Re: [AMBER] modeling a Schiff base with GAFF atom types

From: David Case <>
Date: Wed, 15 Jan 2020 13:54:42 +0000

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:

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.


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Received on Wed Jan 15 2020 - 06:00:04 PST
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