Amber Archive Oct 2006: by date

Sunday, 1 October 2006
- Re: AMBER: chemical shift restrains David A. Case
- Re: AMBER: RE: Amber8: problem related to antechamber David A. Case
- Re: AMBER: Multiple Timestep MD David A. Case
- Re: AMBER: RE: Amber8: problem related to antechamber David A. Case
- Re: AMBER: Multiple Timestep MD Robert Duke
- AMBER: polarization effects Vitor Manuel Sousa F?x
- AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
Monday, 2 October 2006
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case
- Re: AMBER: proposed patch for ptraj/evec.c (Amber 9.0) David A. Case
- Re: AMBER: problem to center solvateshell David A. Case
- AMBER: Pressure in MD Fenghui Fan
- Re: AMBER: Pressure in MD Thomas Steinbrecher
- AMBER: how to run a mm_pbsa on a minimized structure? Wang, Xuelin
- AMBER: mdcrd file Fenghui Fan
- Re: AMBER: mdcrd file Bill Ross
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
- Re: AMBER: mdcrd file Fenghui Fan
- Re: AMBER: mdcrd file Bill Ross
- RE: AMBER: mdcrd file Ross Walker
- AMBER: How to get the VDW contacts' messages from the mdcrd files Jiapu.Zhang.csiro.au
- RE: AMBER: problem to center solvateshell Bonnet, Pascal [PRDBE]
Tuesday, 3 October 2006
- AMBER: Pressure problem with restraint Jianhui
- AMBER: hbond analysis Vlad Cojocaru
- Re: AMBER: hbond analysis Thomas Cheatham
- AMBER: MM_PBSA error Shozeb Haider
- Re: AMBER: hbond analysis Vlad Cojocaru
- Re: AMBER: hbond analysis Thomas Cheatham
- Re: AMBER: hbond analysis Vlad Cojocaru
- AMBER: how to calculate rmsd for non hydrogen at oms? yxiong99
- Re: AMBER: how to calculate rmsd for non hydrogen at oms? Viktor Hornak
- Re: AMBER: how to calculate rmsd for non hydrogen at oms? JunJun Liu
- AMBER: mm_pbsa PBCAL William Wei
- AMBER: Distance between two atoms Fenghui Fan
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
- AMBER: Re: Distance between two atoms Fenghui Fan
- Re: AMBER: Re: Distance between two atoms Fenghui Fan
Wednesday, 4 October 2006
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Scott Brozell
- AMBER: RMSD: is it related to flexibility? a a
- Re: AMBER: RMSD: is it related to flexibility? Carlos Simmerling
- AMBER: Distance between 2 atoms Fenghui Fan
- AMBER: on rst file Fenghui Fan
- Re: AMBER: hbond analysis Sergey Samsonov
- Re: AMBER: Pressure problem with restraint David A. Case
- Re: AMBER: RMSD: is it related to flexibility? David A. Case
- Re: AMBER: hbond analysis Vlad Cojocaru
- AMBER: atom nomination in the PDB file produced by Amber Fenghui Fan
- AMBER: Re: atom nomination in the PDB file produced by Amber Fenghui Fan
- AMBER: change from .rst file to .mdcrd file Wang, Xuelin
- Re: AMBER: on rst file Bill Ross
- AMBER: Is GB/SANDER slower than TIP3P/PMEMD b86203054.ntu.edu.tw
- Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD Robert Duke
- Re: AMBER: Pressure problem with restraint Jianhui
- RE: AMBER: Is GB/SANDER slower than TIP3P/PMEMD Ross Walker
- Re: AMBER: Pressure problem with restraint David A. Case
- Re: Re: AMBER: Pressure problem with restraint Jianhui
- Re: AMBER: change from .rst file to .mdcrd file JunJun Liu
- AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim
- Re: AMBER: AMBER minimization vs. Gaussian optimization Thomas Cheatham
- Re: AMBER: hbond analysis Thomas Cheatham
- AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth
- Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham
- Re: AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim
- Re: Re: AMBER: Pressure problem with restraint David A. Case
- Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham
- AMBER: VMD PDB into LEAP Readable PDB Akshay Patny
- Re: AMBER: RMSD: is it related to flexibility? a a
- Re: AMBER: AMBER minimization vs. Gaussian optimization FyD
- Re: AMBER: hbond analysis Sergey Samsonov
Thursday, 5 October 2006
- AMBER: Missing values for MM VDW bala
