Dear Gromacs Users, I am calculating the hydrophobic interface area using g_sas between ligands (their hydrophobic solvent accessible surface area (SASA) >95%) and hydrophobic residues of coiled coil fragment of protein (two helical strands) as follows:
Protein SASA + ligand SASA - Protein&Ligand SASA = Interface Area between ligands protein I obtained the hydrophobic interface area increasing during the simulation time -> so everything seems to be ok, because from my simulation 10 ligands occupy hydrophobic residues (the helical terminal strands open allowing ligands to come inside the protein). However, 10 ligands aggregates during the simulation covering their hydrophobic surface which obviously has the influence on the final interface between protein and ligands. Do you know how to calculate the interface area between all 10 ligands during the simulation time in order to subtract from final result? How should I define index files? The second question: I also calculated the hydrogen bonds between ligands and the protein. What is interesting: app. 70% of hydrogen bonds between hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue what is happening as final conformation involve ligands between hydrophobic surfaces of the protein? All the best, Jan
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