Amber Archive Dec 2003: by date

Monday, 1 December 2003
- Re: AMBER: Re: Nmode problem Wu Yingliang
- AMBER: NAD+ and NADH amber parameters Jiten
- Re: AMBER: Re: Nmode problem Holger Gohlke
- Re: AMBER: NAD+ and NADH amber parameters David A. Case
- RE: AMBER: NAD+ and NADH amber parameters Ross Walker
- AMBER: partial charge Li Ying
- AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg
- AMBER: Sander / Anal Emmanuel Giudice
- Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case
- Re: AMBER: Sander / Anal David A. Case
- AMBER: basic questions Wei Wang
- AMBER: sander output Dave S Walker
- Re: AMBER: sander output Carlos Simmerling
- Re: AMBER: basic questions David A. Case
- Re: AMBER: partial charge David A. Case
Tuesday, 2 December 2003
- Re: AMBER: Pseudouridine force field parameters Peter Gannett
- Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde
- AMBER: about H-bond definition for TIP3P Nikolai Smolin
- Re: AMBER: basic questions Wei Wang
- Re: AMBER: basic questions David A. Case
- AMBER: Ptraj-HBOND Taner E. Dirama
- Re: AMBER: partial charge Li Ying
- Re: AMBER: partial charge David A. Case
- AMBER: Anal/MMPBSA Wu Yingliang
- Re: AMBER: Anal/MMPBSA David A. Case
- AMBER: segmentation fault Do Anh Tuan
Wednesday, 3 December 2003
- AMBER: GIBBS - PMFquestion Jiri Matousek
- AMBER: how to calculate vibration frequency? A. Hungie
- Re: AMBER: missing of VdW Parameters for N3 wendy.cornell.pharma.novartis.com
- Re: AMBER: how to calculate vibration frequency? David A. Case
- AMBER: MM-PBSA question Giovanni
- Re: AMBER: segmentation fault David A. Case
- Re: AMBER: partial charge Li Ying
- Re: AMBER: MM-PBSA question Holger Gohlke
- AMBER: Resp Esp charge Derive (RED v-1.0) release FyD
Thursday, 4 December 2003
- AMBER: Paramters for beta and gamma peptides Jagannadh B
Wednesday, 3 December 2003
- RE: Re: AMBER: ANAL/MMPBSA Wu Yingliang
Thursday, 4 December 2003
- Re: AMBER: ANAL/MMPBSA Holger Gohlke
- AMBER: TFE solvent box John
Wednesday, 3 December 2003
- Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg
- Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg
- Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg
Thursday, 4 December 2003
- Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg
- Re: Re: AMBER: ANAL/MMPBSA Wu Yingliang
- Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case
- AMBER: NO2-TYR arubin.unmc.edu
- AMBER: Amber - compiler help Malone, Scott
- RE: AMBER: Amber - compiler help Chris Moth
- Re: AMBER: sander output Dave S Walker
- Re: AMBER: sander output David A. Case
- Re: AMBER: Amber - compiler help David A. Case
- AMBER: TFE solvent box RAJA SWAMINATHAN
Friday, 5 December 2003
- RE: AMBER: TFE solvent box John
- Re: AMBER: Sander / Anal Emmanuel Giudice
- Re: Re: AMBER: Compiling on Suse 9 Pro with ifc... Ye Mei
Sunday, 7 December 2003
- Re: AMBER: NAD+ and NADH amber parameters Jiten
- Re: AMBER: NAD+ and NADH amber parameters Ross Walker
Monday, 8 December 2003
- Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde
- AMBER: initial structures Raghunadha Reddy Burri
- Re: AMBER: initial structures Carlos Simmerling
- AMBER: Temperature dependent properties of TIP4P and TIP5P rluo.uci.edu
- AMBER: Re: initial structures Raghunadha Reddy Burri
- Re: AMBER: Re: initial structures David A. Case
- AMBER: MD L Jin
- AMBER: Small problems L Jin
Tuesday, 9 December 2003
- AMBER: gaff atom types for phosphor compouds astrid.maass
- Re: AMBER: gaff atom types for phosphor compouds Junmei Wang
Wednesday, 10 December 2003
- AMBER: xleap-N/C terminus John
- Re: AMBER: xleap-N/C terminus Jiten
- AMBER: Mg2+ parameters for RNA usage Vlad Cojocaru
- Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer
- AMBER: RESP charges Youyi Peng
- AMBER: About Temperature Regulation L Jin
- AMBER: Antechamber & Ptraj/Rdparm L Jin
