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#748 12/18/03 04:31 AM
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cao Offline OP
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Dear All,

I want to select all those atom or residue that are right on the surface of a protein, But, I don't know how to do so in CHARMM. Could anybody please show me figure out it? Any tips will be appreciated.
Thanks in advance!

cao

Last edited by cao; 12/18/03 03:29 PM.
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rmv Online Content
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You can use the COOR SURF command described in corman.doc to compute the solvent accessible surface exposure of atoms, and use an atom selection based on that result.

Assuming the protein is segid A, and hydrogens are to be excluded:

coor surf acce sele segid A .and. .not. type H* end
define surfatm sele prop wmain .gt. 2.0 .and. .not. type H* end

You may need to use a different surface area threshhold (2.0 may be too large or small for your application), or perhaps use a larger probe radius to reduce the exposed area for more buried atoms.


Rick Venable
computational chemist


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