Hi Dachuan,
The message should be fairly clear. You have the incorrect number of
electrons specified for your QM region. This means you specified the charge
of your QM system incorrectly. You have it set to +6 which gives you an odd
number of electrons. I suggest going through your QM region specification
carefully and counting the number of electrons along with the nuclear
charges (number of protons) to calculate the correct charge for your QM
region. Be careful here because if you get this wrong (say just set it to
+7) the code will run but your system will be in some kind of weird
ionization state.
Note this is same approach you would have to do for any QM code, say
Gaussian for example, where you have to set charge and spin state.
All the best
Ross
> -----Original Message-----
> From: Dachuan Guo [mailto:dcguo.hust.gmail.com]
> Sent: Monday, April 18, 2011 6:57 AM
> To: AMBER.ambermd.org
> Subject: [AMBER] SQM
>
> Hi all,
> I got a problem when I used SQM to calculate charges of a protein. I
> got
> these messages from output file *mdout:*
> QMMM: System specified with odd number of electrons ( 2697)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.
> How could I deal with the error？
> the input file:
> &qmmm
> qm_theory = 'PM3',
> qmcharge = 6,
> ! SCF settings
> scfconv = 1.0d-8, ! kcal/mol
> errconv = 1.d-02, ! au
> tight_p_conv = 0,
> diag_routine = 1,
> itrmax = 100,
> ! Geometry optimization settings
> maxcyc = 0,
> grms_tol = 0.02, ! kcal/(mol*A)
> ! Output
> ntpr = 101,
> verbosity = 0,
> /
> 7 N 19.375 -10.157 -8.443
> 1 H1 19.512 -9.748 -9.356
> *************************************
> The pdb file used here was generated by *tleap *and *ambpdb *in order
> to add
> H atoms and other missing heavy atoms*, *and the value of qmcharge was
> calculate by pdb2pqr.
>
> Thanks,
> Daniel
> --
> Dachuan Guo
> ------------------------------------------------------------------
> Biomolecular Physics and Simulation Group, Department of Physics,
> Huazhong University of Science and Technology, Wuhan 430074, Hubei,
> China
> Tel：86-27-87558335-606
> ------------------------------------------------------------------
> Chinese Version:
> ------------------------------------------------------------------
> 郭大川
> 华中科技大学物理学院 生物分子物理与模拟研究组
> 湖北省武汉市洪山区珞瑜路1037号
> 邮编：430074
> 电话：86-27-87558335-606
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Received on Mon Apr 18 2011 - 09:00:11 PDT
