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"))?
Cheers,
Bernhard
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