# jupyter notebook /biobb

**URL:** https://ask.bioexcel.eu/t/jupyter-notebook-biobb/2506
**Category:** Uncategorized
**Created:** [October 7, 2020, 4:15pm UTC](https://ask.bioexcel.eu/t/jupyter-notebook-biobb/2506 "2020-10-07T16:15:29Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![aishen](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@aishen](https://ask.bioexcel.eu/u/aishen)
#### Post date: [October 7, 2020, 4:15pm UTC](https://ask.bioexcel.eu/t/jupyter-notebook-biobb/2506/1 "2020-10-07T16:15:29Z")

</div>

Hi,

In ubuntu I can’t use anaconda because it messed my config. I install bioexcel the native way ubuntu python. It seems to work except I have problems with gromacs

fixed\_pdb = pdbCode + “\_fixed.pdb”

# Create and launch bb

FixSideChain(input\_pdb\_path=downloaded\_pdb,  
output\_pdb\_path=fixed\_pdb).launch()  
!grep -v HOH 1AKI.pdb \> 1AKI\_fixed.pdb

I have to create namually the file, can you help me fixing that ?

Here too :

from biobb\_chemistry.acpype.acpype\_params\_gmx import AcpypeParamsGMX

# Create prop dict and inputs/outputs

output\_acpype\_gro = ligandCode + ‘params.gro’  
output\_acpype\_itp = ligandCode + ‘params.itp’  
output\_acpype\_top = ligandCode + ‘params.top’  
output\_acpype = ligandCode + ‘params’  
prop = {  
‘basename’ : output\_acpype,  
‘charge’ : mol\_charge  
}

#Create and launch bb  
AcpypeParamsGMX(input\_path=output\_babel\_min,  
output\_path\_gro=output\_acpype\_gro,  
output\_path\_itp=output\_acpype\_itp,  
output\_path\_top=output\_acpype\_top,  
properties=prop).launch()

It seems to be a problem with path in bash ?

amber20 and gromacs work perfect I have done many tutorials.

If I can fix it and translate le tutorial in french would it be of interest for you ?

best regards

Henri

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<div class="post-metadata">

### Author: ![aishen](https://avatars.discourse-cdn.com/v4/letter/a/6de8d8/32.png) [@aishen](https://ask.bioexcel.eu/u/aishen)
#### Post date: [October 7, 2020, 9:56pm UTC](https://ask.bioexcel.eu/t/jupyter-notebook-biobb/2506/2 "2020-10-07T21:56:19Z")

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I do to replay to my question : The latest example Biobb\_MDsetupAPI\_tutorial is the solution  
I run the complete example without any problem (no anaconda)