Re: gmx_MMPBSA_test IndexError

[Mario Ernesto]

did you install Parmed from out repository?

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

El lun, 16 may 2022 a las 22:18, zengshuai yan (<zengsh...@gmail.com>) escribió:

Hello everyone. I'm running gmx_MMPBSA_test by using command-line " gmx_MMPBSA_test  -n 6". But, the nine test examples were all error. When I check the log in detail, I found this error :

 [INFO   ] Starting gmx_MMPBSA v1.5.2

[INFO   ] Command-line

  mpirun -np 6 gmx_MMPBSA MPI -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2 -nogui

[INFO   ] Checking mmpbsa.in input file...

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

[INFO   ] Checking external programs...

[INFO   ] cpptraj found! Using /mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/bin/cpptraj

[INFO   ] tleap found! Using /mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/bin/tleap

[INFO   ] parmchk2 found! Using /mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/bin/parmchk2

[INFO   ] sander found! Using /mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/bin/sander

[INFO   ] Using GROMACS version > 5.x.x!

[INFO   ] gmx found! Using /mnt/nature/softmatter/gromacs-2020.6/install/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   ] Generating ligand parameters from ligand.mol2 file...

[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...

[INFO   ] Cleaning normal complex trajectories...

[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa

    app.file_setup()

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 127, in file_setup

    create_inputs(INPUT, self.normal_system, self.pre)

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 213, in create_inputs

    gb_mdin = SanderGBInput(INPUT)

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 264, in __init__

    self.mdin.change(self.parent_namelist[key], key, self.input_items[key])

  File "/mnt/nature/yanzs/apps/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/amber/mdin/mdin.py", line 197, in change

    if (value[0] == value[-1] == "'") or (value[0] == value[-1] == '"'):

IndexError: string index out of range

Error occurred on rank 0.

Exiting. All files have been retained.

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------

Hope this helps, thanks!

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/458032f8-c218-45ae-a746-ea1e94323108n%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.