I don't have the parameters. You could possibly fudge it by
extrapolating out from SER->CYS->Se_CYS based scaled by
electronegativities of O,S,Se. I'm not saying that this is rigorous,
just that its possible to do. My main point here, though, is to ask if
you *really* need to bother with this.
Thioredoxin ~ 100 amino acids. Sampling is a real problem in
simulations, and I highly doubt that you're going to see a difference
in CYS vs. Se_CYS in the context of a 100 aa protein on simulation
timescales (I also doubt you'd see a difference for CYS vs. SER).
Besides, wouldn't crystallographers be basically out of business if
Se_CYS mucked up the structure as compared to CYS?
Chris.
Please
Someone know Gromos parameters for selenium. WE need to simulate the
Thioredoxin and we need to simulate a cisteine with a selenium.
Thanks
regards
Luis Scott
--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de Matemática, Computação e Cognição
Universidade Federal do ABC
Grupo de Pesquisa em Biologia Computacional
--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de Matemática, Computação e Cognição
Universidade Federal do ABC
--
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