[gmx-users] Alcohol Dehydrogenase MD simulation....Reg

Kishore kris.vempali at gmail.com
Tue Mar 22 18:38:43 CET 2011

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.

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