Jennifer,
I recommend leaving the envelope radius at 10. It is used to define the
outer limits of the molecule, thus defining what the openings of the
cavities look like. Feel free to try different settings, though.
As for the probe radius, we just borrow 1.4 or 1.2 from the protein
literature. It's certainly an approximation. I'm not aware of any other
probe radius definitions.
Bob Hanson
On Mon, Oct 6, 2008 at 6:17 AM, Jennifer Williams <
[EMAIL PROTECTED]> wrote:
>
>
> Hi Users,
>
> I want to use the isosurface cavity command to look at the cavities
> available within my structure (a mesoporous silica) to CO2 and other
> small gaseous molecules. My question is: what should I use as a
> realistic probe radius?
>
> In my modelling I simulate CO2 as below:
>
> name epsilon sigma
> O_CO2 1.10765301 2.9847
> C_CO2 0.000 0.000
>
> Is there a formula for determining the probe radius so it can
> represent the CO2 molecule as my simulation "sees it" i.e using the
> Lennard Jones parameters? I have seen from some internet searching
> that water is represented by a probe radius of 1.4. How was this
> determined? Is there a list of species with their probe radii for Jmol?
>
> Also I suppose the envelope will also influence the final result of
> the cavity search. Is 10 a reasonable value?
>
> Thanks
>
> Jennifer
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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