Hello,
I am using a steered MD to steer a substrate to the reaction center of a heme-containing enzyme. I am using a LCOD as the rxn coordinate. I am comparing the wild-type PMF to that of two mutants. Is there a way to compare across different starting rxn coordinates. For example, the LCOD for the substrate to the heme is 8 angstroms total while the LCOD for the same substrate in the mutant is 6 angstroms total. Is there a way to correct for the differences in initial distances? I found that the PMF is much larger in the wild-type than the mutant and I think it might be because of the wild-type having to travel a larger distance based on my initial ASMD start.
Sincerely,
Peter Ramdhan
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Received on Fri Nov 22 2024 - 16:30:02 PST
