# BioBB **URL:** https://ask.bioexcel.eu/c/bioexcel-building-blocks-library/23.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About the BioBB category](https://ask.bioexcel.eu/t/about-the-biobb-category/2037)
**Author:** [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Replies:** 0\ **Last updated:** [May 26, 2020, 11:28am UTC](https://ask.bioexcel.eu/t/about-the-biobb-category/2037 "2020-05-26T11:28:41Z")
BioExcel Building Blocks BioBB is a software library for interoperable biomolecular simulation workflows. The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomol… --- ## [Problems running BD simulation in flexserv workflow](https://ask.bioexcel.eu/t/problems-running-bd-simulation-in-flexserv-workflow/6137)
**Author:** [@giulya](https://ask.bioexcel.eu/u/giulya)\ **Replies:** 1\ **Last updated:** [May 29, 2026, 2:40pm UTC](https://ask.bioexcel.eu/t/problems-running-bd-simulation-in-flexserv-workflow/6137 "2026-05-29T14:40:03Z")
Hello, I’ve been using the Macromolecular Coarse-Grained Flexibility workflow ( Jupyter Notebook Macromolecular Coarse-Grained Flexibility tutorial ) with an api.alphafold module. My main problem is that the Brownian dyn… --- ## [Using biobb\_gromacs image on runpod](https://ask.bioexcel.eu/t/using-biobb-gromacs-image-on-runpod/5541)
**Author:** [@pducrot](https://ask.bioexcel.eu/u/pducrot)\ **Replies:** 2\ **Last updated:** [March 26, 2025, 4:48pm UTC](https://ask.bioexcel.eu/t/using-biobb-gromacs-image-on-runpod/5541 "2025-03-26T16:48:43Z")
Hi, I’m trying to run a Gromacs simulation using the biobb\_gromacs docker image running on runpod. It doesn’t seem to be using the GPU regardless the gmx mdrun options I set. In runpod I selected a RTX A4000 GPU pod. Do… --- ## [Utilizing GROMACS Simulation Files for DNA Structure Analysis with the biobb\_dna Package](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003)
**Author:** [@fatemeh](https://ask.bioexcel.eu/u/fatemeh)\ **Replies:** 11\ **Last updated:** [August 19, 2024, 10:41am UTC](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003 "2024-08-19T10:41:46Z")
Hello, I would like to use biobb\_dna to analyze the DNA structure. I have used GROMACS, so I have .tpr and .xtc files. Can I use these files with biobb\_dna ? thank you in advance --- ## [Exploring the Limitations of biobb\_dna in Handling Large DNA Sequences](https://ask.bioexcel.eu/t/exploring-the-limitations-of-biobb-dna-in-handling-large-dna-sequences/5017)
**Author:** [@fatemeh](https://ask.bioexcel.eu/u/fatemeh)\ **Replies:** 3\ **Last updated:** [August 19, 2024, 10:39am UTC](https://ask.bioexcel.eu/t/exploring-the-limitations-of-biobb-dna-in-handling-large-dna-sequences/5017 "2024-08-19T10:39:34Z")
Hello, Can biobb\_dna support a specific length of DNA? I have 90 base pairs, but it only considers 45 base pairs during calculation. --- ## [Problems with MD](https://ask.bioexcel.eu/t/problems-with-md/3954)
**Author:** [@jonaramirez](https://ask.bioexcel.eu/u/jonaramirez)\ **Replies:** 7\ **Last updated:** [April 29, 2024, 7:56am UTC](https://ask.bioexcel.eu/t/problems-with-md/3954 "2024-04-29T07:56:31Z")
Hi, I am doing MD with a protein which has a magnesium atom and I have problems in the step “create protein system topology”. The FATAL error said: “Atom .R\.A\ does not have a type”, and I don’t know how ca… --- ## [BioBB not working?](https://ask.bioexcel.eu/t/biobb-not-working/4751)
**Author:** [@gcdomingo](https://ask.bioexcel.eu/u/gcdomingo)\ **Replies:** 3\ **Last updated:** [January 12, 2024, 3:15am UTC](https://ask.bioexcel.eu/t/biobb-not-working/4751 "2024-01-12T03:15:36Z")
Hi! I try to use BioBB server but it won’t work, I cannot submit a project. It only says uploading data when i submit my protein-ligand structure it does not go to step 2:protonation state. can you help me with this? --- ## [Challenges in Installing biobb\_dna on Ubuntu: Seeking Solutions](https://ask.bioexcel.eu/t/challenges-in-installing-biobb-dna-on-ubuntu-seeking-solutions/4733)
