[gmx-users] free energy calculation on amino acid mutation

[Yi An]

Hi Gromacs users,

I'm trying to calculate the relative binding free energy of a certain
ligand when a leucine in the ligand binding site is mutated to glycine. The
concept is simple but I have met some difficulties creating topology files
for free energy calculation. I have two questions I wish you guys can help:

1. Let's say my protein have 200 residues and the leucine I want to mutate
is in the middle (80 for example). When I tried to edit the topology of
this protein, I found that since the number of atoms changed, I need to
make lots of changes for bond, angle, and dihedral parameters. Is my
feeling correct?

2. If my understanding is correct, I wish there are some existing scripts
which can help people create topology file for mutational free energy
calculation. I will highly appreciate if you guys tell me where I can find
them.

Thank you very much.

Yi An
Postdoctoral Research Associate
UNC-Chapel Hill