On 9/28/12 2:19 PM, Archana Sonawani wrote:
Dear Justin,
So do I have to carry out umbrella sampling simulations separately for the
three complexes or put the three ligands together with the protein and pull
the ligands one by one to calculate the binding energy. I am confused.
Each complex has to be treated separately. Simultaneously pulling three
molecules won't make any physical sense and the simulations would crash anyway.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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