Thanks for the response, Dan. I also looked into using molsurf, but it
didn't look like it gave the contribution of the surface area of <mask> to
the total surface area, like 'surf' does. For instance, if I specified as
my mask ":2.H", it would give me the total surface area of the hydrogen
atom as an independent object, not the exposed surface area within the
protein. Is this correct? If so, is there a way to get the exposed
surface area from 'molsurf'? Thanks for your help.
Sid
On Wed, May 9, 2012 at 5:41 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
