Hi,
> So I don't understand fully your notice "The analytical correction does
> not have any connection to this, but is a separate step (without MD
> simulation) you probably have to do.".
> Probably you had on your mind just k*T*ln(Fr), k*T*ln(Ft*C0) corrections
> or there is some way how to estimate also dGsite_r and dGsite_t
> contributions without special TI run ?
> Maybe usually these contributions are neglected as especially in cases of
> strongly interacting ligands these corrections are sufficiently small ?
ok, what I said may have been imprecise, the analytical correction is a
separate step, but the cost of switching on the restraints while the
ligand fully interacts is yet another third leg of your cycle that indeed
needs a numerical result from MD simulations. I dont think it is a
contribution that can typically be neglected, unless you set very weak
restraints.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jan 26 2012 - 09:30:04 PST
