mahbubeh zarrabi wrote:
Dear all
I have 3 complexes of docking.(one receptor with 3
different ligands).I studied MD of 3 complexes in 15
ns by gromacs.how can i compare binding energy and
affinity of 3 ligands with receptor.(how can i
analysis gromacs result)
Shouldn't you have asked this question before designing your
simulations? :-) You can't measure binding affinity without taking a
difference between "before" and "after", which you don't seem to have.
You probably need to look at literature on thermodynamic integration, or
some such.
Mark
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