From: Revthi Sanker (revthi.sanker1990_at_gmail.com)
Date: Fri Nov 21 2014 - 03:23:19 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 1:52 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:
> set sel [atomselect top "protein and noh"]
> $sel writepsf protein.psf
> $sel writepdb protein.pdb
>
>
>
> From: Revthi Sanker <revthi.sanker1990_at_gmail.com>
> Reply-To: <namd-l_at_ks.uiuc.edu>, Revthi Sanker <revthi.sanker1990_at_gmail.com
> >
> Date: Thu, 20 Nov 2014 23:56:48 +0530
> To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: namd-l: create psf file without hydrogens
>
> 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
> -------------------------------------------------------
>
>
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