GROMACS version:5.0.7
GROMACS modification: Yes/No
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Hi, i need for help
i don`t know what happen
ile “/home/icaro/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/icaro/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py”, line 118, in buildTopology
tops = self.gmxtop2prmtop()
File “/home/icaro/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/icaro/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/icaro/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py”, line 251, in init
self.read(fname, defines, parametrize)
File “/home/icaro/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py”, line 461, in read
self.parametrize()
File “/home/icaro/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py”, line 1021, in parametrize
raise ParameterError(‘Not all bond parameters found’)
ParameterError: Not all bond parameters found
Exiting. All files have been retained.
somebody can help me?
i used ff gromos54a7_atb_lipid.ff and command is
gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md_teste_louco_4.xtc -ci index_chains.ndx -cg 22 23 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv -nogui