gmx_MMPBSA error

[maral afshinpour]

Hello, I'm new to gmx_MMPBSA. I used one of the examples for the QM calculation, and I downloaded all the sample files, but when I ran the command, I faced the following error. I would really appreciate if you could help me to solve this issue. I use version 1.4.3 and python 3.8.12

I used all the input files of this link:
https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examples/QM_MMGBSA

Do I need to change any variable in mmpbsa.in file?

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Starting
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO   ] Checking external programs...
[ERROR  ] MMPBSA_Error AMBERHOME is not set!.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
    app.make_prmtops()
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 566, in make_prmtops
    external_progs = find_progs(self.INPUT, self.mpi_size)
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/findprogs.py", line 66, in find_progs
    my_progs[prog] = ExternProg(prog, used_progs[prog], search_path).full_path
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/findprogs.py", line 165, in __init__
    if needed: self.find()
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/findprogs.py", line 169, in find
    self.full_path = which(self.prog_name, self.search_path, self.force_path)
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/findprogs.py", line 132, in which
    amberhome = get_amberhome()
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/findprogs.py", line 123, in get_amberhome
    GMXMMPBSA_ERROR('AMBERHOME is not set!')
  File "/gpfs/shared/apps_local/python/3.7-1.20/envs/ambertools/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: AMBERHOME is not set!. Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Thanks,

Maral

[Mario Sergio Valdes]

What installation method did you use? If you compiled AmberTools, you must be sure to set the AMBERHOME environment variable. The versions of AmberTools we recommend already do this automatically, just make sure you source the amber.sh file. Additionally, I recommend you use the latest version (v1.5.6) since you get the same results as version 1.4.3, but it is more stable, faster, with many more methodologies available, and with the most robust analysis tool.
Note:
If you have limitations for the installation of the new version because you are working on an HPC, it is possible to use a local environment that does not require additional permissions and has all the requirements for the installation of the latest version.