The chemistry of molecular interactions is a matter of shape and electrostatics, but doing electrostatics poorly is worse than doing none at all. Accurate charges are required, and the best charge models are of limited value if protonation states are wrong. QUACPAC offers everything necessary to do charges well. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and quality, and electrostatic potential map construction and storage.

The primary features of the QUACPAC include:

• pKa state enumeration for pH 2-14
• Tautomer enumeration and canonicalization
• MMFF [1] partial charges at about 1000 molecules per second
• HF/6-31G* quality charges with AM1-BCC [2] at 1 molecule per second for drug-sized molecules
• Protein charge assignment and protein pKa via Poisson-Boltzmann (PB) electrostatics [3]
• Electrostatic descriptors
• Compact storage of electrostatic potential maps
• OEChemplete - all I/O and molecular information processing by OEChem
• pKa and tautomer enumeration and partial charges are available as OEChempatible C++ toolkits
• Robust reading and specification-compliant writing of SMILES, SDF, MOL, MOL2, PDB, FASTA, MacroModel, XYZ, and OEBinary file formats
• Support for LINUX, HP-UX, Tru64UNIX, AIX, IRIX, Solaris, Windows, OS X
• 64-bit processing on HP-UX, Tru64, AIX, IRIX, Itanium®2 and PowerPC Linux

[1] Merck Molecular Force Field: I-V: Halgren, T.A., J. Comp. Chem, 1996, 17, 490-641; VI-VII: Halgren, T.A., J. Comp. Chem, 1999, 20, 720-748.

[2] Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: Jaklian, A., Jack, D.B. and Bayly, C., J. Comp. Chem, 2002, 23, 1623-1641.

[3] On the Calculation of pKas in Proteins: Yang, A.-S., Gunner, M.R., Sampogna, R., Sharp, K.A. and Honig, B., 1993.