recipe pmx_biobb

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling



LGPL / GNU General Public License (GPL)



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:

``pmx`` is a python library that allows users to setup and analyse molecular dynamics simulations with the `Gromacs <>`_ package. Among its main features are the setup and analysis of alchemical free energy calculations for protein, nucleic acid, and small molecule mutations.

Citations --------- ``pmx`` is a research software. If you make use of it in scientific publications, please cite the following papers::


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}



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

(downloads) docker_pmx_biobb



depends boost-cpp:


depends cxx-compiler:

depends libgcc-ng:


depends libgfortran-ng:

depends libgfortran5:


depends libstdcxx-ng:


depends matplotlib-base:

depends python:


depends python_abi:

3.7.* *_cp37m

depends rdkit:

depends scipy:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pmx_biobb

and update with::

   mamba update pmx_biobb

To create a new environment, run:

mamba create --name myenvname pmx_biobb

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `pmx_biobb/tags`_ for valid values for ``<tag>``)

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