question about free energy calculation through FEP method in NAMD

From: M. A (
Date: Wed Jul 14 2021 - 01:35:05 CDT

Dear Jérôme,

Do you have any suggestions to solve this problem?
I want to calculate the free energy (ΔG) between a ligand and protein
through FEP method in NAMD. In my structure, the ligand is located on the
surface of the protein, not inside the protein, lt means a part of the
ligand that is closed to the protein surface has interaction with protein,
and the other part of the ligand which is in contact with water molecules,
has interaction with these molecules. So, when I change the B column of
atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns
off for all atoms of ligand (all atoms in contact with protein and water
molecules both) while I need to eliminate the only interaction between the
ligand and protein. How can I specify that it eliminates just the
interaction between the ligand and protein and does not consider the
interaction of ligand and water molecules.
I appreciate all your help.

best regards

Maryam Atabay
Ph.D in Nano Computational Chemistry
Department of Physics, Sharif University of Technology

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST