You could also consider using the 'native contacts' option to compute the
number of water residues in contact with your ASP at each frame.
As for membrane metrics, one option would be to use the cpptraj vector
command to compute the center of mass of the lipid headgroups in the
appropriate membrane leaflet over time and compare that with the center of
mass of the ASP group over time.
On Mon, Jul 9, 2018 at 10:32 AM, Stephan Schott <schottve.hhu.de> wrote:
> Hi Elisa,
> To do what Kenneth is suggesting you, I would recommend to take a look at
> the vector command in the cpptraj manual. This would allow you to extract
> the component of the distance in a certain direction. You could choose a
> reference point like the center of mass of the last atom from your lipids
> and evaluate the z-distance component only. A histogram of the distance
> measurements should show you the bimodal behavior you are describing.
> Hope it helps,
>
> El lun., 9 jul. 2018 a las 19:22, Kenneth Huang (<khuang8.student.gsu.edu
> >)
> escribió:
>
> > Hi,
> >
> >
> > You could try to use measuring the distance in cpptraj if you know a
> fixed
> > reference point that you can measure the aspartate distance to and see
> how
> > it changes with time.
> >
> >
> > You could also look at the waters around it, ie watershell, if your
> > residue is becoming buried in the membrane, but that might be trickier to
> > interpret if there happens to be enough water around in both positions.
> >
> >
> > Best,
> >
> >
> > Kenneth
> >
> > ________________________________
> > From: Elisa Pieri <elisa.pieri90.gmail.com>
> > Sent: Monday, July 9, 2018 9:12 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Help on
> >
> > Hello everyone,
> >
> > I'm running a simulation of a protein in membrane (explicit solvent). I
> > have a ASP residue that is located at the frontier between water and
> > membrane, and it is dynamically flipping from being embedded in the
> > membrane and facing the water. I would like to plot this property against
> > the time coordinate. Since I have no MM analysis background on this
> topic,
> > could you tell me what kind of analysis should/could I run (presumably
> with
> > cpptraj)?
> >
> > Sorry for this trivial question..could you help me?
> >
> > Elisa
> > _______________________________________________
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> > --
> > Stephan Schott Verdugo
> > Biochemist
> >
> > Heinrich-Heine-Universitaet Duesseldorf
> > Institut fuer Pharm. und Med. Chemie
> > Universitaetsstr. 1
> > 40225 Duesseldorf
> > Germany
> >
> > <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Mon Jul 09 2018 - 11:00:02 PDT
