This is just how the LCPO algorithm is implemented; you can sort of
think the of the hydrogens as being included within the radii of the
heavy atoms. LCPO is a very approximate algorithm anyway - you may
want to try the 'molsurf' command in cpptraj which uses a more
accurate Connolly-type surface area calc. Try with either the default
settings or set the probe radius to 0 and specify an offset of 1.4.
-Dan
On Wed, May 9, 2012 at 8:33 PM, Sidney Elmer <paulymer.gmail.com> wrote:
> Hi,
>
> Is there a reason that hydrogen atoms are not included in the calculation
> of surface area using the "surf" command in cpptraj? I would like to
> calculate the exposed surface area of the peptide hydrogen, which should
> correlate with hydrogen/deuterium exchange rates of that hydrogen. But
> since hydrogens are not included, the best I can do is measure the exposed
> surface area of the peptide nitrogen, but I'm not convinced that will give
> me the answers I'm looking for. Any insights would be appreciated.
>
> Sid
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Received on Wed May 09 2012 - 18:00:04 PDT
