When modeling hydrogen bonds explicitly, it is necessary to add polar hydrogens to the macromolecule. Then the appropriate partial atomic charges must be assigned. This can be achieved by the user's preferred method, e.g. using InsightII , Quanta , Sybyl , AMBER or CHARMm . Alternatively, one of the shell scripts described in the Appendix can be used. The charged macromolecule must be converted to PDBQS format so that AutoGrid can read it.
Note that most modeling systems add polar hydrogens in a default orientation, typically assuming each new torsion angle is 0° or 180°. Without some form of refinement, this can lead to spurious locations for hydrogen-bonds. One option is to relax the hydrogens and perform a molecular mechanics minimization on the structure. Another is to use a program like "pol_h" which takes as input the default-added polar hydrogen structure, samples favorable locations for each movable proton, and selects the best position for each. This "intelligent" placement of movable polar hydrogens can be particularly important for tyrosines, serines and threonines.