Amber Archive Jun 2008: by date

Sunday, 1 June 2008
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra
- AMBER: PCA - analysis Ibrahim Moustafa
Monday, 2 June 2008
- Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra
- AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith
- Re: AMBER: ptraj has trouble with x-plor psf file from VMD Jufang Shan
- Re: AMBER: Jarzynski David Mobley
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker
- Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 David A. Case
- AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick
- Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling
- AMBER: MAXAT can not be changed for AMBERTool 1.0 Hu, Shaowen (JSC-SK)[USRA]
- RE:AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick
- Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling
- AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick
- AMBER: PCA analysis Ibrahim Moustafa
- AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan
- AMBER: Error message: Install Amber9 on fedora 9 Chih-Ying Lin
- Re: AMBER: Error message: Install Amber9 on fedora 9 David A. Case
- Re: AMBER: MAXAT can not be changed for AMBERTool 1.0 David A. Case
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case
- AMBER: writing a script in amber Taufik Al-Sarraj
- Re: AMBER: gasteiger is not working with ambertools 1.0 David A. Case
Tuesday, 3 June 2008
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko
- AMBER: corrupted restart file yavuzturkm.prc.boun.edu.tr
- AMBER: Temperature controlling method in AMBER tinni sona
- Re: AMBER: corrupted restart file Cenk \(Jenk\) Andac
- Re: AMBER: corrupted restart file Carlos Simmerling
- AMBER: Trajectory in "Sietraj" Alfredo Quevedo
- RE: AMBER: Trajectory in "Sietraj" Purisima, Enrico
- Re: AMBER: Trajectory in "Sietraj" Alfredo Quevedo
- Re: AMBER: Trajectory in "Sietraj" Florian Haberl
- RE: AMBER: Trajectory in "Sietraj" Purisima, Enrico
- Re: AMBER: gasteiger is not working with ambertools 1.0 Alan
- Re: AMBER: Temperature controlling method in AMBER David A. Case
- Re: AMBER: Trajectory in "Sietraj" Alfredo Quevedo
- AMBER: solvate box : buffer list fatima.chami.durham.ac.uk
- Re: AMBER: solvate box : buffer list David A. Case
- RE: AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan
- RE: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Ross Walker
- Re: AMBER: drawing repeated units Taufik Al-Sarraj
- RE: AMBER: drawing repeated units Ross Walker
- Re: AMBER: Missing gaff angle parameters for dimethyl esters Junmei Wang
- Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith
- Re: AMBER: drawing repeated units Taufik Al-Sarraj
- RE: AMBER: drawing repeated units Ross Walker
Wednesday, 4 June 2008
- Re: AMBER: solvate box : buffer list fatima.chami.durham.ac.uk
- AMBER: problems with sleap Alan
- AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen
- AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei
- Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case
- AMBER: amber installation on cluster Pankaj R. Daga
- Re: AMBER: amber installation on cluster David A. Case
- RE: AMBER: amber installation on cluster Ross Walker
- AMBER: NAB documentation for programmers ramu.vt.edu
- AMBER: ptraj imaging issue Vlad Cojocaru
- Re: AMBER: drawing repeated units Taufik Al-Sarraj
- AMBER: syn and anti conformation Rabin
- Re: AMBER: syn and anti conformation Carlos Simmerling
- Re: AMBER: ptraj imaging issue Jianyin Shao
- Re: AMBER: problems with sleap David A. Case
- Re: AMBER: Error message: Install Amber9 on fedora 9 Chih-Ying Lin
- RE: AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme
- Re: AMBER: problems with sleap Alan
Thursday, 5 June 2008
- AMBER: problem of install amber9 Xioling Chuang
- Re: AMBER: ptraj imaging issue Vlad Cojocaru
- RE: AMBER: problem of install amber9 Xioling Chuang
- AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal
- AMBER: Free energy of dissociation fatima.chami.durham.ac.uk
- Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Carlos Simmerling
- AMBER: Vaccum Simulations in PMEMD !! Sampath Koppole
- Re: AMBER: Free energy of dissociation Gustavo Seabra
- AMBER: netcdf configure returned 1 Jens Lattig
- Re: AMBER: Vaccum Simulations in PMEMD !! Robert Duke
- Re: AMBER: ptraj imaging issue Vlad Cojocaru
- AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig
- Re: AMBER: Free energy of dissociation fatima.chami.durham.ac.uk
- AMBER: A problem of installing Amber10 Yicun Ni
- Re: AMBER: Free energy of dissociation David Mobley
- Re: AMBER: ptraj imaging issue Jianyin Shao
- AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat
- Re: AMBER: A problem of installing Amber10 David A. Case
- Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case
- Re: AMBER: A problem of installing Amber10 Harry Ni
- Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint? David A. Case
- Re: AMBER: A problem of installing Amber10 David A. Case
