Error running gmx_MMPBSA

[cmpla...@gmail.com]

Hi! I am trying to run a BFE calculation with 3D-RISM on a Carbon nanotube-ligand system. There seems to be no problem in the pdb files generated by gmx_MMPBSA, however I encounter the following error:

Would appreciate any help! Thanks

[INFO   ] Starting gmx_MMPBSA v1.5.0.3
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs cnt_ligand.pdb -ct md_0_1-removepbc.xtc -ci index_system.ndx -cg 2 3 -cp topol.top

[WARNING] Default TOLERANCE value is 0.00001! However 0.001 is been used. Check documentation for more details...
[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /opt/amber/bin/cpptraj
[INFO   ] tleap found! Using /opt/amber/bin/tleap
[INFO   ] parmchk2 found! Using /opt/amber/bin/parmchk2
[INFO   ] sander found! Using /opt/amber/bin/sander
[INFO   ] rism3d.snglpnt found! Using /opt/amber/bin/rism3d.snglpnt
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs-2021.4/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 2_3 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 2 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 3 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[WARNING] No reference structure was found and the complex structure not contain any chain ID. Assigning chains ID automatically...
  File "/home/christian/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 391, in gmx2pdb
    self.check_structures(self.complex_str, self.receptor_str, self.ligand_str)
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 1132, in check_structures
    self._assign_chains_IDs(com_str, rec_str, lig_str)
  File "/home/christian/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 1185, in _assign_chains_IDs
    curr_chain_id = chains_letters[chains_letters.index(chains_ids[-1]) + 1]
IndexError: list index out of range

Exiting. All files have been retained.

[Mario Sergio Valdes]

The method we use for assigning the chain ID, if it doesn't exist and no reference structure is defined, is quite simple and primitive, so it may fail on some systems. Consequently, you should ideally define a properly annotated reference structure, that is, with only the complex and chain IDs.
In any case, it would be helpful to improve the chain ID assignation method if you send us your files (*.tpr, 5 frames *.xtc, *.ndx, groups, and *.top with associated files). These files will not be shared and will be deleted once we prove that the method works.

Mario S.

[cmpla...@gmail.com]

Here's the link to the shared drive containing my working files if anyone has the time to take a look at them. Thanks in advance!

[cmpl...@gmail.com]

Here's the link to the shared drive containing my working files. Thanks in advance!

[Mario Sergio Valdes]

Unfortunately, I have bad news. The problem is fixed if you use the *.tpr instead of the PDB in the -cs option. However, since it is 3D-RISM, a different program than SANDER is used for its calculation. This implies that it is less flexible with the composition of the topology, which causes it to end in error since it is a topology converted from OPLSA. To fix this, we are working on implementing the 3D-RISM calculation with SANDER (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/153).
Do you have a particular preference/need for 3D-RISM? You may consider using PB instead until we resolve this issue.

Sincerely.

Mario S.

[cmpl...@gmail.com]

I'm exploring 3D-RISM since it considers hydrophobic interactions and hydrogen bonds which may be helpful in studying my system. I tried running a BFE calculation using the PB model, however, I ran into this error: 

Thanks for the help!

[INFO   ] Starting gmx_MMPBSA v1.5.0.3
[DEBUG  ] WDIR          : /home/christian/gromacs/CNT/Methyl_Paraben/MP/3DRISM
[DEBUG  ] AMBERHOME     : /opt/amber
[DEBUG  ] PYTHON EXE    : None
[DEBUG  ] PYTHON VERSION: 3.8.10 (default, Nov 26 2021, 20:14:08) [GCC 9.3.0]
[DEBUG  ] MPI           : /usr/bin/mpirun
[DEBUG  ] ParmEd        : 3.4.1
[DEBUG  ] OS PLATFORM   : Linux-5.8.0-36-generic-x86_64-with-glibc2.29
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #40~20.04.1-Ubuntu SMP Wed Jan 6 10:15:55 UTC 2021
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ct last10ns.xtc -ci index_system.ndx -cg 2 3 -cp topol.top

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |;Sample input file for MM/3D-RISM &general
[DEBUG  ] |
[DEBUG  ] |&general
[DEBUG  ] |sys_name="CNTMP-PB"
[DEBUG  ] |startframe=95
[DEBUG  ] |endframe=102
[DEBUG  ] |/
[DEBUG  ] |PBinput:
[DEBUG  ] |&pb
[DEBUG  ] |/
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ]

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /opt/amber/bin/cpptraj
[INFO   ] tleap found! Using /opt/amber/bin/tleap
[INFO   ] parmchk2 found! Using /opt/amber/bin/parmchk2
[INFO   ] sander found! Using /opt/amber/bin/sander

[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs-2021.4/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...

