HydraMap v1.0

	
wsitem: the main program for predicting water locations.
usage:
./wsitem protein_file ligand_file apo/holo [ D=4.0 Cutoff=5.0 radius=2.0 N=10 ]

protein_file: PDB format;
ligand_file: Mol2 format, used for defining the protein binding pocket;
apo/holo: determine whether the ligand is included in the prediction of water locations;
D: the distance between the cubic boundary and the nearest ligand atom, default 4.0Å; 
Cutoff: cutoff value for defining favorable PMF values in water site clustering, default 5.0;
radius: the distance defining the region around the center point, default 2.0Å;
N: the least number of grids in a cluster for a valid hydration site, default 10.

Three default parameter files are required including:
PARA_PRO.TXT: PMF parameters for protein atom and water molecule;
PARA_WAT.TXT: PMF parameters between water molecules, used for calculating interactions between water molecules;
PARA_LIG.TXT: PMF parameters for ligand atom and water molecule, only required if the "holo" state is assigned.
After running the command, a log file "wsite.log", a Mol2 file "wsite.pdb" and a grid file "grid.txt" with PMF energies are generated.


getwat: used to select the water molecules within a defined distance from the protein and ligand atoms.
usage:
./getwat protein_file ligand_file wat_file [ distance=4.0 ]

protein_file: PDB format;
ligand_file: Mol2 format;
wat_file: PDB format;
distance: a value defines the distance between the oxygen atom of the water molecule and the protein/ligand atom, default 4.0Å.


analws: used to calculate the distance between a pair of nearest water molecules.
usage: 
./analws ligand_file wat_file1 wat_file2 [ distance=4.0 ]

ligand_file: Mol2 format;
wat_file1 and wat_file2: PDB format, including the coordinates of water molecules;
distance: a value defines the distance between the oxygen atom of the water molecule and the ligand atom, default 4.0Å.


dG: used to calculate the interaction energies of the predicted water molecules from the protein atoms and other water molecules.
usage:
./dG hs_file grid_file 

hs_file: PDB format, including the coordinates of the predicted water molecules;
grid_file: "grid.txt", generated by "wsitem" program, including the coordinates and PMF energies of each grid;