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Parameterization for diazonium-tyrosine
#36055 12/01/16 07:15 PM
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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 Files
azo-tyr.mol2.txt (4.05 KB, 259 downloads)
azo-tyr.str.txt (5.9 KB, 276 downloads)
Re: Parameterization for diazonium-tyrosine
jingjieyeo #36056 12/01/16 07:30 PM
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In this case, it's possible that a more complete parametrization may be needed, with QM calculations.


Rick Venable
computational chemist

Re: Parameterization for diazonium-tyrosine
jingjieyeo #36076 12/11/16 08:21 PM
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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?

Re: Parameterization for diazonium-tyrosine
jingjieyeo #36077 12/11/16 08:36 PM
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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.


Rick Venable
computational chemist

Re: Parameterization for diazonium-tyrosine
jingjieyeo #36107 12/30/16 04:36 PM
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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?

Last edited by jingjieyeo; 12/30/16 05:52 PM.

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