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?. Cheers, Amit.
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