aug 06 2002 - 11:25:31 PDT)
am1-bcc charges
Sophia Kondratova
(Tue Aug 06 2002 - 11:26:22 PDT)
Re: am1-bcc charges
David A. Case
(Tue Aug 06 2002 - 12:32:12 PDT)
Leap error: PDB file with more than 10000 residues
Pratul Agarwal
(Tue Aug 06 2002 - 12:50:04 PDT)
Re: Leap error: PDB file with more than 10000 residues
David A. Case
(Tue Aug 06 2002 - 14:13:30 PDT)
Re: Leap error: PDB file with more than 10000 residues
Pratul Agarwal
(Tue Aug 06 2002 - 14:47:00 PDT)
Re: Leap error: PDB file with more than 10000 residues
jim caldwell
(Tue Aug 06 2002 - 14:57:34 PDT)
charges
Cozmuta
(Tue Aug 06 2002 - 16:24:14 PDT)
Re: charges
David A. Case
(Wed Aug 07 2002 - 18:35:07 PDT)
Re: charges-again
Cozmuta
(Wed Aug 07 2002 - 18:47:14 PDT)
mpich, I/O, Master node, filesystem
Jianhui Wu
(Wed Aug 07 2002 - 21:24:13 PDT)
Re: mpich, I/O, Master node, filesystem
David Case
(Wed Aug 07 2002 - 22:14:25 PDT)
nmode segmentation fault
zhongh_at_umich.edu
(Thu Aug 08 2002 - 06:56:08 PDT)
Re: nmode segmentation fault
Holger Gohlke
(Thu Aug 08 2002 - 11:16:11 PDT)
Re: nmode segmentation fault
Haizhen Zhong
(Fri Aug 09 2002 - 06:46:19 PDT)
problems runing gibbs on a IBM SP2 machine
ramon kleber da rocha
(Fri Aug 09 2002 - 07:48:11 PDT)
Re: nmode segmentation fault
jim caldwell
(Thu Aug 08 2002 - 11:21:03 PDT)
Gentoo vs. Redhat Linux, shared/distributed filesystem
Jianhui Wu
(Thu Aug 08 2002 - 12:44:53 PDT)
protonation pH dependent
Cozmuta
(Thu Aug 08 2002 - 14:14:46 PDT)
Re: protonation pH dependent
David A. Case
(Thu Aug 08 2002 - 15:05:25 PDT)
LINMIN failure during minimization
Giulio Rastelli
(Fri Aug 09 2002 - 01:46:18 PDT)
Re: LINMIN failure during minimization
David A. Case
(Fri Aug 09 2002 - 09:09:09 PDT)
namelist error with sander
Andreas Kerzmann
(Fri Aug 09 2002 - 01:47:53 PDT)
Re: namelist error with sander
David A. Case
(Fri Aug 09 2002 - 08:50:27 PDT)
Re: namelist error with sander
Andreas Kerzmann
(Mon Aug 12 2002 - 05:40:12 PDT)
Constant pressure MD problems (sander)
Pratul Agarwal
(Mon Aug 12 2002 - 07:45:15 PDT)
Re: Constant pressure MD problems (sander)
David A. Case
(Mon Aug 12 2002 - 08:47:10 PDT)
Memory and swap in sander
William Wei
(Mon Aug 12 2002 - 08:11:35 PDT)
Re: Memory and swap in sander
David A. Case
(Mon Aug 12 2002 - 08:55:55 PDT)
Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system.
jeff dyason
(Wed Aug 07 2002 - 21:45:49 PDT)
Re: Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system.
Sanjeev B.S.
(Wed Aug 07 2002 - 21:46:08 PDT)
Re: Amber trajectory movies in Powerpoint
Elsa de Sousa Henriques
(Tue Aug 06 2002 - 18:58:15 PDT)
(no subject)
Giulio Rastelli
(Wed Aug 07 2002 - 02:07:21 PDT)
Re: your mail
darden
(Wed Aug 07 2002 - 04:58:17 PDT)
SHAKE problem
Rosalia Pascual
(Wed Aug 07 2002 - 08:13:12 PDT)
Amber+Mosix
Jianhui Wu
(Wed Aug 07 2002 - 13:40:15 PDT)
RE: Amber+Mosix
Ross Walker
(Sun Aug 11 2002 - 14:33:04 PDT)
using belly with GB
David A. Case
(Wed Aug 07 2002 - 18:36:18 PDT)
PROTON_INFO
Cozmuta
(Fri Aug 02 2002 - 20:25:37 PDT)
Re: PROTON_INFO
Qing Zhang
(Sat Aug 03 2002 - 18:12:24 PDT)
Re: look for benchmark with myrinet vs. 100-BT
C. Klein
(Sun Aug 04 2002 - 01:21:29 PDT)
problems with parallel sander on linux clusters?
