I wish to estimate the hydrophobic interactions between a protein and ligand for a GROMACS trajectory. While the obvious and tedious way is to calculate distances and angles for each specific interaction, please share any other way to accurately determine the hydrophobic interactions based on geometric criteria.
you can download LigPLOT (or LigPLOT+ with GUI), a simple program that quantifies the number of non-bonded interactions and hydrogen bonds between any ligand and the protein.
What else did you have in mind apart from the distances and angles of specific interactions? Maybe you can come up with some hybridization of specific atoms and work towards electron cloud shapes which can cancel out. (since you wanted a geometric solution ).
Dear Mahesh, LigPLOT would allow quantification of interactions for a single pose. I wish to calculate the hydrophobic interactions throughout a MD trajectory such that I get the percentage of time the interaction was formed (occupancy). While hydrogen bonds can be calculated by gmx hbond, I want to calculate interactions like pi-stacking and pi-cation throughout the trajectory, similar to one calculated in the simulation interaction diagram after Desmond simulation in Schrödinger.
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