Option -pbc mol requires a .tpr file for the -s option

[raweru]

Executable: /path/miniforge3/envs/abfe/bin.AVX2_256/gmx
Data prefix: /path/miniforge3/envs/abfe
Working dir: /path/ABFE_workflow/examples/data/CyclophilinD_min/output/ligand-2/1/ligand
Command line:
gmx trjconv -s /path/ABFE_workflow/examples/data/CyclophilinD_min/output/ligand-2/1/ligand/fep/fep-topology/ligand.gro -f /path/ABFE_workflow/examples/data/CyclophilinD_min/output/ligand-2/1/ligand/fep/fep-topology/nojump.gro -o /path/ABFE_workflow/examples/data/CyclophilinD_min/output/ligand-2/1/ligand/fep/fep-topology/equil.gro -pbc mol -center -ur compact

Will write gro: Coordinate file in Gromos-87 format

---

Program: gmx trjconv, version 2024.3-conda_forge
Source file: src/gromacs/tools/trjconv.cpp (line 789)

Fatal error:
Option -pbc mol requires a .tpr file for the -s option

[philbiggin]

This is related to the gromacs implementation of this -pbc option. So you have two choices I think:

1. Omit the option
2. Script up something to supply the .tpr

[IAlibay]

@raweru am I correct in understanding this is happening with the test files under default settings with gromacs 2024?

@philbiggin - I suspect something changed in gmx 2024, I encountered that bug elsewhere (different project) and couldn't work out why it suddenly started failing for me.

[raweru]

@IAlibay Yes that is correct. Does it run fine with some older gromacs?

[IAlibay]

If it's the standard workflow i.e. you aren't calling any extra gmx commands outside of what snakemake does for you, then it "should work" (at least it has worked with previous versions of gromacs)