How I can clean & prepare Protein for MD simulations from the ligand-protein complex?
Cleaning of protein define removal of water molecules, extra chain's and cofactors, for that purpose, you can use CHIMERA. Use command "delete :.b" to delete the chain b (you can select any chain you want to delete by replacing b with a or c) and for deletion of cofactor, you can edit the file in WordPad where you can delete the HET atoms (cofactors and water molecules)
Preparation process takes into account the insertion of missing atoms and chains. For that you can use "Swiss-Pdb viewer".
Dear Amit,
Please go through this link:
https://www.researchgate.net/post/protein_chain_detect_and_delete
You can also consider Meastro (Schrodinger) protein preparation module for this purpose.
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