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标题: 用gmx_MMPBSA计算遇到IndexError: list index out of range Exiting [打印本页]

作者
Author: 风神Mukhta 时间: 2025-3-22 14:05
标题: 用gmx_MMPBSA计算遇到IndexError: list index out of range Exiting
我模拟了几种小分子在水体系中的结合，想导出其中两种小分子的结合自由能，gmx_MMPBSA已安装完毕，.top .ndx .in .tpr文件已上传。
运行 gmx_MMPBSA -i mmpbsa_pb.in -cs md1.tpr -ct traj_centered.xtc -ci index.ndx -cg 4 5 -cp BMA.top -o results_mmpbsa.dat -eo MMPBSA.csv
显示
[INFO ] Starting gmx_MMPBSA v1.6.3
[INFO ] Command-line
  gmx_MMPBSA -i mmpbsa_pb.in -cs md1.tpr -ct traj_centered.xtc -ci index.ndx -cg 4 5 -cp BMA.top -o results_mmpbsa.dat -eo MMPBSA.csv

[INFO ] Checking mmpbsa_pb.in input file...
[INFO ] Checking mmpbsa_pb.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/xjb/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/xjb/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/xjb/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/xjb/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/xjb/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group VBT_PLA (4_5) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group VBT (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group PLA (5) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 124, in buildTopology
tops = self.gmxtop2prmtop()
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 565, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 854, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 346, in __init__
self.read(fname, defines, parametrize)
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 407, in read
bond, bond_type = self._parse_bonds(line, bond_types, molecule.atoms)
  File "/home/xjb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 600, in _parse_bonds
funct = int(words[2])
IndexError: list index out of range
Exiting. All files have been retained.
这个问题好像是无法识别【bond】的有关信息么？我有一个问题，在模拟体系仅有小分子的时候，我选择其中一个小分子的.top文件去include各种分子的 .itp文件，这一步是对是错。如果是对的话，它应该会识别BMA.top中include的 .itp文件中的【bond】吧。
希望各位老师能够指导我一下，让我有修改的方向，目前我实在无从下手。

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