Amber Archive Dec 2009: by date

Monday, 30 November 2009
- Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu
- Re: [AMBER] Regarding rigid bond aneesh cna
Tuesday, 1 December 2009
- [AMBER] ptraj utility Neha Bharat Gajaria
- Re: [AMBER] Regarding rigid bond Carlos Simmerling
- Re: [AMBER] problem with FAD in tleap M. Shahid
- Re: [AMBER] trajout problem Daniel Roe
- Re: [AMBER] ptraj utility Daniel Roe
- Re: [AMBER] distance-dependent dielectric constant minimization case
- Re: [AMBER] ptraj utility Carlos Simmerling
- Re: [AMBER] Regarding rigid bond case
- Re: [AMBER] Regarding rigid bond Carlos Simmerling
- Re: [AMBER] ptraj utility case
- Re: [AMBER] distance-dependent dielectric constant minimization Robert Duke
- RE: [AMBER] trajout problem Anna Reymer
- RE: [AMBER] trouble with antechamber Jennifer L. Muzyka
- Re: [AMBER] Regarding rigid bond Bill Ross
- Re: [AMBER] Regarding rigid bond Adrian Roitberg
- Re: [AMBER] Regarding rigid bond Bill Ross
- Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin
- Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin
- [AMBER] XLEaP Error on Closing Edit Wallace Kunin
- RE: [AMBER] XLEaP Error on Closing Edit Ross Walker
- Re: [AMBER] SGLD in pmemd?? Dean Cuebas
- Re: [AMBER] SGLD in pmemd?? Robert Duke
- [AMBER] Re: looking for parameters for DHFR substrates and inhibitors... [one more try] Sidney Elmer
- Re: [AMBER] ptraj utility Neha Bharat Gajaria
- Re: [AMBER] Regarding rigid bond aneesh cna
Wednesday, 2 December 2009
- Re: [AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try] FyD
- [AMBER] How to get total energy of a system from QM/MM gunajyoti das
- Re: [AMBER] How to get total energy of a system from QM/MM steinbrt.rci.rutgers.edu
- Re: [AMBER] Regarding rigid bond Bill Ross
- [AMBER] MMGBSA Zhongjie Liang
- [AMBER] look at Amber's slides, email Sally Pias
- [AMBER] Segmentation fault gurunath katagi
Thursday, 3 December 2009
- [AMBER] NAB example scripts in AmberTools (Amber 10) Christopher Wassman
- [AMBER] binding energy of multiple ligand-receptor complex 欧阳德方
- Re: [AMBER] NAB example scripts in AmberTools (Amber 10) case
- [AMBER] QM/MM input file error mahesh kumar
- [AMBER] semiempirical copper Jacopo Sgrignani
- [AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950
- RE: [AMBER] semiempirical copper Ross Walker
- RE: [AMBER] QM/MM input file error Ross Walker
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane Ross Walker
- Re: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD
- [AMBER] AmberTools modifications for Ubuntu 9.10 peker milas
- [AMBER] help with TIP4P and mpi pmemd Hashem Taha
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke
- [AMBER] parameter file for the sulphate ion Fenghui Fan
- [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño
- Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Mengjuei Hsieh
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Jason Swails
- [AMBER] clarification DNA forcefield Taufik Al-Sarraj
- [AMBER] sodium ions before or after solvation makes a difference Naser Alijabbari
- Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke
- Re: [AMBER] Scripting tleap Jio M
Friday, 4 December 2009
- Re: [AMBER] binding energy of multiple ligand-receptor complex Oliver Kuhn
- Re: [AMBER] clarification DNA forcefield Jiri Sponer
- [AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić
- Re: [AMBER] binding energy of multiple ligand-receptor complex steinbrt.rci.rutgers.edu
- [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950
- [AMBER] aromatic ring getting distorted Jio M
- Re: [AMBER] mm_pbsa- Decomposition: bad atom type Hannes Kopitz
- Re: [AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić
- [AMBER] problem with antechamber sculiujl
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño
- Re:Re: [AMBER] problem with antechamber sculiujl
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found case
