SZMAP Input and Output¶
SZMAP takes molecule files as input—usually molecules representing a protein and a corresponding ligand—and generates an OEBinary file as output. The molecular input is assumed to have explicit hydrogens and partial charges. Making sure the input molecules are properly prepared is essential in order to obtain useful results and we recommend using OEDesignUnit generated with SPRUCE for this. See the SZMAP Workflow chapter for more information on preparing molecules.
When using OEDesignUnits, note that they potentially include both solvent and
a bound ligand, depending on the structure. There are two flags that are crucial to keep
-excludeDUligand, to control whether those two
components should be part of the calculation or not.
When SZMAP reads input molecules, it checks for missing hydrogens
and missing partial charges and will halt if the protein input does not appear to
be complete; for ligands AM1BCC charges and Zap9 radii are assigned if partial charges are not pre-assigned.
When the ligand(s) are already split out from the protein, MolCharge
may be used to add partial different partial charges to the ligands.
-warn_if_missing_hydrogens can be used to
prevent halting, but before using it you should analyze the problem to see
if it is due to an error in the input or something else, such as a disagreement with OEChem
as to the proper bond order or charge state for your molecule.
Mistakes in encoding alternate conformation codes can, for example, lead to
very long and very short bonds, with the short ones interpreted as double bonds.
And aromatic or double bonds that are not flat enough can cause OEChem to
interpret them as single bonds.
If SZMAP is given an input .pdb file which still contains the usual occupancy and B-factor, rather than radii and partial charges, any energies it generates will be meaningless.
SZMAP output contains the input molecules along with either one or more computed grids or with computed values attached to individual atoms. The output file can be opened in VIDA where the results will be displayed in the context of the input molecules. See the SZMAP Workflow and the chapters describing the WaterColor VIDA Extension, the Water Orientation VIDA Extension and the Color By Atom Properties for step-by-step information on visualizing the results.
Calculations done at specific coordinates produce a tab-delimited table listing the results, which can be processed by Excel or other programs.
The output file can also be interpreted by the utility programs SzmapGrid, GridComp and SzmapReport. Although VIDA is the best tool for analyzing SZMAP results, SzmapGrid can be used to write out grid data in other formats.