Amber Archive Jun 2005 by author
370 messages
:
Starting
Wed Jun 01 2005 - 02:53:00 PDT,
Ending
Fri Jul 01 2005 - 02:53:00 PDT
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acb15885.uprm.edu
AMBER: pb_pgb test fail
(Mon Jun 27 2005 - 11:17:48 PDT)
alice
Re: Re: AMBER: bad atom type: H
(Wed Jun 15 2005 - 18:35:00 PDT)
AMBER: bad atom type: H
(Wed Jun 15 2005 - 03:53:50 PDT)
AMBER: How to run amber more efficiently?
(Tue Jun 07 2005 - 19:59:26 PDT)
Ananda Rama Krishnan Selvaraj
Re: AMBER: Extended bonds-MD
(Wed Jun 15 2005 - 05:55:41 PDT)
AMBER: Extended bonds-MD
(Wed Jun 15 2005 - 00:02:25 PDT)
AMBER: Extended bonds-MD
(Tue Jun 14 2005 - 09:29:29 PDT)
AMBER: Restrained-MD
(Mon Jun 13 2005 - 16:04:14 PDT)
Re: RE: AMBER: problem in minimization
(Thu Jun 02 2005 - 00:39:36 PDT)
AMBER: problem in minimization
(Wed Jun 01 2005 - 01:48:46 PDT)
Andreas Kerzmann
AMBER: Sander is changing directories
(Wed Jun 08 2005 - 02:37:58 PDT)
AMBER: Sander is changing directories
(Wed Jun 08 2005 - 02:39:23 PDT)
Andreas Svrcek-Seiler
Re: AMBER: GCC for AMBER on 64 bit machine
(Thu Jun 23 2005 - 11:44:44 PDT)
RE: AMBER: Installation problem - wrong address
(Fri Jun 17 2005 - 10:28:43 PDT)
RE: AMBER: Installation problem. .
(Fri Jun 17 2005 - 10:12:10 PDT)
Re: AMBER: Installation problem. .
(Thu Jun 16 2005 - 21:54:42 PDT)
Re: AMBER: Installation problem. .
(Wed Jun 15 2005 - 05:31:46 PDT)
Andy Purkiss
Re: AMBER: fail of minimization in sander
(Tue Jun 07 2005 - 05:17:24 PDT)
Angela Liu
AMBER: amber 8 leap topology file dihedral term problem
(Tue Jun 28 2005 - 06:59:57 PDT)
Angelo Pugliese
Re: AMBER: time and lifetime in hbond analysis (ptraj)
(Tue Jun 14 2005 - 07:57:56 PDT)
Re: AMBER: creating pdb file....
(Tue Jun 14 2005 - 04:11:41 PDT)
Anthony Cruz
Re: AMBER: Solvate question?
(Tue Jun 07 2005 - 05:31:30 PDT)
AMBER: Solvents
(Mon Jun 06 2005 - 09:00:07 PDT)
Re: AMBER: Solvate question?
(Mon Jun 06 2005 - 08:59:06 PDT)
Re: AMBER: Compile question??
(Mon Jun 06 2005 - 06:24:40 PDT)
AMBER: Compile question??
(Mon Jun 06 2005 - 04:59:13 PDT)
AMBER: Solvate question?
(Mon Jun 06 2005 - 03:30:44 PDT)
Re: AMBER: Protein ions?
(Thu Jun 02 2005 - 09:45:34 PDT)
AMBER: Protein ions?
(Thu Jun 02 2005 - 07:12:56 PDT)
Bill Ross
Re: AMBER: question about Carnal
(Wed Jun 22 2005 - 13:51:34 PDT)
RE: AMBER: vdw for terminal phosphate
(Mon Jun 13 2005 - 13:22:47 PDT)
Re: AMBER: vdw for terminal phosphate
(Fri Jun 10 2005 - 11:10:32 PDT)
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 12:27:14 PDT)
Re: AMBER: AMBER frcmod+off input vs. prep input
(Tue Jun 07 2005 - 10:58:06 PDT)
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 09:47:42 PDT)
Re: AMBER: segmentation fault in sander
(Tue Jun 07 2005 - 09:35:27 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 17:03:38 PDT)
Re: AMBER: segmentation fault in sander
(Mon Jun 06 2005 - 15:18:45 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 10:58:54 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 07:34:39 PDT)
Re: AMBER: fail of minimization in sander
(Sun Jun 05 2005 - 20:50:48 PDT)
Biswaroop Mukherjee
AMBER: Argon Box
(Thu Jun 02 2005 - 01:44:46 PDT)
Brent Krueger
AMBER: gaff.dat typo
(Wed Jun 01 2005 - 18:35:58 PDT)
caoch.cherry.bio.titech.ac.jp
AMBER: nonbond_list question .
