Hi Amali,
gmx hbond identifies typical acceptor and donor groups by default. In fact, analysing non-standard donors/acceptors is a bit underdeveloped. What the program basically does, if memory serves me right, is to identify N and O with H bound to them, or optionally without H in case of acceptors. If you wish to analyse the hbonds separated by residue number you may wan to either run vmx bond multiple times with one group being a single residue and the other the ligand, or you can run it once with the -hbm and -hbn options and extract the information from the resulting matrix. Kind regards, Erik > On 28 Jun 2016, at 08:59, Amali Guruge <[email protected]> wrote: > > Thank you very much for the answer. How we identify residues involving in H > bonds? In index file do we have to specify them? > > On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky <[email protected]> > wrote: > >> Hello, >> >> Please use the "hbond" utility in gromacs. >> >> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n >> [<.ndx>]][-num [<.xvg>] >> >> >> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge <[email protected]> >> wrote: >> >>> Dear Gromacs users, >>> >>> I carried out 20 ns long MD simulation for my receptor-ligand complex >> using >>> Gromacs software. Now I want to calculate number of hydrogen bonds formed >>> in the ligand and receptor corresponding to the residue number. Can >> anyone >>> help me? >>> >>> >>> Thank you. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to [email protected]. >>> >> >> >> >> -- >> Yours Sincerely, >> -------------------------- >> SUBHOMOI BORKOTOKY, >> Centre for Bioinformatics >> Pondicherry University >> Pondicherry,INDIA. >> >> Alternate Email: [email protected] >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
