Amber Archive May 2005: by date

Sunday, 1 May 2005
- AMBER: Identifying water molecules with ptraj Joseph Fernandez
Monday, 2 May 2005
- AMBER: fast 1/r methods Brent Krueger
- Re: AMBER: fast 1/r methods fangyu liang
- Re: AMBER: fast 1/r methods Andreas Svrcek-Seiler
- Re: AMBER: ipol=1 & use_pme= ?? David A. Case
- AMBER: How to fix the atom in NPT case? george Chen
- Re: AMBER: How to fix the atom in NPT case? David A. Case
- Re: AMBER: Re: R.E.D. question Yanze Zhang
- Re: AMBER: How to fix the atom in NPT case? george Chen
- Re: AMBER: Re: R.E.D. question FyD
- AMBER: sander run YoungJin Cho
Tuesday, 3 May 2005
- AMBER: GB with dipoles ! Pradipta Bandyopadhyay
- Fwd: Re: AMBER: AMBER Test Anthony Cruz
- AMBER: Can I add iodide anione? Myunggi Yi
- AMBER: rborn(i) in egb.f Harianto Tjong
- Re: AMBER: rborn(i) in egb.f John Mongan
- AMBER: NOE constraints Hui-Hsu Tsai
- Re: AMBER: rborn(i) in egb.f Harianto Tjong
- Re: AMBER: rborn(i) in egb.f David A. Case
- Re: AMBER: NOE constraints David A. Case
- Re: AMBER: How to fix the atom in NPT case? george Chen
- Re: AMBER: rborn(i) in egb.f Harianto Tjong
- Re: AMBER: rborn(i) in egb.f David A. Case
- Re: AMBER: How to fix the atom in NPT case? David A. Case
Wednesday, 4 May 2005
- AMBER: Relative stability with MMPBSA Angelo Pugliese
- AMBER: Bromelain PDF xleap load error Thomas Patko
- AMBER: mm/pbsa error Eric Hu
- AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac
- Re: AMBER: Meaning of induced dipole moments for atom pairs? David A. Case
- AMBER: How can I read parm99.dat file? Myunggi Yi
- Re: AMBER: How can I read parm99.dat file? Bill Ross
Thursday, 5 May 2005
- Re: AMBER: How can I read parm99.dat file? Vineet Pande
- Re: AMBER: How can I read parm99.dat file? David A. Case
- AMBER: ibelly in nmode Dawei Zhang
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko
- Re: AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) JunJun Liu
- AMBER: keeping two domains closed together during a simulation Sergio E. Wong
- AMBER: problem with gb md emilia wu
- RE: AMBER: problem with gb md Ross Walker
- Re: RE: AMBER: problem with gb md emilia wu
Friday, 6 May 2005
- Re: RE: AMBER: problem with gb md Andreas Svrcek-Seiler
- AMBER: No vdW parameters for HO.. Vineet Pande
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Andy Purkiss
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi
- Re: AMBER: No vdW parameters for HO.. David A. Case
- Re: AMBER: No vdW parameters for HO.. Vineet Pande
- AMBER: a nomenclature question Kenley Barrett
- Re: AMBER: No vdW parameters for HO.. Yong Duan
- AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth
- Re: AMBER: How can I read parm99.dat file? Bill Ross
Saturday, 7 May 2005
- Re: AMBER: ibelly in nmode David A. Case
Monday, 9 May 2005
- AMBER: langevin, GB and simulated annealing - 5 pascal.baillod.epfl.ch
- AMBER: radial distribution function Myunggi Yi
- Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling
- Re: AMBER: langevin, GB and simulated annealing - 5 David A. Case
- AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari
Tuesday, 10 May 2005
- Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling
- Re: AMBER: radius parameter for F atom Scott Pendley
- Re: AMBER: mm/pbsa error Scott Pendley
Wednesday, 11 May 2005
- AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko
- AMBER: Trouble with example tutorial Maciej
- AMBER: Parameter for alpha-lactose Sagarika Dev
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Mark Rance
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko
- AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 Thomas E. Cheatham, III
- Fwd: Re: AMBER: AMBER Test Anthony Cruz
- AMBER: SANDER BOMB: volume of ucell too big Stern, Julie
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 FyD
- RE: AMBER: Asking how to creat alanine "dipeptide" in amber8 Ross Walker
- AMBER: Problem with xleap Ilyas Yildirim
- Re: AMBER: Problem with xleap FyD
- AMBER: maximum number of processors MURAT CETINKAYA
Thursday, 12 May 2005
- Re: AMBER: Problem with xleap JunJun Liu
- Re: AMBER: Parameter for alpha-lactose David A. Case
- Re: Fwd: Re: AMBER: AMBER Test David A. Case
- Re: AMBER: maximum number of processors Asim Okur
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons David A. Case
- Re: AMBER: maximum number of processors Michael Crowley
- Re: AMBER: Trouble with example tutorial David A. Case
- AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski
- Re: AMBER: SANDER BOMB: volume of ucell too big Michael Crowley
- RE: AMBER: SANDER BOMB: volume of ucell too big Stern, Julie
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Bill Ross
- Re: AMBER: SANDER BOMB: volume of ucell too big David A. Case
- Re: AMBER: SANDER BOMB: volume of ucell too big Robert Duke
- AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen
- RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside Spero Manolatos
- Re: AMBER: a nomenclature question David A. Case
- RE: AMBER: Tutorial #1 ptraj/sander problem Ross Walker
- Re: AMBER: Problem with xleap Ilyas Yildirim
- AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang
- Re: AMBER: RESP charge fitting for N-methylguanine cation Kara Di Giorgio
- AMBER: amber8 test error Cordova, Luis E.
