[gmx-users] binding energy (score) of single trajectory frames

Justin Lemkul jalemkul at vt.edu
Wed Oct 30 16:51:40 CET 2013

On 10/30/13 11:26 AM, Knapp Bernhard wrote:
> Hi users,
> I was wondering if there is an easy and quick way to get a frame-wise binding
> energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory.
> This is not indented to be an actual binding free energy approach but rather a
> rough indicator if the binding between two chains increases or decreases during
> simulation time. This should work like a protein/protein docking scoring
> function which assigns binding scores to single conformations. Is there a direct
> approach on an existing xtc (even if water was removed and not all steps were
> written)? Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation,
> Ghydrophobic etc. Alternatively (and probably much more time and resource
> consuming), would it be possible to obtain this by the rerun option of mdrun
> (adjusted energy monitoring groups (the original setup was "energygrps =
> protein    SOL"))?

Using energygrps is the closest you'll get without modifying the code.  You'll 
get decomposed short-range nonbonded terms, which can perhaps provide some 
indicator of the strength of the interaction between the two entities.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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