Amber Archive Apr 2005: by date

Thursday, 31 March 2005
- AMBER: GB dynamics mathew k varghese
- AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! chaiann ng
- AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj
- Re: AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! Jiri Matousek
Friday, 1 April 2005
- Re: AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj
- AMBER: scaleCharges with polarisable force fields Phineus Markwick
- AMBER: Problems with protonate on Linux Atro Tossavainen
- Re: AMBER: GB dynamics David A. Case
- Re: AMBER: scaleCharges with polarisable force fields David A. Case
- Re: AMBER: How to fix the torsion angles during energy minimization David A. Case
- Re: AMBER: Problems with protonate on Linux David A. Case
- AMBER: trajectory alignment using ptraj Wen Li
- Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III
- Re: AMBER: trajectory alignment using ptraj Wen Li
- Re: AMBER: trajectory alignment using ptraj Wen Li
- Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III
- Re: AMBER: trajectory alignment using ptraj Wen Li
- Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III
- Re: AMBER: trajectory alignment using ptraj Wen Li
- AMBER: reference of Targeted MD xhu1.memphis.edu
- Re: AMBER: GB dynamics Bill Ross
- AMBER: oxo-heme Peter Gannett
- Re: AMBER: trajectory alignment using ptraj Wen Li
Saturday, 2 April 2005
- Re: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Robert Duke
Sunday, 3 April 2005
- AMBER: problem with input files when using ff02EP + pol3 Phineus Markwick
- Re: AMBER: All the tests passed except prmtop and prepin... shuli
- Re: AMBER: problem with input files when using ff02EP + pol3 David A. Case
Saturday, 2 April 2005
- AMBER: helical parameters obtaining Kateryna Miroshnychenko
Monday, 4 April 2005
- AMBER: surface area John
- AMBER: Sander minimization & dynamic question chaiann ng
- Re: AMBER: Sander minimization & dynamic question Carlos Simmerling
- Re: AMBER: Sander minimization & dynamic question Andreas Svrcek-Seiler
- AMBER: ff02EP + pol3 (2) Phineus Markwick
- AMBER: emilia wu
- AMBER: single-stranded poly(rC) simulation Kateryna Miroshnychenko
- Re: AMBER: All the tests passed except prmtop and prepin... shuli
- AMBER: force constant Unit used in TMD xhu1.memphis.edu
- Re: AMBER: surface area Tim Meyer
- Re: AMBER: force constant Unit used in TMD Carlos Simmerling
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu
- Re: AMBER: force constant Unit used in TMD Viktor Hornak
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu
- Re: AMBER: force constant Unit used in TMD Asim Okur
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu
- AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wu Yingliang
- Re: AMBER: David A. Case
- Re: AMBER: ff02EP + pol3 (2) David A. Case
- Re: AMBER: single-stranded poly(rC) simulation David A. Case
- Re: Re: AMBER: emilia wu
Tuesday, 5 April 2005
- RE: Re: AMBER: Wells, David H
Monday, 4 April 2005
- AMBER: AMBER 8.0 problems with impose (tleap) on linux Guillermo Mulliert Carlín
Tuesday, 5 April 2005
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wei Zhang
- AMBER: how to make a nonsymmetric box around the solute Lina Nilsson
- AMBER: doble C and N terminal Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- Re: RE: Re: AMBER: emilia wu
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters David A. Case
- AMBER: GB with Langevin dynamics problem Peter Varnai
- Re: AMBER: GB with Langevin dynamics problem Carlos Simmerling
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Bill Ross
- Re: AMBER: GB with Langevin dynamics problem Andreas Svrcek-Seiler