- Re: [AMBER] AmberTools modifications for Ubuntu 9.10 case
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham III
- Re: [AMBER] sodium ions before or after solvation makes a difference Thomas Cheatham III
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Jason Swails
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD
- Re: [AMBER] sodium ions before or after solvation makes a difference Bill Ross
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane Ross Walker
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham III
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD
- Re: [AMBER] binding energy of multiple ligand-receptor complex Jason Swails
- Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha
- Re: [AMBER] help with TIP4P and mpi pmemd case
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke
- Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha
- RE: [AMBER] binding energy of multiple ligand-receptor complex 欧阳德方
- Re: [AMBER] help with TIP4P and mpi pmemd Lizzard Man
Saturday, 5 December 2009
- Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu
- Re: [AMBER] distance-dependent dielectric constant minimization Bill Ross
- Re: [AMBER] distance-dependent dielectric constant minimization case
- Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu
Sunday, 6 December 2009
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov
- [AMBER] COOH group troubling Jio M
- Re: [AMBER] COOH group troubling Jason Swails
- Re: [AMBER] COOH group troubling Bill Ross
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham
- Re: [AMBER] COOH group troubling Jio M
- Re: [AMBER] COOH group troubling Bill Ross
- Re: [AMBER] ambpdb water removal for rst files Andrew Voronkov
- Re: [AMBER] ambpdb water removal for rst files Bill Ross
- Re: [AMBER] ambpdb water removal for rst files Bill Ross
- Re: [AMBER] Scripting tleap case
- Re: [AMBER] aromatic ring getting distorted case
- [AMBER] how to restart the stopped MM-GBSA job Zhongjie Liang
- [AMBER] Problem of MM-PBSA 欧阳德方
- Re: [AMBER] Scripting tleap Jio M
- Re: [AMBER] aromatic ring getting distorted Jio M
- [AMBER] force field parameters Piotr Cieplak
Monday, 7 December 2009
- [AMBER] phosphorus to carbon on minimization Alexander Boncheff
- [AMBER] Topology Reorder for EVB Andrea Coletta
- [AMBER] Parametrizing charges for modified DNA bases Bob Johnson
- Re: [AMBER] Problem of MM-PBSA Ray Luo
- Re: [AMBER] phosphorus to carbon on minimization Jason Swails
- Re: [AMBER] phosphorus to carbon on minimization FyD
- Re: [AMBER] Topology Reorder for EVB Jason Swails
- Re: [AMBER] Topology Reorder for EVB E.M.
- Re: [AMBER] Parametrizing charges for modified DNA bases FyD
- RE: [AMBER] Problem of MM-PBSA 欧阳德方
- Re: [AMBER] Problem of MM-PBSA Ray Luo
- Re: [AMBER] clarification DNA forcefield Taufik Al-Sarraj
- [AMBER] question about failures peker milas
- Re: [AMBER] question about failures Jason Swails
- Re: [AMBER] question about failures peker milas
- Re: [AMBER] question about failures Jason Swails
- Re: [AMBER] question about failures peker milas
Tuesday, 8 December 2009
- Re: [AMBER] Topology Reorder for EVB Andrea Coletta
- Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov
- Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Carlos Simmerling
- [AMBER] myristate to palmitate transformation Anthony Pemberton
- [AMBER] Re: EEL = ************* Taufik Al-Sarraj
- [AMBER] Custom RNA modeling Wallace Kunin
- [AMBER] ptraj image Taufik Al-Sarraj
- Re: [AMBER] ptraj image Thomas Cheatham
- Re: [AMBER] Custom RNA modeling Ilyas Yildirim
- Re: [AMBER] ptraj image Bill Ross
- Re: [AMBER] ptraj image Taufik Al-Sarraj
- Re: [AMBER] ptraj image Bill Ross
- [AMBER] Nmode "not running properly" problem in MM_PBSA Du Yun
- [AMBER] PIMD test stalling peker milas
- [AMBER] Re: PIMD test stalling peker milas
- [AMBER] how to add desired number of water balaji nagarajan
- Re: [AMBER] ATP/GTP parameters E.M.