- Re: AMBER: Mg2+ parameters for RNA usage Pascal Auffinger
- RE: AMBER: xleap-N/C terminus John
- Re: AMBER: Mg2+ parameters for RNA usage Peter VARNAI
- Re: AMBER: About Temperature Regulation David A. Case
- Re: AMBER: xleap-N/C terminus David A. Case
- Re: AMBER: RESP charges David A. Case
- AMBER: Nitrated Tyr arubin.unmc.edu
- Re: AMBER: About Temperature Regulation L Jin
- Re: AMBER: RESP charges Youyi Peng
- AMBER: MOPAC from antechamber Beale, John
- Re: AMBER: RESP charges Jiten
- Re: AMBER: RESP charges Joey Harriman
- Re: AMBER: Mg2+ parameters for RNA usage Bill Ross
- Re: AMBER: MOPAC from antechamber Joey Harriman
- Re: AMBER: xleap-N/C terminus Bill Ross
- Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross
- Re: AMBER: RESP charges David A. Case
- Re: AMBER: RESP charges Junmei Wang
- Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Junmei Wang
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Junmei Wang
Thursday, 11 December 2003
- AMBER: a simple question about HBond energy... Florent Barbault
- AMBER: Carbohydrate connectivity Bimo Ario Tejo
- Re: AMBER: Carbohydrate connectivity Jiten
- Re: AMBER: Carbohydrate connectivity David A. Case
- Re: AMBER: How to use quasih? David A. Case
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Junmei Wang
- RE: AMBER: xleap-N/C terminus Dalmaris, John
- RE: AMBER: xleap-N/C terminus Bill Ross
- AMBER: GBSA problem northrop.chem.ucla.edu
- Re: AMBER: GBSA problem Wu Yingliang
Friday, 12 December 2003
- AMBER: lifetime in ptraj hbond Fajar Rakhman Wibowo
- AMBER: ambpdb L Jin
- Re: AMBER: ambpdb ch cureton
- Re: AMBER: ambpdb L Jin
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin
- Re: AMBER: ambpdb ch cureton
- Re: AMBER: lifetime in ptraj hbond Martin Lepsik
- AMBER: adding extra salt Vlad Cojocaru
- AMBER: Antechamber:charges missing L Jin
- Re: AMBER: adding extra salt Bill Ross
- AMBER: nmode, trajectory kbyun.wesleyan.edu
- AMBER: parmscan Jessica Swanson
- AMBER: order parameter myang
- Re: AMBER: order parameter David A. Case
- Re: AMBER: a simple question about HBond energy... David A. Case
- Re: AMBER: a simple question about HBond energy... Bill Ross
Saturday, 13 December 2003
- AMBER: non-zero 10-12 coefficient Bimo Ario Tejo
- Re: AMBER: nmode, trajectory Holger Gohlke
- Re: AMBER: non-zero 10-12 coefficient David A. Case
Thursday, 11 December 2003
- AMBER: How to use quasih? A. Hungie
Sunday, 14 December 2003
- AMBER: Heme and Zn parameters Vema Aparna
Monday, 15 December 2003
- AMBER: Energy map L Jin
- Re: AMBER: Energy map Tammy Smith
- AMBER: Message removed at request of author Name Removed
- Re: AMBER: Energy map Tammy Smith
- AMBER: length of deltaG calcs Heather A.Carlson
- AMBER: question about namelist aini.UMDNJ.EDU
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Holger Gohlke
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs David Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Thomas E. Cheatham, III
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: Energy map Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: length of deltaG calcs Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith
- Re: AMBER: question about namelist Tammy Smith
- Re: AMBER: question about namelist Suse Broyde
- Re: AMBER: question about namelist Ioana Cozmuta
- Re: AMBER: water neighborhood of amide hydrogens Bill Ross
- AMBER: minimization on sander Herbert Georg
- Re: AMBER: minimization on sander Bill Ross
- Re: AMBER: minimization on sander Herbert Georg
- Re: AMBER: question about namelist Piotr Cieplak
- AMBER: no "Input orientation" in g98 log Lee, Matt
Tuesday, 16 December 2003
- AMBER: Ibelly and Ewald error message when ewald should be off Ben Cossins
- AMBER: Nmode analysis ptn-ligand complex Jory Zmuda
Wednesday, 17 December 2003
