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@peastman and I discussed the potential for implementing something like the CHARMM [BLOCK](https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/block/) facility for OpenMM to make i…
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We should make sure our constant-pH code http://github.com/choderalab/protons will generate ffxml files that work with the latest `simtk.openmm.app.ForceField` and the forcefields we convert here.
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See [this comment](https://github.com/pandegroup/openmm/issues/1611#issuecomment-340553081) and subsequent comments.
We have to decide whether to merge AMBER protein, DNA, and RNA parameters into a…
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- [x] Localize the subsystem.
- [x] Finalize balancing.
- [x] Fix a display issue where forcefields make ships think they have a lot more HP than they actually have.
- [x] Find and implement a way …
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The connectivity of residues to one another (for example the peptide bond between two amino acids in a protein) is not assigned for valid PDBs. Currently, bonds are assigned based on a distance criter…
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I want to use the Charmm36 force fields. I can add it, I'm just making sure that no one has done it yet.
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We want to be able to begin Yank calculations (especially, hydration free energy calculations) with SMIRNOFF forcefields (such as via the `ForceField` class which currently lives in https://github.com…
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It appears the current `convert_amber.py` script is not Python 3 compatible:
```
mski1776:amber choderaj$ python convert_amber.py
Traceback (most recent call last):
File "convert_amber.py", lin…
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I'm getting this error:
```
Traceback (most recent call last):
File "pdb2lmp.py", line 299, in
conv.collect_types()
File "pdb2lmp.py", line 99, in collect_types
dbmol = self.moldb.m…