unable to install

[shrijoshi20]

i tried to install AMDock using the given method but getting following errors

(base) shrikant@shrikant-HP:~$ amdock
Traceback (most recent call last):
File "/home/shrikant/miniconda3/envs/AMDock/bin/AMDock", line 5, in
from AMDock.Docking_Program import run
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in
from AMDock.result_tab import Results
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in
from AMDock.variables import Variables
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/variables.py", line 6, in
import AutoDockTools, pymol
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/pymol/init.py", line 558, in
import pymol._cmd
ImportError: /home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/pymol/../../../libnetcdf.so.19: undefined symbol: H5Pset_fapl_ros3

[Valdes-Tresanco-MS]

Please, show me the output of conda list

[shrijoshi20]

(base) shrikant@shrikant-HP:~$ conda list

packages in environment at /home/shrikant/miniconda3:

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
adblockparser 0.7 pypi_0 pypi
attrs 23.1.0 pypi_0 pypi
automat 22.10.0 pypi_0 pypi
boltons 23.0.0 py38h06a4308_0
brotlipy 0.7.0 py38h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.0 h5eee18b_0
ca-certificates 2023.05.30 h06a4308_0
certifi 2023.5.7 py38h06a4308_0
cffi 1.15.1 py38h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 23.5.2 py38h06a4308_0
conda-content-trust 0.1.3 py38h06a4308_0
conda-libmamba-solver 23.5.0 py38h06a4308_0
conda-package-handling 2.1.0 py38h06a4308_0
conda-package-streaming 0.8.0 py38h06a4308_0
constantly 15.1.0 pypi_0 pypi
cryptography 39.0.1 py38h9ce1e76_2
fmt 9.1.0 hdb19cb5_0
funcparserlib 1.0.1 pypi_0 pypi
h2 4.1.0 pypi_0 pypi
hpack 4.0.0 pypi_0 pypi
hyperframe 6.0.1 pypi_0 pypi
hyperlink 21.0.0 pypi_0 pypi
icu 58.2 he6710b0_3
idna 3.4 py38h06a4308_0
incremental 22.10.0 pypi_0 pypi
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
libarchive 3.6.2 h6ac8c49_2
libcurl 8.1.1 h251f7ec_1
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_0
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libmamba 1.4.1 h2dafd23_1
libmambapy 1.4.1 py38h2dafd23_1
libnghttp2 1.52.0 h2d74bed_1
libsolv 0.7.22 he621ea3_0
libssh2 1.10.0 hdbd6064_2
libstdcxx-ng 11.2.0 h1234567_1
libxml2 2.10.3 hcbfbd50_0
lz4-c 1.9.4 h6a678d5_0
ncurses 6.4 h6a678d5_0
openssl 3.0.9 h7f8727e_0
packaging 23.0 py38h06a4308_0
pcre2 10.37 he7ceb23_1
pillow 10.0.0 pypi_0 pypi
pip 23.1.2 py38h06a4308_0
pluggy 1.0.0 py38h06a4308_1
priority 1.3.0 pypi_0 pypi
psutil 5.9.5 pypi_0 pypi
pybind11-abi 4 hd3eb1b0_1
pycosat 0.6.4 py38h5eee18b_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py38h06a4308_0
pyqt5 5.15.9 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.12.2 pypi_0 pypi
pysocks 1.7.1 py38h06a4308_0
python 3.8.17 h955ad1f_0
qt5reactor 0.6.3 pypi_0 pypi
readline 8.2 h5eee18b_0
reproc 14.2.4 h295c915_1
reproc-cpp 14.2.4 h295c915_1
requests 2.29.0 py38h06a4308_0
ruamel.yaml 0.17.21 py38h5eee18b_0
ruamel.yaml.clib 0.2.6 py38h5eee18b_1
setuptools 67.8.0 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_1
splash 3.5 pypi_0 pypi
sqlite 3.41.2 h5eee18b_0
tk 8.6.12 h1ccaba5_0
toolz 0.12.0 py38h06a4308_0
tqdm 4.65.0 py38hb070fc8_0
twisted 22.10.0 pypi_0 pypi
typing-extensions 4.7.1 pypi_0 pypi
urllib3 1.26.16 py38h06a4308_0
wheel 0.38.4 py38h06a4308_0
xvfbwrapper 0.2.9 pypi_0 pypi
xz 5.4.2 h5eee18b_0
yaml-cpp 0.7.0 h295c915_1
zlib 1.2.13 h5eee18b_0
zope-interface 6.0 pypi_0 pypi
zstandard 0.19.0 py38h5eee18b_0
zstd 1.5.5 hc292b87_0

