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bigginlab / ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
GNU General Public License v3.0
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Option -pbc mol requires a .tpr file for the -s option #31

Open raweru opened 2 weeks ago

raweru commented 2 weeks ago

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 commented 1 week ago

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 commented 1 week ago

@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 commented 1 week ago

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

IAlibay commented 1 week ago

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)