Hello,
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,
Rafal
--
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
