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links.ff
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;-----------------------------------
; P3HT LINKS
;-----------------------------------
[link]
resname "P3HT"
[ bonds ]
CT2 +CT5 2 0.1430 9.2100e+06 {"group": "connection"}
[ pairs ]
CT2 +HT4 1 {"group": "connection"}
[ angles ]
CT3 CT2 +CT5 2 130.0 760.0 {"group": "connection"}
CT2 +CT5 +CT4 2 130.0 760.0 {"group": "connection"}
ST1 CT2 +CT5 2 120.0 780.0 {"group": "connection"}
CT2 +CT5 +ST1 2 120.0 780.0 {"group": "connection"}
[ dihedrals ]
; propers
ST1 CT2 +CT5 +ST1 1 0.0 1.80 1 {"group": "connection", "version":"1"}
ST1 CT2 +CT5 +ST1 1 0.0 -9.50 2 {"group": "connection", "version":"2"}
; impropers
CT2 +ST1 +CT4 +CT5 2 0.0 167.42309 {"group": "connection"}
CT2 CT3 ST1 +CT5 2 0.0 167.42309 {"group": "connection"}
;-----------------------------------
; P3HT-TERMINI LINKS
;-----------------------------------
[link]
resname "Hter|P3HT"
[ atoms ]
; compensate for the 0.245 charge of the H being added
CT5 {"replace": {"charge": -0.394}}
[ bonds ]
-H1 CT5 2 0.1090 1.2300e+07 {"comment":"H-CT5-link", "group": "termini"}
[ pairs ]
-H1 CT2 1 {"comment":"H-CT5-link", "group": "termini"}
-H1 CT3 1 {"comment":"H-CT5-link", "group": "termini"}
-H1 HT4 1 {"comment":"H-CT5-link", "group": "termini"}
[ angles ]
-H1 CT5 ST1 2 119.0 575.0 {"comment":"H-CT5-link", "group": "termini"}
-H1 CT5 CT4 2 126.0 575.0 {"comment":"H-CT5-link", "group": "termini"}
[ dihedrals ]
-H1 ST1 CT4 CT5 2 0.0 167.42309 {"comment":"H-CT5-link", "group": "termini"}
[link]
resname "P3HT|Hter"
[ atoms ]
; compensate for the 0.245 charge of the H being added
CT2 {"replace": {"charge": -0.394}}
[ bonds ]
CT2 +H1 2 0.1090 1.2300e+07 {"comment":"H-CT2-link", "group": "termini"}
[ pairs ]
C09 +H1 1 {"comment":"H-CT2-link", "group": "termini"}
H14 +H1 1 {"comment":"H-CT2-link", "group": "termini"}
H15 +H1 1 {"comment":"H-CT2-link", "group": "termini"}
[ angles ]
ST1 CT2 +H1 2 119.0 575.0 {"comment":"H-CT2-link", "group": "termini"}
CT3 CT2 +H1 2 126.0 575.0 {"comment":"H-CT2-link", "group": "termini"}
[ dihedrals ]
+H1 ST1 CT3 CT2 2 0.0 167.42309 {"comment":"H-CT2-link", "group": "termini"}
[ link ]
[ atoms ]
CT2 {"resname": "P3HT"}
[ warning ]
You should patch P3HT with a H-terminal residues. Use -seq Hter:1 P3HT:4 Hter:1
[ non-edges ]
CT2 +H1
CT2 +CT5