Amber Archive Apr 2008: by date

Monday, 31 March 2008
- AMBER: Amber 8 on Redhat 4 X86_64 yavuzturkm.prc.boun.edu.tr
Tuesday, 1 April 2008
- AMBER: TIP5P water simulation with AMBER7 Biman Jana
- AMBER: hybrid remd imaging Geoff Wood
- AMBER: working with unformatted restart files in AMBER9 Vlad Cojocaru
- AMBER: atomic posiltional fluctuation Furia Gargano
- RE: AMBER: Protein rotating out of box Steve Spronk
- Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin
- Re: AMBER: atomic posiltional fluctuation Thomas Cheatham III
- AMBER: Electric field on atoms in equallibrium Lishan Yao
- Re: AMBER: Electric field on atoms in equallibrium Tom Darden
- Re: AMBER: Electric field on atoms in equallibrium Lishan Yao
- AMBER: B-factor Furia Gargano
- Re: AMBER: Electric field on atoms in equallibrium Tom Darden
- AMBER: Simulating DNA Backbone in NAB Adelene Sim
- AMBER: LEap error message for parmBSC0 force field Cenk Andac
- Re: AMBER: LEap error message for parmBSC0 force field Thomas Cheatham III
- Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin
- AMBER: meet problems in adding ions and waterbox Qiang Li
- Re: AMBER: meet problems in adding ions and waterbox David A. Case
- Re: AMBER: meet problems in adding ions and waterbox Qiang Li
Wednesday, 2 April 2008
- AMBER: LJ parameters aneesh cna
- Re: AMBER: Protein rotating out of box Lars Skjærven
- AMBER: REMD simulation error Guillaume Renvez
- RE: AMBER: Protein rotating out of box Steve Spronk
- AMBER: ANNOUNCE: Release of AmberTools, version 1.0 David A. Case
- Re: AMBER: Protein rotating out of box Thomas Cheatham III
- Re: AMBER: B-factor Thomas Cheatham III
- Re: AMBER: working with unformatted restart files in AMBER9 Thomas Cheatham III
- Re: AMBER: LJ parameters Thomas Steinbrecher
- Re: AMBER: Protein rotating out of box Qiang Li
- Re: AMBER: Nmode segmentation fault David A. Case
- Re: AMBER: residual dipolar couplings - alignment tensor energy David A. Case
- Re: AMBER: Regarding SHAKE David A. Case
- AMBER: ptraj / covariance / quasiharmonic approximation / entropy Seth Lilavivat
- Re: AMBER: Protein rotating out of box Lars Skjærven
- Re: AMBER: Simulating DNA Backbone in NAB David A. Case
- Re: AMBER: multiple dihedral restraints using group David A. Case
- Re: AMBER: Protein rotating out of box Lars Skjærven
- Re: AMBER: ptraj / covariance / quasiharmonic approximation / entropy Chris Moth
- Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth
- Re: AMBER: meet problems in adding ions and waterbox David A. Case
- Re: AMBER: AMBER 9 testing Taufik Al-Sarraj
Thursday, 3 April 2008
- Re: AMBER: LJ parameters aneesh cna
- Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac
- Re: AMBER: LEap error message for parmBSC0 force field Alberto Perez
- AMBER: NAD parameters Urszula Uciechowska
- Re: AMBER: NAD parameters David A. Case
- RE: AMBER: NAD parameters Ross Walker
- AMBER: dockmolecules in examples directory of AmberTools-1.0 M. L. Dodson
- AMBER: mm_pbsa error rams rams
- AMBER: MPI run problem Qi Yan
- AMBER: problem with Mg2+ during MD Zhenwei Lu
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross
- Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac
- AMBER: Using mdcrd files to look at minor charge changes Cooper, Matthew
- Re: AMBER: Using mdcrd files to look at minor charge changes David A. Case
- AMBER: Simple Minimization - Error dpandit.brandeis.edu
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross
- Re: AMBER: Simple Minimization - Error David A. Case
- Re: AMBER: Simple Minimization - Error Daniel Smith
- Re: AMBER: mm_pbsa error stephane acoca
- Re: AMBER: MPI run problem David A. Case
- AMBER: imem keyword using mmpbsa Sergio Wong
- Re: AMBER: MPI run problem Robert Duke
- RE: AMBER: MPI run problem Qi Yan
- Re: AMBER: imem keyword using mmpbsa Sergio Wong
- Re: AMBER: imem keyword using mmpbsa David A. Case
Friday, 4 April 2008
