Error running gmx_MMPBSA

[Jay Lim]

Hello, I am new to use gmx_MMPBSA. I am trying to using gmx_MMPBSA to calculate the binding free energy of protein and ligand that contains Pt atom. The error "The complex, receptor, and ligand trajectories must be the same length. " occurs. I have used "gmx check" to check the .xtc file. There are 10001 frames in both complex_edited.xtc and ligand_edited.xtc. Additionally, I am not sure if it is proper to get the ligand file (ligand.xtc,ligand.top) when I simulated the ligand in water with Gromacs.

Thanks in advance!

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct complex_edited.xtc -ci index.ndx -cp topol.top -cg 1 12 -ls ligand.tpr -li lig_index.ndx -lp ligand_topol.top -lt ligand_edited.xtc -lg 0 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Starting gmx_MMPBSA v1.6.1+16.gc99f0b4
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct complex_edited.xtc -ci index.ndx -cp topol.top -cg 1 12 -ls ligand.tpr -li lig_index.ndx -lp ligand_topol.top -lt ligand_edited.xtc -lg 0 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

tets
[INFO   ] Checking mmpbsa.in input file...
[WARNING] The startframe variable must be >= 1. Changing startframe from 0 to 1
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/johnson/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/johnson/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/johnson/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/johnson/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/johnson/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/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_Other (1_12) 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 Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] A ligand structure file was defined. Using MT approach...
[INFO   ] Making gmx_MMPBSA index for ligand...
[INFO   ] Normal Ligand: Saving group System (0) in _GMXMMPBSA_LIG_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...
/home/johnson/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:1030: GromacsWarning: 136 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!
  warnings.warn('%i 1-4 pairs were missing from the [ pairs ] '
[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   ] A Ligand Topology file was defined. Using MT approach...
[INFO   ] Building AMBER Ligand Topology from GROMACS Ligand Topology...
/home/johnson/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/parmed/gromacs/gromacstop.py:1030: GromacsWarning: 136 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!
  warnings.warn('%i 1-4 pairs were missing from the [ pairs ] '
[INFO   ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Cleaning normal ligand trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[ERROR  ] MMPBSA_Error

The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 we have simplified a few things to make the code easier to maintain. Please check the documentation

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/johnson/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/home/johnson/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.file_setup()
  File "/home/johnson/miniconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 142, in file_setup
    GMXMMPBSA_ERROR('The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 '
  File "/home/johnson/miniconda3/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:

The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 we have simplified a few things to make the code easier to maintain. Please check the documentation

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

[marioe911116]

could you please share the files you are using? That way is easier for us to see what's going on...

thanks

[marioe911116]

solved offline

take into account that this will probably increase the error as the internal energy terms won't cancel exactly... Also, make sure your trajectories are fitted properly, there seem to be some issues with the dihedrals of the ligand as per my quick calculation with only 10 frames

El jue, 14 sept 2023 a las 2:19, Zexiong Lin (<shes...@gmail.com>) escribió:

Hello,

It can work now. Could I ask another question? How can the ligand file be obtained?  Is it proper to get the ligand file (ligand.xtc,ligand.top) as I ran the simulation of the ligand in water without the receptor in Gromacs.

I am sincerely grateful for your unwavering support throughout this process.

Regards,

On Thu, 14 Sept 2023 at 19:00, Mario Ernesto <marioe...@gmail.com> wrote:

Please, update gmx_MMPBSA as follows and let me know if this solves the issue:

pip install gmx-mmpbsa -U

El mié, 13 sept 2023 a las 16:55, Zexiong Lin (<shes...@gmail.com>) escribió:

Dear Mario,

I appreciate your response a lot. The files are attached to this email.

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct complex_fit.xtc -ci index.ndx -cp topol.top -cg 1 12 -ls ligand.tpr -li lig_index.ndx -lp ligand_topol.top -lt ligand_fit.xtc -lg 0 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

I am sincerely grateful for your unwavering support and patience.

On Thu, Sep 14, 2023 at 10:47 AM Mario Ernesto <marioe...@gmail.com> wrote:

This is my email address 

marioe...@gmail.com

On Wed, Sept 13, 2023, 4:28 p.m. Jay Lim <shes...@gmail.com> wrote:

Dear Marioe,

the files exceeds 24 M and could not be uploaded? could you provide your email address?

Regards,