Amber Archive Jun 2002 by date

155 messages: Starting Sun Jun 02 2002 - 20:29:38 PDT, Ending Sun Jun 30 2002 - 15:40:39 PDT
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Sunday, 2 June 2002
- Problem with Gibbs 2D run Asif Rahaman
- Re: Intel ifc Compiler Joachim Reichelt
Monday, 3 June 2002
- (no subject) Ishita sharma
- Re: mm_pbsa in parallel system David Case
- Parallel Amber on Solaris 2.6 Thomas A. Spraggins
- Re: mm_pbsa in parallel system (fwd) Jianhui Wu
- Re: Parallel Amber on Solaris 2.6 William Gropp
Tuesday, 4 June 2002
- Clarification R.Sathyapriya
- Re: SHAKE troubles Arvid Soederhaell
Wednesday, 5 June 2002
- Amber PGF77 comilation error + MPICH problem Fabrice Yerly
- Parameters for hexachloroethane Bjorn-Olav Brandsdal
- Machine_file for Hitachi SR8000 A. Hungie
- PME box ? Yi ming Cheng
- Re: PME box ? David Smith
- reference Marcela Madrid
- Question TL Poulos
- Re: PME box ? Long Hai
- Amber7, sander, restart, blast up Jianhui Wu
- Running amber7 and nab on FreeBSD bdodson_at_scms.utmb.EDU
- cap water eric hu
Thursday, 6 June 2002
- Re: Intel Kernel Math Library case
- Intel Kernel Math Library Joffre Heredia
- Mac OS X compiliation? Randy M. Wadkins
- amber on MAC OSX case
- analysis of Gibbs 2D run Asif Rahaman
Friday, 7 June 2002
- no mdcrd, no mden file Arvid Soederhaell
- benchmark for Amber7 A. Hungie
- charges for peptides Marcela Madrid
- Re: cap water eric hu
- Re: amber on MAC OSX Randy M. Wadkins
- Re: Suggestion to Bill and Case Bill Ross
- Suggestion to Bill and Case William Wei
Saturday, 8 June 2002
- model molecules for getting charges of DNA Jiyoung Heo
Sunday, 9 June 2002
- Re: model molecules for getting charges of DNA Qing Zhang
- C=C=C bending parameters Jones de Andrade
- cold belly run error eric hu
- (no subject) Snyder, James
Monday, 10 June 2002
- Re: amber on MAC OSX Tru
- RE: xaLeap make fails on AIX Thomas A. Spraggins
- Re:xaLeap make fails on AIX Bill Ross
- entropy calculation X. Tan
- Re: cold belly run error Asim Okur
- Re: Floating Invalid Bill Ross
Tuesday, 11 June 2002
- Reorder water in amber7 Peter Varnai
- Re: Reorder water in amber7 Carlos Simmerling
- Amber protein-ion problem Emma.Sigfridsson_at_astrazeneca.com
- RE: Reorder water in amber7 case
- RE: entropy calculation case
- Re: Floating Invalid jim caldwell
- minimization probs Amesh Patel
- Re: Reorder water in amber7 Peter VARNAI
- RE: minimization probs case
- Re: cold belly run error eric hu
- Protonated database Andrew Petersen
- Re: cold belly run error eric hu
- sander input for a newbie Randy M. Wadkins
- test of mm_pbsa Yongjun Jiang
Wednesday, 12 June 2002
- igb problem in sander Emma.Sigfridsson_at_astrazeneca.com
- vlimit exceeded A. Hungie
- perturbed type DH not found Mao Xiang
- Re: vlimit exceeded Carlos Simmerling
- Re: sander input for a newbie Randy M. Wadkins
- Application of Amber Monica
- Re: vlimit exceeded Thomas Cheatham
- sander parallel eric hu
- RE: Floating Invalid lifang xu
Thursday, 13 June 2002
- Re: sander parallel Joffre Heredia
- How to set the dielctric constant equals 1, when running MD simulations in real solvent water? Ling Zhang
- The atom number mismatch in coord and topology file. Ling Zhang
- Re: sander parallel eric hu
- Re: The atom number mismatch in coord and topology file. Carlos Simmerling
- Using TIP4P water S. Yamasaki
- (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com
Friday, 14 June 2002
- Re: sander parallel St�phane Teletch�a
- Periodic water box Rudesh Toofanny
- The atom number mismatch in coord and topology file in AMBER6. Ling Zhang
- Re: The atom number mismatch in coord and topology file in AMBER6. Robert Duke
- tleap error for systems with 64-bit pointers Karen Haskell
- free energy for binding Qing Zhang
