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

[imren bayıl]

hi,ı want to calculate binding energy for my system.

The calculation is starting and continuing without any error but suddenly ı am getting this error.how to fix it

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /home/imren/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
             82%|#####################################################################5               | 9/11 [elapsed: 08:18 remaining: 01:52][ERROR  ] CalcError

/home/imren/miniconda3/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/imren/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/imren/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/imren/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/imren/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/imren/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/imren/miniconda3/envs/gmxMMPBSA/lib/python3.9/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.')
CalcError:

/home/imren/miniconda3/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.

[Mario Sergio Valdes]

It seems like it's an internal sander error. Please attach the *.mdout file

[imren bayıl]

2 Haziran 2023 Cuma tarihinde saat 18:23:36 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

[Mario Sergio Valdes]

Attach the *.mdout file, not the mdp

[imren bayıl]

2 Haziran 2023 Cuma tarihinde saat 18:34:06 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

[Mario Sergio Valdes]

As you can see in the mdout file, the energetic terms are huge

 BOND    = *************  ANGLE   =    12783.2715  DIHED      =     2302.5615
 UB      =  3352876.0076  IMP     =      999.6468  CMAP       =        0.0000
 VDWAALS =     -947.5539  EEL     =    15758.3869  EPB        =   -22620.0847
 1-4 VDW =     1058.8864  1-4 EEL =    -6410.9680  RESTRAINT  =        0.0000
 ECAVITY =       77.5211  EDISPER =        0.0000
minimization completed, ENE= 0.11000585E+09 RMS= 0.844900E+04

Probably, sander is out of RAM. Please, follow the instruction in this section https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/gmx_MMPBSA_running/#before-running-gmx_mmpbsa

Also, check the RAM consumption when the calculation is running. If this is the problem, maybe you want to decrease the value of fillratio to 2.5 or less