- AMBER: solvateOct produces strange residues compared to solvateCap Markus Kaukonen
- AMBER: GAFF Eric Germaneau
- Re: AMBER: GAFF Vlad Cojocaru
- Re: AMBER: GAFF Vlad Cojocaru
- Re: AMBER: GAFF Eric Germaneau
- Re: AMBER: GAFF Eric Germaneau
- AMBER: Restraintmask and Restraint_WT : Question dpandit.brandeis.edu
- Re: AMBER: GAFF David A. Case
- AMBER: ligand slips out of pocket Hannes Wallnoefer
- Re: AMBER: mm_pbsa error Scott Pendley
- AMBER: sander.MPI setup with SGE Sasha Buzko
- Re: AMBER: GAFF Eric Germaneau
- Re: AMBER: Restraintmask and Restraint_WT : Question Thomas Steinbrecher
Saturday, 5 April 2008
- AMBER: artifacts in ptraj avg output stephane acoca
- Re: AMBER: artifacts in ptraj avg output Barbault Florent
- Re: AMBER: artifacts in ptraj avg output stephane acoca
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- AMBER: Minimisation: cis-azobenzene parameters Chih-Ying Lin
- RE: AMBER: sander.MPI setup with SGE Ross Walker
- Re: AMBER: Minimisation: cis-azobenzene parameters David A. Case
- AMBER: RE: amber help Ross Walker
Sunday, 6 April 2008
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
Monday, 7 April 2008
- AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: NAB examples David A. Case
- Re: AMBER: running minimisation on cis-azobenzene David A. Case
- RE: AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: NAB examples David A. Case
- RE: AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: NAB examples Andreas Svrcek-Seiler
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher
- Re: AMBER: NAB examples David A. Case
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- AMBER: Trans-azobenzene and cis-azobenzene Chih-Ying Lin
- Re: AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water David A. Case
- AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: sander.MPI setup with SGE Sasha Buzko
- AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin
- Re: AMBER: Build a MPI NAB David A. Case
- Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case
- Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case
Tuesday, 8 April 2008
- AMBER: restraint box dimension aneesh cna
- RE: AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher
- AMBER: Amber 9 run error Andrew Borgert
- Re: AMBER: Build a MPI NAB David A. Case
- Re: AMBER: running minimisation on cis-azobenzene Junmei Wang
- Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin
- Re: AMBER: running minimisation on cis-azobenzene----an electron-withdrew atom Chih-Ying Lin
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- RE: AMBER: Amber 9 run error Ross Walker
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case
- Re: AMBER: running minimisation on cis-azobenzene Junmei Wang
- Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin
- Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin
- Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin
- AMBER: anything wrong with this script Chih-Ying Lin
- Re: AMBER: restraint box dimension David A. Case
- AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin
- AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin
- Re: AMBER: Protein rotating out of box David A. Case
- AMBER: converting from CNS file format Sally Pias
Wednesday, 9 April 2008
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) zachary hartman
- RE: AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA]
- AMBER: Estimating dielectric constant Marcelo Puiatti
- Re: AMBER: Build a MPI NAB David A. Case
- AMBER: Collect dihedral angles Chih-Ying Lin
- AMBER: ASSERTion ' ier == 0 ' failed in nmode.f Qi Yan
- AMBER: Tutorial B3- Section6 Chih-Ying Lin
- Re: AMBER: Tutorial B3- Section6 David A. Case
- Re: AMBER: Tutorial B3- Section6 Chih-Ying Lin
- AMBER: Force field Parameters Chih-Ying Lin
- Re: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f David A. Case
- Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s
- Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s
- Re: AMBER: FAD and NAD parameters Thomas Leonard
Thursday, 10 April 2008
- AMBER: tempi in Replica Exchange rebeca.mmb.pcb.ub.es
- Re: AMBER: tempi in Replica Exchange Carlos Simmerling
- AMBER: WHAM: how frequently do I need data on the system coordinates? David Cerutti
- AMBER: Gbsa in NAB Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: Gbsa in NAB David A. Case
- Re: AMBER: WHAM: how frequently do I need data on the system coordinates? John Chodera
- Re: AMBER: solvateOct produces strange residues compared to solvateCap David A. Case
- AMBER: Initial Equilibration dpandit.brandeis.edu
- AMBER: protein-ligand complex problem Lynn
- Re: AMBER: Tutorial B3- Section6 Chih-Ying Lin
- RE: AMBER: protein-ligand complex problem Ross Walker
- Re: AMBER: protein-ligand complex problem David A. Case
- AMBER: trans-azobenzene under minimisation Chih-Ying Lin
- RE: AMBER: Initial Equilibration Ross Walker
- Re: AMBER: converting from CNS file format Sally Pias
Friday, 11 April 2008
- Re: AMBER: restraint box dimension aneesh cna
- Re: AMBER: restraint box dimension Carlos Simmerling
- Re: AMBER: Tutorial B3- Section6 Carlos Simmerling
- AMBER: query about Generalized Born simulation gurvisha.leadinvent.com
- Re: AMBER: query about Generalized Born simulation Carlos Simmerling
- Re: AMBER: query about Generalized Born simulation rpaduri.chem.wayne.edu
- AMBER: Amber installation jacopo.sgrignani.unifi.it
- RE: AMBER: Amber installation Ross Walker
- AMBER: Imaging before HBond analysis? Evan Kelly
- Re: AMBER: Amber installation Mengjuei Hsieh
- Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III
- Re: AMBER: Imaging before HBond analysis? Evan Kelly
- RE: AMBER: Amber installation Ross Walker
- Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III
- Re: AMBER: Imaging before HBond analysis? Evan Kelly
Sunday, 13 April 2008
- AMBER: installing pmemd with fftw YangMingjun
- Re: AMBER: installing pmemd with fftw Robert Duke
- Re: Re: AMBER: installing pmemd with fftw YangMingjun
Monday, 14 April 2008
- AMBER: topology file Giuseppe De Marco
- AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer
- AMBER: error in compilation elsize.cc snoze pa
- Re: AMBER: error in compilation elsize.cc David A. Case
- AMBER: ANNOUNCEMENT: release of Amber 10 David A. Case
- Re: AMBER: error in compilation elsize.cc snoze pa
- AMBER: loadPdb returns extra atoms Seth Lilavivat
- AMBER: Problems compiling Amber with MKL Sasha Buzko
- Re: AMBER: loadPdb returns extra atoms Thomas Cheatham III
- AMBER: JavaGenes Shultz, Jack
- AMBER: Whole System Equilibration & Pressure dpandit.brandeis.edu
- RE: AMBER: Problems compiling Amber with MKL Ross Walker
- RE: AMBER: Whole System Equilibration & Pressure Ross Walker
- RE: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f Qi Yan
- RE: AMBER: Problems compiling Amber with MKL Sasha Buzko
- RE: AMBER: Problems compiling Amber with MKL Sasha Buzko
- AMBER: energy decomposition vs ala scan Sergio Wong
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case
Tuesday, 15 April 2008
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer
- AMBER: imaging problem Marcin Krol
- Re: AMBER: imaging problem Carlos Simmerling
- AMBER: mmpbsa with gromacs trajectory jacopo.sgrignani.unifi.it
- Re: AMBER: imaging problem Marcin Krol
- Re: AMBER: imaging problem David Smith
- Re: AMBER: imaging problem Marcin Krol
- AMBER: loading pdb in leap to create parameter files Cristina Sisu
- Re: AMBER: loading pdb in leap to create parameter files Da-Wei Li
- RE: AMBER: Whole System Equilibration & Pressure dpandit.brandeis.edu
- Re: AMBER: loading pdb in leap to create parameter files Cristina Sisu
- Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj
- AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji
- RE: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? Ross Walker
