[gmx-users] complex topology file

Justin Lemkul jalemkul at vt.edu
Thu Feb 11 02:42:19 CET 2016

On 2/10/16 8:34 PM, Sana Saeed wrote:
> please someone help me. i 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

I already replied:




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


More information about the gromacs.org_gmx-users mailing list