Known issues and bugs (@striketeam)

Created by Pavan Behara

Team members interested in following/pursuing/raising issues (please add yourself if you’re missed): 

striketeam: @Chapin Cavender @Chris Ringrose @Christopher Bayly @Daniel Cole @David Dotson @David Mobley @Diego Nolasco @Hyesu Jang @Jeffrey Wagner @Jessica Maat @John Chodera @Josh Mitchell @Joshua Horton @Lee-Ping Wang @Lorenzo D'Amore @Matt Thompson @Michael Gilson @Michael Shirts @Pavan Behara @Simon Boothroyd @Tobias Huefner @Trevor Gokey

 

Time horizon: On-going

Goals

List of FF issues raised by internal/external members

Issue/task

Preliminary work/progress/comments

Team

Status/Timeline

Issue/task

Preliminary work/progress/comments

Team

Status/Timeline

Halogenated compounds

Discussion link: https://openforcefieldgroup.slack.com/archives/CKSHCE7SB/p1611592728000200

Brief summary: Large discrepancies with experiment for the COVID Moonshot on compounds containing a chloro group on aromatic scaffolds

 

 

Boron parameters in FF (Feature request and does not belong here???)

Discussion link:

https://openforcefieldgroup.slack.com/archives/C01HSKCUEBZ/p1615499784058000

Brief summary: Lack of parameters for Boron.

 

 

Amide issue

Discussion link:

https://openforcefieldgroup.slack.com/archives/CKSHCE7SB/p1596485145006600

Brief summary:

High preference to non-planar amides using Parsley 1.2.0

 

 

Sulfonic and phosphonic acids

Discussion link:

Brief summary:

Bad O-S-O and O-P-O angles in sulfonic and phosphonic acids, need more coverage in training data.

 

 

 

Sulfoximine, sulfonimidamines (dataset coverage and does not belong here???)

Discussion link:

https://openforcefieldgroup.slack.com/archives/C0ZE3KUHJ/p1617385968001000

Brief summary:

Dataset coverage

 

 

 

 

Problem chemistries from benchmark analysis by Thomas Fox, an industry partner.
Additional analysis by Lorenzo D’Amore and Xavier Lucas

Discussion link:

https://openforcefieldgroup.slack.com/archives/C01BN0C5AKF/p1623935171007300

https://openforcefieldgroup.slack.com/archives/C01BN0C5AKF/p1623935450009200

https://openforcefield.atlassian.net/wiki/spaces/~954728248/pages/2110488578

 

https://openforcefieldgroup.slack.com/archives/C01BN0C5AKF/p1631634575020600

Brief summary:

RMSD analysis of the QM minimum energy conformer and MM optimized conformer with 1.3.0

Observations of Thomas Fox:

  • CC bond in oxirane 0.12A too long
    ("C1CO1")

  • CC bond between the two C=O in quadratic acid 0.1A too long
    ("Oc1c(O)c(=O)c1=O")

  • sulfoximide S=N bond 0.18A too long
    (Eg. "CCCCS(=N)(=O)CCC(N)C(O)=O")

  • 2-vinyl-furan ("C=CC1=CC=CO1") is not planar

  • aromatic nitro groups not in plane with ring (Eg. "C1=CC=C(C=C1)[N+](=O)[O-]")

  • aromatic thioethers out of plane (Eg. "CSC1=CC=CC=C1")

  • ring puckering of spiro-pyrrolidine
    (Eg. "C1CNCC12NC3=CC=CC=C3C(=O)N2")

  • aryl-methoxy groups not planar (45°)
    (Eg. "COC1=CC=CC=C1")

    Disclaimer: added some smiles as a starting point/reference in case of general chemical space observations, may not be the exact molecules Thomas Fox is referring to when you see Eg..

 

 

Cyclobutane is flat (not puckered) with 1.2.0, 1.3.0.

QM in green above (from PhalkEtOH dataset)

1.2.0 in magenta above

1.3.0 in cyan above

 

 

Nitrogen-oxygen bonds in constrained systems (like rings) might result in long bonds with lengthy MM runs

Discussion link: https://openforcefield.atlassian.net/wiki/spaces/MEET/pages/2021228567

  • From Josh Horton’s lengthy MM run

 

 

Bicyclo pentane moieties difficult to converge with MM

Discussion link:

https://openforcefieldgroup.slack.com/archives/CK5MQG0TC/p1626985095050500