Amber Archive Nov 2002: by date

Friday, 1 November 2002
- flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 Pascal Bonnet
- molsurf reference Giulio Rastelli
- Re: molsurf reference David A. Case
- Re: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 David A. Case
- Re: carnal output trajectory Francesca Mocci
- Re: total energies during MM-PBSA Lepsa
Sunday, 3 November 2002
- problem about cut and cap sxzheng
Monday, 4 November 2002
- Re: carnal St�phane Teletch�a
- periodic box Craig A Bayse
- P4_GLOBMEMSIZE problem Jean-Christophe Ducom
- Re: periodic box David A. Case
- Visualizing AMBER coordinates trajectory in VMD Pratul Agarwal
- restart Ioana Cozmuta
- Re: Visualizing AMBER coordinates trajectory in VMD David A. Case
- Re: restart David A. Case
- RUNMIN hung_at_atc.atccu.chula.ac.th
- Re: RUNMIN Ioana Cozmuta
- procheck hung_at_atc.atccu.chula.ac.th
Tuesday, 5 November 2002
- pseudoatoms and NMR restraints david
- Re: Visualizing AMBER coordinates trajectory in VMD Tom Bishop
- CCl4 as solvent Aldo Jongejan
- Snapshot stuff Layi Adekoya
- Re: pseudoatoms and NMR restraints David A. Case
- Re: equilibrium problem about cut and belly David A. Case
- Re: torsion restraints in GIBBS David A. Case
- Re: procheck David A. Case
- RE: P4_GLOBMEMSIZE problem Ross Walker
- Re: equilibrium problem about cut and belly Thomas Steinbrecher
- Re: P4_GLOBMEMSIZE problem Jean-Christophe Ducom
- entropy calcs in mm_pbsa giulio_at_unimo.it
- Re: entropy calcs in mm_pbsa Holger Gohlke
- RE: P4_GLOBMEMSIZE problem Ross Walker
- torsion restraints in GIBBS Jose Ramon Blas
Wednesday, 6 November 2002
- Bugfixes William Wei
- average and runningaverage in ptraj Vlad Cojocaru
- Re: average and runningaverage in ptraj Holger Gohlke
- Re: average and runningaverage in ptraj Thomas Cheatham
- time-averaged restraint developer Jake Isaacs
- restrt format problem Marcela Madrid
- nbflag Ioana Cozmuta
- nbflag Ioana Cozmuta
Thursday, 7 November 2002
- surface Ioana Cozmuta
- Re: amber on RH8 Scott Brozell
Friday, 8 November 2002
- averaging with ptraj and carnal Vlad Cojocaru
- ramdomized start velocities Arvid Soederhaell
- Sander: check COM velocity, temp: 0.000000 0.00(Removed) Miguel de Federico de la R�a
- more about averaging Vlad Cojocaru
- residue cross-correlation Bimo Ario Tejo
- Roar capabilities M. L. Dodson
- residue cross-correlation Bimo Ario Tejo
- Re: ramdomized start velocities David A. Case
- Re: ramdomized start velocities Andy Purkiss
- Re: residue cross-correlation Andreas Svrcek-Seiler
- Re: ramdomized start velocities James W. Caldwell
- Re: residue cross-correlation Thomas Cheatham
- Re: more about averaging Bill Ross
- Problem in run Monica
- Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) Thomas Cheatham
- MEP g98_option FyD
- Re: Problem in run Monica Jain
- Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) David Case
- Re: Problem in run David Case
Saturday, 9 November 2002
- Forwarded mail.... Narang Manpreet Kaur
- drifting from average structure Vlad Cojocaru
- carnal7 produces memory fault and a core Giulio Rastelli
- belly and EWALD in amber7 Zhang Jian
Sunday, 10 November 2002
- Re: belly and EWALD in amber7 darden
- Re: belly and ivcap conflict in gibbs David A. Case
- Re: Forwarded mail.... David A. Case
- Re: belly and EWALD in amber7 Zhang Jian
Monday, 11 November 2002
- .top files read into xLeap? Arvid Soederhaell
- Re: MEP g98_option Pascal Bonnet
- nonpeoridic boundary + mm/gbsa Yongjun Jiang
- Re: nonpeoridic boundary + mm/gbsa Holger Gohlke
- saveAmberParm of leap Sichun Yang
- Re: saveAmberParm of leap David A. Case
