From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 09 2009 - 10:46:49 CDT

On Wed, 2009-09-09 at 08:55 -0600, Ronald Salesky wrote:
> Hello,

ron,

> I'm new to VMD and am having some difficulties generating
> a .psf file for a CNT. I use the plugin extension to
> generate the nanotube on the VMD main menu. The generated
> tube is then saved w/ the file extension .pdb. Running
> autopsf fails which I tracked to the residue named "CNT".

autopsf (or rather the underlying psfgen) is not at all
designed to handle CNT-type structures.

> I then renamed all 'CNT' residues to 'CA'. Autopsf then
> appears to complete OK, but the VMD command line window
> shows a long list of "can't locate coordinates" for each
> line from the pdb file (which of course HAS valid
> coordinates). The resulting .psf file contains nothing
> useful and the autopdb file generated only has a single
> atom in it.

to understand why you see those error messages, you
have to understand how psfgen works. it is _not_ looking
for the coordinates in the .pdb file. to explain what and
why would take too long here.

> Could someone more knowledgeable about VMD please describe
> what I'm doing wrong?

actually, you don't need to use autopsf to generate a usable
.psf file, but you can generate it directly, potentially with
some additional scripting, from within VMD.
first of all, you have to know what force-field atom type you
want to use for the CNT carbons. to set the atom type you can do:
set sel [atomselect top "resname CNT"]
$sel set type MYTYPE ; # set MYTYPE to the desired atom type, \
                          e.g. for phenyl ring carbons

then you have to decide whether you want to keep the CNT rigid or
you'd have to identify a proper bond parameter (and angle/dihedral as
needed). for that you have to study what kind of settings have already
been used successfully. if you want the CNT to be free floating, you
should be all set and can just save the .psf file with.

animate write psf cnt.psf

if you want model in infinitely long periodic CNT you have to
add the missing bonds across the PBC. that can be done by mouse
or via: topo addbond id1 id2 (with id1/id2 being 0-based atom indices)
if you need to add angle/dihedral potentials it gets a bit messy,
since no simple helper script exists (yet) to derive angles from
bonding information. the writing out of the psf file is then the same.

HTH,
   axel.
>
> Thanks much,
>
> Ron
> Research assistant, nanoscience program at UNM
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Research Associate Professor
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.