On Mon, Apr 11, 2005, Kenley Barrett wrote:
> I am in something of a circular
> predicament in that I need to know the coordinates of the added
> protons so that I can run the file through GAMESS to find the
> electrostatic point charges...
The problem of figuring where protons are in a general organic molecule is
a difficult one, and there is no general solution in the Amber suite of
programs. You can build them by hand in LEaP, and then clean them up using
the "relax selection" option. Or, if you are feeling lucky, you can use the
"add H and build" option in LEaP, starting from a structure that is missing
protons. Be prepared to backtrack, since LEaP doesn't always make the best
choices. But that may get you close enough to allow GAMESS to optimize the
geometry for you.
You might ask here or on the CCL whether people know of better solutions.
....good luck...dac
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Received on Tue Apr 12 2005 - 02:53:00 PDT
