Problem of installing LigParGen Server Locally

[sbkk000]

• [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.

1. python=3.6.13
2. ligpargen = 2.1
3. numpy = 1.19.5
4. openbabel = 2.4.1
5. pandas = 1.1.5
6. 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?

[RaphaelRobidas]

The scripts that are "not found" use csh. I had the same issue and fixed it by installing csh.

[eastsheng]

I had the same issue, did you fix it?

[GsGithub17]

I have the same issue.

Is this solved? Any suggestions?