AMBER Archive (2004)

Subject: Re: AMBER: Trajectory file

From: Bill Ross (
Date: Wed Jun 09 2004 - 16:19:36 CDT

> 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

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