Amber Archive Sep 2007: by date

Saturday, 1 September 2007
- AMBER: Solvent in closest contact with solute Francesco Pietra
Monday, 3 September 2007
- AMBER: ntt parameter in vacuum Age.Skjevik.student.uib.no
- Re: AMBER: ntt parameter in vacuum Carlos Simmerling
- Re: AMBER: ntt parameter in vacuum David A. Case
- AMBER: creating topology files for RNA DNA hybrid.molecule msubhamoy.ibab.ac.in
- Re: AMBER: creating topology files for RNA DNA hybrid.molecule saurabh agrawal
- AMBER: installing LMOD error Xioling Chuang
- AMBER: Catein Catherine
Tuesday, 4 September 2007
- AMBER: Running mpirun -np 1 on different processors Francesco Pietra
- Re: AMBER: Running mpirun -np 1 on different processors Adrian Roitberg
- Re: AMBER: Running mpirun -np 1 on different processors Carlos Simmerling
- AMBER: decomposition energy Pankaj R. Daga
- Re: AMBER: Running mpirun -np 1 on different processors Francesco Pietra
- Re: AMBER: installing LMOD error David A. Case
- AMBER: Problem compiling AMBER 9 on ppc64 Eric Shamay
- Re: AMBER: Problem compiling AMBER 9 on ppc64 David A. Case
- Re: AMBER: Using ntr=1 in xleap Lili Peng
- AMBER: Problem with modelling ammonium ion? David Cerutti
- Re: AMBER: installing LMOD error Xioling Chuang
- Re: AMBER: Problem with modelling ammonium ion? David Cerutti
Wednesday, 5 September 2007
- Re: AMBER: refinement of NMR struture using AMBER andy ng
- AMBER: Comparing explicit solvent/vacuum qmmm Francesco Pietra
Tuesday, 4 September 2007
- Re: AMBER: installing LMOD error David A. Case
Wednesday, 5 September 2007
- AMBER: PMF calculation - minimum conformer Catein Catherine
- AMBER: Fwd: Comparing explicit solvent/vacuum qmmm Francesco Pietra
- RE: AMBER: decomposition energy Catein Catherine
- Re: AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak
- AMBER: amber md movie using Chimera Wang, Xuelin
- Re: AMBER: amber md movie using Chimera Mingfeng Yang
- Re: AMBER: amber md movie using Chimera David A. Case
- RE: AMBER: amber md movie using Chimera. . Wang, Xuelin
- Re: AMBER: amber md movie using Chimera Bill Ross
- AMBER: chiral surfaces Hector A. Baldoni
- Re: AMBER: chiral surfaces Carlos Simmerling
Thursday, 6 September 2007
- AMBER: DelPhi Urszula Uciechowska
- AMBER: RE: Tutorial5 -- sustiva and xleap Ross Walker
- AMBER: electron density difference Ozlem Demir
- Re: AMBER: refinement of NMR struture using AMBER Seth Lilavivat
- RE: AMBER: Dihedrals in Sander Steve Spronk
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: installing LMOD error Xioling Chuang
- Re: AMBER: Prepin error (?) in xleap David A. Case
- Re: AMBER: Prepin error (?) in xleap Junmei Wang
- Re: AMBER: Prepin error (?) in xleap Eduardo Mendez
Friday, 7 September 2007
- Re: AMBER: refinement of NMR struture using AMBER andy ng
- AMBER: Harmonic constraints Johan Qvist
- Re: AMBER: Harmonic constraints Carlos Simmerling
- Re: AMBER: Harmonic constraints Ilyas Yildirim
- AMBER: System extending beyond of (non existent) virtual box Francesco Pietra
- Re: AMBER: Harmonic constraints Carlos Simmerling
- AMBER: for NMR restrains files Wenyong Tong
- Re: AMBER: Harmonic constraints Thomas Cheatham
- Re: AMBER: Harmonic constraints Carlos Simmerling
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: Prepin error (?) in xleap Ilyas Yildirim
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: Prepin error (?) in xleap Ilyas Yildirim
- Re: AMBER: for NMR restrains files Prem Prakash Pathak
- Re: AMBER: Harmonic constraints Jiri Sponer
Saturday, 8 September 2007
- AMBER: Fwd: System extending beyond of (non existent) virtual box Francesco Pietra
- AMBER: solvent box pyridine Francesco Pietra
- AMBER: rms and rms nofit Alana Canfield
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- AMBER: Targeted MD Beale, John
- Re: AMBER: Targeted MD Adrian Roitberg
Sunday, 9 September 2007
- AMBER: Explicit water in implicit enviornment? Hayden Eastwood
Monday, 10 September 2007
- RE: AMBER: Harmonic constraints Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: Harmonic constraints Carlos Simmerling
