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 - 06:30:04 PDT
