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

[Mohamad Koohi-Moghadam]

Yes, That was really a good news. Thanks AMBER.
As you suggest I try to find the free energy for these two situations. I
hope can find any result.

Mohamad

On Wed, Feb 8, 2017 at 11:48 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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