Amber Archive Oct 2005: by date

Monday, 3 October 2005
- AMBER: Error check COM velocity!! jpragati.ibab.ac.in
- AMBER: cut-offs in non-periodic simulations Fabien Cailliez
- Re: AMBER: cut-offs in non-periodic simulations Andreas Svrcek-Seiler
- Re: AMBER: amber8 parallel sander Kathleen Erickson
- AMBER: question temperature coupling tautp value for RNA Zhuang
- AMBER: question temperature coupling tautp value for RNA Zhuang
- RE: AMBER: question temperature coupling tautp value for RNA Ross Walker
- Re: AMBER: amber8 parallel sander MURAT CETINKAYA
- Re: AMBER: amber8 parallel sander Robert Duke
Tuesday, 4 October 2005
- AMBER: Problem during production!! jpragati.ibab.ac.in
- AMBER: Can I trust ANAL result? Madjid Taghdir
- AMBER: Manganese ion parameter nadtanet
- AMBER: Energy output problem! Pradipta Bandyopadhyay
- Re: AMBER: question temperature coupling tautp value for RNA Carlos Simmerling
- AMBER: The default of HIS in leaprc : HID or HIE ? Jiten
- AMBER: Fw: The default of HIS in leaprc : HID or HIE ? Jiten
- AMBER: Installation error - icc: command not found Sukjoon Yoon
- AMBER: AMBER compilation - RH Enterprise 4, Xeon EM64T Sukjoon Yoon
Wednesday, 5 October 2005
- AMBER: Is AMBER package suitable for simulating multiple molecule in solvent? wulei
- Re: AMBER: Installation error - icc: command not found Andreas Svrcek-Seiler
- Re: AMBER: Installation error - icc: command not found Mingfeng Yang
Thursday, 6 October 2005
- AMBER: antechamber dimesion size, again Toshifumi Yui
- Re: AMBER: Minimization in sander and nmode David A. Case
- AMBER: question about grid in ptraj Linchen Gong
- AMBER: R factors in NMR intensity refinement Yuqin Cai
- Re: AMBER: R factors in NMR intensity refinement YoungJin Cho
- RE: AMBER: antechamber dimesion size, again Junmei Wang
- Re: AMBER: antechamber dimesion size, again Toshifumi Yui
- AMBER: AMBER compilation error Sukjoon Yoon
- AMBER: QMMM question xiaoqin huang
Friday, 7 October 2005
- Re: AMBER: question about grid in ptraj Angelo Pugliese
- Re: AMBER: AMBER compilation error Andreas Svrcek-Seiler
- AMBER: parameters for pyridoxal phosphate Anna Feldman-Salit
- AMBER: problem with temperature weights Manish Datt
- Re: AMBER: problem with temperature weights Carlos Simmerling
- Re: AMBER: problem with temperature weights Manish Datt
Saturday, 8 October 2005
- Re: AMBER: problem with temperature weights Carlos Simmerling
- Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac
Sunday, 9 October 2005
- AMBER: sander error Yam
Monday, 10 October 2005
- Re: AMBER: sander error Guanglei Cui
- Re: AMBER: QMMM question Guanglei Cui
- RE: AMBER: sander error Ross Walker
- RE: AMBER: QMMM question Ross Walker
- AMBER: Parameters and topology for Diacylglycerol (DAG) Nitin Bhardwaj
- Re: AMBER: QMMM question xiaoqin huang
Tuesday, 11 October 2005
- RE: AMBER: sander error Yam
- AMBER: how to constitute T-phosphotyrosine group? luaj.sohu.com
- AMBER: PCA Claire Zerafa
- AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com
- Re: AMBER: sander error David A. Case
- Re: AMBER: PCA David A. Case
- AMBER: maxgrp error Javier Pérez Mirón
- AMBER: warning in leap Marcela Madrid
- Re: AMBER: warning in leap David A. Case
- AMBER: How to simulate a crystal structure? Chunhu Tan
Wednesday, 12 October 2005
- AMBER: F,Cl,Br,I in MMPBSA Yong Xu
- Re: AMBER: How to simulate a crystal structure? David A. Case
- Re: AMBER: How to simulate a crystal structure? Joseph Nachman
- AMBER: troubleshooting replica exchange Zhuang
- Re: AMBER: troubleshooting replica exchange Sergio E. Wong
- AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com
