In addition to the atomic affinity grid maps, AutoDock requires an electrostatic potential grid map. Polar hydrogens must be added, if hydrogen-bonds are being modeled explicitly. Partial atomic charges must be assigned to the macromolecule. The electrostatic grid can be generated by AutoGrid , or by other programs such as MEAD 1 or DELPHI 2 , which solve the linearized Poisson-Boltzmann equation. AutoGrid calculates Coulombic interactions between the macromolecule and a probe of charge e , +1.60219x10 -19 C; there is no distance cutoff used for electrostatic interactions. A sigmoidal distance-dependent dielectric function is used to model solvent screening, based on the work of Mehler and Solmajer 3 ,
where: B = e0 - A ; e0 = the dielectric constant of bulk water at 25°C = 78.4; A = -8.5525, l = 0.003627 and k = 7.7839 are parameters.
Charges must be stored in PDBQ format in order for AutoGrid to read them. PDBQ is an augmented form of the standard PDB format, in which an extra column is used to store the partial atomic charges (hence the "Q" in "PDBQ"). Columns 71-76 of the PDB file hold the partial atomic charge (the older form of PDBQ contains charges in columns 55-61).
Charges can be assigned using a molecular modeling program. Unix shell scripts are provided to convert from
Insight95
4
".car" files ("cartopdbq") and
SYBYL
5
".mol2" files ("
mol2topdbq"
). See also "q.amber" and "q.kollua", in the appendices.
1. Bashford, D. and Gerwert, K. (1992) "Electrostatic calculations of the pK a values of ionizable groups in bacteriorhodopsin", J. Mol. Biol. , 224 , 473-486; Bashford, D. and Karplus, M. (1990) "pK a s of ionizable groups in proteins - atomic detail from a continuum electrostatic model.", Biochemistry , 29 , 10219-10225; MEAD is available from Donald E. Bashford, Dept. Molecular Biology, Mail Drop MB1, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037.
2. Gilson, M.K. and Honig, B. (1987) Nature, 330 , 84-86; DELPHI is available from Biosym Technologies, 9685 Scranton Road, San Diego, CA 92121-2777, USA.