AMBER Archive (2004)

Subject: AMBER: Trajectory file

From: Joseph Nachman (
Date: Wed Jun 09 2004 - 14:22:45 CDT

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 Nachman				Department of Biochemistry		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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