ONIOM tips

ONIOM tips:

To get out the model system from an oniom calculation include iop(1/33=2). In the output file, search for: "ONIOM: generating point 2 high level on model system". All atoms without the label -1 belong to the model system (this list includes also the link hydrogens).

Force Fields not implemented To use force fields which are not implemented in Gaussian09, you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER.

In Gaussview: When selecting MM regions in QM/MM methods you can change the status (H/L) of several atoms at same time, by:i) select the upper atom in the list ii) go to the last one and press control+shift 3) change the last atom status to low level.

GaussView can help assigning atom types and it will also add point charges according to the AMBER convention for atoms in standard protein residues. For other molecules that are not standard residues, there is no information about appropriate charges (GaussView will try to assign reasonable atom types), so one would need to derive charges for the atoms in such molecule, or look in the literature to see if other researchers have derived charges and parameters for such molecule.

Only the "amber96" version is internally hardwired in the G09 code and that is the one selected when using the AMBER keyword. The "amber.prm" file in the "g09" directory is simply a text file that shows this same parameter file that is internally hardwired in the code, but the program does not read that file. It is included for illustrative purposes so one see examples of how to specify MM parameters manually. The files that you mentioned (amber98.prm and oplsaa.prm) unfortunately are not ready to be used. You can make modifications to the internally hardwired parameter file by adding the modifications to the input file, for instance: example_amber96

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