Hi Ya,
There are several options you can choose in AMBER: the nonbonded model,
bonded model and cationic dummy atom model to simulate the metal ion.
Here is a tutorial about metal ion modeling:
http://ambermd.org/tutorials/advanced/tutorial20/.
Here are two papers about nonbonded model of divalent metal ions and the
parameters are all available in AMBER (please check *Amber force
fields-->Molecular mechanics force fields-->Ions *section in AMBER2015
manual):
http://pubs.acs.org/doi/abs/10.1021/ct400146w
http://pubs.acs.org/doi/abs/10.1021/ct400751u
If you have any questions, please feel free to email me.
Best,
Pengfei
2015-05-07 9:18 GMT-04:00 Ya Gao <gaoyaaaa.gmail.com>:
> Dear all,
>
> I need parameter files for mercuric ion (Hg2+), which is linked to GLU,
> CYS, and GLN, to perform simulations. However, I cannot find it in
> parm99.dat . Would anyone give me some help or tell me any source where
> these can be available.
>
> Thanks very much.
>
> Best wishes,
>
> Ya
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 07 2015 - 07:00:04 PDT