- Re: AMBER: Error message: Install Amber9 on fedora 9 David A. Case
- AMBER: RE: solvating RNA in 8M urea box Ross Walker
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme
- AMBER: Query on MM-PBSA Neha Gandhi
Friday, 6 June 2008
- AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig
Thursday, 5 June 2008
- Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal
Friday, 6 June 2008
- AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian
- AMBER: Problem While Installing Amber Ranga Swamy
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru
- AMBER: NAN errors still exist Praveena Gopal
- Re: AMBER: NAN errors still exist Carlos Simmerling
- AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick
- Re: AMBER: VMD Movie .mdcrd file ptraj David Watson
- RE: AMBER: Problem While Installing Amber Ross Walker
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory David Case
- AMBER: NAB documentation David Case
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David Case
- AMBER: Problems simulating a protein-ligand complex Sasha Buzko
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru
- Re:AMBER:VMD Movie.mdcrd Campbell, Patrick
- Re: AMBER: Problems simulating a protein-ligand complex David A. Case
- Re: AMBER: A problem of installing Amber10 Harry Ni
- Re: AMBER: A problem of installing Amber10 David A. Case
- Re: AMBER: A problem of installing Amber10 Harry Ni
- Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko
- RE: AMBER: Problems simulating a protein-ligand complex Ross Walker
- RE: AMBER: Problems simulating a protein-ligand complex Sasha Buzko
- RE: AMBER: Problems simulating a protein-ligand complex Ross Walker
- RE: AMBER: Problems simulating a protein-ligand complex Sasha Buzko
- Re: AMBER: NAB documentation Ramu Anandakrishnan
- AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg
- RE: AMBER: Problems simulating a protein-ligand complex Ross Walker
- RE: AMBER: 100 short MD runs within a single Sander script? Ross Walker
- Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko
Saturday, 7 June 2008
- Re: AMBER: Problems simulating a protein-ligand complex Adrian Roitberg
- Re: AMBER: Problems simulating a protein-ligand complex M. L. Dodson
- AMBER: Problem of Ptraj analyze matrix Qi Yan
Sunday, 8 June 2008
- AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra
- AMBER: problem in starting sander Qiuting Hong
- Re: AMBER: Combine mdcrd while stripping WAT problem Gustavo Seabra
- Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling
- Re: AMBER: problem in starting sander Carlos Simmerling
- Re: AMBER: problem in starting sander Qiuting Hong
- RE: AMBER: problem in starting sander Ross Walker
- Re: AMBER: Problem of Ptraj analyze matrix David A. Case
- Re: AMBER: NAB documentation David A. Case
- Re: AMBER: problem in starting sander Qiuting Hong
- Re: AMBER: problem in starting sander Carlos Simmerling
- AMBER: MM-PBSA and delphi Neha Gandhi
- Re: AMBER: MM-PBSA and delphi Neha Gandhi
Monday, 9 June 2008
- Re: AMBER: MM-PBSA and delphi Navnit Kumar Mishra
- Re: AMBER: MM-PBSA and delphi Neha Gandhi
- AMBER: Problem of Ptraj analyze matrix Qi Yan
- Re: AMBER: Problem of Ptraj analyze matrix Adrian Roitberg
- RE: AMBER: Problem of Ptraj analyze matrix Qi Yan
- Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko
- RE: AMBER: MM-PBSA and delphi Qi Yan
- AMBER: Calcium and Magnesium LJ parameters Daniel Smith
Tuesday, 10 June 2008
- Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig
- Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Mark Williamson
- AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang
- AMBER: SMD pulling velocity fatima.chami.durham.ac.uk
- Re: AMBER: SMD pulling velocity Gustavo Seabra
- Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang
- Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case
- AMBER: how to calculate the interaction energy Wang,Ying
- Re: AMBER: how to calculate the interaction energy Thomas Steinbrecher
- Re: AMBER: how to calculate the interaction energy Wang,Ying
- AMBER: amber10 installation problem Ed Pate
- AMBER: Simulating complexes with magnesium atoms Sasha Buzko
- AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu
- Re: AMBER: amber10 installation problem Robert Duke
- RE: AMBER: amber10 installation problem Ross Walker
Wednesday, 11 June 2008
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian
- AMBER: box shape changed at NVT fatima.chami.durham.ac.uk
- Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra
- AMBER: QM/MM Taufik Al-Sarraj
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David A. Case
- Re: AMBER: box shape changed at NVT David A. Case
- Re: AMBER: QM/MM Gustavo Seabra
- Re: AMBER: QM/MM Taufik Al-Sarraj
- AMBER: Equilibration/Heating - Protein fixed -Problem dpandit.brandeis.edu
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Jianyin Shao
- Re: AMBER: PTRAJ - Segmentation Fault Jianyin Shao
- RE: AMBER: Equilibration/Heating - Protein fixed -Problem Vahdati N.