Friday, 13 May 2005
- Re: AMBER: the restraint MD fail with amber8,but success with amber7 Carlos Simmerling
- AMBER: creating residues - charge assign problems Hayden Eastwood
- Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang
- Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang
- Re: AMBER: creating residues - charge assign problems FyD
- Re: AMBER: RESP charge fitting for N-methylguanine cation FyD
- Re: AMBER: creating residues - charge assign problems David A. Case
- Re: AMBER: amber8 test error David A. Case
- AMBER: platinum atom in Xleap Chen Chengwen
- Re: AMBER: maximum number of processors Abd Ghani Abd Aziz
Saturday, 14 May 2005
- AMBER: How to create a parallel job for amber 8? 易虹
- Re: AMBER: How to create a parallel job for amber 8? Shulin Zhuang
- Re: AMBER: maximum number of processors C J Kenneth Tan -- OptimaNumerics
- AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch.cherry.bio.titech.ac.jp
- Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? Carlos Simmerling
- AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee
- RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? ross.rosswalker.co.uk
- Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross
Sunday, 15 May 2005
- AMBER: how to reduce box size and delete excess solvent hj zou
- AMBER: How to set constraint Li Su
- Re: AMBER: how to reduce box size and delete excess solvent Bill Ross
Monday, 16 May 2005
- AMBER: strange mm_pbsa.pl bug Nelson Fonseca
- AMBER: How to set up dihedral constraints in amber Li Su
- AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee
- Re: AMBER: How to set constraint David A. Case
- AMBER: output of force field info Stern, Julie
- AMBER: nmode in mmpbsa Joseph Fernandez
- Re: AMBER: output of force field info David A. Case
- AMBER: *** Proper torsion parameters missing *** Ilyas Yildirim
- Re: AMBER: output of force field info Thomas E. Cheatham, III
- AMBER: ATOM TYPE Ilyas Yildirim
- Re: AMBER: nmode in mmpbsa Holger Gohlke
Tuesday, 17 May 2005
- AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x
- Re: AMBER: MMPBSA calculations on Highly charged systems Nelson Fonseca
- Re: AMBER: generating over 16 bps of DNA in nucgen Garhan Attebury
- AMBER: Message in .out file Atilio Anzellotti
- Re: AMBER: generating over 16 bps of DNA in nucgen aanzellotti.mail2.vcu.edu
- AMBER: GAFF angle parameters Monica Civera
- AMBER: molsurf error mingche Pan
- AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi
- Re: AMBER: compiling pmemd on dual xeon Robert Duke
- Re: AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh
- AMBER: gaff: ca-ca-c -o torsion parameter Oliver Hucke
- AMBER: amber 8 REM possible test problem Sergio E. Wong
- RE: AMBER: GAFF angle parameters Junmei Wang
- AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker
- AMBER: MD on surface Yanze Zhang
- AMBER: error with ptraj Xiaowei (David) Li
- AMBER: loading pdb cbala.igib.res.in
- Re: AMBER: Message in .out file David A. Case
- Re: AMBER: loading pdb David A. Case
- Re: AMBER: error with ptraj David A. Case
- Re: AMBER: gaff: ca-ca-c -o torsion parameter David A. Case
Wednesday, 18 May 2005
- AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan
- Re: AMBER: loading pdb Rajeev Ranjan Singh
- RE: AMBER: Using AMBER for Carbon nanotubes Ross Walker
- AMBER: error during MD run cbala.igib.res.in
- Re: AMBER: error during MD run Thomas E. Cheatham, III
- Re: AMBER: error during MD run Rajeev Ranjan Singh
- AMBER: frcmod info for Nickel Kara Di Giorgio
- Re: AMBER: loading pdb Ilyas Yildirim
- AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari
- Re: AMBER: parameter for sulfur in thio-glucoside residue Ilyas Yildirim
- AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Bill Ross
