Amber Archive Feb 2008: by date

Friday, 1 February 2008
- AMBER: hbonds in first solvation shells Ignacio J. General
- AMBER: silica slab / FF Arturas Ziemys
- AMBER: Entropy calculations using NMODE saurabh agrawal
Saturday, 2 February 2008
- Re: AMBER: Entropy calculations using NMODE Eddie Mende
- Re: AMBER: Entropy calculations using NMODE saurabh agrawal
Monday, 4 February 2008
- AMBER: twin cut-off radii Sandeep Kaushik
- AMBER: principal component analysis rams rams
- Re: AMBER: principal component analysis Mark Williamson
- AMBER: (no subject) Syed Tarique Moin
- Re: AMBER: principal component analysis rams rams
- Re: AMBER: twin cut-off radii David A. Case
- Re: AMBER: twin cut-off radii Robert Duke
- AMBER: Re: bad atom type f(fluorine) in MM-PBSA kanazta1.yahoo.co.jp
- AMBER: time autocorrelation: ?? fatima.chami.durham.ac.uk
- RE: AMBER: principal component analysis Marco A. Lopez
- AMBER: Using antechamber without AMBER program Surasak Chunsrivirot
- Re: AMBER: Using antechamber without AMBER program Scott Brozell
- Re: AMBER: Using antechamber without AMBER program David A. Case
- AMBER: Amber 9 installation Taufik Al-Sarraj
- Re: AMBER: Amber 9 installation Yu Chen
- RE: AMBER: Amber 9 installation Ross Walker
- AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert
- Re: AMBER: VLIMIT units; TGTFITMASK David A. Case
- Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot
- Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot
- Re: AMBER: Using antechamber without AMBER program David A. Case
Tuesday, 5 February 2008
- AMBER: mm_pbsa: vertex atom mismatch Marc Lindner
- RE: AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert
- AMBER: Amber 9 installation Taufik Al-Sarraj
- AMBER: infinite polymers in CHARMM David A. Case
- AMBER: silica slab Arturas Ziemys
- Re: AMBER: silica slab David A. Case
- Re: AMBER: silica slab Arturas Ziemys
- AMBER: Problem with energy decomposition in MMPBSA alfredoq.mail.fcq.unc.edu.ar
- AMBER: segmentation fault while generating the covariance matrix rams rams
- AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member Vidana.Epa.csiro.au
Wednesday, 6 February 2008
- Fwd: AMBER: (no subject) Syed Tarique Moin
- AMBER: Query related to implicit solvent EXTDIEL S.Sundar Raman
- AMBER: Binary restart file !! Sampath Koppole
- Re: AMBER: Query related to implicit solvent EXTDIEL David A. Case
- Re: AMBER: Binary restart file !! David A. Case
- Re: AMBER: Binary restart file !! Sampath Koppole
- AMBER: using NAB to calculate entropy Wang, Xuelin
- RE: AMBER: silica slab Steve Spronk
- Re: AMBER: using NAB to calculate entropy David A. Case
- RE: AMBER: using NAB to calculate entropy. . Wang, Xuelin
- AMBER: Amber compilation with ifort Andrey Semichaevsky
- Re: AMBER: using NAB to calculate entropy. . David A. Case
- Re: AMBER: Amber compilation with ifort David A. Case
- RE: AMBER: Amber compilation with ifort Ross Walker
- AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail
- Re: AMBER: Amber compilation with ifort Mark Williamson
- Re: AMBER: silica slab Steven Winfield
- Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Bill Ross
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Ross Walker
- AMBER: Problem:neturalization jani sahil
- AMBER: A new program for doing RESP David Cerutti
- Re: AMBER: Amber compilation with ifort Atro Tossavainen
- Re: AMBER: Problem:neturalization David Cerutti
Thursday, 7 February 2008
- AMBER: disulfide bridge with ff03ua FF Marcin Krol
- AMBER: Deleting solute from box Kevin Davies
