VMD-L Mailing List

From: Revthi Sanker (revthi.sanker1990_at_gmail.com)
Date: Fri Nov 21 2014 - 03:23:41 CST

Thank you very much

Revathi.S
M.S. Research Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute Of Technology, Madras
India
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On Fri, Nov 21, 2014 at 1:25 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
> -------------------------------------------------------
>
>
>