Issue while setting up MD simulation with AMBER

1

Hi,

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
&cntrl
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
&end
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.

Any ideas?

Kind regards