Hi,
Just to add a bit to Jason's response:
On Tue, Mar 26, 2013 at 5:54 AM, Jason Swails <jason.swails.gmail.com> wrote:
> In my opinion, it's an inadequacy of using the LCPO method to calculate
> these kinds of surface areas (i.e., decomposed surface areas). Obviously
> the SAs should never be negative, and the fact that they are is simply an
> artifact of the P1, P2, P3, and P4 fitting parameters of LCPO. The method
> was parametrized to calculate total surface areas, so it doesn't
> necessarily surprise me that it doesn't work well when decomposed like this.
What 'surf' is reporting here are the selected atoms *contribution* to
the overall LCPO surface area. Atoms that are more buried tend to have
low or negative values in the LCPO method, which of course is a very
rough approximation (certainly only good for qualitative analysis).
> 2. Why there is a huge difference between 'surf' and 'molsurf' SASA
>> outputs? (-9.497 vs 139.179)
>>
>
> Because I believe that the molsurf method does _not_ calculate a decomposed
> surface area. That is, the surface area of a mask is calculated as though
> no other atom exists. You can verify this by comparing the output of:
Jason is correct here. The 'molsurf' command treats selected atoms as
being isolated and is not currently decomposable.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Mar 26 2013 - 08:00:04 PDT
