Hi Harry,
You could always write a script that does this automatically through ptraj.
I've attached an example that I've written in Python, though it prints all
of the data for each phi/psi dihedral of a specific residue to a separate
file (so a ramachandran plot can be plotted for each residue over the course
of the whole simulation).
Hope this helps,
Jason
On Fri, Sep 24, 2010 at 7:07 AM, Harald Lanig <
harald.lanig.chemie.uni-erlangen.de> wrote:
> Dear amber users,
>
> within ptraj there is the functionality of extracting dihedral angles by
> explicitly stating the 4 necessary atoms. Is there also an easy way of
> getting the phi and psi angles of a complete protein? I want to avoid to
> define all angles of a 200 residue protein manually:-)
>
> Any hint is highly appreciated!
> -Harry
> --
> ------------------------------------------------------------------------
> Dr. Harald Lanig Universitaet Erlangen/Nuernberg
> Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen
>
> Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de
> Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig
> ------------------------------------------------------------------------
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 24 2010 - 06:30:04 PDT