- Re: AMBER: questions about run MD at different pH David A. Case
- AMBER: xleap segmentation fault on SaveAmberParm Brendan Duggan
- Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj
- Re: AMBER: xleap segmentation fault on SaveAmberParm Wei Zhang
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case
- Re: AMBER: xleap segmentation fault on SaveAmberParm David A. Case
- Re: AMBER: questions about run MD at different pH David A. Case
- Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj
- AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera
- AMBER: PMF calculation for rate constant or binding constant? Catein Catherine
- AMBER: PMF calculation for binding constant or rate constant? Catein Catherine
Wednesday, 16 April 2008
- AMBER: leap - using default radius 1.500000 for HO3 Nina Fischer
- AMBER: Protonation states in Constant pH Simulations Neil Bruce
- AMBER: Distance in z dimension Age.Skjevik.student.uib.no
- Re: AMBER: topology file David A. Case
- Re: AMBER: PMF calculation for binding constant or rate constant? David A. Case
- Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms Tom Darden
- AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko
- RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker
- Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera
- RE: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko
- RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker
- RE: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko
- Re: AMBER: Amber9 with MPICH2 failure at runtime David A. Case
- Re: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko
- RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker
- Re: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko
- AMBER: xLeap unit editor "seg fault" inonshar.post.tau.ac.il
Thursday, 17 April 2008
- AMBER: Scale LJ parameters fatima.chami.durham.ac.uk
- AMBER: Accessing Equilibration Results dpandit.brandeis.edu
- AMBER: uccabke.ucl.ac.uk
- AMBER: H atom names in Amber David A. Case
- Re: AMBER: Da-Wei Li
- Re: AMBER: Florian Haberl
- Re: AMBER: H atom names in Amber uccabke.ucl.ac.uk
- AMBER: Performance issues on Ethernet clusters Sasha Buzko
- Re: AMBER: Performance issues on Ethernet clusters David A. Case
- AMBER: Conformation search... Anthony Cruz
- Re: AMBER: Performance issues on Ethernet clusters Robert Duke
- AMBER: Short trajectory segments / frequent restarts causes explosion David Cerutti
- Re: AMBER: Performance issues on Ethernet clusters Sasha Buzko
- AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Kevin Abbey
- Re: AMBER: Short trajectory segments / frequent restarts causes explosion Robert Duke
- Re: AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Sasha Buzko
- Re: AMBER: xLeap unit editor "seg fault" David A. Case
- Re: AMBER: Scale LJ parameters David A. Case
Friday, 18 April 2008
- AMBER: compile Amber9 on 64bit AMD Opteron Jeffrey
- AMBER: nmode problem Hannes Wallnoefer
- Re: AMBER: nmode problem Hannes Wallnoefer
- Re: AMBER: compile Amber9 on 64bit AMD Opteron David A. Case
- AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case
- AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling
- Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai
- Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai
- RE: AMBER: hydrogens are flying in replica exchange simulations Ross Walker
Saturday, 19 April 2008
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling
Sunday, 20 April 2008
- Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai
- AMBER: How to add radius of an atom saurabh agrawal
Monday, 21 April 2008
- AMBER: Average structure James Thomas
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen
- Re: AMBER: hydrogens are flying in replica exchange simulations Adrian Roitberg
- Re: AMBER: hydrogens are flying in replica exchange simulations Adrian Roitberg
- Re: AMBER: Average structure David Cerutti
