AMBER Archive (2005)

Subject: Re: AMBER: mesure dihedral angle during MD

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Sun Mar 13 2005 - 12:10:46 CST

Hi, Julien

You can do it with a simple UNIX command awk. Assuming column 2 has the
torsion angle in your ptraj output file,

awk '{if($2 < 0){print $2 + 360}else{print $2}}' _your_ptraj_output_

or

awk '{$2>0?a=$2:a=$2+360;print a}' _your_ptraj_output_

You can replace _your_ptraj_output_ with your ptraj output filename.

Guanglei

julien wrote:
> Dear all,
>
> I tried to measure a dihedral observed during MD simulation using ptraj. The
> value oscillate between +180 and -180. Is it possible to get in the ouput only
> positive values ? Do I have to chnage the source code for that ? If yes how
> since I am not a programmer and I have no knowledge in C...
>
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