MMPBSA and Protein files issue

[noumanistic]

Hi Pablo, the notebook was working fine till today, but now I am facing two issues.

1. MMPBSA calculations
   error: Error: Creating complex topology failed!
   b''
   b'Traceback (most recent call last):\n File "/usr/local/bin/parmed", line 11, in \n sys.exit(clapp())\n File "/usr/local/lib/python3.10/site-packages/parmed/scripts.py", line 119, in clapp\n amber_prmtop.add_parm(parm)\n File "/usr/local/lib/python3.10/site-packages/parmed/tools/parmlist.py", line 36, in add_parm\n parm = load_file(name, structure=True)\n File "/usr/local/lib/python3.10/site-packages/parmed/formats/registry.py", line 194, in load_file\n return cls.parse(filename, *args, **kwargs)\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/amberformat.py", line 353, in parse\n return LoadParm(filename, *args, **kwargs)\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/readparm.py", line 48, in LoadParm\n parm = parm.view_as(AmberParm)\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/amberformat.py", line 420, in view_as\n return cls.from_rawdata(self)\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/_amberparm.py", line 233, in from_rawdata\n inst.initialize_topology()\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/_amberparm.py", line 204, in initialize_topology\n self.box = list(box[1:]) + [box[0], box[0], box[0]]\n File "/usr/local/lib/python3.10/site-packages/parmed/amber/_amberparm.py", line 2150, in box\n box = np.array(box, dtype=np.float64, copy=False, subok=True).reshape((-1, 6))\nValueError: Unable to avoid copy while creating an array as requested.\nIf using np.array(obj, copy=False) replace it with np.asarray(obj) to allow a copy when needed (no behavior change in NumPy 1.x).\nFor more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.'
   File "/usr/local/bin/MMPBSA.py", line 98, in
   app.loadcheck_prmtops()
   File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 613, in loadcheck_prmtops
   self.normal_system = MMPBSA_System(FILES.complex_prmtop,
   File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py", line 98, in init
   self.complex_prmtop = LoadParm(complex_prmtop)
   File "/usr/local/lib/python3.10/site-packages/parmed/amber/readparm.py", line 42, in LoadParm
   parm = AmberFormat(parmname)
   File "/usr/local/lib/python3.10/site-packages/parmed/amber/amberformat.py", line 374, in init
   self.rdparm(fname)
   File "/usr/local/lib/python3.10/site-packages/parmed/amber/amberformat.py", line 450, in rdparm
   ret = _rdparm.rdparm(fname)
   OSError: Could not open com.prmtop for reading

Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
mkdir: cannot create directory ‘/content/drive/MyDrive/ww/MMPBSA_igb_1’: File exists
mv: cannot stat '_MMPBSA*': No such file or directory
mv: cannot stat 'com.prmtop': No such file or directory
mv: cannot stat 'rec.prmtop': No such file or directory
mv: cannot stat 'ligand.prmtop': No such file or directory
mv: cannot stat 'reference.frc': No such file or directory

FileNotFoundError Traceback (most recent call last)
in <cell line: 68>()
66 get_ipython().system('bash run_MMPBSA.sh 2>&1 1>/dev/null')
67
---> 68 f_mmpbsa = open(final_mmpbsa + '.dat', 'r')
69 file_contents = f_mmpbsa.read()
70 print(file_contents)

FileNotFoundError: [Errno 2] No such file or directory: '/content/drive/MyDrive/ww/hh.dat'

2. ** Unable to create protein ligand files from the very start.**
error: ERROR: Check your inputs!

please fix this