Amber Archive May 2008: by date

Wednesday, 30 April 2008
- Re: AMBER: calibration of constant pH simulations Pradipta Bandyopadhyay
- Re: AMBER: regarding segfault during energy minimization Anamika Awasthi
Thursday, 1 May 2008
- Re: AMBER: Cysteine sulphonic acid parameters FyD
- AMBER: Discontinuous Constant pH Restarts Neil Bruce
- Re: AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri
- AMBER: Water residue tracking Steve Seibold
- AMBER: Installation problem of AMBER on cluster sudipta sinha
- Re: AMBER: Installation problem of AMBER on cluster David A. Case
- AMBER: Amber10 installation error juyong Lee
- RE: AMBER: Amber10 installation error Ross Walker
- Re: AMBER: Amber10 installation error juyong Lee
Friday, 2 May 2008
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell
- AMBER: test.parallel.QMMM problem Carra, Claudio (JSC-SK)[USRA]
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 sychen
- AMBER: Help with NMODE Seth Lilavivat
- RE: AMBER: Amber10 installation error Ross Walker
- RE: AMBER: Installation problem of AMBER on cluster Ross Walker
- RE: AMBER: test.parallel.QMMM problem Ross Walker
- Re: AMBER: Amber10 installation error David A. Case
- Re: AMBER: Water tracking Thomas Cheatham III
- Re: AMBER: Help with NMODE David A. Case
- AMBER: cfortran.h error with xlf90 compiler juyong Lee
- Re: AMBER: Help with NMODE Seth Lilavivat
- RE: AMBER: cfortran.h error with xlf90 compiler Ross Walker
- Re: AMBER: cfortran.h error with xlf90 compiler David A. Case
- Re: AMBER: Help with NMODE David A. Case
- Re: AMBER: Help with NMODE Seth Lilavivat
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- AMBER: Compiling amber10 with xlf90 fortran compiler juyong Lee
- AMBER: Mn2+ parameters in AMBER jitrayut jitonnom
- RE: AMBER: Installation problem of AMBER on cluster Ross Walker
- Re: AMBER: Help with NMODE David A. Case
- AMBER: Inquiry on B-factor of NMR James Thomas
- Re: AMBER: Discontinuous Constant pH Restarts David A. Case
- AMBER: printing dipoles in Amber10 (and earlier) Piotr Cieplak
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- AMBER: Water tracking Steve Seibold
- AMBER: point charges Chih-Ying Lin
- Re: AMBER: Installation problem of AMBER on cluster Gustavo Seabra
- RE: AMBER: printing dipoles in Amber10 (and earlier) Ross Walker
- RE: AMBER: Installation problem of AMBER on cluster Ross Walker
- RE: AMBER: point charges Ross Walker
- RE: AMBER: Installation problem of AMBER on cluster Ross Walker
- AMBER: Example .prepi file for nonstandard amino acids finke.oakland.edu
- Re: RE: AMBER: point charges Chih-Ying Lin
- Re: AMBER: Example .prepi file for nonstandard amino acids David A. Case
- RE: RE: AMBER: point charges Ross Walker
- Re: AMBER: Example .prepi file for nonstandard amino acids finke.oakland.edu
Saturday, 3 May 2008
- Re: RE: RE: AMBER: point charges Chih-Ying Lin
Friday, 2 May 2008
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
Saturday, 3 May 2008
- AMBER: about glycam06 WANG,YING
- Re: AMBER: about glycam06 David A. Case
- Re: AMBER: about glycam06 WANG,YING
- Re: AMBER: Installation problem of AMBER on cluster David A. Case
- Re: AMBER: about glycam06 WANG,YING
- Re: AMBER: about glycam06 David A. Case
- Re: RE: RE: AMBER: point charges David A. Case
- Re: AMBER: about glycam06 Austin B. Yongye
- Re: AMBER: about glycam06 WANG,YING
- Re: AMBER: about glycam06 WANG,YING
Sunday, 4 May 2008
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- AMBER: Amber10 Installation error - incorrect file suffix juyong Lee
- AMBER: Deriving Force Field Parameters Shultz, Jack
- Re: AMBER: Help with NMODE Seth Lilavivat
- AMBER: GAFF Schema Shultz, Jack
- Re: AMBER: about glycam06 Bill Ross
- Re: AMBER: GAFF Schema David A. Case
- Re: AMBER: Amber10 Installation error - incorrect file suffix David A. Case
- Re: AMBER: Help with NMODE David A. Case
- Re: AMBER: Installation problem of AMBER on cluster David A. Case
- Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell
- Re: AMBER: Amber10 Installation error - incorrect file suffix juyong Lee
- AMBER: Jarzinsky relationship E.M.
