VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 27 2011 - 14:37:59 CDT

I'd suggest that you begin by seeing what that "iC" error is about.
Is there something named "iC" (or perhaps "iC" is a truncation of
something longer) in your input files?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 27, 2011 at 06:13:05PM +0300, seda demirci wrote:
> 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 

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