Finding Water Bridges

to create solvated and neutralized box, run command:
this script will find all the PDB files under current directory and solvate and neutralize them. the final files will be named *_wb_ionized.pdb *_wb_ionized.psf *_wb_ionized.ref(fix one CA in middle residue) *.namd(before you run the simulation it is better to check the file to set the temperature and output frequency etc.).
then run namd2 +p * *.namd > *_equi.log to equilibrate the solvate the box.
Check the progress by: tail -f *_equi.log
load trajectory into VMD:
vmd *.psf *_equi.dcd
open tcl terminal:
source ~/toolset/water_bridge.tcl
then click the play button, let the program calculate bridges for every frame.
Following is the trajectory of BPTI(6PTI.pdb)