HEM residue in NAMD

From: Peter Bazeley (petebazeley_at_yahoo.com)
Date: Tue Nov 02 2004 - 02:23:50 CST

Hi

I need a little help here. I have a PDB file of HETATM
atoms for a heme group. Each atom has "HEM" in the PDB
residue column (I've attached the PDB file). I am
trying to generate a psf file, but get the following:

building segment HEME
reading residues from pdb file
../../pdb_segments/2D6H/2D6H_fixed_heme.pdb
unknown residue type HEM
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type HEM

and

ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to
start over.
ERROR: failed on guessing coordinates
ERROR: failed on writing structure to psf file
ERROR: failed on writing coordinates to pdb file

There were quite a few coordinates that couldn't be
guessed, but I've had that problem before and was
still able to generate a psf file. Has anyone else
used a Heme group in a NAMD simulation, or know what I
am doing wrong?

Thanks,
Peter Bazeley

                
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