[gmx-users] typeB in FEP calculations

Rui Neves rppneves at gmail.com
Mon Sep 26 19:34:25 CEST 2016

Hi Gromacs users,

I am trying to determine a relative binding free-energy of two hypothetical
ligands (A -> B).

To do this, I must indicate a typeB for the atomtypes in B.
Once this is done, do I have to explicitly include the bonded parameters
for the B state, if I started by loading all the parameters of the force
field that parameterizes both ligands?

Thank you for any help,


Rui Neves

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