Amber Archive Aug 2009: by date

Friday, 31 July 2009
- Re: [AMBER] query Ashish Runthala
- Re: [AMBER] ambpdb problem Ashish Runthala
- Re: [AMBER] problem from xleap Qinghua Liao
- Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala
- Re: [AMBER] problem from xleap Ashish Runthala
- [AMBER] radial distribution function Dharmik Meghana shankar
- [AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov
Saturday, 1 August 2009
- Re: [AMBER] problem from xleap Tom Joseph
- [AMBER] Re: query bharat lakhani
- Re: [AMBER] Re: query Ashish Runthala
- [AMBER] Showing error bharat lakhani
- Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov
- [AMBER] Showing error in energy minimization bharat lakhani
- Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Vivek Sharma
Sunday, 2 August 2009
- Re: [AMBER] Showing error in energy minimization case
- Re: [AMBER] Showing error in energy minimization Ashish Runthala
- [AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues? Catein Catherine
- RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine
- Re: [AMBER] xleap installation error Bokun Cho
Monday, 3 August 2009
- [AMBER] showing error when creating topology and coordinate file bharat lakhani
- [AMBER] optimization step length ondrej.prenosil.marge.uochb.cas.cz
- [AMBER] Problem with Amber8 Sebastian Petruczynik
- Re: [AMBER] Problem with Amber8 ondrej.prenosil.marge.uochb.cas.cz
- Re: [AMBER] optimization step length Ashish Runthala
- [AMBER] What is the meaning of IED values for PCA analysis? Catein Catherine
- [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin
- Re: [AMBER] nonbon.f question Rizwan Tai
- Re: [AMBER] xleap installation error Scott Brozell
- [AMBER] Lennard Jones potential Rizwan Tai
- RE: [AMBER] nonbon.f question Ross Walker
- RE: [AMBER] Lennard Jones potential Ross Walker
- RE: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Ross Walker
- RE: [AMBER] Problem with Amber8 Ross Walker
- [AMBER] Re: showing error when creating topology and coordinate file bharat lakhani
Tuesday, 4 August 2009
- RE: [AMBER] Re: showing error when creating topology and coordinate file Olotu Odunayo
- [AMBER] parmchk problem isaac sugden
- [AMBER] Protein Activity Chih-Ying Lin
- Re: [AMBER] Protein Activity Bill Ross
- Re: [AMBER] Protein Activity Chih-Ying Lin
- Re: [AMBER] Protein Activity Bill Ross
- Re: [AMBER] Protein Activity Ashish Runthala
- [AMBER] problem of mm_pbsa Qinghua Liao
Wednesday, 5 August 2009
- [AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill
- Re: [AMBER] Problem with Amber8 Sebastian Petruczynik
- [AMBER] TWO restraints with different force constants s. Bill
- Solved THNAKS Re: [AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill
- Re: [AMBER] TWO restraints with different force constants A. Gomez-Sicilia
- AW: [AMBER] TWO restraints with different force constants Aust, Susanne
- [AMBER] Computational Resources s. Bill
- Re: [AMBER] problem of mm_pbsa case
- RE: [AMBER] Computational Resources Ross Walker
- Re: [AMBER] parmchk problem case
- Re: [AMBER] What is the meaning of IED values for PCA analysis? case
- [AMBER] ptraj failure to parse psf input Sasha Buzko
- Re: [AMBER] parmchk problem isaac sugden
- Re: [AMBER] ptraj failure to parse psf input case
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko
- [AMBER] nmode output Vahdati N.