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling
- AMBER: nmode jacopo.sgrignani.unifi.it
- RE: AMBER: loading pdb in leap to create parameter files Steve Spronk
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Scott Brozell
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Scott Brozell
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen
- AMBER: aromatic residues lost planarity during MD simulation cniu.ualberta.ca
- Re: AMBER: aromatic residues lost planarity during MD simulation Carlos Simmerling
- Re: AMBER: hydrogens are flying in replica exchange simulations Karl Kirschner (kkirschn)
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case
- Re: AMBER: nmode David A. Case
- Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai
- AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong
- Re: AMBER: Can sander provide ESP with PBC? John Chodera
- RE: AMBER: Average structure Ross Walker
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen
- AMBER: How to change default radius assigned to an atom saurabh agrawal
- Re: AMBER: How to change default radius assigned to an atom David A. Case
- AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari
Tuesday, 22 April 2008
- RE: AMBER: Average structure Francesco Pietra
- AMBER: vlimit-problems after image and restart Anselm Horn
- AMBER: matrxi dist command priya priya
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Mike Summers
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers Mike Summers
- AMBER: RESP charges Jena M
- AMBER: minimization san_amber roy
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case
- Re: AMBER: pressure varies in constant pressure membrane simulation David A. Case
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling
- AMBER: refine cyana structures! Hongyan Li
- Re: AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari
- RE: AMBER: vlimit-problems after image and restart Ross Walker
- AMBER: RE: amber tutorial A3 Ross Walker
- AMBER: Topology file format for Amber9 Xioling Chuang
Wednesday, 23 April 2008
- AMBER: cross time correlation function fatima.chami.durham.ac.uk
- AMBER: ESP on atoms (2) Khatcharin Siriwong
- AMBER: 2D-RMSD Tom McGrory
- Re: AMBER: How to change default radius assigned to an atom Wei Zhang
- Re: AMBER: cross time correlation function David A. Case
- Re: AMBER: Topology file format for Amber9 David A. Case
- Re: AMBER: cross time correlation function fatima.chami.durham.ac.uk
- Re: AMBER: cross time correlation function David A. Case
- AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen
- Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error David A. Case
- Re: AMBER: Can sander provide ESP with PBC? Thomas Steinbrecher
- Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen
- AMBER: Tutorial B5 Chih-Ying Lin
- Re: AMBER: Tutorial B5 Alessandro Nascimento
- AMBER: saveamberparm taufik.alsarraj.utoronto.ca
- AMBER: saveamberparm taufik.alsarraj.utoronto.ca
- Re: AMBER: Tutorial B5 Chih-Ying Lin
- Re: AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong
- RE: AMBER: Tutorial B5 Ross Walker
- Re: RE: AMBER: Tutorial B5 Chih-Ying Lin
Thursday, 24 April 2008
- AMBER: sander & imin=5 Xioling Chuang
- AMBER: water in the binding site MMPBSA jacopo.sgrignani.unifi.it
- AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists)
- Re: AMBER: saveamberparm David A. Case
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Gustavo Seabra
- AMBER: double strand DNA break up (imaging) Seth Lilavivat
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists)
- Re: AMBER: double strand DNA break up (imaging) Thomas Cheatham III
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke
- AMBER: How to print out the improper dihedral angles/wilson angles? Chih-Ying Lin
Friday, 25 April 2008
- AMBER: nmode output jacopo.sgrignani.unifi.it
- AMBER: query regarding loadpadb Anamika Awasthi
- Re: AMBER: query regarding loadpadb Reena .....