- AMBER: PBSA calculation fail .... Changge Ji
- Re: AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth
- Re: AMBER: ptraj hbond analysis troubles Robert Duke
- Re: AMBER: VMD PDB into LEAP Readable PDB David A. Case
- Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham
- Re: AMBER: RMSD: is it related to flexibility? Gustavo Seabra
- Re: AMBER: PBSA calculation fail .... Ray Luo
- AMBER: Building polymer with sequence command gtg549i.mail.gatech.edu
- Re: AMBER: ptraj hbond analysis troubles Robert Duke
- Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham
- AMBER: generating resp input files with antechamber dhruva chakravorty
- Re: AMBER: Building polymer with sequence command David A. Case
- AMBER: water prmtop/inpcrd problem Akshay Patny
- Re: AMBER: ptraj hbond analysis troubles Robert Duke
- Re: AMBER: water prmtop/inpcrd problem David A. Case
- Re: Re: AMBER: PBSA calculation fail .... Changge Ji
- AMBER: (no subject) Prashanth Athri
- AMBER: Calculation of Dihedral constants Prashanth Athri
- Re: AMBER: RMSD: is it related to flexibility? a a
Friday, 6 October 2006
- Re: AMBER: water prmtop/inpcrd problem Ilyas Yildirim
- RE: AMBER: water prmtop/inpcrd problem Akshay Patny
- Re: AMBER: PBSA calculation fail .... Ray Luo
- Re: AMBER: (no subject) David A. Case
- Re: AMBER: RMSD: is it related to flexibility? Feng X Zhou
- AMBER: LEAP error Akshay Patny
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell
- Re: AMBER: LEAP error Scott Brozell
- AMBER: How to merge two molecules to one Myunggi Yi
- Re: AMBER: LEAP error Akshay Patny
- Re: AMBER: LEAP error Ilyas Yildirim
Saturday, 7 October 2006
- AMBER: MM_PBSA Rajendra P. OJHA
Sunday, 8 October 2006
- AMBER: question about building molecules Rita Cassia
- Re: AMBER: question about building molecules David A. Case
- Re: AMBER: LEAP error David A. Case
- AMBER: Potential of Mean Force calculation or Steered molecular dynamics a a
Monday, 9 October 2006
- Re: AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
- AMBER: some puzzles in equilibration MD Zhihong Yu
- AMBER: Trouble with Leap Biswa Ranjan Meher
- RE: AMBER: some puzzles in equilibration MD Ross Walker
- RE: AMBER: some puzzles in equilibration MD Zhihong Yu
- RE: AMBER: LEAP error (Test Case) Akshay Patny
- Re: AMBER: question about building molecules Rita Cassia
- AMBER: how to combine NEB method with QM/MM approach caoch.cherry.bio.titech.ac.jp
- AMBER: MMPBSA vDW error Shozeb Haider
- AMBER: Announcement: Parameters for Modified Nucleosides in RNA Raviprasad Aduri
- RE: AMBER: how to combine NEB method with QM/MM approach Ross Walker
- RE: AMBER: some puzzles in equilibration MD Ross Walker
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Scott Brozell
- Re: AMBER: Trouble with Leap Scott Brozell
- RE: AMBER: some puzzles in equilibration MD Bill Ross
Tuesday, 10 October 2006
- AMBER: Steered molecular dynamics with Amber 8.0 a a
- AMBER: partial charges Fabian Alejandro Rodriguez
- AMBER: Ｆｅ complex Toshifumi Yui
- AMBER: generalized born model for organic solvent Eric Hu
- AMBER: Re: AMBER: Ｆｅ complex　(correction) Toshifumi Yui
- AMBER: adding polar hydrogens Sean Rathlef
Wednesday, 11 October 2006
- AMBER: Reducind trajectory Sergey Samsonov
- Re: AMBER: Reducing trajectory Sergey Samsonov
- Re: AMBER: ptraj hbond analysis troubles Reinhard Klement
- AMBER: Parameters for Nickel a a
- Re: AMBER: partial charges David A. Case
- Re: AMBER: adding polar hydrogens David A. Case
- Re: AMBER: generalized born model for organic solvent David A. Case
- Re: AMBER: adding polar hydrogens Sean Rathlef
- Re: AMBER: adding polar hydrogens David A. Case
- AMBER: amber force field Noriaki Okimoto
- Re: AMBER: amber force field Carlos Simmerling
- Re: AMBER: adding polar hydrogens Sean Rathlef
- AMBER: problems for running sander.MPI Qizhi Cui
- RE: AMBER: problems for running sander.MPI Ross Walker
