AMBER Archive (2002)

Subject: free energy for binding

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Fri Jun 14 2002 - 17:50:54 CDT

Dear Amber users:

I'm studying a protein-DNA system in which a bulky
carcinogen is covalently linked to one or another
adenine on the DNA. Experimentally the binding free
energy of protein to the carcinogen modified DNA is
different in the two cases. I would like to do free
energy simulations to see how well the free energy
difference can be reproduced.

What dynamics should I run? Should I ALSO run dynamics
on the single protein and single carcinogen modified
DNA?

Thanks a lot,

Qing Zhang

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