ERROR while running pb and pb_decomp analysis

[Paul Schrank]

Dear all,

Sorry to bother but it seems I have an error while running PB and PB Decomposition analysis for my system, when starting to analyze the trajectory. My input command looks like this:

(I run on my google colab jupiter notebook, so that nobody is confused by the directories ;)

!source activate /content/conda_env/mmPBSA; mpirun -np 2 gmx_MMPBSA -O -i /content/mmPBSA_test/mmpbsa_test.in -cs /content/mmPBSA_test/smTG_Gln.pdb -ci /content/mmPBSA_test/smTG_Gln.ndx -cg 1 13 -ct /content/mmPBSA_test/smTG_Gln_pb_fit.xtc -lm /content/mmPBSA_test/CBZ_Gln_Gly.mol2 -nogui

And the console output till ERROR looks something like this:

[INFO ] Starting gmx_MMPBSA v1.6.0 [INFO ] Command-line mpirun -np 2 gmx_MMPBSA -O -i /content/mmPBSA_test/mmpbsa_test.in -cs /content/mmPBSA_test/smTG_Gln.pdb -ci /content/mmPBSA_test/smTG_Gln.ndx -cg 1 13 -ct /content/mmPBSA_test/smTG_Gln_pb_fit.xtc -lm /content/mmPBSA_test/CBZ_Gln_Gly.mol2 -nogui [INFO ] Checking /content/mmPBSA_test/mmpbsa_test.in input file... [INFO ] Checking /content/mmPBSA_test/mmpbsa_test.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /content/conda_env/mmPBSA/bin/cpptraj [INFO ] tleap found! Using /content/conda_env/mmPBSA/bin/tleap [INFO ] parmchk2 found! Using /content/conda_env/mmPBSA/bin/parmchk2 [INFO ] sander found! Using /content/conda_env/mmPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /content/gromacs-2022/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 Protein_CBZ (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] Generating ligand parameters from /content/mmPBSA_test/CBZ_Gln_Gly.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 Protein (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 CBZ (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 ] Selecting residues by distance (8 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 31 residues: R:A:TYR:67 R:A:GLY:68 R:A:CYM:69 R:A:VAL:70 R:A:GLY:71 R:A:VAL:72 R:A:HIS:206 R:A:ASN:244 R:A:ILE:245 R:A:PRO:246 R:A:PHE:256 R:A:VAL:257 R:A:ASN:258 R:A:PHE:259 R:A:ASH:260 R:A:TYR:261 R:A:HIS:279 R:A:GLY:280 R:A:ASN:281 R:A:HIS:282 R:A:TYR:283 R:A:LEU:290 R:A:ALA:292 R:A:MET:293 R:A:HIS:294 R:A:TYR:296 R:A:TRP:303 R:A:TYR:307 R:A:ASP:309 R:A:PHE:310 L:Z:CBZ:1 [INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation... [INFO ] 5 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 2 CPUs... [WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM. [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /content/conda_env/mmPBSA/bin/sander [INFO ] calculating complex contribution... 0%| | 0/5 [elapsed: 00:00 remaining: ?]At line 143 of file /home/conda/feedstock_root/build_artifacts/ambertools_1661778969278/work/AmberTools/src/sander/rgroup.F90 (unit = 5, file = '_GMXMMPBSA_pb_decomp_com.mdin') Fortran runtime error: End of file Error termination. Backtrace: At line 143 of file /home/conda/feedstock_root/build_artifacts/ambertools_1661778969278/work/AmberTools/src/sander/rgroup.F90 (unit = 5, file = '_GMXMMPBSA_pb_decomp_com.mdin') Fortran runtime error: End of file Error termination. Backtrace: #0 0x7f9f6a3e9068 in read_sf_internal at ../../../libgfortran/io/transfer.c:325 #1 0x7f9f6a3e6d7d in read_default_char1 at ../../../libgfortran/io/read.c:455 #2 0x7f9f6a3ea007 in formatted_transfer_scalar_read at ../../../libgfortran/io/transfer.c:1787 #3 0x7f9f6a3eac66 in formatted_transfer at ../../../libgfortran/io/transfer.c:2491 #4 0x55e493a31f31 in ??? #5 0x55e4939bcd2f in ??? #6 0x55e4939685b1 in ??? #7 0x55e493965d6d in ??? #8 0x55e493965de5 in ??? #9 0x7f9f6a0a7082 in ??? #10 0x55e493797838 in ??? [ERROR ] CalcError /content/conda_env/mmPBSA/bin/sander failed with prmtop COM.prmtop! If you are using sander and PB calculation, check the *.mdout files to get the sander error . Check the gmx_MMPBSA.log file to report the problem. File "/content/conda_env/mmPBSA/bin/gmx_MMPBSA", line 8, in <module> sys.exit(gmxmmpbsa()) File "/content/conda_env/mmPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa app.run_mmpbsa() File "/content/conda_env/mmPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/content/conda_env/mmPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/content/conda_env/mmPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) + File "/content/conda_env/mmPBSA/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.') CalcError: /content/conda_env/mmPBSA/bin/sander failed with prmtop COM.prmtop! If you are using sander and PB calculation, check the *.mdout files to get the sander error Check the gmx_MMPBSA.log file to report the problem. Error occurred on rank 1. Exiting. All files have been retained. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1

I also tried running GB calculation using the programm and it work without any issues.

I annotated a test run (with also all binary files from the failed test run) in the appendix, if anyone wants to replicate the run.

For troubleshooting, I already tried:

- not using MPI, because I though maybe RAM wasn't enough for the job to run

- Rerunning while using V5.1 of ccptraj

- Replicated the removal of PBC and fitting like suggested in another post (https://groups.google.com/g/gmx_mmpbsa/c/ZbB19AvnuJo)

I greatly appreciate any help and thank all of you in advance for your time :)

Best regards

Paul Schrank

[Mario Ernesto]

Thank Paul for reporting... This is an issue that has been fixed already... Please check: 

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/352#issuecomment-1456630847

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[Mario Sergio Valdes]

We will release v1.6.1 with this fix in a few days.

[Paul Schrank]

Oh I see so it had something to do with my python :D Thanks I just input: 

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U (as provided in your mentioned issue)

after activating the envoirment and it installed all neccessary dependencies :)

Now it works

Thank you very much and have a nice evening

[Mario Sergio Valdes]

Actually, this is a bug in version v1.6.0. As in this version, we introduced some internal structural changes to improve the implementation of new methods, then we had this little bug that escaped us during testing. Installing the development version as you did, solved the problem. However, we will release version v1.6.1 to prevent other users from having the same bug.