David Case
(Sun Aug 04 2002 - 11:34:20 PDT)
(no subject)
sepideh ameli
(Sun Aug 04 2002 - 12:01:20 PDT)
Import of CHARMM force field and GB potential parameters into Amber7
Soonmin Jang
(Sun Aug 04 2002 - 19:19:20 PDT)
Re: Import of CHARMM force field and GB potential parameters into Amber7
David Case
(Sun Aug 04 2002 - 22:25:28 PDT)
MD in alcohol
Marc DOBLER
(Sun Aug 04 2002 - 19:33:52 PDT)
Re: MD in alcohol
David Case
(Sun Aug 04 2002 - 22:31:40 PDT)
Re: MD in alcohol
Marc DOBLER
(Mon Aug 05 2002 - 01:46:17 PDT)
Information request - where to buy software
Claire Edmonds
(Mon Aug 05 2002 - 06:23:59 PDT)
distance restraint stuff
Layi Adekoya
(Thu Aug 01 2002 - 08:24:50 PDT)
Re: distance restraint stuff
CUI, Guanglei
(Thu Aug 01 2002 - 08:44:25 PDT)
Re: "number of processors must be a power of two"
Sanjeev B.S.
(Tue Aug 06 2002 - 09:17:35 PDT)
Re: "number of processors must be a power of two"
David A. Case
(Tue Aug 06 2002 - 09:40:33 PDT)
Re: "number of processors must be a power of two"
Michael Crowley
(Tue Aug 06 2002 - 10:31:50 PDT)
creating a solvent box
Bimo Ario Tejo
(Tue Aug 06 2002 - 10:23:13 PDT)
Re: creating a solvent box
David A. Case
(Tue Aug 06 2002 - 11:53:50 PDT)
check-up question
Cozmuta
(Tue Aug 06 2002 - 12:13:31 PDT)
Re: check-up question
David A. Case
(Tue Aug 06 2002 - 14:14:56 PDT)
FW: Compiling on HP-UX 11.00
Hagedorn, Dan N
(Fri Aug 09 2002 - 11:45:00 PDT)
Amber/Gentoo linux
Jianhui Wu
(Fri Aug 09 2002 - 12:53:16 PDT)
RE: Amber/Gentoo linux
Ross Walker
(Sun Aug 11 2002 - 14:32:37 PDT)
RE: Amber/Gentoo linux
Margaret Cheung
(Sun Aug 11 2002 - 16:31:02 PDT)
Nanotubes with AMBER
Stefan Andreev Andreev
(Sun Aug 11 2002 - 16:59:26 PDT)
Re: Nanotubes with AMBER
David Case
(Sun Aug 11 2002 - 21:13:23 PDT)
literature for NVE
Khatcharin Siriwong
(Mon Aug 12 2002 - 02:07:05 PDT)
Re: literature for NVE
David A. Case
(Mon Aug 12 2002 - 08:38:45 PDT)
Re: literature for NVE
Khatcharin Siriwong
(Mon Aug 12 2002 - 09:19:03 PDT)
chesey.panther.gsu.edu
Michael G Cooney
(Mon Aug 12 2002 - 12:03:37 PDT)
misdirected message
Michael G Cooney
(Mon Aug 12 2002 - 12:35:35 PDT)
Format of prep input files
dianah_at_unm.edu
(Tue Aug 13 2002 - 10:42:11 PDT)
Re: Format of prep input files
David A. Case
(Tue Aug 13 2002 - 11:13:47 PDT)
sander minimizations failing
John Bushnell
(Tue Aug 13 2002 - 17:03:12 PDT)
minimization in amber7 for nonperiodic systems
David Case
(Tue Aug 13 2002 - 22:47:43 PDT)
Re: minimization in amber7 for nonperiodic systems
Giulio Rastelli
(Wed Aug 14 2002 - 08:03:11 PDT)
Re: minimization in amber7 for nonperiodic systems
David A. Case
(Wed Aug 14 2002 - 08:28:21 PDT)
dihedral parameter for conjugated double bonds in GAFF
Giulio Rastelli
(Wed Aug 14 2002 - 01:37:50 PDT)
GB in Amber7
Jithesh
(Wed Aug 14 2002 - 01:37:54 PDT)
Re: GB in Amber7
David A. Case
(Wed Aug 14 2002 - 08:33:57 PDT)
Running amber7 on Param10000
Sanjeev B.S.
