Try using X-ray data structures from on-line databases (
http://www.ccdc.cam.ac.uk/products/csd/ ) or even a PDB file that has Fe
atoms in it and use the bond, angle and dihedral distances for your own
parameters. Thats a start.
Hope it helps.
Good luck,
Rodrigo.
2010/10/9 juan zeng <azengjuan.gmail.com>
> ok ,thank you very much.But where can I get the bond length of FE atom with
> other atom and angle and so on.
>
> 2010/10/9 case <case.biomaps.rutgers.edu>
>
> > On Sat, Oct 09, 2010, juan zeng wrote:
> >
> > > 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.
> >
> > ...good luck.....dac
> >
> >
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Received on Sat Oct 09 2010 - 11:00:02 PDT
