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From: seda demirci (seda.demirci_at_stu.khas.edu.tr)
Date: Fri May 27 2011 - 10:13:05 CDT

Dear all

I am triying to create a psf file for protein(620 residues) that is created via homology modelling. I was using the following commands

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias atom SER HG HG1
pdbalias atom CYS HG HG1
pdbalias atom ILE 1HD1 HD1
pdbalias atom ILE 2HD1 HD1
pdbalias atom ILE 3HD1 HD1
pdbalias atom HIS HD1 HE2
segment P1 {pdb HDKL.pdb}
coordpdb HDKL.pdb P1
guesscoord
writepdb HDKL_B.pdb
writepsf HDKL_B.psf

when executing this script psf file occurs but I got this message:

CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum
Created by CHARMM version 31 1
cross-term entries present in topology definitions
ERROR! FAILED TO RECOGNIZE iC
ERROR! FAILED TO RECOGNIZE iC
ERROR! FAILED TO RECOGNIZE iC
ERROR! FAILED TO RECOGNIZE iC
ERROR! FAILED TO RECOGNIZE iC

I would like to know how to solve this problem, thanks in advance

seda