Gmx grompp: reading tpx file (md_0_1.tpr) version 129 with version 103 program

GROMACS version: 2023.4
GROMACS modification: Yes/No

Hi, I am trying to convert tpr and xtc file generated by GROMACS version 2023.4 to older version of GROMACS (5.1.5). I am doing this due to the latest compatible version of g_mmpbsa being gmx 5.1.x. Some older discussion have mentioned the solution, running gmx grompp using older gmx version to convert the tpr. However, it seems that executing gmx grompp also resulted in the same error. Here is my prompt:

gmx grompp -f md.mdp -c md_0_1.tpr -p topol.top -o md_0_1_gmx515.tpr

And it reported this error:

Fatal error:
reading tpx file (md_0_1.tpr) version 129 with version 103 program
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

I would also appreciate it if anyone have any suggestion on newer method to calculate binding affinity for protein-ligand or protein-peptide. Thanks in advance!

Hello,

have you tried rerunning the grompp command as you did for generating the md_0_1.tpr file? So, if in GROMACS 2023.4 you did something like: gmx grompp -f md.mdp -c file.gro -p topol.top -o md_0_1.tpr you now do the same with the old GROMACS version, so you will get a md_0_1.tpr file that is in the binary form of GROMACS 5.1.5. If the mdp options are compatible, it should work instantly.

The error you get is because you using GROMACS 5.1.5 to read from a structure file with the -c flag that points to a binary compiled with a more recent software, so it won’t work. I think the .tpr comment about converting means what I wrote beforehand, that is, re-run the same grompp command you used for generating the md_0_1.tpr BUT with the oldest version of GROMACS. This will give you a binary that is compatible with 5.1.5, as it was generated by it, and now you can use that one as a .tpr for analysis within the 5.1.5 version.

i suggest using this for MM/PBSA calculations