[nayanmondal1337]

me too have similar issue. the output is

(base) nayan@nayan:~/Desktop$ conda list

packages in environment at /home/nayan/miniconda3:

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
amdock 1.6.2 pypi_0 pypi
autodocktools-py3 1.5.7.post1+9.gda0c87c pypi_0 pypi
brotlipy 0.7.0 py39h27cfd23_1003
ca-certificates 2021.7.5 h06a4308_1
certifi 2021.5.30 py39h06a4308_0
cffi 1.14.6 py39h400218f_0
chardet 4.0.0 py39h06a4308_1003
conda 4.10.3 py39h06a4308_0
conda-package-handling 1.7.3 py39h27cfd23_1
cryptography 3.4.7 py39hd23ed53_0
docutils 0.17.1 pypi_0 pypi
idna 2.10 pyhd3eb1b0_0
ld_impl_linux-64 2.35.1 h7274673_9
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libstdcxx-ng 9.3.0 hd4cf53a_17
mmcif-pdbx 2.0.1 pypi_0 pypi
mpi4py 3.1.4 pypi_0 pypi
ncurses 6.2 he6710b0_1
numpy 1.25.2 pypi_0 pypi
openssl 1.1.1k h27cfd23_0
pdb2pqr 3.6.1 pypi_0 pypi
pip 21.1.3 py39h06a4308_0
propka 3.5.0 pypi_0 pypi
pycosat 0.6.3 py39h27cfd23_0
pycparser 2.20 py_2
pyopenssl 20.0.1 pyhd3eb1b0_1
pyqt5 5.15.9 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.12.2 pypi_0 pypi
pysocks 1.7.1 py39h06a4308_0
python 3.9.5 h12debd9_4
readline 8.1 h27cfd23_0
requests 2.25.1 pyhd3eb1b0_0
ruamel_yaml 0.15.100 py39h27cfd23_0
setuptools 52.0.0 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_0
sqlite 3.36.0 hc218d9a_0
tk 8.6.10 hbc83047_0
tqdm 4.61.2 pyhd3eb1b0_1
tzdata 2021a h52ac0ba_0
urllib3 1.26.6 pyhd3eb1b0_1
wheel 0.36.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3

[shrijoshi20]

Kindly help me out in getting issue solved and install AMDock. Thanks.

[Valdes-Tresanco-MS]

I apologize for my delayed response. It seems like pymol changes. I will check what's going on and try to fix it ASAP.

[deepakshilkar]

Same error

Apps$ AMDock Traceback (most recent call last): File "/home/user/anaconda3/envs/AMDock/bin/AMDock", line 5, in <module> from AMDock.Docking_Program import run File "/home/user/anaconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 3, in <module> from AMDock.checker import Checker File "/home/user/anaconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/checker.py", line 1, in <module> from AMDock.warning import (prot_with_metal_warning, metal_no_ADzn_warning1, File "/home/user/anaconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/warning.py", line 1, in <module> from PyQt5.QtWidgets import * ImportError: /home/user/anaconda3/envs/AMDock/lib/python3.9/site-packages/PyQt5/QtWidgets.abi3.so: undefined symbol: _ZdlPvm, version Qt_5