Amber Archive May 2003: by date

Thursday, 1 May 2003
- problem about virtual box? Youyi Peng
- Re: problem about virtual box? Carlos Simmerling
- Ewald: coeff, error estimate Paula Petrone
- Re: problem about virtual box? pengyo.rwja.umdnj.edu
- Re: problem about virtual box? Thomas Cheatham
- Re: problem about virtual box? Youyi Peng
- Re: problem about virtual box? Thomas E. Cheatham, III
- Simple math of memory calculation for nmode Masaki Tomimoto
- problem on MD simulation of damage DNA Shuang Ding
- Re: problem on MD simulation of damage DNA Carlos Simmerling
- Re: Ewald: coeff, error estimate darden
- Re: Simple math of memory calculation for nmode David A. Case
- Questoin about temperature Maverick
Friday, 2 May 2003
- initial velocity Youyi Peng
- Re: initial velocity Natasja Brooijmans
- Re: initial velocity Carlos Simmerling
- Question about BELLY NMODE Masaki Tomimoto
- RE: Question about BELLY NMODE Masaki Tomimoto
- Re: Residual dipolar couplings David A. Case
- Help with Sander test output error Donald Keidel
- multiple timesteps Ioana Cozmuta
- upper limited of memory for nmode wentaofu
- (no subject) Narang Manpreet Kaur
Saturday, 3 May 2003
- (no subject) smolnar.jadeinc.com
Sunday, 4 May 2003
- Latest Leap Compile Errors smolnar.jadeinc.com
- Re: Latest Leap Compile Errors David A. Case
- SPC/E water model Ioana Cozmuta
- SPC/E model -LJ parameters Ioana Cozmuta
- Re: SPC/E water model Holger Gohlke
Monday, 5 May 2003
- can not minimize tang kwa
- Re: can not minimize Carlos Simmerling
- Re: Latest Leap Compile Errors Stephen P. Molnar, Ph.D.
- Re: can not minimize Guanglei Cui
- Re: can not minimize tang kwa
- Re: can not minimize tang kwa
- Re: can not minimize Guanglei Cui
- Re: can not minimize tang kwa
- minimizaiton in vacuum David A. Case
- how to set up a carbon nanotube pdb file zhaoxc.puccini.che.pitt.edu
Tuesday, 6 May 2003
- ANAL in AMBER A.Madhumalar
- saveAmberParm problems in xleap Wayne Dawson
- Re: minimizaiton in vacuum tang kwa
- minimization with restraints A. Hungie
Tuesday, 20 May 2003
- Re: minimization with restraints Carlos Simmerling
Tuesday, 6 May 2003
- Re: saveAmberParm problems in xleap caldwell.heimdal.compchem.ucsf.edu
- Re: saveAmberParm problems in xleap Guanglei Cui
- Re: saveAmberParm problems in xleap Wayne Dawson
- Pi-Pi stacking Fernando Martin
- Re: saveAmberParm problems in xleap Ioana Cozmuta
Wednesday, 7 May 2003
- non bonded pairlist? Arvid Soederhaell
- Re: SPC/E water model Ioana Cozmuta
- Re: MD steps limit in sander (Amber 6) Carlos Simmerling
- help me switching from amber5 to amber6 Asif Rahaman
- Re: help me switching from amber5 to amber6 David A. Case
Thursday, 8 May 2003
- Phosphotyrosine parametrization Obdulia Rabal
- Re: saveAmberParm problems in xleap Wayne Dawson
- current AMBER citation? Jake Isaacs
- RMSD fluctuation too much Youyi Peng
- Re: current AMBER citation? David A. Case
- Re: RMSD fluctuation too much Carlos Simmerling
- Use of Mg2+ in AMBER 7 Peter Anderson
Friday, 9 May 2003
- 2 questions FyD
- Re: 2 questions Carlos Simmerling
- Etot is not constant in NVE ensemble A. Hungie
- Re: Etot is not constant in NVE ensemble darden
- RE: Etot is not constant in NVE ensemble Yong Duan
