error running gmx_MMPBSA for files prepared using CHARMM-GUI

[gagandeep singh]

Dear Mario,

I am running binding energy calculations of a protein-ligand system of my friend.The MD simulation system was prepared using CHARMM-GUI and it is showing the error:

[ERROR  ] MMPBSA_Error /home/gsk/anaconda3/envs/AmberTools20/bin/tleap failed when querying _GMXMMPBSA_leap.in.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/gsk/anaconda3/envs/AmberTools20/bin/gmx_MMPBSA", line 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==0+unknown', 'console_scripts', 'gmx_MMPBSA')())
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/app.py", line 97, in gmxmmpbsa
    app.make_prmtops()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/main.py", line 579, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/make_top.py", line 115, in buildTopology
    tops = self.makeToptleap()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/make_top.py", line 1168, in makeToptleap
    GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + 'leap.in'))
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/gsk/anaconda3/envs/AmberTools20/bin/tleap failed when querying _GMXMMPBSA_leap.in. Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Logfile is attached for your reference where leap has added few atoms and couldn't assign a type to it along with missing angle parameters.

Kindly help in this regard.

Best Regards,

Gagandeep Singh

--

Assistant Research Officer (Biotechnology)

Central Ayurveda Research Institute, Jhansi

Ph.D. Scholar

KSBS, IIT Delhi

Mob- 8178163366, 8285477478

[Mario Sergio Valdes]

For the CHARMM force field you must include the topology (-cp topol.top)

Cheers!

Mario S