There is mismatch in the pdbs of ligand while preparing system for MD simulation in CHARMM-GUI. Can somone help me out in this ?

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Aashish Bhatt

You can upload your ligand to the CGenFF server (https://cgenff.silcsbio.com/).

Then you will get a ligand.str file. Check the atom names with your ligand that is inside the protein.

Supply your .rtf and .prm files in Charmm-gui after converting the STR file, and it will work.

Arunima Verma

Thank you, Aashish Bhatt