I think you misunderstand the problem.
What you really see is the finite representation of floating numbers
and the associated problem in rounding. As far as I can see the
antechamber toolchain writes charges with six digits which means that
those figures have already been subject to rounding (or truncation).
Summing up all partial charges may thus not result in an integer charge.
Sander and pmemd will however neutralise any non-zero charges. As long
as this non-zero charge is "small" that should be no problem. If you
still feel that your total charge deviates too much you can
redistribute the charges and write to "higher" precision.
Alternatively, you could modify the antechamber code to write out in
higher precision. But neither changes the nature of the problem.
On Mon, 7 Mar 2016 16:00:44 +0530
SHAILESH KUMAR <shaile27_sit.jnu.ac.in> wrote:
> Hello All,
>
> I am working on a series of small molecules (8) experimentlly know to
> bind to a kinase receptor, I want to prepare these molecules for
> simulation. But while preparing I noticed that AM1-BCC charges
> generated with antechamber suit, Net charge is not an integer
> multiple of 1e, but it is like 0.001e, 0.002e on different small
> molecules, But as we know to be able to use PBC for simulation we
> need to have 0 charge on system, hence fractional Net charge is
> problematic. So, can anyone suggest me ways to adjust charges to get
> rid of fractional charge.
>
> In the mean while I thought, probably this issues is due to
> semi-empirical nature of charge generation method, So I tried running
> gammes with RHF-6-31G(d,p) level of theory with parameters:
>
> ________________________________________________________________
>
> $CONTRL ICHARG=0 MPLEVL=0
> RUNTYP=OPTIMIZE SCFTYP=RHF EXETYP=RUN
> MULT=1 UNITS=ANGS MAXIT=200
> ! INTTYP=HONDO QMTTOL=1.0E-08 ITOL=30 ICUT=20
> COORD=CART $END
> $SCF DIRSCF=.T. CONV=1.0E-08 $END
> $SYSTEM MWORDS=96 MEMDDI=480 $END
> $STATPT NSTEP=200 OPTTOL=1.0E-06
> HESS=CALC IHREP=10 $END
> $FORCE METHOD=ANALYTIC VIBANL=.F. $END
> $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=0
> DIFFSP=.F. $END
> $GUESS GUESS=HUCKEL $END
>
> __________________________________________________________________
> then tried generating RESP charges with RED-III.52-Tools but again I
> noticed in case of two of the 8 molecules, there were hydrogens which
> had partial negative charges, which makes me suspicious about such
> RESP charges thats why I thought It is better to proceed with AM1-BCC
> charges. But with AM1-BCC I have above stated problem. Any
> advice/suggestion in this regared is greatly appreciated.
>
>
> Thanks in advance
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Received on Mon Mar 07 2016 - 03:00:04 PST
