Re: top file for CNT

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 17 2010 - 13:49:44 CDT

On Sun, Oct 17, 2010 at 4:10 AM, sara <sara_15_s_at_yahoo.com> wrote:
>
> Hi All
>
> I work on carbon nanotubes, and made pdb file of CNT (8,2) in methanol by vegazz. but in namd, i want to make its psf file. for this work, which top file i must use?

i don't think that is possible as such with psfgen (unless you write
a topology for the whole CNT). the basic assumption behind psfgen
is that you have molecules and chains of residues. a CNT does not
fit into this scheme.

that being said, generating a .psf file for a CNT is pretty straightforward
from the bond topology. for this you can use the topotools plugin in VMD,
e.g. in combination with the nanotube builder plugin.
you can get the latest version of topotools either in the latest
VMD alpha test versions here:
http://www.ks.uiuc.edu/Research/vmd/alpha/
or from my home page:
http://sites.google.com/site/akohlmey/software/topotools

create or load the carbon nanotube (only) into VMD.
then type on the command prompt.

package require topotools
topo retypebonds
topo guessangles
topo guessdihedrals
mol reanalyze 0
animate write psf cnt.psf

the VMD nanotube plugin sets the atom type for
CNTs to CA. if you want something else, you need
to change it using atom selections.

cheers,
   axel.

> please send me the usefull topology file for CNT in methanol
>
> TNX alot
> Sara

--
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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