The result of Autodock Vina is an output.pdbqt file, which is having only the ligand pose but no protein structure to which this ligand has docked to. If this file is opened in PyMOL and protein is inserted to see the interactions between the protein-ligand complex, I am unable to save this complex in PDB format for later reference . I docked a protein & ligand, but output showing only ligand pose. therefore ligplot is not able to read this output file.
These outputs are text files and the pdb files are also text files. So, you can open and edit them in notepad/gedit. First you open both the Vina output and the protein pdb files in notepad. Then copy the ATOM/HETATM information under "Model 1" heading from the Vina output file and paste that at the end of the protein pdb file. Now, you have the complex and it should work with LigPlot.
Dear Naiju Thomas
Just copy complex file content to receptor files and save it as PDB
File. You also can use discovery studio to create 2D-interactions plot between receptor and ligand.
Dear Naiju,
I have exactly the same problem. I docked compounds with iGEMDOCK and the pharmacological interactions with the docked compounds can be viewed in Rasmol but the files can't be exported in pdb format but only in BMP or RAST format. I need to use to PDB format of the ligand-receptor complex in order to see the hydrogen bonds in the binding site. Could you explain me how you succeed in it?
Uttam Pal Naiju Thomas
hi,
I have followed the same steps but not able to open the complex file in ligplot.
It shows error: Unable to create log file in temporary directory:C:/tmp though I have changed my advanced directory settings too. Could u explain more on it.
Hi Mrs Sharma and Mr Galani, you can go through thw following link. I was facing the same issue. Finally I was able to solve this by changing the temporary file location.
https://www.researchgate.net/post/How_to_solve_C_tmp_error_of_LigPlot
Md. Mahbubur Rahman
Hi It was resolved.
Actually in my case, the path in ligPlot was wrong. I have changed it to c:\temp, it was initially c:\tmp
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