- AMBER: Re:Re:single-stranded poly(rC) simulation Kateryna Miroshnychenko
- Re: AMBER: Re:Re:single-stranded poly(rC) simulation Thomas E. Cheatham, III
- Re: AMBER: doble C and N terminal David A. Case
- AMBER: Protein with structural ions Kara Wald
- Re: AMBER: Protein with structural ions Oliver Hucke
- Re: Re: AMBER: Protein with structural ions Yong Xu
- Re: AMBER: AMBER 8.0 problems with impose (tleap) on linux David A. Case
- Re: AMBER: Problems with protonate on Linux Atro Tossavainen
Wednesday, 6 April 2005
- AMBER: FW: Amber installation Eric Mullins
- Re: AMBER: Problems with protonate on Linux David A. Case
- AMBER: a bimolecular reaction Eric Hu
- Re: AMBER: FW: Amber installation David A. Case
- AMBER: About Gaussian Key Words Katagiri Daisuke
- AMBER: value of SALTCON mathew k varghese
- AMBER: combine mdcrd using ptraj xueping
- Re: AMBER: combine mdcrd using ptraj Asim Okur
- Re: AMBER: combine mdcrd using ptraj xueping
Thursday, 7 April 2005
- Re: AMBER: combine mdcrd using ptraj Lihua Wang
- RE: AMBER: About Gaussian Key Words Vineet Pande
- Re: AMBER: combine mdcrd using ptraj xueping
- AMBER: RADIOPT=1 Fabien Cailliez
- Re: AMBER: Protein with structural ions Tim Meyer
- AMBER: RE: system comparison for amber Ross Walker
- Re: AMBER: RE: system comparison for amber Carlos Simmerling
- AMBER: leap single precision Guanglei Cui
- Re: AMBER: value of SALTCON David A. Case
- Re: AMBER: About Gaussian Key Words (fwd) duan_list.albert.genomecenter.ucdavis.edu
- AMBER: makeDIST_RST ERROR Y. Xu
- AMBER: problems with "protonate" Kenley Barrett
- AMBER: how to get the parameters for modified amino acid residue? ying xiong
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- Re: Re: AMBER: Protein with structural ions Y. Xu
Friday, 8 April 2005
- Re: AMBER: leap single precision Scott Brozell
- AMBER: linit in mm-pbsa Fabien Cailliez
- Re: AMBER: linit in mm-pbsa Arantxa Sanz
- AMBER: Disulfide bond michael chen
- Re: AMBER: Disulfide bond Carlos Simmerling
- Re: AMBER: makeDIST_RST ERROR David A. Case
- Re: AMBER: Protein with structural ions David A. Case
- Re: AMBER: problems with "protonate" David A. Case
- Re: AMBER: how to get the parameters for modified amino acid residue? FyD
- Re: AMBER: Disulfide bond FyD
- Re: AMBER: leap single precision Guanglei Cui
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- AMBER: GB with Langevin dynamics problem 2 Peter Varnai
Thursday, 7 April 2005
- Re: AMBER: linit in mm-pbsa Ray Luo
Friday, 8 April 2005
- AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released David A. Case
- Re: AMBER: Protein with structural ions David A. Case
- Re: AMBER: GB with Langevin dynamics problem 2 David A. Case
- Re: AMBER: GB with Langevin dynamics problem 2 Andreas Svrcek-Seiler
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- Re: AMBER: GB with Langevin dynamics problem 2 Carlos Simmerling
- AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu
- Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak
- Re: AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu
- Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak
- Re: AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu
Saturday, 9 April 2005
- AMBER: average structure-ptraj xueping
- Re: AMBER: average structure-ptraj Carlos Simmerling
- Re: AMBER: leap single precision David A. Case
- Re: AMBER: GB with Langevin dynamics problem 2 David A. Case
- Re: AMBER: how to get the parameters for modified amino acid residue? David A. Case
Sunday, 10 April 2005
- Re: AMBER: average structure-ptraj xueping
- Re: AMBER: average structure-ptraj xueping
