[AMBER] principal axes calculation in ptraj

From: Asmita Gupta <asmita4des.gmail.com>
Date: Tue, 19 Aug 2014 14:42:48 +0530

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

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Received on Tue Aug 19 2014 - 02:30:02 PDT
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