- Re: AMBER: Deleting solute from box Bill Ross
- RE: AMBER: QMMM with printcharges Ross Walker
- Re: AMBER: Deleting solute from box Kevin Davies
- AMBER: Error while compiling Amber Lili Peng
- Re: AMBER: Error while compiling Amber David A. Case
- AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams
Friday, 8 February 2008
- AMBER: Which install compiler and flags? Sam Kaye
- AMBER: PB Bomb in pb_atmlist(): maxnba too short Eddie Mende
- Re: AMBER: Using antechamber without AMBER program Junmei Wang
- Re: AMBER: disulfide bridge with ff03ua FF raja pandian
- RE: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! Ross Walker
- RE: AMBER: Which install compiler and flags? Ross Walker
- RE: AMBER: PB Bomb in pb_atmlist(): maxnba too short Ross Walker
- Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol
- Re: AMBER: Which install compiler and flags? David A. Case
- AMBER: Antechamber/mopac query Lynn F. Ten Eyck
- Re: AMBER: Error while compiling Amber Lili Peng
- Re: AMBER: disulfide bridge with ff03ua FF raja pandian
Saturday, 9 February 2008
- RE: AMBER: Error while compiling Amber Ross Walker
- Re: AMBER: Error while compiling Amber Lili Peng
- RE: AMBER: Error while compiling Amber Ross Walker
- AMBER: Input file for Minimization Campbell, Patrick
- Re: AMBER: Error while compiling Amber chen
Sunday, 10 February 2008
- RE: AMBER: Input file for Minimization Ross Walker
- Re: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams
Monday, 11 February 2008
- Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol
- Re: AMBER: Input file for Minimization Carlos Simmerling
- AMBER: leaprc help snoze pa
- Re: AMBER: leaprc help Carlos Simmerling
- Re: AMBER: leaprc help snoze pa
- AMBER: mm_pbsa problem Badry Bursulaya
- Re: AMBER: leaprc help Reena .....
Tuesday, 12 February 2008
- AMBER: Non-polar Parameters For MM_PBSA Calculation Neil Bruce
- AMBER: PKa calculation Wang, Xuelin
- Re: AMBER: PKa calculation David A. Case
- RE: AMBER: Input file for Minimization Campbell, Patrick
- Re: AMBER: Input file for Minimization Carlos Simmerling
- Re: AMBER: disulfide bridge with ff03ua FF Ray Luo
- RE: AMBER: Non-polar Parameters For MM_PBSA Calculation rluo.uci.edu
- AMBER: RDCs in AMBER 10 Douglas Kojetin
- Re: AMBER: RDCs in AMBER 10 David A. Case
- Re: AMBER: RDCs in AMBER 10 Douglas Kojetin
Wednesday, 13 February 2008
- AMBER: (no subject) Syed Tarique Moin
- AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen
- AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes
- RE: AMBER: (no subject) Ross Walker
- RE: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Ross Walker
- Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol
- AMBER: sander error on Make test.serial Evan Kelly
- Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen
- Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case
- Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen
- Re: AMBER: sander error on Make test.serial Evan Kelly
- AMBER: ambmask problem Hopkins, Robert
- AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran
- AMBER: xmgr graphics display program Hopkins, Robert
- Re: AMBER: xmgr graphics display program Gustavo Seabra
- RE: AMBER: (no subject) Syed Tarique Moin
- Re: AMBER: xmgr graphics display program David A. Case
- Re: AMBER: sander error on Make test.serial David A. Case
- Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen
Thursday, 14 February 2008
- AMBER: mpd error in submitting parallel job Lili Peng
- Re: AMBER: Error while compiling Amber Lili Peng
- Re: AMBER: Error while compiling Amber Jack Lei
