From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 08 2011 - 16:38:35 CST

jacob,

the topotools plugin offers an alternate route in VMD to achieve
the same thing that you are trying to do with psfgen and
your personal codes. the philosophy behind the topotools
scripts is to be more flexible, but don't try to replicate psfgen,
but rather be convenient for problems that are not so easy
to do with psfgen. merging multiple structures is just a
simple function call, though. have a look at:

http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2

it is still work in progress (updates are in the VMD alpha test versions and
posted to the same webserver) and user feedback in the form of bug reports
and feature requests is highly welcome.

cheers,
     axel.

On Tue, Feb 8, 2011 at 11:11 AM, Goldsmith, Jacob <jgoldsmith_at_uky.edu> wrote:
> The problem I have is this:  resetpsf does not reset the topology structure.  I have been trying to make multiple systems of CNTs and I have all the peices of the system in separate .pdb files.  I generally write my .pdb file "by hand" with a script.  Is there a way to reset the topology structure stored?  Simply reloading a different topology file fails.  The number of atoms in the first topology file is preserved.  Thus far, I've had to exit VMD for each separate instance.
>
>  vmd > resetpsf
> clearing structure, preserving topology and aliases
>
> What I want it to say is:
>  vmd > resetpsf
> clearing structure, topology, and aliases
>
> Below is my construction script for reference, run in VMD 1.8.7
>
> Thanks all,
> Jacob
>
> ####################################
> resetpsf
> topology 12nn25c.top
> # above is the topology file that changes each time
> topology ru_bi_pry.top
>
> segment BIP {
>  auto angles dihedrals
>  pdb ru_bi_pry.pdb
> }
> coordpdb ru_bi_pry.pdb
>
> segment  NT {
>  auto none
>  pdb 12nn25c.pdb
> }
> coordpdb 12nn25c.pdb NT
>
> writepsf my_wonderful_md_trial.psf
> writepdb my_wonderful_md_trial.pdb
> ####################################
> # first few .pdb lines
> ATOM      1 C000 ARM     1       8.115  -0.710 -14.757  1.00  0.00      NT   C
> ATOM      2 C001 ARM     1       8.115   0.710 -14.757  1.00  0.00      NT   C
> ATOM      3 C002 ARM     1       7.383   3.443 -14.757  1.00  0.00      NT   C
> ATOM      4 C003 ARM     1       6.673   4.673 -14.757  1.00  0.00      NT   C
> ####################################
> # and ... the spacing was mutilated when I c.c.p. this below
> ####################################
> ATOM      1  RU   BIPYX   1      -0.151   0.086   0.086  1.00  0.00      BIP
> ATOM      2  C10 BIPYX   1      -0.051   0.708   2.913  1.00  0.00      BIP
> ATOM      3  C6   BIPYX   1      -0.051   2.676   1.661  1.00  0.00      BIP
> ATOM      4  C9   BIPYX   1       0.087   1.378   4.109  1.00  0.00      BIP
> ATOM      5  C1   BIPYX   1      -0.221  -0.753   2.841  1.00  0.00      BIP
>
>
>

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