[gmx-users] Using GROMACS to simulate As-Protein interaction

[Mohamad Koohi-Moghadam]

Dear Mark,

Thanks for your reply,
Recently I came across the following tool that is developed by AMBER and it
seems it can define a FF to model for As. It actually covers 80 different
metals:
http://ambermd.org/tutorials/advanced/tutorial20/bonded_model.htm
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674

But my question is, suppose I make the FF for Zn-Protein and As-Protein,
can I use MD to find which one of them are more stable?

Thank yo,
Mohamad

On Wed, Feb 8, 2017 at 6:11 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> First, you need to find a force field that can model As, and then show it
> has some usefulness for relative binding affinity. But it seems wildly
> unlikely that any will exist that are useful. Classical force field models
> are very unlikely to be able to do a good job of this.
>
> Mark
>
> On Wed, Feb 8, 2017 at 4:53 AM Mohamad Koohi-Moghadam <m.koohi.m at gmail.com
> >
> wrote:
>
> > Dear Friends,
> >
> > I have a protein with a receptor that experimentally showed has an
> > interaction with Zn. I want to find if As also bind to this receptor or
> not
> > and want to compare the stability of Zn-protein and As-protein. What is
> > your suggestion to solve this problem.
> >
> > Thank you,
> > Mohamad
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