They will if your protonation states are known and not likely to change for
the states sampled during md.
I would be surprised if HIP was appropriate for pH 8. Maybe, but not
without a pKa shift.
On Mon, Mar 18, 2019, 9:18 AM Bharat Manna <bharatmanna.gmail.com> wrote:
> Dear AMBER Users,
>
> If I assign the protonation states of the amino acid residues manually in
> the PDB file (e.g. at pH 8.0, HIS -> HIP, LYS -> LYS etc.) while generating
> the topology in Leap, and perform conventional MD simulation of the
> protein, will it be similar to Constant pH MD simulation? To be more
> precise, will the results obtained from the simulation be comparable to the
> behaviour of the protein at that particular pH?
>
> Thanks,
> B Manna
> PhD Scholar
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Received on Mon Mar 18 2019 - 07:30:03 PDT
