Amber Archive Dec 2007: by date

Saturday, 1 December 2007
- AMBER: Minimization amber9 segmentation fault Francesco Pietra
- Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg
- Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra
- Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg
Sunday, 2 December 2007
- Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra
- AMBER: mm_pbsa continue run Christopher Gaughan
- AMBER: I need some help in PTRAJ Vijay Manickam Achari
- Re: AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer
Monday, 3 December 2007
- AMBER: sander and pmemd Nadia Vahdati
- Re: AMBER: sander and pmemd Robert Duke
- Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra
- AMBER: Re: divcon on AIX using xlf 10.1 Joachim Hein
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault David A. Case
- AMBER: Free energy for part of the system jialei
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Ilyas Yildirim
- Re: AMBER: I need some help in PTRAJ Chris Moth
- AMBER: During the Sander process, does the pH of the solution change orr not Fenghui Fan
- Re: AMBER: Free energy for part of the system David A. Case
Tuesday, 4 December 2007
- AMBER: Restraintmask syntax Francesco Pietra
- RE: AMBER: Restraintmask syntax Steve Spronk
- AMBER: Solution Structure Determination Protocols - Simulated Annealing Seth Lilavivat
- RE: AMBER: Restraintmask syntax Francesco Pietra
- RE: AMBER: Free energy for part of the system jialei
- AMBER: correlation time Tuncel, Aytug
- Re: AMBER: Free energy for part of the system David A. Case
- Re: AMBER: correlation time David A. Case
- Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case
- Re: AMBER: angle between vectors Prem
- AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey
- Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File David A. Case
- RE: AMBER: Free energy for part of the system jialei
- AMBER: phosphorylation bosco
Wednesday, 5 December 2007
- AMBER: (no subject) Madjid Taghdir
- AMBER: nmode ntrun=2 JM Beames
- AMBER: leap restrainTorsion fatima.chami.durham.ac.uk
- RE: AMBER: Restraintmask syntax Andrew Purkiss-Trew
- AMBER: calcium and zinc parameter Madjid Taghdir
- Re: AMBER: calcium and zinc parameter Mattia Mori - CERM
- AMBER: THF parameters Yves Boulard
- Re: AMBER: THF parameters FyD
- Re: AMBER: leap restrainTorsion David A. Case
- AMBER: Amber 9 - bugfix.40 fails Kevin Davies
- Re: AMBER: Amber 9 - bugfix.40 fails Holger Gohlke
- Re: AMBER: THF parameters David A. Case
- Re: AMBER: nmode ntrun=2 David A. Case
- RE: AMBER: Restraintmask syntax Francesco Pietra
- AMBER: Bulk water simulation with centre of mass position restrain Biman Jana
- Re: AMBER: calcium and zinc parameter Taufik Al-Sarraj
- Fwd: Re: AMBER: leap restrainTorsion fatima.chami.durham.ac.uk
- AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat
- Re: AMBER: THF parameters Piotr Cieplak
- AMBER: amber on AMD opteron-250 servaas michielssens
- Re: AMBER: amber on AMD opteron-250 Robert Duke
- Re: AMBER: amber on AMD opteron-250 David LeBard
- Re: AMBER: THF parameters FyD
- Re: AMBER: amber on AMD opteron-250 Robert Duke
- AMBER: MD_model Urszula Uciechowska
- Re: AMBER: MD_model Thomas Steinbrecher
- AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. Boutheina Kerkeni
- Re: AMBER: MD_model Ilyas Yildirim
- Re: AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. David A. Case
- AMBER: Making movies in VMD Lili Peng
- Re: AMBER: Making movies in VMD Vijay Singh
- Re: AMBER: How to apply psuedo-bonds for restraints David A. Case
- Re: Fwd: Re: AMBER: leap restrainTorsion David A. Case