(Fri Jun 17 2005 - 18:38:27 PDT)
Carlos Simmerling
Re: AMBER: fail of minimization in sander
(Thu Jun 16 2005 - 04:06:42 PDT)
Re: AMBER: fail of minimization in sander
(Wed Jun 15 2005 - 04:24:04 PDT)
Re: AMBER: Extended bonds-MD
(Wed Jun 15 2005 - 04:22:29 PDT)
Re: AMBER: transfer data from Linux to windows
(Thu Jun 09 2005 - 15:41:26 PDT)
Re: AMBER: GB/SA/LD parallel sander
(Wed Jun 08 2005 - 13:09:59 PDT)
Re: AMBER: total energy leaps
(Wed Jun 08 2005 - 04:22:06 PDT)
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 12:34:17 PDT)
Re: AMBER: Solvate question?
(Mon Jun 06 2005 - 09:13:37 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 09:12:38 PDT)
Re: AMBER: Solvate question?
(Mon Jun 06 2005 - 04:26:53 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 04:24:25 PDT)
Re: AMBER: How does Amber8 implemnet ntf=4?
(Thu Jun 02 2005 - 08:53:36 PDT)
Re: AMBER: question whem using leap
(Thu Jun 02 2005 - 04:45:53 PDT)
cbala.igib.res.in
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 12:48:13 PDT)
AMBER: nucgen problem
(Tue Jun 07 2005 - 06:41:27 PDT)
chaiann ng
AMBER: advice needed for minimization and dynamic protocol
(Thu Jun 02 2005 - 18:33:44 PDT)
Chris Harrison
Re: AMBER: Installation problem
(Mon Jun 13 2005 - 17:33:13 PDT)
Re: AMBER: Installation problem
(Sun Jun 12 2005 - 16:04:22 PDT)
Christoph Brockmann
AMBER: nmropt =1 AND ntr=1 in pmemd
(Tue Jun 14 2005 - 02:33:39 PDT)
Cordova, Luis E.
AMBER: precision switch from 64 to 32 bit (double from single precision)
(Wed Jun 08 2005 - 22:39:59 PDT)
cristian obiol
AMBER: total energy leaps
(Wed Jun 08 2005 - 03:44:18 PDT)
RE:AMBER: density problem
(Wed Jun 08 2005 - 01:56:23 PDT)
RE:AMBER: density problem
(Thu Jun 02 2005 - 01:14:21 PDT)
Daniel Wetzler
AMBER: Searching for NAD parameter files / Problems with parameter file creation
(Thu Jun 23 2005 - 07:43:29 PDT)
Dave S Walker
RE: AMBER: runtime error in sander?
(Mon Jun 20 2005 - 11:02:16 PDT)
David A. Case
Re: AMBER: Create new Unit
(Thu Jun 30 2005 - 18:38:42 PDT)
Re: AMBER: antechamber error
(Thu Jun 30 2005 - 14:38:11 PDT)
Re: AMBER: Re: TI tutorial
(Wed Jun 29 2005 - 10:01:23 PDT)
Re: AMBER: Re: TI tutorial
(Wed Jun 29 2005 - 07:30:31 PDT)
Re: AMBER: Re: TI tutorial
(Tue Jun 28 2005 - 18:09:44 PDT)
Re: AMBER: Re: TI tutorial
(Tue Jun 28 2005 - 08:49:53 PDT)
Re: AMBER: pb_pgb test fail
(Mon Jun 27 2005 - 11:48:32 PDT)
Re: AMBER: a question about varying positions of dihedral restraints with step number
(Fri Jun 24 2005 - 08:09:21 PDT)
Re: AMBER: large std error in entropy estimation
(Thu Jun 23 2005 - 11:25:03 PDT)
Re: AMBER: fail of minimization in sander
(Thu Jun 16 2005 - 07:44:21 PDT)
Re: AMBER: How to modify force constants and equalibrium values for standard residues
(Thu Jun 16 2005 - 07:41:18 PDT)
Re: AMBER: Question about "quasih"
(Wed Jun 15 2005 - 14:01:33 PDT)
Re: AMBER: Question about "quasih"
(Wed Jun 15 2005 - 10:43:47 PDT)
Re: AMBER: atom type question
(Wed Jun 15 2005 - 08:18:18 PDT)
Re: AMBER: bad atom type: H
(Wed Jun 15 2005 - 08:09:17 PDT)
Re: AMBER: why the dipeptide always moving out the virtual box
(Tue Jun 14 2005 - 15:50:03 PDT)
Re: AMBER: compiler
(Tue Jun 14 2005 - 11:40:16 PDT)
Re: AMBER: Restrained-MD
(Mon Jun 13 2005 - 16:10:00 PDT)
Re: AMBER: why the dipeptide always moving out the virtual box
(Mon Jun 13 2005 - 15:55:19 PDT)
Re: AMBER: GBSA and thermodynamic ensemble
(Mon Jun 13 2005 - 13:13:14 PDT)
Re: AMBER: atom type question
(Mon Jun 13 2005 - 13:05:44 PDT)
Re: AMBER: Can constant pH be used for minimization?
(Sat Jun 11 2005 - 05:42:51 PDT)
Re: AMBER: Make Distance restraints for non-standard residues
(Fri Jun 10 2005 - 12:59:13 PDT)
Re: AMBER: nmode with ibelly
(Wed Jun 08 2005 - 21:30:01 PDT)
Re: AMBER: TI tutorial in Amber 8
(Wed Jun 08 2005 - 21:27:42 PDT)
Re: AMBER: TI calculation using sander
(Tue Jun 07 2005 - 18:32:34 PDT)
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 13:17:12 PDT)
Re: AMBER: quadrupole in resp
(Tue Jun 07 2005 - 10:30:12 PDT)
Re: AMBER: nmode with ibelly
(Tue Jun 07 2005 - 07:41:41 PDT)
Re: AMBER: nucgen problem
(Tue Jun 07 2005 - 07:38:15 PDT)
Re: AMBER: Protein dynamics.
