Amber Archive May 2005 by author
382 messages
:
Starting
Sun May 01 2005 - 22:53:00 PDT,
Ending
Wed Jun 01 2005 - 04:53:00 PDT
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'Ross Walker'
RE: AMBER: why is snaupe.f is empty?
(Thu May 26 2005 - 11:14:34 PDT)
RE: AMBER: setting up Parallel processing
(Thu May 26 2005 - 11:14:18 PDT)
aanzellotti.mail2.vcu.edu
Re: AMBER: generating over 16 bps of DNA in nucgen
(Tue May 17 2005 - 08:57:45 PDT)
Abd Ghani Abd Aziz
Re: AMBER: maximum number of processors
(Fri May 13 2005 - 23:42:49 PDT)
Andreas Svrcek-Seiler
Re: AMBER: amber code
(Tue May 24 2005 - 07:18:11 PDT)
Re: RE: AMBER: problem with gb md
(Fri May 06 2005 - 02:19:00 PDT)
Re: AMBER: fast 1/r methods
(Mon May 02 2005 - 07:18:22 PDT)
Andrew Box
AMBER: Mol2 to prepin file conversion
(Thu May 26 2005 - 17:08:22 PDT)
Andy Purkiss
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?)
(Fri May 06 2005 - 04:05:36 PDT)
Angelo Pugliese
Re: AMBER: rotating and repositioning molecules in xleap
(Sun May 22 2005 - 02:37:44 PDT)
AMBER: Relative stability with MMPBSA
(Wed May 04 2005 - 09:09:27 PDT)
Anthony Cruz
Fwd: Re: AMBER: AMBER Test
(Wed May 11 2005 - 08:49:38 PDT)
Fwd: Re: AMBER: AMBER Test
(Tue May 03 2005 - 05:25:46 PDT)
Asim Okur
Re: AMBER: maximum number of processors
(Thu May 12 2005 - 08:41:25 PDT)
Atilio Anzellotti
AMBER: Message in .out file
(Tue May 17 2005 - 05:31:36 PDT)
Bill Ross
Re: AMBER: Is the MD simulation normal
(Tue May 31 2005 - 20:41:42 PDT)
RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout
(Tue May 31 2005 - 11:42:50 PDT)
Re: AMBER: STOP 0
(Tue May 31 2005 - 10:43:32 PDT)
Re: AMBER: density profiles in ptraj or carnal
(Tue May 31 2005 - 09:13:28 PDT)
Re: AMBER: density profiles in ptraj or carnal
(Mon May 30 2005 - 10:00:08 PDT)
Re: AMBER: Is the MD simulation normal
(Mon May 30 2005 - 09:49:32 PDT)
RE: AMBER: Is the MD simulation normal
(Sun May 29 2005 - 10:04:01 PDT)
Re: AMBER: Is the MD simulation normal
(Sun May 29 2005 - 08:33:13 PDT)
Re: AMBER: Is the MD simulation normal
(Sat May 28 2005 - 10:00:42 PDT)
Re: AMBER: Is the MD simulation normal
(Fri May 27 2005 - 11:14:30 PDT)
Re: AMBER: dissolving micelle structure in water.. amber7
(Thu May 26 2005 - 09:50:23 PDT)
Re: AMBER: hbond analysis in ptaj/carnal
(Thu May 26 2005 - 09:44:13 PDT)
Re: AMBER: rotating and repositioning molecules in xleap
(Sun May 22 2005 - 08:36:16 PDT)
Re: AMBER: Unexpected stop of Sander run
(Sun May 22 2005 - 13:18:16 PDT)
Re: AMBER: crashing xleap
(Fri May 20 2005 - 12:55:15 PDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 20:56:58 PDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 19:16:22 PDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 21:49:04 PDT)
Re: AMBER: how to reduce box size and delete excess solvent
(Sun May 15 2005 - 12:50:01 PDT)
Re: AMBER: Calculating of radius of gyration in Carnal
(Sat May 14 2005 - 15:26:43 PDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Thu May 12 2005 - 13:08:34 PDT)
Re: AMBER: How can I read parm99.dat file?
(Fri May 06 2005 - 13:08:59 PDT)
Re: AMBER: How can I read parm99.dat file?
(Wed May 04 2005 - 17:12:08 PDT)
Brent Krueger
AMBER: fast 1/r methods
(Mon May 02 2005 - 04:51:56 PDT)
C J Kenneth Tan -- OptimaNumerics
Re: AMBER: maximum number of processors
(Sat May 14 2005 - 07:57:22 PDT)
caoch.cherry.bio.titech.ac.jp
AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?
(Sat May 14 2005 - 10:17:17 PDT)
Carlos Simmerling
Re: AMBER: if setting ntf=4, will it cause someproblem?
(Tue May 31 2005 - 08:12:30 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 10:51:14 PDT)
Re: AMBER: conformational sampling of a peptide
(Tue May 24 2005 - 06:11:53 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 06:57:00 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 04:15:34 PDT)
Re: AMBER: Unexpected stop of Sander run
(Sun May 22 2005 - 13:22:11 PDT)
Re: AMBER: Error in minimization
(Fri May 20 2005 - 05:57:37 PDT)
Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?
