From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Apr 21 2007 - 17:31:53 CDT

On Sat, 21 Apr 2007, Patrick Redmill wrote:

PR> Hi all,
PR> I have a troubling problem that I think some of you may be able to help
PR> me with. I am using SASA to measure, well, the sasa of various caged
PR> particles (like fullerenes). For open ended nanotubes, I want to pick
PR> the size of my probe radius that will reflect the ability (or
PR> inability) for a solvent to go inside the pore. In short, if it's a
PR> thin tube, the probe shouldn't fit inside, if it's a fat one, it
PR> should.

patrick,

i don't think that (ab-)using SASA is a good method for this problem.

i'd rather determine the radius of the nanotube and then try to find
a measure for the diameter of the molecule that has to (not) fit into
the nanotube. for that to be implemented easily, you have to make some
assumptions about the shape of the solvent (more spherical, cylindrical,
disc-like), compute the moment of intertia and then find the diameter
along the proper molecular axis. i expect that you also have to make
some assumptions about how much space you can allow between the
(classical) coordinates of the nanotube and the solven (and how
deformable or flexible its (electron) structure is).

hope that helps,
    axel.

PR> My problem is that I don't see the expected changes in sasa when I
PR> fiddle with my probe size. Intuitively, you'd think smaller probe size
PR> = more solvent accesiblr area. However, when I choose srad = 1.4, I
PR> get:
PR>
PR> 1742.80004883
PR>
PR> Alternatively, when I chose srad = 2.2, I get:
PR>
PR> 1912.75878906
PR>
PR> Obviously, my idea of what srad is, is incorrect, OR I'm setting up the
PR> calculation wrong. For completeness, here are the commands I used to
PR> execute the calculation.
PR>
PR> set var [atomselect 0 "name C"]
PR> $var set radius 1.95 (changing the atomic radii to suit my ff here)
PR> measure sasa 1.4 $var
PR>
PR> Thanks!
PR>
PR> ~Patrick
PR>
PR>
PR>
PR>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.