From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Wed May 11 2005 - 13:49:53 CDT
Now I am using free energy perturbation to calculate free energy difference.
The system is one ligand + one receptor. I want to mutate one
residue in binding pocket from Glycine to Aspartate.
Basically, I grow aspartate and shrink glycine at the same time.
The problem is that aspartate could overlap with other residues due
to its bigger size than glycine. So the VDW energy becomes very large,
even infinite. Anybody has ideas to deal with this situation?
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