- AMBER: A question on connecting residues in xleap Hwankyu Lee
- RE: AMBER: A question on connecting residues in xleap Ross Walker
- Re: AMBER: A question on connecting residues in xleap Hwankyu Lee
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- Re: AMBER: Protein with structural ions David A. Case
- AMBER: Warnings as a file Pavan Ghatty
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- RE: AMBER: A question on connecting residues in xleap Ross Walker
- Re: AMBER: Warnings as a file scopio
Monday, 11 April 2005
- AMBER: Two question about dielectric constant 烨武
- AMBER: rst file problems mathew k varghese
- AMBER:FAD can't be minimized. zhli_2000.126.com
- Re: AMBER: Two question about dielectric constant Carlos Simmerling
- Re: AMBER: rst file problems Carlos Simmerling
- Re: AMBER: A question on connecting residues in xleap Hwankyu Lee
- Re: AMBER: Protein with structural ions David A. Case
- Re: AMBER:FAD can't be minimized. David A. Case
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- Re: AMBER: Two question about dielectric constant Lihua Wang
- RE: AMBER: A question on connecting residues in xleap Ross Walker
- AMBER: GB with Langevin dynamics - solution Peter Varnai
- AMBER: MM_PBSA error Xin Hu
- AMBER: breaking symmetry in minimization Stern, Julie
- Re: AMBER: MM_PBSA error Holger Gohlke
- Re: AMBER: problems with "protonate" Kenley Barrett
- Re: AMBER: breaking symmetry in minimization Bill Ross
- Re: AMBER: MM_PBSA error Xin Hu
- Re: AMBER: problems with "protonate" Bill Ross
- Re: AMBER: About Gaussian Key Words (fwd) Daisuke Katagiri
- AMBER: Fail to load the trajectory file. Jinzhi Lei
- Re: AMBER: Fail to load the trajectory file. Bill Ross
- Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei
- Re: Re: AMBER: Fail to load the trajectory file. Bill Ross
- Re: AMBER: problems with "protonate" David A. Case
- Re: AMBER: Fail to load the trajectory file. Thomas E. Cheatham, III
- Re: AMBER: rst file problems mathew k varghese
- Re: Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei
- Re: AMBER: MM_PBSA error Holger Gohlke
Tuesday, 12 April 2005
- Re: AMBER: rst file problems Carlos Simmerling
- AMBER: peptide side chain modification with LEAP Hannes Barsch
- AMBER: rdparm Tim Meyer
Thursday, 28 April 2005
- AMBER: implementing AMBER in NAMD Lina Nilsson
Tuesday, 12 April 2005
- AMBER: nscm Ilyas Yildirim
- AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs Ye MEI
- RE: AMBER: peptide side chain modification with LEAP Ross Walker
- RE: AMBER: Protein with structural ions Kara Di Giorgio
- Re: AMBER: nscm David A. Case
- AMBER: MM_PBSA problem Xin Hu
- Re: AMBER: Protein with structural ions Carlos Simmerling
- Re: AMBER: problems with "protonate" Bill Ross
- Re: AMBER: MM_PBSA problem Nelson Fonseca
- Re: AMBER: peptide side chain modification with LEAP Bill Ross
- AMBER: Silicon related parameters luckyang.gmail.com
- Re: AMBER: nscm duan_list.albert.genomecenter.ucdavis.edu
- Re: AMBER: MM_PBSA problem Fabien Cailliez
- AMBER: ibelly not working Stern, Julie
- Re: AMBER: GB with Langevin dynamics - solution David A. Case
- Re: AMBER: Protein with structural ions Kara Di Giorgio
- Re: AMBER: a bimolecular reaction David A. Case
- AMBER: vdw or center box dimensions, periodicity, and the jagged edge Stern, Julie
- Re: AMBER: GB with Langevin dynamics - solution Peter Varnai
- AMBER: Protein With Structural Ions Kara Di Giorgio
- AMBER: No. of Snapshots in MM/GB/SA Sagar D Khare
- Re: AMBER: a bimolecular reaction duan_list.albert.genomecenter.ucdavis.edu
- Re: AMBER: ibelly not working Bill Ross
