Hi APBS users,
I have been using APBS to calculate the free energy of protein-protein binding. The electrostatic (PBE) part of the calculations was problem-free thanks to the wonderful PDB2PQR, which rendered my pdb file (3btk) APBS-friendly. However, I was unable to run the apolar calculation, because some of the atom/residue names in my pdb file were not present in the VPARAM parameter base used for this calculation. I tried to fix the problem by using AMBER parameters in PDB2PQR, but that hasn't worked either. Does anyone have a suggestion that does not involve manually fixing atom/residue names in the pdb file or VPARAM?.

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