diff --git a/LIBRARY.md b/LIBRARY.md index 00e98e0de..6e6d774a5 100644 --- a/LIBRARY.md +++ b/LIBRARY.md @@ -24,6 +24,9 @@ |Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)|[martini3](polyply/data/martini3/PTMA.martini3.ff) | | | | |[ibi_cgm3](polyply/data/ibi_cmg3/PTMA.cgm3.ibi.ff) | | | | |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.ibi.ff) | +|poly(N-(methacryloxyethyl) phthalimide)|PMAP |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PMAP_and_PMAPcharged.oplsaa.LigParGen.ff)| | +|poly(2,3-epoxy-propylphthalimide)|PEPP |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged.oplsaa.LigParGen.ff)| | +|poly(N-(vinylbenzyl) phthalimide)|PVBP |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged.oplsaa.LigParGen.ff)| | |Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) | |DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) | |Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) | diff --git a/polyply/data/oplsaaLigParGen/CH3Oter.ff b/polyply/data/oplsaaLigParGen/CH3Oter.ff new file mode 100644 index 000000000..60196ea76 --- /dev/null +++ b/polyply/data/oplsaaLigParGen/CH3Oter.ff @@ -0,0 +1,15 @@ +[ moleculetype ] + CH3O 3 +[ atoms ] + 1 opls_135 1 CH3O C1 1 -0.1104 12.0110 + 2 opls_140 1 CH3O H2 2 0.0368 1.0080 + 3 opls_140 1 CH3O H3 3 0.0368 1.0080 + 4 opls_140 1 CH3O H4 4 0.0368 1.0080 +[ bonds ] + 2 1 1 0.1090 284512.000 + 3 1 1 0.1090 284512.000 + 4 1 1 0.1090 284512.000 +[angles] + 3 1 2 1 107.800 276.144 + 4 1 2 1 107.800 276.144 + 4 1 3 1 107.800 276.144 diff --git a/polyply/data/oplsaaLigParGen/CH3ter.ff b/polyply/data/oplsaaLigParGen/CH3ter.ff new file mode 100644 index 000000000..ba43dc81f --- /dev/null +++ b/polyply/data/oplsaaLigParGen/CH3ter.ff @@ -0,0 +1,15 @@ +[ moleculetype ] + CH3 3 +[ atoms ] + 1 opls_135 1 CH3 C1 1 -0.2451 12.0110 + 2 opls_140 1 CH3 H2 2 0.0817 1.0080 + 3 opls_140 1 CH3 H3 3 0.0817 1.0080 + 4 opls_140 1 CH3 H4 4 0.0817 1.0080 +[ bonds ] + 2 1 1 0.1090 284512.000 + 3 1 1 0.1090 284512.000 + 4 1 1 0.1090 284512.000 +[angles] + 3 1 2 1 107.800 276.144 + 4 1 2 1 107.800 276.144 + 4 1 3 1 107.800 276.144 diff --git a/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged.oplsaa.LigParGen.ff b/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged.oplsaa.LigParGen.ff new file mode 100644 index 000000000..1615f537e --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged.oplsaa.LigParGen.ff @@ -0,0 +1,467 @@ +[ moleculetype ] + PEPP 3 +[ atoms ] + 1 opls_179 1 PEPP O01 1 -0.3532 15.9990 + 2 opls_135 1 PEPP C02 2 0.0851 12.0110 + 3 opls_135 1 PEPP C03 3 0.0893 12.0110 + 4 opls_003 1 PEPP N04 4 -0.8751 14.0070 + 5 opls_145 1 PEPP C05 5 0.6318 12.0110 + 6 opls_002 1 PEPP O06 6 -0.3655 15.9990 + 7 opls_145 1 PEPP C07 7 -0.1524 12.0110 + 8 opls_145 1 PEPP C08 8 -0.0667 12.0110 + 9 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180.000 43.932 2 + 5 7 8 12 4 180.000 10.460 2 + 7 8 9 19 4 180.000 10.460 2 + 8 9 10 20 4 180.000 10.460 2 + 9 10 11 21 4 180.000 10.460 2 + 10 11 12 22 4 180.000 10.460 2 + 11 12 7 13 4 180.000 10.460 2 + 12 13 4 14 4 180.000 43.932 2 +[ pairs ] + 15 4 1 + 15 17 1 + 15 18 1 + 2 5 1 + 2 13 1 + 3 6 1 + 3 7 1 + 3 12 1 + 3 14 1 + 3 23 1 + 3 24 1 + 4 7 1 + 4 8 1 + 4 11 1 + 4 12 1 + 4 1 1 + 4 16 1 + 5 9 1 + 5 11 1 + 5 12 1 + 5 13 1 + 5 14 1 + 5 17 1 + 5 18 1 + 5 19 1 + 6 8 1 + 6 12 1 + 6 13 1 + 7 10 1 + 7 13 1 + 7 14 1 + 7 20 1 + 7 22 1 + 8 11 1 + 8 13 1 + 8 21 1 + 9 12 1 + 9 22 1 + 10 13 1 + 10 19 1 + 11 14 1 + 11 20 1 + 12 19 1 + 12 21 1 + 13 17 1 + 13 18 1 + 13 22 1 + 1 17 1 + 1 18 1 + 1 23 1 + 1 24 1 + 16 17 1 + 16 18 1 + 16 23 1 + 16 24 1 + 19 20 1 + 20 21 1 + 21 22 1 +[ citation ] +2024RAlessandri-JACSAu +OPLSLigParGen1 +OPLSLigParGen2 +polyply + diff --git a/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged_links.ff b/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged_links.ff new file mode 100644 index 000000000..f436c6a64 --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PEPP_and_PEPPcharged_links.ff @@ -0,0 +1,252 @@ +[link] +resname "PEPP" +[ atoms ] +[ bonds ] + +O01 C15 1 0.1410 267776.000 {"comment":"intermonomer"} +[angles] + +O01 C15 C02 1 109.500 418.400 {"comment":"intermonomer"} + +C02 +O01 C15 1 109.500 502.080 {"comment":"intermonomer"} + H08 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} + H09 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} +[ dihedrals ] + +O01 C15 C02 C03 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"intermonomer"} + +C02 +O01 C15 C02 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C15 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + O01 C02 C15 +O01 3 -1.151 1.151 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C02 C15 +O01 3 0.979 2.937 0.000 -3.916 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C02 +O01 C15 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H08 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H09 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C15 +C03 1 {"comment":"intermonomer"} + C15 +C15 1 {"comment":"intermonomer"} + C15 +H01 1 {"comment":"intermonomer"} + C02 +C02 1 {"comment":"intermonomer"} + C03 +O01 1 {"comment":"intermonomer"} + +O01 O01 1 {"comment":"intermonomer"} + +O01 H01 1 {"comment":"intermonomer"} + +C02 H08 1 {"comment":"intermonomer"} + +C02 H09 1 {"comment":"intermonomer"} +[link] +resname "CH3O|PEPP" +[ atoms ] +[ bonds ] + C1 +O01 1 0.1410 267776.000 {"comment":"alpha-C-link"} +[angles] + C1 +O01 +C02 1 109.500 502.080 {"comment":"alpha-C-link"} + H2 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} + H3 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} + H4 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} +[ dihedrals ] + C1 +O01 +C02 +C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"alpha-C-link"} + H2 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +O01 +C02 +C03 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C02 +O01 C1 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C15 C1 1 {"comment":"alpha-C-link"} + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + C1 +H01 1 {"comment":"alpha-C-link"} +[link] +resname "PEPP|CH3" +[ atoms ] +[ bonds ] + C1 -C15 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C15 -C02 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + -H08 -C15 C1 1 110.700 313.800 {"comment":"beta-C-link"} + -H09 -C15 C1 1 110.700 313.800 {"comment":"beta-C-link"} +[ dihedrals ] + C1 -C15 -C02 -O01 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C15 -C02 -C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C02 -C15 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -O01 C1 1 {"comment":"beta-C-link"} + -C02 H2 1 {"comment":"beta-C-link"} + -C02 H3 1 {"comment":"beta-C-link"} + -C02 H4 1 {"comment":"beta-C-link"} + -C03 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + -H08 H2 1 {"comment":"beta-C-link"} + -H08 H3 1 {"comment":"beta-C-link"} + -H08 H4 1 {"comment":"beta-C-link"} + -H09 H2 1 {"comment":"beta-C-link"} + -H09 H3 1 {"comment":"beta-C-link"} + -H09 H4 1 {"comment":"beta-C-link"} +[link] +resname "PEPPcharged" +[ atoms ] +[ bonds ] + +O01 C15 1 0.1410 267776.000 {"comment":"intermonomer"} +[angles] + +O01 C15 C02 1 109.500 418.400 {"comment":"intermonomer"} + +C02 +O01 C15 1 109.500 502.080 {"comment":"intermonomer"} + H08 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} + H09 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} +[ dihedrals ] + +O01 C15 C02 C03 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"intermonomer"} + +C02 +O01 C15 C02 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C15 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + O01 C02 C15 +O01 3 -1.151 1.151 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C02 C15 +O01 3 0.979 2.937 0.000 -3.916 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C02 +O01 C15 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H08 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H09 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C15 +C03 1 {"comment":"intermonomer"} + C15 +C15 1 {"comment":"intermonomer"} + C15 +H01 1 {"comment":"intermonomer"} + C02 +C02 1 {"comment":"intermonomer"} + C03 +O01 1 {"comment":"intermonomer"} + +O01 O01 1 {"comment":"intermonomer"} + +O01 H01 1 {"comment":"intermonomer"} + +C02 H08 1 {"comment":"intermonomer"} + +C02 H09 1 {"comment":"intermonomer"} +[link] +resname "CH3O|PEPPcharged" +[ atoms ] +[ bonds ] + C1 +O01 1 0.1410 267776.000 {"comment":"alpha-C-link"} +[angles] + C1 +O01 +C02 1 109.500 502.080 {"comment":"alpha-C-link"} + H2 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} + H3 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} + H4 C1 +O01 1 109.500 292.880 {"comment":"alpha-C-link"} +[ dihedrals ] + C1 +O01 +C02 +C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"alpha-C-link"} + H2 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +O01 +C02 +C03 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C02 +O01 C1 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C15 C1 1 {"comment":"alpha-C-link"} + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + C1 +H01 1 {"comment":"alpha-C-link"} +[link] +resname "PEPPcharged|CH3" +[ atoms ] +[ bonds ] + C1 -C15 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C15 -C02 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C15 1 110.700 313.800 {"comment":"beta-C-link"} + -H08 -C15 C1 1 110.700 313.800 {"comment":"beta-C-link"} + -H09 -C15 C1 1 110.700 313.800 {"comment":"beta-C-link"} +[ dihedrals ] + C1 -C15 -C02 -O01 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C15 -C02 -C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C02 -C15 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -H08 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C15 -H09 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -O01 C1 1 {"comment":"beta-C-link"} + -C02 H2 1 {"comment":"beta-C-link"} + -C02 H3 1 {"comment":"beta-C-link"} + -C02 H4 1 {"comment":"beta-C-link"} + -C03 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + -H08 H2 1 {"comment":"beta-C-link"} + -H08 H3 1 {"comment":"beta-C-link"} + -H08 H4 1 {"comment":"beta-C-link"} + -H09 H2 1 {"comment":"beta-C-link"} + -H09 H3 1 {"comment":"beta-C-link"} + -H09 H4 1 {"comment":"beta-C-link"} +[link] +resname "PEPP|PEOPHcharged" +[ atoms ] +[ bonds ] + +O01 C15 1 0.1410 267776.000 {"comment":"intermonomer"} +[angles] + +O01 C15 C02 1 109.500 418.400 {"comment":"intermonomer"} + +C02 +O01 C15 1 109.500 502.080 {"comment":"intermonomer"} + H08 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} + H09 