- Re: AMBER: Harmonic constraints Carlos Simmerling
- Re: AMBER: Missplaced TERs David A. Case
- AMBER: RE: Asking for help Ross Walker
- AMBER: AMBER parametrization (??) for OAA and Mg++ Eduardo Mendez
Tuesday, 11 September 2007
- Re:AMBER: AMBER parametrization (??) for OAA and Mg++ Qiang Zhong
- Re: AMBER: AMBER parametrization (??) for OAA and Mg++ FyD
- AMBER: heme forcefield atom types john chen
- Re: AMBER: heme forcefield atom types Vlad Cojocaru
- AMBER: heme force-field (2) john chen
- Re: AMBER: heme force-field (2) Vlad Cojocaru
- AMBER: Tutorial protein-small-molecule-associates Francesco Pietra
- AMBER: PBradii Steve Seibold
- Re: AMBER: PBradii Carlos Simmerling
- RE: AMBER: PBradii Steve Seibold
- AMBER: TIP5P questions Prashanth Athri
Wednesday, 12 September 2007
- AMBER: Problems with Carbohydrate Non-standard Residue Moruz Luminita
- Re: AMBER: Problems with Carbohydrate Non-standard Residue David A. Case
- AMBER: Complexe Energy Analysis saccenti.cerm.unifi.it
- RE: AMBER: Problems with Carbohydrate Non-standard Residue Irene Newhouse
- AMBER: for makeDIST_RST Wenyong Tong
Thursday, 13 September 2007
- AMBER: LINMIN Failure vs Parallelization Sandeep Kaushik
- Re: AMBER: LINMIN Failure vs Parallelization linfu
- Re: AMBER: LINMIN Failure vs Parallelization Gustavo Seabra
- AMBER: Too big EEL energy in energy minimization Wang, Xuelin
- RE: AMBER: Too big EEL energy in energy minimization Ross Walker
- RE: AMBER: Too big EEL energy in energy minimization. . Wang, Xuelin
- RE: AMBER: Too big EEL energy in energy minimization. . Ross Walker
- Re: AMBER: TIP5P questions Thomas Cheatham III
- AMBER: Problem with Sander anna duraj
- Re: AMBER: Problem with Sander Carlos Simmerling
- Re: AMBER: TIP5P questions David A. Case
Friday, 14 September 2007
- AMBER: FF02: sander problem with irstdip=1 Anselm Horn
- AMBER: parallel implementation of Amber 9 Beale, John
- Re: AMBER: FF02: sander problem with irstdip=1 David A. Case
- Re: AMBER: parallel implementation of Amber 9 David A. Case
- Re: AMBER: for makeDIST_RST David A. Case
- AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA]
- AMBER: calcium ion force-fields john chen
- Re: AMBER: Tutorial protein-small-molecule-associates Scott Brozell
- Re: AMBER: DNA base planarity restraint Carlos Simmerling
- AMBER: xleap question Anna Díaz Cirac
- Re: AMBER: xleap question Carlos Simmerling
- RE: AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: DNA base planarity restraint Carlos Simmerling
- Re: AMBER: for makeDIST_RST Wenyong Tong
- RE: AMBER: FF02: sander problem with irstdip=1 Yong Duan
- Re: AMBER: for makeDIST_RST Wenyong Tong
- AMBER: Torsion terms in xleap Lili Peng
- Re: AMBER: Torsion terms in xleap Carlos Simmerling
- Re: AMBER: Torsion terms in xleap Wenyong Tong
- AMBER: AMBER sander Eduardo Mendez
- Re: AMBER: Torsion terms in xleap Davide Moiani
- Re: AMBER: Torsion terms in xleap David A. Case
- Re: AMBER: AMBER sander David A. Case
- AMBER: Can I set harmonic constraints in SMD simulations ? James W
Saturday, 15 September 2007
- AMBER: Problem encountered during thermodynamic integration ming hui
- Re: AMBER: Can I set harmonic constraints in SMD simulations ? David A. Case
- Re: AMBER: Problem encountered during thermodynamic integration David A. Case
- AMBER: Problem with Getting SHAKE to work David Cerutti
- AMBER: replica exchange simulation Ji-Lai Li
- Re: AMBER: Problem with Getting SHAKE to work David Cerutti
- Re: AMBER: Problem with Getting SHAKE to work David A. Case
Sunday, 16 September 2007
- Re: AMBER: Problem with Getting SHAKE to work David Cerutti
Monday, 17 September 2007
- Re: AMBER: replica exchange simulation Carlos Simmerling
- Re: AMBER: Explicit water in implicit enviornment? Carlos Simmerling
- AMBER: Solvation net forces Tyler Luchko
- Re: AMBER: Problem with Getting SHAKE to work David A. Case
- Re: AMBER: Problem with Getting SHAKE to work David Cerutti
- Re: AMBER: Torsion terms in xleap Lili Peng
- Re: AMBER: Torsion terms in xleap David A. Case
- AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Ilyas Yildirim
Tuesday, 18 September 2007
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- AMBER: Potential of mean force: how to extract the min structure? Catein Catherine
- AMBER: GBSA or PBSA: GPB or GGB are +ve or -ve? Catein Catherine
- Re: AMBER: Potential of mean force: how to extract the min structure? Jerome.GOLEBIOWSKI.unice.fr
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Jiri Sponer
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- Re: AMBER: Solvation net forces David A. Case
- AMBER: A question related with periodic boundary condition Jun Liu
- AMBER: How to fix the distance between two atoms. nag raj
- AMBER: Targetted MD and ptraj analysis Ilyas Yildirim
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Francesco Pietra
Wednesday, 19 September 2007
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- AMBER: problem with Thermodynamic Integration Martin Stennett
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood
- Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett
- Re: AMBER: problem with Thermodynamic Integration Ilyas Yildirim
- RE: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood
- Re: AMBER: Problem encountered during thermodynamic integration ming hui
- Re: AMBER: A question related with periodic boundary condition Jun Liu
- Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett
- Re: AMBER: Torsion terms in xleap Lili Peng
- AMBER: A question related with periodic boundary condition Jun Liu
Thursday, 20 September 2007
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD
- AMBER: RE: AMBER9 Installation Help Ross Walker
- RE: AMBER: Targetted MD and ptraj analysis Catein Catherine
Friday, 21 September 2007
- AMBER: Problems loading parameter file in tleap Eduardo Mendez
- Re: AMBER: Problems loading parameter file in tleap Eddie Men
- Re: AMBER: Problems loading parameter file in tleap FyD
- Re: AMBER: Targetted MD and ptraj analysis Carlos Simmerling
- AMBER: MM_PBSA with complex plus Ion saccenti.cerm.unifi.it
- AMBER: kanon gemini
- Re: AMBER: Targetted MD and ptraj analysis Ilyas Yildirim
- AMBER: about restraining atoms san_amber roy
Saturday, 22 September 2007
- AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim
- Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling
- Re: AMBER: about restraining atoms Carlos Simmerling
- Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim
- Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling
- Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim
Sunday, 23 September 2007
- AMBER: Water Question Eddie Men
- Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling
- AMBER: about MD outputs saccenti.cerm.unifi.it
- Re: AMBER: about MD outputs Carlos Simmerling
- Re: AMBER: about MD outputs saccenti.cerm.unifi.it
- Re: AMBER: about MD outputs Carlos Simmerling
- Re: AMBER: about MD outputs saccenti.cerm.unifi.it
- AMBER: Water question Eddie Men
- Re: AMBER: MM_PBSA with complex plus Ion Pankaj Daga
- Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim
- AMBER: Pribelm with Minimization & MD saccenti.cerm.unifi.it
- Re: AMBER: TMD and "Current RMSD from reference" Thomas Cheatham III
- Re: AMBER: Water question David Cerutti
- Re: AMBER: David A. Case
- AMBER: MAXPR san_amber roy
Monday, 24 September 2007
- AMBER: MacOSX installation help Quantum Mechanics
- AMBER: Bertrand P. S. Russell
- AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation.. cgji
- AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it
- RE: AMBER: MacOSX installation help Ross Walker
- RE: AMBER: MAXPR Ross Walker
- AMBER: calcium parameters Mattia Mori - CERM
- RE: AMBER: Pribelm with Minimization & MD Ross Walker
- AMBER: RE: 回复： RE: Asking for help about heating Ross Walker
- RE: AMBER: calcium parameters Ross Walker
- AMBER: effective step period for constant pH simulations Lillian chong
- Re: AMBER: effective step period for constant pH simulations Adrian Roitberg