- Re: AMBER: No. of Snapshots in MM/GB/SA Guangyu Sun
- Re: AMBER: MM_PBSA problem Xin Hu
- Re: AMBER: MM_PBSA problem Xin Hu
- Re: AMBER: rst file problems Furse, Kristina Elisabet
- Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei
- Re: AMBER: MM_PBSA problem Nelson Fonseca
- Re: AMBER: a bimolecular reaction Eric Hu
- AMBER: ptraj, hbond problem Joseph W.Toporowski
- Re: AMBER: a bimolecular reaction Yong Duan
- AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu
- Re: AMBER: MM-PBSA in protein-Zn-ligand system Kara Di Giorgio
- Re: Re: AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu
Wednesday, 13 April 2005
- AMBER: freee energy calculation without minimised structure S.Sundar Raman
- RE: AMBER: freee energy calculation without minimised structure Yong Duan
- AMBER: Watson-Crick restraints YoungJin Cho
- Re: AMBER: MM_PBSA problem David A. Case
- Re: AMBER: MM_PBSA problem Xin Hu
- Re: AMBER: MM_PBSA problem Xin Hu
- Re: AMBER: a bimolecular reaction Eric Hu
- AMBER: what is wrong with my amber job or installation? Amber
- RE: AMBER: a bimolecular reaction Yong Duan
- RE: AMBER: what is wrong with my amber job or installation? Ross Walker
- AMBER: Formatting a restraint file Kara Wald
- Re: AMBER: Formatting a restraint file Carlos Simmerling
- AMBER: xleap, lib file question opitz.che.udel.edu
- RE: AMBER: xleap, lib file question Ross Walker
- AMBER: About NAB Ilyas Yildirim
- Re: AMBER: Formatting a restraint file Kara Di Giorgio
- Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet
- Re: AMBER: About NAB David A. Case
- Re: AMBER: Watson-Crick restraints David A. Case
- AMBER: solvate water box bybaker.itsa.ucsf.edu
Thursday, 14 April 2005
- AMBER: Antechamber -reorders atom sequence Austin B. Yongye
- AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd Fabien Cailliez
- Re: AMBER: Antechamber -reorders atom sequence David A. Case
- Re: AMBER: Formatting a restraint file Kara Di Giorgio
- Re: AMBER: Formatting a restraint file Carlos Simmerling
- Re: AMBER: Formatting a restraint file Kara Di Giorgio
- Re: AMBER: Formatting a restraint file David A. Case
- Re: AMBER: solvate water box David A. Case
- Re: AMBER: About NAB Andreas Svrcek-Seiler
- AMBER: periodic boundaries and repeating structure Stern, Julie
- AMBER: antechamber for cyano group nlxc
- Re: AMBER: periodic boundaries and repeating structure Bill Ross
- Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet
- AMBER: Sander/Mpich2 error with mpd_singinit Joe Nolan
- Re: AMBER: Sander/Mpich2 error with mpd_singinit David LeBard
- AMBER: small target pressure in constant pressure dynamics Eric Hu
- Re: AMBER: small target pressure in constant pressure dynamics Thomas E. Cheatham, III
- Re: AMBER: small target pressure in constant pressure dynamics Eric Hu
- AMBER: big fluctuation in MM-PBSA/GA Eric Hu
- RE: AMBER: small target pressure in constant pressure dynamics Yong Duan
- Re: AMBER: big fluctuation in MM-PBSA/GA David A. Case
- Re: AMBER: big fluctuation in MM-PBSA/GA Thomas E. Cheatham, III
- Re: AMBER: About NAB Ilyas Yildirim
- Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu
- Re: AMBER: About NAB David A. Case
- AMBER: parameters in gaff.dat Lihua Wang
- Re: AMBER: parameters in gaff.dat David A. Case
Friday, 15 April 2005
- AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 Ananda Rama Krishnan Selvaraj
- Re: AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 David A. Case
- Re: AMBER: Antechamber -reorders atom sequence FyD
- AMBER: carnal problem Ed Pate
- AMBER: SollvateBox with ethanol Huaer XC
- AMBER: gaff atom types Claudio Morgado
- Re: AMBER: carnal problem Bill Ross
