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The attached example crashes when the trying to use PTR in residue #6 on the ligand because there are no rotamers for PTR, even though we want to use the WT rotamer.
The field that is causing the …
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It would be useful if we could refactor [`stats.py`](https://github.com/OpenFreeEnergy/cinnabar/blob/main/cinnabar/stats.py) into a class API so that we could drop in different solvers.
Right now, …
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When I tried the script to convert pdbqt to pdbs without any options it converted pdbqt.vina into individual pdb files. The following are the individual pdb files with binding free energies.
Gen_1_…
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We would like to analyze a subset of the simulation (e.g. 1000 iterations out of 20000 iterations) in order to have the calculated free energies and the convergence plots.
Is there a way to automat…
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I would like to calculate the dG of a ligand binding to a protein via the LIE method:
dG = alpha(Uvdw(bound) - Uvdw(free)) + beta(Uelec(bound) - Uelec(free)) + gamma
It appears that some special s…
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When you tell me what I am doing wrong.... Can you tell me how you know? Or what I should have looked for. This debugging log is just a bunch or random words to me. Almost ALL my books had DRM rem…
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Especially if this ends up being a per-release benchmark run, it would be good to have a simple manner for folks to work out what historical computed free energies were for a given edge based on a giv…
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### Description of the enhancement or error report
We need to add .md documentation for the grand potential model. This needs to include a page on derivations and a page with examples how to use this…
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## Motivation
Membrane-protein systems account for ~ 60% of possible target space. Being able to calculate binding free energies for membrane-containing systems would be a significant advantage.
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Using this issue to track and plan the next features. Any additional, comment in this issue and this top post will be edited to include them, link to sub-issues, and list relevant PRs for each item.
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