RE: [gmx-users] CHARMM27 Force field

thank you mark Date: Wed, 4 Jan 2012 09:55:28 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM27 Force field On 4/01/2012 6:49 AM, najwa drici wrote: Hi all, I

[gmx-users] CHARMM27 Force field

Hi all, I want to know if I can implement the CHARMM27 parameter file in gromacs-4.0.7 thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] PROCHEK-NMR instalation problem

hi all Anybody guide me in installig the PROCHECK software and how to run it ?? best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] gromos96 charges

Hi all I would like to know, Where gromos96 charges and vdw parameters come from? And how the total charge, for a protein fragment is determined with gromacs? Cordially DRICI nedjoua -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] how to fixe distance

hi all How can I fix some distances and angles in manner, that I can set up long molecular dynamic simulation without structural lost?cordially DRICI nedjoua -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] extracting a structure from confout.gro file

hi all I would like to extract my protein structure with the first hydration shell around the active site which contains an ion from counfout.gro. Is there any program script able to do this? Cordially DRICI nedjoua -- gmx-users mailing list

[gmx-users] System has non-zero total charge: 2.570000e+00

hello Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform molecular dynamic simulation in box of SPC water. before energy minimization step , I performed the preprosessing step using grompp . However, there’s a note that : System has

RE: [gmx-users] number of grid cells is zero

i want to ask you question about how can i deprotonate or use deprotonated cysteine because I have protein with “cys” in active site, and I want to use deprotonated“cys”. when i run “pdb2gmx “ no option appearing of choosing Cys deprotonated state possibility Date: Sun, 27 Jul 2008 13:16:20

RE: [gmx-users] antechamber topologies to gromacs format

i want to ask you question about how can i deprotonate or use deprotonated cysteine because I have protein with “cys” in active site, and I want to use deprotonated“cys”. when i run “pdb2gmx “ no option appearing of choosing Cys deprotonated state possibility Subject: RE: [gmx-users]

[gmx-users] help

Hi allI work with a protein where 3 CYS redisidues make bond with a Zn atom by its SG atoms and HIS redisidue makes bond with a Zn atom by its NE2 in active siteI want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says on option of choosing Cys protonated state possibility but