Hi, all users of amber
Recently, i have to deal with a case of a protein with a enzyme cofactor,
the original complex crystal structure is a complex without substrate.
So i exrtact a substrate from its family and then merge it into my model.
The minimize and MD calculation have been carried out to search the best
conformation to do QMMM analysis and PBSA analysis
my question is that how to choose the desired conformation?
>From the references, i have obtain the residues which are to be involved in
the catalysis reaction. And the residues which are adjacent to the enzyme.
Thank you for your kind help,
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Received on Mon Sep 06 2010 - 03:30:03 PDT
