AMBER Archive (2009)

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

From: Jordan Monnet (
Date: Wed Jul 15 2009 - 17:56:12 CDT


This ptraj input will convert you trajectory to pdb files:

trajin traj
image origin
trajout traj.pdb pdb nobox

You will get traj.pdb.1, traj.pdb.2 etc...

* Myeong Lee ( wrote:
> 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
> _______________________________________________
> AMBER mailing list


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