(Mon Jun 06 2005 - 15:37:10 PDT)
Re: AMBER: nmode with ibelly
(Mon Jun 06 2005 - 13:09:08 PDT)
Re: AMBER: New problem of parallel sander
(Fri Jun 03 2005 - 08:00:30 PDT)
Re: AMBER: pressure output
(Fri Jun 03 2005 - 08:05:59 PDT)
Re: AMBER: TI in Amber8
(Fri Jun 03 2005 - 08:04:45 PDT)
Re: AMBER: How does Amber8 implemnet ntf=4?
(Thu Jun 02 2005 - 08:52:10 PDT)
Re: AMBER: Protein ions?
(Thu Jun 02 2005 - 08:25:07 PDT)
Re: AMBER: amber8 installation problems
(Thu Jun 02 2005 - 08:07:19 PDT)
Re: AMBER: amber question about leap
(Thu Jun 02 2005 - 08:05:12 PDT)
Re: AMBER: gaff.dat typo
(Thu Jun 02 2005 - 08:01:58 PDT)
David LeBard
Re: AMBER: dielectric constant
(Tue Jun 28 2005 - 13:01:30 PDT)
Re: AMBER: compiler
(Tue Jun 14 2005 - 10:45:27 PDT)
Don.Bashford.stjude.org
Re: AMBER: Installation problem. .
(Mon Jun 13 2005 - 10:56:46 PDT)
Douali, Latifa
AMBER: Create new Unit
(Thu Jun 30 2005 - 16:45:37 PDT)
AMBER: inpcrd file
(Fri Jun 10 2005 - 16:04:24 PDT)
du yongchun
AMBER: question whem using leap
(Thu Jun 02 2005 - 00:25:16 PDT)
AMBER: amber question about leap
(Wed Jun 01 2005 - 22:12:12 PDT)
emilia wu
AMBER: average structure
(Sun Jun 19 2005 - 17:15:53 PDT)
Eric Hu
AMBER: normal mode mm/pbsa interupted
(Thu Jun 09 2005 - 11:46:04 PDT)
Re: AMBER: mm/pbsa error
(Wed Jun 01 2005 - 10:23:53 PDT)
Fabian Boes
Re: AMBER: INTRA molecular hbonds
(Mon Jun 27 2005 - 07:45:13 PDT)
Re: AMBER: Hbond analysis
(Mon Jun 27 2005 - 06:12:34 PDT)
Fabien CAILLIEZ
AMBER: 10-12 potential and create atom type
(Thu Jun 30 2005 - 10:19:41 PDT)
Fajar Rakhman Wibowo
Re: AMBER: transfer data from Linux to windows
(Thu Jun 09 2005 - 16:11:33 PDT)
Furse, Kristina Elisabet
Re: AMBER: nmropt =1 AND ntr=1 in pmemd
(Fri Jun 17 2005 - 12:16:13 PDT)
FyD
Re: AMBER: RED question
(Wed Jun 29 2005 - 09:34:16 PDT)
Re: AMBER: RED question
(Sun Jun 26 2005 - 20:37:59 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Wed Jun 22 2005 - 14:56:30 PDT)
Re: AMBER: Request for g98 (IOP...)
(Tue Jun 14 2005 - 08:55:27 PDT)
Re: AMBER: Need help in charge fitting through RESP
(Mon Jun 13 2005 - 09:15:42 PDT)
Germán Sciaini
AMBER: dielectric constant
(Wed Jun 29 2005 - 04:02:24 PDT)
Re: AMBER: SHAKE in md with partial solvation
(Mon Jun 06 2005 - 03:34:09 PDT)
AMBER: pressure output
(Thu Jun 02 2005 - 15:27:13 PDT)
Gert Kiss
AMBER: Build of AMBER for YDL ?
