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

Navneet Chaturvedi 14.navneet at gmail.com
Wed Oct 14 14:11:56 CEST 2015

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).

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

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

*Your Sincerely*

*Dr Navaneet Chaturvedi*
C/O Dr Gali Prag
Department of Biochemistry & Mol Biology,
Sherman Building (The George S. Wise Faculty of Life Sciences)
Tel Aviv University, Tel Aviv 69978
Email: navaneettau at post.tau.ac.il
Skype: navneetonskype1
Web: http://www.praglab.org/#!members/cso6

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