- AMBER: nmode statistics kbyun.wesleyan.edu
- Re: AMBER: nmode statistics Holger Gohlke
Thursday, 18 December 2003
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Junmei Wang
- Re: AMBER: RESP charges Youyi Peng
- Re: AMBER: RESP charges Junmei Wang
- AMBER: PMEMD Performance on Beowulf systems Stephen.Titmuss.csiro.au
- Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke
Friday, 19 December 2003
- AMBER: MD: restrt L Jin
- AMBER: special gaff atom types available? astrid.maass
- AMBER: Ewald in Amber 7 Ben Cossins
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling
- Re: AMBER: Ewald in Amber 7 David A. Case
- AMBER: Vibration frequency of nucleobases A. Hungie
- AMBER: Toolchest Shuang Ding
- AMBER: initial velocity Fan Gao
- Re: AMBER: initial velocity Peter Oelschlaeger
- AMBER: Curves parameters UU and PP Peter Gannett
Saturday, 20 December 2003
- Re: AMBER: Curves parameters UU and PP Surjit Dixit
- Re: AMBER: special gaff atom types available? David A. Case
Sunday, 21 December 2003
- AMBER: vlimit? Ran Ye
- Re: AMBER: vlimit? Bill Ross
- AMBER: using sander without SHAKE Wayne Dawson
- RE: RE: AMBER: PMEMD Performance on Beowulf systems Aldo Jongejan
Monday, 22 December 2003
- AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? Jiri Matousek
- Re: AMBER: PMEMD Performance on Beowulf systems Viktor Hornak
- Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling
- Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke
- Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding
- Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling
- Re: AMBER: using sander without SHAKE David A. Case
- Re: AMBER: vlimit? David A. Case
- AMBER: HT vs no HT John Mongan
- AMBER: RESP charge redistribution Youyi Peng
- AMBER: umbrella sampling with AMBER Mey Khalili
- Re: AMBER: umbrella sampling with AMBER David A. Case
- 2 FREE Worldwide Airline Tickets Worth $1600 for just $189! Bette Pagan
Tuesday, 23 December 2003
- AMBER: MSMS Salma B. Rafi
- Re: AMBER: MSMS David A. Case
- Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? David A. Case
- AMBER: PMEMD Performance on IBM SP David Skinner
- Re: AMBER: vlimit? Ryan Ye
Wednesday, 24 December 2003
- AMBER: Basic potential question: a b
- AMBER: Basic potential question: Wayne Dawson
- AMBER: MSE Wen Li
- Re: AMBER: using sander without SHAKE Wayne Dawson
- Re: AMBER: using sander without SHAKE David A. Case
- Re: AMBER: MSE David A. Case
- Re: AMBER: Basic potential question: FyD
- Re: AMBER: Basic potential question: Piotr Cieplak
- Re: AMBER: using sander without SHAKE Bill Ross
Thursday, 25 December 2003
- Re: AMBER: Basic potential question: Wayne Dawson
Friday, 26 December 2003
- Re: AMBER: vlimit? David A. Case
Saturday, 27 December 2003
- AMBER: Constant temperature L Jin
- Re: AMBER: Constant temperature Bill Ross
- Re: AMBER: Constant temperature David A. Case
Monday, 29 December 2003
- AMBER: roar topology and coordinate files PSR04996.mailstudenti.unimi.it
- Re: AMBER: roar topology and coordinate files M. L. Dodson
- Re: AMBER: roar topology and coordinate files M. L. Dodson
- AMBER: The restart file generated by Ptraj Ling Zhang
- AMBER: The lost velocities in the restart file generated by Ptraj Ling Zhang
- Re: AMBER: The lost velocities in the restart file generated by Ptraj Bill Ross
- Re: AMBER: roar topology and coordinate files Bill Ross
- Re: AMBER: roar topology and coordinate files M. L. Dodson
Tuesday, 30 December 2003
- AMBER: problems with pressure control Endres, Robert G.
- Re: AMBER: problems with pressure control David A. Case
Wednesday, 31 December 2003
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin
- Re: AMBER: Antechamber & Ptraj/Rdparm David A. Case

Last message date: Wed Jan 14 2004 - 15:53:13 PST
Archived on: Mon Nov 03 2025 - 05:53:22 PST

Amber Archive Dec 2003 by date