Problem Passing Arguement to do loop

[stephenmolnar]

This code now works without any complaints:

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Mon May 13 09:50:54 2019

@author: comp
"""

import subprocess
with open('ligand') as infile:
ligand = infile.read().strip().split()
for nvar in ligand:
command = [
"./pythonsh", "./prepare_ligand4.py",
"-l", nvar + ".mol2",
"-o", nvar + ".pbdqt" ]
proc = subprocess.Popen(command, stdout=subprocess.PIPE)
out, err = proc.communicate()
if proc.returncode:
print ('Subprocess FAILED:', proc.command)

Many thanks for the help.