From: Revthi Sanker (
Date: Thu Nov 20 2014 - 12:26:13 CST

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,​


.S. Research Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute Of Technology, Madras