Re: Asking for some sample PDB and PSF files of carbon nanotube

From: Axel Kohlmeyer (
Date: Wed Dec 15 2010 - 10:52:08 CST

2010/12/15 ع <>:
> Dear All,
> I am now trying to construct pdb and psf files for a single-layer
> graphene. I followed the constructing approach of SiN shown in tutorial
> "Modeling Nanopores for Sequencing DNA", but it did not work well.

> Therefore, I hope to take sample PDB and PSF files of carbon nanotubes
> as a reference. So could anyone give me some help?

building graphene structures should be extremely simple.
just write a small script that computes the coordinates
and writes out a .xyz for them.

you can then load the .xyz file into VMD and that should
automatically determine the bonding pattern for you.
now you have to decide what force field you want to use
and whether you need to define angles, dihedrals, and
impropers for it. those you could reconstruct using either
the psfgen or the topotools plugin. you then have to make
sure that all atoms have the correct atom type matching
your parameter file.
(set sel [atomselect top all]; $sel set type ??)

with topotools the commands

topo guessangles
topo guessdihedrals
topo guessimpropers

can be used to reconstruct the missing information
for the psf file from the bonding topology. you may
have to update topotools to the latest version from here:

topotools can then also be used to merge multiple .psf files.

with psfgen you have to be careful that you issue the
commands to guess angles and dihedrals in the correct order.
it can also be used to merge multiple psf files.


> Thanks very much!
> --
> Ph. D Yuhui He (ع)
> Institute of Scientific and Industrial Research, Osaka University;
> Mihogaoka 8-1, Ibaraki, Osaka 567-0047. JAPAN

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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