Dear Amber Developers and users,
I'm trying to use pbsa with active site focusing,
Thus restricting space to solve Poisson Boltzmann eq.
By AmberTools 13.
Although I set information of spacial boudary,
by setting xmax, ymax, etc in input file,
"pbsa" did not work only for the active site
But for all space.
(I checked it due to the file size and result:
they were same With no regard to setteing of active site boundary)
I attatched my pbsa input.
I am most grateful if you give me some advices.
e.g. I should have set additional flags in input file.
Yours sincerely,
Ikuo KURISAKI
The pbsa input is below:
Sample PB visualization input
&cntrl
ntx=1,
imin=0,
ipb=1,
inp=0
/
&pb
npbverb=1, istrng=0, epsout=80.0, epsin=1.0,
space=1., accept=0.001,
sprob=1.4, cutnb=0,
phiout=1, phiform=2
xmax=25.00, xmin=20.00,
ymax=33.00, ymin=27.00,
zmax=31.00, zmin=37.00,
/
PS I gave patches already...
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Received on Mon Jul 08 2013 - 06:30:03 PDT
