Error in running gmx_MMPBSA

[Ayushi Gupta]

Hi,

I'm running this module for the first time. While building the amber topology files it is giving the following error - 

[INFO   ] Starting

[INFO   ] Command-line

  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_10.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/iiita/miniconda3/envs/AmberTools21/bin/cpptraj

[INFO   ] tleap found! Using /home/iiita/miniconda3/envs/AmberTools21/bin/tleap

[INFO   ] parmchk2 found! Using /home/iiita/miniconda3/envs/AmberTools21/bin/parmchk2

[INFO   ] sander found! Using /home/iiita/miniconda3/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 1_13 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 1 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb

[INFO   ] Building Normal Complex Amber Topology...

  File "/home/iiita/miniconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa

    app.make_prmtops()

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops

    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 117, in buildTopology

    tops = self.gmxtop2prmtop()

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 318, in gmxtop2prmtop

    com_top = self.cleantop(self.FILES.complex_top, self.indexes[0] + self.indexes[1])

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 598, in cleantop

    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__

    self.read(fname, defines, parametrize)

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 311, in read

    molecule.add_atom(*self._parse_atoms(line, params))

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 492, in _parse_atoms

    return atom, words[3], int(words[2])

ValueError: invalid literal for int() with base 10: '30A'

Exiting. All files have been retained.

Kindly help me with the same

[Mario Sergio Valdes]

Hi and welcome!

This is a parmed bug that we have already reported (https://github.com/ParmEd/ParmEd/issues/1153)

     Currently, we are focused on gmx_MMPBSA, but we will try to contribute to the resolution of some of these errors in parmed

Cheers!

Mario S.

[Ayushi Gupta]

Hi,

Thank you so much for that tip, it worked for that particular error 

But moving on it encountered another error - 

Running calculations on normal system...

Beginning PB calculations with /home/iiita/miniconda3/envs/AmberTools21/bin/sander

  calculating complex contribution...

[ERROR  ] CalcError /home/iiita/miniconda3/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/iiita/miniconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa

    app.run_mmpbsa()

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

  File "/home/iiita/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

  File "/home/iiita/miniconda3/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/iiita/miniconda3/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/iiita/miniconda3/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.

Exiting. All files have been retained.

Thankyou again for helping me out on this 

[Mario Sergio Valdes]

Give me more information, because this error is due to many factors.

Are you using the CHARMM force field?

Check the * .mdout file and show me the end, where the error is reported

Mario S.

[Ayushi Gupta]

Yes, I'm using charmm ff

As for in the *mdout file. I couldn't find any error reported on it. I am attaching the same for your reference. 

[marioe911116]

I see the BOND and UB energies are extremely high... did you remove PBC from your trajectory? you can send us the files (*tpr, *ndx, *in, *top with all the *itp and folders associated and 10 frames of your *xtc) you are using, so we can check in detail what's going on... 

cheers!

Mario E.

[Ayushi Gupta]

I didn't remove PBC from my trajectory files

[Ayushi Gupta]

https://drive.google.com/drive/folders/1-s6TYJbKITfoXX_lOZ5Nrjj66SCg4JEe?usp=sharing

The remaining files

[marioe911116]

could you please attach the file "jz4.prm"?

cheers!

Mario

[Ayushi Gupta]

Hi,

Please find the attached file

[marioe911116]

Indeed, the problem is that your trajectory wasn't fitted... in order to remove the PBC from the traj, run these commands:

echo 22 0 | gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -pbc mol -center -ur compact -o md_0_1_noPBC.xtc -n

echo 22 0 | gmx trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -fit rot+trans -n -o md_0_1_fit.xtc

this means you are gonna use group 22 for centering and group 0 for output in the first command, and group 22 for fitting, and group 0 for output in the second command

Then, use "md_0_1_fit.xtc" for your calculations:

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 1 13 -ct md_0_1_fit.xtc -cp topol.top

cheers!

Mario E.

[Ayushi Gupta]

Hi,

Sorry to have disturbed you again and again.

But I'm still getting the same error.

Beginning PB calculations with /home/ayushi/miniconda3/envs/AmberTools21/bin/sander
  calculating complex contribution...
[ERROR  ] CalcError /home/ayushi/miniconda3/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/ayushi/miniconda3/envs/AmberTools21/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ayushi/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/ayushi/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/ayushi/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/ayushi/miniconda3/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/ayushi/miniconda3/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/ayushi/miniconda3/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.
Exiting. All files have been retained.

Thanks

[Bejo Ropii]

Hi. I do have the same problem. [ERROR  ] CalcError /share/apps/amber20/bin/sander failed with prmtop COM.prmtop!

have you solved this?

[Mario Ernesto]

The error here was that the trajectory wasn't fitted properly... make sure your trajectory is ok by checking the time.evolution of RMSD for example... Make sure there is no abrupt changes in RMSD due to periodic conditions artifacts...

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