[AMBER] Can restraints on protein substitute membrane?

From: Rafał Madaj via AMBER <amber.ambermd.org>
Date: Mon, 26 Sep 2022 19:59:57 +0200


I am working on a huge hexameric structure that forms ion channel that I
am going to investigate in terms of permeability for some ligands
(investigated through ASMD/REMD/USMD).

As it is membrane channel, it should be placed within the membrane to
mimic real behavior. However, such calculations, due to size of system
(500k+ atoms) are extremely expensive, especially when applied to dozen
of ligands and/or mutations.

Therefore I am wondering: could application of strong restraints, in
order to freeze position (like 1000 kcal/mol*A2 with dt of 1fs) on the
protein backbone in the areas that *should *be located inside the
membrane, substitute membrane? Of course it would only include outer
transmembrane helices, whereas inner parts could not be affected.

Best regards,


dr inż. Rafał Madaj
Laboratorium Bioinformatyki Strukturalnej
Instytut Biologii Ewolucyjnej
Wydział Biologii UW
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Received on Mon Sep 26 2022 - 11:30:04 PDT
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