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

Rajan Kumar kumarrajan513 at gmail.com
Sat Dec 20 06:13:43 CET 2014

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.


Rajan Kumar
Department of Chemical Engineering
Indian Institute of Technology, Guwahati

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