Dear All, I had been in the look out for someone who has a reasonable amount of expertise in dealing with the MD simulation of an Alcohol Dehydrogenase. I have a problem dealing with the NADPH. I was unable to maintain the planarity of the carboxamide of the nicotinamide moiety in the simulation as a result of which important sidechain hydrogen bonds are being lost in the simulation. Is such behaviour expected or is it because of the non quantum mechanical treatment of the NADPH molecule that these kind of situations occur? If anyone has some experience please share it.
-- KRISHNA KISHORE@IIT-MADRAS
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