[AMBER] modeling a Schiff base with GAFF atom types

From: Sally Pias <sallypias.gmail.com>
Date: Tue, 14 Jan 2020 16:16:57 -0700

Hello developers and users,

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. (For the
structure, see https://en.wikipedia.org/wiki/Bacteriorhodopsin.) One option
is to use all GAFF atom types for the lysine-retinal residue's "side
chain." Another option is to use GAFF atom types for the retinal portion
and protein atom types for the lysine part.

Our difficulty revolves specifically around choosing atom types for the
Schiff base nitrogen and neighboring carbon atoms. We have found parmcheck
to be largely unhelpful.

I would appreciate any guidance or ideas.

Sally Pias

Associate Professor of Chemistry
New Mexico Tech
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Received on Tue Jan 14 2020 - 15:30:02 PST
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