- Re: AMBER: generalized born model for organic solvent Eric Hu
- Re: AMBER: generalized born model for organic solvent David A. Case
- Re: AMBER: generalized born model for organic solvent Adrian Roitberg
Thursday, 12 October 2006
- AMBER: puzzles about solvatoct or solvatebox Zhihong Yu
- AMBER: High Values in MMPBSA Shozeb Haider
- Re: AMBER: problems for running sander.MPI Christophe Deprez
- Re: AMBER: High Values in MMPBSA Thomas Steinbrecher
- AMBER: angle between two vectors Lwin, ThuZar
- Re: AMBER: angle between two vectors M. L. Dodson
- RE: AMBER: problems for running sander.MPI Ross Walker
- Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross
- Re: AMBER: generalized born model for organic solvent Eric Hu
- Re: AMBER: generalized born model for organic solvent David A. Case
- Re: AMBER: angle between two vectors David A. Case
- AMBER: Phenyl Ring atom types sethl.gatech.edu
- AMBER: Ptraj problems Charlisa Daniels
- Re: AMBER: generalized born model for organic solvent Eric Hu
- AMBER: TFE parameters for Amber Mingfeng Yang
- AMBER: BioBlade Sean Rathlef
Friday, 13 October 2006
- AMBER: klambda Sergey Samsonov
- AMBER: Updated Tutorials Page Ross Walker
- AMBER: force fiels for a-rna asli ertekin
- Re: AMBER: force fiels for a-rna Carlos Simmerling
- Re: AMBER: restraints and constant pressure Joshua
- Re: AMBER: force fiels for a-rna asli ertekin
Saturday, 14 October 2006
- AMBER: SURFTEN/SURFOFF values in amber9 ferranna.unimo.it
- AMBER: Grid command of ptraj Atsutoshi Okabe
- Re: AMBER: force fiels for a-rna Jiri Sponer
- Re: AMBER: Grid command of ptraj Sean Rathlef
Sunday, 15 October 2006
- AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang
- Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Fenghui Fan
- AMBER: simulation of protein in non-aq or organic solvent bath Smriti Sharma
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
Monday, 16 October 2006
- AMBER: Amber8: problem related to antechamber priya priya
- AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya
- Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang
- RE: AMBER: Grid command of ptraj Atsutoshi Okabe
- Re: AMBER: Amber8: problem related to antechamber David A. Case
- RE: AMBER: Amber8: problem related to antechamber Ross Walker
- RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration Ross Walker
- Re: AMBER: angle between two vectors Myunggi Yi
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case
- AMBER: Interbox interactions Austin B. Yongye
- AMBER: modeling of ligand concentrations Sean Rathlef
- AMBER: Density calculation Jianhui
- RE: AMBER: angle between two vectors. . Lwin, ThuZar
- AMBER: How to find equillibration time for my system in a generalised born solvation model Gobind Singh Bisht
- Re: AMBER: modeling of ligand concentrations David A. Case
- Re: AMBER: Density calculation David A. Case
- Re: AMBER: How to find equillibration time for my system in a generalised born solvation model David A. Case
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- AMBER: regarding PBCAL in MM-PBSA Cenk Andac
- AMBER: General Coding Problem Elijah Gregory
- Re: AMBER: General Coding Problem David A. Case
- Re: AMBER: modeling of ligand concentrations David A. Case
- Re: AMBER: regarding PBCAL in MM-PBSA Ray Luo
- Re: AMBER: General Coding Problem Bill Ross
- Re: AMBER: regarding PBCAL in MM-PBSA Cenk Andac
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya
- Re: AMBER: Amber8: problem related to antechamber priya priya
Tuesday, 17 October 2006
- AMBER: Problem working with Antechamber nur avneet
- AMBER: RDF calculation Xioling Chuang
- Re: AMBER: puzzles about solvatoct or solvatebox Zhihong Yu
- AMBER: How did the coordinates change in xleap? Zhihong Yu
- Re: AMBER: puzzles about solvatoct or solvatebox Thomas Cheatham
- Re: AMBER: Amber8: problem related to antechamber David A. Case
- Re: AMBER: RDF calculation Thomas Cheatham
