Hi,
Try the MCPB tutorial as a start (
http://ambermd.org/tutorials/advanced/tutorial20/). Once you work through this tutorial you should be in a good position to tackle your system. Good luck!
Kennie
> On Nov 28, 2014, at 11:50 PM, sailu <sai.ktp.gmail.com> wrote:
>
> Dear Amber users;
>
> I have a protein with two metal ions: one is Zinc (ZN) and other one is
> Nickle (Ni). I want parameterise those metal ions to start my
> simulation using Amber modules. The ZN is coordinated with four Cys
> residues and Ni is coordinated with two residues including His and Glu. I
> am new to amber and I don't know how to parameterise these metals. I
> really appreciate you if someone helps in this regards.
>
> Thanking.
>
> --
> *Sarvagalla sailu,*
> *Ph.D.scholar,*
> *Centre for Bioinformatics,*
> *School of Life Sciences,*
> *Pondicherry University**,*
> *Kalapet,*
> *Puducherry - 605014**,*
> *INDIA**.*
> *Mobile: +91-9963202788,**+91-9943923258*
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Received on Sat Nov 29 2014 - 05:30:02 PST