- Re: [AMBER] problem of mm_pbsa Qinghua Liao
- [AMBER] implicit solvent simulation Manish Kumar
- Re: [AMBER] implicit solvent simulation Ashish Runthala
- Re: [AMBER] implicit solvent simulation Manish Kumar
- RE: [AMBER] implicit solvent simulation Ross Walker
- Re: [AMBER] implicit solvent simulation Manish Kumar
Thursday, 6 August 2009
- [AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st Harald Lanig
- [AMBER] Extreme optimization problems ondrej.prenosil.marge.uochb.cas.cz
- Re: [AMBER] parameters for HIV protease inhibitors Carlos Simmerling
- Re: [AMBER] Extreme optimization problems case
- Re: [AMBER] problem of mm_pbsa Rubben Torella
- [AMBER] Regd : gaff force field KIRTANA S
- Re: [AMBER] Regd : gaff force field Nicholas Musolino
- RE: [AMBER] Regd : gaff force field Ross Walker
- Re: [AMBER] Regd : gaff force field KIRTANA S
- Re: [AMBER] problem of mm_pbsa Qinghua Liao
- [AMBER] How to keep the closest solvent mols to each atoms by PTRAJ? u8613020.msg.ndhu.edu.tw
- [AMBER] implicit solvent simulation with new ligand Manish Kumar
Friday, 7 August 2009
- Re: [AMBER] Regd : gaff force field Ashish Runthala
- [AMBER] query bharat lakhani
- [AMBER] pmemd michael
- [AMBER] query regarding resp subarna thakur
- [AMBER] (no subject) Beale, John
- Re: [AMBER] (no subject) Ashish Runthala
- [AMBER] MM-PBSA results Dmitry Osolodkin
- Re: [AMBER] pmemd case
- RE: [AMBER] (no subject) Ross Walker
- RE: [AMBER] Regd : gaff force field Ross Walker
- [AMBER] Appropriate nmode input file for gas and vacuum phase simulation Scott Pendley
- [AMBER] antechamber am1-bcc issues David Mobley
- [AMBER] Re: implicit solvent simulation with new ligand Manish Kumar
- Re: [AMBER] Re: implicit solvent simulation with new ligand Carlos Simmerling
- [AMBER] Parameters for haloacetates Joseph Nachman
- Re: [AMBER] Re: implicit solvent simulation with new ligand Manish Kumar
- Re: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin
- [AMBER] Error in equilibration: file _ew_box.f Biswaranjan Meher
- Re: [AMBER] Error in equilibration: file _ew_box.f case
- Re: [AMBER] problem of mm_pbsa Jordan Monnet
- Re: [AMBER] (no subject) case
- [AMBER] Re: antechamber am1-bcc issues case
- Re: [AMBER] problem of mm_pbsa Qinghua Liao
- Re: [AMBER] Parameters for haloacetates Lili Peng
Saturday, 8 August 2009
- [AMBER] Why..QM/MM s. Bill
- Re: [AMBER] Regd : gaff force field Ashish Runthala
- Re: [AMBER] Re: antechamber am1-bcc issues gilbert.bluemarble.net
- RE: [AMBER] Why..QM/MM Ross Walker
- Re: [AMBER] Re: antechamber am1-bcc issues case
- Re: [AMBER] Appropriate nmode input file for gas and vacuum phase simulation case
Sunday, 9 August 2009
- [AMBER] hydrogen bond? Jio M
- [AMBER] Regarding Minimization maxcyc Ashish Runthala
Monday, 10 August 2009
- [AMBER] DivCon - QM/MM s. Bill
- Re: [AMBER] Re: implicit solvent simulation with new ligand Carlos Simmerling
- Re: [AMBER] Regarding Minimization maxcyc case
- Re: [AMBER] Parameters for haloacetates Joseph Nachman
- Re: [AMBER] problem of mm_pbsa Jordan Monnet
- Re: [AMBER] pmemd michael
- [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin
- RE: [AMBER] pmemd Ross Walker
- Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross
- Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin
- Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross
Tuesday, 11 August 2009
- Solved thanks Re: [AMBER] DivCon - QM/MM s. Bill
- [AMBER] Any Comment, please s. Bill
- AW: [AMBER] Any Comment, please Aust, Susanne
- Re: AW: [AMBER] Any Comment, please s. Bill
- AW: AW: [AMBER] Any Comment, please Aust, Susanne
- [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case
