solvate.sh
usage： solvate.sh
dependancies: mmtsb toolset; vmd; solvate_ionized.tcl
description: it finds all the pdbs file under current directory, and solvate them one by one. it converts each PDB to pure peptide then solvate and neutralize it, and it is SSBONDS tolerate. It also create *(name of pdb).namd file.

water_bridge.tcl

load md trajectory into vmd. open tcl/tk console, source water_bridge.tcl. the available commands includes:

start_hbonding [options]

options:

-protein (calculate hbonds within protein)

-water (calculate hbonds between water molecules)

deg.R

community.R

waterbridge_pipeline.sh

solvate.inp

hphmd_phrex.inp

 

 

packmol:

http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml