Is it possible to flip the nucleotide alone when we do molecular dynamic simulation for ATP bound kinase (without sustrate)?

09 September 2013 0 5K Report

I subjected ATP bound kinase (ATP+protein+2MG2+ ions) for 100ns simulations using gromos force field in Gromacs package. When I analysed the trajectory, the nucleotide end of the ATP (Adenine+ sugar) has got around 90 degree flip during the simulation, which means that the previous hydrogen bond interactions were broken. However the tail of the ATP seems to be located in the same position. Can this result be expected or am I doing something wrong with the selection of force field?

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