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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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prepare_dual_topology.py --config_file=step2.ini issues #139

Open wenzeyu126553 opened 7 months ago

wenzeyu126553 commented 7 months ago

(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

wenzeyu126553 commented 7 months ago

(FEP) zhyx@zhyx:~/PyAutoFEP$ conda list

packages in environment at /home/zhyx/anaconda3/envs/FEP:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alchemlyb 0.6.0 pypi_0 pypi alsa-lib 1.2.11 hd590300_1 conda-forge attr 2.5.1 h166bdaf_1 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.3.11 h06a4308_0 defaults cairo 1.18.0 h3faef2a_0 conda-forge certifi 2024.2.2 py38h06a4308_0 defaults chardet 5.2.0 py38h578d9bd_1 conda-forge contourpy 1.1.1 py38h7f3f72f_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge dbus 1.13.18 hb2f20db_0 defaults decorator 5.1.1 pyhd3eb1b0_0 defaults expat 2.6.2 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_1 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.50.0 py38h01eb140_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge glib 2.80.0 hf2295e7_1 conda-forge glib-tools 2.80.0 hde27a5a_1 conda-forge graphite2 1.3.14 h295c915_1 defaults greenlet 3.0.3 py38h17151c0_0 conda-forge gst-plugins-base 1.22.9 hfa15dee_1 conda-forge gstreamer 1.22.9 h98fc4e7_1 conda-forge harfbuzz 8.3.0 h3d44ed6_0 conda-forge icu 73.2 h59595ed_0 conda-forge importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge joblib 1.3.2 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py38h7f3f72f_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h7b6447c_0 defaults lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.38 h1181459_1 defaults lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 21_linux64_openblas conda-forge libboost 1.84.0 h8013b2b_2 conda-forge libboost-python 1.84.0 py38hae673b5_2 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 21_linux64_openblas conda-forge libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge libclang13 18.1.2 default_h5d6823c_1 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20230828 h5eee18b_0 defaults libevent 2.1.12 hdbd6064_1 defaults libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgcrypt 1.10.3 hd590300_0 conda-forge libgfortran-ng 13.2.0 h69a702a_5 conda-forge libgfortran5 13.2.0 ha4646dd_5 conda-forge libglib 2.80.0 hf2295e7_1 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libgpg-error 1.48 h71f35ed_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 21_linux64_openblas conda-forge libllvm15 15.0.7 hb3ce162_4 conda-forge libllvm18 18.1.2 h2448989_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libogg 1.3.5 h27cfd23_1 defaults libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7b6447c_0 defaults libpng 1.6.43 h2797004_0 conda-forge libpq 16.2 h33b98f1_1 conda-forge libsndfile 1.2.2 hc60ed4a_1 conda-forge libsqlite 3.45.2 h2797004_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libsystemd0 255 h3516f8a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h7b6447c_0 defaults libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h662e7e4_0 conda-forge libxml2 2.12.6 h232c23b_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 h6a678d5_0 defaults matplotlib 3.7.2 py38h06a4308_0 defaults matplotlib-base 3.7.2 py38h1128e8f_0 defaults mpg123 1.32.4 h59595ed_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.3.0 hf1915f5_4 conda-forge mysql-libs 8.3.0 hca2cd23_4 conda-forge ncurses 6.4 h6a678d5_0 defaults networkx 3.1 pypi_0 pypi nspr 4.35 h6a678d5_0 defaults nss 3.98 h1d7d5a4_0 conda-forge numpy 1.24.4 py38h59b608b_0 conda-forge openbabel 3.1.1 py38h8a87c98_9 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.2.1 hd590300_1 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pandas 2.0.3 py38h01efb38_1 conda-forge pcre2 10.43 hcad00b1_0 conda-forge pillow 10.2.0 py38ha43c96d_0 conda-forge pip 23.3.1 py38h06a4308_0 defaults pixman 0.43.2 h59595ed_0 conda-forge ply 3.11 py38_0 defaults pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulseaudio-client 17.0 hb77b528_0 conda-forge pycairo 1.26.0 py38h1a1917b_0 conda-forge pymbar 3.0.5 pypi_0 pypi pyparsing 3.0.9 py38h06a4308_0 defaults pyqt 5.15.10 py38h6a678d5_0 defaults pyqt5-sip 12.13.0 py38h5eee18b_0 defaults python 3.8.18 hd12c33a_1_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.8 4_cp38 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge qt-main 5.15.8 h112747c_20 conda-forge rdkit 2024.03.1 py38h924c20c_0 conda-forge readline 8.2 h5eee18b_0 defaults reportlab 4.1.0 py38h01eb140_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge scikit-learn 1.3.2 pypi_0 pypi setuptools 68.2.2 py38h06a4308_0 defaults sip 6.7.12 py38h6a678d5_0 defaults six 1.16.0 pyh6c4a22f_0 conda-forge sqlalchemy 2.0.29 py38h01eb140_0 conda-forge sqlite 3.41.2 h5eee18b_0 defaults threadpoolctl 3.4.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 py38h06a4308_0 defaults tornado 6.3.3 py38h5eee18b_0 defaults typing-extensions 4.10.0 hd8ed1ab_0 conda-forge typing_extensions 4.10.0 pyha770c72_0 conda-forge unicodedata2 15.1.0 py38h01eb140_0 conda-forge wheel 0.41.2 py38h06a4308_0 defaults xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xkeyboard-config 2.41 hd590300_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.4.6 h5eee18b_0 defaults zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge