error while making psf file for bacteriorhodopsin system

From: Faezeh Mottaghitalab (
Date: Thu May 08 2014 - 15:11:26 CDT

Hello everyone

I’m working on bacteriorhodopsin system.

The problem I have is the retinal molecule that is a part of
bacteriorhodopsin protein.

I download the topology and the parameter file for the retinal from the
NAMD site. But when I want to make the psf structure the vmd tells that :

psfgen) building segment U

psfgen) reading residues from pdb file 1fbb.pdb

psfgen) unknown residue type RET

psfgen) extracted 225 residues from pdb file

psfgen) Info: generating structure...psfgen) unknown residue type RET


ERROR: failed on end of segment

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

the question I have is that how can I merge the retinal topology file and
top_all27_protein_lipid.inp in order to make a correct psf file of whole
protein with retinal.

The commands I use is:

set 1fbb [atomselect top “all”]

$1fbb writepdb 1fbb.pdb

package require psfgen

topology top_all27_prot_lipid.inp

topology top_ret.inp

pdbalias residue HIS HSE

segment U {pdb 1fbb.pdb}

coordpdb 1fbb.pdb U


writepdb fbb.pdb

writepsf fbb.psf

I really appreciate any help because I’m tired of trying over and over
without any good result!

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