- Re: AMBER: Making movies in VMD rdauria.uci.edu
Thursday, 6 December 2007
- AMBER: Problem in running CARNAL Vijay Manickam Achari
- AMBER: Problem in running CARNAL Vijay Manickam Achari
- RE: AMBER: correlation time Tuncel, Aytug
- Re: AMBER: nmode ntrun=2 JM Beames
- AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Ye Mei
- Re: AMBER: calcium and zinc parameter Mattia Mori - CERM
- AMBER: PMEMD compilation problems !! Sampath Koppole
- Re: AMBER: PMEMD compilation problems !! Robert Duke
- Re: AMBER: PMEMD compilation problems !! Robert Duke
- AMBER: pmend vs sander.MPI Francesco Pietra
- Re: AMBER: pmend vs sander.MPI Robert Duke
- Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Andreas Svrcek-Seiler
- Re: AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat
- Re: AMBER: How to apply psuedo-bonds for restraints David A. Case
- Re: AMBER: nmode ntrun=2 David A. Case
- Re: AMBER: correlation time David A. Case
- AMBER: Surface Taufik Al-Sarraj
- Re: AMBER: Problem in running CARNAL Bill Ross
- Re: AMBER: phosphorylation FyD
- Re: AMBER: Surface David A. Case
- Re: Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran10.1.008 and IMKL 10.0.1.014 Ye Mei
- AMBER: Problem in running CARNAL Vijay Manickam Achari
- Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey
Friday, 7 December 2007
- Re: AMBER: Problem in running CARNAL Bill Ross
- AMBER: Troubles installing amber Margaret Doll
- Re: AMBER: Troubles installing amber Wei Zhang
- Re: AMBER: Troubles installing amber Alessandro Nascimento
- Re: AMBER: Troubles installing amber Margaret Doll
- AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni
- Re: AMBER: Troubles installing amber David A. Case
- AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni
- Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT Bill Ross
- Re: AMBER: Troubles installing amber Margaret Doll
- AMBER: running equilibration Boutheina Kerkeni
- RE: AMBER: running equilibration Ross Walker
- Re: AMBER: running equilibration Bill Ross
- Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT David A. Case
- AMBER: Continuing an amber 8 simulation with amber 9 ming hui
Saturday, 8 December 2007
- AMBER: protein_model Urszula Uciechowska
- Re: AMBER: Continuing an amber 8 simulation with amber 9 David A. Case
- Re: AMBER: protein_model steinbrt.scripps.edu
- AMBER: Backbone atoms Boutheina Kerkeni
- Re: AMBER: Backbone atoms David A. Case
- AMBER: website problems Sally Pias
Sunday, 9 December 2007
- AMBER: ptraj with protein-ligand Francesco Pietra
- AMBER: Fwd: ptraj with protein-ligand Francesco Pietra
- AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI#
- AMBER: some input problem Urszula Uciechowska
- AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny
- Re: AMBER: website problems David A. Case
- Re: AMBER: some input problem David A. Case
- Re: AMBER: Re: Amber_ifort_x86_64 test error David A. Case
- Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny
- Re: AMBER: Troubling with installing Amber8 David A. Case
- Re: AMBER: website problems Andreas Svrcek-Seiler
- Re: AMBER: pmend vs sander.MPI Francesco Pietra
- RE: AMBER: website problems Ross Walker
- RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker
- Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny
- Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny
- Re: AMBER: website problems Sally Pias
- RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker
- RE: AMBER: website problems Ross Walker
- RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert
- RE: AMBER: Re: Amber_ifort_x86_64 test error Ilyas Yildirim
- Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny
Monday, 10 December 2007
- AMBER: Ligand-Residue interaction tracking Evan Kelly
- AMBER: TI Approach - mass perturbation Ilyas Yildirim
- AMBER: implicit solvent simulations with calcium ion Akansha Saxena
- Re: AMBER: TI Approach - mass perturbation David A. Case
- Re: AMBER: calcium and zinc parameter Madjid Taghdir
- Re: AMBER: TI Approach - mass perturbation Ilyas Yildirim
Tuesday, 11 December 2007
- Re: AMBER: amber on AMD opteron-250 servaas michielssens
- Re: AMBER: calcium and zinc parameter Mattia Mori - CERM
- RE: AMBER: amber on AMD opteron-250 Ross Walker
- AMBER: tleap crashing Ranjib Dey
- AMBER: implicit solvent simulations WANG,YING
- RE: AMBER: amber on AMD opteron-250 servaas michielssens
- AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang
- RE: AMBER: amber on AMD opteron-250 Ross Walker
- RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker
- RE: AMBER: amber on AMD opteron-250 Christopher Jones
- Re: AMBER: tleap crashing David A. Case
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Gustavo Seabra
- Re: AMBER: implicit solvent simulations liu junjun
- Re: AMBER: implicit solvent simulations WANG,YING
- Re: AMBER: tleap crashing Ranjib Dey
Wednesday, 12 December 2007
- RE: AMBER: implicit solvent simulations Steve Spronk
- AMBER: equilibration Urszula Uciechowska
- AMBER: AMBER7 Si atom type Taufik Al-Sarraj
- AMBER: Free Energy Calculations Mike Wykes
- Re: AMBER: Free Energy Calculations Thomas Steinbrecher
- AMBER: New 2 the board Campbell, Patrick
- Re: AMBER: New 2 the board David A. Case
- AMBER: loading a crystal PDB file Taufik Al-Sarraj
Thursday, 13 December 2007
- AMBER: make test.parallel not complete Prem Prakash Pathak
- AMBER: MMPBSA Syed Tarique Moin
- AMBER: protein-ligand binding affinity Francesco Pietra
- RE: AMBER: make test.parallel not complete Ross Walker
- Re: AMBER: nmode ntrun=2 JM Beames
- RE: AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI#
- AMBER: help in QM/MM simulation Pankaj R. Daga
Friday, 14 December 2007
- AMBER: PMEMD internals !! Sampath Koppole
- Re: AMBER: PMEMD internals !! Robert Duke
- Re: AMBER: Troubling with installing Amber8 David A. Case
- AMBER: replica exchange out files continually overwritten David Mobley
- Re: AMBER: replica exchange out files continually overwritten David A. Case
- Re: AMBER: nmode ntrun=2 David A. Case
- Re: AMBER: replica exchange out files continually overwritten Adrian Roitberg
- Re: AMBER: replica exchange out files continually overwritten David Mobley
- Re: AMBER: replica exchange out files continually overwritten Carlos Simmerling
- Re: AMBER: replica exchange out files continually overwritten David Mobley
- Re: AMBER: replica exchange out files continually overwritten Carlos Simmerling
- AMBER: xleap loading files Taufik Al-Sarraj
- Re: AMBER: replica exchange out files continually overwritten David Mobley
- Re: AMBER: xleap loading files David A. Case
Saturday, 15 December 2007
- AMBER: Time step & non-bonded interactions updating Francesco Pietra
- Re: AMBER: xleap loading files FyD
- RE: AMBER: Time step & non-bonded interactions updating Ross Walker
Sunday, 16 December 2007
- RE: AMBER: Time step & non-bonded interactions updating Francesco Pietra
Monday, 17 December 2007
- AMBER: pmemd: same rst, different result? Anselm Horn
- Re: AMBER: pmemd: same rst, different result? Benjamin Juhl
- AMBER: MMTSB Toolset Urszula Uciechowska
- Re: AMBER: MMTSB Toolset Carlos Simmerling
- Re: AMBER: pmemd: same rst, different result? Robert Duke
