Intermolecular interaction for Absolute binding free energy

User discussions
1

GROMACS version:2023.2
GROMACS modification: No

I need to run a ABFE and need help in defining intermolecular interaction section atoms and parameters.

2

We can’t provide help without more details.

3

I am trying to follow the tutorial provided here Absolute Binding Free Energy - Gromacs 2016 - AlchemistryWiki and for my protein-ligand complex how can I derive the intermolecular_interactions section mentioned in the top file of the tutorial along with parameters associated with it.

4

In the intermolecular interactions section you supply global atom numbers. Otherwise everything is the same as with intramolecular interactions.

5

Thanks for the reply.

I wanted to understand how to pick 3 atoms on protein and 3 atoms on ligand for this intramolecular interactions section.

6

Hello Chetan

I am trying to follow the same tutorial, were you able to reproduce their results upto the analysis part?

7

No I didn’t run the tutorial example

I was trying to understand the process of calculating ABFE in gromacs.

8

Okay thank you, have done any ABFE calculations? If so do you mind share with the tutorial/resources you used

9

I haven’t done any ABFEP calculations yet.