Why to carry the bound ligand structure in docking calculations. Rather use any molecule editor i.e. PMV and delete the existing ligand (You can also use text editor for the purpose). Even this will lead you towards the right interpretations. Ideal docking cases doesnt involves the additionally bound ligand.
Why to carry the bound ligand structure in docking calculations. Rather use any molecule editor i.e. PMV and delete the existing ligand (You can also use text editor for the purpose). Even this will lead you towards the right interpretations. Ideal docking cases doesnt involves the additionally bound ligand.
Hello.
Although not for VINA, if you really need two ligands, there is a Autodock modification called MLSD (multiple ligand simultaneous docking) that can dock two ligands simultaneously (Li, H., & Li, C. (2010). Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein. J Comput Chem, 31(10), 2014–22. doi:10.1002/jcc.21486).
If not, it is better to delete the bound ligand. If you use AutoDockTools, when preparing the receptor, the program will do this automatically (only considering the protein).
Ricardo
I have already downloaded chimera but didn't test it, yet. Thank you!
All the PDB and PDBQT files are basically text files. You can just open them in any text editor (notepad or gedit) and remove all the lines started with HETATM, which indicates heteroatoms (ligands, water etc). It is always good to know your PDB files. There are many unwanted things in it which no visualization software shows.
There are different ways to exclude the ligand from .pdb file. The simpliest are PyMol, as mentioned above, and ... downloading Receptor from PDB databases.
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