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
Monday, 5 May 2008
- Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell
- AMBER: Torsion angle restrains and Jarzinsky E.M.
- Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell
- AMBER: Re: amber 9 compilation problem on IBM SP5 Andrew Emerson
- AMBER: Installation error on IBM cluster juyong Lee
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- AMBER: misplacement of TER by leap Jena M
- Re: AMBER: Installation problem of AMBER on cluster sudipta sinha
- Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell
- Re: AMBER: misplacement of TER by leap Tim Meyer
- Re: AMBER: Deriving Force Field Parameters FyD
- Re: AMBER: about glycam06 WANG,YING
- Re: AMBER: Jarzinsky relationship Adrian Roitberg
- Re: AMBER: Jarzinsky relationship E.M.
- RE: AMBER: Installation error on IBM cluster Ross Walker
- Re: AMBER: Jarzinsky relationship Adrian Roitberg
- AMBER: unable to compile AmberTools 1.0 Rabin
- AMBER: NON-BONDED parameters Chih-Ying Lin
- Re: AMBER: error in compilation elsize.cc Scott Brozell
- AMBER: About reading in heme and CO molecule together with myoglobin Yang, Lee-Wei
- Re: AMBER: NON-BONDED parameters Thomas Steinbrecher
- Re: AMBER: unable to compile AmberTools 1.0 David A. Case
- AMBER: AMBER Parallel test error jitrayut jitonnom
- Re: AMBER: misplacement of TER by leap David A. Case
- Re: AMBER: unable to compile AmberTools 1.0 Yu Chen
- Re: AMBER: Help with NMODE Seth Lilavivat
- RE: AMBER: AMBER Parallel test error Ross Walker
- AMBER: DCCM correlation analysis Ibrahim Moustafa
- Re: AMBER: NON-BONDED parameters Chih-Ying Lin
- AMBER: Units, units units E.M.
- Re: AMBER: Units, units units David A. Case
- Re: AMBER: About reading in heme and CO molecule together with myoglobin David A. Case
- Re: AMBER: NON-BONDED parameters David A. Case
Tuesday, 6 May 2008
- AMBER: Minimization in Octahedric Box guardiani.fi.infn.it
- Re: AMBER: AMBER Parallel test error jitrayut jitonnom
- Re: AMBER: AMBER Parallel test error jitrayut jitonnom
- AMBER: rmsd per residue Furia Gargano
- RE: AMBER: AMBER Parallel test error Ross Walker
- AMBER: steered MD initial state M. L. Dodson
- Re: AMBER: steered MD initial state Gustavo Seabra
- Re: AMBER: steered MD initial state Adrian Roitberg
- Re: AMBER: steered MD initial state M. L. Dodson
- Re: AMBER: Minimization in Octahedric Box David A. Case
- RE: AMBER: Minimization in Octahedric Box Ross Walker
- Re: AMBER: steered MD initial state M. L. Dodson
- AMBER: mm_pbsa.pl not reading parameters for nmode Seth Lilavivat
- Re: AMBER: mm_pbsa.pl not reading parameters for nmode David A. Case
- AMBER: Improper dihedral parameters Chih-Ying Lin
- Re: AMBER: Improper dihedral parameters Bill Ross
- Re: AMBER: Improper dihedral parameters Da-Wei Li
- AMBER: single stranded DNA Taufik Al-Sarraj
- AMBER: DFTB parameters for O-P Carra, Claudio (JSC-SK)[USRA]
- Re: AMBER: single stranded DNA David A. Case
- Re: AMBER: single stranded DNA Taufik Al-Sarraj
- AMBER: Amber Parameter Schema Shultz, Jack
Wednesday, 7 May 2008
- AMBER: Ewald error estimate 欧阳德方
- AMBER: molsurf jacopo.sgrignani.unifi.it
- AMBER: uninstall of AMBER sudipta sinha
- Re: AMBER: Ewald error estimate David A. Case
- Re: AMBER: uninstall of AMBER David A. Case
- Re: AMBER: AMBER Parallel test error sudipta sinha
- RE: AMBER: uninstall of AMBER Ross Walker
- AMBER: nmode: number of atoms limitation Qi Yan
- AMBER: GBSA SA calculation Titus, Jamie $bairdje$
- AMBER: Hydroxyprolines!!! Titus, Jamie $bairdje$
- Re: AMBER: GBSA SA calculation Carlos Simmerling
- Re: AMBER: DFTB parameters for O-P Gustavo Seabra
- AMBER: Harmonic Force Constant Shultz, Jack
- AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan
- Re: AMBER: Discontinuous Constant pH Restarts Neil Bruce
- Re: AMBER: GBSA SA calculation David A. Case
- Re: AMBER: Discontinuous Constant pH Restarts David A. Case
- RE: AMBER: nmode: number of atoms limitation Ross Walker
- AMBER: Azobenzene: AMBER+Gromos Force Field parameters Chih-Ying Lin
- Re: AMBER: GBSA SA calculation Carlos Simmerling
- AMBER: nmode: number of atoms limitation Qi Yan
- Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case
- Re: AMBER: Hydroxyprolines!!! David A. Case
- AMBER: xleap (draw using edit) Taufik Al-Sarraj
- RE: AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan
- RE: AMBER: Ewald error estimate 欧阳德方
- RE: AMBER: Ewald error estimate Thomas Cheatham
- AMBER: reset time and comments E.M.
