[AMBER] angle between DNA (vector) and a plane

From: Taufik Al-Sarraj <taufik.alsarraj.utoronto.ca>
Date: Thu, 15 Apr 2010 13:04:14 -0400


Please forgive me if this has already been addressed.

1. Can i use the vector function in amber (ptraj) to describe single or
double stranded oligonucleotide? (eg if i have a 10-mer ssDNA the
command can be vector A ':2-12')

2. is there a function in ptraj that can be used to define a plane by
using three atoms? (e.g. plane A ':1.x1' ':1.x2' ':1.x3')

3. Finally, can i calculate the angle between a vector and a plane (e.g.
Angle abc vectorA planeA outfile time)

a script can be written to calculate this for a specific coordinate,
there is a thread in 2007 by Ilyas Yildirim that discusses this. But i
really wish to get this angle calculated over a trajectory, preferably
using ptraj.

in the time correlation section of ptraj there is a vector command
defined by two atoms, can this command be extended?


vector DNA :2-12.CA or vector DNA :2-12
plane SUR ':1.x1' ':1.x2' ':1.x3'
angle DNA SUR abc.dat time 10

Many thanks,

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Received on Thu Apr 15 2010 - 10:30:02 PDT
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