Re: creating .psf file for a nanotube

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 11 2011 - 05:18:57 CST

On Fri, Mar 11, 2011 at 3:36 AM, sakthi kumaran <persakthi_at_gmail.com> wrote:
> Dear all,
>           I have coordinates of a (5,5)nanotube in a .pdb file.To create a
> .psf file the autopsf builder in vmd requires some topology file to be
> included. I just need to have that required file as needed my autopsf
> builder to have my psf file for my nanotube.
>
>
> a small doubt that I am not getting cleared What makes a topology file
> different from a parameter file?

they are very different, just have a look. to know more, you should
work your way through the topology file tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/#specializedtopics

you will also see from that, that you need different
strategy to get a psf file. all you need is to assign
 the correct atom type and then generate all angle,
dihedral and improper definitions.

cheers,
    axel.

>
>
>
> thank you
> Kind regards,
> Sakthi
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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