- RE: AMBER: Ewald error estimate 欧阳德方
Thursday, 8 May 2008
- Re: AMBER: reset time and comments Benjamin Juhl
- Re: AMBER: AMBER Parallel test error jitrayut jitonnom
- Re: AMBER: Jarzinsky relationship E.M.
- Re: AMBER: Discontinuous Constant pH Restarts Smriti Sharma
- AMBER: Compilation of PMEMD sudipta sinha
- AMBER: mm_pbsa problem: bad atom type: IP mori.cerm.unifi.it
- Re: AMBER: Compilation of PMEMD Robert Duke
- AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat
- RE: AMBER: reset time and comments Ross Walker
- RE: AMBER: Ewald error estimate Ross Walker
- AMBER: can amber read .xyz files? WANG,YING
- AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif
- Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case
- Re: AMBER: Ewald error estimate David A. Case
- RE: AMBER: Ewald error estimate Thomas Cheatham III
- RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands Ross Walker
- Re: AMBER: Discontinuous Constant pH Restarts David A. Case
- RE: AMBER: can amber read .xyz files? Ross Walker
- Re: AMBER: mm_pbsa problem: bad atom type: IP David A. Case
- Re: AMBER: velocity autocorrelation function for SPC felxible water model David A. Case
- Re: AMBER: xleap (draw using edit) David A. Case
- AMBER: AmberTools on OS X fails tests Hans Martin Senn
- Re: AMBER: AmberTools on OS X fails tests Wei Zhang
- Re: AMBER: AmberTools on OS X fails tests David A. Case
- Re: AMBER: xleap (draw using edit) Taufik Al-Sarraj
- Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat
- RE: AMBER: Harmonic Force Constant Shultz, Jack
- RE: AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif
- Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands David A. Case
- Re: AMBER: Jarzinsky relationship David Mobley
- Re: AMBER: velocity autocorrelation function for SPC felxible water model David A. Case
- AMBER: Adjust Force Field parameters Chih-Ying Lin
Friday, 9 May 2008
- AMBER: QM/MM Syed Tarique Moin
- AMBER: drawing repeated units Taufik Al-Sarraj
- Re: AMBER: QM/MM Gustavo Seabra
- AMBER: distance Urszula Uciechowska
- Re: AMBER: distance E.M.
- AMBER: help to install AMBER9 Jeffrey
- Re: AMBER: distance Ibrahim Moustafa
- Re: AMBER: help to install AMBER9 Ye Mei
- Re: AMBER: help to install AMBER9 Gustavo Seabra
- RE: AMBER: drawing repeated units Ross Walker
- AMBER: MM_PBSA output file Qi Yan
- RE: AMBER: help to install AMBER9 Ross Walker
- Re: AMBER: MM_PBSA output file Navnit Kumar Mishra
- Re: AMBER: drawing repeated units Taufik Al-Sarraj
- AMBER: neutral C-terminus and N-terminus parameters for amber Lisa Perez
- AMBER: Prepgen does not give correct result? Rajendra P. OJHA
- Re: AMBER: MM_PBSA output file Alessandro Nascimento
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- AMBER: cannot read big .pdb files WANG,YING
Saturday, 10 May 2008
- Re: AMBER: neutral C-terminus and N-terminus parameters for amber FyD
- AMBER: parmbsc0 parameters for RNA.DNA systems Cenk $Jenk$ Andac
- Re: AMBER: cannot read big .pdb files David A. Case
- Re: AMBER: parmbsc0 parameters for RNA.DNA systems David A. Case
- Re: AMBER: cannot read big .pdb files Lynn F. Ten Eyck
- AMBER: Calculate number of ions Dong Xu
Sunday, 11 May 2008
- Re: AMBER: help to install AMBER9 Jeffrey
- Re: AMBER: cannot read big .pdb files WANG,YING
- Re: AMBER: cannot read big .pdb files WANG,YING
- AMBER: Solvent mixture box Francesco Pietra
- AMBER: Ewald PARAMETER RANGE WRONG WANG,YING
Monday, 12 May 2008
- AMBER: rms Urszula Uciechowska
- Re: AMBER: rms Vlad Cojocaru
- Re: AMBER: rms Urszula Uciechowska
- Re: AMBER: rms Cenk $Jenk$ Andac
- Re: AMBER: cannot read big .pdb files Wei Zhang
- Re: AMBER: cannot read big .pdb files WANG,YING
- Re: AMBER: help to install AMBER9 Gustavo Seabra
- AMBER: to unsubscribe email Rabin
- Re: AMBER: Ewald PARAMETER RANGE WRONG David A. Case
- AMBER: About Hydrophobic Interactions. cgji
- Re: AMBER: Ewald PARAMETER RANGE WRONG WANG,YING
- Re: AMBER: to unsubscribe email Bill Ross
- AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger
- Re: AMBER: cannot read big .pdb files WANG,YING
- Re: AMBER: to unsubscribe email Rabin
