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 - 03:00:03 PST
