Error when trying to use GROMACS on PDB of Protein-Protein Complex

I am trying to follow the MD simulation with GROMACS tutorial (Running molecular dynamics simulations using GROMACS) on a PDB file, 2XQW, which contains 3 protein chains. However, when I try to run the initial GROMACS set up tool, I get an error that the job cannot run:

The full error says “This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.”

Is there a way to follow this tutorial on a PDB file containing more than 1 protein chain?

Hi @christos-efthymiou, can you submit a bug report (using the bug icon on the failed dataset?)

There should also be a log file created by the job which should provide more information.

Hi @simonbray, I have submitted a bug report. I am also placing several screenshots of information about the error below:





@simonbray I also wanted to add that I have tried this again with separate PDB files with only a single protein chain and the same error occurs.

@christos-efthymiou thanks for the bug report, I replied by email.

I also wanted to add that I have tried this again with separate PDB files with only a single protein chain and the same error occurs.

The reason would be that the error is not due to the multiple chains, but unexpected atom naming in the original PDB file.