From: Bryan Roessler (
Date: Tue Oct 13 2015 - 14:08:02 CDT


When parameterizing novel molecular fragments that will eventually be
bonded to a residue with an existing forcefield, it is necessary to
incorporate some of the atoms near the bond from the residue with existing
forcefields that contribute to the dihedral, angle and bond parameters in
the QM/MM optimization scheme.

Is it then suggested that when performing the charge optimization step in
fftk, I maintain the charges on those overlapping atoms as they exist in
the CHARMM ffs as best as possible? In other words, should I create an
upper and lower bound (so that the optimizer still has some 'play') that
are very near the charge values on those atoms provided in the existing
forcefield? Or should I let all of the charges optimize independently of
the existing forcefield charge parameters?

When I allow all of the charges to optimize without strict bounding, I can
attain a total objective that is very near zero after several iterative
optimization passes. However, when I loosely 'fix' the charges of some of
the overlapping atoms that already exist in the forcefield, the charge
optimization objective values are not nearly as good (which is to be
expected as the degrees of freedom are reduced). However, in some cases the
charges on the overlapping atoms can be quite different than the existing
charge values in the the CHARMM ff if I let them optimize without

Thanks for your help in advance,


*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
* <>*
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