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.
