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