- Re: [AMBER] parmchk problem case
- Re: [AMBER] query regarding resp Oliver Kuhn
- [AMBER] Amber99SB eric johnson
- Re: [AMBER] Amber99SB Carlos Simmerling
- Re: [AMBER] parameters for HIV protease inhibitors Oliver Kuhn
- [AMBER] suggestions pls Jio M
- [AMBER] measuring volume of the binding pocket Mannan
- Re: [AMBER] suggestions pls Ashish Runthala
- [AMBER] Measuring volume of the binding pocket Mannan
- [AMBER] query regarding fes cluster subarna thakur
Wednesday, 12 August 2009
- Re: [AMBER] parameters for HIV protease inhibitors FyD
- Re: [AMBER] query regarding fes cluster FyD
- Re: [AMBER] suggestions pls Jio M
- [AMBER] gaussian 98 input/output for antechamber/resp wong105.llnl.gov
- [AMBER] REMD using hybrid solvent model Morad Mustafa
- [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Manish Kumar
- Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB case
- Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Hector A. Baldoni
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko
- [Amber]: REMD using hybrid solvent model Morad Mustafa
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling
- [AMBER] sourcing leap commands in log file Donald Keidel
- Re: [AMBER] sourcing leap commands in log file Bill Ross
- [AMBER] reset velocity Parimal Kar
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
- Re: [AMBER] ptraj failure to parse psf input Thomas Cheatham
- Re: [AMBER] reset velocity Tom Joseph
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner
Thursday, 13 August 2009
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner
- [AMBER] ptraj imaging of namd generated trajectories Vlad Cojocaru
- [AMBER] Re: ptraj imaging of namd generated trajectories Vlad Cojocaru
- [AMBER] ptraj-image Nancy
- [AMBER] box problem Nancy
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case
- Re: [AMBER] box problem case
- Re: [AMBER] Re: antechamber am1-bcc issues David Mobley
- [AMBER] NAB optimization ondrej.prenosil.marge.uochb.cas.cz
- [AMBER] drying of solvent possible ? Jio M
- Re: [AMBER] NAB optimization case
- Re: [AMBER] problem of mm_pbsa Qinghua Liao
- [AMBER] Strange QM/MM Divcon - help me out s. Bill
- [AMBER] QM/MM types. ros.servidor.unam.mx
- Re: [AMBER] Strange QM/MM Divcon - help me out case
- RE: [AMBER] QM/MM types. Ross Walker
- Re: [AMBER] drying of solvent possible ? Bill Ross
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko
- [AMBER] Protein Domain Motion Chih-Ying Lin
- Re: [AMBER] Protein Domain Motion Carlos Simmerling
- Re: [AMBER] problem of mm_pbsa Jordan Monnet
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko
- Re: [AMBER] Protein Domain Motion Chih-Ying Lin
- Re:Re: [AMBER] box problem Nancy
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
Friday, 14 August 2009
- [AMBER] Charge Problem s. Bill
- Re: [AMBER] Charge Problem Karl Kirschner
- Re: [AMBER] Protein Domain Motion Carlos Simmerling
- Re: [Amber]: REMD using hybrid solvent model Morad Mustafa
- [AMBER] MM_PBSA not successful workalemahu berhanu
- Re: [AMBER] MM_PBSA not successful Jordan Monnet
- Re: [AMBER] MM_PBSA not successful Qinghua Liao
- Re: [AMBER] MM_PBSA not successful workalemahu berhanu
- Re: [AMBER] MM_PBSA not successful workalemahu berhanu
- Re: [AMBER] MM_PBSA not successful Qinghua Liao
- Re: [AMBER] MM_PBSA not successful workalemahu berhanu
- Re: [AMBER] drying of solvent possible ? Jio M
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala
- Re: Re: [AMBER] box problem Ashish Runthala
- Re: [AMBER] Strange QM/MM Divcon - help me out Ashish Runthala
- Re: [AMBER] sourcing leap commands in log file Ashish Runthala
