Re: creating .psf file for a nanotube

From: Axel Kohlmeyer (
Date: Fri Mar 11 2011 - 08:26:58 CST

On Fri, Mar 11, 2011 at 7:34 AM, sakthi kumaran <> wrote:
> does this mean that the .psf file generated from topotools is incorrect. I
> will take a look at the link and reply you back.

topotools does what you tell it to do. it _cannot_ think for you.
psfgen works well, because with amino acids and small molecules,
you can generate templates and then match your coordinate file
with those templates, but _only_ if your coordinate file follows the
conventions stipulated by the PDB and the CHARMM topology syntax.

the approach of topotools is the other way around. it doesn't assume
anything, but you have to tell it what needs to be done. the way charmm
works is that it looks up the parameters for bonds, angles, dihedrals and
impropers from the atom types that are involved in that interaction.
so you have to set the correct atom type. the one chosen by the
VMD nanotube builder should be correct (benzene carbon atom),
but you have to check to make sure. all that topotools then can do
for you is to take the existing bond topology information and derive
angle, dihedral and improper definitions from it.
since you have a pretty narrow nanotube, you probably need to
loosen the "flatness" parameter to get the improper definitions
(the default assumes that only 5% deviation from planarity justifies
defining an improper dihedral).

in any case, it is up to you to check and validate the outcome of
the procedure in the very same way you have to double check the
output of psfgen when matching a compound against charmm
topology templates.


> regards,
> Sakthi

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

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