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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Wed, 7 Nov 2018 08:54:30 -0500

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

Date: Wed, 7 Nov 2018 08:54:30 -0500

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:

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Received on Wed Nov 07 2018 - 06:00:08 PST

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