AMBER Archive (2002)

Subject: Re: carnal output trajectory

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Wed Oct 30 2002 - 07:50:19 CST

Le Mercredi 30 Octobre 2002 14:25, Vlad Cojocaru a écrit :
> Dear Amber users,
> I found out that OUTPUT COORD option in carnal has an option BOX which
> is not written in the manual.
> With this option I managed to output trajectories in a proper way for
> visualizing them with VMD.
> Now the question is that I want to see the trajectory after fitting
> all the structures to the first frame.
> The BOX option seems not to work anymore when I give to carnal the
> following:
> DECLARE
> GROUP g1 (RES 1-17);
> IMAGE img g1%cmass;
> RMS fit1 FIT g1;
> OUTPUT
> COORD crd fit1 BOX;
> The program gives an error message that tells me that the BOX option
> does not work with fit. If I do not use the BOX option the trajectories
> are again impossible to visualize with VMD.
> Does anyone have any suggestions about this??
> Thanks a lot!
> vlad

Use vmd 1.8a28 and see if the option crd or crd box solves your problem.
Stef