Hello all,
Thank you for your reply, I have read the papers as suggested, and i found
that the peak in my rmsd plot is somewhat different than the one shown in
the paper. So i am suspecting that my peptide did dissociate from the
receptor... and this is strange, as the peptide was shown to has highest
inhibition activity compare to others.
I did some experiment using 1. autoimage, 2. center origin + image
familiar, and 3. without any reimage keyword.
The rmsd plots for the autoimage and without reimage keyword are identical,
but the one using center origin + image familiar has no sharp peak towards
the end of the graph (red arrow). I am not sure why... The rmsd plots for
peptide alone and receptor alone are all identical for the three cases.
The trajectory movie without any processing, showed that the peptide
dissociated, and the trajectory with autoimage processing, also showed that
the peptide dissociated, but the peptide was at the other side of receptor
(see image, location 3). I feel strange, and confuse...
Pls enlighten me. Thank you!
On Thu, Jun 16, 2016 at 6:31 PM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> > 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
>
>
>
>
>
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Received on Fri Jun 17 2016 - 00:30:02 PDT
