Re: [AMBER] antechamber

From: Jason Swails <>
Date: Wed, 20 Aug 2014 07:41:36 -0400

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
> 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 -o sqm.out
> Error: cannot run "/home/yanyuna/Programs/amber11/bin/sqm -O -i -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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 05:00:02 PDT
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