- AMBER: Ligand energy minimization Dong Xu
- Re: AMBER: cannot read big .pdb files David Watson
- AMBER: nab Rabin
- Re: Re: AMBER: help to install AMBER9 Jeffrey
- Re: AMBER: nab Alessandro Nascimento
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu
Tuesday, 13 May 2008
- Re: AMBER: Calculate number of ions Mathy Froeyen
- Re: AMBER: nab Andreas Svrcek-Seiler
- AMBER: from Gromax to AMBER Cristina Sisu
- AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- Catein Catherine
- RE: AMBER: from Gromax to AMBER jacopo.sgrignani.unifi.it
- Re: AMBER: nab Rabin
- AMBER: building quadruplex with nab Rabin
- Re: AMBER: cannot read big .pdb files WANG,YING
- AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Marcin Krol
- Re: AMBER: from Gromax to AMBER Cristina Sisu
- AMBER: periodic boundary condition WANG,YING
- RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Ross Walker
- RE: AMBER: Ligand energy minimization Ross Walker
- AMBER: Free Energy Calculations - parameters for MM Seth Lilavivat
- AMBER: initial velocities of MD Jena M
- AMBER: divcon E.M.
- Re: AMBER: initial velocities of MD Carlos Simmerling
- RE: AMBER: initial velocities of MD Ross Walker
- Re: AMBER: GBSA SA calculation Carlos Simmerling
- Re: AMBER: divcon Gustavo Seabra
- AMBER: Amber10 testing problem Cenk $Jenk$ Andac
- RE: AMBER: Amber10 testing problem Ross Walker
- AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER yuan li
Wednesday, 14 May 2008
- Re: AMBER: Calculate number of ions Ruchi Sachdeva
- RE: AMBER: Amber10 testing problem Cenk $Jenk$ Andac
- AMBER: AMBER PBSA Thomas Leonard
- AMBER: Prepgen Rajendra P. OJHA
- Re: AMBER: periodic boundary condition David A. Case
- Re: AMBER: rms Vlad Cojocaru
- AMBER: MM_PBSA problem in binding_energy mori.cerm.unifi.it
- AMBER: about addles:“forrtl: severe (71): integer divide by zero”. 成全
- AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. Ross Walker
- Re: AMBER: MM_PBSA problem in binding_energy jacopo sgrignani
- AMBER: subscribe amber wangluohuaxue
- AMBER: simulate dipole moment Qiuting Hong
- Re: AMBER: simulate dipole moment Neelanjana Sengupta
- RE: AMBER: simulate dipole moment Ross Walker
- AMBER: AMBER entropy calculation Thomas Leonard
- AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. 成全
- Re: AMBER: AMBER entropy calculation Dong Xu
- Re: AMBER: AMBER entropy calculation Swarup Gupta
Thursday, 15 May 2008
- AMBER: Amber10:Compiling with gcc 2.4.1 yongleli
- Re: AMBER: Prepgen Junmei Wang
- Re: Re: AMBER: Prepgen yongleli
- AMBER: Points on a Sphere Justine Condo
- AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. Ross Walker
- AMBER: MKL libraries/Amber10 Francesco Pietra
- AMBER: RESP and Jaguar Seth Lilavivat
- AMBER: solvatebox error WANG,YING
- RE: AMBER: solvatebox error Ross Walker
- RE: AMBER: solvatebox error WANG,YING
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 Gustavo Seabra
- Re: AMBER: MKL libraries/Amber10 Gustavo Seabra
- Re: AMBER: MKL libraries/Amber10 yongleli
- RE: AMBER: MKL libraries/Amber10 Ross Walker
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case
- AMBER: reading PDB trajectory Mark Abraham
- Re: AMBER: Problems installing Amber Tools for Amber 10 David A. Case
- Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 yongleli
- AMBER: RE: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by z 成全
Friday, 16 May 2008
- AMBER: PGI amber9 problems Lorenzo Gontrani
- AMBER: RESP charges of an unusual substrate Jiayun Pang
- Re: AMBER: PGI amber9 problems David A. Case
- Re: AMBER: PGI amber9 problems Lorenzo Gontrani
- AMBER: Weighting factors in RESP charge fitting Anselm Horn
- Re: AMBER: Problems installing Amber Tools for Amber 10 Lynn F. Ten Eyck
- AMBER: STEERED MD fatima.chami.durham.ac.uk
- RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger
- Re: AMBER: STEERED MD Robert Duke
- Re: AMBER: STEERED MD Robert Duke
- Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger
- AMBER: about addles:“forrtl: severe (71): integer divide by z Ross Walker
- RE: AMBER: PGI amber9 problems Ross Walker
- RE: AMBER: MKL libraries/Amber10 Ross Walker
- Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger
- Re: AMBER: Weighting factors in RESP charge fitting Piotr Cieplak
- Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case
- Re: AMBER: Problems installing Amber Tools for Amber 10 David A. Case
- Re: AMBER: MKL libraries/Amber10 David A. Case
- Re: AMBER: MKL libraries/Amber10 Thomas Patko
- AMBER: build proline Qiuting Hong
- AMBER: Versions of mopac David A. Case
Saturday, 17 May 2008
- Re: AMBER: STEERED MD fatima.chami.durham.ac.uk
- Re: AMBER: STEERED MD Robert Duke
- RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- AMBER: Amber 10 ambpdb bug? Sam Danziger
- Re: AMBER: Amber 10 ambpdb bug? David A. Case
Sunday, 18 May 2008
- Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Re: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- David A. Case
- Re: AMBER: Amber 10 ambpdb bug? Sam Danziger
- Re: AMBER: RESP charges of an unusual substrate FyD
Monday, 19 May 2008
- AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Alan
- Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Hans Martin Senn
- AMBER: parameters in ff03 and ff99 Peter Kiss
- AMBER: Hybrid REMD amber10 Geoff Wood
- AMBER: anal Marina Grabar
- Re: Fw: RE: AMBER: MKL libraries/Amber10 Gustavo Seabra
- AMBER: nfft1-3 too large WANG,YING
- AMBER: gasteiger is not working with ambertools 1.0 Alan
- Re: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- RE: AMBER: Hybrid REMD amber10 Ross Walker
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- AMBER: atom type in glycam06 tinni sona
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- AMBER: bye frustrated modeller
- AMBER: analysis REMD rebeca
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- AMBER: 3rd Annual CMM Workshop on QM/MM Simulations Ross Walker
- AMBER: MM-PBSA for carbohydrates Neha Gandhi
- AMBER: how to calculate delta G from IC50 Thomas Leonard
- Re: AMBER: analysis REMD Carlos Simmerling
- Re: AMBER: Hybrid REMD amber10 Carlos Simmerling
Tuesday, 20 May 2008
- AMBER: massively parallel computation Mingfeng Yang
- Re: AMBER: anal David A. Case
- Re: AMBER: anal Marina Grabar
- Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es
- Re: AMBER: MM-PBSA for carbohydrates Navnit Kumar Mishra
- Re: AMBER: analysis REMD Carlos Simmerling
- Re: AMBER: how to calculate delta G from IC50 Chris Moth
- Re: AMBER: massively parallel computation Adrian Roitberg
- Re: AMBER: bye Sara Alexandra Moura
- Re: AMBER: massively parallel computation Robert Duke
- Re: AMBER: Hybrid REMD amber10 Geoff Wood
- Re: AMBER: massively parallel computation Lars Skjærven
- Re: AMBER: massively parallel computation Robert Duke
- Re: AMBER: massively parallel computation Robert Duke
- Re: AMBER: massively parallel computation Mingfeng Yang
- Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es
- Re: AMBER: analysis REMD Adrian Roitberg
- Re: AMBER: building quadruplex with nab Rabin
- AMBER: xLeap compilation issues Sasha Buzko
- AMBER: How to set a ZN atom radius for PB calculations Sam Danziger
- Re: AMBER: building quadruplex with nab David A. Case
- Re: AMBER: xLeap compilation issues David A. Case
Wednesday, 21 May 2008
- AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj
- Re: AMBER: massively parallel computation Atro Tossavainen
- AMBER: $AMBERHOME/dat/slko Francesco Pietra
- Re: AMBER: atom type in glycam06 Lachele Foley (Lists)
- Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra
- AMBER: ptraj analyze matrix Seth Lilavivat
- AMBER: amber tools installation vijayaraj.clri.info
- Re: AMBER: amber tools installation David A. Case
- Re: AMBER: xLeap compilation issues Sasha Buzko
- AMBER: pressure regulation methods Vlad Cojocaru
- Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es
- Re: AMBER: analysis REMD Carlos Simmerling
- Re: AMBER: massively parallel computation Robert Duke
- Re: AMBER: massively parallel computation Atro Tossavainen
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- AMBER: ff99 and ff03 forcefield parameters Peter Kiss
- AMBER: Parallel Self-guided Langevin simulation Dirar Homouz