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim
- AMBER: Amber 8 and LAM compilation problem Glen Otero
- AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari
Thursday, 19 May 2005
- RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ross Walker
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ilyas Yildirim
- AMBER: GB - igb=1 versus dielc=? milion.c-box.cz
- Re: AMBER: Amber 8 and LAM compilation problem Robert Duke
- AMBER: write format of restart crd in sander/pmemd Peter Varnai
- AMBER: Using amber4 generated prep files in amber8? Simon Whitehead
- Re: AMBER: Using amber4 generated prep files in amber8? David A. Case
- Re: AMBER: GB - igb=1 versus dielc=? David A. Case
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Cenk Andac
- AMBER: read pdb back to xleap after solvation of chloroform chaiann ng
- Re: AMBER: read pdb back to xleap after solvation of chloroform David A. Case
- RE: AMBER: read pdb back to xleap after solvation of chloroform Ross Walker
- Re: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng
- RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross
- RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross
Friday, 20 May 2005
- AMBER: MM_PBSA for NMR restrained structures Cenk Andac
- AMBER: Representation of cations in MD Thomas Steinbrecher
- AMBER: leap problem: savepdb Hannes Barsch
- AMBER: Re: antechamber not working .. for thio residue.. Vijay Manickam Achari
- AMBER: how to creat leaprc.gaff Vijay Manickam Achari
- Re: AMBER: how to creat leaprc.gaff Ilyas Yildirim
- Re: AMBER: Re: antechamber not working .. for thio residue.. Shulin Zhuang
- AMBER: Error in minimization Priti Hansia
- Re: AMBER: Error in minimization Carlos Simmerling
- Re: AMBER: Representation of cations in MD David A. Case
- Re: AMBER: leap problem: savepdb David A. Case
- AMBER: Steve Seibold
- Re: AMBER: luckyang.gmail.com
- AMBER: crashing xleap Kenley Barrett
- AMBER: 1-4 scaling factors Stern, Julie
- Re: AMBER: 1-4 scaling factors Thomas E. Cheatham, III
- Re: AMBER: crashing xleap Bill Ross
- Re: AMBER: crashing xleap Scott Brozell
Sunday, 22 May 2005
- AMBER: Unexpected stop of Sander run Grzegorz Jezierski
- Re: AMBER: rotating and repositioning molecules in xleap Angelo Pugliese
Friday, 20 May 2005
- Re: AMBER: read pdb back to xleap after solvation of chloroform Furse, Kristina Elisabet
Saturday, 21 May 2005
- AMBER: Copyright for PBSA Cenk Andac
Friday, 20 May 2005
- Re: AMBER: crashing xleap Ilyas Yildirim
- AMBER: Citing the PBSA module of AMBER8 Cenk Andac
- AMBER: rotating and repositioning molecules in xleap Hwankyu Lee
Sunday, 22 May 2005
- Re: AMBER: rotating and repositioning molecules in xleap Hwankyu Lee
Friday, 20 May 2005
- Re: AMBER: crashing xleap Kenley Barrett
- Re: AMBER: JunJun Liu
- AMBER: modeller Zhang Bing
Sunday, 22 May 2005
- Re: AMBER: Unexpected stop of Sander run Bill Ross
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling
Friday, 20 May 2005
- Re: AMBER: crashing xleap Furse, Kristina Elisabet
Saturday, 21 May 2005
- Re: AMBER: Copyright for PBSA David A. Case
Sunday, 22 May 2005
- Re: AMBER: rotating and repositioning molecules in xleap Bill Ross
- AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee
- RE: AMBER: Error in sander: stack trace terminated abnormally. Ross Walker
- AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari
- Re: AMBER: antechamber not working .. for thio residue.. Shulin Zhuang
Monday, 23 May 2005
- Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski
- AMBER: Setting Amber force field parameters Chen Chengwen
- AMBER: using antechamber ... to get prepin file Vijay Manickam Achari
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling
- RE: AMBER: using antechamber ... to get prepin file Vineet Pande
- Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling
- Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski
- Re: AMBER: Unexpected stop of Sander run David A. Case
- AMBER: Connecting two molecules Hwankyu Lee
- Re: AMBER: Connecting two molecules David A. Case
- Re: AMBER: Connecting two molecules Hwankyu Lee
- Re: AMBER: crashing xleap; bugfix.44 Scott Brozell
- AMBER: hbond detailed analysis over time? pascal.baillod.epfl.ch
- AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari
- RE: AMBER: how to generate frcmod file for using prepin file.. chaiann ng
- AMBER: my frcmod file created using parmchk Vijay Manickam Achari
- Re: AMBER: my frcmod file created using parmchk Ilyas Yildirim
Tuesday, 24 May 2005
- AMBER: my prepin file in lowe-case Vijay Manickam Achari
- AMBER: Which forcefield? Simon Whitehead
- AMBER: conformational sampling of a peptide Hannes Barsch
- AMBER: amber code Juan Fernandez Carmona
- Re: AMBER: conformational sampling of a peptide Carlos Simmerling
- Re: AMBER: amber code Andreas Svrcek-Seiler
- AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke
- Re: AMBER: conformational sampling of a peptide Joseph Nachman
- AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger
- AMBER: Sander Restart Problem Garhan Attebury
- AMBER: How to fix certain bond angles Li Su
- Re: AMBER: How to fix certain bond angles Guanglei Cui
- RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' Ross Walker
- AMBER: Error: vlimit exceeded for step Hwankyu Lee
- Re: AMBER: Error: vlimit exceeded for step Carlos Simmerling
- Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee
- Re: AMBER: Error: vlimit exceeded for step Thomas E. Cheatham, III
- Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee
- Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac
- AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su
- Re: AMBER: Error: vlimit exceeded for step David Mobley
- Re: AMBER: Solute-solvent boundary in pbsa Ray Luo
- AMBER: charges difference of atom in xleap and prmtop chaiann ng
- Re: AMBER: charges difference of atom in xleap and prmtop David A. Case
- Re: AMBER: Which forcefield? David A. Case
Wednesday, 25 May 2005
- AMBER: PARMSCAN program Philippe ARNAUD
- AMBER: average structure after MD kuljeets.igib.res.in
- AMBER: quadrupole in resp riccardo nifosi
- Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek
- Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Guanglei Cui
- AMBER: error in chirality.c? Kenley Barrett
- Re: AMBER: error in chirality.c? David A. Case
- Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac
- Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac
Tuesday, 24 May 2005
- Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa Ray Luo
- Re: AMBER: Solute-solvent boundary in pbsa Ray Luo
Wednesday, 25 May 2005
- AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari
- Re: AMBER: average structure after MD kuljeets.igib.res.in
Thursday, 26 May 2005
- AMBER: distance restraints between two centers of mass JAVIER PEREZ
- Re: AMBER: distance restraints between two centers of mass Fabien Cailliez
- Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek
- AMBER: Is the MD simulation normal Shulin Zhuang
- AMBER: setting up Parallel processing mathew k varghese
- Re: AMBER: setting up Parallel processing Robert Duke
- AMBER: hbond analysis in ptaj/carnal Jana Precechtelova
- Re: AMBER: dissolving micelle structure in water.. amber7 David A. Case
- Re: AMBER: hbond analysis in ptaj/carnal Bill Ross
- Re: AMBER: dissolving micelle structure in water.. amber7 Bill Ross
- Re: AMBER: hbond analysis in ptaj/carnal Thomas E. Cheatham, III
- RE: AMBER: Is the MD simulation normal Yong Duan
- AMBER: why is snaupe.f is empty? Cordova, Luis E.
