Thank you much. I find it
2014-08-20 19:41 GMT+08:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, 2014-08-20 at 10:31 +0800, 闫玉娜 wrote:
> > Hi all,
> > I have a small molecule named 'HEM'. I want to use antechamber to build
> its
> > parameters. I use the command 'antechamber -i HEM_ideal.pdb -fi pdb -o
> > hem.mol2 -fo mol2 -c bcc -s 2 -nc 0'.But there are errors as follows:
> >
> >
> > “Running: /home/yanyuna/Programs/amber11/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> >
> >
> > Running: /home/yanyuna/Programs/amber11/bin/atomtype -i
> ANTECHAMBER_AC.AC0
> > -o ANTECHAMBER_AC.AC -p gaff
> >
> > Total number of electrons: 305; net charge: 0
> > INFO: Number of electrons is odd: 305
> > Please check the total charge (-nc flag) and spin multiplicity (-m
> > flag)
> >
> > Running: /home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
> > Error: cannot run "/home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in
> -o
> > sqm.out" of bcc() in charge.c properly, exit”
> >
> > I have attached its structure file. How can I solve it? Thank you
>
> Amber error messages do not get much clearer than this. You requested a
> QM calculation telling antechamber that the net charge was zero and the
> multiplicity was 1. When the net charge is 0, then the number of
> electrons is the same as the number of protons -- in this case 305. It
> is impossible to have a singlet with an odd number of electrons, so you
> get this error.
>
> What's more is that no charge method that uses a semi-empirical
> Hamiltonian (like am1-bcc) can handle open-shell systems (like your
> iron-containing Heme complex is). So you can't use antechamber unless
> you first compute the electrostatic potential with Gaussian and ask for
> "resp" charges.
>
> Alternatives are: look to see if your Heme complex has already been
> parametrized (search for "amber heme" in Google and you will get lots of
> hits). Use MCPB or R.E.D. to derive charges and force field parameters.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Aug 20 2014 - 05:30:04 PDT
