From: avl211_at_lehigh.edu
Date: Thu Jul 16 2009 - 16:06:31 CDT

Hello,
I am trying to create a psf file based on a pdb file of a molecule
that is not a protein and would technically not have a classification
in a topology file. When the pdb file was created the residue name was
called MOL because there was not anything else it could have been
called. The molecule is made up of carbon rings with hydrogen and a
ammonia tail. Now since the residue name is not in a topology file it
is not being recognized by psfgen so I keep getting the error:
building segment M
reading residues from pdb file rider-molecule1
unknown residue type
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetp

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

Is there anything I could put in the residue column that would allow
me to generate a psf or is there anyway for me to tell psfgen to
ignore the unknown residue? Thank you.
Sincerely,
Adrienne LaFleur

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