To set up MD simulations in CHARMM-GUI for a protein with multiple docked ligands, start by preparing a single PDB file that combines the protein and all the ligands, giving each ligand a unique residue name like LIG1 or LIG2, and adding hydrogens if needed using tools such as PyMOL or Chimera. Then, head to charmm-gui.org and use the Input section's PDB Reader: upload your PDB, select the protein chains and ligand segments, parameterize any unknowns with CGenFF (or upload your own pre-generated parameters from the Ligand Reader tool). Once that's done, move to the Solution Builder or Membrane Builder depending on your system—upload the resulting PDB and PSF files, add water, ions, and a simulation box with about 10Å padding, and choose your force field like CHARMM36m for the protein paired with CGenFF for ligands, along with your preferred MD engine such as GROMACS. If you're dealing with a bunch of ligands or poses, the High-Throughput Simulator can handle batch processing of multiple PDBs. Finally, download the zip file containing your topology (.top or .psf), coordinates (.pdb or .gro), and input scripts (.mdp or .inp), and you're ready to run equilibration and production steps as usual.

Thank you, Sir, for your valuable input. I have converted UNK K to LIG1/LIG2/LIG3 and uploaded it to CHARMM, but it says parsing error. I was wondering if you would be willing to share your email address so I could reach out with a few questions in more detail.

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