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Switch to default OPLS atomtype names #317

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Apr 26, 2023
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Merged

Switch to default OPLS atomtype names #317

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10 changes: 5 additions & 5 deletions polyply/data/oplsaaLigParGen/OHter.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@
OHter 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_803 1 OHter OA1 1 -0.6887 15.9990
2 opls_800 1 OHter C2 2 0.1070 12.0110
3 opls_802 1 OHter HA3 3 0.4173 1.0080
4 opls_802 1 OHter H4 4 0.0822 1.0080
5 opls_802 1 OHter H5 5 0.0822 1.0080
1 opls_154 1 OHter OA1 1 -0.6887 15.9990
2 opls_135 1 OHter C2 2 0.1070 12.0110
3 opls_004 1 OHter HA3 3 0.4173 1.0080
4 opls_140 1 OHter H4 4 0.0822 1.0080
5 opls_140 1 OHter H5 5 0.0822 1.0080
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.1410 267776.000
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24 changes: 7 additions & 17 deletions polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff
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Original file line number Diff line number Diff line change
@@ -1,25 +1,15 @@
;;;;
;;;; GENERATED BY LigParGen Server
;;;; Jorgensen Lab @ Yale University
;;;;
;;;[ atomtypes ]
;;; opls_800 C800 6 12.0110 0.000 A 3.50000E-01 2.76144E-01 ; C
;;; opls_801 O801 8 15.9990 0.000 A 2.90000E-01 5.85760E-01 ; O
;;; opls_802 H802 1 1.0080 0.000 A 2.50000E-01 1.25520E-01 ; H
;;; opls_803 O803 8 15.9990 0.000 A 3.12000E-01 7.11280E-01 ; O (ALCOHOL, TERMINI)
;;;
[ moleculetype ]
; Name nrexcl
PEO 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 PEO C01 1 0.0089 12.0110
2 opls_801 1 PEO O02 2 -0.3846 15.9990
3 opls_800 1 PEO C03 3 0.0089 12.0110
4 opls_802 1 PEO H04 4 0.0917 1.0080
5 opls_802 1 PEO H05 5 0.0917 1.0080
6 opls_802 1 PEO H06 6 0.0917 1.0080
7 opls_802 1 PEO H07 7 0.0917 1.0080
1 opls_135 1 PEO C01 1 0.0089 12.0110
2 opls_179 1 PEO O02 2 -0.3846 15.9990
3 opls_135 1 PEO C03 3 0.0089 12.0110
4 opls_140 1 PEO H04 4 0.0917 1.0080
5 opls_140 1 PEO H05 5 0.0917 1.0080
6 opls_140 1 PEO H06 6 0.0917 1.0080
7 opls_140 1 PEO H07 7 0.0917 1.0080
[ bonds ]
2 1 1 0.1410 267776.000
3 2 1 0.1410 267776.000
Expand Down
160 changes: 80 additions & 80 deletions polyply/tests/test_data/library_tests/oplsaaLigParGen/PEO/polyply/PEO.itp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,86 +9,86 @@
PEO 3

