ok, thank you very much,I will follow your suggestion.
2010/10/11 FyD <fyd.q4md-forcefieldtools.org>
> Dear Juan Zeng,
>
> >> Firstly I use the command"antechamber" to obtain the
> >> gaussian input file(ligand.gjf),then make optimization and calculate the
> >> single-point energy.Finally I want to use the output
> file(ligand_esp.log) of
> >> calculating the single-point energy to get the ligand.prepi and
> >> ligand.frcmod file.But I get the wrong ligand.prepi file which has no
> the
> >> parameter of FE atom .
> >
> > Antechamber doesn't handle transition metals. You can use the procedure
> > you followed to get started, but plan to do some hand-editing at the end.
> > I'd recommend using the mol2 format, rather than prepi, since it is
> easier to
> > edit.
>
> You can use the R.E.D. Tools or R.E.D. Server to generate your FF
> library for heme since R.E.D. handles chemical elements up to Bromine.
> May be the R.E.D. Tools is even the best bet in a first approach...
>
> For heme, you need to know which QM theory level you are going to use.
> Then, you need to know how to build a molecular fragment so that you
> can include your heme in your protein.
> Finally, be prepared to run many time-consuming QM jobs.
>
> You should find many pieces of information by starting from the
> tutorials . q4md-forcefieldtools.org
>
> regards, Francois
>
>
>
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Received on Mon Oct 11 2010 - 04:00:02 PDT
