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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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Glycam.ipynb Error generating Amber Topology #98

Closed pramsland closed 6 months ago

pramsland commented 8 months ago

I get the following error when trying to generate the Amber Topology using the default parameters on Glycam.ipynb

NameError Traceback (most recent call last) in <cell line: 77>() 75 vol = float(line.split()[1]) 76 ---> 77 vol_lit = vol pow(10, -27) 78 atom_lit = 9.03 pow(10, 22) 79 conc = float(Concentration)

NameError: name 'vol' is not defined

pablo-arantes commented 7 months ago

Hi @pramsland,

Sorry for the delay. You have an issue on AMBER tleap, probably the atom name or other issue in your PDB file are creating some problems in the topology generation step. Can you please double-check your file and compare with our example file? This notebook was created to run glycan systems from GLYCAM server (https://glycam.org/#). Are you using a PDB file from GLYCAM?

Thank you.