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Right now, the SmallMoleculeProposalEngine does not correctly respect protonation states, due to code that converts the OpenMM topology to an oemol (will raise issue there).
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When I run the FM1 tutorial example with the following execution:
```
(sire) spadavec@Crandall:~/itx/sire_example/ligandswap$ ligandswap -t0 rec_fmc.top -c0 fmc.30.crd -l0 FM1 -t1 rec_cti.top -c1…
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- [ ] Go through all tutorials and note down all bugs
- [ ] Go through reference manual and note down all bugs and errors
- including installation/dependency bugs
- [ ] Fix them
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Hi,
Quaternion is very convenient for describing the orientation of a molecule (and the relative orientation of molecule A with respect to B). However, I didn't find a simple way to define quaterni…
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Trying to enumerate all the ways that perses can be used, and might be used in future
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I've been using YANK (0.23.4) to simulate a protein-ligand system (6069 atoms and water box and around 100 replicas for both the complex and solvent phase), on a system with two GTX 1080Ti GPUs, and s…
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**In broad terms, what are you trying to do?**
Run absolute binding free energies (ABFE) for host-guest or protein-ligand systems on a scale ranging from 100-1000 systems. This is for benchmark…
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Reviewer `#3` (Remarks to the Author):
In Table 6, why are the computational domains chosen as cubics for all proteins for APBS? It is unfair for APBS in terms of efficiency.
In Table 7, solvat…
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Hi, I recently used this package to generate some statistical data, it failed when some of the molecules' experiment values were not provided. Is there a solution to this kind of data?
Error:
```…
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From Module-HTML-CSS created by [kfklein15](https://github.com/kfklein15): CodeYourFuture/Module-HTML-CSS#43
### Coursework content
This is the first exercise for you to build your Career Developm…