AMBER Archive (2004)

Subject: AMBER: Trajectory file

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
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 

-- 
--------------------------------------------------------------------
Joseph Nachman				Department of Biochemistry
nachman_at_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
--------------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu