find strongly bound waters
This tool searches for crystal waters that
* either interact very strongly with the receptor
* or that interact strongly with receptor and reference ligand,
thus functioning as a water bridge.
Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
As input we need:
* a file containing a protonated protein in pdb-format.
This file should contain water molecules that are to be evaluated by this tool.
However, you can also use a separate pdb-file as input for the water molecules (see below).
* a file containing a reference ligand.
This reference ligand should be located in the binding pocket.
Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
* optionally a file in pdb-format containing water molecules.
If you specify such a file , all water molecules appearing in the
protein input-file (if any) will be ignored.
Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.