- Re: AMBER: Help WARNING: The unperturbed charge of the unit Ilyas Yildirim
- AMBER: problem with ptraj Terry Lang
- Re: AMBER: problem with ptraj Carlos Simmerling
- AMBER: energy calculation gurpreet singh
Tuesday, 25 September 2007
- Re: AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it
- AMBER: Copper and Chlorine parameters Syed Tarique Moin
- RE: AMBER: Help WARNING: The unperturbed charge of the unit Steve Spronk
- RE: AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it
- AMBER: total energy in sander and nmode mbrut.laas.fr
- Re: AMBER: energy calculation David A. Case
- Re: AMBER: total energy in sander and nmode David A. Case
- AMBER: atomicfluct Andres Palencia
- AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Minimization and MD input files Carlos Simmerling
- RE: AMBER: Help WARNING: The unperturbed charge of the unit Ilyas Yildirim
- Re: AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Solvation net forces Tyler Luchko
- RE: AMBER: Minimization and MD input files Ross Walker
- Re: AMBER: Minimization and MD input files David A. Case
- Re: AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Minimization and MD input files Carlos Simmerling
- RE: AMBER: Minimization and MD input files Ross Walker
- Re: AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Solvation net forces Nicolas Lux Fawzi
- Re: AMBER: Minimization and MD input files Carlos Simmerling
- Re: AMBER: Minimization and MD input files Su Nwe
- Re: AMBER: Minimization and MD input files Carlos Simmerling
- AMBER: Re: using RESP Ilyas Yildirim
- AMBER: regarding energy calculation gurpreet singh
- Re: AMBER: Re: using RESP FyD
Wednesday, 26 September 2007
- Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin
- Re: AMBER: regarding energy calculation Abi Ghanem josephine
- AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Carlos Simmerling
- RE: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Ross Walker
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Harianto Tjong
- AMBER: NMR refinement Wenyong Tong
- Re: AMBER: NMR refinement David A. Case
- AMBER: Solvation Issues Eddie Men
- Re: AMBER: Solvation Issues David A. Case
- AMBER: solvation issues Eddie Men
- Re: AMBER: Solvation Issues David Cerutti
- Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin
- AMBER: Reproducing constant pH results !! Pradipta Bandyopadhyay
Thursday, 27 September 2007
- AMBER: force field question Eddie Men
- AMBER: needing more detailed knowledge of tautp than the manual 宫维斌
- AMBER: plotdat: Amber Data Plotting Program S. Ravichandran
- AMBER: restarting REMD simulations Austin B. Yongye
- AMBER: step-by-ste weight changes of dwt -- patch? Douglas Kojetin
- Re: AMBER: force field question David A. Case
- Re: AMBER: needing more detailed knowledge of tautp than the manual David A. Case
- Re: AMBER: restarting REMD simulations Carlos Simmerling
- Re: AMBER: step-by-ste weight changes of dwt -- patch? David A. Case
- 回复:Re: AMBER: needing more detailed knowledge of tautp than the manual 宫维斌
- AMBER: implicit minimization Dr. Devanathan Raghunathan
Friday, 28 September 2007
- AMBER: the box vectors for a Leap generated truncated octahedron Vlad Cojocaru
- Re: AMBER: implicit minimization David A. Case
- Re: AMBER: NMR refinement Wenyong Tong
- AMBER: follow-up Wenyong Tong
- Re: AMBER: follow-up David A. Case
- Re: AMBER: follow-up Wenyong Tong
- Re: AMBER: Solvation Issues Eddie Men
Saturday, 29 September 2007
- AMBER: cyclohexane and decalin on amber Jones de Andrade
- AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía
- Re: AMBER: fragment parametrization tutorial? Carlos Simmerling
- Re: AMBER: Solvation Issues David Cerutti
- Re: AMBER: fragment parametrization tutorial? David A. Case
Sunday, 30 September 2007
- Re: AMBER: fragment parametrization tutorial? FyD
- Re: AMBER: cyclohexane and decalin on amber FyD
- Re: AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía

Last message date: Wed Oct 03 2007 - 06:07:04 PDT
Archived on: Fri Nov 22 2024 - 05:53:36 PST

Amber Archive Sep 2007 by date