Thursday, 13 October 2005
- Re: AMBER: troubleshooting replica exchange Peter Varnai
- AMBER: AMBER goes in a Loop Imran Khan
Friday, 14 October 2005
- AMBER: Scaling factor of NMR restraint FyD
- RE: AMBER: Scaling factor of NMR restraint Ross Walker
- Re: AMBER: Scaling factor of NMR restraint David A. Case
- Re: AMBER: AMBER goes in a Loop David A. Case
- AMBER: oxidised methionine residue Megan G
- Re: AMBER: AMBER goes in a Loop Imran Khan
- Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac
- Re: AMBER: AMBER goes in a Loop Robert Duke
- AMBER: again: F, Cl, Br, I in MMPBSA Yong Xu
- RE: AMBER: Scaling factor of NMR restraint FyD
Sunday, 16 October 2005
- AMBER: GNU Autotool integration for Amber8! mk mk
- AMBER: Free energy for L and D amino acids S.Sundar Raman
- Re: AMBER: Free energy for L and D amino acids Carlos Simmerling
- AMBER: Cyclohexane solvent Box chaiann ng
Monday, 17 October 2005
- RE: AMBER: Cyclohexane solvent Box Ross Walker
- Re: AMBER: Cyclohexane solvent Box chai ann ng
- Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case
- AMBER: antechamber -- missing improper torsions David Mobley
- RE: AMBER: antechamber -- missing improper torsions Ross Walker
- AMBER: pca with ptraj Claire Zerafa
- AMBER: sander error Yam
- AMBER: Question about NVE simulation. tanc.uci.edu
Tuesday, 18 October 2005
- AMBER: program to visualize crystal symmetries Hannes Loeffler
- Re: AMBER: program to visualize crystal symmetries Karsten Suhre
- Re: AMBER: Question about NVE simulation. Carlos Simmerling
- AMBER: problem with xleap Vlad Cojocaru
- Re: AMBER: problem with xleap Mark Williamson
- Re: AMBER: problem with xleap Heike.Meiselbach.chemie.uni-erlangen.de
- RE: AMBER: sander error Ross Walker
- Re: AMBER: sander error Robert Duke
- Re: AMBER: sander error David A. Case
- Re: AMBER: sander error Robert Duke
- Re: AMBER: program to visualize crystal symmetries Joseph Nachman
- AMBER: Simple 3D Molecule Visualization Alec M. Resnick
- Re: AMBER: Simple 3D Molecule Visualization Joachim Reichelt
- Re: AMBER: Simple 3D Molecule Visualization Karsten Suhre
- Re: AMBER: Simple 3D Molecule Visualization Mark Williamson
- Re: AMBER: GNU Autotool integration for Amber8! David A. Case
- Re: AMBER: Simple 3D Molecule Visualization FyD
- Re: AMBER: antechamber -- missing improper torsions David Mobley
- Re: AMBER: Question about NVE simulation. Chunhu Tan
- Re: AMBER: Question about NVE simulation. Carlos Simmerling
- Re: AMBER: Simple 3D Molecule Visualization Furse, Kristina Elisabet
- RE: AMBER: antechamber -- missing improper torsions Ross Walker
Wednesday, 19 October 2005
- AMBER: Neutral C-terminal residue Sébastien Fiorucci
- Re: AMBER: Neutral C-terminal residue Carlos Simmerling
- AMBER: Fw: pca with ptraj Claire Zerafa
- Re: AMBER: Neutral C-terminal residue FyD
- AMBER: ptraj hbond analysis S.Sundar Raman
- Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao
- Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang
- Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang
- AMBER: amber file formats. Shishir
- Re: AMBER: GNU Autotool integration for Amber8! David A. Case
- AMBER: (no subject) mathew k varghese
Thursday, 20 October 2005
- Re: AMBER: (no subject) Yam
- Re: AMBER: (no subject) mathew k varghese
- AMBER: porblem in ptraj julien
- AMBER: Simulating transition metals in amber Thomas Steinbrecher
- AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin
- Re: AMBER: ptraj hbond analysis haixiao jin
- AMBER: REMD error!!! Anthony Cruz
- Re: AMBER: REMD error!!! Carlos Simmerling
- Re: AMBER: REMD error!!! Anthony Cruz
- Re: AMBER: REMD error!!! Carlos Simmerling
- Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao
- AMBER: delphi and surface in MMPBSA Yong Xu
- Re: AMBER: REMD error!!! Anthony Cruz
- Re: AMBER: REMD error!!! Carlos Simmerling
- Re: AMBER: REMD error!!! Guanglei Cui
- Re: AMBER: delphi and surface in MMPBSA David A. Case
- Re: AMBER: REMD error!!! Carlos Simmerling
- Re: AMBER: REMD error!!! Wei Zhang
- Re: AMBER: amber file formats. David A. Case
- Re: AMBER: REMD error!!! Carlos Simmerling
- Re: AMBER: REMD error!!! Anthony Cruz
- Re: AMBER: REMD error!!! Carlos Simmerling
- AMBER: Targeted MD Whitney Allen
- AMBER: xleap with modified residue Whitney Allen
- Re: AMBER: xleap with modified residue Kenley Barrett
- Re: AMBER: Targeted MD Carlos Simmerling
- RE: AMBER: xleap with modified residue Ross Walker
- Re: AMBER: amber file formats. Shishir
- Re: AMBER: amber file formats. David A. Case
- Re: Re: AMBER: delphi and surface in MMPBSA Yong Xu
- Re: Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu
- Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu
- Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue Thomas Cheatham
- Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin
- Re: AMBER: ptraj hbond analysis Thomas Cheatham
Friday, 21 October 2005
- AMBER: Dipolar coupling refinement s0344557.sms.ed.ac.uk
- Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case
- Re: AMBER: antechamber -- missing improper torsions David Mobley
- Re: AMBER: antechamber -- missing improper torsions David A. Case
- AMBER: using position restraints in target MD? Ben-Zhuo Lu
- Re: AMBER: using position restraints in target MD? Viktor Hornak
- Re: AMBER: Dipolar coupling refinement David A. Case
Saturday, 22 October 2005
- Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA JunJun Liu
- Re: Re: AMBER: delphi and surface in MMPBSA David A. Case
- Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac
- Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac
- AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)... konnipati murali
Sunday, 23 October 2005
- AMBER: Problem with the QMMM example in AMBER 2004 tutorial Cenk Andac
- RE: AMBER: Problem with the QMMM example in AMBER 2004 tutorial Ross Walker
Monday, 24 October 2005
- Re: Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II FyD
- Re: AMBER: Simulating transition metals in amber FyD
- Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD
- AMBER: rdparm: a parameter array overflowed ying xiong
- AMBER: compiling amber with pgi 5.2.4 Hannes Barsch
- Re: AMBER: compiling amber with pgi 5.2.4 Robert Duke
- AMBER: error in safe Claire Zerafa
- RE: AMBER: error in safe Ross Walker
- Re: AMBER: compiling amber with pgi 5.2.4 Xuebin Qiao
- Re: AMBER: error in safe Xuebin Qiao
- Re: AMBER: rdparm: a parameter array overflowed David A. Case
- Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac
- RE: AMBER: xleap with modified residue Whitney Allen
- Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac
- AMBER: Is MM-PBSA doable for transition metals ? Cenk Andac
- Re: AMBER: Is MM-PBSA doable for transition metals ? Bill Ross
- AMBER: QMMM for copper complexes! Cenk Andac
- Re: AMBER: xleap with modified residue David A. Case
- AMBER: atmtypenumbers Yong Xu
- Re: Re: AMBER: rdparm: a parameter array overflowed ying xiong
- Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD
Tuesday, 25 October 2005
- AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules? haixiao jin
- AMBER: Using RED to calculate partial charges of new amino acid Donald Thomas
- AW: AMBER: compiling amber with pgi 5.2.4 Hannes Barsch
- AMBER: I am looking forward to hearing from you. Mehdi Davari
- AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj
- Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit David A. Case
- Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj
- AMBER: Antechamber error Nitin Bhardwaj
- Re: AMBER: Antechamber error Nitin Bhardwaj
Wednesday, 26 October 2005
- AMBER: AMBER tests (x86-64, PGI / Intel) Hannes Barsch
- AMBER: Increase the runtime of Amber benchmarks Imran Khan
- Re: AMBER: I am looking forward to hearing from you. Majid moghaddam
- Re: AMBER: Using RED to calculate partial charges of new amino acid FyD
- Re: AMBER: Increase the runtime of Amber benchmarks Carlos Simmerling
- AMBER: seg fault error in resp Kateryna Miroshnychenko
- AMBER: xleap, opteron, pgi and segmentation fault. Lars Packschies
- Re: AMBER: seg fault error in resp FyD
- Re: AMBER: seg fault error in resp Kateryna Miroshnychenko
- Re: AMBER: seg fault error in resp FyD
- Re: AMBER: seg fault error in resp Bill Ross
- AMBER: using constraints with QM/MM Jakub Kostal
- AMBER: Re: restraints xiaoqin huang
- AMBER: some questions when using ATP du yongchun
Thursday, 27 October 2005
- Re: AMBER: seg fault error in resp Kateryna Miroshnychenko
- Re: AMBER: seg fault error in resp FyD
- AMBER: restart file and crd file Lishan Yao
- AMBER: problems installing amber 7 on a RH Linux 8 machine Marios Constantinou
- Re: AMBER: restart file and crd file Mingfeng Yang
- Re: AMBER: restart file and crd file Carlos Simmerling
- Re: AMBER: restart file and crd file Lishan Yao
- AMBER: Unknown atomtypes in amber Nitin Bhardwaj
- Re: AMBER: restart file and crd file Lishan Yao
- Re: AMBER: restart file and crd file Melinda Layten
- Re: AMBER: seg fault error in resp Bill Ross
- Re: AMBER: restart file and crd file Lishan Yao
- Re: AMBER: restart file and crd file Carlos Simmerling
- Re: AMBER: problems installing amber 7 on a RH Linux 8 machine David A. Case
- Re: AMBER: restart file and crd file Lishan Yao
- Re: AMBER: restart file and crd file Mingfeng Yang
- Re: AMBER: restart file and crd file Carlos Simmerling
- Re: AMBER: restart file and crd file Lishan Yao
- Re: AMBER: AMBER tests (x86-64, PGI / Intel) Scott Brozell
Friday, 28 October 2005
- Re: AMBER: problems installing amber 7 on a RH Linux 8 machine Andreas Svrcek-Seiler
- Fwd: Re: AMBER: REMD error!!! Anthony Cruz
- AMBER: Cluster analysis by MMTSB or ptraj Shuting Wei
- Re: Re: AMBER: REMD error!!! Melinda Layten
- AMBER: REMD trajectory error!!! Anthony Cruz
- Re: AMBER: REMD trajectory error!!! Carlos Simmerling
- AMBER: Metals with Amber Anton B. Guliaev
- Re: Fwd: Re: AMBER: REMD error!!! Carlos Simmerling
- AMBER: vdw of h atoms Gustavo Pierdominici Sottile
- Re: AMBER: vdw of h atoms Jiri Sponer
- Re: AMBER: Metals with Amber Bill Ross
- Re: AMBER: vdw of h atoms Bill Ross
- RE: AMBER: vdw of h atoms Rhoad, Jonathan S.
- RE: AMBER: vdw of h atoms Bill Ross
- AMBER: Improper Torsional Parameters Ilyas Yildirim
- AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim
Saturday, 29 October 2005
- AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu
- AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu
- Re: AMBER: Unknown atomtypes in amber David A. Case
- Re: AMBER: Unknown atomtypes in amber Nitin Bhardwaj
Sunday, 30 October 2005
- AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex? haixiao jin
Monday, 31 October 2005
- AMBER: GBSA simulation problem Guillaume Bollot
- Re: AMBER: GBSA simulation problem Carlos Simmerling
- AMBER: tkbc2 Mingfeng Yang

Last message date: Mon Oct 31 2005 - 23:53:01 PST
Archived on: Wed Apr 24 2024 - 05:53:27 PDT

Amber Archive Oct 2005 by date