Amber Archive Dec 2004: by date

Wednesday, 1 December 2004
- AMBER: FEP along a reaction coordinate in sander Tomasz Borowski
- Re: AMBER: Implicit 4r md Stefano.Pieraccini.unimi.it
- Re: AMBER: FEP along a reaction coordinate in sander Masataka Nagaoka
- Re: AMBER: FEP along a reaction coordinate in sander David A. Case
- Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) David A. Case
- AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu
- RE: AMBER: question about parallel simulation Ross Walker
- AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Ilyas Yildirim
- AMBER: ntt parameter tang kwa
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu
- Re: AMBER: ntt parameter David A. Case
- RE: AMBER: question about parallel simulation Ross Walker
- Re: AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Cenk Andac
- Re: AMBER: increasing the maximum value of NPHB parameter Alena Shmygelska
Thursday, 2 December 2004
- Re: AMBER: ntt parameter David Smith
- AMBER: restrainted torsion tang kwa
- Re: AMBER: restrainted torsion David A. Case
- (long) Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) Tru Huynh
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu
- Re: AMBER: extracting energy from trajector? David Smith
- RE: AMBER: question about parallel simulation Ross Walker
- AMBER: nmode & mm-pbsa Shekter, Lee
- Re: AMBER: Implicit 4r md yen li
- AMBER: Residue Loading Problem Garhan Attebury
- Re: AMBER: ntt parameter Ross Walker
- Re: AMBER: Residue Loading Problem Furse, Kristina Elisabet
Friday, 3 December 2004
- Re: AMBER: Residue Loading Problem david.evans.ulsop.ac.uk
- Re: AMBER: Implicit 4r md David A. Case
Saturday, 4 December 2004
- AMBER: Dielectric Constant Marsita M
- Re: AMBER: Dielectric Constant Bill Ross
- Re: AMBER: Dielectric Constant David A. Case
Sunday, 5 December 2004
- AMBER: one question about dielectric dependent model Xiaowei (David) Li
- AMBER: Compiling Antechamber/Amber8 with ia64_ifort Toru Yagi
Monday, 6 December 2004
- Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort Andreas Svrcek-Seiler
- AMBER: strange bond energies Magne Olufsen
- Re: AMBER: strange bond energies Carlos Simmerling
- AMBER: Wanxin Sun
- Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort Jack Lei
- AMBER: md's yen li
- AMBER: cut-off & MD bybaker.itsa.ucsf.edu
- RE: AMBER: cut-off & MD Ross Walker
- AMBER: converting from NAMD trajectory format Stern, Julie
- AMBER: FW: two processor amd 64 bit pc Spero Manolatos
- RE: AMBER: FW: two processor amd 64 bit pc Ross Walker
- AMBER: (no subject) Andrew Box
Tuesday, 7 December 2004
- AMBER: install problem Kevin Murphy
- Re: AMBER: install problem David A. Case
- Re: AMBER: (no subject) David A. Case
- AMBER: Gigabit Ethernet Switch/Opteron 246 jianhui wu
- AMBER: 1-4 EEL tang kwa
- RE: AMBER: Gigabit Ethernet Switch/Opteron 246 Ross Walker
- AMBER: imin=5 in sander MURAT CETINKAYA
Monday, 6 December 2004
- Re: AMBER: imin=5 in sander Carlos Simmerling
Tuesday, 7 December 2004
- Re: AMBER: imin=5 in sander Asim Okur
- Re: AMBER: imin=5 in sander Asim Okur
- AMBER: question about mmpbsa xhu1.memphis.edu
- AMBER: NMR constraint problem Andrew Box
- AMBER: Why the surface calculations sometimes fail? hj zou
Wednesday, 8 December 2004
- AMBER: some questions.... Germán Sciaini
- Re: AMBER: question about mmpbsa cailliez
- Re: AMBER: some questions.... David A. Case
- Re: AMBER: NMR constraint problem David A. Case
- Re: AMBER: 1-4 EEL David A. Case
- Re: AMBER: David A. Case
- Re: AMBER: Why the surface calculations sometimes fail? David A. Case
- Re: AMBER: NMR constraint problem John Bushnell
- Re: AMBER: question about mmpbsa xhu1.memphis.edu
- Re: AMBER: converting from NAMD trajectory format Thomas E. Cheatham, III
- Re: Re: AMBER: Why the surface calculations sometimes fail? hj zou
- AMBER: calculate ligand's rmsd Yong Xu
- RE: AMBER: calculate ligand's rmsd Ross Walker
Thursday, 9 December 2004
