may be try both ways in a small file. feed it to pdb2gmx and then check the topol.top file to see if it uses the correct forcefield name?
On Sat, Dec 20, 2014 at 12:12 AM, Rajan Kumar <kumarrajan...@gmail.com> wrote: > Dear all, > > I am trying to study wetting of Graphene oxide. I have prepared a structure > file using material studio, which I will simulate in GROMACS. > > My structure contain some epoxy and hydroxyl functional group in Graphene > sheet. However, the structure file generated does not differentiate between > carbon atoms with and without functional group in the "Name" column of .pdb > file. Also there is no differentiation in naming format of oxygen atom in > epoxy and hydroxyl group. > > Since, these atoms will have different atom type in atomtype.atp file of > force filed.(I will be using OPLS-AA for simulation). Do I have to make > edits in .pdb file for different atomtypes as well. > > > Thanks > > Rajan Kumar > Department of Chemical Engineering > Indian Institute of Technology, Guwahati > -- > 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.