Query on use of forcefeilds.

[Arikite-netizen]

Respected Sir, Based on your advice I increased the number Strides. However, while running the cell for making topology of the molecule. I thought to use amber03(ff94/ff99) forcefeild, for its extensive modifications providing better QM solvent continuum model. Thus, I tried to edit the code to source that forcefeild. However, everytime I run it , it can't enerate topology; It says that ligand_gaff.pdb file couldn't be found. Thus, I would like to request you to consider adding the amber03 forcefeild too. Regards

[pablo-arantes]

Hi @Arikite-netizen,

Thank you for your feedback. Regarding your question, we have chosen the most up-to-date AMBER force fields (Amber 14 and Amber 99SB). If you want to use something different from that, you can prepare your system on your workstation and then use the fifth notebook in the main Making it Rain page (https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Amber_inputs.ipynb). This notebook uses inputs from AMBER suite of biomolecular simulation program. Just submit your pdb, crd and prmtop, and you can run your system.

I hope it helps. Please, let me know if you have any questions.

I'm closing the issue for now.

Thank you.

Best,

Pablo