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Posted By: jingjieyeo Parameterization for diazonium-tyrosine - 12/01/16 07:15 PM
Dear users,

I would like to parameterize a non-standard residue derived from sulfonic acid and tyrosine. I've attached the corresponding .mol2 file. I've used paramchem with the capped amino acid but the penalties are way off the charts. I've attached the .str file as well.

May I know whether there is a better method to cobble together the parameters? Should I separate the parameterization of the diazonium from that of tyrosine and would that give me better results?

Attached File
azo-tyr.mol2.txt  (258 downloads)
Attached File
azo-tyr.str.txt  (275 downloads)
Posted By: rmv Re: Parameterization for diazonium-tyrosine - 12/01/16 07:30 PM
In this case, it's possible that a more complete parametrization may be needed, with QM calculations.
I noticed that parameters for sulfonic acid can be parameterized in CGENFF, but the main problem comes from the '-N=N-' portion which joins the sulfonic acid to the tyrosine sidechain.

Is it not possible to parameterize the '-N=N-' portion and re-fit the charges for the overall molecule?
Posted By: rmv Re: Parameterization for diazonium-tyrosine - 12/11/16 08:36 PM
Sure, but some QM calcs may still be needed. CHARMM FFs are developed using a fragment approach. There are some tutorials and other reference info noted in the "sticky" posts at the top of this forum.
I've been trying to tackle the problem using the fragment approach. Would it be correct to say that with the tyrosine and sulfonic acid fragment's partial charges already in hand, I should derive water interaction charges for the diazene group and merge the hydrogen charges such that the tyrosine sidechain, diazene, and sulfonic charge groups have an integer charge individually? Wouldn't this end up with the diazene group having zero charge?
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