(Wed Aug 14 2002 - 08:38:34 PDT)
Re: Running amber7 on Param10000
Jithesh
(Thu Aug 15 2002 - 00:35:46 PDT)
force field name
A. Hungie
(Thu Aug 15 2002 - 06:50:48 PDT)
RE: force field name
Yong Duan
(Thu Aug 15 2002 - 09:11:19 PDT)
sander on NEC-SX5
C. Klein
(Thu Aug 15 2002 - 09:12:24 PDT)
RE: sander on NEC-SX5
Karen Haskell
(Thu Aug 15 2002 - 09:38:57 PDT)
trajectory file limit???
Vlad Cojocaru
(Thu Aug 15 2002 - 09:43:54 PDT)
Re: trajectory file limit???
David A. Case
(Thu Aug 15 2002 - 10:26:34 PDT)
Re: trajectory file limit???
jim caldwell
(Thu Aug 15 2002 - 12:26:13 PDT)
Order of a protein, bound waters and ligand in saveamberparm
Masaki Tomimoto
(Thu Aug 15 2002 - 13:25:45 PDT)
RE: Order of a protein, bound waters and ligand in saveamberparm
Masaki Tomimoto
(Thu Aug 15 2002 - 15:04:18 PDT)
Extra points
Sarah Tschampel
(Thu Aug 15 2002 - 13:25:45 PDT)
Re: Extra points
jim caldwell
(Thu Aug 15 2002 - 14:54:21 PDT)
Re: Extra points
David A. Case
(Thu Aug 15 2002 - 16:01:21 PDT)
Re: trajectory file limit???
Pratul Agarwal
(Thu Aug 15 2002 - 14:12:35 PDT)
RE: trajectory file limit???
Ross Walker
(Thu Aug 15 2002 - 14:48:30 PDT)
RE: force field name
Peter Gannett
(Thu Aug 15 2002 - 16:03:52 PDT)
GB in amber6
Prabal Maiti
(Thu Aug 15 2002 - 17:26:22 PDT)
Re: GB in amber6
CUI, Guanglei
(Thu Aug 15 2002 - 19:33:27 PDT)
Re: GB in amber6
David Case
(Thu Aug 15 2002 - 22:23:23 PDT)
Re: GB in amber6
CUI, Guanglei
(Fri Aug 16 2002 - 06:25:52 PDT)
dihedral parameter for conjugated double bonds in GAFF
Giulio Rastelli
(Fri Aug 16 2002 - 09:37:03 PDT)
Etot drops after restarting MD in sander
Pratul Agarwal
(Fri Aug 16 2002 - 11:18:58 PDT)
antechamber's prepc option
Matthew Lee
(Fri Aug 16 2002 - 12:20:59 PDT)
Re: antechamber's prepc option
David A. Case
(Fri Aug 16 2002 - 13:10:55 PDT)
mol2_to_off
Matthew Randolph Lee, Ph.D.
(Fri Aug 16 2002 - 15:15:41 PDT)
average of LES copies
mer_at_chem.wayne.edu
(Sun Aug 18 2002 - 18:00:22 PDT)
Antibody residue numbering
Mark Hsieh
(Mon Aug 19 2002 - 13:56:00 PDT)
Re: Antibody residue numbering
David A. Case
(Mon Aug 19 2002 - 14:15:45 PDT)
RE: Antibody residue numbering
Mark Hsieh
(Mon Aug 19 2002 - 18:00:03 PDT)
RE: Antibody residue numbering
Mark Hsieh
(Tue Aug 20 2002 - 09:52:24 PDT)
Im lost
Sankha Subhra Som
(Mon Aug 19 2002 - 22:16:00 PDT)
Re: Im lost
David A. Case
(Tue Aug 20 2002 - 08:15:29 PDT)
PC (principal component) analysis
Soonmin Jang
(Tue Aug 20 2002 - 01:02:24 PDT)
mail host switchover
jim caldwell
(Mon Aug 19 2002 - 14:58:11 PDT)
a couple missing gaff angle terms
Matthew Lee
(Fri Aug 16 2002 - 14:55:44 PDT)
follow-up post on missing gaff terms
Matthew Randolph Lee, Ph.D.
