FEP

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Tue Feb 01 2005 - 11:15:24 CST

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Hi,

I am studying the binding affinity between two protein molecules. Now I want
to mutate one residue in one molecule and calculate the free energy difference
between the wild type one and the mutant. I have looked at "the tutorial to set
up ...". But I still don't know how to get the psf_file for hybrid molecule
using psfgen before I do any exclusion definition.

Because I have only NAMD. Could I do exclusion definition by hand?

Thank you!

Wei Chen

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