[gmx-users] Parameters for selenium

[chris.neale at utoronto.ca]

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