Dear Professor Case:
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0002,
tight_p_conv=1, scfconv=1.d-10, qmcharge=-1,
/
7 N9 31.5580 25.3660 39.2430
............................
Apparently you are right. I repeated the job, making sure to have inserted
"-m 2". Could that be fixed?
Although I fully agree with your warning about trying to parameterize
organic radicals, I tried to have the antechamber output, on which to
substitute data from the ab initio calculation, as I find it difficult to
build the entire FF without a layout.
The spin density distribution calculated ab initio agrees fairly well with
the EPR spectrum, which is encouraging, although the nonbonded remain
unknown.
thanks a lot
francesco pietra
On Sun, Nov 16, 2014 at 10:20 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Nov 16, 2014, Francesco Pietra wrote:
> >
> > antechamber -fi pdb -i filename.pdb -fo ac -nc -1 -m 2 -c bcc -o
> > filename.ac -pf y -s
> >
> > reports sqm.out
> > QMMM: System specified with odd number of electrons ( 61)
> > QMMM: but odd spin ( 1). You most likely have the charge of
> > QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> > calculation.
> >
> >
> > There are four N-atoms in the small molecule. Two normal tricoord N, one
> > dicoord N with lone pair, one dicoord N with single electron. I could
> > calculate RESP charges and carried out frequency analysis ab initio HF
> > 6-31G* with a qm package, though still interested in the ac file. Can't
> > understand why with 85 electrons, charge -1 mult 2 is said impossible by
> > antechamber. I am at ambertools 12.
>
> Check the sqm.in file: it looks like antechamber might not be correctly
> passing the "-m " flag info(?).
>
> Also note that bcc charges (and the who antechaber typing scheme) are only
> parameterized for closed shell systems. Since you have (or can get) RESP
> charges, those would seem to best way to go. Setting up force fields for
> organic radicals is uncharted territory, certainly for antechamber.
>
> ....dac
>
>
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Received on Sun Nov 16 2014 - 14:00:02 PST
