Amber Archive Jun 2002: by subject

(no subject)
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 03:09:11 PDT)
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Thu Jun 13 2002 - 22:30:15 PDT)
- Snyder, James (Sun Jun 09 2002 - 17:45:03 PDT)
- Ishita sharma (Mon Jun 03 2002 - 04:07:38 PDT)
a problem with AMBER7
- Vlad Cojocaru (Thu Jun 27 2002 - 03:12:58 PDT)
amber on MAC OSX
- Tru (Mon Jun 10 2002 - 02:18:03 PDT)
- Randy M. Wadkins (Fri Jun 07 2002 - 12:29:58 PDT)
- case (Thu Jun 06 2002 - 17:22:44 PDT)
Amber PGF77 comilation error + MPICH problem
- Fabrice Yerly (Wed Jun 05 2002 - 01:31:26 PDT)
Amber protein-ion problem
- Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 04:41:29 PDT)
Amber tutorial
- rino ragno (Sat Jun 15 2002 - 02:53:53 PDT)
Amber7, sander, restart, blast up
- Jianhui Wu (Wed Jun 05 2002 - 10:07:51 PDT)
analysis of Gibbs 2D run
- Asif Rahaman (Thu Jun 06 2002 - 21:46:34 PDT)
Analysis of LES simulation
- mer_at_chem.wayne.edu (Sun Jun 30 2002 - 15:40:39 PDT)
antechamber charges don't sum up to zero
- Michael Jakusch (Mon Jun 24 2002 - 12:38:15 PDT)
Application of Amber
- Monica (Wed Jun 12 2002 - 08:24:49 PDT)
benchmark for Amber7
- A. Hungie (Fri Jun 07 2002 - 07:37:07 PDT)
box size & 1st equilibrium
- Carlos Simmerling (Fri Jun 28 2002 - 04:56:09 PDT)
- yuann (Thu Jun 27 2002 - 23:16:51 PDT)
bug in .../sander/egb.f ?
- Thomas A. Spraggins (Thu Jun 20 2002 - 10:45:28 PDT)
C=C=C bending parameters
- Jones de Andrade (Sun Jun 09 2002 - 13:55:33 PDT)
cap water
- eric hu (Fri Jun 07 2002 - 11:39:22 PDT)
- eric hu (Wed Jun 05 2002 - 17:14:10 PDT)
charges for peptides
- Marcela Madrid (Fri Jun 07 2002 - 08:14:59 PDT)
Clarification
- R.Sathyapriya (Tue Jun 04 2002 - 00:45:19 PDT)
cold belly run error
- eric hu (Tue Jun 11 2002 - 12:42:19 PDT)
- eric hu (Tue Jun 11 2002 - 10:41:47 PDT)
- Asim Okur (Mon Jun 10 2002 - 21:58:30 PDT)
- eric hu (Sun Jun 09 2002 - 15:55:47 PDT)
Compilation ov Amber 7
- Sanjeev B.S. (Sun Jun 30 2002 - 10:42:28 PDT)
- Dov Barak (Fri Jun 21 2002 - 09:40:58 PDT)
dummy torsional parameters
- David A. Case (Thu Jun 27 2002 - 08:38:49 PDT)
- Giulio Rastelli (Thu Jun 27 2002 - 03:31:50 PDT)
entropy calculation
- case (Tue Jun 11 2002 - 06:56:37 PDT)
- X. Tan (Mon Jun 10 2002 - 16:42:59 PDT)
error in rMD
- Monica (Fri Jun 28 2002 - 06:35:34 PDT)
even more van der Waals explosion
- Arvid Soederhaell (Fri Jun 21 2002 - 02:23:17 PDT)
EWALD BOMB (The system has extended beyond ...)