- Re: .top files read into xLeap? David A. Case
Tuesday, 12 November 2002
- Re: residue cross-correlation St�phane Teletch�a
- problem in PME Monica
- Re: problem in PME David A. Case
- RE: problem in PME Kristina Furse
- re: the removal of global motion Shixiang Yan
- NMR restraints on a 10-mer DNA in Sander Jo.Vinje_at_kj.uib.no
- Re: NMR restraints on a 10-mer DNA in Sander Michael G Cooney
- Amber7/CYGWIN compiling James W. Caldwell
- Re: problem in PME David A. Case
- Re: the removal of global motion David A. Case
- Re: NMR restraints on a 10-mer DNA in Sander David A. Case
- Re: the removal of global motion Ioana Cozmuta
- Re: the removal of global motion David A. Case
Wednesday, 13 November 2002
- help! Non bond list overflow! Zhang Jian
- help on VMD movie Zhang Jian
- Re: help on VMD movie St�phane Teletch�a
- Re: help on VMD movie Francesca Mocci
- Ewald Monica
- Re: help on VMD movie Zhang Jian
- Re: Ewald David A. Case
- CMM method Ioana Cozmuta
- Re: CMM method David A. Case
- Re: help! Non bond list overflow! David A. Case
- Re: help on VMD movie Zhang Jian
- Re: input format for gibbs restraints David A. Case
- Re: help! Non bond list overflow! Zhang Jian
- Re: help! Non bond list overflow! Jian Zhang
- input format for gibbs restraints Jose Ramon Blas
- (no subject) Monica
Thursday, 14 November 2002
- restart mm_pbsa Layi Adekoya
- Re: restart mm_pbsa Lepsa
- Re: restart mm_pbsa Pascal Bonnet
- Amber on PC-Linux Philippe Aplincourt
- error in reading .crd file with GIBBS hagop demirdjian
- Re: your mail David A. Case
- Linmin question... Andrei Leit�o
- Linmin question... Andrei Leit�o
- Amber Perl module Tod Pascal
- Re: Amber Perl module Luis Gracia
- Re: Amber Perl module Michael Ford
- non-zero 10-12 coefficient Anonymous
Friday, 15 November 2002
- Re: Linmin question... David A. Case
- simulating dna Tod Pascal
- polarizabitlity X. Tan
- Re: question David A. Case
- Re: question Ioana Cozmuta
- RE: question Yong Duan
Saturday, 16 November 2002
- Conterions Monica
- (no subject) Narang Manpreet Kaur
- Re: your mail David Case
- Re: Conterions David Case
Sunday, 17 November 2002
- Are posters to the Amber list being spammed? Nicholson, James D Mr ARO
- choose dt in gibbs sxzheng
- NATOM mismatch in coord and topology files. Narang Manpreet Kaur
Monday, 18 November 2002
- creating a pdb trajectory with carnal Vlad Cojocaru
- makeDIST_RST? Sichun Yang
- Re: makeDIST_RST? David A. Case
- Re: EWALD crash David A. Case
- Re: simulating dna David A. Case
- Re: polarizabitlity David A. Case
Tuesday, 19 November 2002
- defining groups on dif. sets in carnal Vlad Cojocaru
- Re: question St�phane Teletch�a
- limit of RMSD value Bimo Ario Tejo
- FEP/Gibbs question meiselba
- GIBBS - Error message. Miguel de Federico
- Re: GIBBS - Error message. David A. Case
- Re: limit of RMSD value Thomas Cheatham
- Re: polarizabitlity X. Tan
- Frictional forces in gB Kristina Furse
- Nz-Acetyllysine parameters Luis Gracia
Wednesday, 20 November 2002
- intdiel & extdiel Fredrick Robin Devadoss
- Re: intdiel & extdiel David A. Case
- Bulk Email Sending & Bullet Proof Web Hosting pposton
- Re: intdiel & extdiel Fredrick Robin Devadoss
Thursday, 21 November 2002
- P.3 in antechamber Giulio Rastelli
- PARMSET sara nunez
- RE: PARMSET Ross Walker
- Re: intdiel & extdiel Holger Gohlke
- Re: PARMSET David A. Case
- ion distances Marcela Madrid
- targeted MD for more than 2 groups Sichun Yang
- Re: PARMSET John Bushnell
- Re: ion distances 남기엽
- Restraint Ambiguities Neema Salimi
- Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu
- Re: ion distances Thomas E. Cheatham, III