- AMBER: about hydrogen bond in amber force field WANG,YING
- RE: AMBER: about hydrogen bond in amber force field Ross Walker
Thursday, 22 May 2008
- Re: AMBER: about hydrogen bond in amber force field Carlos Simmerling
- Re: AMBER: amber tools installation vijayaraj.clri.info
- Re: AMBER: $AMBERHOME/dat/slko Francesco Pietra
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Re: AMBER: Parallel Self-guided Langevin simulation David A. Case
- RE: AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj
- AMBER: COM RESTRAINT fatima.chami.durham.ac.uk
- AMBER: potassium ion Lars Skjærven
- AMBER: amber10 installation vijayaraj.clri.info
- AMBER: AMBER file preparation for protein-carbohydrate complex Neha Gandhi
- Re: AMBER: amber10 installation Ibrahim Moustafa
- RE: AMBER: $AMBERHOME/dat/slko Ross Walker
- AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Pavan G
- RE: AMBER: amber10 installation Ross Walker
- RE: AMBER: $AMBERHOME/dat/slko Francesco Pietra
- AMBER: Force field in water and in vacuum ?? Chih-Ying Lin
- RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Ross Walker
- RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz
- RE: AMBER: Force field in water and in vacuum ?? Ross Walker
- Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra
- Re: AMBER: $AMBERHOME/dat/slko Francesco Pietra
- Re: AMBER: potassium ion Bill Ross
- Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra
- RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Ray Luo
- RE: AMBER: How to set a ZN atom radius for PB calculations Ray Luo
- Re: AMBER: AMBER file preparation for protein-carbohydrate complex Lachele Foley (Lists)
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- AMBER: Calculate the RESP charge Fe3+ of heme (p450) chen bents
- Re: AMBER: COM RESTRAINT David A. Case
- Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450) David A. Case
- Re: AMBER: Mn2+ parameters in AMBER Guillermo Mulliert Carlín
Friday, 23 May 2008
- AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas.cbt.uhp-nancy.fr
- AMBER: help MD running error Qiuting Hong
- Re: AMBER: Mn2+ parameters in AMBER jitrayut jitonnom
- Re: AMBER: self-diffusion coefficient and Berendsen Andreas Svrcek-Seiler
- Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru
- Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru
- AMBER: PBC in 2D fatima.chami.durham.ac.uk
- Re: AMBER: ff99 and ff03 forcefield parameters Peter Kiss
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: AMBER: help MD running error Ross Walker
- Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- Re: AMBER: ff99 and ff03 forcefield parameters Peter Kiss
- AMBER: how generate the final output file using mmpbsa luzhenw1.msu.edu
- AMBER: Restart MD Simulation dpandit.brandeis.edu
- RE: AMBER: Restart MD Simulation Ross Walker
- AMBER: ff94 vs. ff03 Swarup Gupta
- AMBER: how to extract energy WANG,YING
- AMBER: periodic bondary condition WANG,YING
- AMBER: ptraj mask not working with psf file Dong Xu
- RE: AMBER: ff94 vs. ff03 Ross Walker
- RE: AMBER: how to extract energy Ross Walker
- RE: AMBER: periodic boundary condition Ross Walker
- Re: AMBER: how generate the final output file using mmpbsa Miguel Ortiz-Lombardía
Saturday, 24 May 2008
- RE: AMBER: how to extract energy Francesco Pietra
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: AMBER: Restart MD Simulation dpandit.brandeis.edu
- AMBER: Amber9 vs Amber10+MKL benchmark Francesco Pietra
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra
- AMBER: calculating the energy from the restart file priya priya
- Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params ke dong
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra
- AMBER: caculating nonpolar solvation energies ke dong
- Re: AMBER: self-diffusion coefficient and Berendsen David A. Case
- Re: AMBER: how to extract energy David A. Case
Sunday, 25 May 2008
- Re: AMBER: AMBER file preparation for protein-carbohydrate complex n.gandhiau.gmail.com
- Re: AMBER: AMBER file preparation for protein-carbohydrate complex Karl Kirschner
- Re: AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas.cbt.uhp-nancy.fr
