I have a pdb file of docked complex of protein and ligand from patchdock, but there is an error occurring when I am importing it to LigPlot.
you need to prepare docked complex for protein-ligand in .pdb format, and then use ligplot fo lr visualization.
You could alternatively use either Discovery studio visualiser or schrondinger visualiser should also work in your case.
Can you provide a sample pdb file and quote the error message you get? You might also use LIgPlot+, the successor to the Ligplot program (https://www.ebi.ac.uk/thornton-srv/software/LigPlus/)
Hi Anne I provided you the complex pdb file generated from patchdock server...please suggest change in file so that I am able to draw 2D interaction plot by ligplus.
I agree with Uttam Pal 's analysis of the problems: file extensions such as .zip and .gz indicate compressed files or multifile archives that need to be unpacked before further analysis.
The image he created show a ligand present in all files, that probably was present in the file you submitted for docking - did you really want to dock your compound on top of this endogenous ligand? If not, you need to remove it before docking. The attached image shows an overlay of all your docking solution.
you need to prepare docked complex for protein-ligand in .pdb format, and then use ligplot fo lr visualization.
You download protein structure from rcsb database by which protein you wants to work with and also download the ligand file. Now open Swiss pdb viewer and go on windows and select those sequence you need and then save that file and open again in spdb viewer and ligate them. It is more easier than any other methods.
You can obtain 2D figures with the academic version of Maestro Schrodinguer (ligand interaction diagram).
Before you do the docking of two proteins, you should make sure that your receptor and ligand carry different chain labels. In your example, You have residues A30-A664, followed by residue A1 to A223. Therefore, you have the same combination of chain label and residue label referring to two different amino acids! If I try to look at this in PyMol, it looks like sol_5_ref.png, as the program cannot resolve the conflict. Two resolve the issue, I used a text editor to cut-and-paste residue A1 to A223 to a separate file (Rec.pdb: A30-A664, Lig: A1 to A223).
After importing both files to PyMOL, I changed the chain label of the Lig file to "B" with the command:
alter Lig, chain="B"
and saved Rec and Lig into the same pdb file
Now the complex appears correctly: (RecLig.png), although ligand residues B47-B62 seem to clash badly with the receptor, and LigPlot+/Dimplot can properly analyze the interactions
Sorry, I attached the original pdb instead of the png file: sol_5_ref.png
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