I am following this tutorial AMBER Protein MD Setup tutorial - BioExcel Building Blocks.
When I execute Step 1: Minimize Hydrogens in Jupyter Notebook it runs without any issues. However, when I do so via cli with python calling the .yaml file I get the following error (log file):
Here is the input file:
This mdin file has been created by the biobb_amber module from the BioBB library
Type of mdin: min_vacuo
imin = 1 ! BioBB simulation_type minimization
maxcyc = 500 ! BioBB property
ntpr = 5 ! BioBB property
ntr = 1 ! BioBB property
restraintmask = ":*&!@H=\ ! BioBB property
restraint_wt = 50.0 ! BioBB property
error in reading namelist cntrl
My .yaml file for this step is:
step4_minH: paths: input_top_path: dependency/step3_leaptop/output_top_path input_crd_path: dependency/step3_leaptop/output_crd_path input_ref_path: dependency/step3_leaptop/output_crd_path output_traj_path: sander_hmin.x output_rst_path: sander_hmin.rst output_log_path: sander_hmin.log properties: simulation_type: min_vacuo mdin: maxcyc: 500 ntpr: 5 ntr: 1 restraintmask: '\":*&!@H=\"' restraint_wt: 50.0
However, if I remove the restraints it works, so the issue must be related to the introduction of restraints. I am a bit lost as the restraints works when running it in Jupyter Notebook.