[gmx-users] Center of mass restraints

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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