>
>
>
2) The histidine and cystein should be parameterized for the md simulation
> in Amber 12 OR NOT
If I'm understanding your question here, which I think is to asking if you
need parameters for phosphorylated histidine and cysteine, I think that
phosphohistidine should be in one of the forcefields since it's a fairly
common target, although I'm not sure which forcefield it'd be. At the very
least, there's parameters for varying states of phosphohistidine on the
Bryce database.
Phosphocystine seems like a pretty unusual target, so you'd probably have
to parameterize it yourself. I could be wrong, though.
Best,
Kenneth
On Sun, May 10, 2015 at 10:57 AM, muhammad tahir ayub <tahirgp0.gmail.com>
wrote:
> 1) my protein(4KIK) contain two protomers (a) and (b), both have the
> binding site, but protomer (b) undergo phosphorylation and make the SEP
> residue while the serine of protomer (a) does not undergo phosphorylation
> so which protomer should be used for molecular dynamics simulation.
>
> 2) The histidine and cystein should be parameterized for the md simulation
> in Amber 12 OR NOT
>
> *Muhammad Tahir*
> *Ayub*
>
> *Junior Research Fellow*
>
> *H.E.J Research Institute of Chemistry*
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>
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Received on Sun May 10 2015 - 09:00:02 PDT
