I'm trying to run a MD simulation of protien-ligand complex with
dUMP(monoanionic) as cofactor. The gaff parameters for dUMP generated by
parmchk has reasonable penalty values but after minimisation step two
atoms(one O and the other hydroxyl-H) attached to the P-atom are sitting
on top of each other and 1-4 EEL value is very large (*************) .Is
it due to wrong force field parameters or wrong charges ??Are the
parameters for dUMP available ??
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Received on Sun Mar 05 2017 - 07:30:03 PST
