alchemical FEP question

From: Nandhini Sokkalingam (
Date: Fri Dec 19 2008 - 21:44:52 CST

Hello all,
I am trying to mutate an aromatic compound to another one. The charges on the
atomic sites for the initial and the target molecule are different while some of the
sites have similar vdw parameters. can i fix the positions of the specific atoms with
similar vdw parameters to account for only electrostatic perturbation and not for
the non-bonded perturbation like in the charging of the sodium atom alchemical
FEP tutorial.


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