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} +[ dihedrals ] + +O01 C15 C02 C03 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"intermonomer"} + +C02 +O01 C15 C02 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C15 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + O01 C02 C15 +O01 3 -1.151 1.151 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C02 C15 +O01 3 0.979 2.937 0.000 -3.916 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C02 +O01 C15 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H08 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H09 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C15 +C03 1 {"comment":"intermonomer"} + C15 +C15 1 {"comment":"intermonomer"} + C15 +H01 1 {"comment":"intermonomer"} + C02 +C02 1 {"comment":"intermonomer"} + C03 +O01 1 {"comment":"intermonomer"} + +O01 O01 1 {"comment":"intermonomer"} + +O01 H01 1 {"comment":"intermonomer"} + +C02 H08 1 {"comment":"intermonomer"} + +C02 H09 1 {"comment":"intermonomer"} +[link] +resname "PEPPcharged|PEOPH" +[ atoms ] +[ bonds ] + +O01 C15 1 0.1410 267776.000 {"comment":"intermonomer"} +[angles] + +O01 C15 C02 1 109.500 418.400 {"comment":"intermonomer"} + +C02 +O01 C15 1 109.500 502.080 {"comment":"intermonomer"} + H08 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} + H09 C15 +O01 1 109.500 292.880 {"comment":"intermonomer"} +[ dihedrals ] + +O01 C15 C02 C03 3 2.874 0.582 2.092 -5.548 -0.000 0.000 {"comment":"intermonomer"} + +C02 +O01 C15 C02 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + +C15 +C02 +O01 C15 3 1.715 2.845 1.046 -5.607 -0.000 0.000 {"comment":"intermonomer"} + O01 C02 C15 +O01 3 -1.151 1.151 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C02 C15 +O01 3 0.979 2.937 0.000 -3.916 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C02 +O01 C15 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H08 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} + H09 C15 +O01 +C02 3 1.590 4.770 0.000 -6.360 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C15 +C03 1 {"comment":"intermonomer"} + C15 +C15 1 {"comment":"intermonomer"} + C15 +H01 1 {"comment":"intermonomer"} + C02 +C02 1 {"comment":"intermonomer"} + C03 +O01 1 {"comment":"intermonomer"} + +O01 O01 1 {"comment":"intermonomer"} + +O01 H01 1 {"comment":"intermonomer"} + +C02 H08 1 {"comment":"intermonomer"} + +C02 H09 1 {"comment":"intermonomer"} diff --git a/polyply/data/oplsaaLigParGen/PMAP_and_PMAPcharged.oplsaa.LigParGen.ff b/polyply/data/oplsaaLigParGen/PMAP_and_PMAPcharged.oplsaa.LigParGen.ff new file mode 100644 index 000000000..19f870aaa --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PMAP_and_PMAPcharged.oplsaa.LigParGen.ff @@ -0,0 +1,579 @@ +[ moleculetype ] + PMAP 3 +[ atoms ] + 1 opls_135 1 PMAP C01 1 -0.1723 12.0110 + 2 opls_135 1 PMAP C02 2 -0.0197 12.0110 + 3 opls_135 1 PMAP C03 3 -0.2521 12.0110 + 4 opls_145 1 PMAP C04 4 0.4454 12.0110 + 5 opls_002 1 PMAP O05 5 -0.4516 15.9990 + 6 opls_179 1 PMAP O06 6 -0.3462 15.9990 + 7 opls_135 1 PMAP C07 7 -0.0020 12.0110 + 8 opls_135 1 PMAP C08 8 0.1061 12.0110 + 9 opls_003 1 PMAP N09 9 -0.9059 14.0070 + 10 opls_145 1 PMAP C10 10 0.6392 12.0110 + 11 opls_002 1 PMAP O11 11 -0.3800 15.9990 + 12 opls_145 1 PMAP C12 12 -0.1462 12.0110 + 13 opls_145 1 PMAP C13 13 -0.0674 12.0110 + 14 opls_145 1 PMAP C14 14 -0.1311 12.0110 + 15 opls_145 1 PMAP C15 15 -0.1331 12.0110 + 16 opls_145 1 PMAP C16 16 -0.0662 12.0110 + 17 opls_145 1 PMAP C17 17 -0.1502 12.0110 + 18 opls_145 1 PMAP C18 18 0.6374 12.0110 + 19 opls_002 1 PMAP O19 19 -0.3684 15.9990 + 20 opls_140 1 PMAP H01 20 0.1209 1.0080 + 21 opls_140 1 PMAP H02 21 0.1209 1.0080 + 22 opls_140 1 PMAP H03 22 0.1024 1.0080 + 23 opls_140 1 PMAP H04 23 0.1024 1.0080 + 24 opls_140 1 PMAP H05 24 0.1024 1.0080 + 25 opls_140 1 PMAP H06 25 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new file mode 100644 index 000000000..86e8cd0bd --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PMAP_and_PMAPcharged_links.ff @@ -0,0 +1,428 @@ +[link] +resname "PMAP" +[ atoms ] +[ bonds ] + C02 +C01 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + C02 +C01 +C02 1 112.700 488.273 {"comment":"intermonomer"} + C03 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + C04 C02 +C01 1 111.100 527.184 {"comment":"intermonomer"} + C01 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + C02 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + C03 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + C04 C02 +C01 +C02 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + O05 C04 C02 +C01 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + O06 C04 C02 +C01 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"intermonomer"} + C01 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H04 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H05 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + C02 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + +C04 C02 1 {"comment":"intermonomer"} + +C02 C03 1 {"comment":"intermonomer"} + +C02 C04 1 {"comment":"intermonomer"} + +C02 C01 1 {"comment":"intermonomer"} + +C03 C02 1 {"comment":"intermonomer"} + +C01 O05 1 {"comment":"intermonomer"} + +C01 O06 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C01 H03 1 {"comment":"intermonomer"} + +C01 H04 1 {"comment":"intermonomer"} + +C01 H05 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +H01 1 {"comment":"intermonomer"} + C04 +H02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PMAP" +[dihedrals] + C02 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] +++C01 C02 1 {"comment":"intermonomer"} +[link] +resname "CH3|PMAP" +[ atoms ] +[ bonds ] + C1 +C01 1 0.1529 224262.400 {"comment":"alpha-C-link"} +[angles] + C1 +C01 +C02 1 112.700 488.273 {"comment":"alpha-C-link"} + H2 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H3 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H4 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + +H01 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} + +H02 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} +[ dihedrals ] + H2 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + +C04 C1 1 {"comment":"alpha-C-link"} + H2 +H01 1 {"comment":"alpha-C-link"} + H2 +H02 1 {"comment":"alpha-C-link"} + H3 +H01 1 {"comment":"alpha-C-link"} + H3 +H02 1 {"comment":"alpha-C-link"} + H4 +H01 1 {"comment":"alpha-C-link"} + H4 +H02 1 {"comment":"alpha-C-link"} +[link] +; for bonded terms spanning three residues +resname "CH3|PMAP" +[dihedrals] + C1 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} +[pairs] +++C01 C1 1 {"comment":"alpha-C-link"} +[link] +resname "PMAP|CH3" +[ atoms ] +[ bonds ] + C1 -C02 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C02 -C01 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + C1 -C02 -C03 1 112.700 488.273 {"comment":"beta-C-link"} + C1 -C02 -C04 1 111.100 527.184 {"comment":"beta-C-link"} +[ dihedrals ] + H2 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C04 -O05 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C04 -O06 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H02 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H03 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H04 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H05 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -C01 H2 1 {"comment":"beta-C-link"} + -C01 H3 1 {"comment":"beta-C-link"} + -C01 H4 1 {"comment":"beta-C-link"} + -C03 H2 1 {"comment":"beta-C-link"} + -C03 H3 1 {"comment":"beta-C-link"} + -C03 H4 1 {"comment":"beta-C-link"} + -C04 H2 1 {"comment":"beta-C-link"} + -C04 H3 1 {"comment":"beta-C-link"} + -C04 H4 1 {"comment":"beta-C-link"} + -O05 C1 1 {"comment":"beta-C-link"} + -O06 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + C1 -H02 1 {"comment":"beta-C-link"} + C1 -H03 1 {"comment":"beta-C-link"} + C1 -H04 1 {"comment":"beta-C-link"} + C1 -H05 1 {"comment":"beta-C-link"} +[link] +; for bonded terms spanning three residues +resname "PMAP|CH3" +[dihedrals] + C1 -C02 -C01 --C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} +[pairs] +--C02 C1 1 {"comment":"beta-C-link"} +[link] +resname "PMAPcharged" +[ atoms ] +[ bonds ] + C02 +C01 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + C02 +C01 +C02 1 112.700 488.273 {"comment":"intermonomer"} + C03 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + C04 C02 +C01 1 111.100 527.184 {"comment":"intermonomer"} + C01 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + C02 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + C03 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + C04 C02 +C01 +C02 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + O05 C04 C02 +C01 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + O06 C04 C02 +C01 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"intermonomer"} + C01 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H04 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H05 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + C02 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + +C04 C02 1 {"comment":"intermonomer"} + +C02 C03 1 {"comment":"intermonomer"} + +C02 C04 1 {"comment":"intermonomer"} + +C02 C01 1 {"comment":"intermonomer"} + +C03 C02 1 {"comment":"intermonomer"} + +C01 O05 1 {"comment":"intermonomer"} + +C01 O06 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C01 H03 1 {"comment":"intermonomer"} + +C01 H04 1 {"comment":"intermonomer"} + +C01 H05 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +H01 1 {"comment":"intermonomer"} + C04 +H02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PMAPcharged" +[dihedrals] + C02 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] +++C01 C02 1 {"comment":"intermonomer"} +[link] +resname "CH3|PMAPcharged" +[ atoms ] +[ bonds ] + C1 +C01 1 0.1529 224262.400 {"comment":"alpha-C-link"} +[angles] + C1 +C01 +C02 1 112.700 488.273 {"comment":"alpha-C-link"} + H2 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H3 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H4 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + +H01 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} + +H02 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} +[ dihedrals ] + H2 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + +C04 C1 1 {"comment":"alpha-C-link"} + H2 +H01 1 {"comment":"alpha-C-link"} + H2 +H02 1 {"comment":"alpha-C-link"} + H3 +H01 1 {"comment":"alpha-C-link"} + H3 +H02 1 {"comment":"alpha-C-link"} + H4 +H01 1 {"comment":"alpha-C-link"} + H4 +H02 1 {"comment":"alpha-C-link"} +[link] +; for bonded terms spanning