Here you will find specific NDDO semiempirical parameters developed to model phosphate reactions.
Parameters for H, C, O, P and S atoms have been specifically calibrated to thiolysis and
alcoholysis of phosphate mono and tri-esters, and proton transfers from related thiols, alcohols
and phospho-esters. Further information may be found in PCCP, 8, 347-353, 2006.
Only H, C, O, P and S parameters are distributed. One may try combinations with AM1 or MNDO
parameters for other elements, but this is untested and potentially unreliable.
Given that several different versions of DYNAMO are in use, parameters in either FORTRAN format (for
the fDynamo version) and in both formats used in pDynamo, XPK (for versions < 1.7.2) and YAML
(for versions >= 1.7.2), are provided.
The mopac_parameters.F90 FORTRAN code should be placed in the fDynamo/source directory and the
library re-compiled. To use the parameter set, CALL MOPAC_SETUP ( "AM1" ).
The XPK or YAML files should be included in the appropriate parameters directory (e.g.,
pdynamo-1.5/pMolecule-1.5/parameters/ or pDynamo-1.7.2/parameters/mndoParameters/). It is
unecessary to re-compile. To use the parameter set, call QCModelMNDO ( "mndoModel" = "chops" ),
where "chops" is the folder where the parameter files are included.
Small differences (up to ~2 kJ/mol) may be found between the energies published (PCCP) and those
obtained with pDynamo due to slight differences in numerical constants in the two programs used
(geomop and pDynamo).