Hi, after docking my drug structure gets changed( a single bond became double bond). does anyone know how to solve this problem. Thanks
It's essential to consider the following possibilities:
To address these issues and potentially prevent undesired structural changes, you can consider the following steps:
- Confirm the correctness of the input file and its format.
- Experiment with different software settings, including constraints and flexibility options.
- Consult the AutoDock Vina and PyRx documentation for specific options that may influence the output structure.
- Validate the output structures using multiple visualization tools to ensure consistency.
Single bond vs double bond is most likely due to visualization error or rather your structure error. It normally happens when your bond are not fully satisfied, so the software thinks that there might be double bond here as with PDB and, I hope, with pdbqt, there is no bonding information in the file. Therefore, visualization software has to guess these bonds based on proximity and sometimes they are not very accurate.
I hope you have provided the minimized or clean inputs before docking. Also carefully check the ligand file when you convert them in PDBQT. I faced similar problem latter I found there was a problem during the ligands format conversion.
Vikas Kumar bro how did you solve this problem? could you please give me your email in the inbox so that I can communicate with you
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