- AMBER: Implicit Solvent Models Nelson Fonseca
- AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins
- Re: AMBER: pbsa error in mm_pbsa amber 8 david.evans.ulsop.ac.uk
- AMBER: No radius found for 2412 Zn Zn Yong Xu
- AMBER: how to prepare Zn.lib Yong Xu
Friday, 10 December 2004
- Re: AMBER: No radius found for 2412 Zn Zn Holger Gohlke
- Re: Re: AMBER: No radius found for 2412 Zn Zn Yong Xu
- Re: AMBER: No radius found for 2412 Zn Zn Holger Gohlke
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins
- Re: AMBER: No radius found for 2412 Zn Zn Jack Lei
- AMBER: question about md's yen li
- Re: AMBER: Implicit Solvent Models David A. Case
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo
- RE: AMBER: how to prepare Zn.lib Ross Walker
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo
- AMBER: question about MGB and PB xhu1.memphis.edu
- Re: Re: AMBER: No radius found for 2412 Zn Zn Yong Xu
Sunday, 12 December 2004
- AMBER: Why the charge is not an integer? mmv
- Re: AMBER: Why the charge is not an integer? Guanglei Cui
- Re: AMBER: Why the charge is not an integer? FyD
- Re: AMBER: Why the charge is not an integer? David A. Case
- AMBER: Binding free energy from separate/single trajectory yuann
Monday, 13 December 2004
- AMBER: ptraj hbond memory allocation on opteron Fabian Boes
- Re: AMBER: ptraj hbond memory allocation on opteron Andreas Svrcek-Seiler
- RE: AMBER: Why the charge is not an integer? Ross Walker
- AMBER: cobalt parameters Peter Gannett
- Re: Re: AMBER: Why the surface calculations sometimes fail? David A. Case
- AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ilyas Yildirim
- AMBER: Why the charge is not an integer? Annette Höglund
Tuesday, 14 December 2004
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins
- Re: AMBER: ptraj hbond memory allocation on opteron Fabian Boes
- Re: AMBER: pbsa error in mm_pbsa amber 8 david.evans.ulsop.ac.uk
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo
- AMBER: entropy implementation in ptraj Raik Grünberg
- RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ross Walker
- AMBER: Compiling question Yanze Zhang
- Re: AMBER: Compiling question David A. Case
- RE: AMBER: Compiling question Ross Walker
- Re: AMBER: Compiling question Robert Duke
- Re: AMBER: Compiling question James W. Caldwell
- Re: AMBER: Compiling question Yanze Zhang
- Re: AMBER: Why the charge is not an integer? John Mongan
Wednesday, 15 December 2004
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins
- AMBER: Ewald tang kwa
- AMBER: unknown elements Youyi Peng
Thursday, 16 December 2004
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo
Wednesday, 15 December 2004
- Re: AMBER: unknown elements David A. Case
- Re: AMBER: entropy implementation in ptraj David A. Case
- Re: AMBER: Ewald David A. Case
- AMBER: mm_pbsa Carsten Detering
- AMBER: About MM/PBSA, PB Calculation nlxc
- RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ilyas Yildirim
- AMBER: Free Energy Perturbation using Sander (TI Method) Ilyas Yildirim
- AMBER: General Question about AMBER's Free Energy Perturbation Method Ilyas Yildirim
- Re: Re: Re: AMBER: Why the surface calculations sometimes fail? hj zou
- Re: AMBER: General Question about AMBER's Free Energy Perturbation Method David A. Case
Thursday, 16 December 2004
- AMBER: sander imin=5 MURAT CETINKAYA
- Re: Re: Re: AMBER: Why the surface calculations sometimes fail? David A. Case
- Re: AMBER: About MM/PBSA, PB Calculation David A. Case
- Re: AMBER: About MM/PBSA, PB Calculation nlxc
- Re: AMBER: Residue Loading Problem David A. Case
- AMBER: nmode problem Yong Xu
Friday, 17 December 2004
- AMBER: Question concerning ANAL total energy calculation Daniel Wetzler
- Re: AMBER: entropy implementation in ptraj Raik Grünberg
- Re: AMBER: Question concerning ANAL total energy calculation David A. Case
- Re: AMBER: entropy implementation in ptraj David A. Case
- AMBER: MD: Water network analysis + visualization Sanjeev B.S.
