From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Mon Oct 02 2000 - 01:07:39 CDT

Hello,

On Mon, Oct 02, 2000 at 12:22:25AM -0500, Justin Gullingsrud wrote:
> David,
>
> Since you're using NAMD, I assume you had some way of generating psf files,
> i.e. either charmm or xplor? Either of these programs would be able to
> modify the structure file to include, say, just the protein.
>
> You could probably do what you want with VMD, but it would be rather
> laborious. Briefly, you could create an atom selection in the text
> console containing only the atoms you want, then write pdb files for
> each time step in the trajectory. After loading each pdb back into VMD,
> you could have VMD write the frames back out as a DCD file.

        Just to clarify, you wouldn't really have to manually save,
say, 500 frames. You'd just have to write the 3 or 4 line tcl script
to loop through the frames, saving each frame with the appropriate
filename (say frame-001.pdb, frame-002.pdb, etc .) Same approach for
reasing the files back in.

                                        Cheers,

                                        Barry

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: barryi_at_ks.uiuc.edu      http://www.ks.uiuc.edu/~barryi