Amber Archive Aug 2006: by date

Monday, 31 July 2006
- Re: AMBER: Xmgr in Windows Ilyas Yildirim
- AMBER: How to set Bondi Radii using xleap Ilyas Yildirim
Tuesday, 1 August 2006
- AMBER: regarding diffusion command output Arvind Marathe
- Re: AMBER: Re: Confusion re AMBER SMD output Adrian Roitberg
- Re: AMBER: Xmgr in Windows Fabián Alejandro Rodríguez
- Re: AMBER: Xmgr in Windows Florian Haberl
- Re: AMBER: Distance between two regions Guanglei Cui
- Re: AMBER: from traj to crd Guanglei Cui
- Re: AMBER: from traj to crd Fabián Alejandro Rodríguez
- Re: AMBER: GB tutorials and disulphide bonds David A. Case
- Re: AMBER: How to set Bondi Radii using xleap David A. Case
- Re: AMBER: How to set Bondi Radii using xleap. . Don.Bashford.stjude.org
- Re: AMBER: Using a trajectory and some PDB files as input for PCA David A. Case
- Re: AMBER: How to set Bondi Radii using xleap Carlos Simmerling
- AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Carlos Simmerling
- AMBER: pdb error AYTUG TUNCEL
- Re: AMBER: pdb error Ilyas Yildirim
- AMBER: any work-around for 80 character mask string limit? Tanya Johannsen
- Re: AMBER: any work-around for 80 character mask string limit? David A. Case
Wednesday, 2 August 2006
- AMBER: brookhaven to amber pdb format AYTUG TUNCEL
- AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo
- Re: AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo
- AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru
- Re: AMBER: brookhaven to amber pdb format David A. Case
- AMBER: Bugfixes available for pmemd iwrap problem Robert Duke
- Re: AMBER: brookhaven to amber pdb format Ilyas Yildirim
- AMBER: where can I find the force field paramete r for Silica yxiong99
- AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta
- AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher
- Re: AMBER: TI-FEP for ILE--->VAL. Ilyas Yildirim
Thursday, 3 August 2006
- Re: AMBER: Maximum system size in simulated annealing Andreas Svrcek-Seiler
- Re: AMBER: PhosphoThreonine Parms for use with ff03 Vlad Cojocaru
- Re: AMBER: Maximum system size in simulated annealing Carlos Simmerling
- AMBER: ff03 and ff99SB force fields Carlos Simmerling
- AMBER: problems with ptraj anna.schrey.gmx.de
- AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Lwin, ThuZar
- AMBER: about Silica's polarizability yxiong99
- Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Carlos Simmerling
- Re: AMBER: about Silica's polarizability David A. Case
- Re: AMBER: TI-FEP for ILE--->VAL. David A. Case
- Re: AMBER: problems with ptraj David A. Case
- AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar
- AMBER: restraint=0.0000 during minimization? Evan Kelly
- AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly
- AMBER: SURFTEN in GB (mm_pbsa calculations) Shuting Wei
- RE: AMBER: ff03 and ff99SB force fields Yong Duan
- Re: AMBER: SURFTEN in GB (mm_pbsa calculations) Carlos Simmerling
- Re: AMBER: ff03 and ff99SB force fields Ray Luo
Friday, 4 August 2006
- Re: AMBER: ff03 and ff99SB force fields Vlad Cojocaru
- RE: AMBER: ff03 and ff99SB force fields Yong Duan
- AMBER: HBOND ANALYSIS Claire Zerafa
- AMBER: H-bonds of peptide with water sangeeta
- AMBER: Residue connection points on prep.in Gloria T. Anderle
- Re: AMBER: question on chargning free energy in solvent vs vacuum David A. Case
- AMBER: parameter for Cd2+? JunJun Liu
- AMBER: to do tutorial 4 using tleap Come On
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar
- RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar
Saturday, 5 August 2006
- Re: AMBER: neutral N-terminal amino-acid parameters for ff03 FyD
- Fw: AMBER: HBOND ANALYSIS Claire Zerafa
Monday, 7 August 2006
- AMBER: Amber Installation Help Kirk Hevener
