[gmx-users] Constraint of active site in gromacs

[Nataraj Balakrishnan]

Thanks Mark, I will do that .
Regards,
Raja
On May 6, 2015 8:07 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Yes, but you need distance restraints (not constraints, which are
> different) like Justin said. You also need to get both ligating water
> molecules, protein and ion into the same moleculetype to make that work.
> That's not trivial, so make sure you really need that EM for something.
>
> Mark
>
> On Wed, 6 May 2015 15:57 Raj D <gromacs.for.f at gmail.com> wrote:
>
> > Thanks Justin , but I have a modelled protein download from Modbase and
> > added Fe iron into the approximate ligating distance of three ligating
> > atoms of the amino acids. Now I am aiming to bring the octahedral
> geometry
> > of the Fe coordinating atoms which include two more water molecules using
> > EM engine of Gromacs. Will it be possible to let the EM to optimize the
> > distances between the atoms of the octahedral by constraining the angles
> > and positions of the atom positions for a octahedral geometry ?
> > Regards,
> > Raja
> > On May 6, 2015 5:14 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 5/6/15 3:09 AM, Raj D wrote:
> > >
> > >> Dear User,
> > >> I would like to constraint the Iron bound active site of the protein
> in
> > >> octahedral shape in EM and MD steps ... Is there a direct routine to
> > >> create
> > >> such a constraint in gromacs by feeding information of ligating atoms
> of
> > >> amino acids with Iron at the center of the octahedral geometry.
> > >>
> > >
> > > What you need are distance restraints, which you will have to write in
> > the
> > > topology yourself.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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