New force field implantation for ONIOM(QM:MM): Difference between revisions

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New force field implantation for ONIOM(QM:MM):
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.


* REMEMBER; all ONIOM calculations should contain the connectivity and the atom types correctly set up (as in MM calculations). And should be the same for all species you wish to compare
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.


* Partial charges for AMBER and ONIOM calculations can be generated in a couple of different ways.
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.
1) For known AMBER residues, GaussView will generate the standard charges and supply them in the input file.


2) For non-standard AMBER residues no charge will be generated but you can use AMBER=QEq and use the charge equilibration method of Rappe and Goddard developed for UFF.
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.  


3) You can generate charges from a single point calculation with Pop=MK. For example LSDA/3-21G or HF/6-31G(d) depending on the size of your system. Then get charges either from the Mulliken analysis or the electrostatic potential fitting. You will need to supply these manually in the input.
More info in [[Feliu Maseras and Group]]

Latest revision as of 16:31, 26 March 2014

go back to Main Page, Computational Resources, Chemistry & More, Computational Codes, GAUSSIAN, G09


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.

More info in Feliu Maseras and Group

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