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Modify opls_validation ".top" impropers (#506)
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* Modify opls_validation ".top" impropers

This PR aims to fix bugs in the opls_validation files. More
specifically, improper parameters that were added to those files
for testing do not using the correct "funct" value to designate
them as periodic impropers. They had previously all been given
the value of "1", which designates them as periodic propers. Parmed
doesn't treat periodic propers any differently than periodic impropers,
except to use a "dihedral.improper" boolean. They are still stored in
structure.dihedrals.

This is relevant when doing conversion from a parmed object to GMSO,
as GMSO has explicit container for impropers. This will be necessary
when parameterizing in GMSO as opposed to ParmEd, and testing that
the parameters are stored in this impropers container in GMSO.

See this link for more information about gromacs topology files.
https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html

    * Change funct values from "1" to "4" in opls_validation top files
    * Add test to "test_opls.py" to validate the correct number of
    impropers are found

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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CalCraven and pre-commit-ci[bot] authored May 27, 2022
1 parent 24a5d5c commit 298b3c6
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Showing 19 changed files with 134 additions and 97 deletions.
12 changes: 6 additions & 6 deletions foyer/opls_validation/124-trimethylbenzene/124-trimethylbenzene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -200,12 +200,12 @@

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
2 1 3 7 1 180 4.6 2
3 2 4 9 1 180 4.6 2
4 3 5 13 1 180 4.6 2
5 4 6 8 1 180 4.6 2
6 5 7 14 1 180 4.6 2
7 2 6 15 1 180 4.6 2
2 1 3 7 4 180 4.6 2
3 2 4 9 4 180 4.6 2
4 3 5 13 4 180 4.6 2
5 4 6 8 4 180 4.6 2
6 5 7 14 4 180 4.6 2
7 2 6 15 4 180 4.6 2

[ system ]
124-trimethylbenzene GAS
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12 changes: 6 additions & 6 deletions foyer/opls_validation/13-difluorobenzene/13-difluorobenzene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -114,12 +114,12 @@
10 9 11 12 3

; added, improper
1 11 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 7 6 1 180 4.6 2
7 5 9 8 1 180 4.6 2
9 7 11 10 1 180 4.6 2
11 9 1 12 1 180 4.6 2
1 11 3 2 4 180 4.6 2
3 1 5 4 4 180 4.6 2
5 3 7 6 4 180 4.6 2
7 5 9 8 4 180 4.6 2
9 7 11 10 4 180 4.6 2
11 9 1 12 4 180 4.6 2
; ring_180
1 3 5 7 1 180 4.6 2
3 5 7 9 1 180 4.6 2
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12 changes: 6 additions & 6 deletions foyer/opls_validation/2-methylphenol/2-methylphenol.top
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Original file line number Diff line number Diff line change
Expand Up @@ -143,12 +143,12 @@
12 14 15 16 3

; added, improper
5 14 6 1 1 180 4.6 2
6 5 8 7 1 180 4.6 2
8 6 10 9 1 180 4.6 2
10 8 12 11 1 180 4.6 2
12 10 14 13 1 180 4.6 2
14 12 5 15 1 180 4.6 2
5 14 6 1 4 180 4.6 2
6 5 8 7 4 180 4.6 2
8 6 10 9 4 180 4.6 2
10 8 12 11 4 180 4.6 2
12 10 14 13 4 180 4.6 2
14 12 5 15 4 180 4.6 2
; 1 3 5 7 1 0 4.6 2
; 3 5 7 9 1 0 4.6 2
; 5 7 9 11 1 0 4.6 2
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24 changes: 12 additions & 12 deletions foyer/opls_validation/3-methylphenol/3-methylphenol.top
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Original file line number Diff line number Diff line change
Expand Up @@ -143,19 +143,19 @@
12 14 15 16 3

