FEP and solvent

From: Matthew Wilce (Matthew.Wilce_at_med.monash.edu.au)
Date: Sun Jun 12 2005 - 22:35:32 CDT

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Dear NAMDers

I have been working through using FEP. I am applying it to a 100aa
protein complexed with a trioligonucleotide. I am wondering whether I
should be considering the solvent that is displaced by the
oligonucleotide. In other words should I be considering someway of
shrinking a set of water molecules that are in the position occupied
by the oligo? Has anyone done this?

Associate Professor Matthew Wilce
Monash University

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