- Re: [AMBER] MM_PBSA not successful Qinghua Liao
Saturday, 15 August 2009
- [AMBER] AMBER job restart problem Kefa Lu
- Re: [AMBER] AMBER job restart problem Ashish Runthala
- Re: [AMBER] Charge Problem FyD
- Re: [AMBER] AMBER job restart problem Kefa Lu
- Re: [AMBER] pmemd michael
- Re: [AMBER] AMBER job restart problem case
- Re: [AMBER] AMBER job restart problem Ashish Runthala
- Re: [AMBER] AMBER job restart problem case
- Re: [AMBER] AMBER job restart problem Thomas Cheatham
- Re: [AMBER] MM_PBSA not successful monnet.jordan.free.fr
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
- [AMBER] Can I do DNA bending with AMBER? Catein Catherine
- [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues Catein Catherine
- [AMBER] What is the parameters for Mg2+? Catein Catherine
- Re: [AMBER] AMBER job restart problem Kefa Lu
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ross Walker
- Re: [AMBER] AMBER job restart problem Thomas Cheatham
- Re: [AMBER] AMBER job restart problem Kefa Lu
Sunday, 16 August 2009
- Re:Re: Re: [AMBER] box problem Nancy
- Re: [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues case
- Re: [AMBER] Can I do DNA bending with AMBER? case
- Re: Re: Re: [AMBER] box problem Ashish Runthala
- [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani
- Re: [AMBER] What is the parameters for Mg2+? Tom Joseph
- RE: [AMBER] Strange QM/MM Divcon - help me out Ross Walker
- RE: Re: [AMBER] box problem Ross Walker
- RE: [AMBER] AMBER on a Mac Mini cluster PoC Ross Walker
- Re: [AMBER] MM_PBSA not successful workalemahu berhanu
- RE: [AMBER] MM_PBSA not successful Ross Walker
- Re: [AMBER] MM-PBSA: decompose energy error Maria Mirza
- [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu
- Re: [AMBER] AMBER on a Mac Mini cluster PoC Alan
- RE: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj Ross Walker
- [AMBER] Conference or workshop on AMBER? Catein Catherine
- RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine
- RE: [AMBER] What is the parameters for Mg2+? Catein Catherine
- RE: [AMBER] Can I do DNA bending with AMBER? Catein Catherine
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala
Monday, 17 August 2009
- [AMBER] gaussain output subarna thakur
- Re: [AMBER] gaussain output FyD
- Re: [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani
- [AMBER] [AmberTool] xleap problem 주태성
- Re: [AMBER] AMBER on a Mac Mini cluster PoC Alan
- Re: [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani
- [AMBER] amber 10 test fails with pathscale 3.2 Raj
- Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu
- RE: [AMBER] Conference or workshop on AMBER? Ross Walker
- Re: [AMBER] AMBER on a Mac Mini cluster PoC - solved Abdul Rehman Gani
- [AMBER] amber test fails with ICC 11.0.081 Raj
- Re: [AMBER] amber test fails with ICC 11.0.081 Carlos Simmerling
- [AMBER] Can i link and refine two domains of a single protein Ashish Runthala
- RE: [AMBER] amber 10 test fails with pathscale 3.2 Ross Walker
- Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj Paul Frybarger
- Re: [AMBER] gaussain output FyD
- [AMBER] Re: [q4md-fft] charge calculation FyD
- [AMBER] AMBER is running silently Kefa Lu
- Re: [AMBER] AMBER is running silently Bill Ross
- Re: [AMBER] AMBER is running silently Kefa Lu
- RE: [AMBER] AMBER is running silently Ross Walker
- Re: [AMBER] AMBER is running silently Kefa Lu
- RE: [AMBER] Conference or workshop on AMBER? Catein Catherine
- Re:Re: [AMBER] box problem Nancy
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case
- RE: [AMBER] Conference or workshop on AMBER? Ross Walker
- Re: [AMBER] box problem Nancy
- Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala
- Re: [AMBER] Conference or workshop on AMBER? Ashish Runthala
- Re: [AMBER] box problem Ashish Runthala
- Re:Re: [AMBER] box problem Nancy
- Re:Re: [AMBER] box problem Nancy
- RE: [AMBER] Conference or workshop on AMBER? Ross Walker
- [AMBER] Is it the correct procedures to strip water for MM/GBSA calculations? Catein Catherine
- RE: [AMBER] Conference or workshop on AMBER? Dharmik Meghana shankar
- [AMBER] antechamber execution subarna thakur
- RE: [AMBER] Conference or workshop on AMBER? Thank you. Catein Catherine
Tuesday, 18 August 2009
- [AMBER] Can i link and refine the modeled domains with different proteins bound on it Ashish Runthala
- [AMBER] RDC import from PALES Thomas Pochapsky
- [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja
- Re: [AMBER] antechamber execution FyD
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? FyD
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Bill Ross
- [AMBER] ***PROBLEMS WITH GROUPLRES Maria Mirza
- [AMBER] Distance restraint and periodic boundary conditions Cyril Falvo
- Re: [AMBER] Distance restraint and periodic boundary conditions Thomas Cheatham
- Re: [AMBER] Distance restraint and periodic boundary conditions case
Wednesday, 19 August 2009
- [AMBER] RESP charges of Fe4S4 cluster subarna thakur
- AW: [AMBER] Conference or workshop on AMBER? Aust, Susanne
- Re: [AMBER] RESP charges of Fe4S4 cluster vhakkim boy
- [AMBER] resp calculation for rubredoxin vhakkim boy
- [AMBER] Problem with loading PDB into tleap Kamali Sripathi
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala
- Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala
- Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai
- [AMBER] why is nonpolar solvation energy not implemented for dynamic in amber TaoPaul
- Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai
- Re: [AMBER] Distance restraint and periodic boundary conditions Keith Van Nostrand
- Re: [AMBER] Problem with loading PDB into tleap ksripath.umich.edu
- [AMBER] angle with ptraj E.M.
- RE: [AMBER] angle with ptraj Seetin, Matthew
- [AMBER] Re: angle with ptraj E.M.
- Re: [AMBER] Problem with loading PDB into tleap case
- Re: [AMBER] Distance restraint and periodic boundary conditions case
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala
Thursday, 20 August 2009
- [AMBER] ptraj cluster - snapshot number of a representative structure Marcin Krol
- Re: [AMBER] antechamber am1-bcc issues Alan
- Re: [AMBER] antechamber am1-bcc issues case
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja
- Re: [AMBER] antechamber am1-bcc issues gilbert.bluemarble.net
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja
- [AMBER] box volume not understood? Jio M
- RE: [AMBER] antechamber am1-bcc issues Ross Walker
- Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai
- RE: [AMBER] box volume not understood? Ross Walker
- Re: [AMBER] ptraj cluster - snapshot number of a representative structure Jianyin Shao
- RE: [AMBER] box volume not understood? Jio M
- [AMBER] center of mass dhacademic
- RE: [AMBER] box volume not understood? Ross Walker
- RE: [AMBER] box volume not understood? Bill Ross
- RE: [AMBER] box volume not understood? Jio M
Friday, 21 August 2009
- [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić
- [AMBER] How to strip water for MM/GBSA calculations? Catein Catherine
- Re: [AMBER] How to strip water for MM/GBSA calculations? Carlos Simmerling
- Re: [AMBER] RESP charges of Fe4S4 cluster case
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen
- RE: [AMBER] box volume not understood? Bill Ross
- Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja
- [AMBER] update on am1-bcc charge problem in antechamber case
- Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja
- RE: [AMBER] PMEMD 10 overflow issues Ross Walker
- RE: [AMBER] PMEMD 10 overflow issues ben rodriguez
- Re: [AMBER] mm_pbsa-Binding and Stability tests? Ray Luo
- [AMBER] Gaussian network model (GNM) Chih-Ying Lin
- Re: [AMBER] Gaussian network model (GNM) Adrian Roitberg
- Re: [AMBER] PMEMD 10 overflow issues Ashish Runthala
- [AMBER] protein-ligand binding simulation times Andrew Voronkov
- [AMBER] ambpdb water removal for rst files Andrew Voronkov
Saturday, 22 August 2009
- Re: [AMBER] protein-ligand binding simulation times steinbrt.rci.rutgers.edu
- Re: [AMBER] protein-ligand binding simulation times Andrew Voronkov
- Re: [AMBER] ambpdb water removal for rst files Bill Ross
- RE: [AMBER] PMEMD 10 overflow issues Ross Walker
- RE: [AMBER] PMEMD 10 overflow issues Ross Walker
Sunday, 23 August 2009
- [AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift Andrew Voronkov
- [AMBER] Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Voronkov
- Re: [AMBER] Distance restraint and periodic boundary conditions Robert Duke
- [AMBER] acetone lib and frcmod files? Jose Borreguero
- [AMBER] ABMD Reaction Coordinates stephane acoca
- [AMBER] ABMD Reaction Coordinates stephane acoca
- [AMBER] ABMD Reaction Coordinates stephane acoca
- [AMBER] ABMD Reaction Coordinates stephane acoca
- RE: [AMBER] acetone lib and frcmod files? Ross Walker
- [AMBER] Note regarding posting of the same message multiple times Ross Walker
Monday, 24 August 2009
- RE: [AMBER] acetone lib and frcmod files? FyD
- [AMBER] Meaning of GMAX E.M.
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić
- Re: [AMBER] Meaning of GMAX case
- Re: [AMBER] acetone lib and frcmod files? Jose Borreguero
- Re: [AMBER] pmemd Robert Duke
- [AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis TaoPaul
- Re: [AMBER] Meaning of GMAX Ashish Runthala
- Re: [AMBER] Meaning of GMAX Adrian Roitberg
- Re: [AMBER] Meaning of GMAX Ashish Runthala
- [AMBER] ptraj limit on trajectory size Sasha Buzko
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen
- Re: [AMBER] acetone lib and frcmod files? FyD
- Re: [AMBER] acetone lib and frcmod files? Jose Borreguero
- RE: [AMBER] ptraj limit on trajectory size Ross Walker
- Re: [AMBER] ptraj limit on trajectory size Sasha Buzko
- [AMBER] problem compiling amber tools with gcc-4.4.1 gilbert.bluemarble.net
- [AMBER] sander does not print out all residues in range. Maria Mirza
- [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Maria Mirza
- RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker
- RE: [AMBER] sander does not print out all residues in range. Ross Walker
- Re: [AMBER] sander does not print out all residues in range. Maria Mirza
- Re: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ashish Runthala
Tuesday, 25 August 2009
- Re: [AMBER] acetone lib and frcmod files? FyD
- Re: [AMBER] acetone lib and frcmod files? FyD
- [AMBER] ambertools test faied subarna thakur
- Re: [AMBER] ambertools test faied case
- [AMBER] Epsilon value for Iron bharat lakhani
- Re: [AMBER] problem compiling amber tools with gcc-4.4.1 case
- RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker
- [AMBER] Single Adenine ros
Wednesday, 26 August 2009
- [AMBER] Chirality error in pdb xiawei
- [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić
- Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? Hannes Loeffler
- [AMBER] ZPVE simple question ondrej.prenosil.marge.uochb.cas.cz
- Re: [AMBER] ZPVE simple question Jerome.GOLEBIOWSKI.unice.fr
- Re: [AMBER] Single Adenine case