(Wed Jun 01 2005 - 16:15:57 PDT)
Giulio Rastelli
AMBER: INTRA molecular hbonds
(Mon Jun 27 2005 - 07:09:23 PDT)
AMBER: adenine test for LMOD in amber8
(Thu Jun 16 2005 - 02:57:16 PDT)
AMBER: time and lifetime in hbond analysis (ptraj)
(Tue Jun 14 2005 - 07:23:50 PDT)
gsciaini
Re: AMBER: How to modify force constants and equalibrium values for standard residues
(Fri Jun 17 2005 - 06:41:44 PDT)
gtg549i.mail.gatech.edu
Re: AMBER: Make Distance restraints for non-standard residues
(Fri Jun 10 2005 - 13:45:00 PDT)
AMBER: Make Distance restraints for non-standard residues
(Fri Jun 10 2005 - 08:47:41 PDT)
AMBER: transfer data from Linux to windows
(Thu Jun 09 2005 - 15:24:05 PDT)
Guanglei Cui
Re: AMBER: atom type for -CH=CH-
(Fri Jun 10 2005 - 06:56:52 PDT)
Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation
(Sat Jun 04 2005 - 08:17:11 PDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Wed Jun 01 2005 - 07:18:37 PDT)
Gustavo Pierdominici Sottile
AMBER: sp2 carbon atom parametrization
(Tue Jun 14 2005 - 09:30:16 PDT)
AMBER: checkoverlap
(Thu Jun 02 2005 - 10:45:19 PDT)
haixiao jin
AMBER: how the phosphated threonine to be recognized in leap
(Thu Jun 23 2005 - 02:03:26 PDT)
AMBER: no corrected reaction field energy in *.out files after running mm_pbsa
(Sun Jun 12 2005 - 19:04:40 PDT)
Herbert Georg
Re: AMBER: Question about GAFF atom types
(Mon Jun 20 2005 - 09:47:38 PDT)
Re: AMBER: Question about GAFF atom types
(Fri Jun 17 2005 - 15:31:52 PDT)
Re: AMBER: Question about GAFF atom types
(Fri Jun 17 2005 - 12:49:53 PDT)
AMBER: Question about GAFF atom types
(Thu Jun 16 2005 - 12:18:50 PDT)
hj zou
AMBER: antechamber problems
(Sun Jun 19 2005 - 06:50:08 PDT)
AMBER: antechamber problems
(Fri Jun 17 2005 - 06:32:27 PDT)
huhu
AMBER: TI tutorial in Amber 8
(Wed Jun 08 2005 - 02:52:24 PDT)
Husni Fattayer
Re: AMBER: how to pull out frames
(Mon Jun 13 2005 - 04:22:40 PDT)
Hwankyu Lee
Re: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 16:48:56 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 16:26:16 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 15:47:29 PDT)
AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 06:55:57 PDT)
AMBER: eigenvalues in vector of ptraj
(Wed Jun 01 2005 - 05:53:51 PDT)
Ilyas Yildirim
Re: AMBER: TI-FEP for ALA --> GLY
(Mon Jun 27 2005 - 22:46:17 PDT)
Re: AMBER: TI-FEP for VAL --> ALA
(Mon Jun 27 2005 - 16:43:16 PDT)
Re: AMBER: TI-FEP for VAL --> ALA
(Sat Jun 25 2005 - 16:39:11 PDT)
Re: AMBER: TI-FEP for ALA --> GLY
(Fri Jun 24 2005 - 23:48:36 PDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Wed Jun 22 2005 - 15:13:19 PDT)
AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
(Mon Jun 20 2005 - 18:51:11 PDT)
Re: AMBER: Question about GAFF atom types
(Mon Jun 20 2005 - 12:51:59 PDT)
Re: AMBER: Analysing my simulation data..
(Sat Jun 18 2005 - 09:47:06 PDT)
Re: AMBER: Question about GAFF atom types
(Fri Jun 17 2005 - 18:29:24 PDT)
Re: AMBER: Question about GAFF atom types
(Fri Jun 17 2005 - 13:42:18 PDT)
Istvan Kolossvary
Re: AMBER: adenine test for LMOD in amber8
(Thu Jun 16 2005 - 06:16:22 PDT)
AMBER: Announcing the LMOD website
(Mon Jun 13 2005 - 11:18:52 PDT)
ivan.mmb.pcb.ub.es
AMBER: Gibbs perturb DNA strands separate
(Tue Jun 07 2005 - 04:16:41 PDT)
JAVIER PEREZ
AMBER: center-of-mass distance restraints
(Thu Jun 02 2005 - 04:14:15 PDT)
Jiten
Re: AMBER: Re: TI tutorial
(Wed Jun 29 2005 - 10:24:19 PDT)
Re: AMBER: Re: TI tutorial
(Wed Jun 29 2005 - 09:22:04 PDT)
Re: AMBER: Re: TI tutorial
(Tue Jun 28 2005 - 20:46:17 PDT)
Re: AMBER: Re: TI tutorial
(Tue Jun 28 2005 - 09:36:59 PDT)
AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation
(Tue Jun 28 2005 - 08:02:42 PDT)
AMBER: Re: TI tutorial
(Tue Jun 28 2005 - 07:17:39 PDT)
Re: AMBER: TI-FEP for ALA --> GLY
(Mon Jun 27 2005 - 19:24:56 PDT)
Re: AMBER: TI-FEP for VAL --> ALA
(Sun Jun 26 2005 - 19:11:03 PDT)
Re: AMBER: MM_PBSA !
(Sun Jun 26 2005 - 17:43:13 PDT)
Re: AMBER: TI-FEP for VAL --> ALA
(Sat Jun 25 2005 - 09:13:44 PDT)
AMBER: TI-FEP for ALA --> GLY
(Fri Jun 24 2005 - 22:07:03 PDT)
John Mongan
Re: AMBER: Can constant pH be used for minimization?
(Tue Jun 14 2005 - 17:03:38 PDT)
Julien Michel
Re: AMBER: GBSA and thermodynamic ensemble
(Mon Jun 13 2005 - 12:51:23 PDT)
JunJun Liu
AMBER: How to read unformatted restart file in PTRAJ ?
