[gmx-users] Center of mass restraints

[Daniel Burns]

Thank you!

If I use the coordinates of the center of mass for the spherical restraint,
will the ligand remain restrained to that coordinate if the protein rotates
or translates the binding site away from that original position? Or am I
going about this wrong?  Can I set up that spherical restraint with a
genrestr command without calculating the coordinates of the center of mass
from a visualization software?

I haven't been able to find an example of this.

On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/10/19 2:54 PM, Daniel Burns wrote:
> > Hello,
> >
> > I have identified a set of amino acid residues that surround a small
> > molecule binding site.  How would I go about restraining the small
> molecule
> > ligand to the center of mass of the surrounding residues?  I want the
> > molecule to be able to bounce around in the binding site to let if find
> the
> > most energetically favorable configuration.
>
> You could either set up a spherical flat-bottom restraint with the
> origin of that restraint coincident with the COM of the desired
> residues, or you could use the pull code to set a restraint between the
> COM of the protein residues and the COM of the ligand.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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> Virginia Tech Department of Biochemistry
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>
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