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rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
https://rinikerlab.github.io/reeds/
MIT License
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Add the notebook and code to generate hybrid topologies to the pipeline #70

Closed candidechamp closed 1 year ago

candidechamp commented 2 years ago

Description

I added the code I was using to generate Hybrid topologies for RE-EDS simulations, such that it is backed up safely, and can also be used by others.

The program needs to use pygromos v3, which can be done by having a pygromos v3 version installed and importing it first in the jupyter notebook, or by changing branches temporarily in the reeds submodule directly.

The program also requires rdkit to perform a maximum common substructure search (MCS).

A few paths need to be tweaked in the notebook, but essentially the program works form a list of .cnf and .top files as input.

The code was also tested on simple cases where the hybrid topologies has multiple -R groups per ligand.

lgtm-com[bot] commented 2 years ago

This pull request introduces 15 alerts when merging 9036ebad9a104990e0f84637fde5ab73027a39e2 into d7f578197f6b65fde3c3416c9164da11ac5431b4 - view on LGTM.com

new alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 15 alerts when merging 7aef6cdbb5062d57e486539a8e786fd330b69c28 into d7f578197f6b65fde3c3416c9164da11ac5431b4 - view on LGTM.com

new alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 15 alerts when merging 7c6e2b64dd5556949853ce388e0d7b93127820d8 into 20bee60fb8bd5b1e309472f4cf5ccfae3cb34fe2 - view on LGTM.com

new alerts: