Hi,
Just wanted to follow up and see if this issue was ever resolved.
-Dan
On Tue, Oct 30, 2018 at 8:53 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What version of cpptraj are you using? Using the PDB and input you
> gave me I get a value of 20.6452 deg (see attached output). One thing
> I often find useful when working with the 'vector' command is writing
> the resulting vectors into vector "trajectories" so I can visualize
> them, e.g.:
>
> writedata vecs.mol2 name1 name2 vectraj trajfmt mol2
>
> This will write vector data from vector data sets name1 and name2 to a
> Mol2 file named trajfmt, which can then be visualized using e.g. VMD
> alongside the original trajectory. The name1 and name2 vector data
> sets must of course exist and be populated (so this should be done
> after a trajectory Run). An example of this is in the attached cpptraj
> output.
>
> -Dan
> On Mon, Oct 29, 2018 at 6:35 PM Matthew Turner <TurnerM13.cardiff.ac.uk>
> wrote:
> >
> > Dear AMBER users,
> >
> > I'm looking to calculate the angle between the planes of aromatic
> residues over a trajectory using cpptraj.
> > I've looked through the manual and the mailing list (particularly noting
> http://archive.ambermd.org/201512/0291.html) and found the commands
> needed:
> >
> > vector name1 corrplane <mask1>
> > vector name2 corrplane <mask2>
> >
> > vectormath vec1 name1 vec2 name2 dotangle out name1_name2_angle.dat
> >
> > This calculates the vectors normal to the planes defined by <mask1> and
> <mask2> and then does the inverse cos of the dot product of those two
> vectors.
> >
> > However, the results are not what I expected. I have selected a single
> frame pdb file (attached, zipped) and was looking at the interplane angle
> between His13 and His14 as a test case. In this frame, the residues sit
> nearly parallel - max 20 degrees out of parallel, by eye.
> > Using masks :13.CG,ND1,CD2,CE1,NE2 and :14.CG,ND1,CD2,CE1,NE2 to select
> the aromatic rings of His (rather than the whole residue) and running the
> above commands gives a dotangle value of 127.3200 degrees.
> >
> > Firstly, this is clearly not correct, so where have I gone wrong? And
> secondly, shouldn't the angle between planes should be between 0 and 90
> degrees (as simply explained here: https://youtu.be/C6ElQdRbHaE?t=287),
> or am I missing something? Calculating the dot product of name1 and name2
> above gives -0.6063. If I was to take the modulus of that, arccos(0.6063)
> = 52 degrees, still not the near zero value I expected.
> >
> > Any help appreciated!
> >
> > Kind regards,
> > Matthew Turner
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 07 2018 - 06:00:08 PST
