From: D.J. Cole <djc56.cam.ac.uk>
Date: 29 Jul 2010 15:03:52 +0100


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.


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Received on Thu Jul 29 2010 - 07:30:03 PDT
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