Sir,
I run some DNA-ligand1 complexes. Though the ligand remains bind throughout
the simulation, (the ligand binds experimentally also), I am not getting a
favorable binding energy from MMPBSA (single trajectory approach). The
ligand has a CH2-CH2-CH2 chain on one end which causes the ligand some
movement (entropy changes) and hence a stable binding energy is not
possible. Is there any other way to quantify the binding energy. Would you
please suggest a reliable approach in such situations where the ligand has
much flexibility?
thanking you
mary
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Received on Wed Mar 16 2016 - 02:30:05 PDT
