Hello. After a long discussion on the parameterization of an active
site containing zinc and a hydroxyl molecule
(
http://archive.ambermd.org/201205/0452.html), I've started
parameterization of the same active site, but this time with the water
molecule instead of a hydroxyl bound to zinc. Everything seems to go
ok, including gaussian calculations, but once I get to the creation of
the xml files and after that, to the creation of the prep file, I see
that the charge distribution is nothing like I would expect. The
procedure places 0 charge on the zinc atom, 0 charge on the oxygen
(water) atom and very small charges on the water hydrogen atoms.
Furthermore, I've checked with the ZAFF xml files distributed with the
original paper, and the charges are very different than the ones they
got. The charges are very different than the ones on the ESP fit in
the gaussian output file. Could it be something with the espgen or
respgen routines as written in the getcharges.sh file?
The ESP CHARGES calculated by gaussian are : (O, H and H are the atoms
that form the water molecule).
Zn 0.85630372D+00
O -0.94007825D+00
H 0.50049376D+00
H 0.41322947D+00
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Received on Tue Jul 31 2012 - 13:00:03 PDT