(Tue Jun 28 2005 - 23:20:57 PDT)
Re: AMBER: PBSA error: PB bomb in pd_aaradi
(Wed Jun 22 2005 - 08:17:43 PDT)
Re: AMBER: Is the MD simulation normal
(Tue May 31 2005 - 19:01:07 PDT)
Junmei Wang
RE: AMBER: antechamber problems
(Mon Jun 20 2005 - 09:35:12 PDT)
RE: RE: AMBER: Antechamber RESP failed for large organic molecule
(Wed Jun 01 2005 - 09:54:42 PDT)
junwang
Re: AMBER: Need help in charge fitting through RESP
(Mon Jun 13 2005 - 10:51:41 PDT)
Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule
(Wed Jun 01 2005 - 14:18:05 PDT)
justin litchfield
AMBER: leap issues on a powerbook
(Sun Jun 12 2005 - 16:21:02 PDT)
K. Yarem
AMBER: AMBER frcmod+off input vs. prep input
(Tue Jun 07 2005 - 09:57:19 PDT)
Kara Di Giorgio
Re: AMBER: RED question
(Sun Jun 26 2005 - 22:13:13 PDT)
AMBER: RED question
(Sat Jun 25 2005 - 15:44:23 PDT)
Kenley Barrett
AMBER: position of protonation info from constant pH run
(Wed Jun 15 2005 - 18:27:44 PDT)
AMBER: Can constant pH be used for minimization?
(Fri Jun 10 2005 - 14:34:41 PDT)
Re: AMBER: segmentation fault in sander
(Tue Jun 07 2005 - 08:36:44 PDT)
AMBER: segmentation fault in sander
(Mon Jun 06 2005 - 15:07:59 PDT)
L Jin
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Wed Jun 01 2005 - 08:05:12 PDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Wed Jun 01 2005 - 03:24:12 PDT)
RE: AMBER: Error on restrained MD equilibration (AMBER 7)
(Wed Jun 01 2005 - 03:20:40 PDT)
L.C. Heady
AMBER: Saturated DNA bases
(Wed Jun 01 2005 - 01:55:54 PDT)
Latifa Douali
AMBER: TI calculation using sander
(Tue Jun 07 2005 - 17:10:54 PDT)
Laurence Lavelle
AMBER: Protein dynamics.
(Tue Jun 07 2005 - 22:52:00 PDT)
AMBER: Protein dynamics.
(Mon Jun 06 2005 - 14:43:50 PDT)
Li Su
AMBER: a question about varying positions of dihedral restraints with step number
(Wed Jun 22 2005 - 12:42:02 PDT)
AMBER: How to turn off pme when using periodic box
(Mon Jun 20 2005 - 11:31:09 PDT)
AMBER: How to set the virtual box size for a calculation run in vacuum
(Mon Jun 20 2005 - 06:27:33 PDT)
Re: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians
(Thu Jun 16 2005 - 16:17:46 PDT)
AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians
(Thu Jun 16 2005 - 14:19:36 PDT)
AMBER: How to modify force constants and equalibrium values for standard residues
(Thu Jun 16 2005 - 06:30:41 PDT)
Re: AMBER: why the dipeptide always moving out the virtual box
(Tue Jun 14 2005 - 14:11:41 PDT)
AMBER: why the dipeptide always moving out the virtual box
(Mon Jun 13 2005 - 14:40:47 PDT)
AMBER: How does Amber8 implemnet ntf=4?
(Thu Jun 02 2005 - 08:32:30 PDT)
Lihua Wang
Re: AMBER: transfer data from Linux to windows
(Thu Jun 09 2005 - 15:32:14 PDT)
Lukasz Bielecki
AMBER: stripwater
(Wed Jun 01 2005 - 07:16:05 PDT)
Lwin, ThuZar
AMBER: setting up restraint with ntr option
(Thu Jun 09 2005 - 14:49:04 PDT)
AMBER: GB/SA/LD parallel sander
(Wed Jun 08 2005 - 12:36:41 PDT)
AMBER: GB/SA/LD parallel sander
(Mon Jun 06 2005 - 09:48:27 PDT)
Mark Williamson
Re: AMBER: Installation problem. .
(Thu Jun 16 2005 - 08:15:58 PDT)
Re: AMBER: Installation problem. .
(Thu Jun 16 2005 - 08:06:57 PDT)
Re: AMBER: Vibrational spectrum? [SOLUTION]
(Fri Jun 10 2005 - 03:33:51 PDT)
Martin Sippel
Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA
(Thu Jun 30 2005 - 03:32:11 PDT)
Re: AMBER: nmode with ibelly
(Wed Jun 08 2005 - 10:48:04 PDT)
Re: AMBER: nmode with ibelly
(Tue Jun 07 2005 - 03:11:44 PDT)
AMBER: nmode with ibelly
(Mon Jun 06 2005 - 02:38:42 PDT)
AMBER: Nmode calculations
(Fri Jun 03 2005 - 10:17:48 PDT)
AMBER: Nmode with residues excluded
(Fri Jun 03 2005 - 09:56:42 PDT)
mfyang
AMBER: GCC for AMBER on 64 bit machine
(Thu Jun 23 2005 - 10:55:01 PDT)
Michael Crowley
Re: AMBER: nonbond_list question .