[DEBUG  ] Running command: echo name 2 GMXMMPBSA_REC\n name 3 GMXMMPBSA_LIG\n  2 | 3\n q\n | /usr/local/gromacs-2021.4/bin/gmx make_ndx -n index_system.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                      :-) GROMACS - gmx make_ndx, 2021.4 (-:
[DEBUG  ]
[DEBUG  ]                             GROMACS is written by:
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[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
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[DEBUG  ] check out http://www.gromacs.org for more information.
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[DEBUG  ]
[DEBUG  ] GROMACS:      gmx make_ndx, version 2021.4
[DEBUG  ] Executable:   /usr/local/gromacs-2021.4/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs-2021.4
[DEBUG  ] Working dir:  /home/christian/gromacs/CNT/Methyl_Paraben/MP/3DRISM
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index_system.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ]
[DEBUG  ]
[DEBUG  ] GROMACS reminds you: "C++ is tricky. You can do everything. You can even make every mistake." (Nicolai Josuttis, CppCon2017)
[DEBUG  ]
[DEBUG  ] Going to read 1 old index file(s)
[DEBUG  ] Counted atom numbers up to 12124 in index file
[DEBUG  ]
[DEBUG  ]   0 System              : 12124 atoms
[DEBUG  ]   1 Other               :   487 atoms
[DEBUG  ]   2 CNT                 :   468 atoms
[DEBUG  ]   3 UNK                 :    19 atoms
[DEBUG  ]   4 Water               : 11637 atoms
[DEBUG  ]   5 SOL                 : 11637 atoms
[DEBUG  ]   6 non-Water           :   487 atoms
[DEBUG  ]   7 System              : 12124 atoms
[DEBUG  ]
[DEBUG  ]  nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
[DEBUG  ]  'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
[DEBUG  ]  't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
[DEBUG  ]  'r': residue              'res' nr         'chain' char
[DEBUG  ]  "name": group             'case': case sensitive           'q': save and quit
[DEBUG  ]  'ri': residue index
[DEBUG  ]
[DEBUG  ] >
[DEBUG  ]
[DEBUG  ] >
[DEBUG  ]
[DEBUG  ] >
[DEBUG  ] Copied index group 2 'GMXMMPBSA_REC'
[DEBUG  ] Copied index group 3 'GMXMMPBSA_LIG'
[DEBUG  ] Merged two groups with OR: 468 19 -> 487
[DEBUG  ]
[DEBUG  ]   8 GMXMMPBSA_REC_GMXMMPBSA_LIG:   487 atoms
[DEBUG  ]
[DEBUG  ] >

[INFO   ] Normal Complex: Saving group 2_3 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[DEBUG  ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs-2021.4/bin/gmx trjconv -f last10ns.xtc -s md_0_1.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[ERROR  ] MMPBSA_Error /usr/local/gromacs-2021.4/bin/gmx trjconv failed when querying last10ns.xtc.
           Check the gmx_MMPBSA.log file to report the problem.

[Mario Sergio Valdes]

Please, show me the output of this command-line 

echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs-2021.4/bin/gmx trjconv -f last10ns.xtc -s md_0_1.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0

[cmpl...@gmail.com]

Hi Mario! I was able to run BFE calculations using the PB model in my system by following the steps mentioned here. Waiting for 3D-RISM to work in the OPLSAA force field. 

[marioe911116]

Hello there! We just released a new version of gmx_MMPBSA (v1.5.2) that should work fine with your system... please upgrade ParmEd and gmx_MMPBSA as follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

python -m pip install gmx_MMPBSA -U

let us know if that solves the issue...

cheers!