- Re: AMBER: Error while compiling Amber Lili Peng
- Re: AMBER: sander error on Make test.serial Evan Kelly
- Re: AMBER: mpd error in submitting parallel job Gustavo Seabra
- Re: AMBER: xmgr graphics display program Junmei Wang
- Re: AMBER: Error while compiling Amber Junmei Wang
- AMBER: Distance restraints between com of two groups of residues Sudha Mani Karra
- Re: AMBER: Error while compiling Amber Lili Peng
- RE: AMBER: mpd error in submitting parallel job Ross Walker
Friday, 15 February 2008
- AMBER: print distance between atoms during simulation within sander itsself Vlad Cojocaru
- AMBER: setbox for solvateoct model Wang, Xuelin
- RE: AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes
- Re: AMBER: Error while compiling Amber Junmei Wang
- Re: AMBER: ambmask problem David A. Case
- AMBER: problem with ambmask David A. Case
- AMBER: using NAB to calculate normal modes Z. Nevin Gerek
- Re: AMBER: using NAB to calculate normal modes David A. Case
- RE: AMBER: using NAB to calculate normal modes. . Wang, Xuelin
- Re: AMBER: using NAB to calculate normal modes Andreas Svrcek-Seiler
- Re: AMBER: using NAB to calculate normal modes. . David A. Case
- Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case
- Re: AMBER: setbox for solvateoct model David A. Case
- RE: AMBER: Is boiling point a good way to validate solvent paramters? FyD
Saturday, 16 February 2008
- AMBER: matrix correl David Beveridge
- Re: AMBER: AMBER parameters for Chlorophyll mathew k varghese
- Re: AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran
- Re: AMBER: AMBER parameters for Chlorophyll David LeBard
Sunday, 17 February 2008
- Re: AMBER: xmgr graphics display program Hopkins, Robert
- AMBER: setting perioding box in AMBER Vijay Manickam Achari
- Re: AMBER: setting perioding box in AMBER David A. Case
Monday, 18 February 2008
- Re: AMBER: matrix correl Holger Gohlke
- AMBER: TERs Steve Seibold
- Re: AMBER: TERs David A. Case
- Re: AMBER: TERs Thomas Cheatham
- RE: AMBER: TERs Steve Seibold
- RE: AMBER: problem with ambmask Hopkins, Robert
- Re: AMBER: setting perioding box in AMBER Vijay Manickam Achari
Tuesday, 19 February 2008
- AMBER: parameters of nonbonded potentials Alexander Klenner
- AMBER: Generating RESP charges Christopher Illingworth
- Re: AMBER: Generating RESP charges Junmei Wang
- Re: AMBER: parameters of nonbonded potentials David A. Case
- Re: AMBER: Generating RESP charges Christopher Illingworth
- Re: AMBER: Generating RESP charges Junmei Wang
- Re: AMBER: Generating RESP charges M. L. Dodson
- Re: AMBER: Generating RESP charges Junmei Wang
- AMBER: united atom force field: antechamber fatima.chami.durham.ac.uk
- Re: AMBER: united atom force field: antechamber David A. Case
- AMBER: NAB to calcuate entropy Wang, Xuelin
- Re: AMBER: NAB to calcuate entropy David A. Case
- AMBER: Regarding:PME and neturalization jani sahil
- AMBER: is that possible fix box size in constant pressure MD Vijay Manickam Achari
Wednesday, 20 February 2008
- Re: AMBER: Regarding:PME and neturalization Lars Skjærven
- AMBER: Dimension of the solvated box? abiram abiram
- Re: AMBER: Dimension of the solvated box? David A. Case
- AMBER: saveAmberPrep in internal coordinates Xu, Huafeng
- AMBER: Problem with "trajout pdb" Yi-Ming Cheng
- RE: AMBER: matrix correl Ibrahim Moustafa
- Re: AMBER: matrix correl Lars Skjærven
- Re: AMBER: saveAmberPrep in internal coordinates Junmei Wang
- RE: AMBER: matrix correl Ibrahim Moustafa
- Re: AMBER: NAB to calcuate entropy Z. Nevin Gerek
- Re: AMBER: NAB to calcuate entropy David A. Case
- RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin
- Re: AMBER: NAB to calcuate entropy. . Z. Nevin Gerek
- RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin
- Re: AMBER: NAB to calcuate entropy. . David A. Case
- Re: AMBER: NAB to calcuate entropy. . David A. Case
- RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin
Thursday, 21 February 2008
- AMBER: XLEaP Anamika Awasthi
- Re: AMBER: XLEaP David A. Case
- Re: AMBER: NAB to calcuate entropy. . David A. Case
- Re: AMBER: NAB to calcuate entropy. . David A. Case
- AMBER: simulated annealing Holly Freedman
- Re: AMBER: simulated annealing David A. Case
- RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin
- Re: AMBER: NAB to calcuate entropy. . David A. Case
- Re: AMBER: simulated annealing Holly Freedman
- AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David Cerutti
- AMBER: (no subject) Syed Tarique Moin
- Re: AMBER: (no subject) Eddie Mende
- Re: AMBER: (no subject) Eddie Mende
Friday, 22 February 2008
- AMBER: problem bull linux compiling Yannick Monclin
- Re: AMBER: problem bull linux compiling Gustavo Seabra
- RE: AMBER: (no subject) Ibrahim Moustafa
- Re: AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David A. Case
- AMBER: gaff paramters servaas michielssens
- Re: AMBER: gaff paramters Servaas Michielssens
- AMBER: More on tweaking a topology file David Cerutti
- Re: AMBER: gaff paramters Servaas Michielssens
Saturday, 23 February 2008
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng
- Fwd: Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng
- AMBER: dihedral energy in amber aneesh cna
- Re: AMBER: More on tweaking a topology file Carlos Simmerling
- Re: AMBER: dihedral energy in amber David A. Case
Monday, 25 February 2008
- Re: AMBER: problem bull linux compiling Yannick Monclin
- Re: AMBER: parameters for silicon atom Scott Brozell
Tuesday, 26 February 2008
- AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento
- Re: AMBER: compiling PMEMD with MKL10.0 Francesco Pietra
- Re: AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento
- Re: AMBER: compiling PMEMD with MKL10.0 Robert Duke
- AMBER: Force fields oguz gurbulak
- AMBER: bond breaking in proteins Eddie Mende
- Re: AMBER: mol2 save Steven Winfield
- Re: AMBER: bond breaking in proteins David A. Case
- AMBER: mol2 save snoze pa
- Re: AMBER: problem bull linux compiling Gustavo Seabra
- Re: AMBER: Force fields David A. Case
- Re: AMBER: mol2 save FyD
- Re: AMBER: mol2 save David A. Case
- Re: AMBER: compiling PMEMD with MKL10.0 Gustavo Seabra
- Re: AMBER: bond breaking in proteins Gustavo Seabra
- Re: AMBER: autodock pdb to obtain parm with tleap David A. Case
- AMBER: autodock pdb to obtain parm with tleap Henar Martínez
- AMBER: bond breaking in proteins Eddie Mende
- AMBER: Using restart files Lili Peng
- AMBER: bond breaking in proteins Eddie Mende
- Re: AMBER: bond breaking in proteins David A. Case
- Re: AMBER: Using restart files David A. Case
- AMBER: charge derivation for modified amino acids Denzil Bernard
- AMBER: "Assuming uniform neutralizing plasma" Evan Kelly
- Re: AMBER: "Assuming uniform neutralizing plasma" Thomas Cheatham
- Re: AMBER: charge derivation for modified amino acids FyD
Wednesday, 27 February 2008
- AMBER: stops writing trajectory Swarup Gupta
- Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez
- Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez
- AMBER: initial command? Anamika Awasthi
- Re: AMBER: initial command? Carlos Simmerling
- Re: AMBER: bond breaking in proteins Gustavo Seabra
