Amber Archive Aug 2005: by date

Sunday, 31 July 2005
- AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler Soo
Monday, 1 August 2005
- AMBER: coordinated water molecules deleted when addions Ye Mei
- Re: AMBER: coordinated water molecules deleted when addions David A. Case
- Re: AMBER: Modeling of a radical L Jin
- Re: AMBER: questions about MG ions JIANING WANG
- AMBER: ptraj help, how to enable disabled ptraj routine? opitz.che.udel.edu
- RE: AMBER: coordinated water molecules deleted when addions Ross Walker
- Re: AMBER: ptraj help, how to enable disabled ptraj routine? Thomas E. Cheatham, III
- AMBER: antechamber problem using RESP luckyang.gmail.com
- AMBER: AMBER8 limitation of memory in QM/MM calculation nadtanet nunthaboot
- RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker
- RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker
- AMBER: memory_mm_pbsa Wei Chen
- RE: AMBER: memory_mm_pbsa Ross Walker
- RE: AMBER: memory_mm_pbsa Wei Chen
Tuesday, 2 August 2005
- AMBER: strange minimalization output blakrose.gazeta.pl
- RE: AMBER: strange minimalization output Ross Walker
- AMBER: Leap set head/tail question Kara Di Giorgio
- RE: AMBER: Leap set head/tail question Rhoad, Jonathan S.
- RE: AMBER: Leap set head/tail question Ross Walker
- AMBER: Boron and Amber Kara Di Giorgio
- AMBER: bond breaking/ energetic ion vannajan.chiangmai.ac.th
- RE: AMBER: bond breaking/ energetic ion Ross Walker
Wednesday, 3 August 2005
- AMBER: power supply crash==>boot problems Kristof Stevens
- AMBER: bond parameters Gustavo Pierdominici Sottile
- Re: AMBER: bond parameters ivan.mmb.pcb.ub.es
- AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA
- RE: AMBER: bond parameters Ross Walker
- Re: AMBER: power supply crash==>boot problems David LeBard
- AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run David.Maxwell.di.mdacc.tmc.edu
- Re: AMBER: bond breaking/ energetic ion Bill Ross
- AMBER: Error with antechamber Joseph Fernandez
- RE: AMBER: Leap set head/tail question Ilyas Yildirim
- RE: AMBER: installing amber7 on 64bit cluster Zhang Bing
- RE: AMBER: installing amber7 on 64bit cluster Ross Walker
Thursday, 4 August 2005
- AMBER: a trivial question Linchen Gong
- Re: AMBER: a trivial question Carlos Simmerling
- Re: AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run Roberto Gomperts
- RE: AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA
- AMBER: nmode Wei Chen
- AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters Grzegorz Jezierski
- RE: AMBER: nmode Yong Duan
- RE: AMBER: nmode Wei Chen
- AMBER: about salt bridges xueping
Friday, 5 August 2005
- AMBER: Conformational energy (QM) for parameterization yuann
- Re: AMBER: about salt bridges Carlos Simmerling
- Re: AMBER: Error with antechamber David A. Case
- RE: Re: AMBER: a trivial question Linchen Gong
- RE: Re: AMBER: a trivial question David LeBard
- AMBER: leap question Kara Di Giorgio
- AMBER: NMR refinement Lei Jia
- Re: AMBER: leap question David A. Case
- Re: AMBER: leap question Kara Di Giorgio
- RE: RE: Re: AMBER: a trivial question Linchen Gong
- AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Hwankyu Lee
Saturday, 6 August 2005
- Re: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) David A. Case
- Re: AMBER: leap question David A. Case
- RE: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Ross Walker
- Re: AMBER: leap question Kara Di Giorgio
Sunday, 7 August 2005
- AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin
- Re: AMBER: is calculated B-factors always smaller than experimental ones? Carlos Simmerling
- AMBER: How to calculate hydrogen bond involved with water molecules quickly? haixiao jin
- Re: AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin
Monday, 8 August 2005
- AMBER: Zymeworks job posting John Vieceli
- AMBER: RE: is calculated B-factors always smaller than experimental ones? Yong Duan
- Re: AMBER: RE: is calculated B-factors always smaller than experimental ones? haixiao jin
- AMBER: Tutorial question and some more... blakrose.gazeta.pl
Tuesday, 9 August 2005
- Re: AMBER: Tutorial question and some more... Bill Ross