- Re: AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu
- Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case
- Re: AMBER: PTRAJ - Segmentation Fault Thomas Cheatham
- RE: AMBER: Equilibration/Heating - Protein fixed -Problem dpandit.brandeis.edu
- AMBER: sander.MPI / openmpi on PBS Arturas Ziemys
- AMBER: 2D RMS plot Steve Spronk
- Re: AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu
- AMBER: Trajectory - Average Structure - Equilibration dpandit.brandeis.edu
- AMBER: Question for how to get all eigenvalues by "analyze matrix" Qi Yan
- Re: AMBER: 2D RMS plot Jianyin Shao
- AMBER: Antechamber and topology file TAEJIN KIM
- AMBER: Coordinated Zinc Khaled Barakat
- Re: AMBER: Combine mdcrd while stripping WAT problem Alexander Metz
Thursday, 12 June 2008
- Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra
- Re: AMBER: Combine mdcrd while stripping WAT problem Alexander Metz
- Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling
- AMBER: updating documentation Alan
- AMBER: using Velocity-Verlet algorithm oguz gurbulak
- AMBER: anisotropic pressure scaling ntp=2 fatima.chami.durham.ac.uk
- Re: AMBER: anisotropic pressure scaling ntp=2 David A. Case
- Re: AMBER: updating documentation David A. Case
- RE: AMBER: 2D RMS plot Steve Spronk
- Re: AMBER: Coordinated Zinc David A. Case
- Re: AMBER: Antechamber and topology file David A. Case
- Re: AMBER: using Velocity-Verlet algorithm David A. Case
- AMBER: SMD RESTRAINTS fatima.chami.durham.ac.uk
- AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell
- Re: AMBER: SMD RESTRAINTS Adrian Roitberg
- Re: AMBER: SMD RESTRAINTS fatima.chami.durham.ac.uk
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell
- Re: AMBER: Compile amber10 parallel with suppied LAM Gustavo Seabra
- AMBER: How to get all eigenvalues by "analyze matrix" Qi Yan
- Re: AMBER: potassium ion Lars Skjærven
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell
- Re: AMBER: Compile amber10 parallel with suppied LAM Gustavo Seabra
- Re: AMBER: SMD RESTRAINTS Adrian Roitberg
- Re: AMBER: updating documentation Alan
- AMBER: Sander crashes >99999 atoms plmallip.mail.uh.edu
- Re: AMBER: Sander crashes >99999 atoms David A. Case
- Re: AMBER: Sander crashes >99999 atoms plmallip.mail.uh.edu
- AMBER: PCAL and polar contribution in the output file Neha Gandhi
Friday, 13 June 2008
- AMBER: MM-GBSA with very positive GB value Catein Catherine
- Re: AMBER: MM-GBSA with very positive GB value Carlos Simmerling
- Re: AMBER: Coordinated Zinc FyD
- Re: AMBER: updating documentation David A. Case
- Re: AMBER: Sander crashes >99999 atoms David A. Case
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell
- AMBER: amber10 make fails for static/parallel James W. Caldwell
- RE: AMBER: MM-GBSA with very positive GB value Catein Catherine
Saturday, 14 June 2008
