I am running protein-ligand simulation in GROMACS. My ligand_ini.pdb and ligand.gro files are not generating properly.Can someone help?

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Susanta Roy

It is difficult to determine the exact cause of the issue without more information on the specific problem you are facing. However, there are a few common issues that can occur during the generation of ligand files for protein-ligand simulations in GROMACS. Here are some suggestions that may help:

Check the ligand topology: Ensure that the ligand topology is correctly generated using the appropriate force field parameters. You can use tools such as Antechamber or CHARMM-GUI to generate the ligand topology.

Check the ligand coordinate files: Ensure that the ligand coordinate files (such as .pdb and .gro files) are generated correctly and contain the correct atom names and positions. You can use tools such as VMD or PyMOL to visualize the ligand structure and verify that it is correct.

Check the ligand parameter files: Ensure that the ligand parameter files (such as .itp and .prm files) are correctly generated and contain the correct force field parameters. You can use tools such as CHARMM-GUI or GROMACS built-in tools to generate the ligand parameter files.

Check the simulation settings: Ensure that the simulation settings are appropriate for the protein-ligand system being simulated. You can use tools such as GROMACS built-in tools or external software such as CHARMM-GUI to set up the simulation.

Madhusudan Dutta

I have performed md simulation with a combination of protein and small molecule ligand but have not used such python script. If you're interested to do with my standardized protocol then feel free to send mail. My mail id: [email protected]