search

pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
385 stars 105 forks source link

Can't run protein-nanoparticle simulation. #99

Closed noumanistic closed 7 months ago

noumanistic commented 8 months ago

can you help me how can i run protein-nanoparticle simulation. i am using https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb but it makes error at generating topology. NameError Traceback (most recent call last) in <cell line: 159>() 157 vol = float(line.split()[1]) 158 --> 159 vol_lit = vol pow(10, 27) 160 atom_lit = 9.03 pow(10, -22) 161 conc = float(Concentration)

NameError: name 'vol' is not defined

pablo-arantes commented 7 months ago

Hi @noumanistic,

Unfortunately this notebook was developed to run protein+ligand systems, I don't think it will work for nanoparticle. That is the reason you're having issue in the topology generation cell, somehow Amber is not recognizing your nanoparticle (probably due to the missing parameters). My suggestion is change the code for your specific case and try it again.

Thank you.

Best,

Pablo