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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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NameError: name 'vol' is not defined #71

Closed jsnwx0 closed 1 year ago

jsnwx0 commented 1 year ago

Hello

The protein_ligand still works well?

When I used it, the error is below:

NameError Traceback (most recent call last)

in () 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 Any good suggestion? Many thanks. WANG
pablo-arantes commented 1 year ago

Hi,

What do you mean with "still works well"? The notebook is working fine, as always. I've tried for differente ligands and everything went well.

You have an issue at topology generation step. 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 the examples PDB that we have here in GitHub for the protein ligand notebook.

Pablo

jsnwx0 commented 1 year ago

Thanks for your information. I checked my my pdb file and it seems different.

Many thanks again.

Best wihses.

WANG

At 2023-06-09 01:00:39, "Pablo Ricardo Arantes" @.***> wrote:

Hi,

What do you mean with "still works well"? The notebook is working fine, as always. I've tried for differente ligands and everything went well.

You have an issue at topology generation step. 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.

Pablo

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