Dear Justin, You said before "you can obtain some idea by using g_mindist to calculate hydrophobic and hydrophilic contacts between the protein and ligand".
That is, I can explore whether there is hydrophobic or hydrophilic feature of ligand using g_mindist tool. is this correct? I did the calculations related to protein_ligand interactions (protein contains two ligand). I plotted the graphs of distance and numcount versus simulation time for each ligand. The number of contacts in ligand x is more than the other ligand y. Which of this ligands are hydrophobic? Which is hydrophilic? I know you are not private tutor. Please don't be angry :( Thanks in advance -- Ahmet YILDIRIM
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