- how to keep aromatic ring flat Qing Zhang
- Re: how to keep aromatic ring flat Bill Ross
Saturday, 15 June 2002
- Amber tutorial rino ragno
Monday, 17 June 2002
- Mn parameters!!! navjot_at_bioinfo.ernet.in
- (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com
- remove COM velocity in Amber7 Peter VARNAI
- WG: Christian.Pilger_at_bc.boehringer-ingelheim.com
Tuesday, 18 June 2002
- question Craig A Bayse
- Re: question jim caldwell
Wednesday, 19 June 2002
- propeller twist of ideal B-DNA A. Hungie
- solvated time-averaged restraint refinement of DNA Jake Isaacs
- parameters for Zn2+ bond to CYS- X. Tan
- Re: Periodic water box Thomas Cheatham
Thursday, 20 June 2002
- Re: remove COM velocity in Amber7 Peter VARNAI
- re: parameters for zn2+ bond to cys- lamon_at_lav.Boehringer-Ingelheim.com
- turning PME off in AMBER7 lamon_at_lav.Boehringer-Ingelheim.com
- Re: turning PME off in AMBER7 Arvid Soederhaell
- Re: turning PME off in AMBER7 David A. Case
- bug in .../sander/egb.f ? Thomas A. Spraggins
- RESP Multiconformer Fitting Miguel de Federico
Friday, 21 June 2002
- van der Waals explosion Arvid Soederhaell
- more van der Waals explosion Arvid Soederhaell
- even more van der Waals explosion Arvid Soederhaell
- j3 coupling Yuguang Mu
- Re: j3 coupling David A. Case
- Re: van der Waals explosion David A. Case
- Compilation ov Amber 7 Dov Barak
- taupt: time constant for heat bath coupling for the SOLUTE Qing Zhang
- Re: taupt: time constant for heat bath coupling for the SOLUTE David A. Case
Monday, 24 June 2002
- SHAKE... Arvid Soederhaell
- Passing arguments with SP2 LoadLeveler Thomas A. Spraggins
- New Residue Monica
- ptraj problem Vlad Cojocaru
- Re: ptraj problem Thomas Cheatham
- Re: SHAKE (actually: new atom types) Bill Ross
- antechamber charges don't sum up to zero Michael Jakusch
- partial charges Osvaldo Santos-Filho
- Re: partial charges Carlos Simmerling
- Re: partial charges David A. Case
Tuesday, 25 June 2002
- Query regarding Gamess Nitin Kumar Singh
Wednesday, 26 June 2002
- plep question FyD
- minimum image cut-off Nikolai Smolin
- transferring structures Matt Hartings
- Re: transferring structures Bill Ross
- Re: transferring structures Matt Hartings
- Using a trucated octahedral box in Amber6 Ling Zhang
- Problem in amber Monica
Thursday, 27 June 2002
- xleap problem FyD
- a problem with AMBER7 Vlad Cojocaru
- dummy torsional parameters Giulio Rastelli
- Re: Problem in amber David Case
- Re: xleap problem David A. Case
- Re: dummy torsional parameters David A. Case
- problems compiling Amber 7 ramon kleber da rocha
- mopac David.Rilett_at_astrazeneca.com
- Re: problems compiling Amber 7 David A. Case
- Re: mopac David A. Case
- iwrap set in sander of Amber6 Ling Zhang
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd
- xmkmf: not found Bill Ross
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd
- box size & 1st equilibrium yuann
Friday, 28 June 2002
- Re: mopac Pascal Bonnet
- EWALD BOMB (The system has extended beyond ...) Michael Jakusch
- Re: box size & 1st equilibrium Carlos Simmerling
- error in rMD Monica
- The crystal water is solute or solvent during solvation Ling Zhang
- Zn/Mg Counterion placement around DNA mdk7p_at_cms.mail.virginia.edu
- Interaction table from minimization kiyean.nam_at_pharma.novartis.com
- van der Waals, hydrogen bond energy Qing Zhang
- Re: van der Waals, hydrogen bond energy Carlos Simmerling
- Re: van der Waals, hydrogen bond energy jim caldwell
Saturday, 29 June 2002
- Re: van der Waals, hydrogen bond energy Andreas Svrcek-Seiler
Sunday, 30 June 2002
- Re: Compilation ov Amber 7 Sanjeev B.S.
- Analysis of LES simulation mer_at_chem.wayne.edu

Last message date: Sun Jun 30 2002 - 15:40:39 PDT
Archived on: Mon Dec 30 2024 - 05:53:13 PST