"_GMXMMPBSA_REC.inpcrd" not found error

[Joo-Chan Kim]

Hello, I have installed gmx_MMPBSA via amber.python method.

I am currently using CUDA 11.2 enabled Docker container with GROMACS 2022.2 and AmberTools21.12.

While I was able to check the successful results from gmx_MMPBSA_test, I got following error from the actual analysis with the command :

mpirun -np 16 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 33 20 -cp topol.top -ct md_fit.xtc -cr md.pdb

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
  File "/mnt/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa
    app.file_setup()
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 127, in file_setup
    create_inputs(INPUT, self.normal_system, self.pre)
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 74, in create_inputs
    rec_top = parmed.load_file('REC.prmtop', xyz=f"{pre}REC.inpcrd")
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/parmed/formats/registry.py", line 196, in load_file
    return cls.parse(filename, *args, **kwargs)
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/parmed/amber/amberformat.py", line 359, in parse
    return LoadParm(filename, *args, **kwargs)
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/parmed/amber/readparm.py", line 70, in LoadParm
    f = load_file(xyz)
  File "/mnt/amber20/miniconda/lib/python3.9/site-packages/parmed/formats/registry.py", line 168, in load_file
    raise FileNotFoundError('%s does not exist' % filename)
FileNotFoundError: _GMXMMPBSA_REC.inpcrd does not exist
Error occurred on rank 0.
Exiting. All files have been retained.

I checked the log file but could not find any error message.

I also changed -np 1 or tried single-thread version but got the same result.

Is there anybody who got the same problem as me?

[Mario Sergio Valdes]

Can you send me a copy of your files (md.tpr, index.ndx topol.top + *.itps, md_fit.xtc and md.pdb) to reproduce the error? 

[Joo-Chan Kim]

I think I found the cause of the problem.

I turned the ALPB approximation option on, but I think it is incompatible with CHARMM radii.

When I changed the alpb = 1 to alpb = 0, the program went well.

2022년 6월 28일 화요일 오전 8시 32분 32초 UTC+9에 mariosergi...@gmail.com님이 작성:

[Mario Sergio Valdes]

We have already identified the problem and it is precisely related to what I have identified. The problem is that the inpcrd file is not generated when using topologies, regardless if it is CHARMM or AMBER. We will try to solve it as soon as possible.

[Mario Ernesto]

Currently, charmm radii is only compatible with &pb calculations... if you plan to use ALPB approximation in the future, please make sure you are using a different radii... also, you can update gmx_MMPBSA from the master, 

conda environment:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA

or 

ambertools compilation:

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA

we have fixed the error of ALPB when using topologies... 

let us know if it works properly...

sincerely...

Mario E.

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