Base Program: HB_Radar
Basic Principle: Finds hydrogen bonds (H-bonds) from X-ray Crystal structures and calculates Potential Energy Surface using Density Functional Theory.
Working protocol:
Harvest .pdb files from RCSB-PDB
Adds hydrogen to each pdb and outputs .atom file
Searches each file and harvest coordinates involved in H-bond formation (updated version can isolate nearby coordinates of H-bond, given certain radius).
Uses NWChem program (https://www.nwchem-sw.org/) as a wrapper to calculate QM single point energy (SPE).
Writes Fortran scripts independently to run NWChem as a sub-process and returns the value to specific array once a SPE calculation finishes.
**Update.v.3: Program can iteratively self-write and try different Fortran scripts for NWChem to try differnt grid size and exchange-correlation function, till a calculation converges.
Outputs the H-bond coordinates and corresponding SPE in single file.
... repeates for every file supplied
Once SPE calculations are over, it plots all the information w.r.t. H-bond's geometric parameters.
Smaple output and studies performed: https://onlinelibrary.wiley.com/doi/10.1002/prot.25271