On Tue, Jan 14, 2020, Sally Pias wrote:
>
>My group would like to model bacteriorhodopsin, and we are having trouble
>determining appropriate atom types to use for the protonated Schiff base
>linkage where the protein's lysine side chain joins retinal.
Have you checked what others have done, e.g. in the Duan group:
https://doi.org/10.1371/journal.pone.0069882
I'm not saying this paper made the best choice, but it would give you a
point of reference. My guess (just that) is that the question of Amber
vs. gaff types won't actually make a lot of difference, but I'd
personally favor keep Amber atom types for the backbone atoms of lysine,
to be more sure of the phi-psi parameters there.
....dac
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Received on Wed Jan 15 2020 - 06:00:04 PST
