error MM(PB)

[negin safaee]

Hello everyone,

I am trying to do MM(PB) calculation by gmx_MMPBSA but i have got the following error, I also cut my xtc file and i defined endframe in my mmpbsa.in file, please help me to solve this error.

gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index2.ndx -cg 17 21 -ct traj-1-10ns.xtc -cp topol.top
[INFO   ] Starting
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ci index2.ndx -cg 17 21 -ct traj-1-10ns.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/safaei/anaconda3/envs/AmberTools21/bin/cpptraj
[INFO   ] tleap found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/tleap
[INFO   ] parmchk2 found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/parmchk2
[INFO   ] sander found! Using /home/safaei/anaconda3/envs/AmberTools21/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/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 17_21 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 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 21 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...
25 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning PB calculations with /home/safaei/anaconda3/envs/AmberTools21/bin/sander
  calculating complex contribution...
[ERROR  ] CalcError /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
        If you are using sander and PB calculation, check the *.mdout files to get the sander error and check this thread (http://archive.ambermd.org/201303/0548.html)
.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/safaei/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 433, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/safaei/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
CalcError: /home/safaei/anaconda3/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
       

[Mario Sergio Valdes]

This is probably a PB convergence error, usually related to inconsistencies in your system. Rarely on certain specific systems (like this one we're still working on), the default parameters should suffice. If you are completely convinced that your system is consistent, you can increase the value of the linit variable to 10000 in the pb namelist defition. Note that this increases computation time. See the documentation for more information about this variable (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/input_file/#pb-namelist-variables)

Also, keep in mind that the trajectory is not enough to be able to test your system. In case you send us your files, please include all the necessary files (tpr, 5 or 10 frames *.xtc, *.ndx, groups, *.top and the associated folder and files if any)

Sincerely

Mario S

[Mario Sergio Valdes]

I refer to this system (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/106)