Re: [AMBER] cpptraj surf

From: Daniel Roe <>
Date: Fri, 24 Aug 2012 08:37:37 -0600


On Fri, Aug 24, 2012 at 7:22 AM, George Tzotzos <> wrote:
> In terms of the ligand, the above matches what has been reported in the literature (ligand effectively buried). I have difficulties interpreting the situation with the protein. I would expect that the proteins SASA during the time evolution of the trajectory would be less than that of the apoprotein.

To me, it doesn't seem unreasonable that the SASA of the complexed
protein is greater than that of the protein by itself. It could be
that there are some subtle conformational changes that occur in the
protein upon binding that result in it having a larger SASA overall.

One thing you could try would be to calculate the surface area with
the 'molsurf' command instead, which gives the more accurate Connolly
surface area ('surf' uses the LCPO algorithm) and see if the trend
still holds.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Aug 24 2012 - 08:00:05 PDT
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