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[Bug-gmx_MMPBSA]: teLeap Error #524

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mkoiral opened this issue Jul 25, 2024 · 30 comments
Open

[Bug-gmx_MMPBSA]: teLeap Error #524

mkoiral opened this issue Jul 25, 2024 · 30 comments

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@mkoiral
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mkoiral commented Jul 25, 2024

Bug summary

I was calculating MMPBSA using my gromacs result and ended up with error.

Terminal output

combine_snap.sh  _GMXMMPBSA_COM_FIXED.pdb  _GMXMMPBSA_leap.in     gmx_mmpbsa.log         _GMXMMPBSA_REC.pdb  index_protein.ndx  ligand           production_2.tpr        receptor                    traj_chainA.xtc
entropy.txt      _GMXMMPBSA_COM_index.ndx  _GMXMMPBSA_LIG_F1.pdb  gmx_MMPBSA.log         gmx_mmpbsa.sh       input.in           LIG.prmtop       production_2.xtc        snapshot_list_ligand.txt    traj_chainB.xtc
gmx_MMPBSA       _GMXMMPBSA_COM.pdb        _GMXMMPBSA_LIG.pdb     _GMXMMPBSA_REC_F1.pdb  index.ndx           leap.log           md_seperate.log  production_noPBC_2.xtc  snapshot_list_receptor.txt  traj_protein.xtc

gmx_MMPBSA.log

Screenshot (15)

Operating system

Linux

gmx_MMPBSA Version

No response

Python version

No response

Installation

conda AmberTools + conda
@Valdes-Tresanco-MS
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Please, use the -cp topol.top instead

@mkoiral
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mkoiral commented Jul 25, 2024 via email

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@Valdes-Tresanco-MS
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Please, attach the gmx_MMPBSA.log file to check your config. Do you check the documentation?

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@Valdes-Tresanco-MS
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Please, use GitHub to attach the file since it is not working via email

@mkoiral
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mkoiral commented Jul 30, 2024

gmx_MMPBSA.log
please see this!

@Valdes-Tresanco-MS
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Valdes-Tresanco-MS commented Jul 30, 2024 •
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Well, the problem is that you are running gmx_MMPBSA in serial mode. To parallelize the calculations you must use mpirun. For example:

mpirun -np 120 gmx_MMPBSA -i input.in -cp topol.top -cs production_2.tpr -ci index.ndx -cg 18 17 -ct production_noPBC_2.xtc -rt traj_chainB.xtc -lt traj_chainA.xtc -o output_MMPBSA.dat -eo output_energy.dat

Which means that you will use 120 CPUs. Please, check the link below to get an example of how to run it in an HPC.

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@Valdes-Tresanco-MS
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This error is related to issues reported with the combination of gmx_mpi and gmx_MMPBSA. You can probably use a gromacs version installed in your conda environment.

conda install -c conda-forge "gromacs<=2023.4" pocl -y -q

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@Valdes-Tresanco-MS
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Yes, gmx_mpi only modified how the calculations are done, parallelizing it with mpi, not the result. Here, gmx_MMPBSA only uses gromacs to generate indexes, PDB files, and clean up the trajectory. Make sure the gromacs you will use is greater than or equal to the one used to generate the trajectory.

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@Valdes-Tresanco-MS
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Unfortunately, no. We tried to implement a GPU base calculation but the efficiency was terrible. You can check our discussion here. We are looking for and implementing new methods, including PBDelphi from your University. At the moment, we don't have any financial support, so it is frozen for now.

@mkoiral
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mkoiral commented Jul 30, 2024 via email

@mkoiral
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mkoiral commented Aug 3, 2024 via email

@Valdes-Tresanco-MS
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The better way is using gmx_MMPBSA_ana. Trying to plot by yourself can be complicated

@mkoiral
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mkoiral commented Aug 4, 2024 via email

@Valdes-Tresanco-MS
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Since HPCs are not designed to work with GUIs it is not recommended trying to install it. You can copy the working folder to your Linux PC and open the result using gmx_MMPBSA_ana

@mkoiral
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mkoiral commented Aug 4, 2024 via email

@mkoiral
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mkoiral commented Aug 6, 2024 via email

@Valdes-Tresanco-MS
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Please, share the conda list output

@mkoiral
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mkoiral commented Aug 7, 2024 via email

@mkoiral
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mkoiral commented Aug 13, 2024 via email

@Valdes-Tresanco-MS
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For gmx_MMPBSA_ana, try to install PyQt6 only. Here you had installed both PyQt5 and PyQt6. If the error persists, try to use PyQt5 instead.
I never used srun before, so I don't know its dependencies and compatibility. But, according to the SLURM forum, this problem requires an admin, so this is not a problem of gmx_MMPBSA. According to other forums, you can use mpirun in SLURM with no problem

@mkoiral
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mkoiral commented Aug 13, 2024 via email

@mkoiral
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mkoiral commented Aug 21, 2024 via email

@Valdes-Tresanco-MS
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Yes. Please, check this section for Quasic-harmonic, Interaction, and C2 Entropies, and this section for Normal modes. Examples, here, here and here

@mkoiral
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mkoiral commented Sep 6, 2024 via email

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@Valdes-Tresanco-MS @mkoiral