Question about an argument in an amber_to_pdb call in Protein MD Setup tutorial using BioExcel Building Blocks (biobb) --AmberTools package version--

BioBB
1

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

2

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!

3

Ok.
Thanks.
Saverio