(Tue Aug 20 2002 - 10:21:50 PDT)
segmentation fault
Vlad Cojocaru
(Tue Aug 20 2002 - 14:21:30 PDT)
Nitro parameters
Jerry Matthew Parks
(Wed Aug 21 2002 - 14:28:48 PDT)
RMSD by residue (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:49:39 PDT)
Re: RMSD by residue (fwd)
Holger Gohlke
(Mon Aug 26 2002 - 18:08:35 PDT)
Re: RMSD by residue (fwd)
Carlos Simmerling
(Mon Aug 26 2002 - 18:10:41 PDT)
Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:02 PDT)
Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd)
David A. Case
(Mon Aug 26 2002 - 18:21:06 PDT)
adding_hydrogens_to_pdb (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:07 PDT)
Re: adding_hydrogens_to_pdb (fwd)
David A. Case
(Mon Aug 26 2002 - 17:34:36 PDT)
ewald bomb in md equilibration (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:14 PDT)
Re: ewald bomb in md equilibration (fwd)
David A. Case
(Mon Aug 26 2002 - 18:23:52 PDT)
why is mm_pbsa broken ? (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:27 PDT)
Re: why is mm_pbsa broken ? (fwd)
Holger Gohlke
(Tue Aug 27 2002 - 10:12:17 PDT)
restraints in parm in amber7
Sarah Tschampel
(Tue Aug 27 2002 - 14:57:33 PDT)
Re: restraints in parm in amber7
Carlos Simmerling
(Tue Aug 27 2002 - 18:38:59 PDT)
problem in MD
Xiang Mao
(Tue Aug 27 2002 - 17:05:11 PDT)
Re: problem in MD
Carlos Simmerling
(Tue Aug 27 2002 - 18:40:06 PDT)
ambpdb problem (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:32 PDT)
Re: ambpdb problem (fwd)
David A. Case
(Mon Aug 26 2002 - 18:27:08 PDT)
Gibbs (FEP) (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:36 PDT)
Re: Gibbs (FEP) (fwd)
David A. Case
(Mon Aug 26 2002 - 18:30:28 PDT)
QUICK HELP! Parameters for neutral amino acids (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:43 PDT)
Re: QUICK HELP! Parameters for neutral amino acids (fwd)
David A. Case
(Mon Aug 26 2002 - 18:32:50 PDT)
amber7, gaff and minimization (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:50 PDT)
Re: amber7, gaff and minimization (fwd)
David A. Case
(Mon Aug 26 2002 - 18:35:26 PDT)
Interface and Amber 7.0
Nigel D Priestley
(Mon Aug 26 2002 - 19:45:55 PDT)
Re: Interface and Amber 7.0
David A. Case
(Tue Aug 27 2002 - 04:53:45 PDT)
Re: Interface and Amber 7.0
David Pearlman
(Tue Aug 27 2002 - 09:35:19 PDT)
amber7: ES40s
Sanjeev B.S.
(Tue Aug 27 2002 - 06:08:49 PDT)
difference 94 99 force field
Vlad Cojocaru
(Tue Aug 27 2002 - 06:34:11 PDT)
Re: difference 94 99 force field
Carlos Simmerling
(Tue Aug 27 2002 - 07:34:50 PDT)
question
Sankha Subhra Som
(Mon Aug 26 2002 - 23:24:32 PDT)
regarding RESP run from gamess output (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:55 PDT)
why is mm_pbsa broken ? (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:50:59 PDT)
add DUMMY atom into coordinate file
yuann
(Fri Aug 16 2002 - 02:12:04 PDT)
Re: add DUMMY atom into coordinate file
Alan Leo
(Fri Aug 16 2002 - 12:51:35 PDT)
Q: waters in NPT & periodic boundary condition
Masaki Tomimoto
(Wed Aug 14 2002 - 09:06:15 PDT)
Re: Q: waters in NPT & periodic boundary condition
David A. Case
(Wed Aug 14 2002 - 09:45:46 PDT)
E going up and down???
Jiyoung Heo
(Wed Aug 14 2002 - 14:13:44 PDT)
Re: E going up and down???
