[gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.

[Justin A. Lemkul]

Quoting SeungPyo Hong <sp1020 at gmail.com>:

> Dear gmx-users,
>
> I want to perform MD with or withou phosphorylated proteins and to compare
> their differences.
> Because the phosphorylation is well known phenomena, I guess there some of
> you had done MD with it.
> I will be glad if you let me know where can I found reliable parametered, or
> residue topologies, for the phosphorylated amino acid.

The Gromos96 43a1p parameter set includes entries for phosphotyrosine,
phosphoserine, and phosphothreonine.  The contributed files on the Gromacs
website are formatted for an older version of Gromacs, and I have re-formatted
them for use with newer versions.  Contact me off-list if you want the files;
I'm happy to send them to you.

If you want phosphohistidine parameters, search the list archive for the
relevant discussion.

-Justin

>
> Sincerely
> Seungpyo Hong.
> --
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'But he created too many objects.'
> -Seungpyo Hong
>
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
> Tel. (82)-18-372-2468
> sphong_ at kaist.ac.kr
> sp1020 at gmail.com
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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