Thank you, Stephan!
When I used 'vector VM ucellz' command the results look good!
Maria
pon., 12 sie 2019 o 12:37 Stephan Schott <schottve.hhu.de> napisał(a):
> Hi Maria,
> I guess since you are calculating the principal Z of your lipids, you don't
> really have a nomal to the membrane and this is causing some issues there
> (depending on the DOPC composition per leaflet). Either try with Dan's
> corrplane suggestion , or try with the unit box vector:
>
> vector VA ^1:;4,5,6.N,CA,C ^1:;25,26,27.N,CA,C
> vector VM ucellz
> vectormath vec1 VM vec2 VA out vector.agr name AngleA dotangle
>
> Unless your membrane is unexpectedly curved, this is fine and will give you
> less noise.
> Hope it helps,
>
> El lun., 12 ago. 2019 a las 11:01, Maria Bzówka (<
> m.bzowka.tunnelinggroup.pl>)
> escribió:
>
> > Thank you all for your suggestions.
> >
> > First, I decided to proceed with Dan's script. After some modifications
> it
> > looks like that:
> > parm x.parm7
> > trajin x.nc
> > vector VA ^1:;4,5,6.N,CA,C ^1:;25,26,27.N,CA,C
> > vector VM principal Z :POPC
> > vectormath vec1 VM vec2 VA out vector.agr name AngleA dotangle
> >
> > These commands work, but I'm pretty sure that the results are not
> correct -
> > what I mean - in my output file the angle values range between 85 and 125
> > and based on the visual inspection of helix behaviour (as well as some
> > previous studies of the systems similar to mine) it is way too much.
> >
> > I've also tried to use 'vector VA principal ^1' command for VA, but it
> > resulted in even higher tilt angles and additionally, within a few
> frames,
> > the values changed drastically (example below):
> > #frame #angle
> > 12.000 118.6092
> > 13.000 19.5291
> > 14.000 109.5863
> > 15.000 63.3221
> > 16.000 104.9826
> > 17.000 67.5767
> >
> > Can I ask for some additional suggestions?
> >
> > Thank you
> >
> > Maria
> >
> >
> > sob., 10 sie 2019 o 15:25 Daniel Roe <daniel.r.roe.gmail.com>
> napisał(a):
> >
> > > Hi,
> > >
> > > Like Callum mentioned, 'vector principal x' will get you the primary
> > > principal axis (i.e. the axis with the highest eigenvector - cpptraj
> > > uses principal X > Y > Z by convention for historical reasons). That
> > > usually works, but you do have to sometimes be careful about sign
> > > flips; in that case you can also get an approximate vector by
> > > calculating the vector between the center of mass of the residues at
> > > the beginning and the end of the helix - I usually use 3 residues
> > > which are ~3 from each end to account for any end-terminal fraying, so
> > > e.g. with an 18 residue helical peptide I'd use residues 4-6 and
> > > 13-15. To get the vector of the membrane itself you can either just
> > > use the Z axis (if your membrane is aligned that way and doesn't
> > > really move a lot) or use 'vector corrplane' to get the vector
> > > orthogonal to the plane that passes through the lipids (or lipid
> > > headgroups). So e.g. your script might look like:
> > >
> > > parm myparm.parm7
> > > trajin mytraj.nc
> > > # Peptide vector (molecule 1)
> > > vector VA ^1:;4,5,6.N,CA,C ^1:;13,14,15.N,CA,C
> > > # or use 'vector VA principal X ^1'
> > > # Membrane vector
> > > vector VM corrplane :DOPC
> > > # Angle of peptide to membrane
> > > vectormath vec1 VM vec2 VA out vector.agr name AngleA dotangle
> > >
> > > Hope this helps,
> > >
> > > -Dan
> > >
> > > On Fri, Aug 9, 2019 at 4:18 AM Maria Bzówka <
> m.bzowka.tunnelinggroup.pl>
> > > wrote:
> > > >
> > > > Dear All,
> > > >
> > > > During the simulation I can see quite a lot of changes in the
> position
> > of
> > > > my TM helix immersed in the lipid bilayer, so I would like to
> calculate
> > > the
> > > > tilt angle between the transmembrane helix principal axis and the
> > vector
> > > > along the Z-axis. However, I'm not so sure how to do that...
> > > > As a principal axis of TM helix I mean the C-alpha atoms from the
> helix
> > > > (which is 30 residues) and I suppose that I should somehow use the
> > vector
> > > > command from cpptraj?
> > > >
> > > > Do you have any suggestions?
> > > >
> > > > Thank you in advance
> > > >
> > > > Maria
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>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
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Received on Mon Aug 12 2019 - 04:30:02 PDT
