Error while running MMPBSA

[Chardi Shahiya]

Hi Sir.

I am getting an error while trying to run MMPBSA for the analysis of the MD of Cyclodextrin and Estradiol.

(gmxMMPBSA) chardi@chardi-Modern-15-B11M:~/Desktop/Test$ gmx_MMPBSA -O -i mmpbsa.in -cs Mass.pdb -ci new_test.ndx -cg 4 3 -ct BetaCD-estradiol.pdb -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs Mass.pdb -ci new_test.ndx -cg 4 3 -ct BetaCD-estradiol.pdb -cp topol.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/chardi/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/chardi/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/chardi/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/chardi/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/chardi/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 4_3 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 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 3 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/chardi/miniconda3/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/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 436, in gmx2pdb
    self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str)
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 558, in res2map
    for e in value['num']:
TypeError: string indices must be integers
Exiting. All files have been retained.

Please find attached my input files and the log file.

I will really appreaciate if you come through for me.

Kind Regards

[Mario Sergio Valdes]

This error is probably because the structure defined in -cs does not match the topology. gmx_MMPBSA accepts pdb in the -cs option, but we recommend using tpr. You can also define a trajectory in pdb format, but it is recommended to use xtc or trr.

Please attach the file gmx_MMPBSA.log to check it

[Mario Sergio Valdes]

Please make sure that the file you send me is valid so I can help you. The actual file has encrypted content. For security reasons, I will not process it. Normally, this file is small (10-50kB) and is plain text.

[gmx_MMPBSA]

We need to have evidence and proof that we interact with the community to continue maintaining and developing gmx_MMPBSA. Please post your doubts and questions in the group or on GitHub. 

If required, you can send us the files directly or through the cloud in complete confidentiality.

Sincerely,

gmx_MMPBSA team

[Mario Sergio Valdes]

Please, send me the following files to check them

- *.top + *.itp + toppar/charmm ff folder (if apply)

- *.tpr

- *.ndx 

- 10 frames *.xtc or *.trr

[Chardi Shahiya]

Thank you very much for your response.

I really appreciate.

In my case, I used a python script that would generate the final md production in .pdb format. So, all other files .ndx, .xtc, where generated from the final .pdb file. For his type of system which MD tool would you recommend me to use in order to easily have the required file for the MMPBSA? 

[Mario Sergio Valdes]

I recommend that you do not use scripts for this unless you are absolutely sure what and how it is done. There are multiple tools to perform MMPB/GBSA calculations. As authors, we suggest using gmx_MMPBSA, however, there are many more. CaFe for NAMD; MMPBSA.py, and mm_pbsa.pl for Amber; MMGBSA for Desmond; MMGBSA for CHARMM; g_mmpbsa, GMXPBSA2.1, and gmx_MMPBSA (this one) for Gromacs. You can use any of them according to your purpose and expertise in the associated MD program.