Protein_ligand.ipynb

[raphaelolipitz]

Hallo There :)

I want to run the colab script Protein_ligand.ipynb but it do not run. Besides its the same code as in the amber.ipynb this line got me the Error: vol not defined.

with open("temp.txt", 'r') as f:
for line in f:
vol = float(line.split()[1])

vol_lit = vol * pow(10, -27)
atom_lit = 9.03 * pow(10, 22)
conc = float(Concentration)
num_ion = int(vol_lit * (conc/0.15) * atom_lit)

if I change the code so that vol gets a global float, the error do not occur anymore, how ever I got the Problem that I got the Error massage that the file: ligand_gff.pdb can not be found.

Maybe the Error is here?
lig_new = os.path.join(workDir, "ligand_gaff.pdb")
.
.
.
f = open(tleap, "w")
f.write("""source """ + str(ff) + "\n"
"""source leaprc.gaff2
LIG = loadmol2 """ + str(ligand_mol2) + "\n"
"""loadamberparams """ + str(ligand_frcmod) + "\n"
"""saveoff LIG """ + str(lib) + "\n"
"""savepdb LIG """ + str(lig_new) + "\n"
"""quit""")
f.close()

tleap_command = "tleap -f " + str(tleap)
cat_command = "cat " + str(starting_end) + " " + str(lig_new) + str(" > ") + str(protein_ligand)

Thanks for your help in advance!
Raphael

[hajnal-adam]

I ran into the same issue. A fix would be very much appreciated!