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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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-requ...@gromacs.org.
