[gmx-users] Constraint of active site in gromacs

[Mark Abraham]

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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>