- RE: AMBER: Tutorial question and some more... Ross Walker
- Re: AMBER: Tutorial question and some more... blakrose.gazeta.pl
Wednesday, 10 August 2005
- Re: AMBER: Tutorial question and some more... Yam
- AMBER: The “crystallographic” waters should be retained or deleted? haixiao jin
- AMBER: Creating protonated cytidine residue Peter Cornish
- AMBER: replica exchange Anthony Cruz
- Re: AMBER: comparing md trajectories Austin B. Yongye
- AMBER: ptraj command inputs opitz.che.udel.edu
- Re: AMBER: ptraj command inputs Thomas E. Cheatham, III
- AMBER: group-based cutoff John Vieceli
- RE: AMBER: group-based cutoff Ross Walker
- Re: AMBER: group-based cutoff Thomas E. Cheatham, III
Thursday, 11 August 2005
- AMBER: solvent problem blakrose.gazeta.pl
- AMBER: Atom type problem nag raj
- Re: AMBER: Atom type problem Ilyas Yildirim
- Re: AMBER: Atom type problem Ilyas Yildirim
Friday, 12 August 2005
- AMBER: molsurf: problem with calculate surface area Magne Olufsen
Sunday, 14 August 2005
- AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu
Monday, 15 August 2005
- AMBER: wtmol and resp Guanglei Cui
Saturday, 13 August 2005
- Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo
Monday, 15 August 2005
- AMBER: difference of energy in sander and nmode in amber 7 sebnem
Tuesday, 16 August 2005
- AMBER: AMBER on g5 10.4 w/g95 or gfortran Rachel Burdge
- Re: AMBER: AMBER on g5 10.4 w/g95 or gfortran justin litchfield
- AMBER: Format of atom specifiication after FIND Joseph Nachman
- Re: AMBER: How is the origin of the grid defined?(PBSA question) Suxin Zheng
- Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo
- AMBER: min problem Gustavo Pierdominici Sottile
- AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim
Wednesday, 17 August 2005
- AMBER: QM/MM jojartb.pharm.u-szeged.hu
- Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem
- Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case
- Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem
- AMBER: glycan Wei Chen
- Re: AMBER: glycan kkirschn.hamilton.edu
- AMBER: residence time of electrons/holes in DNA ioana.pegasus.arc.nasa.gov
- AMBER: Energy Comparisons Kara Di Giorgio
- Re: AMBER: Energy Comparisons Wei Chen
- Re: AMBER: glycan Wei Chen
- AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Angela Liu
- Re: AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Bill Ross
- Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 S. Teletchéa
- Re: AMBER: residence time of electrons/holes in DNA David LeBard
- Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim
- AMBER: ew_bspline.h error khn _
Thursday, 18 August 2005
- Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case
- AMBER: mm_pbsa amit.mbu.iisc.ernet.in
- Re: AMBER: mm_pbsa Ray Luo
- AMBER: parm99.dat non-bonded parameters Angela Liu
- AMBER: parallel amber8 with mpi through qsnet Ye Mei
- AMBER: How to construct a lipid bilayer nag raj
Friday, 19 August 2005
- AMBER: ptraj correlation facility Simon Whitehead
- AMBER: amber8installation cbala.igib.res.in
- Re: AMBER: amber8installation Carlos Simmerling
- Re: AMBER: amber8installation cbala.igib.res.in
- Re: AMBER: ew_bspline.h error Michael Crowley
- AMBER: shake Gustavo Pierdominici Sottile
- Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes
- Re: AMBER: shake Carlos Simmerling
- Re: AMBER: parm99.dat non-bonded parameters Angela Liu
- Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes
- RE: AMBER: QM/MM Ross Walker
- RE: AMBER: ew_bspline.h error Ross Walker
- RE: AMBER: parallel amber8 with mpi through qsnet Ross Walker
- RE: AMBER: min problem Ross Walker
- AMBER: structures extracted from mmpbsa Lwin, ThuZar
Saturday, 20 August 2005
- Re: AMBER: mm_pbsa amit.mbu.iisc.ernet.in
- AMBER: minimization stuck problem blakrose.gazeta.pl
- Re: AMBER: minimization stuck problem Carlos Simmerling
- AMBER: minimization stuck problem blakrose.gazeta.pl
- RE: AMBER: minimization stuck problem Yong Duan
- RE: AMBER: minimization stuck problem Ross Walker
- Re: AMBER: minimization stuck problem blakrose.gazeta.pl
Sunday, 21 August 2005
- Re: AMBER: mm_pbsa Ray Luo
- RE: AMBER: minimization stuck problem Ross Walker
