FEP - Protein binding to Membrane surface

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Feb 10 2011 - 03:50:37 CST


I want to calculate the free energy for the binding process of a Protein to a
Membrane surface. Before I start I have three basic questions:

Is possible to do this?

Regarding the "dual-topology" setup I had in mind to take coordinates from my
MD simulation. One coordinate set from the start where the Protein is ~8A away
from the Membrane interface and one coordinate after 500ns where the protein
has "bound" to the membrane interface.

Does anyone have an example or tutorial for the above? Or can I adapt the
"Binding of a potassium ion to 18–crown–6" protocol? Any thing to keep in mind
while running this kind of FEP/adapting the protocol?

Thanks for your advice.


Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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