- AMBER: trajectories into trajectory Hakkim Boy
- Re: AMBER: trajectories into trajectory Florian Haberl
- RE: AMBER: periodic boundary condition WANG,YING
- RE: AMBER: how to extract energy WANG,YING
- AMBER: mass weighted rms fit Dong Xu
- Re: AMBER: mass weighted rms fit Adrian Roitberg
- AMBER: using amber ports in gromacs Cristina Sisu
- AMBER: using amber ports in Gromacs Cristina Sisu
- Re: AMBER: using amber ports in Gromacs Carlos Simmerling
- Re: AMBER: self-diffusion coefficient and Berendsen David A. Case
- AMBER: is in vacuo simulation neccessary? Anamika Awasthi
- Re: AMBER: is in vacuo simulation neccessary? Mark Abraham
- Re: AMBER: Parallel Self-guided Langevin simulation David A. Case
Monday, 26 May 2008
- AMBER: Umbrella Sampling for proteins German Erlenkamp
- AMBER: peptide at the box center during NVT-MD Darek Czapiewski
- Re: AMBER: peptide at the box center during NVT-MD David A. Case
- AMBER: B-factor calculation from data with different write frequencies Sally Pias
Tuesday, 27 May 2008
- AMBER: Which is best temperature controlling method sudipta sinha
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- Re: AMBER: Problems installing Amber Tools for Amber 10 Scott Brozell
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- AMBER: error when read inpcrd WANG,YING
- RE: AMBER: error when read inpcrd Ross Walker
- RE: AMBER: error when read inpcrd WANG,YING
- Re: AMBER: B-factor calculation from data with different write frequencies Sally Pias
- AMBER: bugfix (imin=5) in amber9 Xioling Chuang
- Re: AMBER: Which is best temperature controlling method David A. Case
- Re: AMBER: bugfix (imin=5) in amber9 David A. Case
- Re: AMBER: Which is best temperature controlling method Reena .....
- AMBER: compilation problem with AMBER10 bhargav patel
- RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz
- Re: AMBER: Which is best temperature controlling method sudipta sinha
- AMBER: Hydration free energies of charged ions using PME Markus Kaukonen
Wednesday, 28 May 2008
- Re: AMBER: Which is best temperature controlling method Mark Abraham
- Re: AMBER: compilation problem with AMBER10 Atro Tossavainen
- AMBER: install amber tools Alejandro Valbuena
- AMBER: energy pairwise decomposition in GB/SA simulation wfli.biophy.nju.edu.cn
- AMBER: Segmentation faults trying to run sander mpi Idan Gabdank
- AMBER: restarting molecular dynamics Germain Vallverdu
- Re: AMBER: restarting molecular dynamics Adrian Roitberg
- Re: AMBER: restarting molecular dynamics Germain Vallverdu
- AMBER: mbondi radii for gaff atom types Sara J
- AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko
- AMBER: protonate in Amber10 Benjamin Juhl
- AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys
- Re: AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys
- Re: AMBER: restarting molecular dynamics Adrian Roitberg
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- Re: AMBER: Hydration free energies of charged ions using PME David A. Case
- Re: AMBER: Parallel Self-guided Langevin simulation David A. Case
- Re: AMBER: install amber tools David A. Case
- Re: AMBER: Segmentation faults trying to run sander mpi David A. Case
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case
- Re: AMBER: mbondi radii for gaff atom types David A. Case
- Re: AMBER: Which is best temperature controlling method David A. Case
- Re: AMBER: Which is best temperature controlling method Adrian Roitberg
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross
- Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg
- Re: AMBER: Which is best temperature controlling method sudipta sinha
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross
- Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg
- AMBER: rmsd vs frame Francesco Pietra
- AMBER: Fw: rmsd vs frame Francesco Pietra
- AMBER: VMD Movie Campbell, Patrick
- Re: AMBER: VMD Movie Carlos Simmerling
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu
- Re: AMBER: Which is best temperature controlling method Germain Vallverdu
Thursday, 29 May 2008
- AMBER: ligand unit charge is not zero amor san juan
