[gmx-users] Element naming format in .pdb file

Johnny Lu johnny.lu128 at gmail.com
Sat Dec 20 13:20:26 CET 2014

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

On Sat, Dec 20, 2014 at 12:12 AM, Rajan Kumar <kumarrajan513 at gmail.com>

> 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
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