(Sat May 14 2005 - 10:52:56 PDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7
(Fri May 13 2005 - 03:50:10 PDT)
Re: AMBER: langevin, GB and simulated annealing - 5
(Tue May 10 2005 - 04:58:42 PDT)
Re: AMBER: langevin, GB and simulated annealing - 5
(Mon May 09 2005 - 12:58:57 PDT)
cbala.igib.res.in
AMBER: error during MD run
(Wed May 18 2005 - 11:39:25 PDT)
AMBER: loading pdb
(Tue May 17 2005 - 22:56:13 PDT)
Cenk Andac
AMBER: Reference (?) for normal-mode analysis in nmode
(Mon May 30 2005 - 02:18:59 PDT)
Re:Re: AMBER: Solute-solvent boundary in pbsa
(Thu May 26 2005 - 13:58:55 PDT)
Re#2:Re: AMBER: Solute-solvent boundary in pbsa
(Wed May 25 2005 - 13:03:47 PDT)
Re: AMBER: Solute-solvent boundary in pbsa
(Wed May 25 2005 - 09:21:52 PDT)
Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA
(Tue May 24 2005 - 11:48:26 PDT)
AMBER: Citing the PBSA module of AMBER8
(Fri May 20 2005 - 14:27:03 PDT)
AMBER: Copyright for PBSA
(Sat May 21 2005 - 01:32:00 PDT)
AMBER: MM_PBSA for NMR restrained structures
(Fri May 20 2005 - 01:36:10 PDT)
Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
(Thu May 19 2005 - 10:03:43 PDT)
Re: AMBER: Meaning of induced dipole moments for atom pairs?
(Thu May 05 2005 - 17:28:49 PDT)
AMBER: Meaning of induced dipole moments for atom pairs?
(Wed May 04 2005 - 13:52:06 PDT)
chaiann ng
AMBER: charges difference of atom in xleap and prmtop
(Tue May 24 2005 - 21:02:33 PDT)
RE: AMBER: how to generate frcmod file for using prepin file..
(Mon May 23 2005 - 20:03:55 PDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 19:55:23 PDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 19:05:27 PDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 18:59:47 PDT)
AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 18:19:04 PDT)
Chen Chengwen
AMBER: Setting Amber force field parameters
(Mon May 23 2005 - 00:55:38 PDT)
AMBER: platinum atom in Xleap
(Fri May 13 2005 - 19:11:12 PDT)
Chris Moth
AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat?
(Fri May 06 2005 - 12:32:23 PDT)
Chutintorn Punwong
Re: AMBER: question about loadiing pdb file of a molecule complex
(Fri May 27 2005 - 15:07:52 PDT)
Cordova, Luis E.
RE: AMBER: meaningful tax for sander question
(Tue May 31 2005 - 13:03:59 PDT)
AMBER: meaningful tax for sander question
(Tue May 31 2005 - 12:19:30 PDT)
AMBER: why is snaupe.f is empty?
(Thu May 26 2005 - 10:06:24 PDT)
AMBER: amber8 test error
(Thu May 12 2005 - 20:26:00 PDT)
cristian obiol
AMBER: density problem
(Tue May 31 2005 - 02:17:46 PDT)
Daniela Kohen
AMBER: Tutorial #1 ptraj/sander problem
(Thu May 12 2005 - 15:03:07 PDT)
Dave S Walker
AMBER: runtime error in sander?
(Tue May 31 2005 - 10:07:13 PDT)
David A. Case
Re: AMBER: meaningful tax for sander question
(Tue May 31 2005 - 12:59:20 PDT)
Re: AMBER: question about loadiing pdb file of a molecule complex
(Tue May 31 2005 - 11:00:59 PDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 08:45:01 PDT)
Re: AMBER: Reference (?) for normal-mode analysis in nmode
(Tue May 31 2005 - 08:30:10 PDT)
Re: AMBER: Force field modification problem
(Mon May 30 2005 - 22:17:06 PDT)
Re: AMBER: Force field modification problem
(Mon May 30 2005 - 09:21:00 PDT)
Re: AMBER: Antechamber RESP failed for large organic molecule
(Mon May 30 2005 - 09:09:27 PDT)
Re: AMBER: question about loadiing pdb file of a molecule complex
(Sat May 28 2005 - 22:29:53 PDT)
Re: AMBER: Mol2 to prepin file conversion
(Thu May 26 2005 - 17:44:36 PDT)
Re: AMBER: dissolving micelle structure in water.. amber7
(Thu May 26 2005 - 09:30:17 PDT)
Re: AMBER: error in chirality.c?
(Wed May 25 2005 - 08:21:48 PDT)
Re: AMBER: Which forcefield?
(Tue May 24 2005 - 22:32:09 PDT)
Re: AMBER: charges difference of atom in xleap and prmtop
(Tue May 24 2005 - 22:27:51 PDT)
Re: AMBER: Connecting two molecules
(Mon May 23 2005 - 08:23:51 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 08:00:46 PDT)
Re: AMBER: Copyright for PBSA
(Sat May 21 2005 - 20:37:45 PDT)
Re: AMBER: leap problem: savepdb
(Fri May 20 2005 - 08:21:13 PDT)
Re: AMBER: Representation of cations in MD
(Fri May 20 2005 - 08:16:15 PDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 18:38:49 PDT)
Re: AMBER: GB - igb=1 versus dielc=?
(Thu May 19 2005 - 09:09:47 PDT)
Re: AMBER: Using amber4 generated prep files in amber8?
(Thu May 19 2005 - 08:31:54 PDT)
Re: AMBER: gaff: ca-ca-c -o torsion parameter
(Tue May 17 2005 - 23:38:33 PDT)
Re: AMBER: error with ptraj
(Tue May 17 2005 - 23:38:22 PDT)
Re: AMBER: loading pdb
(Tue May 17 2005 - 23:38:27 PDT)
Re: AMBER: Message in .out file
(Tue May 17 2005 - 23:38:40 PDT)
Re: AMBER: output of force field info
(Mon May 16 2005 - 17:16:55 PDT)
Re: AMBER: How to set constraint
(Mon May 16 2005 - 08:42:27 PDT)
Re: AMBER: amber8 test error
(Fri May 13 2005 - 10:11:27 PDT)
Re: AMBER: creating residues - charge assign problems
(Fri May 13 2005 - 09:43:41 PDT)
Re: AMBER: a nomenclature question
(Thu May 12 2005 - 15:18:20 PDT)
Re: AMBER: SANDER BOMB: volume of ucell too big
(Thu May 12 2005 - 13:27:50 PDT)
Re: AMBER: Trouble with example tutorial
(Thu May 12 2005 - 10:04:51 PDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Thu May 12 2005 - 09:58:19 PDT)
Re: Fwd: Re: AMBER: AMBER Test
(Thu May 12 2005 - 08:33:15 PDT)
Re: AMBER: Parameter for alpha-lactose
(Thu May 12 2005 - 08:29:08 PDT)
Re: AMBER: langevin, GB and simulated annealing - 5
(Mon May 09 2005 - 16:18:04 PDT)
Re: AMBER: ibelly in nmode
(Sat May 07 2005 - 09:44:21 PDT)
Re: AMBER: No vdW parameters for HO..
(Fri May 06 2005 - 07:38:16 PDT)
Re: AMBER: How can I read parm99.dat file?
(Thu May 05 2005 - 08:10:59 PDT)
Re: AMBER: Meaning of induced dipole moments for atom pairs?
(Wed May 04 2005 - 15:13:14 PDT)
Re: AMBER: How to fix the atom in NPT case?
(Tue May 03 2005 - 17:16:33 PDT)
Re: AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 15:59:23 PDT)
Re: AMBER: NOE constraints
(Tue May 03 2005 - 13:25:44 PDT)
Re: AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 13:23:14 PDT)
Re: AMBER: How to fix the atom in NPT case?
(Mon May 02 2005 - 11:31:26 PDT)
Re: AMBER: ipol=1 & use_pme= ??
(Mon May 02 2005 - 09:44:47 PDT)
David Mobley
Re: AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 12:27:23 PDT)
Dawei Zhang
AMBER: ibelly in nmode
(Thu May 05 2005 - 12:23:13 PDT)
Douali, Latifa
AMBER:Sander errors: Unit 6 Error on OPEN: mdout
(Tue May 31 2005 - 10:34:41 PDT)
drugdesign
AMBER: stack terminated abnormally
(Tue May 31 2005 - 03:20:33 PDT)
Ed Pate
AMBER: question about initial conditions for amber
(Sun May 29 2005 - 19:42:21 PDT)
emilia wu
Re: RE: AMBER: problem with gb md
(Thu May 05 2005 - 23:29:33 PDT)
AMBER: problem with gb md
(Thu May 05 2005 - 19:05:00 PDT)
Eric Hu
AMBER: mm/pbsa error
(Wed May 04 2005 - 11:06:34 PDT)
Fabien Cailliez
Re: AMBER: distance restraints between two centers of mass
(Thu May 26 2005 - 02:01:08 PDT)
fangyu liang
Re: AMBER: fast 1/r methods
(Mon May 02 2005 - 07:17:32 PDT)
Furse, Kristina Elisabet
Re: AMBER: crashing xleap
(Fri May 20 2005 - 15:28:05 PDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform
(Fri May 20 2005 - 14:20:55 PDT)
FyD
Re: AMBER: RESP charge fitting for N-methylguanine cation
(Fri May 13 2005 - 08:33:05 PDT)
Re: AMBER: creating residues - charge assign problems
(Fri May 13 2005 - 08:25:48 PDT)
Re: AMBER: Problem with xleap
(Wed May 11 2005 - 19:21:12 PDT)
Re: AMBER: Asking how to creat alanine "dipeptide" in amber8
(Wed May 11 2005 - 09:06:27 PDT)
Re: AMBER: Re: R.E.D. question
(Mon May 02 2005 - 12:53:35 PDT)
Garhan Attebury
AMBER: Sander Restart Problem
(Tue May 24 2005 - 08:07:49 PDT)
Re: AMBER: generating over 16 bps of DNA in nucgen
(Tue May 17 2005 - 08:27:13 PDT)
george Chen
Re: AMBER: How to fix the atom in NPT case?
