Hi all. I have a question regarding ligplot+ analysis. I did a docking of several ligands with a protein using autodock 4.2. I analysed the binding interactions of some ligands using ligplot+ and it gave the binding interactions between ligand and protein. However, there's one particular ligand that shows quite a good binding energy relative to others, did not show any interaction based on ligplot+. Is there any explanation behind it? I appreciate all your comments. Thank you.
Do the Ligplot+ shows the ligand in the workspace? If no, it is possible that the program is not reading the ligand information file in the input PDB file. A quick check is to try on different web-programs,
PoseView: https://proteins.plus/
PDBSum Generate: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
Yes @prasanth is right. Also, you try PLIP program and check whether the same is observed as in case of LigPlot+
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