David A. Case
(Wed Aug 14 2002 - 15:16:05 PDT)
PMF with sander module
mer_at_gordon.chem.wayne.edu
(Wed Aug 14 2002 - 16:23:25 PDT)
Re: PMF with sander module
Pratul Agarwal
(Wed Aug 14 2002 - 20:49:34 PDT)
Re: PMF with sander module
David A. Case
(Fri Aug 16 2002 - 12:23:16 PDT)
problem with amber7 compiling on SGI
Chris Switzer
(Wed Aug 14 2002 - 18:26:54 PDT)
a question about carnal
Vlad Cojocaru
(Wed Aug 14 2002 - 09:39:36 PDT)
problem reading rstrnt file with pgf77 compiled sander
Michael Petersen
(Wed Aug 14 2002 - 03:13:24 PDT)
Carnal stream problem
Vlad Cojocaru
(Wed Aug 14 2002 - 07:45:04 PDT)
Re: Help needed about mm_pbsa
Holger Gohlke
(Thu Aug 15 2002 - 10:04:03 PDT)
can carnal do the job as anal to break down the energy?
Haizhen Zhong
(Wed Aug 28 2002 - 11:02:48 PDT)
[Re: can carnal do the job as anal to break down the energy?]
Holger Gohlke
(Wed Aug 28 2002 - 11:36:51 PDT)
IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)
Michael Jakusch
(Thu Aug 29 2002 - 00:36:57 PDT)
Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)
Carlos Simmerling
(Thu Aug 29 2002 - 03:54:15 PDT)
Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)
Michael Jakusch
(Thu Aug 29 2002 - 04:56:12 PDT)
MDaemon Warning - Virus Found
postmaster_at_96com.com
(Thu Aug 29 2002 - 05:20:52 PDT)
pbc in amber
Xiang Mao
(Thu Aug 29 2002 - 06:00:04 PDT)
MDaemon Warning - Virus Found
postmaster_at_96com.com
(Thu Aug 29 2002 - 03:14:06 PDT)
Re: problem reading rstrnt file with pgf77
Michael Petersen
(Fri Aug 16 2002 - 06:23:48 PDT)
Re: Can we get trajectories coordinates after FIT in Carnal? (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:03 PDT)
How to make mpeg files from amber trajectories (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:07 PDT)
Re: How to make mpeg files from amber trajectories (fwd)
Jake Isaacs
(Tue Aug 27 2002 - 06:48:24 PDT)
Re: How to make mpeg files from amber trajectories (fwd)
Michal Otyepka
(Wed Aug 28 2002 - 00:22:54 PDT)
What's this "interface" the tutorial talks about?
Andreas Kerzmann
(Wed Aug 28 2002 - 05:41:01 PDT)
Re: What's this "interface" the tutorial talks about?
David Pearlman
(Wed Aug 28 2002 - 12:49:57 PDT)
RE: What's this "interface" the tutorial talks about?
priestle
(Wed Aug 28 2002 - 12:02:52 PDT)
gibbs
sara nunez
(Wed Aug 28 2002 - 12:52:56 PDT)
[Re: can carnal do the job as anal to break down the energy?]
Bill Ross
(Wed Aug 28 2002 - 13:35:40 PDT)
a missing variable
Vlad Cojocaru
(Wed Aug 28 2002 - 13:43:04 PDT)
Re: a missing variable
Matthew Randolph Lee, Ph.D.
(Wed Aug 28 2002 - 15:27:12 PDT)
sorry!!!!maybe another stupid question
Vlad Cojocaru
(Wed Aug 28 2002 - 15:48:03 PDT)
Re: sorry!!!!maybe another stupid question
Pratul Agarwal
(Wed Aug 28 2002 - 18:45:28 PDT)
Tutorial Error Message
Joel Konkle-Parker
(Wed Aug 28 2002 - 16:19:48 PDT)
Re: Tutorial Error Message
Holger Gohlke
(Thu Aug 29 2002 - 08:22:25 PDT)
MDaemon Warning - Virus Found
postmaster_at_96com.com
(Thu Aug 29 2002 - 10:02:23 PDT)
image command
Sophia Kondratova
(Thu Aug 29 2002 - 10:46:01 PDT)
PyMOL + AMBER Trajectories
DeLano, Warren
(Thu Aug 29 2002 - 11:27:01 PDT)
ES40 hangs amber7 jobs.
Sanjeev B.S.
(Thu Aug 29 2002 - 20:09:13 PDT)
Re: ES40 hangs amber7 jobs.
