[gmx-users] Re: gmx-users digest, Vol 1 #1276 - 12 msgs
mrshirts at stanford.edu
Sat Feb 21 07:43:01 CET 2004
> ps: out of couriosity, is this supposed to renstrain a ligand
> in a binding pocket in a free energy calc as suggested by
> by, e.g., Rebecca Wade ? If so, how do you plan to correct dA for the
Basically, we won't be correcting for the restraint, because them it would be
equivalent to putting the ligand ANYWHERE in the box of solvent + protein.
Obviously, if this was a harmonic restraint, it would be a problem, as many of
the configurations we were interested in would be weighted slightly
incorrectly. But with a sufficiently wide flat bottomed potential, the bound
states should all be located in the well. For a tight binder, the it
shouldn't actually matter that much.
Talking to Erik Lindhal, it looks like that implementing such a restraint will
be relatively easy to implement using the distance restraint functionality
usually used for NMR analysis.
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