Hi,
I'm interested in using umbrella sampling to calculate the 1D potential of
mean force along a reaction co-ordinate defined between a protein and
ligand, with additional restraints applied orthogonal to the reaction
co-ordinate, similar to the following paper:
S. Doudou et al., J. Chem. Theory Comput. 5, 909 (2009), "Standard Free
Energy of Binding from a One-Dimensional Potential of Mean Force".
I'm happy defining a reaction co-ordinate between two atoms in AMBER using
nmropt, but I can't see any way to define restraints orthogonal to that
co-ordinate, as the authors appear to do in the above paper (using AMBER9).
Any advice would be much appreciated.
Danny
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Received on Thu Jul 29 2010 - 07:30:03 PDT
