per-residue energy decomposition

[فاطمه بیانی‎]

Hello, 

I am trying to calculate the  decomposition analysis, but it returns the following error:

mpirun -np 2 gmx_MMPBSA MPI -O -i decomp.in -cs model-md.tpr -ci index2.ndx -cg 16 19 -ct traj4550.xtc -cp topol.top
[INFO   ] Starting
[INFO   ] Command-line
  gmx_MMPBSA -O -i decomp.in -cs model-md.tpr -ci index2.ndx -cg 16 19 -ct traj4550.xtc -cp topol.top

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/cpptraj
[INFO   ] tleap found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/tleap
[INFO   ] parmchk2 found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/parmchk2
[INFO   ] sander found! Using /home/yahya/Downloads/yes/envs/AmberTools21/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...
[INFO   ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 16_19 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 Complex: Saving group 16 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 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Building Normal Complex Amber Topology...
[INFO   ] Writing Normal Complex Amber Topology...
[INFO   ] No Receptor topology files was defined. Using ST approach...
[INFO   ] Building AMBER Receptor Topology from Complex...
[INFO   ] No Ligand Topology files was defined. Using ST approach...
[INFO   ] Building AMBER Ligand Topology from Complex...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER Topologies from GROMACS files...Done.

[INFO   ] Loading and checking parameter files for compatibility...

CHAMBER prmtops found. Forcing use of sander
Preparing trajectories for simulation...
26 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/yahya/Downloads/yes/envs/AmberTools21/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...
  File "/home/yahya/Downloads/yes/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 107, in gmxmmpbsa
    app.parse_output_files()
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1060, in parse_output_files
    self.calc_types[key]['delta'] = BindClass(
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 1069, in _init_
    self.delta2()
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 1295, in delta2
    self.rec.fill_composite_terms()
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 370, in fill_composite_terms
    self.data[component] = self.data[key] + self.data[component]
  File "/home/yahya/Downloads/yes/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 59, in _add_
    raise LengthError('length mismatch in energy vectors')
LengthError: length mismatch in energy vectors
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

please help me :(

[Mario Sergio Valdes]

This may be due to internal errors or a failure in the calculation of some components. Please try this same command with version 1.5.2. If the problem persists send us your files.

[فاطمه بیانی‎]

Thank you, I realized my problem was the existence of pbc which was solved with the following command.

gmx trjconv -s model-md.tpr -f traj.xtc -center -pbc mol -ur compact -o md_noPBC.xtc -n index.ndx

mariosergi...@gmail.com در تاریخ جمعه ۶ مهٔ ۲۰۲۲ ساعت ۲۱:۲۱:۳۲ (UTC+4:30) نوشت: