AMBER Archive (2002)

Subject: Re: carnal output trajectory

From: Francesca Mocci (francy_at_mvcch3.unica.it)
Date: Fri Nov 01 2002 - 10:53:31 CST

you can also visualize with vmd the traj without box information:
 edit the parm file and change the "IFBOX" parameter to 0
(for amber 5 parm file format see
http://www.amber.ucsf.edu/amber/doc6/html/AMBER-sh-20.html#sh-20.1)

Hope this helps you,
Francesca

> On Wed, 30 Oct 2002, Vlad Cojocaru wrote:
>
> 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 

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Francesca Mocci
Dipartimento di Scienze Chimiche
http://www.unica.it/~segscchi
Universita' di Cagliari
e-mail: francy_at_mvcch3.unica.it
Phone: +39 070 6754362
Fax:   +39 070 6754388

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