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

[imren bayıl]

Hi,

gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -ci index.ndx -cg 6 11 -ct new.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

I want to calculate binding energy  this is my command.But I am getting error.

this is my mmpbsa.in file 

&general
startframe=1,
endframe=1001,
keep_files=2,
interval=10,
# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only
# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set
PBRadii=7,
/
&pb
# radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP
# calculation
istrng=0.100,inp=1, fillratio=4.0, radiopt=0
/

The error is 

  gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -ci index.ndx -cg 6 11 -ct new.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -ci index.ndx -cg 6 11 -ct new.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/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   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 6_11 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 6 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 11 in _GMXMMPBSA_COM_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...
[INFO   ] Detected CHARMM force field topology format...
[INFO   ] Assigning PBRadii charmm_radii 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 charmm_radii to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii charmm_radii to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

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

[INFO   ] 101 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 1 CPUs...

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
             17%|#############9                                                                     | 17/101 [elapsed: 07:24 remaining: 41:16][ERROR  ] CalcError /home/imren/Downloads/home/imren/Downloads/miniconda33/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/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 132, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 526, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/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/imren/Downloads/home/imren/Downloads/miniconda33/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.

Could you guide me how to fix this problem please ?

[Mario Sergio Valdes]

It is difficult to identify a problem with only this information. Although it is very suspicious that it ends abruptly after processing several frames. It may be a convergence error. Please attach the gmx_MMPBSA.log and *.mdout files.

[imren bayıl]

15 Aralık 2022 Perşembe tarihinde saat 02:47:30 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

[imren bayıl]

I attached the files.Could you help me please

15 Aralık 2022 Perşembe tarihinde saat 23:54:38 UTC+3 itibarıyla imren bayıl şunları yazdı:

[marioe911116]

Please submit teh *.mdout files from amber not gromacs

[imren bayıl]

I dont understand which file neccessary,inside the my folder which one of this your request file         ? 

com.prmtop

com_traj_0.xtc

gmx_MMPSA.log

GMXMMPBSA_COM.inpcrd

GMXMMPBSA_COM.pdb

GMXMMPBSA_COM_FIXED.pdb

GMXMMPBSA_COM_index.ndx

GMXMMPBSA_COM_complex.mdcrd.0

GMXMMPBSA_COM_complex.pdb

GMXMMPBSA_COM_complex_pb.mdout.0

GMXMMPBSA_COM_dummycomplex.inpcrd

GMXMMPBSA_COM_dummyligand.inpcrd
GMXMMPBSA_COM_dummyreceptor.inpcrd

GMXMMPBSA_LIG.inpcrd

GMXMMPBSA_LIG.pdb

GMXMMPBSA_ligand.mdcrd.0

GMXMMPBSA_ligand.pdb

GMXMMPBSA_normal_traj_cpptraj.out

GMXMMPBSA_pb.mdir

GMXMMPBSA_pb.mdin2

GMXMMPBSA_REC.inpcrd

GMXMMPBSA_REC.pdb

GMXMMPBSA_receptor.mdcrd.0

GMXMMPBSA_receptor.pdb

GMXMMPBSA_receptor.restrt.0

LIG.prmtop

REC.prmtop

16 Aralık 2022 Cuma tarihinde saat 08:48:01 UTC+2 itibarıyla marioe911116 şunları yazdı:

[Mario Sergio Valdes]

This GMXMMPBSA_COM_complex_pb.mdout.0

[imren bayıl]

sorry for late  I will be waiting your solution

16 Aralık 2022 Cuma tarihinde saat 20:40:10 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

[marioe911116]

These is no error reproted in teh *mdout file... did you try to run teh system sevral times? do you get the same error alwasy in teh same frame?

[Mario Sergio Valdes]

As I mentioned earlier, I believe this is a convergence problem. In all steps, the convergence limit is reached, so I suspect that your system is not correctly fitted. Please, if possible, share with us your system so that we can check it.