Imaging problems usually show up as jumps in the rmsd, not slow changes. I
suggest you visualize the imaged trajectory and see what is happening. It's
hard to say from snapshot pictures.
On Fri, Jun 17, 2016 at 3:06 AM, colvin <colvin4367.gmail.com> wrote:
> Sorry, the images do not attached correctly, I'm inserting them again.
> Thank you
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Jun 17, 2016 at 3:02 PM, colvin <colvin4367.gmail.com> wrote:
>
> >
> > 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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 17 2016 - 04:30:02 PDT