- Michael Jakusch (Fri Jun 28 2002 - 02:17:20 PDT)
Floating Invalid
- lifang xu (Wed Jun 12 2002 - 20:02:21 PDT)
- jim caldwell (Tue Jun 11 2002 - 07:43:49 PDT)
- Bill Ross (Mon Jun 10 2002 - 22:36:16 PDT)
free energy for binding
- Qing Zhang (Fri Jun 14 2002 - 15:50:54 PDT)
how to keep aromatic ring flat
- Bill Ross (Fri Jun 14 2002 - 16:34:42 PDT)
- Qing Zhang (Fri Jun 14 2002 - 16:00:51 PDT)
How to set the dielctric constant equals 1, when running MD simulations in real solvent water?
- Ling Zhang (Thu Jun 13 2002 - 13:54:53 PDT)
igb problem in sander
- Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 02:11:20 PDT)
Intel ifc Compiler
- Joachim Reichelt (Sun Jun 02 2002 - 23:51:54 PDT)
Intel Kernel Math Library
- Joffre Heredia (Thu Jun 06 2002 - 12:46:32 PDT)
- case (Thu Jun 06 2002 - 08:02:25 PDT)
Interaction table from minimization
- kiyean.nam_at_pharma.novartis.com (Fri Jun 28 2002 - 14:40:59 PDT)
iwrap set in sander of Amber6
- Ling Zhang (Thu Jun 27 2002 - 13:43:41 PDT)
j3 coupling
- David A. Case (Fri Jun 21 2002 - 07:49:40 PDT)
- Yuguang Mu (Fri Jun 21 2002 - 03:38:31 PDT)
Mac OS X compiliation?
- Randy M. Wadkins (Thu Jun 06 2002 - 14:58:18 PDT)
Machine_file for Hitachi SR8000
- A. Hungie (Wed Jun 05 2002 - 04:09:03 PDT)
minimization probs
- case (Tue Jun 11 2002 - 10:36:57 PDT)
- Amesh Patel (Tue Jun 11 2002 - 08:57:12 PDT)
minimum image cut-off
- Nikolai Smolin (Wed Jun 26 2002 - 04:05:08 PDT)
mm_pbsa in parallel system
- David Case (Mon Jun 03 2002 - 07:49:08 PDT)
mm_pbsa in parallel system (fwd)
- Jianhui Wu (Mon Jun 03 2002 - 09:03:12 PDT)
Mn parameters!!!
- navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 02:19:12 PDT)
model molecules for getting charges of DNA
- Qing Zhang (Sun Jun 09 2002 - 12:47:04 PDT)
- Jiyoung Heo (Sat Jun 08 2002 - 17:20:10 PDT)
mopac
- Pascal Bonnet (Fri Jun 28 2002 - 01:49:11 PDT)
- David A. Case (Thu Jun 27 2002 - 11:34:34 PDT)
- David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 10:50:41 PDT)
more van der Waals explosion
- Arvid Soederhaell (Fri Jun 21 2002 - 02:00:59 PDT)
New Residue
- Monica (Mon Jun 24 2002 - 08:01:42 PDT)
no mdcrd, no mden file
- Arvid Soederhaell (Fri Jun 07 2002 - 04:43:30 PDT)
Parallel Amber on Solaris 2.6
- William Gropp (Mon Jun 03 2002 - 12:20:26 PDT)
- Thomas A. Spraggins (Mon Jun 03 2002 - 07:49:45 PDT)
Parameters for hexachloroethane
- Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 02:13:54 PDT)
parameters for zn2+ bond to cys-
- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:17:38 PDT)
- X. Tan (Wed Jun 19 2002 - 17:23:16 PDT)
partial charges
- David A. Case (Mon Jun 24 2002 - 18:52:47 PDT)
- Carlos Simmerling (Mon Jun 24 2002 - 18:38:35 PDT)
- Osvaldo Santos-Filho (Mon Jun 24 2002 - 17:33:15 PDT)
Passing arguments with SP2 LoadLeveler
- Thomas A. Spraggins (Mon Jun 24 2002 - 07:41:26 PDT)
Periodic water box
- Thomas Cheatham (Wed Jun 19 2002 - 20:57:04 PDT)
- Rudesh Toofanny (Fri Jun 14 2002 - 05:41:01 PDT)
perturbed type DH not found
- Mao Xiang (Wed Jun 12 2002 - 03:47:19 PDT)
plep question
- FyD (Wed Jun 26 2002 - 00:28:23 PDT)
PME box ?
