From: zoran (
Date: Fri Jul 03 2015 - 14:56:43 CDT

Hi Hewage,

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

You should according to the namd tutorial do next after topologu hes been communicated:

      pdbalias residue HIS HSE
      pdbalias atom ILE CD1 CD

Tutorials said:
1. Change the residue name of histidine to the proper name found in the topology file. HSE is one of three names for histidine, based on the protonation state of its side group.
2. The atom named ``CD1" ( carbon) in isoleucine residues is renamed as ``CD", its proper name from the topology file. Since isoleucine contains only one carbon atom, the psf file does not use the number label after ``CD".

Hope this help

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