Is it possible to simulate one protein and two ligands simultaneously?

[nyubachi]

Thank you for the wonderful structure you have created. I enjoy using "Protein_ligand.ipynb".

I am a beginner in MD simulation, so this may be a silly attempt, I would like to modify "Protein_ligand.ipynb" to simulate a protein and two ligands simultaneously.

Since it is difficult for me to determine if such an attempt is even possible, I would appreciate your comments and advice.

Thanks in advance.

[pablo-arantes]

Hi @nyubachi,

Yes, it is possible to run with two ligands. I will check the code and let you know which modifications we need to do.

Thank you.

Best,

Pablo

[nyubachi]

Thank you for your response.

I am also trying, but due to my lack of knowledge of MD simulation and my low proficiency in Python, I am having difficulties around the "Parameters to generate the protein topology:" cell.

Any hints or overview of the fixes would be appreciated. Thanks in advance for your help.

[pablo-arantes]

Hi @nyubachi,

Follow the notebook to run a protein complexed two ligands simultaneously. https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_2ligands.ipynb

I hope it helps.

Thank you.

[nyubachi]

I really appreciate you taking the time out of your busy schedule to create the code.

I am currently running a test simulation based on the code you provided, and it seems to be working well.

I will definitely use it effectively and contribute to the development of my research field and the health of patients.

Thank you very much.