mdpow-molconfgen

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Community

Generation of conformers of small molecules.

Background

1. find all N major torsions
2. generate all conformers by rotating all torsions in increments delta for a total of (2π/delta)^N conformers
3. write to a trajectory
4. evaluate the force field energy with gmx mdrun -rerun.
5. find minima in the N-dimensional energy landscape

Implementation notes

1. Load molecules with MDAnalysis.
2. Convert to RDKit molecule.
3. Perform torsion drive with rdkit.Chem.rdMolTransforms

Initial testing systems

From the COW dataset:

• V36-methylacetate : 1 dihedral
• V46-2-methyl-1-nitrobenzene : steric hindrance
• V39-butylacetate : 4 dihedrals

First steps

Community

mdpow-molconfgen is bound by a Code of Conduct.

Installation

To build mdpow-molconfgen from source, we highly recommend using virtual environments. If possible, we strongly recommend that you use mamba as your package manager. Below we provide instructions both for mamba and for pip.

With mamba

Ensure that you have mamba installed.

Create a virtual environment and activate it:

mamba create --name mdpow-molconfgen
mamba activate mdpow-molconfgen

Install the development and documentation dependencies:

mamba env update --name mdpow-molconfgen --file devtools/conda-envs/test_env.yaml
mamba env update --name mdpow-molconfgen --file docs/requirements.yaml

Build this package from source:

pip install -e .

If you want to update your dependencies (which can be risky!), run:

mamba update --all

And when you are finished, you can exit the virtual environment with:

mamba deactivate

With pip

To build the package from source, run:

pip install -e .

If you want to create a development environment, install the dependencies required for tests and docs with:

pip install -e ".[test,doc]"

Copyright

The mdpow-molconfgen source code is hosted at https://github.com/becksteinlab/mdpow-molconfgen and is available under the GNU General Public License, version 2 (see the file LICENSE).

Copyright (c) 2023, Oliver Beckstein

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdpow-molconfgen in published work.