- Long Hai (Wed Jun 05 2002 - 09:07:29 PDT)
- David Smith (Wed Jun 05 2002 - 07:15:44 PDT)
- Yi ming Cheng (Wed Jun 05 2002 - 05:11:15 PDT)
probelms in install of amber (fwd)
- Marcelo Roitburd (Thu Jun 27 2002 - 15:47:41 PDT)
- Marcelo Roitburd (Thu Jun 27 2002 - 15:23:29 PDT)
- Marcelo Roitburd (Thu Jun 27 2002 - 13:59:35 PDT)
Problem in amber
- David Case (Thu Jun 27 2002 - 07:38:30 PDT)
- Monica (Wed Jun 26 2002 - 22:28:21 PDT)
Problem with Gibbs 2D run
- Asif Rahaman (Sun Jun 02 2002 - 20:29:38 PDT)
problems compiling Amber 7
- David A. Case (Thu Jun 27 2002 - 11:27:09 PDT)
- ramon kleber da rocha (Thu Jun 27 2002 - 10:18:50 PDT)
propeller twist of ideal B-DNA
- A. Hungie (Wed Jun 19 2002 - 09:37:29 PDT)
Protonated database
- Andrew Petersen (Tue Jun 11 2002 - 12:12:28 PDT)
ptraj problem
- Thomas Cheatham (Mon Jun 24 2002 - 10:24:30 PDT)
- Vlad Cojocaru (Mon Jun 24 2002 - 08:54:32 PDT)
Query regarding Gamess
- Nitin Kumar Singh (Tue Jun 25 2002 - 08:23:09 PDT)
question
- jim caldwell (Tue Jun 18 2002 - 15:52:19 PDT)
- Craig A Bayse (Tue Jun 18 2002 - 15:04:47 PDT)
- TL Poulos (Wed Jun 05 2002 - 08:49:10 PDT)
reference
- Marcela Madrid (Wed Jun 05 2002 - 08:48:55 PDT)
remove COM velocity in Amber7
- Peter VARNAI (Thu Jun 20 2002 - 05:03:07 PDT)
- Peter VARNAI (Mon Jun 17 2002 - 05:16:27 PDT)
Reorder water in amber7
- Peter VARNAI (Tue Jun 11 2002 - 10:16:00 PDT)
- case (Tue Jun 11 2002 - 06:53:59 PDT)
- Carlos Simmerling (Tue Jun 11 2002 - 04:36:04 PDT)
- Peter Varnai (Tue Jun 11 2002 - 01:38:32 PDT)
RESP Multiconformer Fitting
- Miguel de Federico (Thu Jun 20 2002 - 16:05:11 PDT)
Running amber7 and nab on FreeBSD
- bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 13:31:24 PDT)
sander input for a newbie
- Randy M. Wadkins (Wed Jun 12 2002 - 06:04:55 PDT)
- Randy M. Wadkins (Tue Jun 11 2002 - 16:21:22 PDT)
sander parallel
- St�phane Teletch�a (Fri Jun 14 2002 - 01:58:53 PDT)
- eric hu (Thu Jun 13 2002 - 15:05:13 PDT)
- Joffre Heredia (Thu Jun 13 2002 - 10:39:55 PDT)
- eric hu (Wed Jun 12 2002 - 14:11:24 PDT)
SHAKE (actually: new atom types)
- Bill Ross (Mon Jun 24 2002 - 12:22:02 PDT)
SHAKE troubles
- Arvid Soederhaell (Tue Jun 04 2002 - 01:22:40 PDT)
SHAKE...
