[gmx-users] Metal-Protein interactions
drrahulsuresh at gmail.com
Tue Nov 28 19:00:45 CET 2017
On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/28/17 4:54 AM, RAHUL SURESH wrote:
> > I am trying to simulate a metal-protein interaction using gromacs 2016
> > package and charmm36 ff.
> > I have prepared the initial pdb by performing an oniom calculations
> > protein and metal (at various positions) using gaussian 09 and chose the
> > structure with maximum binding energy. The metal ion is bonded to oxygen
> > atom of His residue. Having a look at gro file after each step
> That's unusual; His typically coordinate metals via their delta or
> epsilon N atoms.
Sorry that I pronounced wrongly as oxygen.. regret the inconvenience.
> > (protein.gro, em.gro, nvt.groand npt.gro) the distance between metal ion
> > and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
> > course of simulations for 10ns, the metal ion is away from the protein.
> > What can be done to have the metal ion restrained at its position? Or if
> > extend the simulation will the metal ion find its appropritae position
> > during the course time?
> Unlikely. This is a fundamental issue with classical mechanical force
> fields approximating ion interactions very poorly, particularly in the
> case of multivalent and/or transition metals. There are many effects
> like polarization and charge transfer that simply can't be modeled. You
> can apply distance restraints (or actual covalent bonds), NBFIX LJ
> parameters, etc.
while restraing the metal ion, it arise an error stating that an atom can
not be mentioned in two groups.
Tc grps = protein_cu water_and_ions.
Cu will already be mentioned in ions.
and that may be enough to preserve the binding pose. In
> reality, one would have to reparametrize any ligating residues because
> the charge distribution on the ion and anything coordinating it is not
> at all what the standard force field uses.
Reparameterize.? Means I have to add additional parameter file to the
charmm36 ff after interacting with metal ion.?
Also Justin, what if I can manually add a bond between N of HIS and metal
ion with most appropriate bond length ..?
(To avoid complexity if it works)
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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