template not found

13 views
Skip to first unread message

N Sridhara Devi

unread,
Feb 17, 2023, 8:49:01 AM2/17/23
to gmx_MMPBSA
dear sir, while doing the gmxMMPBSA run I got this error,
INFO   ] Building Normal Complex Amber topology...
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/saiprasad/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 440, in read
    raise GromacsError('Structure contains %s molecules, but no '
GromacsError: Structure contains unk molecules, but no template defined
Exiting. All files have been retained.
can you please explain about it

Mario Sergio Valdes

unread,
Feb 17, 2023, 9:32:22 AM2/17/23
to gmx_MMPBSA
The *.itp files must be in the same directory as the topology or have their path correctly defined in the *.top file
Reply all
Reply to author
Forward
0 new messages