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Mark Williamson
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David A. Case
- Re: AMBER: potassium ion Bill Ross
Sunday, 15 June 2008
- Re: AMBER: PCAL and polar contribution in the output file Hannes Kopitz
- Re: AMBER: PCAL and polar contribution in the output file Neha Gandhi
- AMBER: Ewald error estimate Pavan G
- AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang
- Re: AMBER: Problem with running refinement of NMR structures with RDCs David A. Case
Monday, 16 June 2008
- AMBER: Eigenmode dynamics in Ptraj fatima.chami.durham.ac.uk
- Re: AMBER: problems with sleap David A. Case
- Re: AMBER: problems with sleap Alan
- AMBER: the SPCFW water model Vlad Cojocaru
- AMBER: sander.MPI / parallel Arturas Ziemys
- Re: AMBER: sander.MPI / parallel Carlos Simmerling
- AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez
- Re: AMBER: sander.MPI / parallel Arturas Ziemys
- Re: AMBER: sander.MPI / parallel David LeBard
- Re: AMBER: sander.MPI / parallel David LeBard
- Re: AMBER: sander.MPI / parallel Arturas Ziemys
- Re: AMBER: sander.MPI / parallel Carlos Simmerling
- Re: AMBER: sander.MPI / parallel David A. Case
- Re: AMBER: problems with sleap Qi Zhang
- AMBER: about resp charges WanJ Ding
- AMBER: IRED to time correlation fatima.chami.durham.ac.uk
- Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case
- Re: AMBER: [Fwd: segmentation fault in nmode] JAMES W CALDWELL
- AMBER: program to calculate rmsd rams rams
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard
Tuesday, 17 June 2008
- Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez
- Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez
- RE: AMBER: program to calculate rmsd Ross Walker
- Re: AMBER: How to solve - Missing BELE for MM in 1 in amber. Hannes Kopitz
- AMBER: improving GAFF sulfonamide parameters Floris Buelens
- AMBER: ligand complexed simulation Siddharth Rastogi
- AMBER: suggestion for next amberTools 1.1 Alan
- Re: AMBER: ligand complexed simulation mori.cerm.unifi.it
- Re: AMBER: about resp charges FyD
- AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? David A. Case
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Jianyin Shao
- Re: AMBER: suggestion for next amberTools 1.1 David A. Case
- RE: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk
- AMBER: to understand GAFF: about A and B coefficients Alan
- Re: AMBER: to understand GAFF: about A and B coefficients David A. Case
- AMBER: multiple dihedral restraints using group (in Amber 10) mkseo
Wednesday, 18 June 2008
- AMBER: MM-PBSA Neha Gandhi
- Re: AMBER: multiple dihedral restraints using group (in Amber 10) fatima.chami.durham.ac.uk
- AMBER: Eigenmode dynamics - imaging traj fatima.chami.durham.ac.uk
- AW: AMBER: MM-PBSA Alexander Metz
- Re: AMBER: Eigenmode dynamics - imaging traj E.M.
