I ran ligand docking and I created a ligand-protein complex PDB in Chimera. Both the ligand and protein are saved and when I open the PDB I can see both structures together. However, I am trying to add a ligand force field using charmm-gui. I know how to make the forefield for the ligand, but whenever I try to load my complex in charmm-gui, the ligand chain is not showing up for me to add the forcefield. Instead only the 312 amino acid structure is reading as chain A. I do know, however, that the ligand exists in that structure, just charmm-gui isn't reading it as a separate chain. Is there something I can do to bypass this? Or alternative ways I can add a forcefield to just the ligand, so that I can run MD simulations with the ligand-protein complex?
look video in link http://www.charmm-gui.org/?doc=demo&id=protein_ligand&lesson=1
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I have tried what was suggested in the video. But the PDB complex I made in chimera is not recognized as separate chains in charmm, so I cannot add the forcefield to the ligand since charmm is not recognizing there is even a ligand in the pdb structure.
Hi Brandon,
It might be because the protein and the ligand are saved as two separate models in the pdb file. You need to combine both the ligand and protein models into a single "MODEL" section in the pdb file you upload to the GUI. Try this: 1) Open both the protein and docked ligand in Chimera, 2) Click on "Favorites > Model Panel", 3) Make sure both models are selected in the left-hand side of the dialog box, 4) Click "copy/combine" in the right-hand side.
From here you should be able to save it as a single, new pdb file where both your protein and ligand are included in the save "MODEL" section of the pdb file. CHARMM-GUI should (hopefully) now be able to recognize your ligand! Hope this helps :)
All the best,
Tom
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