VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 06 2012 - 11:52:27 CST

On Mon, Feb 6, 2012 at 12:02 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> Flavio, Chris and Axel,
>        Thank you for your input. I ended up making a PSF containing the "!
> NATOM" list and the "!NBOND" list, and using topotools (v 1.1) I
> confirmed the number of bonds (52 -- from the partial PSF I loaded along
> with the pdb), angles (0), and dihedrals (0) using:
>
> vmd > topo numbonds
> 52
> vmd > topo numangles
> 0
> vmd > topo numdihedrals
> 0
>
> Then for the actual angle and dihedral creation, I used
>
> vmd > topo guessangles
> vmd > topo numangles
> 99
> vmd > topo guessdihedrals
> vmd > topo numdihedrals
> 139
>
> Then write the psf using
>
> vmd > animate write psf test2.psf
> psfplugin) Writing angles/dihedrals/impropers...
> Info) Opened coordinate file test2.psf for writing.
> Info) Finished with coordinate file test2.psf.
> 1
>
> This process is disconcertingly easy, so I went through a majority of
> the angles and dihedrals by hand and confirmed that they are correct and
> no angle or dihedral is duplicated or missing.
>
>        I consider this solved on the basis of the topotools package. Many
> thanks to Axel and anyone else developing that toolbox.

two comments on that.

please upgrade to the recently released
VMD 1.9.1 to have the latest bugfixes
for topotools included.

the psf file you generated this way, is still missing
vital force field information (atom type and charges)

you may be able to run a simulation with this, but
it may give bogus results.

axel.

>
> rajan
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.