Hi everyone, I have a problem with the ligand display in the output file using autodock vina. When the compound contains "N", it just shows it as an asterix and there are bonds missing towards these atoms. Do you know why? What do I do wrong? I draw the compounds in ChemSketch, Optimize for 3D, safe as mol file, open in pymol, safe as pdb, then open with Autodock Tools and safe as pdbqt. Until here the structure looks fine. Then I run Vina and when I open results in Pymol, the structure is ruined. May someone help or does someone have similar experience?
Hi Marcela,
You should convert your Vina output to mol2 file format by use of Open Babel:
http://openbabel.org/wiki/Main_Page
http://openbabel.org/wiki/Category:Installation
http://macappstore.org/open-babel/
https://www.youtube.com/watch?v=I6xf2itreeQ&ytbChannel=Jinuraj%20Kr
Hi again,
Or save your Vina output as PDB file format by AutoDock Tools.
You can use UCSF Chimera (https://www.cgl.ucsf.edu/chimera/) and LigPlot (http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/) for visualization and analysis of docked file.
the problem may be inside the conversion of pbbqt file so yes it may be solved by extension conversion using openbabel
Save your output as PDB file.
To show interactions between ligand and protein, please run following instruction:
1- save your protein as pdb file;
2- save pdbqt result file as pdb file;
3- Copy the contents of the ligand file to protein pdb file;
4- Use discovery studio visualizer software to display interaction between ligand and protein.
5- Now you can see all bonds of your molecule and its interactions with protein.
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