- [AMBER] ptraj image Neha Bharat Gajaria
- [AMBER] Re: ATP/GTP parameters FyD
Wednesday, 9 December 2009
- [AMBER] Re: COOH troubling Jio M
- Re: [AMBER] Re: COOH troubling case
- Re: [AMBER] ptraj image Thomas Cheatham
- Re: [AMBER] Re: COOH troubling Jio M
- Re: [AMBER] how to add desired number of water Simon Becker
- Re: [AMBER] Custom RNA modeling Wallace Kunin
- Re: [AMBER] ptraj image Daniel Roe
- [AMBER] Re: COOH group trouble Jio M
- Re: [AMBER] how to add desired number of water Bill Ross
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Scott Brozell
- Re: [AMBER] Re: COOH troubling Junmei Wang
- Re: [AMBER] problem with antechamber Junmei Wang
- [AMBER] Re: nab normal mode analysis has imaginary frequencies Junmei Wang
- Re: [AMBER] Re: COOH troubling Dean Cuebas
- Re: [AMBER] Re: COOH troubling Jio M
Thursday, 10 December 2009
- Re: [AMBER] Re: COOH troubling Jio M
- [AMBER] pressure tensor components Silvia Carlotto
- Re: [AMBER] Re: nab normal mode analysis has imaginary frequencies case
- [AMBER] MMPBSA on a selected region ERIK.LAURINI.phd.units.it
- Re: [AMBER] MMPBSA on a selected region Jason Swails
- Re: [AMBER] Re: EEL = ************* case
- Re: [AMBER] Re: COOH troubling Junmei Wang
- RE: [AMBER] antechamber error Mike Hanby
- Re: [AMBER] antechamber error David Watson
- [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei
- Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Carlos Simmerling
- RE: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Ross Walker
- Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei
- Re: [AMBER] Re: COOH troubling Dean Cuebas
Friday, 11 December 2009
- Re: [AMBER] antechamber error case
- Re: [AMBER] Re: COOH troubling case
- [AMBER] QM/MM minimization Hashem Taha
- Re: [AMBER] Re: COOH troubling Jio M
- [AMBER] amber10 pmemd fail Aragorn Steiger
- Re: [AMBER] amber10 pmemd fail Robert Duke
- FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Hopkins, Robert
- Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Bill Ross
- Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Hopkins, Robert
- RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Richard Owczarzy
- RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Bill Ross
- RE: [AMBER] QM/MM minimization Ross Walker
- RE: [AMBER] amber10 pmemd fail Ross Walker
- RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Ross Walker
- Re: [AMBER] Re: COOH troubling Jio M
Saturday, 12 December 2009
- Re: [AMBER] Re: COOH troubling Dean Cuebas
- RE: [Possible Spam: 10%] RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desirednumberof water Hopkins, Robert
Sunday, 13 December 2009
- Re: [AMBER] Nmode "not running properly" problem in MM_PBSA case
- Re: [AMBER] pressure tensor components case
- [AMBER] amber.ambermd.org shumao.cqut.edu.cn
- [AMBER] How to run LEaP in a shell file? SongLin
Monday, 14 December 2009
- [AMBER] Different simulation times for similar systems Oliver Kuhn
- Re: [AMBER] How to run LEaP in a shell file? case
- Re: [AMBER] How to run LEaP in a shell file? SongLin
- [AMBER] how can i include ANP residue Bradley Dickson
- Re: [AMBER] Custom RNA modeling Wallace Kunin
- Re: [AMBER] Different simulation times for similar systems Carlos Simmerling
- Re: [AMBER] AMBER: segmentation fault when running parmchk Scott Brozell
- Re: [AMBER] Custom RNA modeling case
- Re: [AMBER] Custom RNA modeling Thomas Cheatham
- [AMBER] Installation on MacOSX Freedman, Tanya
- Re: [AMBER] Installation on MacOSX David Watson
- Re: [AMBER] how can i include ANP residue FyD
- Re: [AMBER] Custom RNA modeling Wallace Kunin
- Re: [AMBER] Custom RNA modeling Carlos Simmerling
- Re: [AMBER] how can i include ANP residue Bradley Dickson
- Re: [AMBER] Custom RNA modeling Jiri Sponer
- Re: [AMBER] how can i include ANP residue David Watson
