Hello everyone,
I have protein ligand system and I want to understand are there any water mediated interactions between protein and ligand, I have calculated the Hbonds between the ligand with water molecules and some selected residues with water molecules. But it does not provide much of the information, Is there any other method through which I can capture these interactions?
Thanks a lot
Hi,
I do not know if there is a specific tools for this. Maybe you can use gmx select to create a group containing water molecules closer to the ligand and the protein (see here for the selection synthax Selection syntax and usage — GROMACS 2022.2 documentation). My assumption is that to have a water mediated interaction some waters are located between ligand and protein and have with a longer residence time. Then you could monitor for example if the selected water molecules hydrogen bond both protein and ligand at the point in time.
I hope it helps
\Alessandra
Than you for your response.
I had used the similar method to calculate and was able to capture the water molecules, which are having the longer residence time and so, was able to capture the interactions.
I was just interested to know if there are any other methods or any tools available for the same.