prepare_dual_topology.py --config_file=step2.ini issues #139
Description
(FEP) zhyx@zhyx:~/PyAutoFEP$ prepare_dual_topology.py --config_file=step2.ini --output_hidden_temp_dir=False
=============== mdp and run steps=================
Complex Water
min01.mdp min01.mdp
min02.mdp min02.mdp
min03.mdp nve.mdp
nve.mdp nvt.mdp
nvt.mdp npt.mdp
npt.mdp md.mdp
md.mdp -
================= Input ligands ==================
Name Molecule Topology
FXR_12 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(Cl)c1[H] lig_data/FXR_12.itp
FXR_74 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(Br)c1[H] lig_data/FXR_74.itp
FXR_76 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c([H])c1[H] lig_data/FXR_76.itp
FXR_84 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(F)c1[H] lig_data/FXR_84.itp
FXR_85 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(C([H])([H])[H])c1[H] lig_data/FXR_85.itp
FXR_88 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(C(F)(F)F)c1[H] lig_data/FXR_88.itp
================= Perturbations ==================
State A State B
FXR_12 FXR_74
FXR_12 FXR_76
FXR_12 FXR_84
FXR_12 FXR_85
FXR_12 FXR_88
=================== Poses read ===================
Name File Details
FXR_12 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x148eb217ba90>, 'topology': ['lig_data/FXR_12.itp']}
=============== Superimposed poses ===============
Name File Note
FXR_12 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x148eb217ba90>, 'topology': ['lig_data/FXR_12.itp']} Read from saved state
================== Align poses ===================
Molecule FXR_12 aligned
================ Working on pairs ================
Perturbation Pose Coordinates
============ Working on FXR_12-FXR_74 ============
FXR_12→FXR_74
================ Building system =================
Traceback (most recent call last):
File "/home/zhyx/PyAutoFEP/prepare_dual_topology.py", line 4559, in
build_data = prepare_complex_system(
File "/home/zhyx/PyAutoFEP/os_util.py", line 558, in wrap_trace
return f(*args, **kwargs)
File "/home/zhyx/PyAutoFEP/prepare_dual_topology.py", line 680, in prepare_complex_system
copyfiles = build_posres_and_chain_itp(
File "/home/zhyx/PyAutoFEP/os_util.py", line 558, in wrap_trace
return f(*args, **kwargs)
File "/home/zhyx/PyAutoFEP/prepare_dual_topology.py", line 389, in build_posres_and_chain_itp
fix_chain_restraint(this_filename, index_posre_data[prot_group][0], verbosity=verbosity)
File "/home/zhyx/PyAutoFEP/prepare_dual_topology.py", line 174, in fix_chain_restraint
restraint_data = os_util.read_file_to_buffer(restraint_file, die_on_error=True, return_as_list=True)
File "/home/zhyx/PyAutoFEP/os_util.py", line 104, in read_file_to_buffer
data_buffer = input_file.readlines()
File "/home/zhyx/anaconda3/envs/FEP/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x81 in position 47: invalid start byte
Perturbation BUG encountered while submitting generate_perturbation_map.py task Does anyone know how to solve this bug THANKS