From: Axel Kohlmeyer (
Date: Wed Jun 29 2011 - 08:31:02 CDT

On Wed, Jun 29, 2011 at 5:02 AM, safron saif <> wrote:
> Dear vmd users,
> I am using Materials Studio software to get the structure of Carbon Nanotube
> (defective).I  got pdb file for the structure from Material Studio and
> loaded the same to the VMD to create ".txt"  file ( for lammps input ). But

what format is this ".txt" file supposed to be. VMD doesn't know that format.
.txt on windows implies a plain text flile.

> the problem is that the txt file does not included the angle
> information(means it is showing number of angles is zero) .Due to this
> reason, i cant give any angle information in lammps code ( ie angle style or
> angle  coefficient in lammps code) so that some kind of deformation is

please note, that a .pdb file only contains information about atom coordinates
and atom / residue names and numbers. the bonds that you see are based on
heuristics (using an educated guess for atomic radii) inside VMD and may or
may not be correct/complete.

any information about angles, dihedrals, and impropers has to be generated
and how that is best done in VMD with either the psfgen or the topotools
plugin. it is not the .psf file itself, it is how you generate that
information in it
that makes all the difference. once you have that information in VMD you
can try to write it out as you need it.


> undergoing to the structure during simulation .Does the psf file solve this
> problem? If yes ,how can i get the psf file .OR is there any solution for
> this problem ? please suggest me
> thanking you,
> safron.

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