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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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Error on "Parameters to generate the molecule topology on GAFF2 force field:" #70

Closed chemuser168 closed 1 year ago

chemuser168 commented 1 year ago

I am using the program on Google collab and I keep getting an error when I get to the "Parameters to generate the molecule topology on GAFF2 force field:" cell.

It says:

NameError Traceback (most recent call last)

in <cell line: 157>() 155 vol = float(line.split()[1]) 156 --> 157 vol_lit = vol pow(10, -27) 158 atom_lit = 9.03 pow(10, 22) 159 conc = float(Concentration)

NameError: name 'vol' is not defined

pablo-arantes commented 1 year ago

Hi @chemuser168,

This issue is on topology generation. The tleap is not able to create your topology for your protein/ligand structure. Can you please double-check your ligand PDB file? Please, compare with examples PDB that we have here in GitHub for the protein ligand notebook.

I hope it helps.

Thank you.

Best,

Pablo