- Re: AMBER: SollvateBox with ethanol Guanglei Cui
- Re: AMBER: carnal problem Ed Pate
- Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu
- Re: AMBER: carnal problem Bill Ross
- Re: AMBER: parameters in gaff.dat Lihua Wang
- Re: AMBER: carnal problem Ed Pate
- Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu
- Re: AMBER: carnal problem Bill Ross
- Re: AMBER: carnal problem Ed Pate
- Re: AMBER: Antechamber -reorders atom sequence Austin B. Yongye
- Re: AMBER: parameters in gaff.dat David A. Case
- Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu
- AMBER: RESP charges with Gaussian03 and Amber Delon Wilson
- AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Scott E. Boesch
- Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu
- Re: AMBER: RESP charges with Gaussian03 and Amber FyD
Saturday, 16 April 2005
- Re: AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Carlos Simmerling
- AMBER: amber8/antechamber installation problem Xin Hu
Sunday, 17 April 2005
- Re: AMBER: amber8/antechamber installation problem David A. Case
Monday, 18 April 2005
- AMBER: about equilibration dynamics S.Sundar Raman
- AMBER: ATTN REVISION 吕海婷
- AMBER: dielectric constant Nina Fischer
- AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000.126.com
- AMBER: Rep Exch. suggestion Brent Krueger
- AMBER: RESP charges with Gaussian03 and Amber Delon Wilson
- Re: AMBER: Rep Exch. suggestion Guanglei Cui
- Re: AMBER: ATTN REVISION David A. Case
- Re: AMBER: dielectric constant David A. Case
- AMBER: langevin, GB and simulated annealing? pascal.baillod.epfl.ch
- Re: AMBER: langevin, GB and simulated annealing? Adrian E. Roitberg
- Re: AMBER: langevin, GB and simulated annealing? Carlos Simmerling
- RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker
- AMBER: Dual Xeon EM64T Intel Fortran Compiler Shekter, Lee
- AMBER: local dielectric constant Xavier Deupi
- AMBER: Re: Re: AMBER: ATTN REVISION 吕海婷
- AMBER: RESP charges - multiple conformations Austin B. Yongye
- Re: AMBER: Re: Re: AMBER: ATTN REVISION David A. Case
- AMBER: New parametrs Maciej
- Re: AMBER: RESP charges - multiple conformations FyD
Tuesday, 19 April 2005
- AMBER: GAFF: H type on carbon bearing a cyano group Claudio Morgado
- AMBER: Gibbs compilation problem Maciej
- AMBER: solvent accessible surface area John
- AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) Soo Joo
- RE: AMBER: solvent accessible surface area John
- Re: AMBER: RESP charges - multiple conformations Austin B. Yongye
- AMBER: The effect appling paches Yagi Toru
- Re: AMBER: amber8/antechamber installation problem Xin Hu
- AMBER: a problem with mm_pbsa Ye MEI
- Re: AMBER: RESP charges - multiple conformations FyD
- Re: AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) David A. Case
- Re: AMBER: solvent accessible surface area David A. Case
- Re: AMBER: a problem with mm_pbsa Xin Hu
- Re: AMBER: Gibbs compilation problem David A. Case
- AMBER: Amber compilation problem David A. Case
- Re: AMBER: The effect appling paches David A. Case
Monday, 18 April 2005
- Re: AMBER: solvent accessible surface area Ray Luo
Tuesday, 19 April 2005
- RE: AMBER: Re: Re: AMBER: ATTN REVISION Junmei Wang
- AMBER: Non-Bonded Cutoff vs PME Vineet Pande
- RE: AMBER: gaff atom types Junmei Wang
- RE: AMBER: antechamber for cyano group Junmei Wang
- AMBER: langevin, GB and simulated annealing - 2 pascal.baillod.epfl.ch
- Re: AMBER: Non-Bonded Cutoff vs PME David A. Case
- Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III
- Re: AMBER: langevin, GB and simulated annealing - 2 David A. Case
- Re: AMBER: ATTN REVISION lv haiting
- AMBER: Yong Xu
