protein_ligand topology builder (vol is not defined)

[imeldp96]

it gives error like this

---

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]

Hi @imeldp96,

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 (https://github.com/pablo-arantes/making-it-rain/tree/main/PROTEIN_LIGAND) for the protein ligand notebook.

I hope it helps.

Thank you.

Best,

Pablo