Some Basic queries for FEP and TI

From: Debadrita Basu (
Date: Sun Mar 21 2021 - 11:18:50 CDT

Hello Everyone,

My protein of interest has ~850 residues (quite big) where a Magnesium ion
is intrinsically bound. Also some ligands are known to bind to some
specific grooves of this protein. I wanted to see the role of Magnesium on
the ligand binding (ie whether it has a facilitating or inhibiting role).
So, I decided to carry out the FEP calculation where I discharge the
Magnesium atom to a dummy Magnesium atom, (in two different systems: ligand
bound and apo) followed by thermodynamic integration. I used CGENFF to

I decided to follow the FEP algorithm implemented in NAMD, but I have a
couple of questions in my mind:

1. Whether I will get a true result by using the whole protein.
2. While discharging the Magnesium atom I will end up changing the total
charge of the system, is that acceptable? If not, how can it be solved?

Hope, I get something to learn from your answers.

Thank You.

Debadrita Basu.
Senior Research Fellow
Bose Institute
Kolkata, India.

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