On 23/03/2011 4:38 AM, Kishore wrote:
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.
Classical MD simulations use improper dihedrals to maintain such
planarity. You can see this in the amide links in a peptide backbone,
for example. Each set of four co-planar atoms (three arranged around a
central one) needs an improper dihedral. So you need H-N-C-H, N-C-O-Cr4
and C-Cr4-Cr5-Cr3 (where the ring carbons are named Cr and numbered
clockwise from N) in order for the carboxamide to stay coplanar with the
aromatic ring
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