Subject: Removing Translation and Rotation after MD

From: Gerald Loeffler <[email-masked]>
Date: Thu, 12 Jun 1997 12:35:08 +0200

Greetings!

I would very much appreciate your comments to the following problem:

I need to remove the translational and rotational motion of a protein
after a Molecular Dynamics simulation.

I know, this is a seemingly trivial problem.

A) Up to now I didn't care much about the details and just fitted all
protein structures along the MD trajectory to the start structure such
that the C-alpha atoms are optimally (i.e., minimal root-mean-square
deviation) superimposed (e.g. using the excellent profit program).

B) However, it may be that for my current problem the other alternative
that came to my mind would be better suited, namely
	1) removing translation by superimposing the centers of gravity
	   of all structures
	and subsequently
	2) removing rotation by superimposing the "principal axes of
	   inertia" of all structures.

Firstly, I'm not sure if the terminology of B)2) is correct.

Secondly, I'm missing the formulas to do B)1) and B)2).

Thridly, I'd like to know if there are cases where either method A) or
method B) are definitely prefered.

Fourthly, it may be that there are other methods of removing translation
and rotation?!

Fifthly, which free program implements method B) or other intersting
methods?

As always, I thank you very much in advance for your help, and I will
summarize to the list if there is some interest in that.

	Cheers,
	gerald
-- 

Gerald Loeffler
PostDoc in Theoretical Biochemistry

EMail: [email-masked]
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