(Tue May 03 2005 - 13:50:59 PDT)
Re: AMBER: How to fix the atom in NPT case?
(Mon May 02 2005 - 12:35:42 PDT)
AMBER: How to fix the atom in NPT case?
(Mon May 02 2005 - 11:19:54 PDT)
Glen Otero
AMBER: Amber 8 and LAM compilation problem
(Wed May 18 2005 - 22:52:00 PDT)
Grzegorz Jezierski
AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"
(Tue May 31 2005 - 09:04:20 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 07:38:58 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 06:43:51 PDT)
Re: AMBER: Unexpected stop of Sander run
(Mon May 23 2005 - 00:14:54 PDT)
AMBER: Unexpected stop of Sander run
(Sun May 22 2005 - 12:44:55 PDT)
AMBER: RESP charge fitting for N-methylguanine cation
(Thu May 12 2005 - 09:50:17 PDT)
gtg549i.mail.gatech.edu
Re: AMBER: question about loadiing pdb file of a molecule complex
(Tue May 31 2005 - 12:12:39 PDT)
AMBER: Loading pdb-residue (re)numbering in leap
(Tue May 31 2005 - 10:48:13 PDT)
Re: AMBER: question about loadiing pdb file of a molecule complex
(Mon May 30 2005 - 08:56:09 PDT)
AMBER: question about loadiing pdb file of a molecule complex
(Fri May 27 2005 - 14:39:28 PDT)
Guanglei Cui
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 12:02:46 PDT)
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
(Wed May 25 2005 - 06:55:23 PDT)
Re: AMBER: How to fix certain bond angles
(Tue May 24 2005 - 08:40:00 PDT)
Hannes Barsch
AMBER: conformational sampling of a peptide
(Tue May 24 2005 - 01:58:04 PDT)
AMBER: leap problem: savepdb
(Fri May 20 2005 - 02:30:29 PDT)
Harianto Tjong
Re: AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 15:13:16 PDT)
Re: AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 13:31:43 PDT)
AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 12:04:39 PDT)
Hayden Eastwood
AMBER: creating residues - charge assign problems
(Fri May 13 2005 - 04:06:06 PDT)
hj zou
AMBER: how to reduce box size and delete excess solvent
(Sun May 15 2005 - 04:51:32 PDT)
Holger Gohlke
Re: AMBER: nmode in mmpbsa
(Mon May 16 2005 - 23:44:17 PDT)
Hui-Hsu Tsai
AMBER: NOE constraints
(Tue May 03 2005 - 12:18:27 PDT)
Hwankyu Lee
Re: AMBER: density profiles in ptraj or carnal
(Mon May 30 2005 - 21:13:26 PDT)
Re: AMBER: density profiles in ptraj or carnal
(Mon May 30 2005 - 15:58:54 PDT)
AMBER: density profiles in ptraj or carnal
(Sun May 29 2005 - 20:27:37 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 11:34:34 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 11:07:41 PDT)
AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 10:20:10 PDT)
Re: AMBER: Connecting two molecules
(Mon May 23 2005 - 09:51:20 PDT)
AMBER: Connecting two molecules
(Mon May 23 2005 - 08:13:00 PDT)
AMBER: Error in sander: stack trace terminated abnormally.
(Sun May 22 2005 - 14:05:31 PDT)
Re: AMBER: rotating and repositioning molecules in xleap
(Sun May 22 2005 - 06:03:40 PDT)
AMBER: rotating and repositioning molecules in xleap
(Fri May 20 2005 - 23:09:45 PDT)
AMBER: generating over 16 bps of DNA in nucgen
(Mon May 16 2005 - 08:33:04 PDT)
AMBER: Calculating of radius of gyration in Carnal
(Sat May 14 2005 - 11:36:37 PDT)
Ilyas Yildirim
Re: AMBER: my frcmod file created using parmchk
(Mon May 23 2005 - 21:03:42 PDT)
Re: AMBER: crashing xleap
(Fri May 20 2005 - 14:47:09 PDT)
Re: AMBER: how to creat leaprc.gaff
(Fri May 20 2005 - 02:48:14 PDT)
Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
(Thu May 19 2005 - 00:37:22 PDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 21:47:49 PDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 21:00:07 PDT)
AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 19:16:35 PDT)
Re: AMBER: parameter for sulfur in thio-glucoside residue
(Wed May 18 2005 - 19:11:34 PDT)
Re: AMBER: loading pdb
(Wed May 18 2005 - 13:21:24 PDT)
AMBER: ATOM TYPE
(Mon May 16 2005 - 19:10:48 PDT)
AMBER: *** Proper torsion parameters missing ***
(Mon May 16 2005 - 17:19:04 PDT)
Re: AMBER: Problem with xleap
(Thu May 12 2005 - 16:14:38 PDT)
AMBER: Problem with xleap
(Wed May 11 2005 - 18:45:50 PDT)
Jana Precechtelova
AMBER: hbond analysis in ptaj/carnal
(Thu May 26 2005 - 09:25:20 PDT)
JAVIER PEREZ
AMBER: distance restraints between two centers of mass
(Thu May 26 2005 - 01:37:30 PDT)
John Mongan
Re: AMBER: rborn(i) in egb.f
(Tue May 03 2005 - 11:26:15 PDT)
Joseph Fernandez
AMBER: nmode in mmpbsa
(Mon May 16 2005 - 16:36:28 PDT)
AMBER: Identifying water molecules with ptraj
(Sun May 01 2005 - 14:00:59 PDT)
Joseph Nachman
Re: AMBER: conformational sampling of a peptide
(Tue May 24 2005 - 08:26:52 PDT)
Juan Fernandez Carmona
AMBER: amber code
(Tue May 24 2005 - 03:08:00 PDT)
JunJun Liu
Re: AMBER:
(Fri May 20 2005 - 19:41:24 PDT)
Re: AMBER: Problem with xleap
(Thu May 12 2005 - 00:19:24 PDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?)
