From: Davit Hakobyan (
Date: Mon May 03 2004 - 14:04:32 CDT

Hi All,

I have a pdb file of an enzyme (phosphoglycerate mutase) which is complexed
with its substrate (3-phosphoglycerate with HETATM record). As the substrate
is not a valid residue (with name 3PG, which is not a name of any valid
residue) it is rejected by topology file when I try to generate a new *.pdb
file which will contain hydrogen atoms in addition (or a *.psf file).

Is there a way to include substrate (HETATM records) in further simulation
along with the protein (ATOM records) itself ?

Thanks for any help.

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