- AMBER: Info regarding reduced cysteines Rafi Ahmad
- Re: AMBER: Info regarding reduced cysteines David A. Case
- AMBER: transition state John Chuang莊曜遠老師
- Re: AMBER: H-bonds of peptide with water Scott Pendley
- AMBER: Glass, Kevin A
- AMBER: antechamber bond typing questions David Mobley
- Re: AMBER: Scott Brozell
- AMBER: RE: antechamber bond typing questions Junmei Wang
- AMBER: Problem with restarting MD simulation Gobind Bisht
Tuesday, 8 August 2006
- Re: AMBER: Problem with restarting MD simulation Carlos Simmerling
- AMBER: cutting the box after "solvatebox" Vlad Cojocaru
- Re: AMBER: cutting the box after "solvatebox" Carlos Simmerling
- Re: AMBER: cutting the box after "solvatebox" Vlad Cojocaru
- AMBER: PCA: can't complete projection Zu Thur Yew
- Re: AMBER: cutting the box after "solvatebox" Guanglei Cui
- Re: AMBER: PCA: can't complete projection Vlad Cojocaru
- AMBER: ptraj: nofit option for rmsd Joseph Nachman
- Re: AMBER: Amber Installation Help David A. Case
- Re: AMBER: PCA: can't complete projection Zu Thur Yew
- Re: AMBER: Amber Installation Help; link woes Scott Brozell
- AMBER: GAFF parameters: DPPC Bilayer Akshay Patny
- Re: AMBER: GAFF parameters: DPPC Bilayer Nitin Bhardwaj
- RE: AMBER: GAFF parameters: DPPC Bilayer Yong Duan
Wednesday, 9 August 2006
- AMBER: Format of mdcrd files Gobind Bisht
- Re: AMBER: Format of mdcrd files Carlos Simmerling
- Re: AMBER: Format of mdcrd files Mark Williamson
- AMBER: Energy differecnes as using igb=1 and igb=0 backy
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling
- AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu
- AMBER: how to reassign charges Lwin, ThuZar
- Re: AMBER: transition state Eric Hu
- Re: AMBER: how to reassign charges David Mobley
- Re: AMBER: how to reassign charges David A. Case
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition David A. Case
- RE: AMBER: GAFF parameters: DPPC Bilayer Akshay Patny
- RE: AMBER: how to reassign charges Yong Duan
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu
- AMBER: Heme parameters Marcelo Puiatti
- Re: AMBER: Heme parameters Weihua Li
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 backy
Thursday, 10 August 2006
- AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a
- AMBER: Phosphated Tyrosine, not a type (xleap)? a a
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling
- AMBER: Re: Simulated annealing Carlos Simmerling
- Re: AMBER: Phosphated Tyrosine, not a type (xleap)? David A. Case
- AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner
- Re: AMBER: problems with ptraj Thomas Cheatham
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. David A. Case
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? Thomas Cheatham
- Re: AMBER: HBOND ANALYSIS Thomas Cheatham
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a
- Re: AMBER: Phosphated Tyrosine, not a type (xleap)? a a
Friday, 11 August 2006
- AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang
- Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Guanglei Cui
- AMBER: Could mm_pbsa decompose energy only for the receptor ? backy
- AMBER: ptraj quasiharmonic analysis question Shawn yy
- AMBER: how to do a molecular dynamic study on a trimer Abhilash
- AMBER: AMBER8 - RDF bug Petr Kulhanek
- AMBER: Nature of QM scanning protocol for parameter development Isherwood, James
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case
- AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S
- Re: AMBER: Middlebury College Cluster and Amber 8 Robert Duke
- Re: AMBER: Middlebury College Cluster and Amber 8 David A. Case
- AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui
- AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D.
- Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Adrian Roitberg
- AMBER: impose command in leap problem Piotr Cieplak
- Re: AMBER: impose command in leap problem Scott Brozell
Saturday, 12 August 2006
- AMBER: DIELC? backy
- AMBER: parallel pmemd with intel 9 fc bala
- Re: AMBER: how to do a molecular dynamic study on a trimer Gobind Bisht
- Re: AMBER: parallel pmemd with intel 9 fc Robert Duke
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? FyD
Sunday, 13 August 2006
- Re: AMBER: DIELC? David A. Case
- Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file David A. Case
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case
- Re: AMBER: antechamber error -> metals Scott Brozell
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? a a
Monday, 14 August 2006
- AMBER: Problem with sander in Linux Wimal
- AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a
- AMBER: klambda Vitor Manuel Sousa F?x
- AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko
- AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu
- Re: AMBER: problem imposing arbitrary peptide bonds through leap David A. Case
- Re: AMBER: klambda David A. Case
- Re: AMBER: Problem with sander in Linux David A. Case
- Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu
- Re: AMBER: klambda Ilyas Yildirim
- AMBER: source code Yannick Bomble
- AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang
- Re: AMBER: source code Thomas Cheatham
- AMBER: Advice on linux cluster sought Feng X Zhou
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Thomas Cheatham
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang
- Re: AMBER: impose command in leap problem Piotr Cieplak
- Re: AMBER: transition state John Chuang莊曜遠老師
- RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a
Tuesday, 15 August 2006
- AMBER: (no subject) a a
- AMBER: amber9 Test Failer kawamura_hiro.riken.jp
- Re: AMBER: (no subject) Navnit Kumar Mishra
- AMBER: amber 9 intel 9.1 ia64 Tim Robinson
- Re: AMBER: amber 9 intel 9.1 ia64 Fabian Boes
- Re: AMBER: amber9 Test Failer David A. Case
- AMBER: Question about using antechamber with G03 Gustavo Seabra
- AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu
- AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra
- AMBER: antechamber failure on FMN David Mobley
- Re: AMBER: antechamber failure on FMN David Mobley
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner
- Re: AMBER: Question about using antechamber with G03 David A. Case
- AMBER: input conversion error mm_pbsa AYTUG TUNCEL
- AMBER: TI tutorial Mingfeng Yang
- Re: AMBER: input conversion error mm_pbsa David A. Case
- Re: AMBER: (Another) Question about using antechamber with G03 David A. Case
- Re: AMBER: antechamber failure on FMN David A. Case
- Re: AMBER: TI tutorial David A. Case
Wednesday, 16 August 2006
- AMBER: MM_PBSA : Question about Stability? Guillaume Bollot
- Re: AMBER: Question about using antechamber with G03 Gustavo Seabra
- AMBER: MMPBSA: positive energies during nmode Zu Thur Yew
- Re: AMBER: MMPBSA: positive energies during nmode David A. Case
- Re: AMBER: MM_PBSA : Question about Stability? David A. Case
- AMBER: reading ff file into XLeap Petr Jerabek
- Re: AMBER: DOTA-Lanthanide complexes in Amber David A. Case
- AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold
- Re: AMBER: Ptraj selecting specific atoms in specific residues Scott Pendley
- Re: AMBER: reading ff file into XLeap David A. Case
- Re: AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu
- Re: AMBER: Ptraj selecting specific atoms in specific residues Thomas Cheatham
- RE: AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold
- AMBER: checkmask Steve Seibold
- AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng
- AMBER: pmf input files Lauren O'Neil
- AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu
- Re: AMBER: DOTA-Lanthanide complexes in Amber Brent Krueger
- Re: AMBER: generate "template" frcmod from standard residues? David Mobley
- AMBER: help with leap sethl.gatech.edu
- Re: AMBER: help with leap Bill Ross
- RE: AMBER: antechamber error -> metals Junmei Wang
Thursday, 17 August 2006
- Re: AMBER: help with leap Franck_Vendeix.ncsu.edu
- Re: AMBER: generate "template" frcmod from standard residues? David A. Case
- AMBER: 答复: AMBER: pmf input files Chunhu Tan
- Re: AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu
- Re: AMBER: generate "template" frcmod from standard residues? David A. Case
- Re: AMBER: cutting the box after "solvatebox" Ilyas Yildirim
- AMBER: RE: antechamber failure on FMN Junmei Wang
- AMBER: Execution time discrepancies Glass, Kevin A
- Re: AMBER: Execution time discrepancies Bill Ross
- AMBER: identical high energies Tanya Johannsen
