Re: create psf file without hydrogens

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Nov 20 2014 - 14:22:06 CST

set sel [atomselect top "protein and noh"]
$sel writepsf protein.psf
$sel writepdb protein.pdb



From: Revthi Sanker <revthi.sanker1990_at_gmail.com<mailto:revthi.sanker1990_at_gmail.com>>
Reply-To: <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, Revthi Sanker <revthi.sanker1990_at_gmail.com<mailto:revthi.sanker1990_at_gmail.com>>
Date: Thu, 20 Nov 2014 23:56:48 +0530
To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto: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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