; added, improper
5 12 6 1 1 180 4.6 2
6 5 8 7 1 180 4.6 2
8 6 10 9 1 180 4.6 2
10 8 14 11 1 180 4.6 2
14 10 12 15 1 180 4.6 2
12 14 5 13 1 180 4.6 2
5 12 6 1 4 180 4.6 2
6 5 8 7 4 180 4.6 2
8 6 10 9 4 180 4.6 2
10 8 14 11 4 180 4.6 2
14 10 12 15 4 180 4.6 2
12 14 5 13 4 180 4.6 2
; ring_180
5 6 8 10 1 180 4.6 2
6 8 10 14 1 180 4.6 2
8 10 14 12 1 180 4.6 2
10 14 12 5 1 180 4.6 2
14 12 5 6 1 180 4.6 2
12 5 6 8 1 180 4.6 2
; 5 6 8 10 1 180 4.6 2
; 6 8 10 14 1 180 4.6 2 This dihedral doesn't exist
; 8 10 14 12 1 180 4.6 2
; 10 14 12 5 1 180 4.6 2
; 14 12 5 6 1 180 4.6 2
; 12 5 6 8 1 180 4.6 2

[ system ]
3-methylphenol GAS
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24 changes: 12 additions & 12 deletions foyer/opls_validation/4-methylphenol/4-methylphenol.top
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Original file line number Diff line number Diff line change
Expand Up @@ -143,19 +143,19 @@
12 14 15 16 3

; added, improper
1 14 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 10 6 1 180 4.6 2
10 5 12 11 1 180 4.6 2
12 10 14 13 1 180 4.6 2
14 12 1 15 1 180 4.6 2
1 14 3 2 4 180 4.6 2
3 1 5 4 4 180 4.6 2
5 3 10 6 4 180 4.6 2
10 5 12 11 4 180 4.6 2
12 10 14 13 4 180 4.6 2
14 12 1 15 4 180 4.6 2
; ring_180
1 3 5 10 1 180 4.6 2
3 5 10 12 1 180 4.6 2
5 10 12 14 1 180 4.6 2
10 12 14 1 1 180 4.6 2
12 14 1 3 1 180 4.6 2
14 1 3 5 1 180 4.6 2
; 1 3 5 10 1 180 4.6 2
; 3 5 10 12 1 180 4.6 2
; 5 10 12 14 1 180 4.6 2
; 10 12 14 1 1 180 4.6 2
; 12 14 1 3 1 180 4.6 2
; 14 1 3 5 1 180 4.6 2

[ system ]
4-methylphenol GAS
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4 changes: 2 additions & 2 deletions foyer/opls_validation/N-methylformamide/N-methylformamide.top
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Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,8 @@ N-methylformamide 3
6 5 7 9 3

; Added DvdS 2010-12-21
7 9 5 8 1 180 4.6 2
5 1 7 6 1 180 4.6 2
7 9 5 8 4 180 4.6 2
5 1 7 6 4 180 4.6 2
[ system ]
N-methylformamide GAS
[ molecules ]
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4 changes: 2 additions & 2 deletions foyer/opls_validation/NN-dimethylacetamide/NN-dimethylacetamide.top
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Original file line number Diff line number Diff line change
Expand Up @@ -124,8 +124,8 @@ NN-dimethylacetamide 3
8 7 12 15 3

; Added DvdS 2010-12-21
5 1 7 6 1 180 4.6 2
5 8 12 7 1 180 4.6 2
5 1 7 6 4 180 4.6 2
5 8 12 7 4 180 4.6 2
[ system ]
NN-dimethylacetamide GAS
[ molecules ]
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4 changes: 2 additions & 2 deletions foyer/opls_validation/NN-dimethylformamide/NN-dimethylformamide.top
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Original file line number Diff line number Diff line change
Expand Up @@ -98,8 +98,8 @@ NN-dimethylformamide 3
6 5 10 12 3

; Added DvdS 2010-12-21
10 12 5 11 1 180 4.6 2
5 1 6 10 1 180 4.6 2
10 12 5 11 4 180 4.6 2
5 1 6 10 4 180 4.6 2
[ system ]
NN-dimethylformamide GAS
[ molecules ]
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4 changes: 2 additions & 2 deletions foyer/opls_validation/dimethylformamide/dimethylformamide.top
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Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,8 @@
6 5 10 12 3

; Added DvdS 2010-12-21
10 12 5 11 1 180 4.6 2
5 1 6 10 1 180 4.6 2
10 12 5 11 4 180 4.6 2
5 1 6 10 4 180 4.6 2

