Hi,
On Sat, Jan 28, 2012 at 4:21 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com> wrote:
> The interesting point is that :
> SASAR +
> SASAL = SASAC
>
> 3952.9418 + 2466.6582 = 6419.6000
> Why?
As stated in the AmberTools manual, the surface area calculated by
cpptraj 'surf' reflects the contribution of atoms in <mask> to the
overall surface area, not the surface area of <mask> as an isolated
system, therefore it is expected that the areas of R and L should sum
up to C. You could get SASA of each region by stripping everything
else out prior:
trajin prod1.mdcrd 1 1 1
strip :WAT,:Na+,:Cl-
strip !(:1-56)
surf R :1-56 out sasa.dat
Perform a run like that for each region you want the SASA for. Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Sat Jan 28 2012 - 07:30:03 PST
