Hİ,I have installed MMPBSA my computer which is just consist of ubuntu.I used this commands respectively.I didint get any error.
I am getting error.I attached my screenshot.MMPBSA has been installed.but I am getting error.Could you guide me please ,I have to use this tool for my phd thesis.
gmx_MMPBSA -O -i
mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc
[INFO ] Starting gmx_MMPBSA v1.5.7
[INFO ] Command-line
gmx_MMPBSA -O -i
mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc
[INFO ] Checking
mmpbsa.in input file...
[INFO ] Checking
mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/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 1_13 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 1 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Changing the Complex residues name format from GROMACS to AMBER...
[INFO ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO ] Splitting receptor and ligand in PDB files..
[INFO ] Building tleap input files...
[ERROR ] MMPBSA_Error /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/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/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 121, in buildTopology
tops = self.makeToptleap()
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1383, in makeToptleap
self._run_tleap(tleap, '
leap.in', data_path)
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1510, in _run_tleap
GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + arg1))
File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/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: /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.