- Re: targeted MD for more than 2 groups Carlos Simmerling
- Re: Error running AMBER6 on Beowulf cluster David A. Case
- Re: Restraint Ambiguities David A. Case
- Re: Restraint Ambiguities Neema Salimi
Friday, 22 November 2002
- Equilibration output Amber7 Fredrick Robin Devadoss
- Re: Restraint Ambiguities David A. Case
- problem in restrt Marcela Madrid
- Re: Equilibration output Amber7 Thomas Cheatham
- Re: problem in restrt Thomas Cheatham
- restarting simulation Marcela Madrid
- Re: restarting simulation Carlos Simmerling
- solvateOct Kristina Furse
- Re: Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu
- Re: restarting simulation Marcela Madrid
- leap for peptide Sichun Yang
- Re: Error running AMBER6 on Beowulf cluster Carlos Simmerling
- ntx=7, irest=0 Marcela Madrid
- pdb file Ioana Cozmuta
- Re: pdb file Ioana Cozmuta
- Re: solvateOct David A. Case
- Re: ntx=7, irest=0 David A. Case
- Re: ntx=7, irest=0, redux David Case
Saturday, 23 November 2002
- (no subject) Narang Manpreet Kaur
- Calculating atomic charges for AMBER with Gaussian98W Thomas Steinbrecher
- Re: Calculating atomic charges for AMBER with Gaussian98W M. L. Dodson
Sunday, 24 November 2002
- Re: your mail darden
- Hydrophobic protein in water Luo Liu
- atom type not recognized by GB eric hu
- Re: atom type not recognized by GB David A. Case
- Re: atom type not recognized by GB eric hu
- Inquiry software_at_kagaku.com
Monday, 25 November 2002
- (no subject) CHAUMONT Alain
- using SHAKE for solvent only hagop demirdjian
- Re: using SHAKE for solvent only David A. Case
- external electric field Ioana Cozmuta
- a second question Ioana Cozmuta
- Re: ion distances Bill Ross
Tuesday, 26 November 2002
- GIBBS - ERROR: Restraint read error from RSTIN; Check format: Miguel de Federico
- Error in Equilibration Fredrick Robin Devadoss
- RE: solvateOct Kristina Furse
- Re: GIBBS - ERROR: Restraint read error from RSTIN; Check format: David A. Case
- restrain a residue as center of mass eric hu
- Re: solvateOct David A. Case
- Re: restrain a residue as center of mass Carlos Simmerling
- the tree name? Sichun Yang
- Please help. Energy suddenly increase. Protein jump out Lich Nguyen
Wednesday, 27 November 2002
- How Amber calculates electrostatic energy? Daniel Svozil
- Re: Please help. Energy suddenly increase. Protein jump out David A. Case
- esp.sh problem FyD
- Re: esp.sh problem David Smith
- Re: restrain a residue as center of mass eric hu
- RE: Please help. Energy suddenly increase. Protein jump out Yong Duan
- Re: esp.sh problem David A. Case
- Re: restrain a residue as center of mass Carlos Simmerling
- Re: Please help. Energy suddenly increase. Protein jump out Carlos Simmerling
- Re: restrain a residue as center of mass Carlos Simmerling
- external electric field/another try Ioana Cozmuta
- Re: the tree name? David A. Case
- RE: Please help. Energy suddenly increase. Protein jump out Yong Duan
- Re: external electric field/another try darden
- Re: external electric field/another try James W. Caldwell
Thursday, 28 November 2002
- Re: esp.sh problem FyD
- C60 parameter vannajan_at_chiangmai.ac.th
- Re: C60 parameter Pascal Bonnet
- Problem Monica
Friday, 29 November 2002
- parmchk -p option Thomas.Fox_at_bc.boehringer-ingelheim.com
- parameters for cyclic nucleotides Thomas.Fox_at_bc.boehringer-ingelheim.com
- (no subject) Narang Manpreet Kaur
- Re: Problem David Case
- Re: your mail David Case
- Break down energy contributions Numan Oezguen

Last message date: Fri Nov 29 2002 - 13:06:36 PST
Archived on: Wed Apr 24 2024 - 05:53:16 PDT

Amber Archive Nov 2002 by date