cmelab / cmelab/polybinder

Fix atom typing errors when using OPLS

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#17 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
2
Forks
5
PR merge metrics
No merged PRs in 30d

Description

**PEEK**:
gaff: Works
opls: Error

```
Exception: Parameters have not been assigned to all proper dihedrals. Total system dihedrals: 174, Parameterized dihedrals: 158. Note that if your system contains torsions of Ryckaert-Bellemans functional form, all of these torsions are processed as propers.
```
**PEKK:**
gaff: Works

opls: Error
```
Exception: Parameters have not been assigned to all proper dihedrals. Total system dihedrals: 180, Parameterized dihedrals: 154. Note that if your system contains torsions of Ryckaert-Bellemans functional form, all of these torsions are processed as propers.
```

So far, it looks like the errors are not being able to assign all of the dihedrals when using the opls forcefield.

If we pass `assert_dihedral_params=False` when using OPLS, then both PEEK and PEKK will work.

This fix won't require much within this repo, but rather with foyer. We could make a PR that adds missing dihedrals, but I'm not sure how long that would take.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the PEEK and PEKK OPLS cases and inspect foyer's dihedral parameter assignment, since the issue identifies missing OPLS parameters as the failure. The work is done when both systems parameterize all proper dihedrals without passing assert_dihedral_params=False; the required fix may belong in foyer rather than this repository.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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