Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ?
Also what is the real *-t value should I provide ? As I understood this is only Rmin but could I define Rmax cutoff as well? James * 5 апреля 2012 г. 12:36 пользователь Peter C. Lai <p...@uab.edu> написал: > g_saltbr? > > If you have salt bridges you already know about and want to look at, you > can always go with g_dist per pair manually. > > On 2012-04-05 12:23:02PM +0400, James Starlight wrote: > > Dear Gromacs Users! > > > > > > I'd like to monitor origin and destabilisation of salt-bridges during > > simulation time. In particular I want to define some charged residues > > within selection groups to monitor both of intra-protein as well as > > protein-protein interactions. In past I've used only > > g_hbond<http://manual.gromacs.org/online/g_hbond.html>utillity to > > monitor Hbonds within selection. Is there any specified program > > for such task but with salt-bridges only ? > > > > > > Thanks for help, > > > > James > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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