- Re: Etot is not constant in NVE ensemble Thomas Cheatham
- Re: 2 questions David A. Case
- Re: Etot is not constant in NVE ensemble A. Hungie
- Re: ANAL in AMBER David A. Case
- Re: Etot is not constant in NVE ensemble bishop
- What kind of interactions are ignored for end group interactions Huang Zunnan
- Re: What kind of interactions are ignored for end group interactions Carlos Simmerling
- 10-12 H-bond terms Ioana Cozmuta
- Re: Etot is not constant in NVE ensemble darden
Saturday, 10 May 2003
- RMSF problem yuan bo
- Re: 10-12 H-bond terms Andreas Svrcek-Seiler
- a question about scale factor Ye Mei
- Re: a question about scale factor Carlos Simmerling
- difference between iwrap and image? yuann
Monday, 12 May 2003
- Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE Omar Wahab
- unit of vlimit? Fabian Boes
- Heat of Vaporization Karl N. Kirschner
- School Amber Study Treakle, Kirk
- no MD output Youyi Peng
- Re: 10-12 H-bond terms Ioana Cozmuta
- Re: 10-12 H-bond terms David A. Case
- Re: 10-12 H-bond terms Ioana Cozmuta
Tuesday, 13 May 2003
- Simple question about sander parameter set Peng Tao
- Re: Simple question about sander parameter set David A. Case
- Re: Heat of Vaporization David A. Case
- Re: Simple question about sander parameter set Peng Tao
- re: parameters for nitro group Shixiang Yan
- Re: parameters for nitro group David A. Case
- water residence time analysis Mahadevan Seetharaman
- Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU
- Re: Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU
- Re: Increase lastist in the &cntrl namelist Ioana Cozmuta
- Re: Increase lastist in the &cntrl namelist Dodi Heryadi
- H-O-H angle Ioana Cozmuta
- Re: Increase lastist in the &cntrl namelist Ioana Cozmuta
- Re: H-O-H angle Luis Gracia
- Sander help tianxiao yang
- Re: Sander help David A. Case
- Re: H-O-H angle Ioana Cozmuta
- A question about AMBER, leaprc.ff02EP yuming chen
- Re: A question about AMBER, leaprc.ff02EP David A. Case
Wednesday, 14 May 2003
- Re: A question about AMBER, leaprc.ff02EP yuming chen
- mm_pbsa and B/Z DNA relative stabilities Peter Gannett
- serine/tyrosine in charged states Layi Adekoya
- Re: mm_pbsa and B/Z DNA relative stabilities Robert G. Endres
- protonate problem Venkata S Koppuravuri
- Re: protonate problem David A. Case
- Using GLYCAM in sander with a non-zero 10-12 coefficient Peng Tao
- Newton-Raphson minimization for large systems Qing Zhang
Thursday, 15 May 2003
- Simulation under physiological conditions Michal Otyepka
- Re: Simulation under physiological conditions Michal Otyepka
- Re: Simulation under physiological conditions Andreas Svrcek-Seiler
- atomic positional fluctuation pengyo.rwja.umdnj.edu
- nucgen.dat Maria Zavodszky
- Re: nucgen.dat Ioana Cozmuta
- Re: atomic positional fluctuation Holger Gohlke
Friday, 16 May 2003
- using distance restraints in Sander (AIX 4.3 RS6000) Wayne Dawson
- ptraj generated PDB files Fabian Boes
- Re: ptraj generated PDB files caldwell.heimdal.compchem.ucsf.edu
- Re: ptraj generated PDB files David A. Case
- mm_pbsa with PBCAL = 0 wentaofu
- Re: using distance restraints in Sander (AIX 4.3 RS6000) David A. Case
- Re: mm_pbsa with PBCAL = 0 Holger Gohlke
- anal, amber7 and resnum 0 Sanjeev B.S.
