It is of course possible to compare the backbone RMSD of all snapshots to
the average, and then excerpt the closest snapshot, which will certainly
have reasonable solvent and counter-ion positions. But, interpreting the
average structure, or a close snapshot, as "telling us something", would
most likely be a case of over-interpretation. If the MD trajectory
ensemble is "telling you something" - backed by the statistics, _and_ there
is a snapshot that illustrates that point, then OK.. that might have
application...... within the caveat that it still only a snapshot.
On Sat, Mar 26, 2016 at 3:45 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Imagine a moiety that twists and flaps back and forth with respect to
> the rest of the system. A raw average might be an unchemical jumble in
> the middle. My impression is that this situation is less likely in
> crystals.
>
> Quick experiment - run vacuum dynamics and average to see what I mean.
>
> Bill
>
> On 3/26/16 12:45 PM, Michael Shokhen wrote:
> > Dear Jason,
> >
> > Thank you for your response.
> > You wrote: "It is generally a mistake to think that an average structure
> will be
> > physically realistic."
> > What is a crystal structure of protein molecule identified by x-ray?
> > Isn't it an average structure over all protein molecules in real
> physical system?
> > Following your statement what single frame on the MD trajectory should
> be used
> > as a resulting computational structure simulating a protein structure in
> a real physical system?
> >
> > Regards,
> > Michael
> >
> > *****************************
> > Michael Shokhen, PhD
> > Associate Professor
> > Department of Chemistry
> > Bar Ilan University,
> > Ramat Gan, 52900
> > Israel
> > email: shokhen.mail.biu.ac.il
> >
> > ________________________________________
> > From: Jason Swails <jason.swails.gmail.com>
> > Sent: Saturday, March 26, 2016 10:18 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] membrane protein problem
> >
> > On Sat, Mar 26, 2016 at 2:35 PM, Michael Shokhen <
> michael.shokhen.biu.ac.il>
> > wrote:
> >
> >> Dear AMBER experts.
> >>
> >>
> >> Applying AMBE14 and AmberTools15, I have simulated a protein in membrane
> >> by MD in periodic cell.
> >>
> >> The next step is calculation of the average structure from
> >> the fragment of the production trajectory that satisfies a desired
> protein
> >> backbone RMSD condition.
> >>
> >> Finally, to obtain a representative protein structure the latter step
> must
> >> be minimization.
> >>
> >>
> >> The adequate minimization of a membarne protein can be conducted in
> >> membrane environment only. That is why I have accounted in the averaging
> >> procedure
> >>
> >> the whole soup in the periodic cell: protein, membrane, water, and
> counter
> >> ions.
> >>
> >> In this purpose I have applied the following cpptraj script:
> >>
> >>
> >> parm ../*.prmtop
> >>
> >> trajin prod4.mdcrd 3000 10000
> >>
> >> center :1-9308 mass origin
> >>
> >> autoimage origin
> >>
> >> rms first .C,CA,N
> >>
> >> average average_prod4_3000-10000.pdb PDB
> >>
> >> run
> >>
> >> quit
> >>
> >>
> >>
> >> The problem I faced is that despite the final pdb file contains also
> >> solvent water molecules and counter ions their coordinates are
> corrupted.
> >>
> >> Water molecules and counter ions are collapsed
> >>
> >> in a very small condensed area in the center of periodic cell
> >> like in a black hole.
> >>
> > This is exactly what I would expect to happen in a converged simulation.
> > Picture a droplet of water that is suspended in zero-G (free-fall) for a
> > long time. Each molecule is constantly moving, and the ready exchange of
> > water (due to typical diffusion) means that each water molecule spends
> > equal time at every "location" within the droplet as long as it has
> enough
> > time to diffuse everywhere. If its probability density in the droplet is
> > uniform, its *average* position is the center of the droplet. And this
> > holds true for *every* water molecule.
> >
> > It is generally a mistake to think that an average structure will be
> > physically realistic.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > _______________________________________________
> > 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
> >
>
>
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Received on Sat Mar 26 2016 - 15:30:03 PDT
