Good Morning!
I would like to know, currently which metals are parameterized in the MMFF94 and MMFF94s and if there are probable transition metals in a parameterization study?
Thanks
The parameters for MMFF94 are in the papers, e.g.
Halgren, T.A. (1996), Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem., 17: 490-519
I don’t remember off the top of my head, but I think it’s limited only to a few ions:
FE+2 87 87 87 87 87 IRON +2 CATION
FE+3 88 88 88 88 88 IRON +3 CATION
LI+ 92 92 92 92 92 LITHIUM CATION
NA+ 93 93 93 93 93 SODIUM CATION
K+ 94 94 94 94 94 POTASSIUM CATION
ZN+2 95 95 95 95 95 DIPOSITIVE ZINC CATION
CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM CATION
CU+1 97 97 97 97 97 MONOPOSITIVE COPPER CATION
CU+2 98 98 98 98 98 DIPOSITIVE COPPER CATION
MG+2 99 99 99 99 99 DIPOSITIVE MAGNESIUM CATION
In general, if you want metal complexes, I’d recommend UFF as a force field.
Whenever I tried including any of these ions in the system, the optimization in Avogadro with MMFF94 or MMFF94s returned the error: “AutoOpt: Could not setup force field …”. Other FFs (UFF, GAFF, Ghemical) are fine. Any idea? Does that mean Avogadro doesn’t have the MMFF94 parameters for any metal?
It has all the MMFF94 parameters, but is likely not assigning the atom types.
If GAFF is working, I’d go with that - David van der Spoel’s group has spent time checking the parameter assignments. UFF is also a possibility.
I understand that in case the metal ion have different charge (Fe+2, Fe+3, Cu+1, Cu+2) the atom types might be necessary and it could be a problem. But for non transition metal there is no ambiguity. If it is an easy job maybe Avogadro should at least get them correctly.
I’d need to see your system.
The code uses Open Babel to do atom typing and force field optimization, e.g. atom typing for potassium
https://github.com/openbabel/openbabel/blob/mastersrc/forcefields/forcefieldmmff94.cpp#L2588
Certainly the simple cations (Li, Na, K, Zn, Ca, Mg) work, e.g. solvating a \ce{Ca+2} ion with \ce{H2O}