- Re: AMBER: Eigenmode dynamics - imaging traj Myunggi Yi
- Re: AMBER: MM-PBSA Miguel Ortiz-Lombardía
- AMBER: about gaff.dat in ambeTools 1.0 Alan
- AMBER: ptraj fatima.chami.durham.ac.uk
- libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 M. L. Dodson
- AMBER: cross correlation function using iRED matrix fatima.chami.durham.ac.uk
- Re: AMBER: cross correlation function using iRED matrix Myunggi Yi
- AMBER: tip3p water and shake Wang,Ying
- Re: AMBER: about resp charges wanjian ding
- RE: AMBER: tip3p water and shake Ross Walker
- AMBER: sp carbon notation? Laura Benton
- Re: AMBER: sp carbon notation? David A. Case
- Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 David A. Case
- RE: AMBER: tip3p water and shake Wang,Ying
- AMBER: questions about gaff yzhao
- Re: AMBER: questions about gaff Mark Williamson
- RE: AMBER: tip3p water and shake Wang,Ying
- AMBER: [Fwd: failure to load box parameters] Daniel Smith
- AMBER: How to create average structure? Shen, Lingling
- Re: AMBER: How to create average structure? Carlos Simmerling
- Re: AMBER: tip3p water and shake David A. Case
- Re: AMBER: [Fwd: failure to load box parameters] David A. Case
Thursday, 19 June 2008
- AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami.durham.ac.uk
- AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge)
- AMBER: Installation Problem of AMBER10 bhargav patel
- Re: AMBER: Installation Problem of AMBER10 Carlos Simmerling
- Re: AMBER: Correlation functions from iRED analysis Myunggi Yi
- RE: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge)
- Re: AMBER: Correlation functions from iRED analysis Myunggi Yi
- RE: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge)
- RE: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk
- RE: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk
- AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami.durham.ac.uk
- Re: AMBER: Installation Problem of AMBER10 David A. Case
- Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou
- SV: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge)
- Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami.durham.ac.uk
- Re: SV: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk
- Re: AMBER: Correlation functions from iRED analysis Myunggi Yi
- Re: AMBER: Installation Problem of AMBER10 Bill Ross
- SV: SV: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge)
- AMBER: simple sander James W. Caldwell
- Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case
- Re: AMBER: simple sander David A. Case
- Re: AMBER: simple sander JAMES W CALDWELL
Friday, 20 June 2008
- AMBER: ligand complexed simulation Siddharth Rastogi
- AMBER: GAFF for organic crystals Rabone, Jeremy
- Re: AMBER: Installation Problem of AMBER10 bhargav patel
- AMBER: trajout input Thomas Leonard
- Re: AMBER: trajout input Barbault Florent
- Re: AMBER: trajout input Thomas Leonard
- AMBER: rdparm help Alan
- Re: Re: AMBER: questions about gaff Steven
- Re: AMBER: rdparm help Thomas Cheatham
- AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson
- Re: AMBER: AmberTools 1.0 installation error: x86_64 David A. Case
- Re: AMBER: trajout input Thomas Cheatham III
- AMBER: Amber 10 timing Ed Pate
- Re: AMBER: Installation Problem of AMBER10 David A. Case
- Re: AMBER: Installation Problem of AMBER10 Bill Ross
- Re: AMBER: Amber 10 timing Robert Duke
Saturday, 21 June 2008
- AMBER: SIZE.h problems 欧阳德方
- Re: AMBER: SIZE.h problems Mark Williamson
Sunday, 22 June 2008
- AMBER: (no subject) Daniel B. Kaplan
- Re: AMBER: trajout input Swarup Gupta
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme
Monday, 23 June 2008
- AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana
- Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez
- AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang
- AMBER: source of AMBER9 Germain Vallverdu
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber David A. Case
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber Junmei Wang
- AMBER: amber10/dat/leap/cmd/README need update Alan
- Re: AMBER: (no subject) Junmei Wang
- Re: AMBER: amber10/dat/leap/cmd/README need update Vlad Cojocaru
- Re: AMBER: How to adjust the problem of "Vlimit exceeded" David A. Case
