[gmx-users] growing ligands in binding pockets

Xavier Periole periole at inka.mssm.edu
Mon Aug 25 19:18:01 CEST 2003

Hello John,

Remember that the apparition/disparition of your ligand is supposed
to only be a perturbation to your system. This is a necessary condition
for your FEP calculation to be valid. That is why people use a lambda
to decompose the "transformation" into perturbations as small as possible
within the computer feasability.
People have done that for cations alchmistry (good results), or some
mutation studies (not sure it works for all kind of mutants), ligand I don't
know. I am just trying to stress out the bigger the perturbation the less
accurate the result !!


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