From: Axel Kohlmeyer (
Date: Thu Jan 19 2012 - 17:55:01 CST

hi ganesh,

On Thu, Jan 19, 2012 at 5:56 PM, Ganesh Kamath <> wrote:
> Hi All,
>  I have a graphene sheet of 448 C atoms. I have made a top file for
> the graphene sheet.

can you be a bit more specific. may types of files have
the extension .top. which format specifically are you
talking about. a CHARMM topology file? how do you
describe a graphene sheet with that at all?

> I try to build the sheet using psf builder and import the top file. It

do you mean the "psfgen" tool that comes with VMD/NAMD?

> then builds me this psf
> file with Atoms: 173056 and no bonds or angles or dihedrals.
> Could some one provide suggestions.

what script/command are you using to do this process.

> Do we have to specify every atom of the Carbon in the top file?
> Do we have to specify the bond information for the atoms in top file?

if you are talking about a CHARMM topology file,
then yes, there is a tutorial that explains how to
write non-standard residue entries.

for something as simple as a graphene sheet
(for as long as it is finite, i.e. not extending across
a periodic dimension) there are alternate ways,
e.g. manually assigning the proper CHARMM atom
type and mass and then using the topotools plugin
to "guess" the remaining topology components and
then just writing it out as a psf file.

(and remember you need impropers for that, too,
so that it stays flat).


> thanks!
> ganesh

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.