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

Date: Tue, 14 Oct 2014 14:44:30 -0600

Hi,

On Tue, Oct 14, 2014 at 5:25 AM, Asmita Gupta <asmita4des.gmail.com> wrote:

*> This is a very old post from amber mailing list which is apparently
*

*> unanswered..
*

*>
*

*> http://archive.ambermd.org/200107/0059.html
*

This post isn't just old, it's ancient in terms of Amber (13 years ago

we're talking Amber 6)...

*> I have similar doubts as to the the calculation of principal axes in
*

*> cpptraj. Shouldn't the vectors x,y,z be mutually perpendicular to each
*

*> other or align with the coordinate axes of the molecule. I have used
*

*> similar script for calculation but the vectors don't seem to be correct..
*

I did a quick test using benzene (since the original post mentions

using a ring structure) and the results seem fine to me (picture

attached). The picture shows the results after performing 'principal

dorotation' and 'vector principal x' (red), 'vector principal y'

(green), and 'vector principal z' (blue). The structure is aligned and

the principal axes are orthogonal to one another as one would expect.

In cpptraj (as in ptraj before it) the principal axes are (sorted from

largest to smallest eigenvalue) X > Y > Z in both the 'principal' and

'vector principal' commands. Note that this is opposite the usual

convention, which assigns the axis with the largest eigenvalue to Z;

this may have been what confused the original poster. This convention

has been maintained in cpptraj for backwards compatibility.

*> Can you please suggest how can i get the 3 principal axes vectors which are
*

*> aligned w.r.t. coordinate axes..
*

Something like this would work:

parm BNZ.parm7

trajin BNZ.rst7

# Align principal axes to coordinate axes

principal dorotation

# Output rotated structure

trajout rotated.mol2

# Output principal axes vectors as PDB files

vector PX principal x trajout PX.vectraj trajfmt pdb

vector PY principal y trajout PY.vectraj trajfmt pdb

vector PZ principal z trajout PZ.vectraj trajfmt pdb

Hope this helps,

-Dan

*>
*

*> Thanks
*

*>
*

*> Asmita
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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Received on Tue Oct 14 2014 - 14:00:02 PDT

Date: Tue, 14 Oct 2014 14:44:30 -0600

Hi,

On Tue, Oct 14, 2014 at 5:25 AM, Asmita Gupta <asmita4des.gmail.com> wrote:

This post isn't just old, it's ancient in terms of Amber (13 years ago

we're talking Amber 6)...

I did a quick test using benzene (since the original post mentions

using a ring structure) and the results seem fine to me (picture

attached). The picture shows the results after performing 'principal

dorotation' and 'vector principal x' (red), 'vector principal y'

(green), and 'vector principal z' (blue). The structure is aligned and

the principal axes are orthogonal to one another as one would expect.

In cpptraj (as in ptraj before it) the principal axes are (sorted from

largest to smallest eigenvalue) X > Y > Z in both the 'principal' and

'vector principal' commands. Note that this is opposite the usual

convention, which assigns the axis with the largest eigenvalue to Z;

this may have been what confused the original poster. This convention

has been maintained in cpptraj for backwards compatibility.

Something like this would work:

parm BNZ.parm7

trajin BNZ.rst7

# Align principal axes to coordinate axes

principal dorotation

# Output rotated structure

trajout rotated.mol2

# Output principal axes vectors as PDB files

vector PX principal x trajout PX.vectraj trajfmt pdb

vector PY principal y trajout PY.vectraj trajfmt pdb

vector PZ principal z trajout PZ.vectraj trajfmt pdb

Hope this helps,

-Dan

-- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)

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(image/jpeg attachment: BenzenePrincipal.jpg)

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