the plt.pdb do not exist

[unistdJRZ]

Dear authors:
I have finish the installation proceduros with ur instruction and passed test_ligpargen.py.
however when i running ligpargen -s 'c1ccc(cc1)O' -n phenol -p phenol -r MOL -c 0 -o 0 -cgen CM1A that on ur example command, its report File "/mnt/g/BOSS/ligpargen/ligpargen/tools/boss.py", line 208, in run
shutil.copyfile('plt.pdb', pdbFile)
File "/root/miniconda3/envs/py37/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'plt.pdb'

i have no idea whats wrongs, even discusse with GPT

[SARU230]

BOSS works only in 32 bit environment. So when you are installing all the dependencies make sure you use what works in 32 bit.

[unistdJRZ]

appreciate

[unistdJRZ]

thanks for ur answers again，i'm now successfuly running this project, and here is my experience: 1. ur framework writting with py37 and support only 64bit arch (prereleased wheels) and 32bit rdkit/ openbabel support only python 2.7, its hard to build a enviorment on a genuine 32bit vituralmachine, however, in the wsl, only need to run:
sudo dpkg --add-architecture i386
sudo apt update
sudo apt install -y libc6:i386 libstdc++6:i386 libgcc1:i386
libgfortran3:i386 libx11-6:i386 libncurses5:i386

could support BOSS running, besides, the configuration of BOSS have to add two enviorment varible:
export BOSSdir=/mnt/g/BOSS/boss
export PATH=$PATH:$BOSSdir/scripts otherwise the bosscmd could not detect by csh bosscmd.
Thanks for ur codes again and hopes my experience could help u makes the toturial more convience.

[wenjiett]

Hello, I still get the same error even after installing the 32-bit library.
Environment: wsl, ubuntu-22.04

Traceback (most recent call last):
  File "/home/stephen/miniconda3/envs/molyte/bin/ligpargen", line 33, in <module>
    sys.exit(load_entry_point('LigPargen', 'console_scripts', 'ligpargen')())
  File "/home/stephen/ligpargen/ligpargen/ligpargen.py", line 507, in main
    molname=args.molname, workdir= args.path, debug= args.debug)
  File "<string>", line 17, in __init__
  File "/home/stephen/ligpargen/ligpargen/ligpargen.py", line 190, in __post_init__
    self.workdir, self.debug)
  File "/home/stephen/ligpargen/ligpargen/tools/boss.py", line 208, in run
    shutil.copyfile('plt.pdb', pdbFile)
  File "/home/stephen/miniconda3/envs/molyte/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'plt.pdb'

I test my BOSS installation by typing ./BOSS in my terminal and the information is correct. I hope someone can help me figure it out.

(molyte) stephen@DESKTOP-JTTUH0B:~/boss$ ./BOSS
    Insufficient arguments! you need to specify
 at least five, i.e. ./BOSS 001 100000 0.0 0.0 0.0
    Insufficient arguments! you need to specify
 at least five, i.e. ./BOSS 001 100000 0.0 0.0 0.0

[SARU230]

I think its because you are running it on wsl.
On wsl you can create a singularity container and run ligpargen.