[ atoms ]
1 opls_803 1 OHter OA1 1 -0.6887 15.999
2 opls_800 1 OHter C2 2 0.107 12.011
3 opls_802 1 OHter HA3 3 0.4173 1.008
4 opls_802 1 OHter H4 4 0.0822 1.008
5 opls_802 1 OHter H5 5 0.0822 1.008
6 opls_800 2 PEO C01 6 0.0089 12.011
7 opls_801 2 PEO O02 7 -0.3846 15.999
8 opls_800 2 PEO C03 8 0.0089 12.011
9 opls_802 2 PEO H04 9 0.0917 1.008
10 opls_802 2 PEO H05 10 0.0917 1.008
11 opls_802 2 PEO H06 11 0.0917 1.008
12 opls_802 2 PEO H07 12 0.0917 1.008
13 opls_800 3 PEO C01 13 0.0089 12.011
14 opls_801 3 PEO O02 14 -0.3846 15.999
15 opls_800 3 PEO C03 15 0.0089 12.011
16 opls_802 3 PEO H04 16 0.0917 1.008
17 opls_802 3 PEO H05 17 0.0917 1.008
18 opls_802 3 PEO H06 18 0.0917 1.008
19 opls_802 3 PEO H07 19 0.0917 1.008
20 opls_800 4 PEO C01 20 0.0089 12.011
21 opls_801 4 PEO O02 21 -0.3846 15.999
22 opls_800 4 PEO C03 22 0.0089 12.011
23 opls_802 4 PEO H04 23 0.0917 1.008
24 opls_802 4 PEO H05 24 0.0917 1.008
25 opls_802 4 PEO H06 25 0.0917 1.008
26 opls_802 4 PEO H07 26 0.0917 1.008
27 opls_800 5 PEO C01 27 0.0089 12.011
28 opls_801 5 PEO O02 28 -0.3846 15.999
29 opls_800 5 PEO C03 29 0.0089 12.011
30 opls_802 5 PEO H04 30 0.0917 1.008
31 opls_802 5 PEO H05 31 0.0917 1.008
32 opls_802 5 PEO H06 32 0.0917 1.008
33 opls_802 5 PEO H07 33 0.0917 1.008
34 opls_800 6 PEO C01 34 0.0089 12.011
35 opls_801 6 PEO O02 35 -0.3846 15.999
36 opls_800 6 PEO C03 36 0.0089 12.011
37 opls_802 6 PEO H04 37 0.0917 1.008
38 opls_802 6 PEO H05 38 0.0917 1.008
39 opls_802 6 PEO H06 39 0.0917 1.008
40 opls_802 6 PEO H07 40 0.0917 1.008
41 opls_800 7 PEO C01 41 0.0089 12.011
42 opls_801 7 PEO O02 42 -0.3846 15.999
43 opls_800 7 PEO C03 43 0.0089 12.011
44 opls_802 7 PEO H04 44 0.0917 1.008
45 opls_802 7 PEO H05 45 0.0917 1.008
46 opls_802 7 PEO H06 46 0.0917 1.008
47 opls_802 7 PEO H07 47 0.0917 1.008
48 opls_800 8 PEO C01 48 0.0089 12.011
49 opls_801 8 PEO O02 49 -0.3846 15.999
50 opls_800 8 PEO C03 50 0.0089 12.011
51 opls_802 8 PEO H04 51 0.0917 1.008
52 opls_802 8 PEO H05 52 0.0917 1.008
53 opls_802 8 PEO H06 53 0.0917 1.008
54 opls_802 8 PEO H07 54 0.0917 1.008
55 opls_800 9 PEO C01 55 0.0089 12.011
56 opls_801 9 PEO O02 56 -0.3846 15.999
57 opls_800 9 PEO C03 57 0.0089 12.011
58 opls_802 9 PEO H04 58 0.0917 1.008
59 opls_802 9 PEO H05 59 0.0917 1.008
60 opls_802 9 PEO H06 60 0.0917 1.008
61 opls_802 9 PEO H07 61 0.0917 1.008
62 opls_800 10 PEO C01 62 0.0089 12.011
63 opls_801 10 PEO O02 63 -0.3846 15.999
64 opls_800 10 PEO C03 64 0.0089 12.011
65 opls_802 10 PEO H04 65 0.0917 1.008
66 opls_802 10 PEO H05 66 0.0917 1.008
67 opls_802 10 PEO H06 67 0.0917 1.008
68 opls_802 10 PEO H07 68 0.0917 1.008
69 opls_800 11 PEO C01 69 0.0089 12.011
70 opls_801 11 PEO O02 70 -0.3846 15.999
71 opls_800 11 PEO C03 71 0.0089 12.011
72 opls_802 11 PEO H04 72 0.0917 1.008
73 opls_802 11 PEO H05 73 0.0917 1.008
74 opls_802 11 PEO H06 74 0.0917 1.008
75 opls_802 11 PEO H07 75 0.0917 1.008
76 opls_803 12 OHter OA1 76 -0.6887 15.999
77 opls_800 12 OHter C2 77 0.107 12.011
78 opls_802 12 OHter HA3 78 0.4173 1.008
79 opls_802 12 OHter H4 79 0.0822 1.008
80 opls_802 12 OHter H5 80 0.0822 1.008