- Re: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang
- RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker
Tuesday, 18 December 2007
- Re: AMBER: pmemd: same rst, different result? Anselm Horn
- AMBER: amber9/mmtsb Francesco Pietra
- AMBER: Scripts for md analysis Francesco Pietra
- Re: AMBER: pmemd: same rst, different result? Robert Duke
- Re: AMBER: pmemd: same rst, different result? David A. Case
- Re: AMBER: amber9/mmtsb David A. Case
- AMBER: PME and counter ions Lars Skjærven
- Re: AMBER: amber9/mmtsb Francesco Pietra
- RE: AMBER: pmemd: same rst, different result? Yong Duan
- Re: AMBER: PME and counter ions Bill Ross
- Re: AMBER: pmemd: same rst, different result? Robert Duke
- Re: AMBER: PME and counter ions Lars Skjærven
- Re: AMBER: pmemd: same rst, different result? Thomas Cheatham
- AMBER: closest water molecules with 8 angstroms nag raj
Wednesday, 19 December 2007
- Re: AMBER: closest water molecules with 8 angstroms Alessandro Nascimento
- Re: AMBER: pmemd: same rst, different result? Robert Duke
- Re: AMBER: help in QM/MM simulation Gustavo Seabra
- Re: AMBER: amber9/mmtsb David A. Case
- Re: AMBER: PME and counter ions Pablo Englebienne
- Re: AMBER: PME and counter ions David A. Case
- Re: AMBER: PME and counter ions Bill Ross
- Re: AMBER: PME and counter ions Eddie Men
- AMBER: PME and counter ions Chris Moth
- Re: AMBER: PME and counter ions David A. Case
- Re: AMBER: PME and counter ions Lars Skjærven
- Re: AMBER: PME and counter ions David A. Case
- Re: AMBER: PME and counter ions Thomas Cheatham
Thursday, 20 December 2007
- Re: AMBER: make test.parallel not complete Prem Prakash Pathak
- AMBER: Electron density profile Age.Skjevik.student.uib.no
- Re: AMBER: PME and counter ions Lars Skjærven
- AMBER: Use of Counter Ions in binding energy calculations Jonathan Suever
- Re: AMBER: PME and counter ions Bill Ross
- Re: AMBER: PME and counter ions Bill Ross
- AMBER: Steered MD M kutty
Friday, 21 December 2007
- AMBER: No radius found for K+ (MM_PBSA) saurabh agrawal
- AMBER: About protein-ligand binding Francesco Pietra
- Re: AMBER: Steered MD M. L. Dodson
- Re: AMBER: Steered MD M. L. Dodson
- Re: AMBER: No radius found for K+ (MM_PBSA) Thomas Cheatham III
- Re: AMBER: PME and counter ions Thomas Cheatham III
Saturday, 22 December 2007
- Re: AMBER: R.E.D.-III bug fixes snoze pa
- AMBER: RESP using antechamber snoze pa
- Re: AMBER: RESP using antechamber Barbault Florent
Sunday, 23 December 2007
- RE: AMBER: Steered MD M kutty
- AMBER: installation of amber9 on suse linux 10.3 s lal badshah
- Re: AMBER: installation of amber9 on suse linux 10.3 David A. Case
Wednesday, 26 December 2007
- Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 David A. Case
- Re: AMBER: installation of amber9 on suse linux 10.3 s lal badshah
- AMBER: installation s lal badshah
- RE: AMBER: installation of amber9 on suse linux 10.3 Ross Walker
Saturday, 29 December 2007
- Re: AMBER: installation Mark Williamson
- AMBER: RESP charge fitting using antechamber Wei Chen
- Re: AMBER: RESP charge fitting using antechamber David A. Case
Sunday, 30 December 2007
- Re: AMBER: RESP charge fitting using antechamber FyD
- Re: AMBER: RESP charge fitting using antechamber Francesco Pietra
Monday, 31 December 2007
- Re: AMBER: RESP charge fitting using antechamber FyD
- AMBER: About RAMD Francesco Pietra
- Re: AMBER: RESP charge fitting using antechamber FyD
- AMBER: a question of ptraj WANG,YING
- Re: AMBER: a question of ptraj Chris Moth

Last message date: Wed Jan 02 2008 - 06:07:19 PST
Archived on: Fri Apr 26 2024 - 05:53:41 PDT

Amber Archive Dec 2007 by date