Amber Archive Jan 2006: by date

Sunday, 1 January 2006
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews
Monday, 2 January 2006
- Re: AMBER: problem with ssh and xleap Peter Gannett
- RE: AMBER: antechamber problem Baker, Bo-Yang
- Re: AMBER: problem with ssh and xleap Robyn Ayscue
- AMBER: water molecules with in 3 angstroms to the solute nag raj
Tuesday, 3 January 2006
- Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim
- AMBER: requirement of delphi for mm_pbsa Manish Datt
- Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim
Wednesday, 4 January 2006
- AMBER: How to run mm_pbsa_statistics.pl? Peng Tao
- Re: AMBER: requirement of delphi for mm_pbsa David A. Case
- Re: AMBER: requirement of delphi for mm_pbsa Holger Gohlke
- Re: AMBER: How to run mm_pbsa_statistics.pl? Holger Gohlke
- AMBER: minimalization prior to nmode analysis, is it necessary? Magne Olufsen
- AMBER: Ligand charge bybaker.itsa.ucsf.edu
- Re: AMBER: Ligand charge David Mobley
- AMBER: Leap Joseph Fernandez
- Re: AMBER: Leap Bill Ross
- AMBER: Q: results from PB solver in example no.3 Tomimoto_Masaki.takeda.co.jp
- Re: AMBER: Q: results from PB solver in example no.3 Ray Luo
- Re: AMBER: Ligand charge Ilyas Yildirim
Thursday, 5 January 2006
- AMBER: Where to modify the atom type in sander? zhli_2000.126.com
- Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao
- RE: AMBER: Where to modify the atom type in sander? Ross Walker
- Re: AMBER: Ligand charge Bill Ross
- Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao
- Re: AMBER: minimalization prior to nmode analysis, is it necessary? David A. Case
- Re: AMBER: minimalization prior to nmode analysis, is it necessary? Adrian Roitberg
Friday, 6 January 2006
- AMBER: creating a RST file from specific set of binpos/crd file Baird, Jamie \(bairdje\)
- Re: AMBER: creating a RST file from specific set of binpos/crd file Thomas E. Cheatham, III
- RE: AMBER: creating a RST file from specific set of binpos/crd file Ross Walker
- Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type Amber admin
- AMBER: SHAKE - ntc = 3 Jennie Thomas
- Re: AMBER: SHAKE - ntc = 3 David A. Case
Sunday, 8 January 2006
- AMBER: Could you help me about mmpbsa! thank you! linfu
Monday, 9 January 2006
- AMBER: amber alexandratm.sapo.pt
- AMBER: parameters for C=S alexandra.marques.fc.up.pt
- Re: AMBER: SHAKE - ntc = 3 Jennie Thomas
- RE: AMBER: SHAKE - ntc = 3 Ross Walker
- Re: AMBER: SHAKE - ntc = 3 David A. Case
- Re: AMBER: parameters for C=S David A. Case
- Re: AMBER: SHAKE - ntc = 3 Jennie Thomas
- Re: AMBER: SHAKE - ntc = 3 Bill Ross
- AMBER: about mmpbsa linfu
- Re: AMBER: SHAKE - ntc = 3 Jennie Thomas
- AMBER: problem with the output file for free energy perturbation calculation brmeher.iitg.ernet.in
- AMBER: strange result of mm/pbsa snowyowls
- AMBER: regarding Hydrogen bond analysis S.Sundar Raman
Tuesday, 10 January 2006
- Re: AMBER: regarding Hydrogen bond analysis David A. Case
Sunday, 8 January 2006
- AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number? tonglei
Tuesday, 10 January 2006
- AMBER: Problem in Antechamber Sai Kumar Ramadugu
- AMBER: PTRAJ generating wrong dihedral angles hayden
- AMBER: mpich Amber7 problem Jan Dohnalek
- Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao
- Re: AMBER: PTRAJ generating wrong dihedral angles Thomas E. Cheatham, III
- AMBER: ptraj distance matrix Holly Freedman
- Re: AMBER: Leap compilation issues Jiten
Wednesday, 11 January 2006
- Re: AMBER: ptraj distance matrix Holger Gohlke
- Re: AMBER: mpich Amber7 problem Petr Kulhanek
- Re: AMBER: mpich Amber7 problem linfu
- Re: AMBER: mpich Amber7 problem Jan Dohnalek
- AMBER: Gibbs pmf calculation Atsutoshi Okabe
- AMBER: Workshops a a
- AMBER: GLUTATHIONE Joachim Reichelt
- Re: AMBER: GLUTATHIONE Ilyas Yildirim
- Re: AMBER: GLUTATHIONE Tim Meyer
