Hi Ross,
Thanks for your advice, I found that tleap added OXT atom to the end of
the pdb file and -1 charge was added to the system, which may cause that
error.
Thanks,
Dachuan
2011/4/18 Ross Walker <ross.rosswalker.co.uk>
> 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
> > -------------------------------------------------------------------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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>
--
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 - 23:00:02 PDT
