Thanks. On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan <ishe...@iitb.ac.in> wrote:
> > Hi Neha, > > If I understand correctly pdb file is used for extracting information > about the topology of the molecule..in this case the atom name and type. > so it does not matter at which time point of time in your simulation your > pdb file is generated as long as it is whole molecule. > > Best > Sheeja. > > > Hi gromacs users, > > > > In the perl script to calculate hydrogen bond %, the command is > > > > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx > > > > > > What should the structure.pdb file contain? > > > > How to obtain it? > > > > At which point of simulations? > > > > Thanks, > > Neha > > -- > > 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 gmx-users-requ...@gromacs.org. > > > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.