[AMBER] cross angle analysis

From: Antonio Amber Carlesso <antonio.amber.carlesso.gmail.com>
Date: Tue, 24 Mar 2020 13:56:28 +0100

Dear Amber Users,

I performed an angle analysis between two dimer interface defined as any
pair of Cα atoms (example system below)

[image: image.png]

I performed this analysis with four different systems.

Since the systems investigated are rotated to the right and rotated to the
left I was expecting as output (a) positive and (b) negative angles (*i.e.*
for example + 25-30 degrees for right hand and - 25-30 for left hand

Do you have any idea why the value received as output is always positive?

Thank you for the help!

The command line used was:

#Add Modules, etc etc

 module load amber/16.at17


# load prmtop and trajectory

 parm crystal_3FBV_ion_ok.prmtop

 trajin reeim.xtc

#analysis with residue at the interface identify by using Chimera (i.e.
using select > ZONE)

 rms first :1-1687.CA

 vector A corrplane

 vector B corrplane

  vectormath vec1 A vec2 B dotangle out angle_tetramer_YEAST_1.dat



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(image/png attachment: image.png)

Received on Tue Mar 24 2020 - 06:00:02 PDT
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