(Sat Jun 18 2005 - 12:51:01 PDT)
milion.c-box.cz
AMBER: Vibrational spectrum?
(Fri Jun 10 2005 - 09:53:01 PDT)
Mohammed Mayeed
AMBER: Protein-surface interaction
(Wed Jun 08 2005 - 11:37:30 PDT)
AMBER: (no subject)
(Wed Jun 08 2005 - 10:26:15 PDT)
mrbroad.ilstu.edu
AMBER: Free Energy Calculation torsion missing
(Tue Jun 14 2005 - 11:21:54 PDT)
Nadine Homeyer
AMBER: Parameters for phosphorylated amino acids
(Thu Jun 23 2005 - 07:24:08 PDT)
AMBER: Parameters for phosphorylated amino acids
(Thu Jun 23 2005 - 06:54:22 PDT)
Re: AMBER: Need help in charge fitting through RESP
(Mon Jun 13 2005 - 09:20:49 PDT)
Oliver Hucke
AMBER: puzzling gaff parameter
(Tue Jun 14 2005 - 18:16:35 PDT)
Re: AMBER: Request for g98 (IOP...)
(Tue Jun 14 2005 - 09:20:51 PDT)
opitz.che.udel.edu
AMBER: question about Carnal
(Wed Jun 22 2005 - 13:03:45 PDT)
Re: AMBER: atom type question
(Mon Jun 13 2005 - 13:46:18 PDT)
AMBER: atom type question
(Mon Jun 13 2005 - 12:41:30 PDT)
Osmar Norberto de Souza
AMBER: GBSA and thermodynamic ensemble
(Mon Jun 13 2005 - 11:29:18 PDT)
Paramasivam Manikandan
AMBER: Request for g98 (IOP...)
(Tue Jun 14 2005 - 08:04:30 PDT)
Peter Gannett
AMBER: antechamber error
(Thu Jun 30 2005 - 12:05:25 PDT)
AMBER: error - compiling antechamber
(Wed Jun 29 2005 - 12:30:20 PDT)
AMBER: compiler error, SGI Octane
(Tue Jun 28 2005 - 05:54:35 PDT)
Peter Varnai
Re: AMBER: DNA base-flipping: TI vs PMF
(Thu Jun 02 2005 - 10:21:56 PDT)
Petr Kulhanek
Re: AMBER: nonbond_list question .
(Sun Jun 19 2005 - 03:06:31 PDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Wed Jun 01 2005 - 04:03:21 PDT)
Pradipta Bandyopadhyay
AMBER: mm_pbsa script !
(Sun Jun 26 2005 - 23:43:53 PDT)
AMBER: MM_PBSA !
(Sun Jun 26 2005 - 05:43:18 PDT)
Qizhi Cui
AMBER: atom type for -CH=CH-
(Thu Jun 09 2005 - 18:46:13 PDT)
Rhoad, Jonathan S.
RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation
(Thu Jun 23 2005 - 08:08:01 PDT)
RE: AMBER: vdw for terminal phosphate
(Mon Jun 13 2005 - 09:21:49 PDT)
AMBER: vdw for terminal phosphate
(Fri Jun 10 2005 - 09:16:47 PDT)
Robert Duke
Re: AMBER: nonbond_list question .
(Sun Jun 19 2005 - 07:25:37 PDT)
Re: AMBER: nonbond_list question .
(Sat Jun 18 2005 - 20:03:07 PDT)
Re: AMBER: nmropt =1 AND ntr=1 in pmemd
(Fri Jun 17 2005 - 14:58:44 PDT)
Re: AMBER: nmropt =1 AND ntr=1 in pmemd
(Tue Jun 14 2005 - 05:18:20 PDT)
Re: AMBER: precision switch from 64 to 32 bit (double from single precision)
(Thu Jun 09 2005 - 05:20:52 PDT)
Re: AMBER: Compile question??
(Mon Jun 06 2005 - 07:32:06 PDT)
Re: AMBER: Compile question??
(Mon Jun 06 2005 - 07:17:48 PDT)
Re: AMBER: Compile question??
(Mon Jun 06 2005 - 05:38:02 PDT)
Roberto Gomperts
Re: AMBER: error - compiling antechamber
(Wed Jun 29 2005 - 14:11:41 PDT)
Re: [pgannett.hsc.wvu.edu: AMBER: compiler error, SGI Octane]
(Wed Jun 29 2005 - 08:01:00 PDT)
Ross Walker
RE: AMBER: Is the MD simulation normal
(Wed Jun 29 2005 - 09:09:13 PDT)
RE: AMBER: script for calculating hydrogen bond
(Mon Jun 27 2005 - 20:04:43 PDT)
RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation
(Thu Jun 23 2005 - 09:26:56 PDT)
AMBER: RE: tutorial 8
(Wed Jun 22 2005 - 14:15:33 PDT)
RE: AMBER: How to turn off pme when using periodic box
(Mon Jun 20 2005 - 13:31:04 PDT)
RE: AMBER: average structure
(Sun Jun 19 2005 - 17:41:07 PDT)
AMBER: RE: AMBER :LINMIN problem
(Fri Jun 17 2005 - 11:27:25 PDT)
RE: AMBER: Installation problem. .
