Hi,
I am going through a tutorial of relative binding energy calculation between
benzene and phenol (
http://ambermd.org/tutorials/advanced/tutorial9/setup.html)
I am using the exact protocol for generating topology and coordinate file
for benzene molecule....the %FLAG radii is having different radii value for
water molecules.
My values are coming out to be 1.50000000E+00 8.00000000E-01
8.00000000E-01 for O-H1-H2 ....where as the topology file present in the
tutorial are having different values..ie...1.50000000E+00 8.00000000E-01
1.20000000E+00 for O-H1-H2...
I did not understand why the two hydrogen's of water molecule should have
different radii..?
Kindly suggest...as because of this difference my results are varying a lot
while vdw decoupling step.
Thanks in Advance
--
--
SUNITA GUPTA
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Received on Fri Aug 13 2010 - 06:00:06 PDT