- Re: AMBER: ligand unit charge is not zero mori.cerm.unifi.it
- AMBER: how to overcome theunusual bonds formation Thomas Leonard
- AMBER: solvatebox fatima.chami.durham.ac.uk
- Re: AMBER: how to overcome theunusual bonds formation Florian Haberl
- Re: AMBER: how to overcome theunusual bonds formation Thomas Leonard
- Re: AMBER: how to overcome theunusual bonds formation Adrian Roitberg
- Re: AMBER: Which is best temperature controlling method Robert Duke
- Re: AMBER: how to overcome theunusual bonds formation Swarup Gupta
- Re: AMBER: ligand unit charge is not zero amor san juan
- Re: AMBER: ligand unit charge is not zero Swarup Gupta
- AMBER: Installing PMEMD with Amber10 Justin A. Lemkul
- Re: AMBER: Which is best temperature controlling method David A. Case
- Re: AMBER: Installing PMEMD with Amber10 Robert Duke
- Re: AMBER: Segmentation faults trying to run sander mpi Idan Gabdank
- Re: AMBER: Segmentation faults trying to run sander mpi David A. Case
- RE: AMBER: solvatebox Ross Walker
- AMBER: VMD Movie 2 Campbell, Patrick
- Re: AMBER: VMD Movie 2 Carlos Simmerling
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko
- AMBER: ptraj rmsd calculation Pavan G
- AMBER: VMD Movie 3 Campbell, Patrick
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- RE: AMBER: VMD Movie 3 Ross Walker
- Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul
- AMBER: NTC and NTF dpandit.brandeis.edu
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu
- RE: AMBER: NTC and NTF Ross Walker
- AMBER: VMD Movie 4 Campbell, Patrick
- RE: AMBER: NTC and NTF dpandit.brandeis.edu
- Re: AMBER: Installing PMEMD with Amber10 Robert Duke
- AMBER: ptraj has trouble with x-plor psf file from VMD Dong Xu
- Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul
- Re: AMBER: VMD Movie 3 Ibrahim Moustafa
- Re: AMBER: protonate in Amber10 David A. Case
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen
Friday, 30 May 2008
- AMBER: Ptraj | Multiple trajout commands? Ian
- Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul
- AMBER: Jarzynski fatima.chami.durham.ac.uk
- AMBER: nab Joachim Reichelt
- AMBER: Iron-Sulfur Cluster Joachim Reichelt
- AMBER: Sander instead of PMEMD Cristina Sisu
- Re: AMBER: Sander instead of PMEMD Robert Duke
- Re: AMBER: Sander instead of PMEMD Cristina Sisu
- Re: AMBER: Sander instead of PMEMD Robert Duke
- Re: AMBER: nab David A. Case
- AMBER: VMD Movie 3 Campbell, Patrick
- Re: AMBER: Sander instead of PMEMD Florian Haberl
- Re: AMBER: Sander instead of PMEMD Francesco Pietra
- Re: AMBER: Sander instead of PMEMD Cristina Sisu
- Re: AMBER: Sander instead of PMEMD Robert Duke
- Re: AMBER: Sander instead of PMEMD Florian Haberl
- Re: AMBER: Jarzynski David Mobley
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- AMBER: tleap error message Wang,Ying
- RE: AMBER: Sander instead of PMEMD Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao
- Re: AMBER: Sander instead of PMEMD Francesco Pietra
- Re: AMBER: Iron-Sulfur Cluster Justine Condo
- Re: AMBER: Sander instead of PMEMD Francesco Pietra
- AMBER: igb and ibelly Holly Freedman
- RE: AMBER: igb and ibelly Ross Walker
- Re: AMBER: igb and ibelly David A. Case
- RE: AMBER: igb and ibelly Holly Freedman
- AMBER: SANDER and PMEMD with openmpi Ross Walker
- Re: AMBER: igb and ibelly Holly Freedman
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
Saturday, 31 May 2008
- Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen
- Re: AMBER: Jarzynski fatima.chami.durham.ac.uk
- Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul
- Re: AMBER: Iron-Sulfur Cluster FyD
- AMBER: MMPBSA error Cristina Sisu
- Re: AMBER: MMPBSA error Peter Gannett
- Fw: RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra
- Re: AMBER: MMPBSA error Cristina Sisu
- AMBER: ptraj analyze modes from nmode Miguel Ortiz-Lombardía
- Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker
- AMBER: amber9 , ptraj vector commad issue Vijay Singh
- Re: AMBER: Ptraj | Multiple trajout commands? Jianyin Shao

Last message date: Sun Jun 01 2008 - 06:08:25 PDT
Archived on: Wed Apr 24 2024 - 05:53:40 PDT

Amber Archive May 2008 by date