VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Wed Apr 13 2005 - 00:52:34 CDT

dear Kos,

> I'm interested to post-process with VMD
> and to calculate
> - dihedral (main chain phi/psi) values
> time-series and ave/sd
> - g(r) for the salt distributions relative
> to charged sites of a protein
i cannot help you with the first one, but i've recently finished set of
scripts that can be (among other things) used for getting the
distribution of residues of given type around protein (or anything that
can be represented by selection in vmd). these should be available in
the vmd script library soon, however if you need it quickly, please let
me know and i will send it directly to you.
this is something different than g(r), but g(r) in my opinion can be
used (correctly) only for distribution of objects consisting of single
particle. you can get something similar, if you take the distribution
plot and calculate differences...

regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
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