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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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trjconv failed when querying md.tpr #15

Closed mar-ko2020 closed 3 years ago

mar-ko2020 commented 3 years ago

Hi I am trying to calculate the mmpbsa between a protein and DNA. I use the following command gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 15 -ct md.xtc However, it gives me this error and the job stops after a few minutes MMPBSA_Error: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2020.4/bin/gmx trjconv failed when querying md.tpr Exiting. All files have been retained. I used gromacs2020 and the pbc was removed from the trajectory. Any help would be appreciated. Thanks!

Valdes-Tresanco-MS commented 3 years ago

The error information is contained in the make_top.log file. Sorry about that.:sweat_smile: We are working to improve the error output. Can you share the file make_top.log?. If it has sensitive information you can send it to my email.

mar-ko2020 commented 3 years ago

Thanks Valdes. Could you share your email address, please?

Valdes-Tresanco-MS commented 3 years ago

mariosergiovaldes145@gmail.com

gayatripanda5 commented 3 years ago

Hi, I also facing the same issue. gmx_MMPBSA worked perfectly fine with files in Protein-DNA examples but failed while running it for my files.

Command used: gmx_MMPBSA -O -i mmpbsa_onlygbsa.in -cs md_0-900ns-1000ns_nodt_nocpmact.tpr -ci index_prot.ndx -cg 1 12 -ct md_0-900ns-1000ns_nodt_nocpmact.xtc

Error reported: File "/home/gayatrip/miniconda3/envs/amber/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.') MMPBSA_Error: /home/gayatrip/gromacs-2020/build/bin/gmx trjconv failed when querying md_0-900ns-1000ns_nodt_nocpmact.tpr. Check the gmx_MMPBSA.log file to report the problem.

Could you please tell me where am I going wrong?

Thanks in advance

marioernestovaldes commented 3 years ago

Could you please send us the files (.in, .tpr, .xtc, .ndx) for review... That way will be easy for us to determine where the error is quickly... make sure to send just a piece of the xtc (10 frames)

On Fri, Apr 9, 2021, 3:55 AM Gayatri Panda @.***> wrote:

Hi, I also facing the same issue. gmx_MMPBSA worked perfectly fine with files in Protein-DNA examples but failed while running it for my files.

Command used: gmx_MMPBSA -O -i mmpbsa_onlygbsa.in -cs md_0-900ns-1000ns_nodt_nocpmact.tpr -ci index_prot.ndx -cg 1 12 -ct md_0-900ns-1000ns_nodt_nocpmact.xtc

Error reported: File "/home/gayatrip/miniconda3/envs/amber/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.') MMPBSA_Error: /home/gayatrip/gromacs-2020/build/bin/gmx trjconv failed when querying md_0-900ns-1000ns_nodt_nocpmact.tpr. Check the gmx_MMPBSA.log file to report the problem.

Could you please tell me where am I going wrong?

Thanks in advance

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gayatripanda5 commented 3 years ago

Hi, Apologies for the delayed response! Shall I send these files at this email id: mariosergiovaldes145@gmail.com?

Valdes-Tresanco-MS commented 3 years ago

Hi, Apologies for the delayed response! Shall I send these files at this email id: mariosergiovaldes145@gmail.com?

Yes, you can send me the files.

For future errors, doubts or problems, please open a new issue. If you think your issue is similar to an existing one you can simply reference it as #issue number (no spaces, eg #15 for the current one). This makes it easier for us to follow up properly since once an issue is closed it means that it has been solved. We appreciate your understanding and we will help you solve your problem.

Best! Mario S.

gayatripanda5 commented 3 years ago

Dear Mario S.,

Apologies for the inconvenience caused!. I have submitted this as a new issue. It is easier for me also to track down any update associated with this issue. Thanks for this suggestion. Also, as suggested by you, I have shared with you the required files.

Ridwan20-alt commented 1 year ago

Hi I am trying to calculate the mmpbsa between a protein and a ligand with LPH atoms. After following this tutorial(https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examples/Protein_ligand_LPH_atoms_CHARMMff) to prepare my input files I use the following command: gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 18 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv However, it gives me this error and the job stops after a few minutes: [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 1_18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [ERROR ] MMPBSA_Error /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc. Check the gmx_MMPBSA.log file to report the problem. File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa app.make_prmtops() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology self.gmx2pdb() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 232, in gmx2pdb GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0])) File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

Ridwan20-alt commented 1 year ago

I will be glad if you can guide me on to get this error resolved

Thanks

Valdes-Tresanco-MS commented 1 year ago

Please, open a new issue to better follow up on the problem and attach the gmx_MMPBSA.log file

elahehtavili commented 1 year ago

Hi I am trying to calculate the mmpbsa between a protein and protein. I use the following command gmx_MMPBSA -O -i mmpbsa.in -cs md_2_3.tpr -ci index.ndx -cg 17 18 -ct final_noPBC.xtc However, it gives me this error and the job stops after a few minutes /opt/miniconda/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying final_noPBC.xtc

Check the gmx_MMPBSA.log file to report the problem. File "/opt/miniconda/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/opt/miniconda/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/opt/miniconda/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/opt/miniconda/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology self.gmx2pdb() File "/opt/miniconda/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0])) File "/opt/miniconda/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.') MMPBSA_Error:

/opt/miniconda/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv failed when querying final_noPBC.xtc

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

I used gromacs2022 and the pbc was removed from the trajectory. Any help would be appreciated. Thanks!

Valdes-Tresanco-MS commented 1 year ago

@elahehtavili This issue is already closed and corresponds to an old version. Please, open a new issue and attach all required information and files.