Re: [AMBER] solvent accessibility

From: German P. Barletta <>
Date: Sat, 15 May 2021 13:41:01 -0600

> 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
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