[gmx-users] energy minimization

Justin Lemkul jalemkul at vt.edu
Thu Nov 13 19:36:29 CET 2014

On 11/13/14 2:14 AM, md kashif wrote:
> Dear all
> Can anyone suggest that how to compare change in energy of my protein
> before docking and after docking by a ligand.
> Please suggest any suitable tutorial or paper if possible.

You can easily calculate an energy value for the protein (single point energy 
calculation), but it's not a free energy and it's totally force field-dependent. 
  Proteins are generally (mostly) rigid during docking, so any change in the 
energy is probably small.

If this is related to your previous posts about the energy value after 
minimization, it's really not a useful quantity because the systems are simply 



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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