[ system ]
dimethylformamide GAS
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12 changes: 6 additions & 6 deletions foyer/opls_validation/ethylbenzene/ethylbenzene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -166,12 +166,12 @@ ethylbenzene 3
16 15 17 18 3

; added, improper
8 17 9 5 1 180 4.6 2
9 8 11 10 1 180 4.6 2
11 9 13 12 1 180 4.6 2
13 11 15 14 1 180 4.6 2
15 13 17 16 1 180 4.6 2
17 15 8 18 1 180 4.6 2
8 17 9 5 4 180 4.6 2
9 8 11 10 4 180 4.6 2
11 9 13 12 4 180 4.6 2
13 11 15 14 4 180 4.6 2
15 13 17 16 4 180 4.6 2
17 15 8 18 4 180 4.6 2
; 1 3 5 7 1 0 4.6 2
; 3 5 7 9 1 0 4.6 2
; 5 7 9 11 1 0 4.6 2
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12 changes: 6 additions & 6 deletions foyer/opls_validation/fluorobenzene/fluorobenzene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -94,12 +94,12 @@ fluorobenzene 3
7 9 11 1 3

; added, improper
1 11 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 7 6 1 180 4.6 2
7 5 9 8 1 180 4.6 2
9 7 11 10 1 180 4.6 2
11 9 1 12 1 180 4.6 2
1 11 3 2 4 180 4.6 2
3 1 5 4 4 180 4.6 2
5 3 7 6 4 180 4.6 2
7 5 9 8 4 180 4.6 2
9 7 11 10 4 180 4.6 2
11 9 1 12 4 180 4.6 2
; 1 3 5 7 1 0 4.6 2
; 3 5 7 9 1 0 4.6 2
; 5 7 9 11 1 0 4.6 2
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4 changes: 2 additions & 2 deletions foyer/opls_validation/formamide/formamide.top
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,8 @@ formamide 3
3 2 4 6 3

; Added DvdS 2010-12-21
2 1 4 3 1 180 4.6 2
4 5 6 2 1 180 4.6 2
2 1 4 3 4 180 4.6 2
4 5 6 2 4 180 4.6 2

[ system ]
formamide GAS
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26 changes: 13 additions & 13 deletions foyer/opls_validation/nitrobenzene/nitrobenzene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -127,22 +127,22 @@ nitrobenzene 3
9 11 12 14 3

; added, improper
1 11 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 7 6 1 180 4.6 2
7 5 9 8 1 180 4.6 2
9 7 11 10 1 180 4.6 2
11 9 1 12 1 180 4.6 2
1 11 3 2 4 180 4.6 2
3 1 5 4 4 180 4.6 2
5 3 7 6 4 180 4.6 2
7 5 9 8 4 180 4.6 2
9 7 11 10 4 180 4.6 2
11 9 1 12 4 180 4.6 2
; ring_180
1 3 5 7 1 180 4.6 2
3 5 7 9 1 180 4.6 2
5 7 9 11 1 180 4.6 2
7 9 11 1 1 180 4.6 2
9 11 1 3 1 180 4.6 2
11 1 3 5 1 180 4.6 2
; 1 3 5 7 1 180 4.6 2
; 3 5 7 9 1 180 4.6 2
; 5 7 9 11 1 180 4.6 2
; 7 9 11 1 1 180 4.6 2
; 9 11 1 3 1 180 4.6 2
; 11 1 3 5 1 180 4.6 2

[ dihedrals ]
12 13 14 11 1 improper_X_NO_ON_NO
12 13 14 11 4 improper_X_NO_ON_NO
[ system ]
nitrobenzene GAS
[ molecules ]
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2 changes: 1 addition & 1 deletion foyer/opls_validation/nitroethane/nitroethane.top
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ nitroethane 3
7 5 8 10 3

[ dihedrals ]
8 9 10 5 1 improper_X_NO_ON_NO
8 9 10 5 4 improper_X_NO_ON_NO
[ system ]
nitroethane GAS
[ molecules ]
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2 changes: 1 addition & 1 deletion foyer/opls_validation/nitromethane/nitromethane.top
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ nitromethane 3
4 1 5 7 3

