AMBER Archive (2009)

Subject: [AMBER] Protein motions comparison

From: Dmitry Osolodkin (
Date: Thu Feb 19 2009 - 05:58:24 CST

Dear All,

I am working on a project dealing with the comparison of closely related
proteins, and my idea is to compare their motions during simple straight
molecular dynamics simulation. The simulation for different proteins is
performed for 6 ns using the identical parameters. The trajectories
obtained are rather similar, but the difference can be observed, for
example, by rmsd value. Nevertheless, some more comparison parameters
are needed, but also needed is advice about their usage. My ideas are as

1. The principal motion of my proteins is the bending of a rather big
elongated domain. So it would be great to measure the angle between the
halves of the domain during trajectory, but I have no idea how to do it.
Is it possible with ptraj?

2. Is it correct to compare eigenvalues or eigenvectors between
different simulations? The proteins differ only by two or three amino
acid residue substitutions per subunit (ca. 400 residues).

2a. Is there any way of visualisation of eigenvectors and porcupine
plots apart from IED and Dynamite? Is it possible (or does it make
sense) to create the projection of the trajectory on the single
eigenvector for further analysis?

Best regards,

Dmitry Osolodkin
Group of Computer Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
Phone: +7-495-9393557
Fax: +7-495-9390290

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