GROMACS version: 2019.6 and 5.1.5
GROMACS modification: Yes/No
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Hi guys,
I simulated a system of protein and ligand by gromacs 2019.6. In the process of analyzing the results, i am trying to calculate beta-contents using gromacs 5.1.5 using command gmx do_dssp -f md_nopbc_1.xtc -s md_1.tpr -n index.ndx -sc dssp_1.xvg.
I am facing with an incompatibility that gromacs 5.1.5 can not read files of gromacs 2019, so how i can fix this problem. It would be great if you can give me a reference or guidelines to resolve this problem.
This is a typical problem when using old tools with new .tpr files. You can try to regenerate the .tpr file with the old GROMACS version, i.e., re-run the command that you used to generate the .tpr by using the same files but by sourcing the old GROMACS. Ideally, this would produce a .tpr that is compatible with the old version, but for a such old version of GROMACS I’m not completely sure that it will work out of the box.
I have tried to use gmx trjconv to convert file xtc of gromacs 2019 to xtc by gromacs 5.1.5 but it is the same error. What command can i use to create tpr that is compatible with gromacs 5.1.5? I already have the tpr file generated from MD simulation using gromacs 2019.
No you have to go the other way around. Both the index and the .xtc files should (hopefully) be okay with the old GROMACS version. However, you have a .tpr file that is compiled with v2019 and you are trying to read it with v5.1.5.
You generated the .tpr file for the v2019 with something like
You have to rerun the same command with GROMACS v5.1.5. This will generate a new .tpr file that is compatible with v5.1.5, as you generated it with that version. Then you can run the analysis with v5.1.5 by providing the .xtc and .ndx files from the run with v2019 and the .tpr compiled with v5.1.5.
