PermissionError: [Errno 13] Permission denied:

[azbvenkat]

Dear all

I installed  the gmxMMPBSA package in hpc, before that I installed amber tools 20 and set the environment also. I checked the MMPBSA.py and it's working fine.
for trying purpose I used the gmx_MMPBSA tutorial input (Protein_protein), I got  following error

-------------------------------------------------
Protein_protein]$ gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 19 20 -ct com_traj.xtc
[INFO   ] Starting
[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.
[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /opt/amber20/bin/cpptraj
[INFO   ] tleap found! Using /opt/amber20/bin/tleap
[INFO   ] parmchk2 found! Using /opt/amber20/bin/parmchk2
[INFO   ] mmpbsa_py_energy found! Using /opt/amber20/bin/mmpbsa_py_energy
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /opt/gromacs-ramd-release-2020/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...
[INFO   ] Checking if supported force fields exists in Amber data...
  File "/home/subbu/.local/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/subbu/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsa
    app.make_prmtops()
  File "/home/subbu/.local/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
    maketop = CheckMakeTop(self.FILES, self.INPUT, self.external_progs)
  File "/home/subbu/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 98, in __init__
    checkff(self.INPUT['overwrite_data'])
  File "/home/subbu/.local/lib/python3.8/site-packages/GMXMMPBSA/utils.py", line 203, in checkff
    gmxf.mkdir()
  File "/opt/amber20/miniconda/lib/python3.8/pathlib.py", line 1284, in mkdir
    self._accessor.mkdir(self, mode)
PermissionError: [Errno 13] Permission denied: '/opt/amber20/dat/leap/cmd/gmxMMPBSA'
Exiting. All files have been retained.
-----------------------------------------------------------

 I tried for all other examples the same error only getting. Due to the permission error, I checked the folder (/opt/amber20/dat/leap/cmd/) it does not contain gmxMMPBSA ?. After the installation of gmx_MMPBSA I exported the export PATH="/opt/amber20/miniconda/bin:$PATH"

really I don't know what thing is missing here ? kindly provide solution to perform the gmxMMPBSA  

Note: used (Gromacs2020.2, AMBERTools 20 , gmxMMPBSA version 1.4.1 )

Thank you 

[Mario Sergio Valdes]

Hi and welcome!

gmx_MMPBSA tries to create a data folder on that path, containing several force fields (GLYCAM_06h- and Zwitterionic amino acids). Since that folder belongs to the system, it needs write permissions. You can run gmx_MMPBSA with administrative permissions or change the permissions to the /opt/amber20 folder and all subdirectories.

Best!

Mario S.

[Mario Sergio Valdes]

I forgot to mention it. What I described above, you only need to run it only once, it is not necessary to run gmx_MMPBSA always with admin permissions, since executing with admin permissions is somewhat complicated in HPC. You should only run gmx_MMPBSA with these permissions when the data folder is updated, which we will point out appropriately in the changelog. If this is the 1st time you install gmx_MMPBSA then the folder will be created, otherwise, you must use the overwrite_data variable to overwrite it.

If you solved the problem, please tell us so we can identify the thread with a tag and that new users can have an appropriate reference.

Best!

Mario S.

[azbvenkat]

Yes, its permission related issue only and now it's fixed. 

Thank you very much 

[Mario Sergio Valdes]

Excellent!

Best!

Mario S.