three residues +resname "CH3|PMAPcharged" +[dihedrals] + C1 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} +[pairs] +++C01 C1 1 {"comment":"alpha-C-link"} +[link] +resname "PMAPcharged|CH3" +[ atoms ] +[ bonds ] + C1 -C02 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C02 -C01 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + C1 -C02 -C03 1 112.700 488.273 {"comment":"beta-C-link"} + C1 -C02 -C04 1 111.100 527.184 {"comment":"beta-C-link"} +[ dihedrals ] + H2 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C04 -O05 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C04 -O06 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H02 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H03 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H04 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H05 -C03 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -C01 H2 1 {"comment":"beta-C-link"} + -C01 H3 1 {"comment":"beta-C-link"} + -C01 H4 1 {"comment":"beta-C-link"} + -C03 H2 1 {"comment":"beta-C-link"} + -C03 H3 1 {"comment":"beta-C-link"} + -C03 H4 1 {"comment":"beta-C-link"} + -C04 H2 1 {"comment":"beta-C-link"} + -C04 H3 1 {"comment":"beta-C-link"} + -C04 H4 1 {"comment":"beta-C-link"} + -O05 C1 1 {"comment":"beta-C-link"} + -O06 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + C1 -H02 1 {"comment":"beta-C-link"} + C1 -H03 1 {"comment":"beta-C-link"} + C1 -H04 1 {"comment":"beta-C-link"} + C1 -H05 1 {"comment":"beta-C-link"} +[link] +; for bonded terms spanning three residues +resname "PMAPcharged|CH3" +[dihedrals] + C1 -C02 -C01 --C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} +[pairs] +--C02 C1 1 {"comment":"beta-C-link"} +[link] +resname "PMAP|PMAPcharged" +[ atoms ] +[ bonds ] + C02 +C01 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + C02 +C01 +C02 1 112.700 488.273 {"comment":"intermonomer"} + C03 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + C04 C02 +C01 1 111.100 527.184 {"comment":"intermonomer"} + C01 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + C02 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + C03 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + C04 C02 +C01 +C02 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + O05 C04 C02 +C01 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + O06 C04 C02 +C01 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"intermonomer"} + C01 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H04 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H05 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + C02 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + +C04 C02 1 {"comment":"intermonomer"} + +C02 C03 1 {"comment":"intermonomer"} + +C02 C04 1 {"comment":"intermonomer"} + +C02 C01 1 {"comment":"intermonomer"} + +C03 C02 1 {"comment":"intermonomer"} + +C01 O05 1 {"comment":"intermonomer"} + +C01 O06 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C01 H03 1 {"comment":"intermonomer"} + +C01 H04 1 {"comment":"intermonomer"} + +C01 H05 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +H01 1 {"comment":"intermonomer"} + C04 +H02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PMAP|PMAPcharged" +[dihedrals] + C02 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] +++C01 C02 1 {"comment":"intermonomer"} +[link] +resname "PMAPcharged|PMAP" +[ atoms ] +[ bonds ] + C02 +C01 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + C02 +C01 +C02 1 112.700 488.273 {"comment":"intermonomer"} + C03 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + C04 C02 +C01 1 111.100 527.184 {"comment":"intermonomer"} + C01 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + C02 +C01 +C02 +C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + C03 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + C04 C02 +C01 +C02 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + O05 C04 C02 +C01 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + O06 C04 C02 +C01 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"intermonomer"} + C01 C02 +C01 +C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H04 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H05 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + C02 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C04 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + +C04 C02 1 {"comment":"intermonomer"} + +C02 C03 1 {"comment":"intermonomer"} + +C02 C04 1 {"comment":"intermonomer"} + +C02 C01 1 {"comment":"intermonomer"} + +C03 C02 1 {"comment":"intermonomer"} + +C01 O05 1 {"comment":"intermonomer"} + +C01 O06 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C01 H03 1 {"comment":"intermonomer"} + +C01 H04 1 {"comment":"intermonomer"} + +C01 H05 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +H01 1 {"comment":"intermonomer"} + C04 +H02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PMAPcharged|PMAP" +[dihedrals] + C02 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] +++C01 C02 1 {"comment":"intermonomer"} diff --git a/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged.oplsaa.LigParGen.ff b/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged.oplsaa.LigParGen.ff new file mode 100644 index 000000000..fa6cf1fac --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged.oplsaa.LigParGen.ff @@ -0,0 +1,633 @@ +[ moleculetype ] + PVBP 3 +[ atoms ] + 1 opls_135 1 PVBP C01 1 -0.1576 12.0110 + 2 opls_135 1 PVBP C02 2 -0.0695 12.0110 + 3 opls_145 1 PVBP C03 3 -0.0640 12.0110 + 4 opls_145 1 PVBP C04 4 -0.1504 12.0110 + 5 opls_145 1 PVBP C05 5 -0.1236 12.0110 + 6 opls_145 1 PVBP C06 6 -0.1226 12.0110 + 7 opls_135 1 PVBP C07 7 0.1714 12.0110 + 8 opls_003 1 PVBP N08 8 -0.8689 14.0070 + 9 opls_145 1 PVBP C09 9 0.6340 12.0110 + 10 opls_002 1 PVBP O10 10 -0.3836 15.9990 + 11 opls_145 1 PVBP C11 11 -0.1478 12.0110 + 12 opls_145 1 PVBP C12 12 -0.0680 12.0110 + 13 opls_145 1 PVBP C13 13 -0.1342 12.0110 + 14 opls_145 1 PVBP C14 14 -0.1331 12.0110 + 15 opls_145 1 PVBP C15 15 -0.0686 12.0110 + 16 opls_145 1 PVBP C16 16 -0.1477 12.0110 + 17 opls_145 1 PVBP C17 17 0.6338 12.0110 + 18 opls_002 1 PVBP O18 18 -0.3850 15.9990 + 19 opls_145 1 PVBP C19 19 -0.1236 12.0110 + 20 opls_145 1 PVBP C20 20 -0.1504 12.0110 + 21 opls_140 1 PVBP H01 21 0.0964 1.0080 + 22 opls_140 1 PVBP H02 22 0.0964 1.0080 + 23 opls_140 1 PVBP H03 23 0.1077 1.0080 + 24 opls_146 1 PVBP H04 24 0.1524 1.0080 + 25 opls_146 1 PVBP H05 25 0.1600 1.0080 + 26 opls_140 1 PVBP H06 26 0.1261 1.0080 + 27 opls_140 1 PVBP H07 27 0.1261 1.0080 + 28 opls_146 1 PVBP H08 28 0.1794 1.0080 + 29 opls_146 1 PVBP H09 29 0.1618 1.0080 + 30 opls_146 1 PVBP H10 30 0.1617 1.0080 + 31 opls_146 1 PVBP H11 31 0.1790 1.0080 + 32 opls_146 1 PVBP H12 32 0.1600 1.0080 + 33 opls_146 1 PVBP H13 33 0.1524 1.0080 +[ bonds ] + 2 1 1 0.1529 224262.400 + 3 2 1 0.1510 265265.600 + 4 3 1 0.1400 392459.200 + 5 4 1 0.1400 392459.200 + 6 5 1 0.1400 392459.200 + 7 6 1 0.1510 265265.600 + 8 7 1 0.1475 282001.600 + 9 8 1 0.1388 349782.400 + 10 9 1 0.1229 476976.000 + 11 9 1 0.1490 334720.000 + 12 11 1 0.1400 392459.200 + 13 12 1 0.1400 392459.200 + 14 13 1 0.1400 392459.200 + 15 14 1 0.1400 392459.200 + 16 15 1 0.1400 392459.200 + 17 16 1 0.1490 334720.000 + 18 17 1 0.1229 476976.000 + 19 6 1 0.1400 392459.200 + 20 19 1 0.1400 392459.200 + 21 1 1 0.1090 284512.000 + 22 1 1 0.1090 284512.000 + 23 2 1 0.1090 284512.000 + 24 4 1 0.1080 307105.600 + 25 5 1 0.1080 307105.600 + 26 7 1 0.1090 284512.000 + 27 7 1 0.1090 284512.000 + 28 12 1 0.1080 307105.600 + 29 13 1 0.1080 307105.600 + 30 14 1 0.1080 307105.600 + 31 15 1 0.1080 307105.600 + 32 19 1 0.1080 307105.600 + 33 20 1 0.1080 307105.600 + 16 11 1 0.1424 392459.200 + 17 8 1 0.1388 349782.400 + 20 3 1 0.1400 392459.200 +[angles] + 3 2 1 1 114.000 527.184 + 4 3 2 1 120.000 585.760 + 5 4 3 1 120.000 527.184 + 6 5 4 1 120.000 527.184 + 7 6 5 1 120.000 585.760 + 8 7 6 1 111.200 669.440 + 9 8 7 1 116.900 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180.000 10.460 2 + 5 6 7 19 4 180.000 10.460 2 + 7 8 9 17 4 180.000 0.000 2 + 8 9 10 11 4 180.000 43.932 2 + 9 11 12 16 4 180.000 10.460 2 + 11 12 13 28 4 180.000 10.460 2 + 12 13 14 29 4 180.000 10.460 2 + 13 14 15 30 4 180.000 10.460 2 + 14 15 16 31 4 180.000 10.460 2 + 15 16 11 17 4 180.000 10.460 2 + 16 17 8 18 4 180.000 43.932 2 + 6 19 20 32 4 180.000 10.460 2 + 19 20 3 33 4 180.000 10.460 2 +[ pairs ] + 1 4 1 + 1 20 1 + 2 5 1 + 2 19 1 + 2 24 1 + 2 33 1 + 3 6 1 + 3 21 1 + 3 22 1 + 3 25 1 + 3 32 1 + 4 7 1 + 4 19 1 + 4 23 1 + 4 33 1 + 5 8 1 + 5 20 1 + 5 26 1 + 5 27 1 + 5 32 1 + 6 9 1 + 6 17 1 + 6 24 1 + 6 33 1 + 7 10 1 + 7 11 1 + 7 16 1 + 7 18 1 + 7 20 1 + 7 25 1 + 7 32 1 + 8 11 1 + 8 12 1 + 8 15 1 + 8 16 1 + 8 19 1 + 9 13 1 + 9 15 1 + 9 16 1 + 9 17 1 + 9 18 1 + 9 26 1 + 9 27 1 + 9 28 1 + 10 12 1 + 10 16 1 + 10 17 1 + 11 14 1 + 11 17 1 + 11 18 1 + 11 29 1 + 11 31 1 + 12 15 1 + 12 17 1 + 12 30 1 + 13 16 1 + 13 31 1 + 14 17 1 + 14 28 1 + 15 18 1 + 15 29 1 + 16 28 1 + 16 30 1 + 17 26 1 + 17 27 1 + 17 31 1 + 19 25 1 + 19 26 1 + 19 27 1 + 20 23 1 + 20 24 1 + 21 23 1 + 22 23 1 + 24 25 1 + 28 29 1 + 29 30 1 + 30 31 1 + 32 33 1 +[ citation ] +2024RAlessandri-JACSAu +OPLSLigParGen1 +OPLSLigParGen2 +polyply + diff --git a/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged_links.ff b/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged_links.ff new file mode 100644 index 000000000..09857b4e9 --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PVBP_and_PVBPcharged_links.ff @@ -0,0 +1,392 @@ +[link] +resname "PVBP" +[ atoms ] +[ bonds ] + +C01 C02 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + +C01 C02 C01 1 112.700 488.273 {"comment":"intermonomer"} + +C02 +C01 C02 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +C01 C02 C03 1 114.000 527.184 {"comment":"intermonomer"} + H03 C02 +C01 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + +C02 +C01 C02 C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H03 +C02 +C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C02 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C01 +C02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} + C02 +C03 1 {"comment":"intermonomer"} + C02 +H03 1 {"comment":"intermonomer"} + C03 +C02 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +C01 1 {"comment":"intermonomer"} + C20 +C01 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C02 H03 1 {"comment":"intermonomer"} + H03 +H01 1 {"comment":"intermonomer"} + H03 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PVBP" +[dihedrals] +++C01 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] + C02 ++C01 1 {"comment":"intermonomer"} +[link] +resname "CH3|PVBP" +[ atoms ] +[ bonds ] + C1 +C01 1 0.1529 224262.400 {"comment":"alpha-C-link"} +[angles] + C1 +C01 +C02 1 112.700 488.273 {"comment":"alpha-C-link"} + H2 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H3 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H4 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + +H01 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} + +H02 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} +[ dihedrals ] + H2 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} + +H03 +C02 +C01 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + C1 +H03 1 {"comment":"alpha-C-link"} + H2 +H01 1 {"comment":"alpha-C-link"} + H2 +H02 1 {"comment":"alpha-C-link"} + H3 +H01 1 {"comment":"alpha-C-link"} + H3 +H02 1 {"comment":"alpha-C-link"} + H4 +H01 1 {"comment":"alpha-C-link"} + H4 +H02 1 {"comment":"alpha-C-link"} +[link] +; for bonded terms spanning three residues +resname "CH3|PVBP" +[dihedrals] + C1 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} +[pairs] +++C01 C1 1 {"comment":"alpha-C-link"} +[link] +resname "PVBP|CH3" +[ atoms ] +[ bonds ] + C1 -C02 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C02 -C01 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + C1 -C02 -C03 1 114.000 527.184 {"comment":"beta-C-link"} + -H03 -C02 C1 1 110.700 313.800 {"comment":"beta-C-link"} +[ dihedrals ] + H2 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C03 -C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C03 -C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H02 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -C01 H2 1 {"comment":"beta-C-link"} + -C01 H3 1 {"comment":"beta-C-link"} + -C01 H4 1 {"comment":"beta-C-link"} + -C03 H2 1 {"comment":"beta-C-link"} + -C03 H3 1 {"comment":"beta-C-link"} + -C03 H4 1 {"comment":"beta-C-link"} + -C04 C1 1 {"comment":"beta-C-link"} + -C20 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + C1 -H02 1 {"comment":"beta-C-link"} + -H03 H2 1 {"comment":"beta-C-link"} + -H03 H3 1 {"comment":"beta-C-link"} + -H03 H4 1 {"comment":"beta-C-link"} +[link] +; for bonded terms spanning three residues +resname "PVBP|CH3" +[dihedrals] + C1 -C02 -C01 --C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} +[pairs] +--C02 C1 1 {"comment":"beta-C-link"} +[link] +resname "PVBPcharged" +[ atoms ] +[ bonds ] + +C01 C02 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + +C01 C02 C01 1 112.700 488.273 {"comment":"intermonomer"} + +C02 +C01 C02 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +C01 C02 C03 1 114.000 527.184 {"comment":"intermonomer"} + H03 C02 +C01 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + +C02 +C01 C02 C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H03 +C02 +C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C02 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C01 +C02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} + C02 +C03 1 {"comment":"intermonomer"} + C02 +H03 1 {"comment":"intermonomer"} + C03 +C02 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +C01 1 {"comment":"intermonomer"} + C20 +C01 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C02 H03 1 {"comment":"intermonomer"} + H03 +H01 1 {"comment":"intermonomer"} + H03 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PVBPcharged" +[dihedrals] +++C01 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] + C02 ++C01 1 {"comment":"intermonomer"} +[link] +resname "CH3|PVBPcharged" +[ atoms ] +[ bonds ] + C1 +C01 1 0.1529 224262.400 {"comment":"alpha-C-link"} +[angles] + C1 +C01 +C02 1 112.700 488.273 {"comment":"alpha-C-link"} + H2 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H3 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + H4 C1 +C01 1 110.700 313.800 {"comment":"alpha-C-link"} + +H01 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} + +H02 +C01 C1 1 110.700 313.800 {"comment":"alpha-C-link"} +[ dihedrals ] + H2 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H3 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + H4 C1 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + C1 +C01 +C02 +C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} + +H03 +C02 +C01 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H01 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} + +H02 +C01 C1 H4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link"} +[ dihedrals ] +[ pairs ] + +C02 H2 1 {"comment":"alpha-C-link"} + +C02 H3 1 {"comment":"alpha-C-link"} + +C02 H4 1 {"comment":"alpha-C-link"} + +C03 C1 1 {"comment":"alpha-C-link"} + C1 +H03 1 {"comment":"alpha-C-link"} + H2 +H01 1 {"comment":"alpha-C-link"} + H2 +H02 1 {"comment":"alpha-C-link"} + H3 +H01 1 {"comment":"alpha-C-link"} + H3 +H02 1 {"comment":"alpha-C-link"} + H4 +H01 1 {"comment":"alpha-C-link"} + H4 +H02 1 {"comment":"alpha-C-link"} +[link] +; for bonded terms spanning three residues +resname "CH3|PVBPcharged" +[dihedrals] + C1 +C01 +C02 ++C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} +[pairs] +++C01 C1 1 {"comment":"alpha-C-link"} +[link] +resname "PVBPcharged|CH3" +[ atoms ] +[ bonds ] + C1 -C02 1 0.1529 224262.400 {"comment":"beta-C-link"} +[angles] + C1 -C02 -C01 1 112.700 488.273 {"comment":"beta-C-link"} + H2 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H3 