Steered md itself doesn't give a pmf, how are you doing that?
Also make sure you have error bars on both pmfs, to make sure those are
smaller than the differences from mutation.
On Fri, Nov 22, 2024, 7:09 PM Ramdhan,Peter A via AMBER <amber.ambermd.org>
wrote:
> 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 - 16:30:03 PST