- AMBER: nanotube parameters MURAT CETINKAYA
- Re: AMBER: nanotube parameters Bill Ross
- Re: AMBER: General Question about AMBER's Free Energy Perturbation Method Ilyas Yildirim
- Re: AMBER: General Question about AMBER's Free Energy Perturbation Method David A. Case
- Re: AMBER: nanotube parameters David A. Case
Saturday, 18 December 2004
- Re: AMBER: Question concerning ANAL total energy calculation Daniel Wetzler
- Re: AMBER: Question concerning ANAL total energy calculation David A. Case
- AMBER: Kinetics energy Germán Sciaini
- Re: AMBER: Kinetics energy Carlos Simmerling
Monday, 20 December 2004
- AMBER: Question on tleap of amber8 Okimoto Noriaki
- Re: AMBER: nanotube parameters Andreas Svrcek-Seiler
- Re: AMBER: Kinetics energy Andreas Svrcek-Seiler
- AMBER: constraints on atoms cailliez
- Re: AMBER: Question on tleap of amber8 David A. Case
- AMBER: Sander TI Cai, Yufeng
- AMBER: parameter development Sebastian Fernandez Alberti
- Re: AMBER: Question concerning ANAL total energy calculation Daniel Wetzler
- Re: AMBER: Question concerning ANAL total energy calculation David A. Case
- AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ilyas Yildirim
- RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ross Walker
- AMBER: cluster analysis with ptraj in amber 8.0 Eric Hu
Tuesday, 21 December 2004
- AMBER: Dummy torsion paramters for thermodynamic integration Thomas Steinbrecher
- Re: AMBER: cluster analysis with ptraj in amber 8.0 David Smith
- AMBER: a question Germán Sciaini
- AMBER: nrespa=2 Marsita M
- Re: AMBER: Dummy torsion paramters for thermodynamic integration David A. Case
- Re: AMBER: nrespa=2 David A. Case
- Re: AMBER: nrespa=2 Carlos Simmerling
- Re: AMBER: Sander TI David A. Case
- Re: AMBER: parameter development David A. Case
- Re: AMBER: constraints on atoms David A. Case
- AMBER: Ideal bonds and angles Nhat-hang Duong
- Re: AMBER: Ideal bonds and angles David A. Case
- AMBER: TFE parameters Adrian E. Roitberg
- Re: AMBER: a question David A. Case
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Bill Ross
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang
- RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ross Walker
Wednesday, 22 December 2004
- AMBER: Output of sander Harianto
- Re: AMBER: Output of sander David A. Case
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules David A. Case
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules David A. Case
- AMBER: energy unit Chen Song
Thursday, 23 December 2004
- AMBER: amber7 on digital unix anshul.imtech.res.in
- AMBER: Molecular modelling. Osman Gani
- Re: AMBER: energy unit Harianto
- Re: AMBER: amber7 on digital unix David A. Case
- Re: AMBER: amber7 on digital unix anshul.imtech.res.in
- Re: AMBER: amber7 on digital unix David A. Case
- Re: AMBER: Output of sander Harianto
- Re: AMBER: Output of sander David A. Case
- AMBER: RMSD of ligand Yong Xu
- Re: AMBER: Molecular modelling. David A. Case
Friday, 24 December 2004
- AMBER: mm_gbsa results for charged ligands Cenk Andac
- Re: AMBER: mm_gbsa results for charged ligands Holger Gohlke
Saturday, 25 December 2004
- AMBER: Problem with computing Resp charges using RED Cenk Andac
Tuesday, 28 December 2004
- AMBER: input conversion error [Amber8] Bimo Ario Tejo
Wednesday, 29 December 2004
- AMBER: NSCM Alberto p
- Re: AMBER: Problem with computing Resp charges using RED FyD
- AMBER: MM_PBSA calculations Jiten
Thursday, 30 December 2004
- AMBER: MM_PBSA calculation error Jiten
- AMBER: MD simulations on heparin and heparin sulfate Harald Lanig
- Re: AMBER: Problem with computing Resp charges using RED Cenk Andac
- AMBER: Dummy Atoms: How to create them? Ilyas Yildirim
- Re: AMBER: Dummy Atoms: How to create them? David A. Case
- AMBER: How is optimization done during energy minimization of the force field? fangyu liang
Friday, 31 December 2004
- AMBER: mm_pbsa +fillratio Jiten
- Re: AMBER: How is optimization done during energy minimization of the force field? myang

Last message date: Fri Dec 31 2004 - 17:53:00 PST
Archived on: Fri Nov 22 2024 - 05:53:22 PST

Amber Archive Dec 2004 by date