AMBER Archive (2009)

Subject: [AMBER] ptraj (vector and corrplane)

From: taufik.alsarraj_at_utoronto.ca
Date: Fri Apr 10 2009 - 19:45:46 CDT

Hello,

I have a DNA strand on a surface that i would like to analyze using
ptraj. I have not used ptraj before so my question is introductory: I
attached a picture of my system, residues 3-21 are DNA residues and
Residue 1 is the whole surface. I would like to measure the polar
angle between a DNA vector and the surface plane.

i tried
test{
trajin *.mdcrd
trajout *.mdcrd
vector DNA ':3-21@%C' out dna.vector
corrplane Surface ':1@%Si' sur.vector
angle result DNA Surface out result.out
}

> ptraj *.prmtop test

but i got
PTRAJ: vector DNA ':3-21@%C' out dna.vector
Mask [:3-21@%C] represents 23 atoms
Segmentation fault

does this mean vector needs exactly 3 atoms?

Thank you,
Taufik


240ps.jpeg

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