gmx_MMPBSA typeerror and MPI_ABORT

[fred]

Dear all, i am new to MD simulation. i am using charmm36 for protein ligand simulation.  while i am using gmx_MMPBSA command for energy calculation, i received following error. any ideas of  solving this? Thanks in advance

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

[INFO   ] Starting

[INFO   ] Command-line

  gmx_MMPBSA -O -i mmpbsa1.in -cs md_0_20.tpr -ci index.ndx -cg 1 13 -ct md_0_20_center.xtc -cp topol.top -rs 4WKQ_processed.gro

[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 variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use qh_entropy for Quasi-Harmonic approximation and i_entropy for Interaction entropy approximation 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...

[INFO   ] cpptraj found! Using /mnt/c/Users/user/desktop/gromacs-MD/vchemistry5/amber20_src/bin/cpptraj

[INFO   ] tleap found! Using /mnt/c/Users/user/desktop/gromacs-MD/vchemistry5/amber20_src/bin/tleap

[INFO   ] parmchk2 found! Using /mnt/c/Users/user/desktop/gromacs-MD/vchemistry5/amber20_src/bin/parmchk2

[INFO   ] sander found! Using /mnt/c/Users/user/desktop/gromacs-MD/vchemistry5/amber20_src/bin/sander

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

[INFO   ] gmx found! Using /usr/local/gromacs/bin/gmx

[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...

[INFO   ] Checking gmxMMPBSA data folder exists in Amber data...

[INFO   ] Get PDB files from GROMACS structures files...

[INFO   ] Making gmx_MMPBSA index for complex...

[INFO   ] Running command: echo name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n  1 | 13\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx

[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[INFO   ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx editconf -f md_0_20.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx

[INFO   ] A receptor structure file was defined. Using MT approach...

[INFO   ] Normal receptor: Saving group None in None file as _GMXMMPBSA_REC.pdb

  File "/home/bioinfo/.local/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/home/bioinfo/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa

    app.make_prmtops()

  File "/home/bioinfo/.local/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops

    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/bioinfo/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 115, in buildTopology

    self.gmx2pdb()

  File "/home/bioinfo/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 228, in gmx2pdb

    logging.info('Running command: ' + (' '.join(editconf_echo_args)) + ' | ' + ' '.join(editconf_args))

TypeError: sequence item 7: expected str instance, NoneType found

Error occured 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.

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

[LAPTOP-SHNLJKIQ:00035] 1 more process has sent help message help-btl-vader.txt / cma-permission-denied

[LAPTOP-SHNLJKIQ:00035] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages  

[Mario Ernesto]

Hello there! As per the command line you are using:

gmx_MMPBSA -O -i mmpbsa1.in -cs md_0_20.tpr -ci index.ndx -cg 1 13 -ct md_0_20_center.xtc -cp topol.top -rs 4WKQ_processed.gro

I assume you are interested in using a reference structure file?

In that case, the flag should be '-cr'

gmx_MMPBSA -O -i mmpbsa1.in -cs md_0_20.tpr -ci index.ndx -cg 1 13 -ct md_0_20_center.xtc -cp topol.top -cr 4WKQ_processed.pdb

Take into account that the reference structure should be a PDB file, and it's recommended to be the PDB file used to generate the topology in GROMACS or CHARMM-GUI.

Hope this helps!

Cheers!

Mario E.

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[fred]

Thanks Mario! the error is fixed. Although there is another error occurred (ValueError: cannot reshape array of size 14784), it has been fixed through the LP related procedure (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand_LPH_atoms_CHARMMff/). The system now is calculating complex contribution. Lets see how it goes. Thanks for the helps again. 

Fred

[Mario Sergio Valdes]

Excellent Fred...

Since you have obtained previous errors, we recommend that you do some tests prior to your calculations. Although this method is fast, it can take some time depending on your computational resources.

Do a test with a few frames (10  generally, should be enough) and see if the results you get are consistent. Remember to remove the PBC.

We hope that our program is up to the task you need.

Cheers!

Mario S.