I second what Jason said about using the representative structure from
clustering. If the average structure is distorted, then minimizing it will
give good geometries but this can suggest that the ensemble looks like the
minimized average, which it doesn't. With distortions at least people are
aware that there is some diversity. Artificially getting rid of it can be
very misleading. For example, if you have 2 alternate conformations, and
the average is distorted as a result, minimizing it will make it look to
your audience like you only have 1 dominant conformation, and even worse,
it might not look like any of the actual clusters at all. I would only use
the minimized average if you have strong evidence that there is a single
dominant cluster with small fluctuations about the average.
On Thu, Oct 18, 2012 at 10:09 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi Mu,
>
> Jason is absolutely correct here, but for the sake of prettier
> presentations, it is common to take the average structure that amber gives
> you and conduct a short energy minimization of it. This should give you a
> chemically normal-looking structure that is at least somewhat close to the
> average one. Alternatively, you would pick and show the snapshot from your
> MD that has the lowest rmsd compared to the average one. I find that to be
> a good compromise between the true average and a model that people can
> make sense of.
>
> Thomas
>
> On Thu, October 18, 2012 9:44 am, Jason Swails wrote:
> > On Thu, Oct 18, 2012 at 5:40 AM, Mu Xia <muxiachuixue.163.com> wrote:
> >
> >> Hi all,
> >>
> >>
> >> I want to get an average structure of the ligand-protein complex from
> >> the
> >> trajectories generated by MD. So I use the ptraj command. The input file
> >> is
> >> as following.
> >>
> >>
> >> trajin production1.mdcrd
> >> rms first mass .CA,C,N
> >> average a.pdb pdb
> >>
> >>
> >> When examining a.pdb in VMD, I find that the X-H (X is the heavy atom)
> >> bonds are abnormally short.
> >>
> >
> > This makes sense. H atoms typically rotate fairly freely (they are small
> > and there is little steric hindrance in many instances to free rotation).
> > Also, for groups like CH3, the 3 hydrogens are, at least approximately,
> > rotationally degenerate, meaning they should have approximately the same
> > average location (which will be nearly on top of the heteroatom).
> >
> >
> >> My question is, how could I get a correct average structure containing
> >> normal bonds and coordinates?
> >>
> >
> > What you got *is* a correct average structure (i.e., it is *the* average
> > structure). "Normal bonds and coordinates" would be something you would
> > find in a 'representative structure' in cluster analysis or something of
> > the like.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Thu Oct 18 2012 - 07:30:04 PDT
