Error running Protein ligand CHARMff example

[Chandan Choudhury]

Dear user,

I have installed the gmx_MMPBSA using conda and I have downloaded the Protein_ligand_CHARMMff example. 

When I try to execute gmx_MMPBSA gromacs not found error is shown.

Steps performed:

1. $source GMXRC

2. set gmx_path="/scratch/chandan/apps/gmx/2021.5/bin/" in mmpbsa.in

3. $gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2

[INFO ] Starting gmx_MMPBSA v1.5.1
[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
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/chandan/apps/anaconda3/envs/AmberTools21/bin/cpptraj
[INFO ] tleap found! Using /home/chandan/apps/anaconda3/envs/AmberTools21/bin/tleap
[INFO ] parmchk2 found! Using /home/chandan/apps/anaconda3/envs/AmberTools21/bin/parmchk2
[INFO ] sander found! Using /home/chandan/apps/anaconda3/envs/AmberTools21/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.
File "/home/chandan/apps/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/chandan/apps/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/home/chandan/apps/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 523, in make_prmtops
external_progs = utils.find_progs(self.INPUT, self.mpi_size) if self.master else {}
File "/home/chandan/apps/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 683, in find_progs
GMXMMPBSA_ERROR('Could not find necessary program [ GROMACS ]')
File "/home/chandan/apps/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: Could not find necessary program [ GROMACS ]
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Please suggest any workaround.

Thank you!

Chandan

[Mario Sergio Valdes]

Can you show me the output of these commands?

which gmx
ls /scratch/chandan/apps/gmx/2021.5/bin/

It looks like you don't have access to gmx either way.