[gmx-users] Re: selenium parameter

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Jul 12 15:07:22 CEST 2010

Susan. Please use the mailing list instead of personal email.

A google search for electronegativity of selenium provides a useful  
first hit. The .rtp issue is covered often on the mailing list.  
Overall, you will find this link helpful:  

Quoting Susan COSTANTINI <susan.costantini at unina2.it>:

> Dear Chris
> I have read your mail regarding the selenium parameters and I have   
> tried to insert the SEG atom in ffG43a1.rtp but Gromacs gives error.
> Where I can the electronegativities of Se?
> When I run the pdb2gmx comand, Gromacs give this error:
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: pdb2gmx.c, line: 421
> Fatal error:
> Atom SEG in residue CYSH 50 not found in rtp entry with 8 atoms
>              while sorting atoms
> -------------------------------------------------------
> Have you idea how I can solve this problem?
> Thank you in advance!!
> Susan Costantini
> Senior Fellow
> Oncologic Center Research in Mercogliano (Italy)
> 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.

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