(Thu May 05 2005 - 17:37:36 PDT)
Junmei Wang
RE: AMBER: Antechamber RESP failed for large organic molecule
(Tue May 31 2005 - 07:37:35 PDT)
RE: AMBER: GAFF angle parameters
(Tue May 17 2005 - 15:08:47 PDT)
junwang
AMBER: External Field in AMBER?
(Tue May 31 2005 - 19:19:38 PDT)
Re: RE: AMBER: Antechamber RESP failed for large organic molecule
(Tue May 31 2005 - 09:58:33 PDT)
AMBER: Antechamber RESP failed for large organic molecule
(Sun May 29 2005 - 12:57:59 PDT)
Kara Di Giorgio
AMBER: Working with a nickel-organometallic compound
(Tue May 31 2005 - 16:36:30 PDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 21:10:36 PDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap?
(Wed May 18 2005 - 19:45:43 PDT)
AMBER: frcmod info for Nickel
(Wed May 18 2005 - 12:04:44 PDT)
Re: AMBER: RESP charge fitting for N-methylguanine cation
(Thu May 12 2005 - 19:40:17 PDT)
Kenley Barrett
AMBER: error in chirality.c?
(Wed May 25 2005 - 07:27:07 PDT)
Re: AMBER: crashing xleap
(Fri May 20 2005 - 13:57:00 PDT)
AMBER: crashing xleap
(Fri May 20 2005 - 11:48:13 PDT)
AMBER: a nomenclature question
(Fri May 06 2005 - 09:11:24 PDT)
kuljeets.igib.res.in
Re: AMBER: average structure after MD
(Wed May 25 2005 - 22:42:32 PDT)
AMBER: average structure after MD
(Wed May 25 2005 - 02:14:19 PDT)
L Jin
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 09:21:55 PDT)
AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 08:23:51 PDT)
Lauren O'Neil
AMBER: DNA base-flipping: TI vs PMF
(Tue May 31 2005 - 08:40:45 PDT)
Li Su
Re: AMBER: if setting ntf=4, will it cause someproblem?
(Tue May 31 2005 - 14:07:25 PDT)
AMBER: if setting ntf=4, will it cause someproblem?
(Tue May 31 2005 - 07:55:03 PDT)
AMBER: Bond angle restraints setting files
(Mon May 30 2005 - 09:05:15 PDT)
AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
(Tue May 24 2005 - 12:14:09 PDT)
AMBER: How to fix certain bond angles
(Tue May 24 2005 - 08:27:14 PDT)
AMBER: How to set up dihedral constraints in amber
(Mon May 16 2005 - 08:39:50 PDT)
AMBER: How to set constraint
(Sun May 15 2005 - 11:58:51 PDT)
AMBER: Asking how to creat alanine "dipeptide" in amber8
(Wed May 11 2005 - 08:37:07 PDT)
luckyang.gmail.com
Re: AMBER:
(Fri May 20 2005 - 11:28:17 PDT)
Maciej
AMBER: Trouble with example tutorial
(Wed May 11 2005 - 04:08:02 PDT)
Marcin Krol
Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"
(Tue May 31 2005 - 09:17:30 PDT)
Mark Rance
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Wed May 11 2005 - 08:02:05 PDT)
masi.nmr.mpibpc.mpg.de
AMBER: STOP 0
(Tue May 31 2005 - 09:40:25 PDT)
AMBER: MM-PBSA calculation
(Tue May 31 2005 - 09:37:40 PDT)
mathew k varghese
AMBER: setting up Parallel processing
(Thu May 26 2005 - 08:39:00 PDT)
Michael Crowley
Re: AMBER: SANDER BOMB: volume of ucell too big
(Thu May 12 2005 - 10:10:20 PDT)
Re: AMBER: maximum number of processors
(Thu May 12 2005 - 10:00:09 PDT)
milion.c-box.cz
AMBER: GB - igb=1 versus dielc=?
