gives the basic name for the output file or files
containing ligand orientations. In SINGLE mode, there is one output file of
ligand orientations for each sphere cluster that is used for docking. In
SEARCH mode, the number of ligand output files per sphere cluster used for
docking equals the number of types of scoring to be done (twice this number if
molecules are also to be saved according to their normalized scores, that is,
if normalize_save is greater than 0). Each of the top-scoring molecules
is output in its best-scoring orientation. The string norm is appended to
indicate the file containing the top normalized score ligands, the string eel
indicates the top electrostatic score ligands, and the string ff indicates the
top force field score ligands. In all cases the final suffix to the name is
the number of the cluster used in docking. For example, the suffix eelnorm1
indicates that the file contains the ligands with the top normalized
electrostatic scores generated by docking to cluster number 1. The output is
in extended PDB format, which is standard PDB format up through the
coordinates columns, but has additional information in subsequent columns.
Extended PDB format may be converted to standard PDB
format with the x2pdb utility. Depending on the input, not all of this
information may be available; whenever it is not available, zeroes are output.
REMARK cards are used for reporting scores and (if available) molecule names.
output_hydrogens
specifies whether or not ligand hydrogens should be
included in the output, if present in the database. If output_hydrogens
is yes, hydrogens will be included in the output. In any case, ligand hydrogens
are not used for matching, orientation, or contact scoring.
