AMBER Archive (2009)

Subject: [AMBER] Thermodynamic Integration calculation on an artificial anion receptor

From: Huifang (
Date: Wed Oct 28 2009 - 23:38:05 CDT

Hi Amber Users,

I am trying to calculate the relative binding free energies of an
artificial receptor with various anions in explicit solvent by means
of TI. Firstly, I remove the partial charges on the anion, followed by
a mutation to another anion and finally putting the charges on the
mutated anion. However, when removing the charges on the anion, the
anion no longer binds to the receptor. Do I have to put constraints on
the complex or are there any other ways to curb this problem? Any
comment or suggestion is greatly appreciated.

Many thanks,

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