How to create a substrate parameter file ?

From: Davit Hakobyan (
Date: Thu May 06 2004 - 15:09:00 CDT

Hi All,

I need to simulate an MD with a glycolytic enzyme (Phosphoglycerate mutase -
PGM) and its substrate (2-Phophoglycerate - 2PG). Alas there is only a PGM
with 3-Phosphoglycerate (3PG) in complex.

My questions are

1. Is there any available tool which can help to build a 2PG molecule with
its parameters ?

2. Are there methods, which can help one to replace 3PG with 2PG at the
active site of PGM molecule ?

I know these are somewhat abstract questions but I would appreciate any idea
and advice.

Thanks for any help.

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