- [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Jason Swails
- Re: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Dean Cuebas
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs case
- Re: [AMBER] Segmentation fault in antechamber Scott Brozell
Tuesday, 15 December 2009
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer
- [AMBER] Number of Cycles s. Bill
- Re: [AMBER] Installation on MacOSX Alan
- Re: [AMBER] Installation on MacOSX Jason Swails
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Jason Swails
- Re: [AMBER] Number of Cycles Jason Swails
- Re: [AMBER] Installation on MacOSX David Watson
- Re: [AMBER] Number of Cycles Robert Duke
- Re: [AMBER] Number of Cycles Robert Duke
- Re: [AMBER] Number of Cycles Carlos Simmerling
- Re: [AMBER] Number of Cycles Jason Swails
- Re: [AMBER] Number of Cycles Jason Swails
- [AMBER] addles - neb error balaji nagarajan
- Re: [AMBER] Number of Cycles Robert Duke
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Daniel Roe
- Re: [AMBER] Installation on MacOSX Alan
- RE: [AMBER] addles - neb error Ross Walker
- Re: [AMBER] Number of Cycles Carlos Simmerling
- Re: [AMBER] Number of Cycles Robert Duke
- Re: [AMBER] Number of Cycles Jason Swails
- Re: [AMBER] Number of Cycles Carlos Simmerling
- Re: [AMBER] Number of Cycles Jason Swails
- Re: [AMBER] Number of Cycles Robert Duke
- RE: [AMBER] Number of Cycles Niel Henriksen
- Re: [AMBER] Number of Cycles Bill Ross
- Re: [AMBER] Number of Cycles Robert Duke
- RE: [AMBER] Number of Cycles Niel Henriksen
- Re: [AMBER] Number of Cycles Jason Swails
- Re: [AMBER] Number of Cycles Robert Duke
- RE: [AMBER] Number of Cycles Ross Walker
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer
- RE: [AMBER] addles - neb error balaji nagarajan
Wednesday, 16 December 2009
- [AMBER] non standard residue and bond command Neha Bharat Gajaria
- [AMBER] chemical shifts: nter and cter Eliana Asciutto
- Re: [AMBER] chemical shifts: nter and cter case
- Re: [AMBER] addles - neb error case
- [AMBER] NAMD dcd files in ptraj Ganesh Kamath
- Re: [AMBER] non standard residue and bond command case
- Re: [AMBER] non standard residue and bond command Bill Ross
- [AMBER] Parameters for HYP and CGU Rilei Yu
- RE: [AMBER] addles - neb error balaji nagarajan
- Re: [AMBER] Parameters for HYP and CGU Adrian Roitberg
- Re: [AMBER] Parameters for HYP and CGU Jason Swails
- Re: [AMBER] Parameters for HYP and CGU Rilei Yu
- Re: [AMBER] Parameters for HYP and CGU Rilei Yu
Thursday, 17 December 2009
- Re: [AMBER] Parameters for HYP and CGU FyD
- Re: [AMBER] Parameters for HYP and CGU Alessandro Contini
- [AMBER] branched aminoacids Alessandro Contini
- Re: [AMBER] branched aminoacids FyD
- [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel
- [AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message. 木野　亮平
- Re: [AMBER] branched aminoacids Alessandro Contini
- Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 case
- [AMBER] MM_PBSA Problem (no radius for ion) s. Bill
- Re: [AMBER] MM_PBSA Problem (no radius for ion) Scott Brozell
- [AMBER] Compatibility of ONIOM and Amber vaibhav dixit
Friday, 18 December 2009
- Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel
- Re: [AMBER] MM_PBSA Problem (no radius for ion) s. Bill
- [AMBER] Inorganic Phosphate Parameters Cihan Aydin
- Re: [AMBER] Inorganic Phosphate Parameters. . Don.Bashford.stjude.org
- [AMBER] antechamber bond type error Mark M Huntress
- [AMBER] note on Antechamber error Mark M Huntress
- Re: [AMBER] Inorganic Phosphate Parameters. . Jason Swails
- [AMBER] SQM and AMBER Jio M
Saturday, 19 December 2009
- Re: [AMBER] antechamber bond type error case
- Re: [AMBER] Inorganic Phosphate Parameters. . case
- [AMBER] Non-Standard Atoms Jack Shultz
- Re: [AMBER] Non-Standard Atoms Jason Swails
