I am modeling the binding of a substrate to an active site and want to do some MMPBSA-derived binding energy calculations (MMPBSA-py-mpi).
Looking in the literature- I see simulation times <1ns to 40 ns for production simulations. I have determined that my enzyme-substrate structures (there are 10) are stable from the equilibrations steps ( as outlined in Amber tutorial on mmpbsa).
Is there any 'gold standard' for the length of production runs that yeild the most reliable mmpbsa energy outputs?
Thanks,
Chris
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Received on Fri May 03 2013 - 09:30:02 PDT
