Re: [AMBER] Principal Axis

From: Daniel Roe <>
Date: Fri, 16 Jan 2015 11:09:10 -0700


On Fri, Jan 16, 2015 at 3:01 AM, Karl Kirschner <> wrote:
> calculations. The structure of both clusters is the same, but they differ
> in their input coordinates and in the ordering of the TP3 water residues -

Just to make sure I'm understanding you correctly, you mean that the
relative positioning of each water with respect to each other water is
the same in both clusters, correct? Did you ascertain this visually,
or by some other method (not doubting you, just curious)?

> Using cpptraj (fully patched AmberTools14), I then compute the principal
> axes of each cluster. I expected that I obtain the same results. Instead if
> I view the resulting principal axes, overlayed with the output cluster
> structures (as obtained from the dorotation keyword), I see that the axes
> are indeed identical, but the clusters are offset. I have also tried the
> "origin" keyword (both before and after the principal command) to help
> correct the structures' offset, but this doesn't change the final
> coordinates within the mol2 file. As seen in the image, the 4mer-2 has two
> of its principal axes pointing directly at hydrogen atoms, while the 4mer-1
> has the same two axes pointing to the center of hydrogen bonds.

The 'center' command should only be necessary prior to the rotation
from 'principal'.

> I would appreciate if someone could point out if I have made an error in
> my input or in my thinking. My only guess(!) is that perhaps something is
> going wrong with dorotation within the principal command.

Nothing appears wrong with your input at first glance. One thing to
try is to use the 'out <filename>' keyword of the 'principal' command
to ensure you're indeed getting the same eigenvectors (althought the
'principal' and 'vector' commands use the same code for calculating
principal axes so it should match). If you would like, send me
off-list the PDBs for each cluster and I can take a closer look.


> Just to be clear, the attached image shows the output structures (eg.
> 4mer-1.mol2) and principal axes (e.g. 4mer-1.x.pdb) as obtained from
> cpptraj, whose input for the 4mer-1 is below. The two clusters would
> overlay perfectly if one did it manually within a molecular viewer - by an
> ~90 degree rotation of the blue cluster.
> trajin 4mer-1.leap.pdb
> center :1-4 origin
> principal :1-4 dorotation mass
> trajout 4mer-1.mol2
> vector v1 :1-4 principal x out 4mer-1.x.dat
> vector v2 :1-4 principal y out 4mer-1.y.dat
> vector v3 :1-4 principal z out 4mer-1.z.dat
> vector v4 :1-4 principal x trajout 4mer-1.x.pdb trajfmt pdb
> vector v5 :1-4 principal y trajout 4mer-1.y.pdb trajfmt pdb
> vector v6 :1-4 principal z trajout 4mer-1.z.pdb trajfmt pdb
> Thanks in advance,
> Karl
> --
> Karl. N. Kirschner, Ph.D.
> Research Associate
> Bonn-Rhein-Sieg University of Applied Sciences
> Grantham-Allee 20, 54757 Sankt Augustin, Germany
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jan 16 2015 - 10:30:06 PST
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