Hello,
> =>> Treat special parameters
> =>> Calc missing parameters
> =>> Calc delta from raw data
It seems to me that you have an unusual residue that
is not defined in AMBER force field. In that case, I
would suggest that you prepare your parameter-topology
and coordinates files using General AMBER Force Field
which can be called in by typing 'source leaprc.gaff'
in leap.
In that case, I would also recommend that you prepare
a mol2 file for your molecule by antechamber using
GAFF atom types and AM1BCC charges. You could then use
that mol2 file as an input in leap to prepare your
prm/top and crd files.
That is all I can propose to help solve your proplem
looking at your mm-pbsa output. Perhaps, someoneelse
can come up with a better solution.
wishing you a plenty of luck with your reserach.
jenk.
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Received on Tue Nov 01 2005 - 08:53:00 PST