- Re: [AMBER] ZPVE simple question case
- Re: [AMBER] Single Adenine case
- Re: [AMBER] Chirality error in pdb case
- [AMBER] Need you help bharat lakhani
- Re: [AMBER] Need you help Carlos Simmerling
- [AMBER] Re: question_on_MMPBSA jackie
- [AMBER] Inquiries about antechamber Yikan Chen
- Re: [AMBER] Single Adenine ros
- Re: [AMBER] Single Adenine Bill Ross
- Re: [AMBER] Inquiries about antechamber Nicholas Musolino
- Re: [AMBER] Inquiries about antechamber Yikan Chen
- RE: [AMBER] Re: question_on_MMPBSA Catein Catherine
- RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine
- Re: [AMBER] Inquiries about antechamber FyD
Thursday, 27 August 2009
- Re: [AMBER] Single Adenine FyD
- RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Hannes Loeffler
- RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine
- Re: [AMBER] Re: question_on_MMPBSA jackie
- Re: [AMBER] Inquiries about antechamber jackie
- Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? jackie
- Re: [AMBER] Single Adenine ros
- [AMBER] SCC-DFTB MD for mercury ions in proteins Vaida Arcišauskaitė
- Re: [AMBER] SCC-DFTB MD for mercury ions in proteins Adrian Roitberg
- Re: [AMBER] Single Adenine FyD
- [AMBER] Setting a constrain in one direction Darren Yang
- Re: [AMBER] Setting a constrain in one direction Nicholas Musolino
- RE: [AMBER] Chirality error in pdb xiawei
- [AMBER] Regarding principal component analysis using ptraj Arvind Marathe
Friday, 28 August 2009
- Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler
- Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe
- Re: [AMBER] Chirality error in pdb case
- Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler
- Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe
- Re: [AMBER] RDC import from PALES case
- [AMBER] (no subject) workalemahu berhanu
- RE: [AMBER] Setting a constrain in one direction matthew_seetin.urmc.rochester.edu
- Re: [AMBER] (no subject) workalemahu berhanu
- [AMBER] nmr restraint for angle between vectors Peter Varnai
Saturday, 29 August 2009
- [AMBER] about file format Jia Xu
- [AMBER] radius for Manganese ion Chunliyan
- [AMBER] Dyndom Chunliyan
- Re: [AMBER] about file format Tom Joseph
- Re: [AMBER] Dyndom Carlos Simmerling
- [AMBER] (no subject) workalemahu berhanu
- RE: [AMBER] Dyndom Loeffler, Hannes (STFC,DL,CSE)
- Re: [AMBER] about file format Jia Xu
Sunday, 30 August 2009
- [AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu
- [AMBER] Changing pH of the system nicholus bhattacharjee
- Re: [AMBER] Changing pH of the system Adrian Roitberg
- Re: [AMBER] Changing pH of the system nicholus bhattacharjee
- Re: [AMBER] Changing pH of the system Adrian Roitberg
- Re: [AMBER] radius for Manganese ion E.M.
- [AMBER] WATERSHELL Mannan
- Re: [AMBER] (no subject) workalemahu berhanu
- [AMBER] How to derive charges from the output bharat lakhani
Monday, 31 August 2009
- Re: [AMBER] How to derive charges from the output Barbault Florent
- [AMBER] Query regarding watershell command Mannan
- [AMBER] divcon question Andrei Neamtu
- Re: [AMBER] divcon question case
- Re: [AMBER] ATP/GTP parameters case
- Re: [AMBER] How to derive charges from the output bharat lakhani
- [AMBER] momentum in MD simulation dhacademic
- [AMBER] antechamber bug report Matthew Walsh
- Re: [AMBER] antechamber bug report case
- Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial FyD
- Re: [AMBER] ATP/GTP parameters FyD
- Re: [AMBER] How to derive charges from the output FyD
- Re: [AMBER] ATP/GTP parameters E.M.

Last message date: Wed Sep 02 2009 - 23:06:57 PDT
Archived on: Wed Dec 25 2024 - 05:53:55 PST

Amber Archive Aug 2009 by date