LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI

Question

[Aman Vishwakarma]

I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. However, when I pass a PDB file of a protein without ligands, I don't see any interactions. Interestingly, when I run this ligand-free PDB file through LigPlot GUI, it shows the interactions.

PDB ID example: 1BBT

Here is the code I wrote:

filename = "1BBT.pdb"
ligPlotLoc = "LigPlus"
programLoc = f"{ligPlotLoc}/lib/exe_linux64/"
ligplot_prm = f"{ligPlotLoc}/lib/params/ligplot.prm"
atom_number = 82
chain_ID = 1

os.system(f"{programLoc}hbadd {filename} {ligPlotLoc}/components.cif -wkdir ./")
os.system(f"{programLoc}hbplus -L -f hbplus.rc -h 2.90 -d 3.90 -N {filename} -wkdir ./")
os.system(f"{programLoc}hbplus -L -f hbplus.rc -h 2.70 -d 3.35 {filename} -wkdir ./")
os.system(f"{programLoc}ligplot {filename} {atom_number} {atom_number} {chain_ID} -wkdir ./ -prm {ligplot_prm} -ctype 1")

Below is the image of the interaction I obtained from running the LigPlot command line.

Below is the interaction that I am trying to get using the LigPlot command line but haven't been able to. However, I successfully obtained it using the LigPlot GUI. But wanted to get it done through ligplot command

Answer 1

[Aman Vishwakarma]

The issue was resolved by removing the -f hbplus.rc argument. The hbplus.rc file, which is a hydrogen bond file created by the hbadd program, is automatically used by the hbplus program from the tmp folder. We were incorrectly passing this file as an argument in the script.