MM3 embedded to ONIOM
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Gaussian09 is commonly used for ONIOM(QM:MM) calculations. However, this software supports only for three force fields, namely UFF, AMBER, and Dreiding. Of these, UFF is the common method of choice in the QM/MM studies of homogeneous catalysis, while AMBER force field is usually used for enzymatic systems. In common practice, we aware that the UFF is not accurate, and we cannot not find relevant AMBER parameters if the molecular system holds other ligands/residues.
Several force field parameter sets, MM3, MMFFs, OPLS, GROMACS, and etc., are available in the commonly used MM programs, but these force fields cannot be used in Gaussian09. Therefore, there is a keen interest to connect above force field parameter sets to Gaussian09 ONIOM(QM:MM) optimizer. To this end, we implemented the force field parameter sets that are available in the TINKER6.0 program to the Gaussian09 ONIOM(QM:MM) optimizer.
This new implementation uses Gaussian09 standardized interface to run MM programs externally to produce MM energy, dipole moment, gradients, and hessian for ONIOM(QM/MM) calculations, where Gaussian09 uses for QM calculation and the external MM program performs MM calculations. Present implementation uses Tinker6.0 program package as the external MM program, and allows Gaussian09 community to use the Tinker force filed parameter sets for ONIOM(QM/MM) calculations.
New implementation starts with Gaussian09 to provide text files (EIn) with the current structure (real system or model system). Then, our scripts refer these information and setup input files for TINKER6.0, performs MM calculations, and convert functional values and derivatives the into a standard text file (EOu) for recovery by Gaussian09.
Contact Ignacio or Maria for further details.
The tutorial of this implementation is available in this pdf file:
File:Tutorial ignacio corrections.pdf
How to submit "SICTWO" calculations on kimik2[edit]
You can either edit by hand the body.sub or use the QMMM submiting script. To use the QMMM submititng script just type QMMM and press enter. In the following line write the type of queue you wish to use (c12m24, c8m24 or c4m8) and the name of the input without extension. Example:
@kimik2:~/QMMM c4m8 nameinput @kimik2:~/
Limitations:[edit]
So far it can not perform optimizations in solution.