From: Faezeh Mottaghitalab (faezeh.mt258_at_gmail.com)
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
failed!
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
guesscoord
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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