AMBER Archive (2007)

Subject: AMBER: atomicfluct

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sun Feb 11 2007 - 23:45:40 CST

Dear All,

I could like to calculate the atomic fluctuation per residues for a
protein-DNA complex.

It seems to me that I could use the following command line in ptraj for this
purpose:

atomiclfluct out test_mdcrd.apf @C, CA, N byres bfactor

However, I cannot find the results for DNA residues, and the unit of the
atomic fluctuation is not known, as it is very large. What is the unit for
the y-axis? Can I convert them into A unit instead?

Did I do anything wrong here? Could you mind to instruct me how to improve
the command lines used?

Best regards,

Catherine

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