File Error

[Harsh Rajan]

Hi,
can you help me out with this error.
Log file is attached below.

[INFO   ] Starting gmx_MMPBSA v1.6.3
[DEBUG  ] WDIR          : /mnt/d/Harsh/MD_2vwd/1219631
[DEBUG  ] AMBERHOME     : /home/sairam/miniconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/sairam/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.19 (main, May  6 2024, 19:43:03) [GCC 11.2.0]
[DEBUG  ] MPI           : /home/sairam/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 4.2.2
[DEBUG  ] OS PLATFORM   : Linux-5.15.153.1-microsoft-standard-WSL2-x86_64-with-glibc2.35
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #1 SMP Fri Mar 29 23:14:13 UTC 2024
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i LPBE_mmpbsa.in -cs 32-md.tpr -ct 36-md-fit.xtc -ci index.ndx -cg 3 4 -cp topol.top -o LPBE_MMPBSA.dat -eo LPBE_MMPBSA.csv

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |#Binding free energy calculation with Linear PB (LPBE)
[DEBUG  ] |
[DEBUG  ] |#gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG  ] |
[DEBUG  ] |#Sample input file for PB calculation
[DEBUG  ] |#This input file is meant to show only that gmx_MMPBSA works.
[DEBUG  ] |#Although, we tried to use the input files as recommended in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time.
[DEBUG  ] |#Feel free to change the parameters #according to what is better for your system.
[DEBUG  ] |
[DEBUG  ] |&general
[DEBUG  ] |sys_name="Linear_PB",
[DEBUG  ] |startframe=1,
[DEBUG  ] |endframe=100,
[DEBUG  ] |forcefields="leaprc.protein.ff14SB"
[DEBUG  ] |/
[DEBUG  ] |&pb
[DEBUG  ] |radiopt=0, istrng=0.150,
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ]
[INFO   ] Checking LPBE_mmpbsa.in input file...
[INFO   ] Checking LPBE_mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version 4.x.x!
[ERROR  ] MMPBSA_Error

Could not find necessary program [ GROMACS ]

Check the gmx_MMPBSA.log file to report the problem.


Thanks

Regards

[Harsh Rajan]

After sourcing the latest gromacs 
the following error occurred

mpirun -np 2 gmx_MMPBSA -O -i protein_lig_mmpbsa.in -cs 32-md.tpr -ct 36-md-fit.xtc -ci index.ndx -cg 3 4 -cp topol.top -o protein_lig_MMPBSA.dat -eo protein_lig_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.6.3
[INFO   ] Command-line
  mpirun -np 2 gmx_MMPBSA -O -i protein_lig_mmpbsa.in -cs 32-md.tpr -ct 36-md-fit.xtc -ci index.ndx -cg 3 4 -cp topol.top -o protein_lig_MMPBSA.dat -eo protein_lig_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/sairam/miniconda3/envs/gmxMMPBSA/bin/sander

[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/bin/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 C-alpha_Backbone (3_4) 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 C-alpha (3) 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 Backbone (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
  File "/home/sairam/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/sairam/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/sairam/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/sairam/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 122, in buildTopology
    self.gmx2pdb()
  File "/home/sairam/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 523, in gmx2pdb
    self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str)
  File "/home/sairam/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 600, in res2map
    for e in value['num']:
TypeError: string indices must be integers
Error occurred on rank 0.
Exiting. All files have been retained.
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

[Harsh Rajan]

I would suggest it's way easier to use the -cg 1 13 and then use the index_complex index in the command, which is generated using the Protein (1) and (13) as the index_complex file.

mpirun -np 2  gmx_MMPBSA -O -i mmpbsa.in -cs *.tpr -ct **.xtc -ci index_complex.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

This should solve the issue.

Regards 

Harsh