- Re: AMBER: How did the coordinates change in xleap? David A. Case
- Re: AMBER: Interbox interactions Thomas Cheatham
- Re: AMBER: modeling of ligand concentrations David A. Case
- RE: AMBER: Grid command of ptraj Thomas Cheatham
- Re: AMBER: Interbox interactions Austin B. Yongye
- AMBER: Unstable RMS trajectory Dave, Sonya
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- Re: AMBER: Unstable RMS trajectory Carlos Simmerling
- Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross
- Re: AMBER: Unstable RMS trajectory Gustavo Seabra
- Re: AMBER: Unstable RMS trajectory Bill Ross
- Re: AMBER: Unstable RMS trajectory Carlos Simmerling
- Re: AMBER: modeling of ligand concentrations David A. Case
- RE: AMBER: Unstable RMS trajectory Ross Walker
- Re: AMBER: Unstable RMS trajectory Adrian Roitberg
- Re: AMBER: Unstable RMS trajectory Gustavo Seabra
- RE: AMBER: Unstable RMS trajectory Dave, Sonya
- RE: AMBER: Unstable RMS trajectory Dave, Sonya
- AMBER: sander/topology problem Lorenzo Gontrani
- Re: AMBER: sander/topology problem David A. Case
- Re: AMBER: Unstable RMS trajectory Adrian Roitberg
- Re: AMBER: Unstable RMS trajectory Gustavo Seabra
- RE: AMBER: Unstable RMS trajectory Dave, Sonya
- AMBER: question on mm_pbsa_statistics.pl Yongmei Pan
- AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan
- RE: AMBER: Grid command of ptraj Atsutoshi Okabe
- Re: AMBER: Trouble with Leap Biswa Ranjan Meher
- AMBER: Problem loading peptoid residues with antechamber nur avneet
- AMBER: To create methanol solvent box Atsutoshi Okabe
Wednesday, 18 October 2006
- Re: AMBER: questions on mm_pbsa_statitistics.pl Holger Gohlke
- Re: AMBER: To create methanol solvent box Smriti Sharma
- AMBER: how to simulate water flow inside a channel? Gobind Singh Bisht
- AMBER: alanine scan (mm/pbsa) rob yang
- Re: Re: AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan
- RE: AMBER: Problem loading peptoid residues with antechamber Junmei Wang
- Re: AMBER: questions on mm_pbsa_statitistics.pl Holger Gohlke
- AMBER: ptraj atomicfluct Myunggi Yi
- Re: AMBER: ptraj atomicfluct Myunggi Yi
- AMBER: charge models in antechamber Eric Hu
- Re: AMBER: charge models in antechamber Sean Rathlef
- Re: AMBER: charge models in antechamber Sean Rathlef
- AMBER: RESP charges of iron-porphyrin system Shin Tokumoto
- RE: AMBER: Problem loading peptoid residues with antechamber nur avneet
- Re: AMBER: Trouble with Leap Biswa Ranjan Meher
Thursday, 19 October 2006
- AMBER: mmpbsa in parallell Olayiwola Adekoya
- Re: AMBER: Trouble with Leap Ilyas Yildirim
- AMBER: Free-energy using MM-PBSA mathew k varghese
- AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A \(Mina\)
- Re: AMBER: Free-energy using MM-PBSA Yongmei Pan
- Re: AMBER: RESP charges of iron-porphyrin system Gustavo Seabra
- AMBER: Amber 9 installation problem Cenk Andac
- Re: AMBER: Amber 9 installation problem Mark Williamson
- Re: AMBER: RESP charges of iron-porphyrin system Chris Moth
- Re: AMBER: charge models in antechamber David Mobley
- Re: AMBER: Amber 9 installation problem Cenk Andac
- Re: AMBER: Amber 9 installation problem David A. Case
- Re: AMBER: Amber 9 installation problem Cenk Andac
- AMBER: Curve fitting during dihedral parameter calculation Prashanth Athri
- Re: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred David A. Case
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com
- Re: AMBER: RESP charges of iron-porphyrin system Shin Tokumoto
- RE: AMBER: Issue with installation of Amber v9.0 parallel compilation Ross Walker
- Re: AMBER: RESP charges of iron-porphyrin system FyD
Friday, 20 October 2006
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A \(Mina\)
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad
- Re: AMBER: Probelm with running Amber 9 parallelly David A. Case
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker
- AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai Ingvar Lagerstedt
