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Problem of installing LigParGen Server Locally
- [x] I believe this to be a bug with LigParGen
- [x] This is a feature request
Issue Information
Software name & Version : LigParGen Method:
Actual Behavior
I tried to install it strictly according to the tutorial of this blog How to Install LigParGen Server Locally ?
I have created an conda environment for LigParGen installing.
- python=3.6.13
- ligpargen = 2.1
- numpy = 1.19.5
- openbabel = 2.4.1
- pandas = 1.1.5
- networkx = 2.3
Finally, the error message when running the test command is as follows:
$ LigParGen -s 'c1ccccc1' -r BNZ -c 0 -o 0 -l
LBCC converter is activated
1 molecule converted
89 audit log messages
MOLECULE HAS A CHARGE of 0
sh: 1: /home/x/boss/scripts/xZCM1A: Permission denied
cp: cannot stat 'sum': No such file or directory
sh: 1: /home/x/boss/scripts/xSPM: Permission denied
/bin/cp: cannot stat 'sum': No such file or directory
sh: 1: /home/x/boss/scripts/xSPM: Permission denied
/bin/cp: cannot stat 'sum': No such file or directory
Traceback (most recent call last):
File "/home/x/anaconda3/envs/ligpargen/bin/LigParGen", line 8, in <module>
sys.exit(main())
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/Converter.py", line 90, in main
convert(**vars(args))
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/Converter.py", line 144, in convert
mol = BOSSReader('%s.z' % resname, optim, charge, lbcc)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 283, in __init__
self.refine_data(optim, charge, lbcc)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 507, in refine_data
lbcc_MD = self.get_ImpDat(optim, charge)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 447, in get_ImpDat
odat = Refine_file('/tmp/out')
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 266, in Refine_file
flines = open(fname, 'r+')
IsADirectoryError: [Errno 21] Is a directory: '/tmp/out'
I tried the following operation, but I still got an error:
$ chmod +x xZCM1A xSPM xSPM
LBCC converter is activated
1 molecule converted
89 audit log messages
MOLECULE HAS A CHARGE of 0
sh: 1: /home/x/boss/scripts/xZCM1A: not found
cp: cannot stat 'sum': No such file or directory
sh: 1: /home/x/boss/scripts/xSPM: not found
/bin/cp: cannot stat 'sum': No such file or directory
sh: 1: /home/x/boss/scripts/xSPM: not found
/bin/cp: cannot stat 'sum': No such file or directory
Traceback (most recent call last):
File "/home/x/anaconda3/envs/ligpargen/bin/LigParGen", line 8, in <module>
sys.exit(main())
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/Converter.py", line 90, in main
convert(**vars(args))
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/Converter.py", line 144, in convert
mol = BOSSReader('%s.z' % resname, optim, charge, lbcc)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 283, in __init__
self.refine_data(optim, charge, lbcc)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 507, in refine_data
lbcc_MD = self.get_ImpDat(optim, charge)
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 447, in get_ImpDat
odat = Refine_file('/tmp/out')
File "/home/x/anaconda3/envs/ligpargen/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 266, in Refine_file
flines = open(fname, 'r+')
IsADirectoryError: [Errno 21] Is a directory: '/tmp/out'
What should I do to solve this problem?