If the PDB has each protein with separate chain entries (A, B, etc) then this shouldn't be a problem. pdb2gmx will produce separate topologies for each chain and an overall topology that reads from each of the individual topologies and contains the other directives about FF, water model, posre, etc.
J On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH <drrahulsur...@gmail.com> wrote: > Dear all > > I have a PDB entry having 10 models(Aggregated structure). Here I want to > carry out the molecular dynamic simulation as such in aggregated form. But > gromacs is considering only one model in the PDB structure. How can I > simulate it as a whole.? > > Thank you > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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.
