Error running gmxMMPBSA decomp analysis

[Amelia Francis]

Hi,

When I try running a decomposition analysis the command fails with the following error message: 

MMPBSA_Error: 

We expected something like this: A/2-10,35,41 B/104 but we get “within instead

The full error message and mmpbsa.in file is shown below. 

I've checked this with colleagues and it doesn't appear to be an issue with my mmpbsa.in file as it follows the same format as the examples.

Has anyone come across this before/know what causes this error?

Thanks!

Amelia

mmpbsa.in file:

&general

sys_name=“Nb85_GII.4_1”,

startframe=1000,

endframe=50000,

forcefields=“charmm36-jul2022.ff”

temperature=300

/

&gb

igb=5

/

#make sure to include at least one residue from both the receptor

##and ligand in the print_res mask of the &decomp section.

##this requirement is automatically fulfilled when using the within keyword.

##Re: [AMBER] Is there any problem with this input file? from Bill Miller III on 2013-08-05 (Amber Archive Aug 2013)

&decomp

idecomp=2, dec_verbose=3,

print_res=“within 4”

/

Command:

gmx_MMPBSA -O -i ../mmpbsa.in -cs md.tpr -ci ../complex.ndx -cg 17 18 -ct md_nowater.xtc -cp ../topol.top

Error:

[INFO   ] Starting gmx_MMPBSA 1.6.4+21.gccbb3a8

[INFO   ] Command-line

  gmx_MMPBSA -O -i ../mmpbsa.in -cs md.tpr -ci ../complex.ndx -cg 17 18 -ct md_nowater.xtc -cp ../topol.top

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

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

[INFO   ] Checking external programs...

[INFO   ] cpptraj found! Using /shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/bin/cpptraj

[INFO   ] tleap found! Using /shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/bin/tleap

[INFO   ] parmchk2 found! Using /shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/bin/parmchk2

[INFO   ] sander found! Using /shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/bin/sander

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

[INFO   ] gmx found! Using /shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/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 a_1-4702_a_9405-11155 (17_18) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[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 a_1-4702 (17) 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 a_9405-11155 (18) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb

[INFO   ] Checking the structures consistency...

[INFO   ] 

[INFO   ] Using topology conversion. Setting radiopt = 0...

[INFO   ] Building Normal Complex Amber topology...

[INFO   ] Detected CHARMM force field topology format...

[INFO   ] Assigning PBRadii mbondi2 to Complex...

[INFO   ] Writing Normal Complex AMBER topology...

[INFO   ] No Receptor topology file was defined. Using ST approach...

[INFO   ] Building AMBER Receptor topology from Complex...

[INFO   ] Assigning PBRadii mbondi2 to Receptor...

[INFO   ] Writing Normal Receptor AMBER topology...

[INFO   ] No Ligand topology file was defined. Using ST approach...

[INFO   ] Building AMBER Ligand topology from Complex...

[INFO   ] Assigning PBRadii mbondi2 to Ligand...

[INFO   ] Writing Normal Ligand AMBER topology...

[ERROR  ] MMPBSA_Error 

We expected something like this: A/2-10,35,41 B/104 but we get “within instead

Check the gmx_MMPBSA.log file to report the problem.

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 6, in <module>

    sys.exit(gmxmmpbsa())

             ^^^^^^^^^^^

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa

    app.make_prmtops()

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops

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

                                                                          ^^^^^^^^^^^^^^^^^^^^^^^

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 131, in buildTopology

    decomp_res = self.get_selected_residues(self.INPUT['decomp']['print_res'])

                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 892, in get_selected_residues

    dist, res_selection = selector(select)

                          ^^^^^^^^^^^^^^^^

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/utils.py", line 667, in selector

    GMXMMPBSA_ERROR(f'We expected something like this: A/2-10,35,41 B/104 but we get {s} instead')

  File "/shared/home1/c.c25030769/.conda/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__

    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')

MMPBSA_Error: 

We expected something like this: A/2-10,35,41 B/104 but we get “within instead

Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained.

[mariosergi...@gmail.com]

Please attach the gmx_MMPBSA.log file. It appears there are strange characters in the expression. The check is being done with x.
https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/blob/ccbb3a891448cfe5e17a14fde0af46e29ce707d3/GMXMMPBSA/utils.py#L657-L661

In many cases, there may be invisible, strange characters causing the expression to fail. We need to improve the method for these checks :)

[muralidhar pandey]

Ligand topology is not properly generated.

Further,verify the number of atoms in each followed by concept 

No.of atoms in complex=no.of atoms in receptor+No of atoms in ligand 

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[mariosergi...@gmail.com]

Please send me the files (gmx_MMPBSA.log and/or the input files if possible). I don't have a way to check what's happening. In most cases, it's a poor selection of groups in the index, or an unsupported atom that gets removed during processing.

[muralidhar pandey]

Use any text editor to open the file you will find 

To view this discussion visit https://groups.google.com/d/msgid/gmx_mmpbsa/e2e26c70-6fb8-4c7d-8852-29d2ef135cb3n%40googlegroups.com.

[Amelia Francis]

Thanks all for your help!

The problem was strange characters in the mmpbsa.in file. The quotation marks were the wrong 'kind' (Unicode instead of ASCII).

Replacing the quotation marks with ' allowed it to run.