> The molecular surface, (aka the solvent-excluded surface, or SES) as
defined by Connolly and Richards, and implemented in molsurf and many other
codes, includes surface segments that can b
e assigned to a single atom, but also surface segments arising from places
where the probe sphere is in contact with two or more atoms at the same
time. So it's not just a lack of coding
that prevents a per-atom decomposition: one would have to arbitrarily
decide how to assign the latter areas to atoms. And almost any algorithm
one thinks of will lead to some odd behaviors.
------
That's up to the algorithm. Lee & Richards algorithms can be made to slice
each atom instead of the whole protein, thus getting the SAS of each atom.
Shrake & Rupley's algorithm represents the surface of each sphere (atom) as
a set of points so it can also get the SAS of each atom.
I'd love to have the time to volunteer to code these algorithms in cpptraj.
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Received on Sat May 15 2021 - 13:00:02 PDT
