VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Nov 20 2014 - 13:55:24 CST

Hi Revathi,

Can't you just generate a pdb/psf pair with hydrogens like usual, and
then remove the hydrogens as a postprocessing step? I'm unfamiliar with
the dynamic network analysis plugin, but if you want a hydrogenless
pdb/psfpair, the following scriptlet would remove the hydrogens:

set nohsel [atomselect top "noh"]
$nohsel writepdb "noh.pdb"
$nohsel writepsf "noh.psf"

-Josh Vermaas

On 11/20/2014 12:26 PM, Revthi Sanker wrote:
> Dear all,
> I would like to generate a psf file without any hydrogens for a given
> pdb. Simply removing "guesscoord" distorts the structure while
> including it, adds hydrogens.
>
> ( The reason for trying to keep the hydrogens out is to carry out the
> Dynamic network analysis where the atom types of terminal residues
> create problems while designating nodes. Since the tutorial same psf
> and dcd files do not have hydrogens, I am assuming removing hydrogens
> will help me overcome this error. Kindly correct me if I am wrong).
>
> Any help in this direction will be of immense help.
>
> Thank you in advance.
>
> ​Yours sincerely,​
>
> Revathi.S
> ​
> M​
> .S. Research Scholar
> Computational Biophysics Lab
> Department of Biotechnology
> Indian Institute Of Technology, Madras
> India
> -------------------------------------------------------
>