# Issue while setting up MD simulation with AMBER

**URL:** <https://ask.bioexcel.eu/t/issue-while-setting-up-md-simulation-with-amber/3780>\
**Category:** Uncategorized\
**Created:** [June 22, 2022, 1:36pm UTC](https://ask.bioexcel.eu/t/issue-while-setting-up-md-simulation-with-amber/3780 "2022-06-22T13:36:32Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![jcmunoz](https://avatars.discourse-cdn.com/v4/letter/j/a87d85/32.png) [@jcmunoz](https://ask.bioexcel.eu/u/jcmunoz)\
**Post date:** [June 22, 2022, 1:36pm UTC](https://ask.bioexcel.eu/t/issue-while-setting-up-md-simulation-with-amber/3780/1 "2022-06-22T13:36:32Z")

</div>

Hi,

I am following this tutorial [AMBER Protein MD Setup tutorial - BioExcel Building Blocks](https://mmb.irbbarcelona.org/biobb/workflows/tutorials/amber_md_setup).

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:

```auto
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