Hello,
I have use DOCK to dock 10 ligands into the protein structure.
I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in one pdb file.
Now, what I want to know is when I give this file to LIGPLOT, is it possible to generate something like:
%polar interactions XX
%non-polar interactions XX
%hydrogen interactions XX
Is there a way to do it with LIGPLOT, if now is there some other software that can be recommended for this type of assessment?
Best
If I understood your question correctly, you would like to get 2D representations of each of the ten binding conformations in the protein individually, using ligplot. You have a pdb file containing coordinates of all the ligands in the same space. What I would have done is the following:
The page also describes auomated assignment of non-covalent interactions like H-bonds and polar/non-polar interactions.
Hope this helps. If you want relevant scripts to do the same, I'll be happy to help.
You can use ligplot and then the export to Pymol for a 3D view of ligand.
Pymol also have a preset mode for displaying ligands.
You can do it with Ligplot just check the settings and tick what you wanna view.
You can also use, Discovery Studio visualizer, pymol, poseview, LeView etc.
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