Sunday, 20 December 2009
- Re: [AMBER] Non-Standard Atoms case
- Re: [AMBER] Non-Standard Atoms Jack Shultz
- [AMBER] hi ashish pandey
Monday, 21 December 2009
- Re: [AMBER] hi David Watson
- [AMBER] Sander crash, corrupt rst file... Waqas Nasir
- [AMBER] (No reply) Compatibility of ONIOM and Amber vaibhav dixit
- [AMBER] Release of AmberTools, version 1.3 David A. Case
- [AMBER] Gaff compatible with ff899.SB Pol Boudard
- Re: [AMBER] Gaff compatible with ff899.SB Carlos Simmerling
- [AMBER] MM PBSA stats Peter Jones
Tuesday, 22 December 2009
- [AMBER] PQR file - HELP PLEASE s. Bill
- [AMBER] MMGBSA error Zhongjie Liang
- Re: [AMBER] MMGBSA error Carlos Simmerling
- [AMBER] sqm x mopac in AmberTools 1.3 Alan
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson
- Re: [AMBER] PQR file - HELP PLEASE Jason Swails
- [AMBER] Van der Waals and electrostatic Forces Frank X. Vázquez
- [AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ? Marek Maly
- [AMBER] pupil and amber davide branduardi
- Re: [AMBER] PQR file - HELP PLEASE s. Bill
- Re: [AMBER] pupil and amber Ben Roberts
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case
- [AMBER] atom type shamoon siddiqui
- [AMBER] AmberTools-1.3 not compiling on MacOsX Cesar Millan
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX David Watson
Wednesday, 23 December 2009
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh
- [AMBER] typo in AmberTools.pdf (release 1.3) Alan
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh
- [AMBER] using sqm from AmberTools 1.3 Alan
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Jason Swails
- Re: [AMBER] atom type FyD
- 答复: [AMBER] MMGBSA error Zhongjie Liang
- Re: [AMBER] using sqm from AmberTools 1.3 David A. Case
- Re: [AMBER] using sqm from AmberTools 1.3 David A. Case
- Re: [AMBER] typo in AmberTools.pdf (release 1.3) David A. Case
- [AMBER] NEB-error balaji nagarajan
- Re: [AMBER] NEB-error Carlos Simmerling
- [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin
- [AMBER] CHARMM psf file to Amber prmtop file Sarvin Moghaddam
- Re: [AMBER] CHARMM psf file to Amber prmtop file xmzpzengs
- Re: Re: [AMBER] NEB-error xmzpzengs
- Re: Re: [AMBER] NEB-error Carlos Simmerling
- [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin
- Re: [AMBER] CHARMM psf file to Amber prmtop file Jason Swails
- [AMBER] iron in prepi file generation for heme Donald Keidel
- [AMBER] Adding single distance restraint Adler, Marc
- Re: [AMBER] CHARMM psf file to Amber prmtop file David A. Case
- Re: [AMBER] Van der Waals and electrostatic Forces David A. Case
- Re: [AMBER] Adding single distance restraint Jason Swails
- [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin
- [AMBER] SQM and AMBER :again Jio M
Thursday, 24 December 2009
- [AMBER] OE and CG types Jio M
- Re: [AMBER] OE and CG types Jason Swails
- Re: [AMBER] OE and CG types Jio M
- Re: [AMBER] OE and CG types Carlos Simmerling
- Re: [AMBER] How to put another 10 ligands into the simulation system? David A. Case
- Re: [AMBER] iron in prepi file generation for heme David A. Case
- RE: [AMBER] CHARMM psf file to Amber prmtop file Ross Walker
- RE: [AMBER] using sqm from AmberTools 1.3 Ross Walker
- [AMBER] implicit solvent MD with fixed residues Hakan Gunaydin
- [AMBER] RE: Amber question Ross Walker
- [AMBER] a problem in building oligosaccharides using LEaP Song Lin
- [AMBER] MMGBSA error Zhongjie Liang
- Re: [AMBER] OE and CG types Jio M
Friday, 25 December 2009
- [AMBER] FW: how to change velocities balaji nagarajan
- Re: [AMBER] FW: how to change velocities Carlos Simmerling
- Re: [AMBER] OE and CG types Jason Swails
- Re: [AMBER] MMGBSA error Jason Swails
- [AMBER] a question about ptraj qiaoyan
- [AMBER] PQR files s. Bill
- Re: [AMBER] PQR files Jason Swails
