[gmx-users] complex topology file

Justin Lemkul jalemkul at vt.edu
Wed Feb 10 03:25:21 CET 2016

On 2/9/16 10:54 AM, Sana Saeed wrote:
> hi gmx usersi want to find out absolute binding free energy of protein ligand
> complex. fisrt i performed docking and selected best poses and then i made
> topology file of ligand with PRODRGserver. and then included itp file of
> ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in
> tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
> . can i use these complex files for MD for absolute binding free energy? in
> some tutorials the topology file of complex is quite differently organised.
> please guide me, i am following decoupling and coupling steps from
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

PRODRG topologies are inaccurate for even simple MD simulations.  Using it for a 
free energy calculation is certain to result in junk.



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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