Greetings to anyone who reads this question. The problem that I am facing is whenever I try to run Autodock 4.2 and Autodock vina for my compounds that contains Bromine, the error that occurs is, in the poses when visualised through Biovia DS, it prompts that "ligand is not a single fragment" and the Bromine doesn't contains any bonding or interactions. However, on the internet, in several research papers, I have seen simulations run through Autodock, and they have reportedly found the interactions for the compounds that contain halogen especially Bromine as well. Thus, if anyone do knows the solution to this problem, please suggest. It would be much helpful. Thank you.
I have attached a picture of the same where Bromine is identified as a single element after docking. Thank you. Please help.
Hi, can you send the pdbqt input and output file? Seems like something wrong with the connectivities in your ligand atoms. And how did you prepared your ligand for it to become pdbqt?
Regards.
The ligand was drawn through Chemdraw software and then optimised in Chemdraw 3d software using MM2 force field. The ligand was converted to pdbqt in Autodock by using "Save as PDBQT" option. Whenever I convert mol2 ligand files to pdbqt ligand files in autodock the Bromine atom breaks its interaction with the ligand chanin. I am sending you a general template of the pdbqt input and output file for reference which I couldn't share though research gate seems to have some restrictions. Can you share me your email id. I would love to share there. Do check and help me out if possible @Rezi Riadhi Syahdi . Thank you.
Ah I understand. It seems I misunderstood your question. So the problem happened when you visualized your docking output *.pdbqt? Not happen when you want to dock your structure. In that case, you can use RDKit: The AssignBondOrdersFromTemplate function because pdbqt doesn't retain bond in explicit information.
There is a good page on it made by someone at Oxford Protein Informatics Group (OPIG), you can google "Post-processing for molecular docking: Assigning the correct bond order using RDKit." and go to the top page which should be that OPIG page. Hope it'll solve your problem
Thanks for all the help and support. However, I found out a way to make Bromine containing compounds to dock in Autodock via Autodock Vina. Juts use Pyrx docking sofware for the docking purpose and you can easily resolve this issue. Thank you.
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