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])
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()
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