Subject: Re: CCL:Diameter of a globular peptide

From: [email-masked] (Don Gregory)
Date: Fri, 15 Dec 1995 08:21:04 -0500

In response to S.Shapiro's note about calculating the theoretical diameters
of globular peptides, and Per-Ola Norrby's response:

>
>        Of course, you could spend a couple of thousand CPU hours on
>molecular dynamics runs and average....
>

My guess is that the real quantity being sought, is the radius of gyration.
There are a number of tools that can be used to calculate this for
any system, even a protein; for example Quanta does so.
If one has a very elongated system, and one is interested in
the orthogonal components of the general r.g, I would recommend using
the "coor orient mass" command of CHARMm.
This procedure not only orients the molecule with the major moment
along the x axis, secondary moment along y etc. but also prints out
these moments.
Don Gregory
Protein Product Manager : Biosym/MSI