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
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 12 2019 - 02:00:02 PDT