(Fri Jun 17 2005 - 10:39:15 PDT)
RE: AMBER: Installation problem. .
(Fri Jun 17 2005 - 09:33:42 PDT)
RE: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians
(Thu Jun 16 2005 - 15:00:41 PDT)
RE: AMBER: How to modify force constants and equalibrium values for standard residues
(Thu Jun 16 2005 - 14:05:33 PDT)
RE: AMBER: Installation problem. .
(Wed Jun 15 2005 - 09:46:25 PDT)
RE: AMBER: solutions of amber installation problems
(Tue Jun 14 2005 - 21:55:20 PDT)
RE: AMBER: creating pdb file....
(Tue Jun 14 2005 - 10:51:21 PDT)
RE: AMBER: compiler
(Tue Jun 14 2005 - 10:43:58 PDT)
RE: AMBER: Extended bonds-MD
(Tue Jun 14 2005 - 10:28:43 PDT)
RE: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 20:49:05 PDT)
RE: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 16:24:21 PDT)
RE: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 10:25:26 PDT)
RE: AMBER: Error: vlimit exceeded for step
(Mon Jun 06 2005 - 10:19:04 PDT)
RE: AMBER: SHAKE in md with partial solvation
(Mon Jun 06 2005 - 10:12:20 PDT)
RE: AMBER: New problem of parallel sander
(Fri Jun 03 2005 - 09:53:55 PDT)
RE: AMBER:
(Fri Jun 03 2005 - 09:51:48 PDT)
RE: AMBER: Build of AMBER for YDL ?
(Wed Jun 01 2005 - 16:29:49 PDT)
RE: AMBER: problem in minimization
(Wed Jun 01 2005 - 09:56:46 PDT)
RE: AMBER: density problem
(Wed Jun 01 2005 - 09:21:33 PDT)
S.Sundar Raman
AMBER: Request for calculating free energy using AMBER6
(Mon Jun 27 2005 - 04:59:00 PDT)
AMBER: Need help in charge fitting through RESP
(Mon Jun 13 2005 - 06:55:29 PDT)
Scott Pendley
Re: AMBER: MM-PBSA calculation
(Wed Jun 01 2005 - 16:44:05 PDT)
Shulin Zhuang
Re: AMBER: Is the MD simulation normal
(Thu Jun 30 2005 - 08:00:11 PDT)
Re: AMBER: Is the MD simulation normal
(Thu Jun 30 2005 - 07:52:03 PDT)
Re: AMBER: Is the MD simulation normal
(Wed Jun 29 2005 - 08:03:20 PDT)
Re: AMBER: Is the MD simulation normal
(Wed Jun 29 2005 - 03:11:53 PDT)
Re: AMBER: antechamber problems
(Mon Jun 20 2005 - 18:07:56 PDT)
Re: AMBER: Need help in charge fitting through RESP
(Mon Jun 13 2005 - 07:29:02 PDT)
Re: AMBER: density problem
(Tue May 31 2005 - 18:49:47 PDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 18:36:32 PDT)
Simon Whitehead
AMBER:
(Thu Jun 02 2005 - 05:44:03 PDT)
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
Re: AMBER: fail of minimization in sander
(Wed Jun 15 2005 - 04:05:25 PDT)
Re: AMBER: Protein ions?
(Thu Jun 02 2005 - 07:57:02 PDT)
Stern, Julie
AMBER: SOURCE3 in gaff.dat
(Fri Jun 10 2005 - 02:40:20 PDT)
AMBER: eelnb
(Mon Jun 06 2005 - 13:16:31 PDT)
Sukjoon Yoon
AMBER: Installation problem. .
(Thu Jun 16 2005 - 07:49:19 PDT)
AMBER: Installation problem. .
(Tue Jun 14 2005 - 23:08:51 PDT)
AMBER: Installation problem
(Sun Jun 12 2005 - 21:07:26 PDT)
RE: AMBER: Installation problem
(Sun Jun 12 2005 - 19:35:37 PDT)
AMBER: Installation problem
(Sun Jun 12 2005 - 02:21:50 PDT)
Suxin Zheng
AMBER: Have the parameters for dUMP been calculated by somebody?
(Fri Jun 24 2005 - 18:30:12 PDT)
Re: AMBER: Parameters for phosphorylated amino acids
(Thu Jun 23 2005 - 15:41:30 PDT)
AMBER: Compile Problems of Parallel Amber8 on Mac G5
(Wed Jun 08 2005 - 16:02:23 PDT)
Thomas Patko
Re: AMBER: transfer data from Linux to windows
(Thu Jun 09 2005 - 15:49:02 PDT)
Thomas Steinbrecher
Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA
(Thu Jun 30 2005 - 00:14:01 PDT)
Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation
(Mon Jun 06 2005 - 00:23:16 PDT)
Varsha Goyal
Re: AMBER: Analysing my simulation data..
