Hello. For energy minimization of my peptide ligand, I am using Chimera software. Is it necessary to add hydrogen to the ligand prior to docking?
In general, it is advised to add hydrogen atoms to the ligand before docking if you are using a docking program that necessitates explicit hydrogens for precise calculations. However, you might not need to explicitly add hydrogens to the ligand beforehand if you're using a docking program within Chimera that handles hydrogen atoms implicitly or automatically adds hydrogens throughout the docking process.
It is necessary to add polar hydrogens for the molecular docking process. Because these hydrogens can participate in hydrogen bonding. Some programs automatically add polar hydrogens before docking, but to be sure, enter the polar hydrogens manually.
The addition of polar hydrogens is significant for the molecular bonding process and these hydrogens tend to participate in hydrogen bonding.
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