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 - 00:30:02 PDT
