Re: Graphene pdb/psf files cannot be read by psfgen

From: Cruz-Chu Eduardo Roberto (
Date: Wed Feb 15 2012 - 05:06:31 CST

readpsf command must go before coordpdb; that is:

readpsf graphene.psf

coordpdb graphene.pdb

then you add other molecules

readpsf smth.psf
coordpdb smth.pdb

and output the final structure

writepsf final.psf
writepdb final.pdb

a more detailed explanation is provided in the psfgen user guide, available in the website.



On Feb 15, 2012, at 8:14 AM, Wanzhi Qiu wrote:

Dear NAMDers,

I constructed a small graphene sheet using VMD Carbon Nanostructure Builder with options of Bonds, Angles etc are ticked. The result is shown on VMD OpenGL window and pdb/psf files are then generated using writepdb/writepsf commands in Tk console. The files appear to be correct with numbers for bonds, angles etc in the psf file. However, they fail when I try to combine the graphene with other molecules.

The problem is that the generated graphene.pdb/graphene.psf cannot be read by psfgen. In particular, the commands issued in the Tk console and error messages are:

>coordpdb graphene.pdb
gives following result:

psfgen) reading coordinates from pdb file graphene.pdb
psfgen) no segment
psfgen) Warning: failed to set coordinate for atom C GRA:1
(patten repeat for all atoms)

>readpsf graphene.psf
gives following result:

psfgen) reading structure from psf file graphene.psf
psfgen) error reading atoms
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

I suspect that the problem might be related to the residue name "GRA" in the pdb file. The first 3 lines of the pdb file are:

CRYST1 8.508 7.368 100.000 90.00 90.00 90.00 P 1 1
ATOM 1 C GRA X 1 0.000 0.000 0.000 0.00 0.00 C
ATOM 2 C GRA X 2 -0.709 1.228 0.000 0.00 0.00 C

Please let me know if you have any advices/comments/suggestions.

Many thanks,


Wanzhi Qiu, Ph. D.
Senior Researcher
National ICT Australia
Department of Electrical & Electronic Engineering
The University of Melbourne Parkville, Victoria 3010 Australia

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