用gmx_MMPBSA计算遇到IndexError: list index out of range Exiting

Sunca

我模拟了两条相同的糖链的聚集，想计算结合自由能，gmx_MMPBSA是官网下载的没有问题,按照流程准备了ndx,top,tpr,xtc，将两条链分设为ligand和receptor组，但是执行时出现了下面的问题。

(gmxMMPBSA) sunca@WL:~/Gromacs/gromacs-2024.2/project/GM8tip3p/95$ gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 2 -ct gm_md_fit.xtc -cp com.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA 1.6.4
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 2 -ct gm_md_fit.xtc -cp com.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] mmpbsa_py_nabnmode found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ] gbnsr6 found! Using /home/sunca/anaconda3/envs/gmxMMPBSA/bin/gbnsr6
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/sunca/Gromacs/gromacs-2024.2/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
                                                                          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 277, in gmx2pdb
    num_com_lig_group, str_com_lig_group = get_index_groups(self.FILES.complex_index, com_lig_group)
                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sunca/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/utils.py", line 382, in get_index_groups
    return group, groups[group]
                  ~~~~~~^^^^^^^
IndexError: list index out of range
Exiting. All files have been retained.

附上了输入的文件，期待有经验或知道原因的大佬回复。

Loading0760

index.ndx是从0开始编号的，你改成0 1再试试

1.   gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 0 1 -ct gm_md_fit.xtc -cp com.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
   

复制代码

Sunca

Loading0760 发表于 2024-12-12 09:36
index.ndx是从0开始编号的，你改成0 1再试试

换成0 1就好了！谢谢大佬！