Dear Bulletin board, I am looking at protein complexes with ligands containing non-natural amino acids. When I run PISA, I get the total area of the ligand, as well as the area of the ligand-protein interface, but hydrogen bonds and salt links are not recognized. I therefore do not think the calculated DeltaG values can be trusted. Is there a way to specify non-natural ligands for PISA, or does it only work for amino acids which have been calibrated with help of a large number pdb structures?
Thank you for your help! Herman
