[gmx-users] Restraining Protein-ligand distance

Justin Lemkul jalemkul at vt.edu
Mon Mar 27 18:55:48 CEST 2017

On 3/27/17 8:42 AM, Juan José Galano Frutos wrote:
> Hi there,
> I am trying AFEC simulations in complex (ligand-protein), but sometimes I
> get the ligands out the binding site, but I dont want that scenary. I was
> thinking the situation of applying distance retraints between a ligand and
> a protein was already solved in GROMACS version later 5.0... without any
> necessity of making a hybrid system. But, I'm using version 5.1, and it
> seems that's not possible doing so, because I'm obtaining errors.
> Is there currently any happy solution to restraint ligand-protein distance?
> or Has one to still go through the unbrella pulling option to do that?

You need distance as well as orientational restraints.  This is done with 
[intermolecular_interactions], which was a new feature in 5.1.  For theory, see 


> In the case I need to do a hybrid system what would be a good procedure?
> Thank you very much.
> Juan José Galano Frutos
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)


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


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