- AMBER: amber atom type -> length of name Tim Meyer
- AMBER: About preparing Zn.lib Varsha Goyal
- AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim
- Re: AMBER: About preparing Zn.lib Ilyas Yildirim
- Re: AMBER: amber atom type -> length of name David A. Case
Thursday, 12 January 2006
- AMBER: ptraj mask question Vlad Cojocaru
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling
- AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru
- Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss
- Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss
- Re: AMBER: stripping trajectories: ptraj versus Carnal Carlos Simmerling
- Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru
- Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru
- AMBER: ATCOR.dat format Kateryna Miroshnychenko
- Re: AMBER: stripping trajectories: ptraj versus Carnal Thomas E. Cheatham, III
- Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru
- Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru
- AMBER: Na+ with GB/SA? Steve Gwaltney
- AMBER: About tleap Varsha Goyal
- RE: AMBER: About tleap Ross Walker
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling
- Re: AMBER: Na+ with GB/SA? David A. Case
- Re: AMBER: Problem in Antechamber David A. Case
- Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu
Friday, 13 January 2006
- AMBER: problem in saving parameter file for non-standard residue Priti Hansia
- Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim
- Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia
- Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim
- Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia
- AMBER: analysing water behavior during MD Vlad Cojocaru
- Re: AMBER: analysing water behavior during MD Fabian Boes
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker
- AMBER: Trimming ptraj output Andy Purkiss
- Re: AMBER: Trimming ptraj output Thomas E. Cheatham, III
- AMBER: base-base interaction Douali, Latifa
- Re: AMBER: Trimming ptraj output Andy Purkiss
- Re: AMBER: base-base interaction Carlos Simmerling
- RE: AMBER: problem in saving parameter file for non-standard residue Priti Hansia
Monday, 16 January 2006
- AMBER: heme improper torsions nkyx.sohu.com
- AMBER: the problem of mdcrd xiphias xie
- Re: AMBER: heme improper torsions Vlad Cojocaru
- Re: AMBER: the problem of mdcrd Vlad Cojocaru
- AMBER: MPICH on OpenMosix Jan Dohnalek
- AMBER: ACTIVE SITE Claire Zerafa
- AMBER: Release of RESP ESP charge DDatabase FyD
- RE: AMBER: the problem of mdcrd Ross Walker
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker
- Re: AMBER: heme improper torsions David A. Case
- Re: AMBER: problem in saving parameter file for non-standard residue David A. Case
- 回复： RE: AMBER: the problem of mdcrd xiphias xie
- 回复： Re: AMBER: the problem of mdcrd xiphias xie
- RE：AMBER: the problem of mdcrd xiphias xie
Tuesday, 17 January 2006
- AMBER: About the unit of the projection onto eigenvectors zgleo
- AMBER: Re: RE：AMBER: the problem of mdcrd Vlad Cojocaru
- AMBER: Re: RE：AMBER: the problem of mdcrd Carlos Simmerling
- AMBER: nmode calculations error Jiten
- AMBER: rms in principal component analysis Lydia
- AMBER: Amber 8 install problem Andrew Box
Wednesday, 18 January 2006
- RE：AMBER: the problem of mdcrd xiphias xie
- AMBER: Re: RE：AMBER: the problem of mdcrd Vlad Cojocaru
- Re: AMBER: Amber 8 install problem Andreas Svrcek-Seiler
- AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko
- AMBER: IGB=10 Ahammadunny Pathiaseril
- Re: AMBER: rms in principal component analysis David A. Case
- Re: AMBER: rms in principal component analysis Lydia
- AMBER: A few problems on the parameterisation of a Glutamine residue Jason K
- RE: AMBER: A few problems on the parameterisation of a Glutamine residue Ross Walker
- Re: AMBER: rms in principal component analysis David A. Case
