[gmx-users] Ligand interaction

Justin Lemkul jalemkul at vt.edu
Wed Nov 12 13:51:52 CET 2014

On 11/12/14 5:10 AM, md kashif wrote:
> Dear all
> The protein+ligand complex energy is -1.05....e+06  and energy of protein
> only(without docking) is -1.5...e+06, what does it mean?

It means that you have two systems with two different energies.  In order to 
dock the ligand, you must have started from a protein without water.  In 
solvating the system afterwards, you ended up with a different number of solvent 
molecules (because there is now less void space in the protein's binding site) 
and therefore the energy surface during minimization is different.  You're 
comparing apples to oranges.



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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