(Sat Jun 18 2005 - 09:21:28 PDT)
AMBER: Question about tutorial-9
(Tue Jun 07 2005 - 09:27:57 PDT)
Vijay Manickam Achari
AMBER: example script for hbond calculation
(Wed Jun 29 2005 - 23:27:15 PDT)
AMBER: acceptor and donor in hbond calculation
(Wed Jun 29 2005 - 22:01:58 PDT)
AMBER: calculating hydrogen bonds
(Tue Jun 28 2005 - 19:50:36 PDT)
AMBER: calculating torsion angles
(Tue Jun 28 2005 - 01:59:02 PDT)
AMBER: script for calculating hydrogen bond
(Mon Jun 27 2005 - 19:57:30 PDT)
AMBER: using xmgrace....
(Thu Jun 23 2005 - 19:51:37 PDT)
AMBER: Analysing my simulation data..
(Sat Jun 18 2005 - 01:32:13 PDT)
AMBER: creating pdb file....
(Tue Jun 14 2005 - 03:49:09 PDT)
Re: AMBER: how to pull out frames
(Mon Jun 13 2005 - 21:04:42 PDT)
AMBER: how to pull out frames
(Sun Jun 12 2005 - 22:23:51 PDT)
Viktor Hornak
Re: AMBER: setting up restraint with ntr option
(Thu Jun 09 2005 - 16:53:05 PDT)
Wai Keat Yam
AMBER: substitute missing residues?
(Fri Jun 10 2005 - 01:20:29 PDT)
wendy
Re: AMBER: fail of minimization in sander
(Thu Jun 16 2005 - 19:43:11 PDT)
Re: AMBER: fail of minimization in sander
(Thu Jun 16 2005 - 01:19:15 PDT)
Re: AMBER: fail of minimization in sander
(Wed Jun 15 2005 - 00:54:59 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 09:13:10 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 08:57:08 PDT)
Re: AMBER: fail of minimization in sander
(Mon Jun 06 2005 - 03:06:01 PDT)
Re: AMBER: fail of minimization in sander
(Sun Jun 05 2005 - 21:59:15 PDT)
AMBER: fail of minimization in sander
(Sun Jun 05 2005 - 20:01:25 PDT)
xhu1.memphis.edu
AMBER: software for real polymer MD simulation
(Wed Jun 22 2005 - 14:31:51 PDT)
Xin Hu
AMBER: PBSA error: PB bomb in pd_aaradi
(Wed Jun 22 2005 - 07:34:13 PDT)
xinhuang.indiana.edu
AMBER: questions about RNA
(Mon Jun 27 2005 - 20:19:58 PDT)
xueping
AMBER: Hbond analysis
(Sun Jun 26 2005 - 18:27:48 PDT)
Ye Mei
AMBER: large std error in entropy estimation
(Tue Jun 21 2005 - 19:51:43 PDT)
Re: RE: AMBER: SHAKE in md with partial solvation
(Tue Jun 07 2005 - 06:46:49 PDT)
AMBER: Re: Re: AMBER: SHAKE in md with partial solvation
(Mon Jun 06 2005 - 03:49:44 PDT)
Re: AMBER: SHAKE in md with partial solvation
(Sun Jun 05 2005 - 04:19:45 PDT)
AMBER: SHAKE in md with partial solvation
(Sun Jun 05 2005 - 00:30:00 PDT)
AMBER: radius parameter for Mg2+ in mm_pbsa calculation
(Sat Jun 04 2005 - 07:37:04 PDT)
Yen-Ting Lai
Re: AMBER: Question about "quasih"
(Wed Jun 15 2005 - 12:25:57 PDT)
AMBER: Question about "quasih"
(Wed Jun 15 2005 - 09:46:22 PDT)
Yogesh Sabnis
AMBER: Cut pdb files
(Thu Jun 16 2005 - 00:57:18 PDT)
Yong Duan
Re: AMBER: Protein dynamics.
(Wed Jun 08 2005 - 10:24:02 PDT)
Zhang Bing
AMBER: parallel error
(Mon Jun 27 2005 - 05:36:14 PDT)
AMBER: solutions of amber installation problems
(Tue Jun 14 2005 - 19:42:13 PDT)
AMBER: Thanks
(Tue Jun 14 2005 - 19:26:23 PDT)
AMBER: compiler
(Tue Jun 14 2005 - 04:13:19 PDT)
AMBER: compiler
(Tue Jun 14 2005 - 01:14:08 PDT)
AMBER: New problem of parallel sander
(Thu Jun 02 2005 - 19:46:13 PDT)
AMBER: amber8 installation problems
(Wed Jun 01 2005 - 23:55:48 PDT)
AMBER: amber8 installation problems
(Wed Jun 01 2005 - 23:44:47 PDT)
Zhiguo Liu
Re: Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA
(Thu Jun 30 2005 - 02:56:42 PDT)
AMBER: Free energy calculation for protein-protein complex using MM_PBSA
(Wed Jun 29 2005 - 18:59:01 PDT)
建平 胡
AMBER: TI in Amber8
(Fri Jun 03 2005 - 02:49:02 PDT)
Last message date
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Fri Jul 01 2005 - 02:53:00 PDT
Archived on
: Wed Apr 17 2024 - 05:53:19 PDT
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