- Re: AMBER: bugfix for impropers in parmchk David A. Case
- AMBER: is there any relationship between RMSD and B-factor? haixiao jin
- Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling
- Re: AMBER: is there any relationship between RMSD and B-factor? haixiao jin
Thursday, 19 January 2006
- Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling
- Re: AMBER: is there any relationship between RMSD and B-factor? Andy Purkiss
- AMBER: ptraj grid output Vlad Cojocaru
- Re: AMBER: ptraj grid output Thomas E. Cheatham, III
- RE: AMBER: Problem in Antechamber Junmei Wang
- AMBER: ptraj PCA Marcela Madrid
- AMBER: amber: problem in center command xiphias xie
Friday, 20 January 2006
- Re: AMBER: amber: problem in center command Vlad Cojocaru
- AMBER: partial charge glycam Kevin Murphy
- Re: AMBER: partial charge glycam kkirschn.hamilton.edu
- Re: AMBER: bugfix for impropers in parmchk David Mobley
- Re: AMBER: bugfix for impropers in parmchk David Mobley
- Re: AMBER: problem in center command xiphias xie
- Re: AMBER: problem in center command Bill Ross
- Re: AMBER: problem in center command Thomas Cheatham
- Re: AMBER: partial charge glycam FyD
Tuesday, 24 January 2006
- RE: AMBER: partial charge glycam Kevin Murphy
- AMBER: ptraj PCA Vlad Cojocaru
- AMBER: AMBER 8.0 : Octane Implicit Solvent? Guillaume Bollot
- Re: AMBER: AMBER 8.0 : Octane Implicit Solvent? David A. Case
- AMBER: monosaccharide residues Fren T
Wednesday, 25 January 2006
- AMBER: Charges of enantiomers for Amber8 lily ferreira
- RE: AMBER: partial charge glycam FyD
- Re: AMBER: Charges of enantiomers for Amber8 FyD
- Re: AMBER: Charges of enantiomers for Amber8 FyD
- AMBER: ptraj PCA: projection mask bug?? Vlad Cojocaru
- AMBER: MM-PBSA Douali, Latifa
- Re: AMBER: Charges of enantiomers for Amber8 lily ferreira
- Re: AMBER: Charges of enantiomers for Amber8 FyD
Thursday, 26 January 2006
- Re: AMBER: partial charge glycam kkirschn.hamilton.edu
- AMBER: AMBER 7 and restrained bonds. Toomas Kaevand
- Re: AMBER: AMBER 7 and restrained bonds. David A. Case
- AMBER: antechamber ping jiang
- AMBER: Charges from NMR spin densities David LeBard
- Re: AMBER: antechamber David Case
- Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu
Friday, 27 January 2006
- AMBER: h-bond Gustavo Pierdominici Sottile
- Re: AMBER: Charges from NMR spin densities David A. Case
- AMBER: atom type "O3" not recognized by XLeap Kenley Barrett
- AMBER: anal vs sander Piotr Cieplak
- Re: AMBER: anal vs sander David A. Case
- Re: AMBER: atom type "O3" not recognized by XLeap David A. Case
- Re: AMBER: About the unit of the projection onto eigenvectors David A. Case
- Re: AMBER: anal vs sander Piotr Cieplak
- Re: AMBER: anal vs sander David A. Case
Monday, 30 January 2006
- AMBER: lifetimes Gustavo Pierdominici Sottile
- AMBER: NAD parameters alexandra.marques.fc.up.pt
- Re: AMBER: NAD parameters ivan.mmb.pcb.ub.es
- RE: AMBER: NAD parameters Ross Walker
- AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com
- AMBER: Decomposed GB energy in idecomp=3 option Sukjoon Yoon
- Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell
- Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com
Tuesday, 31 January 2006
- Re: AMBER: MM-PBSA Jianyin Shao
- AMBER: About placing counter ions Varsha Goyal
- AMBER: parallel compile problems on amber8 hayden
- RE: AMBER: parallel compile problems on amber8 Ross Walker
- RE: AMBER: parallel compile problems on amber8 Ross Walker
- AMBER: Problem in compiling AMBER8 parallel version luckyang.gmail.com
- Re: AMBER: Problem in compiling AMBER8 parallel version David LeBard
- Re: AMBER: Problem in compiling AMBER8 parallel version luckyang.gmail.com
- Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell

Last message date: Wed Feb 01 2006 - 06:10:06 PST
Archived on: Sun Nov 24 2024 - 05:53:40 PST

Amber Archive Jan 2006 by date