- AMBER: GBSA EGB = NaN William Lianhu Wei
- RE: AMBER: identical high energies Ross Walker
- Re: AMBER: identical high energies Thomas Cheatham
- RE: AMBER: GBSA EGB = NaN Ross Walker
- RE: AMBER: Execution time discrepancies Ross Walker
Friday, 18 August 2006
- Re: AMBER: GBSA EGB = NaN William Wei
- Re: AMBER: generate "template" frcmod from standard residues? David Mobley
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case
- AMBER: Re: antechamber failure on FMN David Mobley
- AMBER: amidine group/ gaff parameters Prashanth Athri
- AMBER: ptraj script Jardas sucuriba
- RE: AMBER: GBSA EGB = NaN Ross Walker
Saturday, 19 August 2006
- Re: AMBER: DIELC? backy
Sunday, 20 August 2006
- AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman
- AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson
Monday, 21 August 2006
- AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya
- Re: AMBER: Details about Gaussian basis set for Cobalt complex FyD
- AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL
- Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Ross Walker
- Re: AMBER: GBSA EGB = NaN William Wei
- Re: AMBER: GBSA EGB = NaN William Wei
- Re: AMBER: GBSA EGB = NaN Ilyas Yildirim
- Re: AMBER: mm_pbsa calculation allocation error Ray Luo
- Re: AMBER: GBSA EGB = NaN William Wei
- Re: AMBER: GBSA EGB = NaN David A. Case
- Re: AMBER: GBSA EGB = NaN William Wei
- Re: AMBER: GBSA EGB = NaN David A. Case
- Re: AMBER: transition state Eric Hu
- Re: AMBER: Calculate interaction energy between small organic molecules David A. Case
Tuesday, 22 August 2006
- AMBER: amber naming conventions for structure files sethl.gatech.edu
- Re: AMBER: amber naming conventions for structure files Bill Ross
- AMBER: holding a pair of residues fixed during minimization Seth Lilavivat
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya
Wednesday, 23 August 2006
- Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling
- AMBER: compiling parallel amber 9 in linux Amber admin
- RE: AMBER: compiling parallel amber 9 in linux Ross Walker
- Re: AMBER: compiling parallel amber 9 in linux David A. Case
- Re: AMBER: holding a pair of residues fixed during minimization David A. Case
- Re: AMBER: holding a pair of residues fixed during minimization Bill Ross
- AMBER: Carnal: Internal error: stream file name 2 out of range Shuting Wei
- Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross
- AMBER: 0 steps the same as 1 step? S. Jamal Rahi
- Re: AMBER: 0 steps the same as 1 step? David A. Case
- AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert
- AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson
Thursday, 24 August 2006
- AMBER: ptraj dumpq feature/bug Markus Kaukonen
- AMBER: Can I run RED/RESP for Platinum Complexes? a a
- AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew
- AMBER: TI vlimit exceeded Andrea Bortolato
- AMBER: increase force constants Mahalakshmi Sahasranaman
- Re: AMBER: Backbone & Sidechain atoms: Definition David A. Case
- AMBER: nmode memory problem William Wei
- AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: nmode memory problem Knut Langsestmo
- AMBER: missing values in md.out Jardas sucuriba
- Re: AMBER: missing values in md.out Carlos Simmerling
- Re: AMBER: nmode memory problem William Wei
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker
- Re: AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew
- RE: AMBER: nmode memory problem Ross Walker
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- AMBER: how to use AddPdbAtomMap sethl.gatech.edu
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley
- Re: AMBER: ptraj dumpq feature/bug Thomas Cheatham
- Re: AMBER: how to use AddPdbAtomMap Ilyas Yildirim
- Re: AMBER: Calculate interaction energy between small organic molecules David LeBard
- Re: AMBER: nmode memory problem William Wei
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker
- Re: AMBER: how to use AddPdbAtomMap David A. Case
- Re: AMBER: increase force constants David A. Case
- Re: AMBER: increase force constants Amber admin
- RE: AMBER: compiling parallel amber 9 in linux Amber admin
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- AMBER: building AMBER9 with gfortran/cygwin Jyh-Shyong Ho
- Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 Scott Brozell
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell
- RE: AMBER: antechamber charge calculation very sensitive to conformations ? Junmei Wang
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell
Friday, 25 August 2006
- Re: AMBER: nmode memory problem Atro Tossavainen
- Re: AMBER: building AMBER9 with gfortran/cygwin Andreas Svrcek-Seiler
- AMBER: atomifluct Miguel Ferreira
- Re: AMBER: missing values in md.out Jardas sucuriba
