Re: AMBER: Trajectory file

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Wed, 9 Jun 2004 14:19:36 -0700 (PDT)

> I'm trying to make a pseudo trajectoryu file from a number of pdb files. I
> know how to combine them and output the "crd" file in Carnal, byut I
> realizr that I have to superimpose the structures. Is there a way to do
> thatin ptraj or Carnal, or do I habve to generate by hand the superimposed
> structures, before inputing them into Carnal?
>
> It looks as if one can use FIT in Carnal to superimpose a structure on
> reference structure, if one calculates, for instance, RMSD - but I'm not
> sure how to save the fitted structures and hopw to write them out.

If carnal, just treat the FIT rmsid as the streamid for the
OUTPUT COORD.

Bill
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Received on Wed Jun 09 2004 - 22:53:00 PDT
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