[gmx-users] Protein Ligand simulation

Justin Lemkul jalemkul at vt.edu
Fri May 6 20:31:29 CEST 2016

On 5/6/16 2:26 PM, Alex Mathew wrote:
> Greetings to all !
> i have completed Protein Ligand simulation as per the tutorial,my aim
>  to proof that ligand A inhibit Ligand B -what are the  possible analysis i
> can perform
> i have done the following
> RMSD - to see the stability of protein with ligands
> RMSF-root mean square deviation of individual residues
> hbond-hydrogen bonds between the ligand and protein
> energy-VdW and Coulomiv energy
> dssp-Secondary structure analysis
> pairdist-mean distance betn the ligand and protein in all time
> gyrate-radius of gyration whether any structural changed happen in MD

Most of those are not informative with respect to determining ligand binding 
affinities, etc.  The hard truth is that there is no recipe for analysis, and 
you should have decided what to analyze before ever doing the simulations; how 
else will you know the correct methodology and required time scale to examine 
phenomena of interest?

> how to find other interactions such as hydrophobic pi-pi etc

Maybe you can look at number of contacts (via gmx mindist) but I doubt you'll 
get any legitimate results related to pi stacking with any current biomolecular 
force field.

> Is is possible to do any competitive inhibition study using gromacs?

If you were to immerse your protein in a dilute solution of different ligands, 
and allow them to sample the binding/active site reversibly, sure.  But that's 
basically impossible.  You could do simulations to calculate binding free 
energies to get relative affinities.



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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