1 opls_154 1 OHter OA1 1 -0.6887 15.999
2 opls_135 1 OHter C2 2 0.107 12.011
3 opls_004 1 OHter HA3 3 0.4173 1.008
4 opls_140 1 OHter H4 4 0.0822 1.008
5 opls_140 1 OHter H5 5 0.0822 1.008
6 opls_135 2 PEO C01 6 0.0089 12.011
7 opls_179 2 PEO O02 7 -0.3846 15.999
8 opls_135 2 PEO C03 8 0.0089 12.011
9 opls_140 2 PEO H04 9 0.0917 1.008
10 opls_140 2 PEO H05 10 0.0917 1.008
11 opls_140 2 PEO H06 11 0.0917 1.008
12 opls_140 2 PEO H07 12 0.0917 1.008
13 opls_135 3 PEO C01 13 0.0089 12.011
14 opls_179 3 PEO O02 14 -0.3846 15.999
15 opls_135 3 PEO C03 15 0.0089 12.011
16 opls_140 3 PEO H04 16 0.0917 1.008
17 opls_140 3 PEO H05 17 0.0917 1.008
18 opls_140 3 PEO H06 18 0.0917 1.008
19 opls_140 3 PEO H07 19 0.0917 1.008
20 opls_135 4 PEO C01 20 0.0089 12.011
21 opls_179 4 PEO O02 21 -0.3846 15.999
22 opls_135 4 PEO C03 22 0.0089 12.011
23 opls_140 4 PEO H04 23 0.0917 1.008
24 opls_140 4 PEO H05 24 0.0917 1.008
25 opls_140 4 PEO H06 25 0.0917 1.008
26 opls_140 4 PEO H07 26 0.0917 1.008
27 opls_135 5 PEO C01 27 0.0089 12.011
28 opls_179 5 PEO O02 28 -0.3846 15.999
29 opls_135 5 PEO C03 29 0.0089 12.011
30 opls_140 5 PEO H04 30 0.0917 1.008
31 opls_140 5 PEO H05 31 0.0917 1.008
32 opls_140 5 PEO H06 32 0.0917 1.008
33 opls_140 5 PEO H07 33 0.0917 1.008
34 opls_135 6 PEO C01 34 0.0089 12.011
35 opls_179 6 PEO O02 35 -0.3846 15.999
36 opls_135 6 PEO C03 36 0.0089 12.011
37 opls_140 6 PEO H04 37 0.0917 1.008
38 opls_140 6 PEO H05 38 0.0917 1.008
39 opls_140 6 PEO H06 39 0.0917 1.008
40 opls_140 6 PEO H07 40 0.0917 1.008
41 opls_135 7 PEO C01 41 0.0089 12.011
42 opls_179 7 PEO O02 42 -0.3846 15.999
43 opls_135 7 PEO C03 43 0.0089 12.011
44 opls_140 7 PEO H04 44 0.0917 1.008
45 opls_140 7 PEO H05 45 0.0917 1.008
46 opls_140 7 PEO H06 46 0.0917 1.008
47 opls_140 7 PEO H07 47 0.0917 1.008
48 opls_135 8 PEO C01 48 0.0089 12.011
49 opls_179 8 PEO O02 49 -0.3846 15.999
50 opls_135 8 PEO C03 50 0.0089 12.011
51 opls_140 8 PEO H04 51 0.0917 1.008
52 opls_140 8 PEO H05 52 0.0917 1.008
53 opls_140 8 PEO H06 53 0.0917 1.008
54 opls_140 8 PEO H07 54 0.0917 1.008
55 opls_135 9 PEO C01 55 0.0089 12.011
56 opls_179 9 PEO O02 56 -0.3846 15.999
57 opls_135 9 PEO C03 57 0.0089 12.011
58 opls_140 9 PEO H04 58 0.0917 1.008
59 opls_140 9 PEO H05 59 0.0917 1.008
60 opls_140 9 PEO H06 60 0.0917 1.008
61 opls_140 9 PEO H07 61 0.0917 1.008
62 opls_135 10 PEO C01 62 0.0089 12.011
63 opls_179 10 PEO O02 63 -0.3846 15.999
64 opls_135 10 PEO C03 64 0.0089 12.011
65 opls_140 10 PEO H04 65 0.0917 1.008
66 opls_140 10 PEO H05 66 0.0917 1.008
67 opls_140 10 PEO H06 67 0.0917 1.008
68 opls_140 10 PEO H07 68 0.0917 1.008
69 opls_135 11 PEO C01 69 0.0089 12.011
70 opls_179 11 PEO O02 70 -0.3846 15.999
71 opls_135 11 PEO C03 71 0.0089 12.011
72 opls_140 11 PEO H04 72 0.0917 1.008
73 opls_140 11 PEO H05 73 0.0917 1.008
74 opls_140 11 PEO H06 74 0.0917 1.008
75 opls_140 11 PEO H07 75 0.0917 1.008
76 opls_154 12 OHter OA1 76 -0.6887 15.999
77 opls_135 12 OHter C2 77 0.107 12.011
78 opls_004 12 OHter HA3 78 0.4173 1.008
79 opls_140 12 OHter H4 79 0.0822 1.008
80 opls_140 12 OHter H5 80 0.0822 1.008

[ bonds ]
2 1 1 0.1410 267776.000
Expand Down