(Thu May 19 2005 - 09:53:00 PDT)
mingche Pan
AMBER: molsurf error
(Tue May 17 2005 - 09:52:57 PDT)
Monica Civera
AMBER: GAFF angle parameters
(Tue May 17 2005 - 09:11:46 PDT)
MURAT CETINKAYA
AMBER: maximum number of processors
(Wed May 11 2005 - 20:53:44 PDT)
Myunggi Yi
AMBER: radial distribution function
(Mon May 09 2005 - 11:36:43 PDT)
Re: AMBER: How can I read parm99.dat file?
(Fri May 06 2005 - 07:14:15 PDT)
Re: AMBER: How can I read parm99.dat file?
(Fri May 06 2005 - 07:14:04 PDT)
Re: AMBER: How can I read parm99.dat file?
(Fri May 06 2005 - 06:18:47 PDT)
AMBER: How can I read parm99.dat file?
(Wed May 04 2005 - 16:08:49 PDT)
AMBER: Can I add iodide anione?
(Tue May 03 2005 - 10:36:07 PDT)
Nelson Fonseca
Re: AMBER: MMPBSA calculations on Highly charged systems
(Tue May 17 2005 - 05:36:16 PDT)
AMBER: strange mm_pbsa.pl bug
(Mon May 16 2005 - 08:39:21 PDT)
Oliver Hucke
AMBER: gaff: ca-ca-c -o torsion parameter
(Tue May 17 2005 - 13:54:24 PDT)
pascal.baillod.epfl.ch
AMBER: ptraj - hbond detailed analysis over time?
(Thu May 26 2005 - 10:38:38 PDT)
AMBER: hbond detailed analysis over time?
(Mon May 23 2005 - 11:04:10 PDT)
AMBER: langevin, GB and simulated annealing - 5
(Mon May 09 2005 - 09:25:12 PDT)
Peter Varnai
AMBER: write format of restart crd in sander/pmemd
(Thu May 19 2005 - 05:12:22 PDT)
Petr Kulhanek
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
(Thu May 26 2005 - 03:44:37 PDT)
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
(Wed May 25 2005 - 04:56:34 PDT)
Philippe ARNAUD
AMBER: PARMSCAN program
(Wed May 25 2005 - 00:28:31 PDT)
Pradipta Bandyopadhyay
AMBER: GB with dipoles !
(Tue May 03 2005 - 04:54:44 PDT)
Priti Hansia
AMBER: Error in minimization
(Fri May 20 2005 - 03:58:36 PDT)
Rajeev Ranjan Singh
Re: AMBER: error during MD run
(Wed May 18 2005 - 11:16:12 PDT)
Re: AMBER: loading pdb
(Wed May 18 2005 - 07:01:34 PDT)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN
(Tue May 17 2005 - 13:15:33 PDT)
Ray Luo
Re: AMBER: Solute-solvent boundary in pbsa
(Wed May 25 2005 - 18:40:39 PDT)
Re: AMBER: Solute-solvent boundary in pbsa
(Tue May 24 2005 - 22:54:50 PDT)
Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa
(Tue May 24 2005 - 22:56:08 PDT)
Re: AMBER: Solute-solvent boundary in pbsa
(Tue May 24 2005 - 01:48:10 PDT)
René Ranzinger
AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_'
(Tue May 24 2005 - 08:04:42 PDT)
riccardo nifosi
AMBER: quadrupole in resp
(Wed May 25 2005 - 03:44:20 PDT)
Robert Duke
Re: AMBER: setting up Parallel processing
(Thu May 26 2005 - 09:15:30 PDT)
AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1
(Tue May 24 2005 - 07:42:15 PDT)
Re: AMBER: Amber 8 and LAM compilation problem
(Thu May 19 2005 - 05:05:48 PDT)
Re: AMBER: compiling pmemd on dual xeon
(Tue May 17 2005 - 10:49:48 PDT)
Re: AMBER: SANDER BOMB: volume of ucell too big
(Thu May 12 2005 - 13:44:11 PDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Wed May 11 2005 - 08:18:12 PDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Wed May 11 2005 - 08:14:50 PDT)
Ross Walker
RE: AMBER: double counting of potentials
(Tue May 31 2005 - 16:21:43 PDT)
RE: AMBER: meaningful tax for sander question
(Tue May 31 2005 - 13:12:10 PDT)
RE: AMBER: meaningful tax for sander question
(Tue May 31 2005 - 12:55:14 PDT)
RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout
(Tue May 31 2005 - 10:45:53 PDT)
RE: AMBER: runtime error in sander?
(Tue May 31 2005 - 10:34:51 PDT)
RE: AMBER: STOP 0
(Tue May 31 2005 - 09:47:20 PDT)
RE: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 09:45:19 PDT)
RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"
(Tue May 31 2005 - 09:09:20 PDT)
RE: AMBER: stack terminated abnormally
(Tue May 31 2005 - 08:35:15 PDT)
RE: AMBER: density problem
(Tue May 31 2005 - 08:33:39 PDT)
AMBER: Workshop Tutorials Downtime this weekend.
