Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms.
This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh <bipinel...@gmail.com> wrote: > You can use g_dist with specific atoms indices to calculate distances, > if you already have the information about atoms involved in salt > bridge interactions. > > On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M <hmkv...@gmail.com> wrote: > > Dear users, > > > > Kindly clarify my doubt regarding salt bridge calculation. > > > > Thank you > > Regards > > Kavya > > > > > > On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M <hmkv...@gmail.com> wrote: > > > >> Dear users, > >> > >> For calculating salt bridge in proteins I > >> am using g_hbond instead of g_saltbr. > >> > >> In g_hbond I use contact and mention two > >> indices consisting of > >> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2: > >> group 2: ARG_LYS_&_NZ_NE_NH1_NH2: > >> > >> I use the command: > >> g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm > >> matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 50000 > >> > >> Is this approach correct? > >> > >> Thank you > >> Kavya > >> > > -- > > 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 > > > > -- > ----------------------- > Thanks and Regards, > Bipin Singh > -- > 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 > -- 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
