The "Automated Frequency Matching Method" (AFMM) is a method to parameterize small organic molecules for which force field parameters are unavailable. As the title implies, we use normal mode analysis and match MM normal modes in order to reproduce the QM normal modes. The method should be ideally used for molecules that are rigid and therefore possess few minima and for parameterizing bond and angle force constants (although dihedrals can be tuned at a certain extent as well.
AFMM is currently implemented for CHARMM and AMBER force fields. Our software cannot handle the Gromacs force field because it is united-atom and therefore matching QMM and MM normal modes does not make much sense.
You can find more information about AFMM here:
Z. Cournia, J. C. Smith, and G. M. Ullmann (2005) A molecular mechanics force-field for biologically-important sterols. J. Comp. Chem., 26:1383-1399.
A. C. Vaiana, Z. Cournia, I. B. Costescu, and J. C. Smith (2005) AFMM: A molecular mechanics force-field vibrational parametrization program. Comput. Phys. Commun., 167:34-42.
Please email me at: zcournia [at] bioacademy.gr if you are interested in receiving the code, the manual and support.
AFMM is currently implemented for CHARMM and AMBER force fields. Our software cannot handle the Gromacs force field because it is united-atom and therefore matching QMM and MM normal modes does not make much sense.
You can find more information about AFMM here:
Z. Cournia, J. C. Smith, and G. M. Ullmann (2005) A molecular mechanics force-field for biologically-important sterols. J. Comp. Chem., 26:1383-1399.
A. C. Vaiana, Z. Cournia, I. B. Costescu, and J. C. Smith (2005) AFMM: A molecular mechanics force-field vibrational parametrization program. Comput. Phys. Commun., 167:34-42.
Please email me at: zcournia [at] bioacademy.gr if you are interested in receiving the code, the manual and support.
RSS Feed
