From: Chitrak Gupta (
Date: Tue Sep 08 2015 - 10:54:19 CDT

Hi! I am new to the FFTK plugin. I am following the steps of the tutorial
but having problems at the water interaction stage. I used the "Auto detect
indices" to select the hydrogen bonding atoms. It included even Hydrogens
bonded to aliphatic C, and atoms like amide C, carboxyl C, etc. There were
also atoms that were included both in lists of donors and acceptors. Is
that normal?

After I ran the Gaussian calculations, some of the waters move away from
the molecule. Some other waters also move away but are still bonded,
resulting in severely elongate bonds. Does anyone know how to fix these?