[gmx-users] Topology parameters for ligand

Justin Lemkul jalemkul at vt.edu
Sat Jan 7 21:15:24 CET 2017

On 1/7/17 6:05 AM, tasneem kausar wrote:
> Dear all
> I am following Justin's tutorial methane in water for free energy
> calculation. I am using Gromacs-5.1.4. The charges of methane in topology
> are set to zero. So following the same protocol, is it relevant to set the
> charges at zero in topology of the drug. I am confused because in tutorial
> of Sander (ethanol in water) charges are present in the topology file.
> Please tell me the difference in both the tutorials and how can I apply it
> to drug that I want to study.

The charges in my tutorial are set to zero because the stated goal of that 
tutorial is to reproduce *only the LJ portion of the hydration free energy* to 
match a published paper.  This creates a very simple, robust system.  If you 
want to calculate a real, meaningful hydration or binding free energy, charge 
transformation is required.



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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