> I am simulating a peptide that has known activity to a receptor, but
> throughout the 20ns simulations, the peptide is no longer at the binding
> site, pls see the image below, on how the peptide moved out from the
> binding site to location 3.
>
> Is this something to do with the trajectory imaging? I have tried 1.
> autoimage and 2. center, image familiar, and both gave the same output.
>
> Or the peptide just doesn't fit to the binding site? The energy at the last
> .out file is still negative.
Normally, you can distinguish a true dissociation event from an imaging
issue by watching the trajectory in a viewing program (like VMD):
dissociation occurs most often in several visible steps (unless your
frame intervall is too large and your bound ligand too small), whereas
imaging causes an instantaneous, several Angstroem-long jump of the
ligand between two trajectory frames, i.e. from one side of the
simulation box to the other.
Another hint is the graph RMSD vs time: If you observe instantanous
jumps in the plot of serveral Angstroems in height, this is indicative
of an imaging issue. (See e.g. DOI 10.1007/s00044-014-1135-5 for an
illustration of the imaging topic.)
The energy in the out file is the total system energy including the
solvent-solvent and solvent-solute contribution; thus it cannot used
simply to monitor dissociation events. For this, you could utilize the
linear interaction energy (LIE) between the ligand and the parent
protein, easily calculated via cpptraj: In case of a dissociation, a
gradual decrease of interaction energy is expected.
Regards,
Anselm
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 16 2016 - 04:00:03 PDT
