ONIOM tips

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ONIOM tips:

• You can use iop(4/33=2) to print out all MM contributions.
• 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).
• To use force fields which are not implemented in Gaussian09: There are two options:

Option1: You can do one-dimensional potential energy surface scans over a reaction coordinate, where the constrained structure optimisations at the potential energy surface can be performed with ONIOM(DFT:UFF), ONIOM(DFT:DREIDING) or ONIOM (DFT:AMBER), where the iop(1/33=2) option helps to obtain QM and MM parts of the molecule. Then you can do MM optimisations on the QM and MM parts of the molecule separately with MACROMODEL or TINKER, where they have various force filed parameters. Option2: ´External´ keyword. There are two examples in the G09 test suite which make use of the ´External´ keyword. (1) Test726 uses a shell script to run g09 as an external process with UFF. The script ´extuffex´ is stored in the g09/bsd directory. (2) Test769 uses a perl script, mygau, which is stored in the g09/bsd subdirectory. Note that you will likely need to edit mygau to change the path to perl, rather than /usr/local/bin, because most machines store it in /usr/bin. In both cases you could use ´External´ keyword in the input file.

Eg:-
ONIOM(B3LYP/6-31G(d):AM1:External="Script_name") Opt

The use of an external MM program is not fully implemented in G09. The Gau_External script in the G09 home is an example where we use Gaussian as an external program, specifically 'Gau_External' script helps to run MOPAC as external procedure for ONIOM. You would need to make a copy of this script and modify it to create an input file for other MM programes (Eg. TINKER), and run the MM program with this input, and then use the output from the MM program to generate result files suitable for processing by Gaussian.

• 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:

ONIOM(<Method>/<Basis Set>:AMBER=SoftFirst) geom=connectivity

<Title>

<Charge and Multiplicity> <Coordinates>

<Connectivity table>

<MM Parameter modifications>

With the "SoftFirst" option, the program will use the internally hardwired parameter file for AMBER and add the modifications given in the input file, with the latter taking preference over the internally hardwired parameters in case of duplicates.

If you do not want for G09 to use the internally hardwired parameter file but to read the full parameter table from an external file, you can do so with the "SoftOnly" option, which takes only the MM parameter specifications given in the input file and nothing from the internally hardwired parameter file. For example:

ONIOM(<Method>/<Basis Set>:AMBER=SoftOnly) geom=connectivity

<Title>

<Charge and Multiplicity> <Coordinates>

<Connectivity table>

@/home/fernando/MM/file_with_parameters.prm /N

The "@" character at the beginning of the line means to include the content of a text file in the input, that way one does not need to type or paste the content of another file in the input, the program will automatically look for that other file and include it in this section of the input file.

Note that there are some differences in the format of the MM parameter specification between AMBER and Gaussian, so AMBER ".dat" files with the whole parameter table specification cannot be used directly in Gaussian, they need to be converted to the correct format. The documentation about MM methods in the Gaussian manual contains detailed descriptions of the input formats for each type of MM parameter.