From: Tim Isgro (
Date: Wed May 05 2004 - 17:24:12 CDT

Hi Davit,
If you want to run simulations with the substrate, you will need to
develop parameters for it (as well as a topology file entry for it). The
program MOE can perform a parameter file search and will give parameters
and atomic charges based on similarities between atoms in your molecule
and those already defined in the Charm parameter files. (If you want to
know more, parameter development is probably a discussion more suited
toward the namd-l list.)

On Mon, 3 May 2004, Davit Hakobyan wrote:

> 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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