- Re: AMBER: GAFF for organic crystals Junmei Wang
- Re: AMBER: rdparm help Alan
- AMBER: Antechamber Question Daniel B. Kaplan
- Re: AMBER: [Fwd: failure to load box parameters] Daniel Smith
- AMBER: problems form the pdb to the mol2 Rilei Yu
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme
- Re: AMBER: MM-PBSA in AMBER 10 David A. Case
- Re: AMBER: problems form the pdb to the mol2 David A. Case
- AMBER: dihedral energy calculation inconsistent with gaussian's result Q733
Tuesday, 24 June 2008
- Re: AMBER: dihedral energy calculation inconsistent with gaussian's result Jerome.GOLEBIOWSKI.unice.fr
- Re: AMBER: Installation Problem of AMBER10 bhargav patel
- AMBER: unsubscribe amber sanket.deshmukh.ucd.ie
- AMBER: A-prime RNA input file 欧阳德方
- Re: AMBER: Antechamber Question Junmei Wang
- Re: AMBER: about gaff.dat in ambeTools 1.0 Junmei Wang
- Re: AMBER: problems form the pdb to the mol2 Junmei Wang
- AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan
- Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais
- Re: AMBER: qmmm_DFTB problem Gustavo Seabra
- AMBER: Compilation of amber8 patched with ramd Francesco Pietra
- Re: AMBER: improving GAFF sulfonamide parameters Junmei Wang
- Re: AMBER: Installation Problem of AMBER10 Atro Tossavainen
- AMBER: dihedral potential with odd periodicity Germain Vallverdu
- Re: AMBER: Installation Problem of AMBER10 David A. Case
- Re: AMBER: Compilation of amber8 patched with ramd David A. Case
- Re: AMBER: Compilation of amber8 patched with ramd Vlad Cojocaru
- Re: AMBER: [Fwd: failure to load box parameters] David A. Case
- AMBER: Using AMBER forces Steven Winfield
- AMBER: rdparm Segmentation fault on Ubuntu Alan
- AMBER: Further request answers from Dr. Junmei Wang Rilei Yu
- ： Re: AMBER: problems form the pdb to the mol2 Rilei Yu
- RE: AMBER: Using AMBER forces Ross Walker
- Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra
- Re: AMBER: Further request answers from Dr. Junmei Wang Junmei Wang
- Re: AMBER: Using AMBER forces Steven Winfield
- RE: AMBER: Using AMBER forces Ross Walker
- Re: AMBER: drawing repeated units Taufik Al-Sarraj
- RE: AMBER: drawing repeated units Ross Walker
- Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra
- Re: AMBER: Compilation of amber8 patched with ramd David A. Case
- AMBER: how to derive torsional angle parameters in gaff Junmei Wang
Wednesday, 25 June 2008
- Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra
- AMBER: Debugf AMBER9 John Palmeri
- Re: AMBER: Compilation of amber8 patched with ramd Vlad Cojocaru
- AMBER: local coordinate system question caoch
- AMBER: TI calculations in Amber10 Samuel Genheden (a03samge)
- AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais
- Re: AMBER: local coordinate system question David A. Case
- AMBER: A problem of dihedral angle Harry (Yicun) Ni
- RE: AMBER: A problem of dihedral angle Ross Walker
- Re: AMBER: A problem of dihedral angle Carlos Simmerling
- Re: AMBER: TI calculations in Amber10 Thomas Steinbrecher
- AMBER: Re: AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2 Junmei Wang
- AMBER: amber10 compile gfortran question James W. Caldwell
- Re: AMBER: [Fwd: failure to load box parameters] Daniel Smith
- Re: AMBER: amber10 compile gfortran question David A. Case
- Re: AMBER: [Fwd: failure to load box parameters] David A. Case
- RE: AMBER: amber10 compile gfortran question James W. Caldwell
- AMBER: sleap - TER-card In Hee Park
- Re: AMBER: A problem of dihedral angle Harry (Yicun) Ni
- AMBER: rdparm Segmentation fault Alan
- Re: AMBER: sleap - TER-card David A. Case
- AMBER: Antechamber/mopac am1-bcc charge Dong Xu
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang
- Re: AMBER: rdparm Segmentation fault David A. Case
- AMBER: unsubscribe amber Rabin
- AMBER: (no subject) Daniel B. Kaplan
- Re: AMBER: Antechamber/mopac am1-bcc charge Dong Xu
Thursday, 26 June 2008
- Re: AMBER: how to derive torsional angle parameters in gaff Balazs JOJART
- AMBER: Amber:unsubscribe amber sanket.deshmukh.ucd.ie
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang
- AMBER: concerning force fields Adrien Delmont
- AMBER: Peseckis, Steven M.
