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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
*

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:

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

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

'dotangle' keyword.

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

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