James W. Caldwell
(Fri Aug 30 2002 - 09:07:11 PDT)
dump coordinate into mdcrd
A. Hungie
(Fri Aug 30 2002 - 01:03:17 PDT)
MDaemon Warning - Virus Found
postmaster_at_96com.com
(Fri Aug 30 2002 - 03:08:15 PDT)
example gibbs file for the methane tutorial
Andreas Kerzmann
(Fri Aug 30 2002 - 03:18:06 PDT)
NTX value
giudice
(Fri Aug 30 2002 - 03:31:19 PDT)
Re: NTX value
James W. Caldwell
(Fri Aug 30 2002 - 09:10:10 PDT)
Re: NTX value
James W. Caldwell
(Fri Aug 30 2002 - 11:35:30 PDT)
Vanderbilt Biomolecular Modeling Symposium
Jarrod Smith
(Fri Aug 30 2002 - 11:00:40 PDT)
RE: Vanderbilt Biomolecular Modeling Symposium
Douglas Kojetin
(Fri Aug 30 2002 - 12:22:19 PDT)
Binding site volume/Sander MD
Jianhui Wu
(Fri Aug 30 2002 - 14:20:09 PDT)
GBSA with IGB=2, setting the PBradii bondi
Sarangan Ravichandran
(Fri Aug 30 2002 - 14:55:28 PDT)
Re: GBSA with IGB=2, setting the PBradii bondi
David Case
(Sat Aug 31 2002 - 10:58:35 PDT)
Re: NTX value
David A. Case
(Fri Aug 30 2002 - 12:07:44 PDT)
MDaemon Warning - Virus Found
postmaster_at_96com.com
(Fri Aug 30 2002 - 03:59:25 PDT)
sander7 on IBM 7040-681 under AIX 5.1
Peter Varnai
(Fri Aug 30 2002 - 06:01:07 PDT)
ewald bomb
Vlad Cojocaru
(Fri Aug 30 2002 - 06:38:49 PDT)
Re: ewald bomb
David A. Case
(Fri Aug 30 2002 - 12:13:14 PDT)
iwrap and image
Sophia Kondratova
(Wed Aug 28 2002 - 05:55:36 PDT)
Re: iwrap and image
James W. Caldwell
(Wed Aug 28 2002 - 07:35:50 PDT)
Carnal RMSDs (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:12 PDT)
Re: Etot drops after restarting MD in sander (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:16 PDT)
turning off ewald (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:21 PDT)
Re: turning off ewald (fwd)
David A. Case
(Mon Aug 26 2002 - 18:12:29 PDT)
a more general question about ff (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:25 PDT)
leaprc file (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:29 PDT)
Torsion restraint between center of mass groups
Pratul Agarwal
(Mon Aug 26 2002 - 14:51:33 PDT)
a more general question (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:41 PDT)
leaprc file (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:44 PDT)
Re: leaprc file (fwd)
David A. Case
(Mon Aug 26 2002 - 18:09:22 PDT)
Re: Extra points (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:49 PDT)
Scaling of Sander on Linux Clusters (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:51:57 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Pratul Agarwal
(Mon Aug 26 2002 - 17:32:24 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Stéphane Teletchéa
(Tue Aug 27 2002 - 01:41:06 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Sanjeev B.S.
(Tue Aug 27 2002 - 01:56:15 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Stéphane Teletchéa
(Tue Aug 27 2002 - 02:31:16 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Sanjeev B.S.
(Tue Aug 27 2002 - 10:59:51 PDT)
Re: Scaling of Sander on Linux Clusters (fwd)
Peter Gannett
(Mon Aug 26 2002 - 17:56:06 PDT)
Re: "number of processors must be a power of two" (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:52:01 PDT)
Using GBSA for a DNA-PROTEIN complex (fwd)
amber_at_heimdal.compchem.ucsf.edu
(Mon Aug 26 2002 - 14:52:06 PDT)
test
James W. Caldwell
(Mon Aug 26 2002 - 15:04:35 PDT)
mail reflector
James W. Caldwell
(Mon Aug 26 2002 - 15:35:53 PDT)
ewald bomb in md equilibration
Sophia Kondratova
(Mon Aug 26 2002 - 15:54:37 PDT)
Re: Carnal RMSDs
Bill Ross
(Mon Aug 26 2002 - 16:56:50 PDT)
Re: how to make mpeg files from amber trajectories
Anke Eisenmann
(Tue Aug 27 2002 - 07:41:01 PDT)
Fw: amber problem
Carlos Simmerling
(Wed Aug 28 2002 - 10:10:26 PDT)
Last message date
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Sat Aug 31 2002 - 10:58:35 PDT
Archived on
: Wed Apr 17 2024 - 05:53:10 PDT
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