Hi,
Without knowing more details about your calculation (what molecule,
what was the input to cpptraj, etc) I can only hazard a guess.
Obviously a negative surface area has no meaning, but remember that
the LCPO surface calculation that cpptraj performs is only a rough
approximation, and as far as I know there's nothing explicit in the
equations to prevent negative surface areas from resulting. If you're
attempting to calculate the surface area of only a fraction of the
molecule (i.e. you're using an atom mask to specify only part of your
solute) and that region is buried it's possible you could get a
negative number.
Of course, there could also be a bug in the code. If you are willing,
could you send me a topology file, cpptraj input, and at least 1
coordinate frame (preferably an Amber restart file or PDB) that
reproduces the negative surface area so I can look into it? Thanks!
-Dan
On Sun, Jun 5, 2011 at 11:30 PM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers,
>
>
>
> Thank you for kind support every time.
>
>
>
> I have a question for using surf command in cpptraj module.
>
> When I used it, negative SASA values were returned for a case.
>
> What do they mean, physically or numerically?
>
>
>
> Sincerely yours,
>
>
>
> Ikuo Kurisaki
>
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>
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Received on Sun Jun 05 2011 - 21:00:04 PDT