**Author:** [@fatemeh](https://ask.bioexcel.eu/u/fatemeh)\ **Replies:** 7\ **Last updated:** [December 27, 2023, 9:19am UTC](https://ask.bioexcel.eu/t/challenges-in-installing-biobb-dna-on-ubuntu-seeking-solutions/4733 "2023-12-27T09:19:09Z")
Hello, I am writing about biobb\_dna. Unfortunately, I am not able to install it on Ubuntu with pip and Anaconda. I encountered the following error with both pip as an example. Does anybody have the same problem, or does… --- ## [Using the Protein MD Setup tutorial using BioExcel Building Blocks (biobb) --AmberTools package version-- with Amber installed frome sources](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702)
**Author:** [@saverio](https://ask.bioexcel.eu/u/saverio)\ **Replies:** 2\ **Last updated:** [November 27, 2023, 3:45pm UTC](https://ask.bioexcel.eu/t/using-the-protein-md-setup-tutorial-using-bioexcel-building-blocks-biobb-ambertools-package-version-with-amber-installed-frome-sources/4702 "2023-11-27T15:45:54Z")
Hi, I’ve used the Protein MD Setup tutorial using BioExcel Building Blocks (biobb) –AmberTools package version– following the instructions: git clone https://github.com/bioexcel/biobb\_wf\_amber\_md\_setup.git cd biobb\_… --- ## [Question about an argument in an amber\_to\_pdb call in Protein MD Setup tutorial using BioExcel Building Blocks (biobb) --AmberTools package version--](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)
**Author:** [@saverio](https://ask.bioexcel.eu/u/saverio)\ **Replies:** 2\ **Last updated:** [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 "2023-11-27T15:44:31Z")
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:Minimi… --- ## [Examples for a section of the Molecular Structure Checking wf](https://ask.bioexcel.eu/t/examples-for-a-section-of-the-molecular-structure-checking-wf/4622)
**Author:** [@saverio](https://ask.bioexcel.eu/u/saverio)\ **Replies:** 2\ **Last updated:** [October 23, 2023, 5:55pm UTC](https://ask.bioexcel.eu/t/examples-for-a-section-of-the-molecular-structure-checking-wf/4622 "2023-10-23T17:55:07Z")
Hi, in the section Metal Ions of the Molecular Structure Checking wf there is written the following: “Presence of heteroatoms being metal ions. Only structural metal ions should be kept in MD simulations, as they requ… --- ## [Problem with Fatal error from gmx pdb2gmx in the Protein MD Setup wf](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600)
**Author:** [@saverio](https://ask.bioexcel.eu/u/saverio)\ **Replies:** 2\ **Last updated:** [October 11, 2023, 10:02am UTC](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600 "2023-10-11T10:02:27Z")
HI, I should like to adapt the “Protein MD Setup tutorial using BioExcel Building Blocks” workflow to the protein of my concern including the Zn and Mg ions present in the solved structure. HI, I should like to adapt… --- ## [Line filtering in a fetched PDB in biobb gromacs tutorial](https://ask.bioexcel.eu/t/line-filtering-in-a-fetched-pdb-in-biobb-gromacs-tutorial/4558)
**Author:** [@xave](https://ask.bioexcel.eu/u/xave)\ **Replies:** 2\ **Last updated:** [October 2, 2023, 5:30pm UTC](https://ask.bioexcel.eu/t/line-filtering-in-a-fetched-pdb-in-biobb-gromacs-tutorial/4558 "2023-10-02T17:30:50Z")
Hi, in the output of the cell relative to the fetching of a PDB structure in the biobb gromacs tutorial whose code is the following: from biobb\_io.api.pdb import pdb Create properties dict and inputs/outputs download… --- ## [Problem with GromacsVersionError: Gromacs version should be 5.1.2 or newer 0 detected](https://ask.bioexcel.eu/t/problem-with-gromacsversionerror-gromacs-version-should-be-5-1-2-or-newer-0-detected/4546)
