- recipe pmx_biobb
Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
- Homepage:
- License:
LGPL / GNU General Public License (GPL)
- Recipe:
pmx: alchemistry in gromacs ===========================
|build| |cov|
**Warning:** this is a development version of ``pmx``, it is not stable or reliable yet. You are welcome to try/test it and provide feedback, but use at your own risk. The current stable version of ``pmx`` can be found in the master branch: https://github.com/deGrootLab/pmx
``pmx`` is a python library that allows users to setup and analyse molecular dynamics simulations with the `Gromacs <http://gromacs.org>`_ package. Among its main features are the setup and analysis of alchemical free energy calculations for protein, nucleic acid, and small molecule mutations.
https://degrootlab.github.io/pmx/
Citations --------- ``pmx`` is a research software. If you make use of it in scientific publications, please cite the following papers::
- @article{Gapsys2015pmx,
title = {pmx: Automated protein structure and topology generation for alchemical perturbations}, author = {Gapsys, Vytautas and Michielssens, Servaas and Seeliger, Daniel and de Groot, Bert L.}, journal = {Journal of Computational Chemistry}, volume = {36}, number = {5}, pages = {348--354}, year = {2015}, doi = {10.1002/jcc.23804}
}
- @article{Seeliger2010pmx,
title = {Protein Thermostability Calculations Using Alchemical Free Energy Simulations}, author = {Seeliger, Daniel and de Groot, Bert L.}, journal = {Biophysical Journal}, volume = {98}, number = {10}, pages = {2309--2316}, year = {2010}, doi = {10.1016/j.bpj.2010.01.051}
}
License ------- ``pmx`` is licensed under the GNU Lesser General Public License v3.0 (LGPL v3).
- package pmx_biobb¶
- Versions:
5.2.2-0,5.2.1-0,4.1.3-1,4.1.3-0,4.1.2-2,4.1.2-1,4.1.2-0,4.0.2-0,3.0.3-4,5.2.2-0,5.2.1-0,4.1.3-1,4.1.3-0,4.1.2-2,4.1.2-1,4.1.2-0,4.0.2-0,3.0.3-4,3.0.3-3,3.0.3-2,3.0.3-1,3.0.3-0,2.0.0-2,2.0.0-1,2.0.0-0,1.0.0-3,1.0.0-2,1.0.0-1,1.0.0-0- Depends:
on boost-cpp
on cxx-compiler
on libgcc
>=13on matplotlib-base
on python
>=3.10,<3.11.0a0on python_abi
3.10.* *_cp310on rdkit
on scipy
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install pmx_biobb
to add into an existing workspace instead, run:
pixi add pmx_biobb
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install pmx_biobb
Alternatively, to install into a new environment, run:
conda create -n envname pmx_biobb
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/pmx_biobb:<tag>
(see pmx_biobb/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pmx_biobb/README.html)
