# Question about an argument in an amber\_to\_pdb call in Protein MD Setup tutorial using BioExcel Building Blocks (biobb) --AmberTools package version--

**URL:** https://ask.bioexcel.eu/t/question-about-an-argument-in-an-amber-to-pdb-call-in-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version/4701
**Category:** BioBB
**Created:** [November 26, 2023, 3:16pm UTC](https://ask.bioexcel.eu/t/question-about-an-argument-in-an-amber-to-pdb-call-in-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version/4701 "2023-11-26T15:16:28Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![saverio](https://avatars.discourse-cdn.com/v4/letter/s/dbc845/32.png) [@saverio](https://ask.bioexcel.eu/u/saverio)
#### Post date: [November 26, 2023, 3:16pm UTC](https://ask.bioexcel.eu/t/question-about-an-argument-in-an-amber-to-pdb-call-in-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version/4701/1 "2023-11-26T15:16:28Z")

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Hi,  
I’m studying the Protein MD Setup tutorial using BioExcel Building Blocks (biobb)  
–AmberTools package version–

I’m reporting the code in three sections.

Energetically minimize the structure section  
Step 1:Minimize Hydrogens  
**Hydrogen** minimization, applying **position restraints** (50 Kcal/mol.Å2) to the **protein heavy atoms**.

…

sander\_mdrun(input\_top\_path=output\_top\_path,  
input\_crd\_path=output\_crd\_path,  
input\_ref\_path=output\_crd\_path,  
output\_traj\_path=output\_h\_min\_traj\_path,  
output\_rst\_path=output\_h\_min\_rst\_path,  
output\_log\_path=output\_h\_min\_log\_path,  
properties=prop)

Step2:Minimizing the system  
**System** minimization, applying **position restraints** (50 Kcal/mol.Å2) to the **protein heavy atoms**.

…

sander\_mdrun(input\_top\_path=output\_top\_path,  
input\_crd\_path=output\_h\_min\_rst\_path,  
input\_ref\_path=output\_h\_min\_rst\_path,  
output\_traj\_path=output\_n\_min\_traj\_path,  
output\_rst\_path=output\_n\_min\_rst\_path,  
output\_log\_path=output\_n\_min\_log\_path,  
properties=prop)

Create solvent box and solvating the system section  
Getting minimized structure

…

amber\_to\_pdb(input\_top\_path=output\_top\_path,  
input\_crd\_path=output\_h\_min\_rst\_path,  
output\_pdb\_path=output\_ambpdb\_path  
)

I’m guessing that second argument in the previous amber\_to\_pdb call should be  
input\_crd\_path=output\_n\_min\_rst\_path  
not  
input\_crd\_path=output\_h\_min\_rst\_path.

Otherwise the results of the the Step2 will not be used.

I’m wrong?

Thanks.

Saverio

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<div class="post-metadata">

### Author: ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)
#### Post date: [November 27, 2023, 10:10am UTC](https://ask.bioexcel.eu/t/question-about-an-argument-in-an-amber-to-pdb-call-in-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version/4701/2 "2023-11-27T10:10:56Z")

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Hi Saverio,

you are absolutely right, this is an error that should be fixed. Luckily it wasn’t affecting much the final result in this case. We are going to fix this issue in the next release of the workflows.

Thanks for spotting the problem and for letting us know!

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<div class="post-metadata">

### Author: ![saverio](https://avatars.discourse-cdn.com/v4/letter/s/dbc845/32.png) [@saverio](https://ask.bioexcel.eu/u/saverio)
#### Post date: [November 27, 2023, 3:44pm UTC](https://ask.bioexcel.eu/t/question-about-an-argument-in-an-amber-to-pdb-call-in-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version/4701/3 "2023-11-27T15:44:31Z")

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Ok.  
Thanks.  
Saverio