On Sun, Mar 05, 2017, Mrinal Arandhara wrote:
> 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 ??
Problems typially arise with the GAFF force fields and protonated phosphates,
exactly as you describe: the hydrogen has no van der Waals radius, and hence
no barrier to getting arbitrarily close to to a neighboring oxygen atom.
Two ideas: (a) add extra angle bending terms to keep this from happening,
as here:
%A T. Steinbrecher
%A J. Latzer
%A D.A. Case
%T Revised AMBER Parameters for Bioorganic Phosphates
%J J. Chem. Theory Comput.
%V 8
%P 4405-4412
%D 2012
(b) use the gaff2 parameters, where all hydrogens have nonzero Lennard-Jones
parameters.
Combinations of (a) and (b) might also be worth exploring. I may be missing
some literature here, and I hope others on the list will chime in if they know
more.
...good luck....dac
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Received on Sun Mar 05 2017 - 10:30:02 PST