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + H4 C1 -C02 1 110.700 313.800 {"comment":"beta-C-link"} + C1 -C02 -C03 1 114.000 527.184 {"comment":"beta-C-link"} + -H03 -C02 C1 1 110.700 313.800 {"comment":"beta-C-link"} +[ dihedrals ] + H2 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C03 -C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + C1 -C02 -C03 -C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"beta-C-link"} + -H01 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + -H02 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H2 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H3 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} + H4 C1 -C02 -H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ dihedrals ] +[ pairs ] + -C01 H2 1 {"comment":"beta-C-link"} + -C01 H3 1 {"comment":"beta-C-link"} + -C01 H4 1 {"comment":"beta-C-link"} + -C03 H2 1 {"comment":"beta-C-link"} + -C03 H3 1 {"comment":"beta-C-link"} + -C03 H4 1 {"comment":"beta-C-link"} + -C04 C1 1 {"comment":"beta-C-link"} + -C20 C1 1 {"comment":"beta-C-link"} + C1 -H01 1 {"comment":"beta-C-link"} + C1 -H02 1 {"comment":"beta-C-link"} + -H03 H2 1 {"comment":"beta-C-link"} + -H03 H3 1 {"comment":"beta-C-link"} + -H03 H4 1 {"comment":"beta-C-link"} +[link] +; for bonded terms spanning three residues +resname "PVBPcharged|CH3" +[dihedrals] + C1 -C02 -C01 --C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} +[pairs] +--C02 C1 1 {"comment":"beta-C-link"} +[link] +resname "PVBP|PSPHcharged" +[ atoms ] +[ bonds ] + +C01 C02 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + +C01 C02 C01 1 112.700 488.273 {"comment":"intermonomer"} + +C02 +C01 C02 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +C01 C02 C03 1 114.000 527.184 {"comment":"intermonomer"} + H03 C02 +C01 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + +C02 +C01 C02 C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H03 +C02 +C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C02 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C01 +C02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} + C02 +C03 1 {"comment":"intermonomer"} + C02 +H03 1 {"comment":"intermonomer"} + C03 +C02 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +C01 1 {"comment":"intermonomer"} + C20 +C01 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C02 H03 1 {"comment":"intermonomer"} + H03 +H01 1 {"comment":"intermonomer"} + H03 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PVBP|PSPHcharged" +[dihedrals] +++C01 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] + C02 ++C01 1 {"comment":"intermonomer"} +[link] +resname "PVBPcharged|PSPH" +[ atoms ] +[ bonds ] + +C01 C02 1 0.1529 224262.400 {"comment":"intermonomer"} +[angles] + +C01 C02 C01 1 112.700 488.273 {"comment":"intermonomer"} + +C02 +C01 C02 1 112.700 488.273 {"comment":"intermonomer"} + +H01 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +H02 +C01 C02 1 110.700 313.800 {"comment":"intermonomer"} + +C01 C02 C03 1 114.000 527.184 {"comment":"intermonomer"} + H03 C02 +C01 1 110.700 313.800 {"comment":"intermonomer"} +[ dihedrals ] + +C02 +C01 C02 C01 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H03 +C02 +C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C03 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 C03 3 0.967 2.900 0.000 -3.866 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C04 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C03 C20 3 -0.523 0.523 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + H01 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H02 C01 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + H03 C02 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H01 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} + +H02 +C01 C02 H03 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ dihedrals ] +[ pairs ] + C01 +C02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} + C02 +C03 1 {"comment":"intermonomer"} + C02 +H03 1 {"comment":"intermonomer"} + C03 +C02 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +C01 1 {"comment":"intermonomer"} + C20 +C01 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + +C02 H03 1 {"comment":"intermonomer"} + H03 +H01 1 {"comment":"intermonomer"} + H03 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PVBPcharged|PSPH" +[dihedrals] +++C01 +C02 +C01 C02 3 1.360 -0.523 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] + C02 ++C01 1 {"comment":"intermonomer"} diff --git a/polyply/data/oplsaaLigParGen/citations.bib b/polyply/data/oplsaaLigParGen/citations.bib index 2b72b60be..88d9119e4 100644 --- a/polyply/data/oplsaaLigParGen/citations.bib +++ b/polyply/data/oplsaaLigParGen/citations.bib @@ -57,3 +57,14 @@ @article{2023RAlessandri-Macromolecules year={2023} } +@article{2024RAlessandri-JACSAu, + title={Structural, Ionic, and Electronic Properties of Solid-State Phthalimide-Containing Polymers for All-Organic Batteries}, + author={Alessandri, Riccardo and Li, Cheng-Han and Keating, Sheila and Mohanty, Khirabdhi T. and Peng, Aaron and Lutkenhaus, Jodie L. and Rowan, Stuart J. and Tabor, Daniel P. and de Pablo, Juan J.}, + journal={JACS Au}, + volume={4}, + number={6}, + pages={2300-2311}, + doi={10.1021/jacsau.4c00276}, + year={2024} +} +