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

[Mark Abraham]

Hi,

Well that's relatively good news :-) You can likely use the same kinds of
free-energy methods that are used e.g. for relative free-energy of binding
of one drug molecule over another to a protein... your "drug" is just the
ion, of course. See various tutorials. First challenge is to understand how
their model works and how you can express the parameters and topologies in
GROMACS file formats (assuming you use GROMACS). If you're really lucky,
your A and B state will just differ by parameters :-)

Mark

On Wed, Feb 8, 2017 at 4:20 PM Mohamad Koohi-Moghadam <m.koohi.m at gmail.com>
wrote:

> 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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