AMBER Archive (2009)

Subject: [AMBER] Can I get the torsion angle between base-pairs using ptraj ?

From: Myeong Lee (wnagne_at_gmail.com)
Date: Wed Jul 15 2009 - 16:51:02 CDT

Dear Amber users:

I want to get the torsion angle between base-pairs (or two planes defined by
DNA bases) from the MD trajectory, so that I can see how the torsion angle
changes with time. Can ptraj do that?? I think maybe not because I should
be able to define plane in ptraj. The other option is to obtain pdb file
(or rst file -- then I can convert into pdb) for each time step from
trajectory, then I can write a simple code and shell script to obtain
torsion angle for each time step. Can you please help me what's the best
way to do this? Many thanks!!

- wnagne
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