- Re: AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai David A. Case
- AMBER: Question about sander code Kijeong Kwac
- AMBER: problem of installing carnal on macosx gtg549i.mail.gatech.edu
- Re: AMBER: Question about sander code David A. Case
- Re: AMBER: problem of installing carnal on macosx Bill Ross
- Re: AMBER: problem of installing carnal on macosx Shuting Wei
- RE: Re: AMBER: Question about sander code Kijeong Kwac
- AMBER: atom type nh vs. n2 sethl.gatech.edu
- Re: Re: AMBER: Question about sander code David A. Case
- RE: Re: Re: AMBER: Question about sander code Kijeong Kwac
- AMBER: question on molsurf Yongmei Pan
- RE: RE: Re: Re: AMBER: Question about sander code Kijeong Kwac
- Re: Re: Re: AMBER: Question about sander code David A. Case
- AMBER: HBON in frcmod file Ilyas Yildirim
Saturday, 21 October 2006
- Re: AMBER: HBON in frcmod file Bill Ross
- Re: AMBER: HBON in frcmod file Ilyas Yildirim
- AMBER: single or dual topology for TI? Holly Freedman
- Re: AMBER: single or dual topology for TI? David Mobley
- Re: AMBER: HBON in frcmod file Bill Ross
- Re: AMBER: single or dual topology for TI? Holly Freedman
- Re: AMBER: single or dual topology for TI? David Mobley
Sunday, 22 October 2006
- AMBER: mmpbsa: fail to run heat in tutorial A3 jitrayut jitonnom
- Re: AMBER: HBON in frcmod file David A. Case
Monday, 23 October 2006
- AMBER: Virus? Peter Gannett
- RE: AMBER: mmpbsa: fail to run heat in tutorial A3 Ross Walker
- AMBER: ff for drug-dna complex and drug atom types assignment Kateryna Miroshnychenko
- RE: AMBER: Grid command of ptraj Thomas Cheatham
- Re: AMBER: modeling of ligand concentrations Thomas Cheatham
- AMBER: PKDIV lone pair dihedrals Lorenzo Gontrani
- Re: AMBER: ff for drug-dna complex and drug atom types assignment Barbault Florent
- AMBER: Using modified NA bases sethl.gatech.edu
- Re: AMBER: PKDIV lone pair dihedrals David A. Case
- Re: AMBER: PKDIV lone pair dihedrals darden
- AMBER: ptraj radial problem: Segmentation fault Jianhui Tian
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- Re: AMBER: modeling of ligand concentrations Carlos Simmerling
- Re: AMBER: modeling of ligand concentrations Thomas Cheatham
- Re: AMBER: Using modified NA bases Fabian Alejandro Rodriguez
- Re: AMBER: modeling of ligand concentrations Adrian Roitberg
- AMBER: splitting LES with ptraj in amber9 bala
Tuesday, 24 October 2006
- AMBER: DIST_RST Urszula Uciechowska
- Re: AMBER: DIST_RST Cenk Andac
- AMBER: problem with calcpka.pl Benjamin Juhl
- Re: AMBER: Using modified NA bases Franck_Vendeix.ncsu.edu
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A \(Mina\)
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker
- AMBER: pmemd installation on linux_p3_athlon ifort gtg549i.mail.gatech.edu
- Re: AMBER: pmemd installation on linux_p3_athlon ifort Robert Duke
- Re: AMBER: Using modified NA bases FyD
- Re: AMBER: pmemd installation on linux_p3_athlon ifort Shuting Wei
- AMBER: load charges to antechamber calculations Wang, Xuelin
- AMBER: Not getting proper structure after minimization Dave, Sonya
- Re: AMBER: Not getting proper structure after minimization Carlos Simmerling
- Re: AMBER: Not getting proper structure after minimization Gustavo Seabra
- Re: AMBER: Not getting proper structure after minimization Elijah Gregory
- RE: AMBER: Not getting proper structure after minimization Dave, Sonya
- Re: AMBER: load charges to antechamber calculations David A. Case
- Re: AMBER: Not getting proper structure after minimization Elijah Gregory
- Re: AMBER: Not getting proper structure after minimization Elijah Gregory
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- AMBER: md and implicit solvation Jardas sucuriba
- Re: AMBER: md and implicit solvation Adrian Roitberg
- Re: AMBER: modeling of ligand concentrations Thomas Steinbrecher
- Re: AMBER: md and implicit solvation David A. Case
