GROMACS version:
GROMACS modification: No
How to calculate the number of hydrophobic interactions in a protein-ligand simulation performed in GROMACS?
Could you explain how you would count the number of hydrophobic interactions?
Strictly speaking there is no such thing as “hydrophobic” interaction. It is rather a hydrophobic effect, which is an entropy-driven process in protein folding.
Nevertheless, you can check contact between hydrophobic side chains of amino acid residues and check for pi-pi, aromatic-amide, cation-pi and CH-pi interactions by determining from trajectories distances, angles etc. of such functions.
After docking of DNA and a druglike molecule , I have observed some hydrogen bonds and hydrophobic bonds(file attached ). After completion of md simulation I can calculate the hydrogen bonds, same way can I calculate hydrophobic bonds?
(Attachment sp.docx is missing)