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Add OPLS Parameters for ADOPA #454

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PR Summary:

ADOPA is molecule similar to that of L-DOPA (https://en.wikipedia.org/wiki/L-DOPA) (See image below).
The atom type for the carbon bonded to the amine group (opls_912) needed to be added to properly atom type the molecule.

Currently the following dihedral parameters are missing:

Missing dihedral with ids (15, 14, 39, 40) and types ['opls_465', 'opls_912', 'opls_900', 'opls_909'].
Missing dihedral with ids (15, 14, 39, 41) and types ['opls_465', 'opls_912', 'opls_900', 'opls_909'].
Missing dihedral with ids (18, 15, 14, 39) and types ['opls_466', 'opls_465', 'opls_912', 'opls_900'].
Missing dihedral with ids (19, 15, 14, 39) and types ['opls_467', 'opls_465', 'opls_912', 'opls_900'].

which corresponds to C_2-CT-NT-H and O_2-C_2-CT-NT. I need to do some further digging to find these dihedral parameters. For this reason, along with lack of unit testing for this molecule, I am opening as a draft right now.

adopa

PR Checklist


  • Includes appropriate unit test(s)
  • Appropriate docstring(s) are added/updated
  • Code is (approximately) PEP8 compliant
  • Issue(s) raised/addressed?

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codecov bot commented Aug 23, 2021

Codecov Report

Merging #454 (9173ce7) into master (b55b416) will not change coverage.
The diff coverage is n/a.

❗ Current head 9173ce7 differs from pull request most recent head e42af3c. Consider uploading reports for the commit e42af3c to get more accurate results

@@           Coverage Diff           @@
##           master     #454   +/-   ##
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  Coverage   73.87%   73.87%           
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  Files          17       17           
  Lines        1849     1849           
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  Hits         1366     1366           
  Misses        483      483           

@rmatsum836
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rmatsum836 commented Aug 23, 2021

Looking at a typed system from LibParGen, the atom type for 466-465-912-900 is:

14.43480 -11.00392  -3.43088   0.00000   0.00000   0.00000

.

For 465-912-900-909, the dihedral parameters are:

-1.26775   3.02085   1.74473  -3.49782   0.00000   0.00000

There isn't an exact match for these in the gromacs bonded parameters (https://github.com/gromacs/gromacs/blob/master/share/top/oplsaa.ff/ffbonded.itp) but perhaps it's worth testing these parameters out.

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