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
Hmm ok if Gromacs does not provide something like this then I ask the
question a little bit different: Does someone know a pure scoring
function for protein/protein interaction? It should not be a complete
docking program but rather something which can simply evaluate given
conformations (coming from an MD trajectory) ... and it should also not
be a webserver (like ClusPro) but a downloadable binary because I want
to test a quite high amount of conformations. Something like XSCORE [J
Comp Aid Des, 16: 11-26. 2002] but instead of ligand/protein for
protein/protein interactions.
Cheers,
Bernhard
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