I am attempting to develop a parameterization set (force field) for a free-base (no metal center) porphyrin. I started from the heme molecule that can be found in the CHARMM36 parameter files. However, the inclusion of an iron atom at the core compared to my metal-free case, should significantly affect the partial charges as well as bond strengths.
According to the CGenFF FAQs, the paradigm is to break the molecule into smaller segments, generate parameters, and then synthesize the full molecule. There are several reasons for this suggestion; in addition to reducing contaminating secondary interactions, fragmentation reduces heavy atom counts, which is essential for some of the high level QM calculations.
But I guess my concern is the "contaminating secondary interactions". The porphyrin core is key to the simulations I'm going to be running. The large aromatic ring structure shares electrons in a non-trivial manner, and I thought the point of re-parameterizing was to accurately estimate the partial charges and bond/torsion strengths that were generated by these secondary interactions.
I'm using a tool ffTK (description at http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
) to assist building the QM calculations required to simulate the interaction of the water with the molecule in order to determine the partial charges. However, when simulating the water moving radially away from one of the interior atoms of the porphyrin core, the water molecules move too close to the atoms on the opposite side. I can move the line of interaction out of the plane of the molecule, but I'm not sure how that would affect the QM calculations for charge. Any guidance?
Alternatively, I can just use pyrrolidine as a base unit for all tetra-pyrroles in the molecule, but as mentioned would be concerned it oversimplifies the charge distribution.
Physics and Astronomy Department
The University of Texas at San Antonio