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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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