- Arvid Soederhaell (Mon Jun 24 2002 - 04:25:05 PDT)
solvated time-averaged restraint refinement of DNA
- Jake Isaacs (Wed Jun 19 2002 - 09:52:35 PDT)
Suggestion to Bill and Case
- William Wei (Fri Jun 07 2002 - 13:49:10 PDT)
- Bill Ross (Fri Jun 07 2002 - 13:16:30 PDT)
taupt: time constant for heat bath coupling for the SOLUTE
- David A. Case (Fri Jun 21 2002 - 17:28:38 PDT)
- Qing Zhang (Fri Jun 21 2002 - 16:44:55 PDT)
test of mm_pbsa
- Yongjun Jiang (Tue Jun 11 2002 - 20:08:23 PDT)
The atom number mismatch in coord and topology file in AMBER6.
- Robert Duke (Fri Jun 14 2002 - 09:27:00 PDT)
- Ling Zhang (Fri Jun 14 2002 - 07:58:45 PDT)
The atom number mismatch in coord and topology file.
- Carlos Simmerling (Thu Jun 13 2002 - 15:27:38 PDT)
- Ling Zhang (Thu Jun 13 2002 - 14:41:08 PDT)
The crystal water is solute or solvent during solvation
- Ling Zhang (Fri Jun 28 2002 - 11:58:08 PDT)
tleap error for systems with 64-bit pointers
- Karen Haskell (Fri Jun 14 2002 - 12:55:16 PDT)
transferring structures
- Matt Hartings (Wed Jun 26 2002 - 13:58:11 PDT)
- Bill Ross (Wed Jun 26 2002 - 12:47:02 PDT)
- Matt Hartings (Wed Jun 26 2002 - 10:24:23 PDT)
turning PME off in AMBER7
- David A. Case (Thu Jun 20 2002 - 06:49:33 PDT)
- Arvid Soederhaell (Thu Jun 20 2002 - 06:45:25 PDT)
- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:28:30 PDT)
Using a trucated octahedral box in Amber6
- Ling Zhang (Wed Jun 26 2002 - 18:28:46 PDT)
Using TIP4P water
- S. Yamasaki (Thu Jun 13 2002 - 18:05:48 PDT)
van der Waals explosion
- David A. Case (Fri Jun 21 2002 - 07:55:26 PDT)
- Arvid Soederhaell (Fri Jun 21 2002 - 01:54:05 PDT)
van der Waals, hydrogen bond energy
- Andreas Svrcek-Seiler (Sat Jun 29 2002 - 05:29:38 PDT)
- jim caldwell (Fri Jun 28 2002 - 17:24:21 PDT)
- Carlos Simmerling (Fri Jun 28 2002 - 16:41:11 PDT)
- Qing Zhang (Fri Jun 28 2002 - 15:57:10 PDT)
vlimit exceeded
- Thomas Cheatham (Wed Jun 12 2002 - 12:35:53 PDT)
- Carlos Simmerling (Wed Jun 12 2002 - 04:42:14 PDT)
- A. Hungie (Wed Jun 12 2002 - 02:49:44 PDT)
WG:
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 22:48:01 PDT)
xaLeap make fails on AIX
- Bill Ross (Mon Jun 10 2002 - 11:19:47 PDT)
- Thomas A. Spraggins (Mon Jun 10 2002 - 09:13:01 PDT)
xleap problem
- David A. Case (Thu Jun 27 2002 - 08:33:16 PDT)
- FyD (Thu Jun 27 2002 - 01:20:53 PDT)
xmkmf: not found
- Bill Ross (Thu Jun 27 2002 - 15:29:08 PDT)
Zn/Mg Counterion placement around DNA
- mdk7p_at_cms.mail.virginia.edu (Fri Jun 28 2002 - 12:46:11 PDT)

Amber Archive Jun 2002 by subject