- Re: AMBER: concerning force fields Carlos Simmerling
- Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra
- AMBER: ligand partial charge and conformation question Dong Xu
- Re: AMBER: concerning force fields Adrien Delmont
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang
- AMBER: output file AMBER9_MPI Vijay Manickam Achari
- Re: AMBER: concerning force fields Carlos Simmerling
- Re: AMBER: improving GAFF sulfonamide parameters David Mobley
- Re: AMBER: Antechamber/mopac am1-bcc charge FyD
- AMBER: Dihedral Angle Parameters Ilyas Yildirim
- Re: AMBER: Dihedral Angle Parameters Carlos Simmerling
- Re: AMBER: Dihedral Angle Parameters Ilyas Yildirim
- RE: AMBER: Dihedral Angle Parameters Ross Walker
- Re: AMBER: Dihedral Angle Parameters Carlos Simmerling
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang
- Re: AMBER: sleap - TER-card In Hee Park
- Re: AMBER: sleap - TER-card David A. Case
Friday, 27 June 2008
- AMBER: REMD Amber10 : error in reading namelist cntrl rebeca
- Re: AMBER: Antechamber/mopac am1-bcc charge FyD
- Re: AMBER: concerning force fields Adrien Delmont
- Re: AMBER: concerning force fields Carlos Simmerling
- AMBER: Group specification problem fatima.chami.durham.ac.uk
- Re: AMBER: concerning force fields Karl Kirschner (kkirschn)
- Re: AMBER: REMD Amber10 : error in reading namelist cntrl Carlos Simmerling
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang
- AMBER: pmemd 10 output Vlad Cojocaru
- RE: AMBER: pmemd 10 output Ross Walker
- Re: AMBER: pmemd 10 output Vlad Cojocaru
- Re: AMBER: pmemd 10 output Vlad Cojocaru
- AMBER: Test scripts James W. Caldwell
- RE: AMBER: pmemd 10 output Ross Walker
- AMBER: ptraj - read in part of trajectory Seth Lilavivat
- Re: AMBER: Test scripts David A. Case
- RE: AMBER: Test scripts James W. Caldwell
- Re: AMBER: ptraj - read in part of trajectory Vlad Cojocaru
- Re: AMBER: ptraj - read in part of trajectory Carlos Simmerling
- Re: AMBER: ptraj - read in part of trajectory Seth Lilavivat
- Re: AMBER: David A. Case
- AMBER: question about the charge Harry (Yicun) Ni
- Re: AMBER: question about the charge Carlos Simmerling
- Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra
- Re: AMBER: question about the charge Harry (Yicun) Ni
Saturday, 28 June 2008
- Re: AMBER: Antechamber/mopac am1-bcc charge FyD
- Re: AMBER: concerning force fields Adrien Delmont
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? David A. Case
- Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra
Sunday, 29 June 2008
- AMBER: Seed for random number generator Francesco Pietra
- Re: AMBER: Antechamber/mopac am1-bcc charge FyD
- AMBER: RE: AMBER 10 failure to run in UBUNTU Peseckis, Steven M.
Monday, 30 June 2008
- AMBER: Constrained group fatima.chami.durham.ac.uk
- AMBER: NMR refinement teresa.ierano.unina.it
- AMBER: nmode analysis Joachim Reichelt
- Re: AMBER: nmode analysis Mark Williamson
- Re: AMBER: nmode analysis Joachim Reichelt
- RE: AMBER: nmode analysis Vahdati N.
- AMBER: hold atoms fixed Boutheina Kerkeni
- Re: AMBER: hold atoms fixed Carlos Simmerling
- Re: AMBER: hold atoms fixed Boutheina Kerkeni
- Re: AMBER: hold atoms fixed fatima.chami.durham.ac.uk
- Re: AMBER: hold atoms fixed Gustavo Seabra
- AMBER: wrapping a restart file fatima.chami.durham.ac.uk
- Re: AMBER: NMR refinement David A. Case
- Re: AMBER: wrapping a restart file Gustavo Seabra
- Re: AMBER: Constrained group Robert Duke
- AMBER: watershell cero? rebeca
- AMBER: (no subject) fatima.chami.durham.ac.uk
- Re: AMBER: wrapping a restart file Robert Duke
- Re: AMBER: (no subject) Robert Duke
- AMBER: MM-PBSA calculation problem Wei Huang
- AMBER: error in reading namelist cntrl Maria Frushicheva
- Re: AMBER: error in reading namelist cntrl David A. Case
- RE: AMBER: error in reading namelist cntrl Ross Walker
- AMBER: Regarding force field ff02 and ion library Abhishek Singh
- AMBER: missing torsion parameters John Bennett
- Re: AMBER: Regarding force field ff02 and ion library David A. Case
- Re: AMBER: Regarding force field ff02 and ion library Thomas Cheatham III
- RE: AMBER: missing torsion parameters Ross Walker

Last message date: Wed Jul 02 2008 - 06:07:29 PDT
Archived on: Mon Apr 22 2024 - 05:53:36 PDT

Amber Archive Jun 2008 by date