CalcError of PB calculation

[jeromeRlon]

My Question is...

The PB calculation failed with : CalcError: /home/jerome/anaconda3/envs/gmxmmpbsa/bin/sander failed with prmtop COM.prmtop!

[jeromeRlon]

[ERROR ] CalcError /home/jerome/anaconda3/envs/gmxmmpbsa/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error . Check the gmx_MMPBSA.log file to report the problem. File "/home/jerome/anaconda3/envs/gmxmmpbsa/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/jerome/anaconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa app.run_mmpbsa() File "/home/jerome/anaconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/home/jerome/anaconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/home/jerome/anaconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 479, in run GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) + File "/home/jerome/anaconda3/envs/gmxmmpbsa/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') CalcError: /home/jerome/anaconda3/envs/gmxmmpbsa/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error

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

[jeromeRlon]

The command: gmx_MMPBSA -i mmpbsa.in -cs md_04.tpr -ci mas1.ndx -cg 1 13 -ct center_md_04.xtc -cp 7ju7.top

The files could be provided by request

[Valdes-Tresanco-MS]

This may be due to multiple factors. Please report future problems using the template we have provided. This template allows us to have a minimum of information and rule out underlying causes that we have already resolved.

Please, attach the file _gmxMMPBSA.log (drag and drop it, do not copy the content here).

[marioernestovaldes]

Could you please also send the *.mdout files?

[jeromeRlon]

SURE!

Here are the file .log and the file .mdout of GB and PB calculation. log and mdout.zip

[marioernestovaldes]

I have checked the output files and there are no visible errors... could you please send the files that you are using to do some tests... my email is marioe911116@gmail.com

[jeromeRlon]

ok, I have sent them to you.

[marioernestovaldes]

haven't received any email so far... could you please double-check?

[jeromeRlon]

All mails should be delivered to your server by now.

[marioernestovaldes]

I ran the calculation on my computer and everything works fine... the files are correct... the only seems that occurs to me is a memory problem... could you try to run only (delete or comment the GB part) PB with 2 frames? I see also that the trajectory is not fit and contains PBC... you may want to remove the PBC and fit the trajectory as this can cause errors down the road...

Input file generated by gmx_MMPBSA (v1.5.2)
Be careful with the variables you modify, some can have severe consequences on the results you obtain.

# General namelist variables
&general
  sys_name             = ""                                             # System name
  startframe           = 4500                                              # First frame to analyze
  endframe             = 4502                                        # Last frame to analyze
  interval             = 1                                              # Number of frames between adjacent frames analyzed
  forcefields          = "oldff/leaprc.ff99SB,leaprc.gaff"              # Define the force field to build the Amber topology
  ions_parameters      = 1                                              # Define ions parameters to build the Amber topology
  PBRadii              = 3                                              # Define PBRadii to build amber topology from GROMACS files
  temperature          = 298.15                                         # Temperature
  qh_entropy           = 0                                              # Do quasi-harmonic calculation
  interaction_entropy  = 0                                              # Do Interaction Entropy calculation
  ie_segment           = 25                                             # Trajectory segment to calculate interaction entropy
  c2_entropy           = 0                                              # Do C2 Entropy calculation
  assign_chainID       = 0                                              # Assign chains ID
  exp_ki               = 0.0                                            # Experimental Ki in nM
  full_traj            = 0                                              # Print a full traj. AND the thread trajectories
  keep_files           = 2                                              # How many files to keep after successful completion
  netcdf               = 0                                              # Use NetCDF intermediate trajectories
  solvated_trajectory  = 1                                              # Define if it is necessary to cleanup the trajectories
  verbose              = 1                                              # How many energy terms to print in the final output
/
# (AMBER) Possion-Boltzmann namelist variables
&pb
  ipb                  = 2                                              # Dielectric model for PB
  inp                  = 2                                              # Nonpolar solvation method
  sander_apbs          = 0                                              # Use sander.APBS?
  indi                 = 1.0                                            # Internal dielectric constant
  exdi                 = 80.0                                           # External dielectric constant
  emem                 = 4.0                                            # Membrane dielectric constant
  smoothopt            = 1                                              # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
  istrng               = 0.15                                           # Ionic strength (M)
  radiopt              = 1                                              # Use optimized radii?
  prbrad               = 1.4                                            # Probe radius
  iprob                = 2.0                                            # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
  sasopt               = 0                                              # Molecular surface in PB implict model
  arcres               = 0.25                                           # The resolution (Å) to compute solvent accessible arcs
  memopt               = 0                                              # Use PB optimization for membrane
  mprob                = 2.7                                            # Membrane probe radius in Å
  mthick               = 40.0                                           # Membrane thickness
  mctrdz               = 0.0                                            # Distance to offset membrane in Z direction
  poretype             = 1                                              # Use exclusion region for channel proteins
  npbopt               = 0                                              # Use NonLinear PB solver?
  solvopt              = 1                                              # Select iterative solver
  accept               = 0.001                                          # Sets the iteration convergence criterion (relative to the initial residue)
  linit                = 1000                                           # Number of SCF iterations
  fillratio            = 4.0                                            # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
  scale                = 2.0                                            # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
  nbuffer              = 0.0                                            # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
  nfocus               = 2                                              # Electrostatic focusing calculation
  fscale               = 8                                              # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
  npbgrid              = 1                                              # Sets how often the finite-difference grid is regenerated
  bcopt                = 5                                              # Boundary condition option
  eneopt               = 2                                              # Compute electrostatic energy and forces
  frcopt               = 0                                              # Output for computing electrostatic forces
  scalec               = 0                                              # Option to compute reaction field energy and forces
  cutfd                = 5.0                                            # Cutoff for finite-difference interactions
  cutnb                = 0.0                                            # Cutoff for nonbonded interations
  nsnba                = 1                                              # Sets how often atom-based pairlist is generated
  decompopt            = 2                                              # Option to select different decomposition schemes when INP = 2
  use_rmin             = 1                                              # The option to set up van der Waals radii
  sprob                = 0.557                                          # Solvent probe radius for SASA used to compute the dispersion term
  vprob                = 1.3                                            # Solvent probe radius for molecular volume (the volume enclosed by SASA)
  rhow_effect          = 1.129                                          # Effective water density used in the non-polar dispersion term calculation
  use_sav              = 1                                              # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
  cavity_surften       = 0.0378                                         # Surface tension
  cavity_offset        = -0.5692                                        # Offset for nonpolar solvation calc
  maxsph               = 400                                            # Approximate number of dots to represent the maximum atomic solvent accessible surface
  maxarcdot            = 1500                                           # Number of dots used to store arc dots per atom
  npbverb              = 0                                              # Option to turn on verbose mode
/

[jeromeRlon]

The same error was reported...

I would try with a better machine, thank you.

[marioernestovaldes]

closing issue...feel free to reopen if you have any question related to this issue...