- Re: [AMBER] PQR files s. Bill
- Re: [AMBER] implicit solvent MD with fixed residues David A. Case
- Re: [AMBER] MMGBSA error David A. Case
- 答复: [AMBER] MMGBSA error Zhongjie Liang
- RE: [AMBER] FW: how to change velocities balaji nagarajan
Saturday, 26 December 2009
- [AMBER] heating system in NEB balaji nagarajan
- [AMBER] preparation of small molecule libraries with most probable conformations using Amber Andrew Voronkov
- Re: [AMBER] FW: how to change velocities Carlos Simmerling
- [AMBER] reg.changing velocity balaji nagarajan
- Re: [AMBER] OE and CG types Dean Cuebas
- Re: [AMBER] reg.changing velocity David A. Case
- [AMBER] neb error while heating balaji nagarajan
Sunday, 27 December 2009
- [AMBER] .rst file error ZhaoLei
- [AMBER] coarse grained Francesco Pietra
- RE: [AMBER] .rst file error ZhaoLei
- RE: [AMBER] .rst file error ZhaoLei
- [AMBER] ERROR: Could not read coords from {filename} Paul Brandt
- [AMBER] problem in installing amber tools on Mac OSX 10.6 Chun-Wei Pao
Monday, 28 December 2009
- Re: [AMBER] .rst file error Jia Xu
- [AMBER] About APBS radiopt Youn Kyeung Lee
- RE: [AMBER] .rst file error ZhaoLei
- Re: [AMBER] ERROR: Could not read coords from {filename} case
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 David Watson
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 case
- RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei
- Re: [AMBER] ERROR: Could not read coords from {filename} case
- [AMBER] NEB-NAN error balaji nagarajan
- Re: [AMBER] About APBS radiopt Robert Konecny
- Re: [AMBER] .rst file error Jason Swails
- Re: [AMBER] neb error while heating Carlos Simmerling
- Re: [AMBER] OE and CG types Carlos Simmerling
- RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei
- RE: [AMBER] .rst file error ZhaoLei
- Re: [AMBER] ERROR: Could not read coords from {filename} Carlos Simmerling
- Re: [AMBER] .rst file error Jason Swails
- RE: [AMBER] .rst file error ZhaoLei
- RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei
- [AMBER] mpirun error Vijay Manickam Achari
Tuesday, 29 December 2009
- RE: [AMBER] ERROR: Could not read coords from {filename} Paul Brandt
- [AMBER] nab installation Lixia Jin Day
- Re: [AMBER] using sqm from AmberTools 1.3 Alan
- [AMBER] can I install amber11 on a windowsPC under cygwin? Lixia Jin Day
- Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan
- Re: [AMBER] nab installation case
- Re: [AMBER] using sqm from AmberTools 1.3 David Watson
- Re: [AMBER] using sqm from AmberTools 1.3 case
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Mengjuei Hsieh
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case
- Re: [AMBER] sqm x mopac in AmberTools 1.3 case
- Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan
- Re: [AMBER] using sqm from AmberTools 1.3 Alan
- [AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan
- Re: [AMBER] using sqm from AmberTools 1.3 case
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me David Watson
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Bill Ross
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me case
- Re: [AMBER] OE and CG types Jio M
Wednesday, 30 December 2009
- [AMBER] Tests to check for proper MMPBSA.py installation RANAJIT SHINDE
- Re: [AMBER] Tests to check for proper MMPBSA.py installation case
- [AMBER] exchange attempt in REMD zgong.hust
- Re: [AMBER] exchange attempt in REMD Carlos Simmerling
- [AMBER] Zinc parameters? xuemeiwang1103
- Re: Re: [AMBER] exchange attempt in REMD zgong.hust
Thursday, 31 December 2009
- [AMBER] hbond analysis qiaoyan
- Re: Re: [AMBER] exchange attempt in REMD Carlos Simmerling
- Re: [AMBER] Zinc parameters? Ray Luo, Ph.D.

Last message date: Thu Dec 31 2009 - 18:30:03 PST
Archived on: Fri Apr 26 2024 - 05:54:00 PDT

Amber Archive Dec 2009 by date