- Re: AMBER: minimization stuck problem Adrian Roitberg
Monday, 22 August 2005
- AMBER: AMBER topology file format santanu chatterjee
- AMBER: Restraints kanon gemini
- Re: AMBER: Restraints Carlos Simmerling
- AMBER: minimization stuck problem blakrose.gazeta.pl
Tuesday, 23 August 2005
- Re: AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu
- RE: AMBER: minimization stuck problem Ross Walker
Monday, 22 August 2005
- Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo
Tuesday, 23 August 2005
- AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Li Su
- RE: AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Ross Walker
Wednesday, 24 August 2005
- AMBER: mm_pbsa energy decomposition error amit.mbu.iisc.ernet.in
- Re: AMBER: mm_pbsa energy decomposition error David A. Case
- AMBER: essential dynamics Anthony Cruz
- AMBER: Replica exchange Anthony Cruz
- Re: AMBER: essential dynamics John Mongan
- AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Li Su
- RE: AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Ross Walker
- AMBER: ptraj efficiency justin litchfield
- RE: AMBER: ptraj efficiency Ross Walker
- AMBER: RED II and Gaussian Raviprasad Aduri
Thursday, 25 August 2005
- Re: AMBER: mm_pbsa energy decomposition error amit.mbu.iisc.ernet.in
- AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" Whitney Allen
- AMBER: PLease remove my post rpaduri.chem.wayne.edu
- AMBER: Add constraints over time Andrew Box
Friday, 26 August 2005
- AMBER: minimization blakrose.gazeta.pl
- AMBER: replica exchange Anthony Cruz
- RE: AMBER: ew_bspline.h error Ross Walker
- RE: AMBER: minimization Ross Walker
- Re: AMBER: replica exchange Carlos Simmerling
- AMBER: compilation problem (Mac OS X.4) Mark H. Schofield
- Re: AMBER: replica exchange Anthony Cruz
- RE: AMBER: Add constraints over time Ross Walker
Saturday, 27 August 2005
- Re: AMBER: RED II and Gaussian FyD
- AMBER: NRESPA Sergio E. Wong
- Re: AMBER: RED II and Gaussian rpaduri.chem.wayne.edu
Sunday, 28 August 2005
- Re: AMBER: Replica exchange Carlos Simmerling
- AMBER: can I setup a simulation with restrain the COM of a group to a reference structure? bzlu.ucsd.edu
Monday, 29 August 2005
- AMBER: Temperature equilibration Anthony Cruz
- Re: AMBER: Replica exchange Anthony Cruz
- RE: AMBER: Temperature equilibration Ross Walker
- Re: AMBER: Temperature equilibration Anthony Cruz
- AMBER: params for cofactors Michael Dolan
- RE: AMBER: params for cofactors Ross Walker
- Re: AMBER: params for cofactors Michael Dolan
- AMBER: anwar.cdfd.org.in
- AMBER: floating point exception anwar.cdfd.org.in
Tuesday, 30 August 2005
- AMBER: in vacuo? Yam
- AMBER: nmode minimization and normal mode calculation Bing Xiong
- AMBER: Temperature regulation Monica Civera
- Re: AMBER: nmode minimization and normal mode calculation David A. Case
- AMBER: Lennard-Jones coeff... Pavan G
- Re: AMBER: Temperature regulation David A. Case
- AMBER: Re:Antechamber Raviprasad Aduri
- AMBER: floating point exception anwar.cdfd.org.in
Wednesday, 31 August 2005
- Re: AMBER: in vacuo? blakrose.gazeta.pl
- AMBER: MM-PBSA and 1-4 nonbonded interactions Nelson Fonseca
- AMBER: disulfide bonds by "bond" or "edit -> draw" ? Benjamin Juhl
- RE: AMBER: floating point exception Ross Walker
- RE: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Ross Walker
- Re: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Bill Ross
- AMBER: Interpreting Amber8 Benchmark Results Nikhil Kelshikar \(nkelshik\)
- AMBER: Why are some of the Lennard-Jones coeffs 0 ? Pavan G
- Re: AMBER: Why are some of the Lennard-Jones coeffs 0 ? Thomas E. Cheatham, III
- RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker
- Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke
- RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross
- RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker
- RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross
- Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke
- AMBER: addles question Kevin Murphy

Last message date: Wed Aug 31 2005 - 22:53:02 PDT
Archived on: Sun Nov 24 2024 - 05:53:39 PST

Amber Archive Aug 2005 by date