gmx_MMPBSA.py报错求解ValueError: could not convert string to float

2535882172

我在使用gmx_MMPBSA.py计算结合能和能量分解时，到了最后一步报错ValueError: could not convert string to float: '*************'
，请教这种问题应该怎么解决

[INFO   ] Parsing results to output files...

  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 112, in gmxmmpbsa
    app.parse_output_files()
  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1038, in parse_output_files
    self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename % 'complex',
  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/data01/home/scy0641/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 549, in _get_energies
    self['BOND'][self.frame_idx] = float(words[2])
ValueError: could not convert string to float: '*************'
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

我的mmpbsa.in文件

Sample input file for decomposition analysis
Make sure to include at least one residue from both the receptor
and ligand in the print_res mask of the &decomp section.
http://archive.ambermd.org/201308/0075.html. This is automally
guaranteed when using "within" keyword.

&general
startframe=4750, endframe=4800, interval=1,
c2_entropy           = 1
/

&gb
igb=5, saltcon=0.150,
/

&decomp
idecomp=2, dec_verbose=3,
# This will print all residues that are less than 4 Ãa

laoman

我也遇到同样的问题，算PB和GB都能正常结束，自由能解构的时候就出现能量值太大显示成星号了。试过用原生的Amber MMPBSA.py模块去跑也一样报错。感觉应该是体系的问题。换了一个体系重跑就能正常decomposition了。

2535882172

我看到这种错误是因为PBC没有处理好，或者结构一致性出问题

ZHIMING123

你好，gmx_MMPBSA.py这个脚本能发下吗 我在官网找不到了

uenh1998

您好，我也遇到了这个问题，请问你解决了吗