- Re: AMBER: missing values in md.out Carlos Simmerling
- Re: AMBER: antechamber charge calculation very sensitive to conformations ? David Mobley
- Re: AMBER: Installation amber 9 on IBM SP4 David A. Case
- Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker
- Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case
- Re: AMBER: Details about Gaussian basis set for Cobalt complex Thomas Cheatham
- AMBER: How to create a modified NA in leap sethl.gatech.edu
- Re: AMBER: How to create a modified NA in leap Bill Ross
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
- Re: AMBER: Installation amber 9 on IBM SP4 Jyh-Shyong Ho
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi
Saturday, 26 August 2006
- Re: AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman
- AMBER: waters closest to specific residues Jardas sucuriba
- Re: AMBER: TI vlimit exceeded David A. Case
- Re: AMBER: How to create a modified NA in leap sethl.gatech.edu
- Re: AMBER: How to create a modified NA in leap Bill Ross
- AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht
Sunday, 27 August 2006
- Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine David A. Case
- AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht
- Re: AMBER: Temperature fluctuation with Langevin Temperature control Adrian Roitberg
Monday, 28 August 2006
- AMBER: TI, mutation eric.henon.univ-reims.fr
- Re: AMBER: TI, mutation Carlos Simmerling
- Re: AMBER: TI, mutation Pradipta Bandyopadhyay
- Re: AMBER: Temperature fluctuation with Langevin Temperature control David A. Case
- AMBER: preparing ligand/rna structure for MD sethl.gatech.edu
- AMBER: Periodic boundary condition (PBC) Rahaman, Asif
- Re: AMBER: Periodic boundary condition (PBC) Carlos Simmerling
- Re: AMBER: Periodic boundary condition (PBC) Bill Ross
- AMBER: nmode: number of atoms limitation AYTUG TUNCEL
- Re: AMBER: preparing ligand/rna structure for MD David A. Case
- Re: AMBER: Periodic boundary condition (PBC) David A. Case
- AMBER: how to limit the simulation space Eric Hu
- Re: AMBER: how to limit the simulation space Bill Ross
- Re: AMBER: nmode: number of atoms limitation David A. Case
- Re: Re: AMBER: nmode: number of atoms limitation Changge Ji
Tuesday, 29 August 2006
- Re: AMBER: TI, mutation eric.henon.univ-reims.fr
- AMBER: counterions and particle-mesh-ewald cristian obiol
- AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp a a
- AMBER: Qingning Shu
- AMBER: RDF output Jardas sucuriba
- Re: AMBER: David A. Case
- Re: Re: AMBER: Qingning Shu
- AMBER: Missing LES reference in Amber 9 manual Chris Moth
- AMBER: mm_pbsa_statistical.pl William Wei
Wednesday, 30 August 2006
- Re: AMBER: nmode: number of atoms limitation Cenk Andac
- AMBER: REMD: Hybrid topology file Austin B. Yongye
- Re: AMBER: REMD: Hybrid topology file Carlos Simmerling
- Re: AMBER: Missing LES reference in Amber 9 manual David A. Case
- Re: AMBER: mm_pbsa_statistical.pl Jianyin Shao
- AMBER: 1-4 interaction in AMBER8 Jianhui
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling
- Re: AMBER: 1-4 interaction in AMBER8 Jianhui
- Re: AMBER: counterions and particle-mesh-ewald David A. Case
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross
- Re: AMBER: mm_pbsa_statistical.pl William Wei
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling
- RE: AMBER: RDF output Jardas sucuriba
- Re: AMBER: RDF output Thomas Cheatham
- Re: AMBER: counterions and particle-mesh-ewald darden
- RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp Ross Walker
Thursday, 31 August 2006
- AMBER: reference of ff99 Myunggi Yi
- Re: AMBER: reference of ff99 Carlos Simmerling
- Re: AMBER: reference of ff99 Myunggi Yi
- Re: AMBER: reference of ff99 Myunggi Yi
- Re: AMBER: reference of ff99 David A. Case
- AMBER: Question about free energy with mm_pbsa William Wei
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham
- AMBER: minimization with my own charges Myunggi Yi
- Re: AMBER: minimization with my own charges Ilyas Yildirim
- Re: AMBER: minimization with my own charges Myunggi Yi
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif
- Re: AMBER: minimization with my own charges Ilyas Yildirim
- Re: AMBER: minimization with my own charges Myunggi Yi
- Re: AMBER: minimization with my own charges Ilyas Yildirim
- Re: AMBER: minimization with my own charges Myunggi Yi
- Re: AMBER: minimization with my own charges Ilyas Yildirim
- Re: AMBER: minimization with my own charges Thomas Cheatham
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham
- Re: AMBER: Question about free energy with mm_pbsa David A. Case

Last message date: Sun Sep 03 2006 - 06:07:18 PDT
Archived on: Fri Apr 26 2024 - 05:53:33 PDT

Amber Archive Aug 2006 by date