# Re: [AMBER] principal axes calculation in ptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 20 Aug 2014 08:11:37 -0600

Hi,

On Wed, Aug 20, 2014 at 1:45 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> okay...so can we assume that X vector represents eigenvector with largest
> eigenvalue and Z with least??

Yes, this is how 'vector principal' works in cpptraj.

> If i want to calculate angle between two X vectors (of different subsets of
> residues), can that be done using simple vector algebra (dot product
> method?)

Yes, see the 'vectormath' analysis command. You probably want the
'dotangle' keyword.

-Dan

>
> Thanks
>
>
> On Tue, Aug 19, 2014 at 8:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Yes, the principal axes of coordinates are calculated as the
>> eigenvectors resulting from diagonalization of the mass-weighted
>> covariance matrix for the specified set of XYZ coordinates.
>>
>> Crankshaft analysis is essentially looking for anti-correlated motion
>> between two data sets. In cpptraj the 'crankshaft' analysis is really
>> primarily intended to look at crankshaft motion of distances and
>> dihedrals (and more specifically dihedrals in DNA), not vectors (I
>> realize this is not documented, sorry; I will need to correct this).
>> For example, in DNA the alpha/gamma pair of torsions usually moves in
>> an anti-correlated fashion.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Tue, Aug 19, 2014 at 3:12 AM, Asmita Gupta <asmita4des.gmail.com>
>> wrote:
>> > Dear users,
>> >
>> > I have a protein of 974 residues. I want to calculate principal axes for
>> a
>> > set of residues using principle command in ptraj. This is my script:
>> >
>> > trajin ../../frun.crd 1 last 3
>> >
>> > center :1-974 mass origin
>> > image origin center familiar
>> >
>> > vector v1_h1 principal x out pa1_h1.dat :1-35.CA
>> > vector v2_h1 principal y out pa2_h1.dat :1-35.CA
>> > vector v3_h1 principal z out pa3_h1.dat :1-35.CA
>> >
>> > vector v1_h2 principal x out pa1_h2.dat :40-60.CA
>> > vector v2_h2 principal y out pa2_h2.dat :40-60.CA
>> > vector v3_h2 principal z out pa3_h2.dat :40-60.CA
>> >
>> > crank angle v3_h1 v3_h2 out ang_h1h2_v3.dat results outz_v1_2.dat
>> >
>> ------------------------------------------------------------------------------------
>> >
>> > I want to ask how this axes calculation is done in AMBER? As in Gromacs,
>> > this kind of calculation involves doing a PCA of the subset of residues
>> and
>> > generating axes vectors. Is the same method followed in AMBER??
>> >
>> > How does X,Y and Z vectors are determined??
>> >
>> > What is the meaning of "crank" angle between two vectors (i referred the
>> > manual, but couldn't understand the meaning...).
>> >
>> >
>> > Thank you
>> >
>> >
>> > Asmita
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> 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

```--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Wed Aug 20 2014 - 07:30:02 PDT
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