AMBER Archive (2007)

Subject: AMBER: choice of alpha carbons vs side chains

From: Christopher Gaughan (clgaughan68_at_gmail.com)
Date: Wed Apr 04 2007 - 17:34:31 CDT

Dear Amber community,

I am doing a study of two alpha helices that form a dimer. I am specifically
looking at the distance between four pairs of residues during the course of
a 2ns md study. I use the distance option in ptraj to track these distances.
Theses pair consists of oppositely charged residues (E and K) and are very
close to one another .

My question is this:

if I want to keep track of the distances between these oppositely charges
pairs, do I measure the distance between their alpha carbons, or do I
measure the distance between an atom father out along each of the side
chains such as N zeta of lysine and C delta of of glutamate)? I suspect in
the latter case the variance in position will be greater than those of the
distances between the alpha carbons.

Does anyone have any thoughts on this?

Thanks,
Chris

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