From: Jinasena Hewage (
Date: Fri Jul 03 2015 - 14:08:04 CDT

I am trying to generate the psf file, and add ACE and CT3 groups to
terminals of my peptide chain. I have been using the following script.

package require psfgen
psfcontext reset
topology top_all22_prot_cmap.inp
segment mgn {
           pdb helix1.pdb
           first ACE
           last CT3
coordpdb helix1.pdb mgn
regenerate angles dihedrals
writepdb mgn1_new.pdb
writepsf mgn1_new.psf

But for this case it give me an error message saying,

psfgen) cross-term entries present in topology definitions
psfgen) building segment MGN
psfgen) reading residues from pdb file helix1.pdb
psfgen) unknown residue type HIS
psfgen) extracted 15 residues from pdb file
psfgen) setting patch for first residue to ACE
psfgen) setting patch for last residue to CT3
psfgen) Info: generating structure...psfgen) unknown residue type HIS
ERROR: failed on end of segment

Can some one please help me.
Thank you

Dr. Jinasena Hewage
Senior Lecturer  in Physical Chemistry
(Current Position: Visiting Academic, Research School of Chemistry,
Australian National University)
Department of Chemistry
University of Ruhuna
Matara, Sri Lanka
(+94) 071 4500 389