[gmx-users] Center of mass restraints

[Daniel Burns]

Thanks Justin,

You're generous with your time, thank you.

The coordinate file where all the ligand atoms are set to the COM
coordinates, will that be pasted in place of the actual ligand coordinates
in the "complex.gro" file or how do I incorporate that into the run?


Dan

On Mon, Nov 11, 2019 at 7:18 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/11/19 3:58 PM, Daniel Burns wrote:
> > 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?
>
> No, that's only possible with the pull code. If you're just trying to do
> a simple pose refinement, you could apply a light restraint on the
> backbone or C-alpha atoms to prevent this from happening.
>
> >   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?
>
> genrestr won't generate what you need.
>
> Obtain the COM coordinates of your desired residues with gmx traj -ox
> -com and a suitable index group. That's the origin of the restraint.
> Create a (physically unrealistic) coordinate file where all the ligand
> atoms are set to those coordinates.
>
> > I haven't been able to find an example of this.
>
> Probably good fodder for my next tutorial...there are lots of practical
> applications to using the flat-bottom restraints.
>
> -Justin
>
> > 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
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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> Gromacs Users mailing list
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