AMBER: Trajectory file

From: Joseph Nachman <nachman.hera.med.utoronto.ca>
Date: Wed, 9 Jun 2004 15:22:45 -0400 (EDT)

Hello all -

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.

Thanks for your help,

Joseph 

-- 
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Joseph Nachman				Department of Biochemistry
nachman.hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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Received on Wed Jun 09 2004 - 21:53:01 PDT
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