- Re: AMBER: autodock pdb to obtain parm with tleap Junmei Wang
- Re: AMBER: autodock pdb to obtain parm with tleap Francesco Pietra
- AMBER: Amber: shared memory vs cluster Francesco Pietra
- Re: AMBER: autodock pdb to obtain parm with tleap David A. Case
- Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez
- Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez
- Re: AMBER: Amber: shared memory vs cluster Robert Duke
Tuesday, 26 February 2008
- Re: AMBER: bond breaking in proteins Eddie Mende
Wednesday, 27 February 2008
- AMBER: Lennard-Jones parameters zhan chen
Tuesday, 26 February 2008
- Re: AMBER: bond breaking in proteins Eddie Mende
- Re: AMBER: bond breaking in proteins Eddie Mende
Wednesday, 27 February 2008
- RE: AMBER: initial command? Steve Spronk
- RE: AMBER: initial command? Bill Ross
- AMBER: DFTB/SCC-DFTB Eddie Mende
- AMBER: varying restraint_wt with nmropt=1 Andrew Borgert
- Re: AMBER: Amber: shared memory vs cluster Francesco Pietra
- Re: AMBER: Amber: shared memory vs cluster Robert Duke
- Re: AMBER: Lennard-Jones parameters Klenner.bioinformatik.uni-frankfurt.de
- Re: AMBER: Lennard-Jones parameters David A. Case
- Re: AMBER: Lennard-Jones parameters Bill Ross
- AMBER: change in secondary structure during MD Ibrahim Moustafa
- RE: AMBER: change in secondary structure during MD Yong Duan
- Re: AMBER: Lennard-Jones parameters Zhan Chen
- AMBER: problem with antechamber aneesh cna
- Re: AMBER: DFTB/SCC-DFTB David A. Case
- Re: AMBER: varying restraint_wt with nmropt=1 Daniel Cappel
Thursday, 28 February 2008
- Re: AMBER: change in secondary structure during MD Carlos Simmerling
- AMBER: problems with Replica Exchange rebeca.mmb.pcb.ub.es
- Re: AMBER: problems with Replica Exchange Carlos Simmerling
- AMBER: Plea for REMD tutorial tushar garud
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling
- AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein Fenghui Fan
- Re: AMBER: problem with antechamber Junmei Wang
- Re: AMBER: problems with Replica Exchange rebeca.mmb.pcb.ub.es
- AMBER: Liquid/Gas Phase Rita Cassia
- Re: AMBER: problems with Replica Exchange Carlos Simmerling
- Re: AMBER: Lennard-Jones parameters Bill Ross
- AMBER: problems with 10-12 potential in amber8 sander Amie Demmel
- AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky
- RE: AMBER: change in secondary structure during MD Ibrahim Moustafa
- Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case
- RE: AMBER: change in secondary structure during MD Fenghui Fan
- Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel
- Re: AMBER: problems with 10-12 potential in amber8 sander Lynn F. Ten Eyck
- Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case
- AMBER: for NMR refinement Wenyong Tong
Friday, 29 February 2008
- Re: AMBER: parameters for silicon atom Scott Brozell
Thursday, 28 February 2008
- AMBER: Visualizing Periodc box Vijay Manickam Achari
Friday, 29 February 2008
- RE: AMBER: initial command? Steve Spronk
- AMBER: Plea for REMD tutorial tushar garud
- AMBER: Re: Amber Force field for CNT: leaprc.ff23 Andrey Semichaevsky
- Re: AMBER: Re: Force field parameter file for CNT David A. Case
- Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel
- Re: AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling
- Re: AMBER: problems with Replica Exchange Carlos Simmerling
- Re: AMBER: for NMR refinement David A. Case
- AMBER: Non aqueous implicit solvation Mike Wykes

Last message date: Sun Mar 02 2008 - 06:07:44 PST
Archived on: Fri Nov 22 2024 - 05:53:38 PST

Amber Archive Feb 2008 by date