sending a gaussian input demonstration (on a simple watermolecule) + some descriptions
about parameterization in general.
!declare checkpoint (restartfile), number of processors, memory etc
!declare method, basis, type of calculation
!blank line
!then comments
!blank line
!charge and multiplicity i.e. (2S+1) and S=N/2 where N = 0,1,2 ...
!(look in text-book if you don't know what spin multiplicity is)
!define initial coordinates: Z-matrix or Cartesian coordinates
!blank line
!END
!blank line
!SAMPLE INPUT WATER / JOHAN BREDENBERG 2004
--------------------------
%chk=/scratch/wat.chk
%nproc=1
%mem=80MW
%NoSave
#p HF/6-31G* SCF=tight opt pop=MK iop(6/33=2) iop(6/42=6)
optimize water at the HF level of theory with 6-31G* basis
and calculate electrostatic potential with the Merz-Kollmann scheme.
Use output for input in antechamber
0 1
O1
H1 O1 r1
H2 O1 r1 H1 a1
variables:
r1=0.98
a1=104.5
END
---------
END SAMPLE INPUT
!Now run antechamber to get amberadapted charges:
antechamber -i water.log -fi gout -o water.prep -fo prepi -c -resp -s 2
!For further parameterization i.e. bond angle and stretching constants,
!Lennard-Jones parameters you'll probably have to clone existing parameters
!for atom types in the parameter-files, or dig in the literature for experimental
!data. This requires a lot of trial-and-errors, experience,
!and some knowlegde about chemistry in general.
!Have fun & good luck