- Re: anal, amber7 and resnum 0 Sanjeev B.S.
- Re: anal, amber7 and resnum 0 David A. Case
Sunday, 18 May 2003
- DNA base-step distortion kbyun.wesleyan.edu
- Re: DNA base-step distortion kbyun.wesleyan.edu
Monday, 19 May 2003
- Re: DNA base-step distortion Jiri Sponer
- RESP, constraining Dipole Moment Artur Galstyan
- Mainchain.dat tang kwa
- force field parameters for torsions cailliez
- Re: force field parameters for torsions David A. Case
- Re: force field parameters for torsions (I am away) Charles Laughton
- Fluorine atom type in mm_pbsa? Lishan Yao
- Calcium in proteins Javier Cuervo
- off-diagonal VDW term Jiyoung Heo
- Re: off-diagonal VDW term Ioana Cozmuta
Tuesday, 20 May 2003
- RE: off-diagonal VDW term Yong Duan
- Re: Fluorine atom type in mm_pbsa? Lishan Yao
- Re: Mainchain.dat Lepsa
- parm99 cailliez
- Re: Fluorine atom type in mm_pbsa? David A. Case
- Re: Calcium in proteins David A. Case
- Re: off-diagonal VDW term David A. Case
- Xleap adding torsions Andrew Petersen
- Problem with CMC/MD Sameer P. Kawatkar
- a question about constructing a periodic box by PLEP. Margaret Shun Cheung
- Re: From Dr. Ekaterina Nikitina caldwell.heimdal.compchem.ucsf.edu
- Amber 7.xx installation on FreeBSD Joseph Maxwell
- Residual dipolar couplings McAteer, Kathleen
- Re: Amber 7.xx installation on FreeBSD M. L. Dodson
- Re: parm99 David A. Case
Wednesday, 21 May 2003
- Hybdrogen bonds and LJ 10-12 Michal Otyepka
- bad atom type f(fluorine) in MM-PBSA? Lishan Yao
- I still have problems with parm99.dat cailliez
- Re: bad atom type f(fluorine) in MM-PBSA? Holger Gohlke
- Re: bad atom type f(fluorine) in MM-PBSA? Lishan Yao
- RE: Residual dipolar couplings McAteer, Kathleen
- Re: parm99 Junmei Wang
- ptraj rdf help tianxiao yang
- non-periodic system Ioana Cozmuta
- Re: ptraj and rdf help tianxiao yang
- Re: non-periodic system Michael Crowley
- Re: non-periodic system Ioana Cozmuta
- RE: non-periodic system Yong Duan
- RE: non-periodic system Yong Duan
- Re: ptraj rdf help Thomas Cheatham
Thursday, 22 May 2003
- Xleap: 'triangular' and 'square' bond Christian Gossens
- leap complains! Layi Adekoya
- rotational and translational motion Jean-François Taly
- Re: rotational and translational motion Carlos Simmerling
- Re: Xleap: 'triangular' and 'square' bond Andreas Svrcek-Seiler
- translational and rotational motion (more information) Jean-François Taly
- RE: parm99 Bayly, Christopher
- Re: leap complains! Jose Ramon Blas
- Re: Minimization problem w/ counter-ion ! David A. Case
- Re: From Dr. Ekaterina Nikitina David A. Case
- Re: Hybdrogen bonds and LJ 10-12 David A. Case
- Questions about statistics output of mm_pbsa? Lishan Yao
- Re: Questions about statistics output of mm_pbsa? Holger Gohlke
- Please help on xleap: FATAL ERROR Margaret Shun Cheung
- RE: leap complains! Kristina Furse
- Re: Please help on xleap: FATAL ERROR David A. Case
- Re: Questions about statistics output of mm_pbsa? David A. Case
- Re: Please help on xleap: FATAL ERROR John Bushnell
- charge fitting for c-term homocysteine. X. Tan
Friday, 23 May 2003
