AMBER Archive (2002)

Subject: RE: Mutations - Molecular Dynamics

From: William Wei (william_at_phm.utoronto.ca)
Date: Mon May 27 2002 - 10:21:04 CDT

Thanks for the replies of Anton, Bill, and Case. Here is my understanding of
mm_pbsa: It take the dynamics trajectory of one protein, mutate one (or
more) residue(s), then calculate the affinity or some other features. The
trajectories of the mutated protein backbone keep unchanged. Is my
understanding right?

Anton: I am interested in what you said. I want to know the backbone
trajectory differences between natural and mutated ones. Could you please me
more details about the GB method (is that GBSA?). Thank you very much.

William Wei.

-----Original Message-----
From: Anton B. Guliaev [mailto:anton_at_vostok.lbl.gov]

you can take a look at GB method (by David Case) which should save you some
time.
THe first thing i would do to compare the wild type with the mutant is to
claculate RMSD values for
the different parts of the protein, including the backbone (carnal should do
a good job).