- AMBER: ptraj - hbond detailed analysis over time? pascal.baillod.epfl.ch
- Re: AMBER: Is the MD simulation normal Thomas E. Cheatham, III
- RE: AMBER: setting up Parallel processing 'Ross Walker'
- RE: AMBER: why is snaupe.f is empty? 'Ross Walker'
- Re:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac
Wednesday, 25 May 2005
- Re: AMBER: Solute-solvent boundary in pbsa Ray Luo
Thursday, 26 May 2005
- AMBER: Mol2 to prepin file conversion Andrew Box
- Re: AMBER: Mol2 to prepin file conversion David A. Case
- Re: AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari
- Re: AMBER: Is the MD simulation normal Shulin Zhuang
- RE: AMBER: Is the MD simulation normal Yong Duan
Friday, 27 May 2005
- Re: AMBER: Is the MD simulation normal Shulin Zhuang
- RE: AMBER: Is the MD simulation normal Yong Duan
- Re: AMBER: Is the MD simulation normal Bill Ross
- AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu
- AMBER: Workshop Tutorials Downtime this weekend. Ross Walker
- Re: AMBER: question about loadiing pdb file of a molecule complex Chutintorn Punwong
Saturday, 28 May 2005
- Re: AMBER: Is the MD simulation normal Shulin Zhuang
- Re: AMBER: Is the MD simulation normal Bill Ross
- Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case
Sunday, 29 May 2005
- Re: AMBER: Is the MD simulation normal Shulin Zhuang
- Re: AMBER: Is the MD simulation normal Bill Ross
- RE: AMBER: Is the MD simulation normal Yong Duan
- RE: AMBER: Is the MD simulation normal Bill Ross
- AMBER: Antechamber RESP failed for large organic molecule junwang
- AMBER: question about initial conditions for amber Ed Pate
- AMBER: density profiles in ptraj or carnal Hwankyu Lee
- AMBER: pairwise energy decomposition using MM-PBSA Xin Hu
Monday, 30 May 2005
- AMBER: Reference (?) for normal-mode analysis in nmode Cenk Andac
- Re: AMBER: question about initial conditions for amber Stefano Federico Pieraccini
- Re: AMBER: question about initial conditions for amber Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- AMBER: Force field modification problem yuann
- Re: AMBER: Is the MD simulation normal Shulin Zhuang
- Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu
- AMBER: Bond angle restraints setting files Li Su
- Re: AMBER: Antechamber RESP failed for large organic molecule David A. Case
- Re: AMBER: Force field modification problem David A. Case
- Re: AMBER: Is the MD simulation normal Bill Ross
- Re: AMBER: density profiles in ptraj or carnal Bill Ross
- Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee
- Re[2]: AMBER: Force field modification problem sychen
- Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee
- Re: AMBER: Force field modification problem David A. Case
Tuesday, 31 May 2005
- AMBER: density problem cristian obiol
- AMBER: stack terminated abnormally drugdesign
- RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang
- AMBER: if setting ntf=4, will it cause someproblem? Li Su
- Re: AMBER: if setting ntf=4, will it cause someproblem? Carlos Simmerling
- AMBER: Error on restrained MD equilibration (AMBER 7) L Jin
- Re: AMBER: Reference (?) for normal-mode analysis in nmode David A. Case
- RE: AMBER: density problem Ross Walker
- RE: AMBER: stack terminated abnormally Ross Walker
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) David A. Case
- AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) Viktor Hornak
- Re: RE: AMBER: Antechamber RESP failed for large organic molecule junwang
- AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski
- RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Ross Walker
- Re: AMBER: density profiles in ptraj or carnal Bill Ross
- Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Marcin Krol
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin
- AMBER: MM-PBSA calculation masi.nmr.mpibpc.mpg.de
- AMBER: STOP 0 masi.nmr.mpibpc.mpg.de
- RE: AMBER: Error on restrained MD equilibration (AMBER 7) Ross Walker
- RE: AMBER: STOP 0 Ross Walker
- AMBER: runtime error in sander? Dave S Walker
- AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa
- RE: AMBER: runtime error in sander? Ross Walker
- Re: AMBER: STOP 0 Bill Ross
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Ross Walker
- AMBER: Loading pdb-residue (re)numbering in leap gtg549i.mail.gatech.edu
- Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Bill Ross
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui
- Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu
- AMBER: meaningful tax for sander question Cordova, Luis E.
- RE: AMBER: meaningful tax for sander question Ross Walker
- Re: AMBER: meaningful tax for sander question David A. Case
- RE: AMBER: meaningful tax for sander question Cordova, Luis E.
- RE: AMBER: meaningful tax for sander question Ross Walker
- Re: AMBER: if setting ntf=4, will it cause someproblem? Li Su
- AMBER: double counting of potentials Stern, Julie
- RE: AMBER: double counting of potentials Ross Walker
- AMBER: Working with a nickel-organometallic compound Kara Di Giorgio
- AMBER: External Field in AMBER? junwang
- Re: AMBER: Is the MD simulation normal Bill Ross

Last message date: Wed Jun 01 2005 - 04:53:00 PDT
Archived on: Fri Nov 22 2024 - 05:53:24 PST

Amber Archive May 2005 by date