- Re: Questions about statistics output of mm_pbsa? Lishan Yao
- Re: Questions about statistics output of mm_pbsa? Lishan Yao
- Re: Please help on xleap: FATAL ERROR Margaret Shun Cheung
- best force field for Protein+DNA Robert G. Endres
- A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations. Margaret Shun Cheung
- distance-dependent dielectric function Robert G. Endres
- Re: distance-dependent dielectric function Shixiang Yan
- water box distortion GUILLERMINA L ESTIU
- Re: water box distortion caldwell.heimdal.compchem.ucsf.edu
- center command Ioana Cozmuta
- problems with anal in amber7 Liliana Wroblewska
- Re: water box distortion David A. Case
Saturday, 24 May 2003
- MD input file for MM-PBSA calculations Thomas Steinbrecher
- Re: water box distortion GUILLERMINA L ESTIU
- Re: MD input file for MM-PBSA calculations Natasja Brooijmans
- IR6 and makeDIST-RST Francisco Blanco
- Re: water box distortion Holger Gohlke
Sunday, 25 May 2003
- Re: From Dr. Ekaterina Nikitina Nikitina Ekaterina
- HBOND energies in sander Francisco Blanco
Monday, 26 May 2003
- Re: MD input file for MM-PBSA calculations Lepsa
- EWALD BOMB tang kwa
Thursday, 22 May 2003
- Re: translational and rotational motion (more information) Carlos Simmerling
Monday, 26 May 2003
- Re: HBOND energies in sander Holger Gohlke
- Re: EWALD BOMB Holger Gohlke
- RE: EWALD BOMB Yong Duan
Tuesday, 27 May 2003
- Order parameters cailliez
- Amber on SGI with Itanium compilers for linux (fwd) Sanjeev B.S.
- Re: Amber on SGI with Itanium compilers for linux Sanjeev B.S.
- NOTIFICATION CLARK WOOD
- NOTIFICATION CLARK WOOD
- Re: EWALD BOMB tang kwa
- Re: EWALD BOMB Michael Crowley
- AMD opteron Hai-Long Wang
- Re: NOTIFICATION Joseph Maxwell
- Re: Order parameters Holger Gohlke
- Re: NOTIFICATION Jiten
- mm_gbsa question Javier Cuervo
- Re: mm_gbsa question Holger Gohlke
- Does Leap has a problem with Isoleucines? Frederico.Miranda.ibmb.uib.no
Wednesday, 28 May 2003
- about the dielectric Ye Mei
- about the dielectric Ye Mei
- RE: about the dielectric Yong Duan
- Re: AMD opteron Tru Huynh
- CFP: Informatics Approaches in Structural Genomics at PSB 2004 Sean Mooney
- Re: Does Leap has a problem with Isoleucines? Holger Gohlke
- Re: AMD opteron Tru Huynh
- Does Anyone Have a Working MACHINE File for Solaris/SPARC? Chen, Ya
- LES analysis tool other than Moil-view Sameer P. Kawatkar
- clustering trajectories chernhoe
Thursday, 29 May 2003
- coordinate files from carnal jaw3.cec.wustl.edu
- antechamber read gaussian file quch quch
- antechamber read gaussian file quch quch
- MD problem Shuang Ding
- Re: MD problem Carlos Simmerling
- Re: MD problem Shuang Ding
- Re: MD problem Guanglei Cui
- Re: MD problem Shuang Ding
- Re: MD problem Guanglei Cui
- RE: MD problem Yong Duan
- information aram joel panay
- (no subject) 你的朋友
Friday, 30 May 2003
- Phosphorylated Serine Library Frederico.Miranda.ibmb.uib.no
Saturday, 31 May 2003
- A simple question about offset, want to make sure Huang Zunnan

Last message date: Sat May 31 2003 - 17:53:01 PDT
Archived on: Wed Dec 25 2024 - 05:53:20 PST

Amber Archive May 2003 by date