- Re: AMBER: md and implicit solvation Jardas sucuriba
- Re: AMBER: md and implicit solvation David A. Case
- Re: AMBER: md and implicit solvation Thomas Cheatham
- Re: AMBER: modeling of ligand concentrations David A. Case
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- Re: AMBER: modeling of ligand concentrations Sean Rathlef
- AMBER: error estimate for free energy perturbation calculation jz7.duke.edu
- Re: AMBER:pls help load peptoid residues in antechamber nur avneet
- AMBER: Question regarding lastrst and taup Priti Hansia
Wednesday, 25 October 2006
- AMBER: parameters !!?? Urszula Uciechowska
- Re: AMBER: parameters !!?? cristian obiol
- AMBER: Shake&Lone Pairs Lorenzo Gontrani
- AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli
- Re: AMBER: parameters !!?? Urszula Uciechowska
- Re: AMBER: Not getting proper structure after minimization Carlos Simmerling
- Re: AMBER: Not getting proper structure after minimization Giulio Rastelli
- AMBER: residence time& hydration density Andres Palencia
- AMBER: reinstall amber8 Rachel
- Re: AMBER: reinstall amber8 Wei Zhang
- RE: AMBER: Question regarding lastrst and taup Ross Walker
- Re: AMBER: Using modified NA bases Qizhi Cui
- RE: AMBER: parameters !!?? Ross Walker
Tuesday, 24 October 2006
- Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo
Wednesday, 25 October 2006
- Re: AMBER: error estimate for free energy perturbation calculation Chris Moth
- Re: AMBER: RESP charges of iron-porphyrin system Marcelo Puiatti
- Re: AMBER: Shake&Lone Pairs David A. Case
- Re: AMBER: error estimate for free energy perturbation calculation David A. Case
- AMBER: mm_pbsa: binding energy calculation Varsha Goyal
- AMBER: How do we simulate deletion mutations Dave, Sonya
- Re: AMBER: How do we simulate deletion mutations Fenghui Fan
- Re: AMBER: error estimate for free energy perturbation calculation Fenghui Fan
- AMBER: Phosphorylated protein MD simulation Fenghui Fan
- RE: AMBER: How do we simulate deletion mutations Dave, Sonya
- AMBER: CARNAL: carnal source code Keerthi Gottipati
- RE: AMBER: How do we simulate deletion mutations Fenghui Fan
- Re: AMBER: CARNAL: carnal source code Carlos Simmerling
- Re: AMBER: error estimate for free energy perturbation calculation Ilyas Yildirim
- RE: AMBER: Question regarding lastrst and taup Priti Hansia
Thursday, 26 October 2006
- AMBER: how to select the problematic residues(atoms) in VMD Rachel
- Re: AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli
- Re: AMBER: how to select the problematic residues(atoms) in VMD Andres Palencia
- AMBER: MM-PBSA memory usage Stefano Pieraccini
- Re: AMBER: CARNAL: carnal source code Keerthi Gottipati
- Re: AMBER: mm_pbsa: binding energy calculation Angelo
- Re: AMBER: Phosphorylated protein MD simulation Myunggi Yi
- Re: AMBER: Phosphorylated protein MD simulation Myunggi Yi
- AMBER: Calculating native contacts for mdcrd files Anna Bowman
- RE: AMBER: how to select the problematic residues(atoms) in VMD Ross Walker
- Re: AMBER: residence time& hydration density Myunggi Yi
- RE: AMBER: amber9: SA Bomb in sa_arc Ross Walker
- Re: AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli
Wednesday, 25 October 2006
- Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo
Thursday, 26 October 2006
- AMBER: how to add hydrogen molecules in the protein Rachel
- RE: AMBER: amber9: SA Bomb in sa_arc Ross Walker
- AMBER: error GRID command in ptraj Andres Palencia
- RE: AMBER: How do we simulate deletion mutations Dave, Sonya
- AMBER: Two different HIS ligands David LeBard
- Re: AMBER: Two different HIS ligands Kristina Furse
- AMBER: parameters for fluoromolecules with more than one single carbon? Jones de Andrade
- Re: AMBER: Two different HIS ligands David LeBard
- Re: AMBER: how to add hydrogen molecules in the protein David A. Case
Friday, 27 October 2006
- AMBER: halogen bondi radii in mm_pbsa_calceneent.pm Giulio Rastelli
