AMBER Archive (2009)

Subject: [AMBER] ptraj (vector and corrplane)

Date: Fri Apr 10 2009 - 19:45:46 CDT


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
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,


AMBER mailing list