Graphene pdb/psf files cannot be read by psfgen

From: Wanzhi Qiu (
Date: Wed Feb 15 2012 - 01:14:04 CST

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 ----------- 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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