- AMBER: mm_pbsa reference Angelo
- AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: Compile AMBER 8 Mark Williamson
- Re: AMBER: Compile AMBER 8 David A. Case
- AMBER: where to set bondi radii for halogens Giulio Rastelli
- AMBER: Amber: Parallel Installation Problems Maniopoulou, A \(Mina\)
- RE: AMBER: Amber: Parallel Installation Problems Ross Walker
- Re: AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: where to set bondi radii for halogens David A. Case
- Re: AMBER: Compile AMBER 8 David A. Case
- Re: AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: Compile AMBER 8 David A. Case
- Re: AMBER: where to set bondi radii for halogens Giulio Rastelli
- AMBER: Help with polarization force field norberto.ualberta.ca
- Re: AMBER: where to set bondi radii for halogens David A. Case
- AMBER: RESP charge fitting Mingfeng Yang
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case
- Re: AMBER: RESP charge fitting FyD
Saturday, 28 October 2006
- AMBER: solvation and His protonation Jardas sucuriba
- Re: AMBER: mm_pbsa: binding energy calculation Varsha Goyal
Sunday, 29 October 2006
- AMBER: imaging issue David Smith
- AMBER: ff02 force fields norberto.ualberta.ca
- AMBER: C -N -CT-CT torsion parameters John Vieceli
- Re: AMBER: problem with calcpka.pl David A. Case
- Re: AMBER: ff02 force fields David A. Case
Monday, 30 October 2006
- Re: AMBER: mm_pbsa: binding energy calculation Angelo
- AMBER: Closest(closest water) Sergey Samsonov
- Re: AMBER: Closest(closest water) Adrian Roitberg
- Re: AMBER: problem with calcpka.pl Benjamin Juhl
- Re: AMBER: Closest(closest water) Sergey Samsonov
- AMBER: periodic boundary condition question... HL Eastwood
- Re: AMBER: periodic boundary condition question... Sergey Samsonov
- Re: AMBER: periodic boundary condition question... HL Eastwood
- AMBER: how to restrain some residues in a NPT MD? Zhihong Yu
- Re: AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: periodic boundary condition question... Sergey Samsonov
- RE: AMBER: periodic boundary condition question... Ross Walker
- Re: AMBER: periodic boundary condition question... David A. Case
- RE: AMBER: how to restrain some residues in a NPT MD? Ross Walker
- Re: AMBER: Compile AMBER 8 HL Eastwood
- Re: AMBER: periodic boundary condition question... HL Eastwood
- Re: AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: Compile AMBER 8 HL Eastwood
- Re: AMBER: Compile AMBER 8 Esther Brugger
- Re: AMBER: problems for running sander.MPI Christophe Deprez
- Re: AMBER: imaging issue Kristina Furse
- Re: AMBER: ff02 force fields norberto.ualberta.ca
- RE: AMBER: problems for running sander.MPI Ross Walker
- Re: AMBER: Closest(closest water) Mingfeng Yang
- Re: AMBER: imaging issue Thomas Cheatham
- Re: AMBER: solvation and His protonation David A. Case
- AMBER: ff99SB vs ff02 (ff02pol.rl) Nicolas Lux Fawzi
- Re: AMBER: ff99SB vs ff02 (ff02pol.rl) Thomas Cheatham
- Re: AMBER: ff99SB vs ff02 (ff02pol.rl) David A. Case
- Re: AMBER: ff99SB vs ff02 (ff02pol.rl) Thomas Cheatham
Tuesday, 31 October 2006
- AMBER: Re: Problems installing antechamber 1.27 andrea carotti
- AMBER: what is the RMS value in resp charge fitting ? jitrayut jitonnom
- AMBER: MMPBSA entropy question Barbault Florent
- Re: AMBER: solvation and His protonation Jardas sucuriba
- AMBER: Problems with carnal (Amber7) anna.schrey.gmx.de
- Re: AMBER: solvation and His protonation David A. Case
- Re: AMBER: Problems with carnal (Amber7) Bill Ross
- AMBER: N1-protonated adenosine, N-terminal myristyl group Michael F. Summers
- Re: AMBER: problem with calcpka.pl Amber admin
- AMBER: mm_pbsa does not terminate Holly Freedman
- Re: AMBER: MMPBSA entropy question David A. Case
- Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo

Last message date: Sun Nov 05 2006 - 06:07:31 PST
Archived on: Sun Nov 17 2024 - 05:53:31 PST

Amber Archive Oct 2006 by date