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 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).
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