Wednesday, 20 April 2005
- Re: AMBER: langevin, GB and simulated annealing - 2 Andreas Svrcek-Seiler
- AMBER: tleap and water thenmalar
- Re: AMBER: Non-Bonded Cutoff vs PME Vineet Pande
- AMBER: GB and mm_pbsa.pl Nelson Fonseca
- AMBER: interaction between residues Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- Re: AMBER: tleap and water Thomas E. Cheatham, III
- RE: AMBER: ATTN REVISION Junmei Wang
- AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000
- Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III
- Re: AMBER: GB and mm_pbsa.pl David A. Case
- Large files to AMBER, RE: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Yong Duan
- Re: AMBER: GB and mm_pbsa.pl Nelson Fonseca
- AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker
- Re: AMBER: GB and mm_pbsa.pl David A. Case
- AMBER: ibelly not working Stern, Julie
- AMBER: intramolecular nonbonded interactions in AMBER force field John Silvio Vieceli
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling
- RE: AMBER: intramolecular nonbonded interactions in AMBER force field Ross Walker
Thursday, 21 April 2005
- AMBER: about run time in GB and PB Yong Xu
- Re: AMBER: about run time in GB and PB Phineus Markwick
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande
- Re: Re: AMBER: about run time in GB and PB Yong Xu
- RE: AMBER: about run time in GB and PB Yong Duan
- Re: AMBER: about run time in GB and PB Phineus Markwick
- AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang
- AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang
- AMBER: Nose-Hoover thermostat Sam Moors
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling
- Re: RE: AMBER: about run time in GB and PB Yong Xu
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande
- Re: AMBER: about run time in GB and PB Phineus Markwick
- AMBER: re: about run time in GB and PB Phineus Markwick
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Thomas E. Cheatham, III
- AMBER: Moil-view and Quicktime movie Steve Seibold
- Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA David A. Case
- Re: AMBER: ibelly not working David A. Case
- Re: AMBER: Nose-Hoover thermostat David A. Case
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field David A. Case
- AMBER: Sander bomb - atom out of bounds Joe Nolan
- RE: AMBER: Sander bomb - atom out of bounds Ross Walker
- AMBER: problem with belly calculation restart Ed Pate
- Re: Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang
Friday, 22 April 2005
- Re: AMBER: about run time in GB and PB Yong Xu
- AMBER: mean structure calculation mmv
- AMBER: PB Bomb in circle(): Stored surface points over limit Nelson Fonseca
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Guanglei Cui
- AMBER: writing MASKs Sagar D Khare
- RE: AMBER: writing MASKs Vineet Pande
- AMBER: strange VDWAALS and EEL energies calculated by pbsa Fabien Cailliez
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Carlos Simmerling
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa David A. Case
- AMBER: Induced dipole in AMBER8 Cenk Andac
Thursday, 21 April 2005
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Ray Luo
Friday, 22 April 2005
- AMBER: Amber Installation pmullins
- Re: AMBER: Amber Installation David A. Case
- AMBER: Calculate vdw parameters for alkaline earth metal ions Kenley Barrett
- Re: AMBER: Calculate vdw parameters for alkaline earth metal ions Bill Ross
- Re: AMBER: Induced dipole in AMBER8 David A. Case
Saturday, 23 April 2005
- AMBER: Problem when converting AMBER trajectories to CHARMM format Chen Hu
- Re: AMBER: Problem when converting AMBER trajectories to CHARMM format Thomas E. Cheatham, III
