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Hello,
In the documentation for [CHARMM36](http://docs.openmm.org/latest/userguide/application/02_running_sims.html#charmm36) options, it suggests that the current CHARMM forcefield being run is th…
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**Describe the bug**
I am reporting this first, there are 12 items in the list but the index seeks more than the actual size, e.g., 12, 13, 14, ... which generates the error:
```
Traceback (most re…
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**Describe the behavior you would like added to Foyer**
Some force fields utilize non-standard functional forms for bonded interactions; in particular, different torsion types within TraPPE. Non-stan…
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The file is at https://github.com/prody/ProDy-website/blob/master/tutorials/watfinder_tutorial/watFinder_tutorial_files/5kqm_all_sci.pdb and https://github.com/prody/ProDy-website/blob/master/tutorial…
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@peastman -- should I add an SWN4-NDP to the water dropdown menu? I'm not really to familiar with it, but I saw that the forcefield was added to the app.
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When taking the expectation of whether a structure is folded (1) or unfolded (0) on an mbar object, often the weights for folded state at high temperature are very small and negative (such as 1E-15 fo…
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Definitely not a big issue, mostly opening it because @mattwthompson told me to raise these issues 😅
**Description**
Passing an uncharged Molecule through `charge_from_molecule` leads to a Type…
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Sorry for the long explanation - the actual issue here is incredibly pointed and I want to make sure I'm highlighting only it.
OpenFE's docstring of the padding option in solvation settings is:
…
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**Describe the bug**
A clear and concise description of what the bug is.
Calling `flow.draw_graph(figsize=(8, 8)).show()` draws graph images with no edges. It appears to be related to how I'm usin…
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Hello,
I am trying to use combine.py to a system of a protein and a ligand, but I am having this error:
```
OSError: Failed to read molecules from: ['QUBE_pro.prm7', 'QUBE_pro.rst7']
```
I got …