(Fri May 27 2005 - 14:49:05 PDT)
RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_'
(Tue May 24 2005 - 08:43:37 PDT)
RE: AMBER: Error in sander: stack trace terminated abnormally.
(Sun May 22 2005 - 14:53:36 PDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform
(Thu May 19 2005 - 18:41:31 PDT)
RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
(Thu May 19 2005 - 00:16:41 PDT)
RE: AMBER: Using AMBER for Carbon nanotubes
(Wed May 18 2005 - 10:12:29 PDT)
AMBER: RE: Tutorial#1 ptraj/sander problem
(Tue May 17 2005 - 15:56:59 PDT)
RE: AMBER: Tutorial #1 ptraj/sander problem
(Thu May 12 2005 - 15:33:44 PDT)
RE: AMBER: Asking how to creat alanine "dipeptide" in amber8
(Wed May 11 2005 - 10:13:30 PDT)
RE: AMBER: problem with gb md
(Thu May 05 2005 - 21:47:40 PDT)
ross.rosswalker.co.uk
RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?
(Sat May 14 2005 - 12:43:46 PDT)
Sagarika Dev
AMBER: Parameter for alpha-lactose
(Wed May 11 2005 - 07:48:21 PDT)
Scott Brozell
Re: AMBER: crashing xleap; bugfix.44
(Mon May 23 2005 - 10:22:51 PDT)
Re: AMBER: crashing xleap
(Fri May 20 2005 - 13:03:40 PDT)
Scott Pendley
Re: AMBER: mm/pbsa error
(Tue May 10 2005 - 12:56:52 PDT)
Re: AMBER: radius parameter for F atom
(Tue May 10 2005 - 12:49:21 PDT)
Sergio E. Wong
AMBER: amber 8 REM possible test problem
(Tue May 17 2005 - 14:51:04 PDT)
AMBER: keeping two domains closed together during a simulation
(Thu May 05 2005 - 17:44:45 PDT)
Shulin Zhuang
Re: AMBER: Is the MD simulation normal
(Mon May 30 2005 - 07:39:50 PDT)
Re: AMBER: Is the MD simulation normal
(Sun May 29 2005 - 07:53:35 PDT)
Re: AMBER: Is the MD simulation normal
(Sat May 28 2005 - 06:02:05 PDT)
Re: AMBER: Is the MD simulation normal
(Fri May 27 2005 - 00:38:05 PDT)
Re: AMBER: Is the MD simulation normal
(Thu May 26 2005 - 21:23:37 PDT)
AMBER: Is the MD simulation normal
(Thu May 26 2005 - 08:30:48 PDT)
Re: AMBER: antechamber not working .. for thio residue..
(Sun May 22 2005 - 19:31:27 PDT)
Re: AMBER: Re: antechamber not working .. for thio residue..
(Fri May 20 2005 - 03:22:39 PDT)
Re: AMBER: How to create a parallel job for amber 8?
(Sat May 14 2005 - 06:45:54 PDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7
(Fri May 13 2005 - 04:21:28 PDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7
(Fri May 13 2005 - 04:19:20 PDT)
AMBER: the restraint MD fail with amber8,but success with amber7
(Thu May 12 2005 - 18:44:04 PDT)
Simon Whitehead
AMBER: Which forcefield?
(Tue May 24 2005 - 01:13:01 PDT)
AMBER: Using amber4 generated prep files in amber8?
(Thu May 19 2005 - 05:51:00 PDT)
Spero Manolatos
RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside
(Thu May 12 2005 - 15:08:49 PDT)
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
Re: AMBER: question about initial conditions for amber
(Mon May 30 2005 - 04:40:59 PDT)
Stefano Federico Pieraccini
Re: AMBER: question about initial conditions for amber
(Mon May 30 2005 - 04:44:54 PDT)
Stern, Julie
AMBER: double counting of potentials
(Tue May 31 2005 - 16:04:43 PDT)
AMBER: 1-4 scaling factors
(Fri May 20 2005 - 12:13:22 PDT)
AMBER: output of force field info
(Mon May 16 2005 - 12:24:37 PDT)
RE: AMBER: SANDER BOMB: volume of ucell too big
(Thu May 12 2005 - 12:34:55 PDT)
AMBER: SANDER BOMB: volume of ucell too big
(Wed May 11 2005 - 09:07:38 PDT)
Steve Seibold
AMBER:
(Fri May 20 2005 - 10:45:24 PDT)
sychen
Re[2]: AMBER: Force field modification problem
(Mon May 30 2005 - 17:05:45 PDT)
Thomas E. Cheatham, III
Re: AMBER: Is the MD simulation normal
(Thu May 26 2005 - 10:41:03 PDT)
Re: AMBER: hbond analysis in ptaj/carnal
(Thu May 26 2005 - 10:05:00 PDT)
Re: AMBER: Error: vlimit exceeded for step
(Tue May 24 2005 - 11:12:58 PDT)
Re: AMBER: 1-4 scaling factors
(Fri May 20 2005 - 12:43:34 PDT)
Re: AMBER: error during MD run
(Wed May 18 2005 - 11:10:36 PDT)
Re: AMBER: output of force field info
(Mon May 16 2005 - 18:21:51 PDT)
Re: AMBER: Asking how to creat alanine "dipeptide" in amber8
(Wed May 11 2005 - 08:38:54 PDT)
Thomas Patko
Re: AMBER: AMBER8 Build on Linux x64 running Opterons
(Wed May 11 2005 - 08:34:18 PDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?)
