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 - 04:00:01 PDT