[ dihedrals ]
5 6 7 1 1 improper_X_NO_ON_NO
5 6 7 1 4 improper_X_NO_ON_NO

[ system ]
nitromethane GAS
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12 changes: 6 additions & 6 deletions foyer/opls_validation/o-xylene/o-xylene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -160,12 +160,12 @@ o-xylene 3
12 14 15 18 3

; added, improper
5 14 6 1 1 180 4.6 2
6 5 8 7 1 180 4.6 2
8 6 10 9 1 180 4.6 2
10 8 12 11 1 180 4.6 2
12 10 14 13 1 180 4.6 2
14 12 5 15 1 180 4.6 2
5 14 6 1 4 180 4.6 2
6 5 8 7 4 180 4.6 2
8 6 10 9 4 180 4.6 2
10 8 12 11 4 180 4.6 2
12 10 14 13 4 180 4.6 2
14 12 5 15 4 180 4.6 2
; ring_180
5 6 8 10 1 180 4.6 2
6 8 10 12 1 180 4.6 2
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12 changes: 6 additions & 6 deletions foyer/opls_validation/phenol/phenol.top
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Original file line number Diff line number Diff line change
Expand Up @@ -119,12 +119,12 @@ phenol 3
9 11 12 13 3

; added, improper
1 11 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 7 6 1 180 4.6 2
7 5 9 8 1 180 4.6 2
9 7 11 10 1 180 4.6 2
11 9 1 12 1 180 4.6 2
1 11 3 2 4 180 4.6 2
3 1 5 4 4 180 4.6 2
5 3 7 6 4 180 4.6 2
7 5 9 8 4 180 4.6 2
9 7 11 10 4 180 4.6 2
11 9 1 12 4 180 4.6 2
; 1 3 5 7 1 0 4.6 2
; 3 5 7 9 1 0 4.6 2
; 5 7 9 11 1 0 4.6 2
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12 changes: 6 additions & 6 deletions foyer/opls_validation/toluene/toluene.top
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Original file line number Diff line number Diff line change
Expand Up @@ -136,12 +136,12 @@ toluene 3
13 12 14 15 3

; added, improper
5 14 6 1 1 180 4.6 2
6 5 8 7 1 180 4.6 2
8 6 10 9 1 180 4.6 2
10 8 12 11 1 180 4.6 2
12 10 14 13 1 180 4.6 2
14 12 5 15 1 180 4.6 2
5 14 6 1 4 180 4.6 2
6 5 8 7 4 180 4.6 2
8 6 10 9 4 180 4.6 2
10 8 12 11 4 180 4.6 2
12 10 14 13 4 180 4.6 2
14 12 5 15 4 180 4.6 2
; 1 3 5 7 1 0 4.6 2
; 3 5 7 9 1 0 4.6 2
; 5 7 9 11 1 0 4.6 2
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37 changes: 37 additions & 0 deletions foyer/tests/test_opls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,43 @@ def test_full_parametrization(self, oplsaa):
assert all(x.type for x in parametrized.dihedrals)
assert parametrized.combining_rule == "geometric"

def test_improper_in_structure(self):
files_with_impropers = [
("o-xylene", 6),
("nitroethane", 1),
("fluorobenzene", 6),
("N-methylformamide", 2),
("formamide", 2),
("toluene", 6),
("3-methylphenol", 6),
("4-methylphenol", 6),
("2-methylphenol", 6),
("nitrobenzene", 7),
("dimethylformamide", 2),
("nitromethane", 1),
("NN-dimethylformamide", 2),
("124-trimethylbenzene", 6),
("phenol", 6),
("ethylbenzene", 6),
("NN-dimethylacetamide", 2),
("13-difluorobenzene", 6),
] # found in the "impropers" sections of molecule_name.top
for molecule, n_impropers in files_with_impropers:
top = os.path.join(
OPLS_TESTFILES_DIR, molecule + "/" + molecule + ".top"
)
gro = os.path.join(
OPLS_TESTFILES_DIR, molecule + "/" + molecule + ".gro"
)
structure = pmd.load_file(top, xyz=gro)
impropers = []
[
impropers.append(dihedral)
for dihedral in structure.dihedrals
if dihedral.improper
]
assert len(impropers) == n_impropers


if __name__ == "__main__":
TestOPLS().find_correctly_implemented()

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