(Wed May 11 2005 - 00:10:53 PDT)
AMBER: AMBER8 Build on Linux x64 running Opterons
(Wed May 11 2005 - 00:10:14 PDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?)
(Thu May 05 2005 - 15:02:40 PDT)
AMBER: Bromelain PDF xleap load error
(Wed May 04 2005 - 10:13:35 PDT)
Thomas Steinbrecher
AMBER: Representation of cations in MD
(Fri May 20 2005 - 02:30:24 PDT)
Tiziano Tuccinardi
Re: AMBER: compiling pmemd on dual xeon
(Tue May 17 2005 - 11:05:49 PDT)
AMBER: compiling pmemd on dual xeon
(Tue May 17 2005 - 10:28:31 PDT)
Vijay Manickam Achari
Re: AMBER: dissolving micelle structure in water.. amber7
(Thu May 26 2005 - 18:19:57 PDT)
AMBER: dissolving micelle structure in water.. amber7
(Wed May 25 2005 - 20:59:22 PDT)
AMBER: my prepin file in lowe-case
(Tue May 24 2005 - 00:51:55 PDT)
AMBER: my frcmod file created using parmchk
(Mon May 23 2005 - 20:44:21 PDT)
AMBER: how to generate frcmod file for using prepin file..
(Mon May 23 2005 - 19:52:18 PDT)
AMBER: using antechamber ... to get prepin file
(Mon May 23 2005 - 01:59:16 PDT)
AMBER: antechamber not working .. for thio residue..
(Sun May 22 2005 - 19:15:20 PDT)
AMBER: how to creat leaprc.gaff
(Fri May 20 2005 - 02:36:25 PDT)
AMBER: Re: antechamber not working .. for thio residue..
(Fri May 20 2005 - 02:32:19 PDT)
AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
(Wed May 18 2005 - 23:55:21 PDT)
AMBER: parameter for sulfur in thio-glucoside residue
(Wed May 18 2005 - 18:58:57 PDT)
AMBER: parameter for sulfur in thio-octyl-glucopyranoside
(Mon May 09 2005 - 20:23:07 PDT)
Viktor Hornak
Re: AMBER: Error on restrained MD equilibration (AMBER 7)
(Tue May 31 2005 - 08:52:48 PDT)
Vineet Pande
RE: AMBER: using antechamber ... to get prepin file
(Mon May 23 2005 - 05:02:26 PDT)
Re: AMBER: No vdW parameters for HO..
(Fri May 06 2005 - 08:40:09 PDT)
AMBER: No vdW parameters for HO..
(Fri May 06 2005 - 03:20:02 PDT)
Re: AMBER: How can I read parm99.dat file?
(Thu May 05 2005 - 02:12:09 PDT)
Vitor Manuel Sousa F?x
AMBER: MMPBSA calculations on Highly charged systems
(Tue May 17 2005 - 04:01:21 PDT)
Xiaowei (David) Li
AMBER: error with ptraj
(Tue May 17 2005 - 21:27:33 PDT)
Xin Hu
AMBER: pairwise energy decomposition using MM-PBSA
(Sun May 29 2005 - 20:38:30 PDT)
Yanze Zhang
AMBER: MD on surface
(Tue May 17 2005 - 16:58:29 PDT)
Re: AMBER: Re: R.E.D. question
(Mon May 02 2005 - 12:19:14 PDT)
Yong Duan
RE: AMBER: Is the MD simulation normal
(Sun May 29 2005 - 09:46:44 PDT)
RE: AMBER: Is the MD simulation normal
(Fri May 27 2005 - 09:31:27 PDT)
RE: AMBER: Is the MD simulation normal
(Thu May 26 2005 - 23:17:00 PDT)
RE: AMBER: Is the MD simulation normal
(Thu May 26 2005 - 10:05:14 PDT)
Re: AMBER: No vdW parameters for HO..
(Fri May 06 2005 - 09:28:25 PDT)
YoungJin Cho
AMBER: sander run
(Mon May 02 2005 - 13:45:01 PDT)
yuann
AMBER: Force field modification problem
(Mon May 30 2005 - 04:16:27 PDT)
Zhang Bing
AMBER: modeller
(Fri May 20 2005 - 21:53:13 PDT)
Zhang Yingyan
AMBER: Using AMBER for Carbon nanotubes
(Wed May 18 2005 - 01:21:42 PDT)
易虹
AMBER: How to create a parallel job for amber 8?
(Sat May 14 2005 - 04:20:15 PDT)
Last message date
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Wed Jun 01 2005 - 04:53:00 PDT
Archived on
: Fri Nov 22 2024 - 05:53:24 PST
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