Sunday, 24 April 2005
- AMBER: serial and parallel Aknb
- AMBER: coordinates translation Ye MEI
- RE: AMBER: serial and parallel Ross Walker
- Re: AMBER: coordinates translation Jack Lei
- AMBER: AMBER Test Error tpatko
- AMBER: Re: AMBER Test Error (Follow Up) tpatko
Monday, 25 April 2005
- AMBER: How to deal with the Non-standard residue lv haiting
- AMBER: the restarting error zhli_2000.126.com
- Re: AMBER: the restarting error Guanglei Cui
- AMBER: Free energy pertubation (thermodynamic intergration) mrbroad.ilstu.edu
- Re: AMBER: Free energy pertubation (thermodynamic intergration) Sichun Yang
- AMBER: radius parameter for F atom Ye MEI
- Re: AMBER: Induced dipole in AMBER8 Cenk Andac
- Re: AMBER: How to deal with the Non-standard residue FyD
- Re: AMBER: Free energy pertubation (thermodynamic intergration) Ilyas Yildirim
- AMBER: mm_pbsa problem Husni Fattayer
- Re: AMBER: radius parameter for F atom scopio
- AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim
Tuesday, 26 April 2005
- AMBER: Free energy Maciej
- AMBER: Re:Gibbs compilation problem Maciej
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Thomas Steinbrecher
- AMBER: langevin, GB and simulated annealing - 3 pascal.baillod.epfl.ch
- AMBER: AMBER Test Anthony Cruz
- Re: AMBER: the restarting error zhli_2000.126.com
- Re: Re: AMBER: radius parameter for F atom Ye MEI
- Re: AMBER: langevin, GB and simulated annealing - 3 David Case
- Re: AMBER: AMBER Test David Case
- AMBER: langevin, GB and simulated annealing - 4 pascal.baillod.epfl.ch
- Re: AMBER: langevin, GB and simulated annealing - 4 David Case
- AMBER: How to restart MM_PBSA or doing the statistics only Xin Hu
- AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee
- AMBER: error in pbsa calculation mingche Pan
- Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke
- Re: AMBER: error in pbsa calculation Ray Luo
- Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee
- AMBER: Solvate with mixture of ethanol and water(Newbie question) Huaer XC
Wednesday, 27 April 2005
- AMBER: capping amit.mbu.iisc.ernet.in
- Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke
- Re: AMBER: mm_pbsa problem Husni Fattayer
- Re: AMBER: error in pbsa calculation mingche Pan
- Re: AMBER: capping FyD
- Re: AMBER: capping John Mongan
- Re: AMBER: error in pbsa calculation Ray Luo
- Re: AMBER: capping Bill Ross
- AMBER: emilia wu
- Re: AMBER: Pyranose pucker parameters Thomas E. Cheatham, III
- AMBER: mixture solvent model Huaer XC
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim
- Re: AMBER: capping amit.mbu.iisc.ernet.in
- Re: AMBER: capping Bill Ross
Thursday, 28 April 2005
- AMBER: distance restraints mathew k varghese
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Petr Kulhanek
- AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error Maciej
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth David Case
- Re: AMBER: capping FyD
- AMBER: false bond created upon coordinate retrieval Stern, Julie
- Re: AMBER: false bond created upon coordinate retrieval Bill Ross
- AMBER: segmentation problem aanzellotti.mail2.vcu.edu
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim
- AMBER: atommask error Sergio E. Wong
Friday, 29 April 2005
- Re: AMBER: atommask error hornak.csb.sunysb.edu
- Re: AMBER: atommask error Sergio E. Wong
- AMBER: Re: R.E.D. question FyD
- AMBER: Odd Antechamber Behavior Kara Di Giorgio
Saturday, 30 April 2005
- AMBER: ipol=1 & use_pme= ?? Cenk Andac

Last message date: Sat Apr 30 2005 - 14:53:00 PDT
Archived on: Mon Nov 03 2025 - 05:53:28 PST

Amber Archive Apr 2005 by date