[gmx-users] Regarding non-bonded parameter of Zn-His for gromos96 53a6 ff

[Justin Lemkul]

On 10/14/15 8:11 AM, Navneet Chaturvedi wrote:
> Dear gmx user
>
> I need help regarding changing the unit. I found a table in article (
> http://pubs.acs.org/doi/abs/10.1021/jp501737x). There are some non bonded
> parameters of metal ion given in *Ai* [kcal 1/2 mol −1/2 Å−6 ] and *Bi*
> [kcal 1/2 mol −1/2 Å−3 ] unit. I want to use these values in c12 and c6
> values (in case of amber ff sigma and epsilon).
>

https://en.wikipedia.org/wiki/Lennard-Jones_potential#AB_form

They've effectively given you sqrt(A) and sqrt(B) rather than A and B directly.

-Justin

> Could you please text some ideas, how could I use this? I want to check the
> binding coordination of Zn with his amino acid residue in YodA (Zn binding
> protein, 1oek.pdb), But after simulation (after 5 - 8ns), Zn-His bond was
> dissociated.
>
> or Could you type down some view on Zn-Nitrogen (Zn-Histidine) atom non
> bonded parameter. I am using gromos96 53a6 ff.
>
> I am new in this field so I would like to get some ideas about the same.
>
> Thanks a lot
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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