My understanding is that adding new bonds with ParmEd is akin to adding new
force field terms such that nonbonded exclusions are updated in the
topology. The only difference is that a bond does not necessitate angles
and dihedrals as in tleap (or a defined bond type). This seems to be
verified by "just doing it" and checking that the energy difference is not
in the BOND term only.
My question is - is there a way _not _ to update the exclusions so that the
new term is exactly like a harmonic restraint? This would trick the
bookkeeping in alchemical calculations, which apply a lambda factor to
nmropt terms.
Cheers,
Brian
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Received on Mon Nov 01 2021 - 12:00:02 PDT
