examples on running protein-ligand relative binding calculations
See original GitHub issueHey @here,
Are there some examples of how to run protein-ligand relative binding calculations using perses
without neq-switching? Only use the equilibrium alchemical simulations.
I have two small-molecule .sdf
files and one protein .pdb
file. Both molecules have been aligned together based on the common core atom mapping.
Thanks!
Best, Pengfei
Issue Analytics
- State:
- Created 2 years ago
- Comments:6 (2 by maintainers)
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Replacing OpenEye toolkit dependencies with the Open Force Field Toolkit—which provides an abstraction layer to multiple toolkits, including the open source RDKit—is on our roadmap, but it is not urgent for the folks funding development at the moment.
This is not currently on our roadmap, but if you like, you could submit a feature request where you would specify prmtop/inpcrd files for each state and have perses run a free energy calculation. I can’t guarantee when we would be able to get to this due to very limited development resources, however.
Hi @freeenergylab , we do have an example for such a system in the
examples/protein-ligand/cli
which you could run with something likeperses-relative ani.yaml
. You might want to to give that a shot.We do have to make the documentation clearer on these examples. We will work on that. Hope this works.