Hi
I desperately try (for months) to generate GROMACS topology for a ligand using Galaxy.EU server ACPYPE tool.
Trying to use PDB or mol2 input file, trying to calculate the charges (bcc) or not, each times the job fails…
Does anyone has same issues.
Any help would be very appreciated.
Xavier
It seems that switching down to version 19.11 allowed the job to run…
Strange that potentally never tools versions fail where older ones succeed…
Welcome, @XavierB
Your observation is interesting, and I’m glad you solved this!
I’m wondering if there is a small bug with the latest wrapper, or if the tools are actually not compatible, or only incompatible with certain use cases. I’ve open an issue ticket with the developers here. → Reported bug: ambertools_acpype/21.10+galaxy0 not accepting gromacs inputs · Issue #180 · galaxycomputationalchemistry/galaxy-tools-compchem · GitHub
They will probably need an example to confirm the problem. You can post a Galaxy history share link to the issue ticket, or back here in this topic. Simple is better – a history with just the inputs and outputs (from both versions) is probably enough.
Thanks! 
Hi Jennifer,
Unfortunately, it was premature rejoincing…
I think everything comes from the molecule I want to generate the topology through ACPYPE, which has different charged positions.
I’ve changed dozen of times the files (PDB or MOL2) but it seems to fail especially when trying to generate Amber14SB FF topology.
The files that succeed do not work when I try to generate my complex under GROMACS.
Xavier
Ok, thanks for the update @XavierB. You are still welcome to share you history for feedback. Or, you can check your job logs to see what the tools are reporting in the logs. These are from the underlying tool mostly, so the error messages might have solutions reported somewhere if you search.
Where to find the logs is in the same link I posted above:
stdout/stderr messages.There still might be an incompatibility between the tool wrappers, but until we have an example, we are mostly just guessing, and that probably won’t find a solution with such complicated tools/data.
If this can help
https://usegalaxy.eu/api/datasets/4838ba20a6d86765dcab01d3a2f6b1d6/display?to_ext=itp
It generates DU atoms… I think everything comes from this.