Subject: Re: CCL:a question about g(r) for heteroatoms

From: Anton Feenstra <feenstra/at/chem.vu.nl>
Date: Mon, 27 Oct 2003 17:50:32 +0100

weiz wrote:
> Dear Sir:
> I have a problem to calculate the g(r) for heteroatoms. the system that I
> am studying is a peptide in DMSO system.now I want to calculate the g(r)
> for the polar H of peptide (which are
[...]

I'm sorry for not having read all of your question in detail, but I thought
I might refer you to existing analysis tools in the Gromacs package.
These are g_rdf for calculating g(r) of arbitrary selections of atoms in
your system, and g_hbond for calculating hydrogen bonds and related
properties. The tools will read concatenated pdb files as trajectory,
which should cover possible output for almost any simulation package you
might (wish to) use. Gromacs if available free of charge (and without
registration) at www.gromacs.org, available in various pre-compiled
binary packages but also as (usually easy to compile) source-code.

-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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