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PDB2FF ligand test #11
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and descend a block by shift+tab. Update: fixed in 8ddfada.
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I googled the tl_getline(): error and it seems that it is not related to the python code itself. Instead, it is related to something with the leap.in file. Something like this: |
*** Error: tl_getline(): not interactive, use stdio.
Traceback (most recent call last):
File "0_MutaGen_main.py", line 34, in
main()
File "0_MutaGen_main.py", line 14, in main
PDB1.PDB2FF('ff_prep_temp/')
File "/gpfs23/scratch/jiany37/HTP_trial/03022021_enzyme_workflow-develop_qz/Class_PDB.py", line 845, in PDB2FF
ligands_pathNchrg = self.stru.build_ligands(lig_dir, ifcharge=1)
File "/gpfs23/scratch/jiany37/HTP_trial/03022021_enzyme_workflow-develop_qz/Class_Structure.py", line 512, in build_ligands
net_charge = lig.get_net_charge(method=c_method, ph=ph)
File "/gpfs23/scratch/jiany37/HTP_trial/03022021_enzyme_workflow-develop_qz/Class_Structure.py", line 1855, in get_net_charge
mol = next(pybel.readfile('pdb', temp_pdb3_path))
File "/home/jiany37/Software_installed/openbabel-3-1-1_installed/lib/python3.8/site-packages/openbabel/pybel.py", line 161, in readfile
raise IOError("No such file: '%s'" % filename)
OSError: No such file: './cache/ligand_temp3.pdb'
3WIW ligand EPE. The error occurs before ff can be generated. But pdb2pqr adds one H atom to each N and O(=S) atoms, which is obviously not reasonable.
Another issue with PDB2PQR: it cannot process selenocysteine correctly and the output PDB will skip this residue. Example: 3F3K
Ions that get_protonation do not support: Mn(II), Co(III), Fe(III) (5HIO)
Transition metal ions Co only has +2 in leap tip3p ff. In the future, we need to figure out a way to determine the charge for these ions because the coordinate parts in PDB files do not have this information. Most common example: Fe.
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