- Re: AMBER: nmode output Lachele Foley (Lists)
- Re: AMBER: sander & imin=5 David A. Case
- AMBER: Si parameters for MD (AMBER9) Taufik Al-Sarraj
- AMBER: parallel error : undefined reference to `MAIN_' Arturas Ziemys
- AMBER: AMD Opteron: compiler recommendations? Sasha Buzko
- Re: AMBER: AMD Opteron: compiler recommendations? Robert Duke
- Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko
Saturday, 26 April 2008
- Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra
- Fw: Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra
- AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal
- Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent
- AMBER: memory usage Ye Mei
- AMBER: Azobenzene: dihedral angle CCNN force field parameter Chih-Ying Lin
- Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko
- Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra
- Re: AMBER: Azobenzene: dihedral angle CCNN force field parameter Adrian Roitberg
- Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko
- RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker
- RE: AMBER: memory usage Ross Walker
Sunday, 27 April 2008
- Re: RE: AMBER: memory usage Ye Mei
- RE: RE: AMBER: memory usage Ross Walker
- RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal
- AMBER: NMR restraints Ilyas Yildirim
Monday, 28 April 2008
- AMBER: Read trajectories generated by CHARMM Jeffrey
- AMBER: query regarding energy minimization Anamika Awasthi
- Re: RE: RE: AMBER: memory usage Ye Mei
- Re: AMBER: query regarding energy minimization rpaduri.chem.wayne.edu
- Re: AMBER: query regarding energy minimization Deepangi Pandit
- Re: AMBER: Read trajectories generated by CHARMM David A. Case
- Re: AMBER: NMR restraints David A. Case
- Re: RE: RE: AMBER: memory usage David A. Case
- AMBER: Parrallel computing Chih-Ying Lin
- Re: Re: AMBER: Read trajectories generated by CHARMM Jeffrey
- Re: AMBER: query regarding energy minimization D.Usharani
- RE: AMBER: Parrallel computing Ross Walker
- RE: AMBER: query regarding energy minimization Ross Walker
Tuesday, 29 April 2008
- AMBER: Charge derivation: RESP vs. antechamber Catein Catherine
- AMBER: Charge derivation: RESP vs. antechamber Catein Catherine
- AMBER: segmentation fault in SANDER Anamika Awasthi
- RE: AMBER: segmentation fault in SANDER Ross Walker
- AMBER: prmtop spec trivia Lachele Foley (Lists)
- RE: AMBER: prmtop spec trivia Ross Walker
- Re: AMBER: prmtop spec trivia Lachele Foley (Lists)
- RE: AMBER: prmtop spec trivia Ross Walker
- Re: AMBER: prmtop spec trivia Lachele Foley (Lists)
- Re: AMBER: prmtop spec trivia David A. Case
- Re: AMBER: prmtop spec trivia Lachele Foley (Lists)
Saturday, 26 April 2008
- Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal
Tuesday, 29 April 2008
- Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent
- RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker
- Re: AMBER: Charge derivation: RESP vs. antechamber David A. Case
- AMBER: regarding segfault during energy minimization Anamika Awasthi
- RE: AMBER: regarding segfault during energy minimization Ross Walker
Wednesday, 30 April 2008
- AMBER: distance matrix command priya priya
- AMBER: Constat area simulation gurpreet singh
- AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA]
- AMBER: amber 9 compilation problem on IBM SP5 Andrew Emerson
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? David A. Case
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke
- AMBER: RE: amber8 files in amber9 Jena M
- AMBER: about glycam06 WANG,YING
- RE: AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA]
- RE: AMBER: RE: amber8 files in amber9 Ross Walker
- AMBER: calibration of constant pH simulations Lillian Chong
- Re: AMBER: about glycam06 Austin B. Yongye
- Re: AMBER: calibration of constant pH simulations Adrian Roitberg
- Re: AMBER: amber 9 compilation problem on IBM SP5 David A. Case
- Re: AMBER: about glycam06 WANG,YING
- Re: AMBER: about glycam06 Austin B. Yongye
- AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri
- Re: AMBER: Cysteine sulphonic acid parameters David A. Case

Last message date: Sun May 04 2008 - 06:07:15 PDT
Archived on: Fri Nov 22 2024 - 05:53:38 PST

Amber Archive Apr 2008 by date