3
$\begingroup$

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. enter image description here

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 enter image description here

Improve this question
$\endgroup$
2
  • $\begingroup$ its not free, so you better ask to the user community or here ebi.ac.uk/thornton-srv/software/LigPlus/contactus.html In case of any problems or questions relating to LigPlot+, please contact (preferably by e-mail): Roman Laskowski European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Phone Number: +44 (0)1223 492 542 Fax Number: +44 (0)1223 494 468 Email: [email protected] Personal Page: ebi.ac.uk/~roman $\endgroup$
    – pippo1980
    Commented Jul 14 at 17:26
  • $\begingroup$ Thank you @pippo1980 $\endgroup$
    – aspergillus
    Commented Jul 19 at 14:40

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.