[gmx-users] Constraint of active site in gromacs

[Raj D]

Dear Mark,

So to make distance restrain of specific  atoms of  protein residues and
the ligand (itp  file produced by antechamber), I may have to cut the
ligating atoms of amino acids in the  topology as produced by pdb2gmx and
paste into the ligand.itp to make the distance restraint to work ...Is it
the right approach to bring all distance restrained atoms to bring into the
same molecule type ?
Regards,
Raja
So
>
> Thanks Mark, I will do that .
> Regards,
> 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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