**Author:** [@xave](https://ask.bioexcel.eu/u/xave)\ **Replies:** 23\ **Last updated:** [October 2, 2023, 7:33am UTC](https://ask.bioexcel.eu/t/problem-with-gromacsversionerror-gromacs-version-should-be-5-1-2-or-newer-0-detected/4546 "2023-10-02T07:33:09Z")
Hi, I’m running the tutorial: Protein MD Setup tutorial using BioExcel Building Blocks (biobb). At the cell: Create system topology Import module from biobb\_gromacs.gromacs.pdb2gmx import pdb2gmx Create inputs/outpu… --- ## [Trajectory File Size](https://ask.bioexcel.eu/t/trajectory-file-size/4077)
**Author:** [@aleiquea](https://ask.bioexcel.eu/u/aleiquea)\ **Replies:** 1\ **Last updated:** [January 16, 2023, 11:48am UTC](https://ask.bioexcel.eu/t/trajectory-file-size/4077 "2023-01-16T11:48:09Z")
I have my final trajectory file and would like to use it for Structural DNA Helical Parameters. However, the file is larger than 500 MB and I am looking for recommendations on how to reduce the size of the file. --- ## [Any foreseen update of BioBB for Ambertools 22?](https://ask.bioexcel.eu/t/any-foreseen-update-of-biobb-for-ambertools-22/4037)
**Author:** [@mverissi](https://ask.bioexcel.eu/u/mverissi)\ **Replies:** 1\ **Last updated:** [December 22, 2022, 7:46am UTC](https://ask.bioexcel.eu/t/any-foreseen-update-of-biobb-for-ambertools-22/4037 "2022-12-22T07:46:43Z")
Hi all, I recently got a Mac with Apple Silicon and I’d like to use it for Python development. I tried installing BioBB (biobb\_amber, in particular) using conda. However, it says it’s not possible to do it because there… --- ## [Str\_check\_add\_hydrogens](https://ask.bioexcel.eu/t/str-check-add-hydrogens/3777)
**Author:** [@pbarletta](https://ask.bioexcel.eu/u/pbarletta)\ **Replies:** 1\ **Last updated:** [July 1, 2022, 2:38pm UTC](https://ask.bioexcel.eu/t/str-check-add-hydrogens/3777 "2022-07-01T14:38:03Z")
Hi all, I’ve run into 2 issues related to the check\_structure tool. keep\_h, listed here is not actually supported with version biobb version 3.7.6 (my check\_structure version is 3.9.11). I get this warning when I try… --- ## [Biobb\_md: set log.out and log.err on any tool](https://ask.bioexcel.eu/t/biobb-md-set-log-out-and-log-err-on-any-tool/3757)
**Author:** [@pbarletta](https://ask.bioexcel.eu/u/pbarletta)\ **Replies:** 4\ **Last updated:** [June 14, 2022, 2:18pm UTC](https://ask.bioexcel.eu/t/biobb-md-set-log-out-and-log-err-on-any-tool/3757 "2022-06-14T14:18:17Z")
Hello, I read on a previous question that log.out and log.err would become editable but it seems only mdrun allows this config, and even though my command (GmxSelect) has global\_log, err\_log and out\_log as None, still I… --- ## [How to prepare input PDB file (not from PDB database) for MD simulation in BioExcel Building Blocks?](https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681)
**Author:** [@Hamza](https://ask.bioexcel.eu/u/Hamza)\ **Replies:** 1\ **Last updated:** [April 25, 2022, 1:24pm UTC](https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681 "2022-04-25T13:24:51Z")
How to prepare input PDB file (not from PDB database) for MD simulation? Please guide me. I am following tutorial on “Protein MD Setup tutorial using BioExcel Building Blocks (biobb)”: Protein MD Setup tutorial - BioExc… --- ## [Add custom flags for GROMACS mdrun](https://ask.bioexcel.eu/t/add-custom-flags-for-gromacs-mdrun/3459)
**Author:** [@mverissi](https://ask.bioexcel.eu/u/mverissi)\ **Replies:** 2\ **Last updated:** [February 17, 2022, 1:07pm UTC](https://ask.bioexcel.eu/t/add-custom-flags-for-gromacs-mdrun/3459 "2022-02-17T13:07:42Z")
Hi all, I have finally managed to start using BioBB. I’m assembling a basic workflow using GROMACS 2021-2 (and perhaps soon I’ll change it to GROMACS 2022). I would like to add custom flags for mdrun, namely: -dlb yes … --- ## [Extending the receptor-ligand tutorial to cofactors and metals?](https://ask.bioexcel.eu/t/extending-the-receptor-ligand-tutorial-to-cofactors-and-metals/3115)
**Author:** [@patc](https://ask.bioexcel.eu/u/patc)\ **Replies:** 13\ **Last updated:** [September 7, 2021, 6:44am UTC](https://ask.bioexcel.eu/t/extending-the-receptor-ligand-tutorial-to-cofactors-and-metals/3115 "2021-09-07T06:44:13Z")
first of all - thank you so much for the excellent tutorial, as well as the biobb package. it really helped me get set up. I am wondering if its possible to extend this to systems with multiple ligands/cofactors and meta… --- ## [How to write the log.out and log.err files to a custom directory](https://ask.bioexcel.eu/t/how-to-write-the-log-out-and-log-err-files-to-a-custom-directory/2812)
**Author:** [@hjuinj](https://ask.bioexcel.eu/u/hjuinj)\ **Replies:** 2\ **Last updated:** [February 8, 2021, 7:35pm UTC](https://ask.bioexcel.eu/t/how-to-write-the-log-out-and-log-err-files-to-a-custom-directory/2812 "2021-02-08T19:35:04Z")
Is it possible to specify the path where log.out and log.err is written to instead of always being written to the path where the python script is called? Or is it possible to turn it this log off completely? --- ## [Conda install of biobb\_md stalls](https://ask.bioexcel.eu/t/conda-install-of-biobb-md-stalls/2585)
**Author:** [@hjuinj](https://ask.bioexcel.eu/u/hjuinj)\ **Replies:** 7\ **Last updated:** [November 19, 2020, 6:23pm UTC](https://ask.bioexcel.eu/t/conda-install-of-biobb-md-stalls/2585 "2020-11-19T18:23:30Z")
I tried to conda install biobb\_md with the command in the documentation: conda install -c bioconda "biobb\_md\>=3.0.1" but this just stalls at “solving environment” I tried to just do conda install -c bioconda biobb\_md. … --- ## [Ligand Binding Free Energies with PMX](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 2\ **Last updated:** [November 12, 2020, 10:13am UTC](https://ask.bioexcel.eu/t/ligand-binding-free-energies-with-pmx/2532 "2020-11-12T10:13:12Z")
Is there an available tutorial for ligand binding free energy calculations? Maybe I should try to apply the available pmx tutorials to a biobb format. Thank you, Dan --- ## [CP2K command to start simulation](https://ask.bioexcel.eu/t/cp2k-command-to-start-simulation/2438)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 2\ **Last updated:** [September 7, 2020, 7:56pm UTC](https://ask.bioexcel.eu/t/cp2k-command-to-start-simulation/2438 "2020-09-07T19:56:24Z")
I’m just getting started on setting up a QMMM run. I’ve watched Salome Llabres’ tutorial. I see there are a lot of exercises available too that I’m going to look into. What is the actual command line command and optio… --- ## [ExtractHeteroAtoms returns empty heteroatom file](https://ask.bioexcel.eu/t/extractheteroatoms-returns-empty-heteroatom-file/2360)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 4\ **Last updated:** [July 29, 2020, 10:58pm UTC](https://ask.bioexcel.eu/t/extractheteroatoms-returns-empty-heteroatom-file/2360 "2020-07-29T22:58:49Z")
I’m following the protein ligand tutorial with my own files. I used ExtractHeteroAtoms but got an empty file for the output\_heteroatom\_path option. input: prop = { ‘heteroatoms’ : \[{“name”: “LIG”}\] ExtractHeteroAtom… --- ## [Charmm parameterization](https://ask.bioexcel.eu/t/charmm-parameterization/2359)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 3\ **Last updated:** [July 28, 2020, 4:01pm UTC](https://ask.bioexcel.eu/t/charmm-parameterization/2359 "2020-07-28T16:01:52Z")
Any plans to wrap a charmm parameterization tool? Thank you, Dan --- ## [Adding pdb file for protein-ligand complex in setup of BioBB MD setup](https://ask.bioexcel.eu/t/adding-pdb-file-for-protein-ligand-complex-in-setup-of-biobb-md-setup/2281)
**Author:** [@sadafrani6](https://ask.bioexcel.eu/u/sadafrani6)\ **Replies:** 1\ **Last updated:** [July 28, 2020, 12:11pm UTC](https://ask.bioexcel.eu/t/adding-pdb-file-for-protein-ligand-complex-in-setup-of-biobb-md-setup/2281 "2020-07-28T12:11:21Z")
Dear All I wonder if I can make the directory of input pdb file in jupyter notebook in BioBB MD protein-ligand setup and create a single topology using -merge all option of gromacs. I need your suggestions, please. Tha…