Gromacs complaining about .gro format
Posted: Mon Dec 17, 2018 6:30 pm
Dear Prof. Wang,
Hope all is well with you at your new position at UC-Davis, and hope you are well in general!
I and some other people at ORNL would like to optimize force fields for intrinsically disordered proteins using small-angle neutron/X-ray scattering intensities as target data. I have implemented quite a few modifications to allow for this (mostly in "liquid.py"), but I am encountering an error that seems unrelated to any of the modifications I have made. Namely, I'm getting an error in 'npt.out' that traces back to Gromacs, complaining about the format of my .gro file, which consists of a small protein in a water box w/ counter ions:
[[91mSource code file: /software/dev_tools/swtree/cs400/gromacs/5.1.2/centos7.2_gnu5.3.0/gromacs-5.1.2/src/gromacs/fileio/confio.c, line: 1048^[[0m
^[[91mFatal error:^[[0m
^[[91mSomething is wrong in the coordinate formatting of file liquid.gro. Note that gro is fixed format (see the manual)^[[0m
^[[91mFor more information and tips for troubleshooting, please check the GROMACS^[[0m
^[[91mwebsite at http://www.gromacs.org/Documentation/Errors^[[0m
This particular line of 'confio.c' has to do with parsing the coordinate fields. Now, I noticed that the liquid.gro file in the 'optimize.tmp/RS-peptide_simulation_saxs/iter_0000/298.15K-1.0atm' has 6 additional decimal places added to each of the x, y, and z fields (as well as the box dimensions on the last line), so I had initially thought that this was the issue. However, I had run a Gromacs-based example that uses condensed-phase properties as targets, the 'studies/003_liquid_bromine' example in the standard distribution, and it too had the same modification to the coordinate fields in the 'optimize.tmp/LiquidBromine/iter_<number>/298.15K-1.0atm' directories, but this example ran successfully!! I am perplexed! I ran both with Gromacs version 5.1.2.
Please let me know if you need more information, and I will gladly provide it.
Best wishes,
Omar Demerdash
Hope all is well with you at your new position at UC-Davis, and hope you are well in general!
I and some other people at ORNL would like to optimize force fields for intrinsically disordered proteins using small-angle neutron/X-ray scattering intensities as target data. I have implemented quite a few modifications to allow for this (mostly in "liquid.py"), but I am encountering an error that seems unrelated to any of the modifications I have made. Namely, I'm getting an error in 'npt.out' that traces back to Gromacs, complaining about the format of my .gro file, which consists of a small protein in a water box w/ counter ions:
[[91mSource code file: /software/dev_tools/swtree/cs400/gromacs/5.1.2/centos7.2_gnu5.3.0/gromacs-5.1.2/src/gromacs/fileio/confio.c, line: 1048^[[0m
^[[91mFatal error:^[[0m
^[[91mSomething is wrong in the coordinate formatting of file liquid.gro. Note that gro is fixed format (see the manual)^[[0m
^[[91mFor more information and tips for troubleshooting, please check the GROMACS^[[0m
^[[91mwebsite at http://www.gromacs.org/Documentation/Errors^[[0m
This particular line of 'confio.c' has to do with parsing the coordinate fields. Now, I noticed that the liquid.gro file in the 'optimize.tmp/RS-peptide_simulation_saxs/iter_0000/298.15K-1.0atm' has 6 additional decimal places added to each of the x, y, and z fields (as well as the box dimensions on the last line), so I had initially thought that this was the issue. However, I had run a Gromacs-based example that uses condensed-phase properties as targets, the 'studies/003_liquid_bromine' example in the standard distribution, and it too had the same modification to the coordinate fields in the 'optimize.tmp/LiquidBromine/iter_<number>/298.15K-1.0atm' directories, but this example ran successfully!! I am perplexed! I ran both with Gromacs version 5.1.2.
Please let me know if you need more information, and I will gladly provide it.
Best wishes,
Omar Demerdash
