From e3b63e1e9975e38873aeebb4aaace25812c784e6 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Mon, 19 Feb 2024 15:03:06 -0600 Subject: [PATCH] Contribute OPLS/CM1A (LigParGen) model for PMMA --- .../PMMA.oplsaa.LigParGen.CM1A.ff | 294 ++++++++++++++++++ 1 file changed, 294 insertions(+) create mode 100644 polyply/data/oplsaaLigParGen/PMMA.oplsaa.LigParGen.CM1A.ff diff --git a/polyply/data/oplsaaLigParGen/PMMA.oplsaa.LigParGen.CM1A.ff b/polyply/data/oplsaaLigParGen/PMMA.oplsaa.LigParGen.CM1A.ff new file mode 100644 index 00000000..d91bc250 --- /dev/null +++ b/polyply/data/oplsaaLigParGen/PMMA.oplsaa.LigParGen.CM1A.ff @@ -0,0 +1,294 @@ +[ moleculetype ] +PMMA 3 +[ atoms ] + 1 opls_135 1 PMMA C01 1 -0.1678 12.0110 + 2 opls_135 1 PMMA C02 2 -0.0163 12.0110 + 3 opls_135 1 PMMA C03 3 -0.2534 12.0110 + 4 opls_145 1 PMMA C04 4 0.4292 12.0110 + 5 opls_002 1 PMMA O05 5 -0.4515 15.9990 + 6 opls_179 1 PMMA O06 6 -0.3487 15.9990 + 7 opls_135 1 PMMA C07 7 -0.0634 12.0110 + 8 opls_140 1 PMMA H01 8 0.1232 1.0080 + 9 opls_140 1 PMMA H02 9 0.1232 1.0080 + 10 opls_140 1 PMMA H03 10 0.1029 1.0080 + 11 opls_140 1 PMMA H04 11 0.1029 1.0080 + 12 opls_140 1 PMMA H05 12 0.1029 1.0080 + 13 opls_140 1 PMMA H06 13 0.1056 1.0080 + 14 opls_140 1 PMMA H07 14 0.1056 1.0080 + 15 opls_140 1 PMMA H08 15 0.1056 1.0080 +[ bonds ] + 2 1 1 0.1529 224262.400 + 3 2 1 0.1529 224262.400 + 4 2 1 0.1522 265265.600 + 5 4 1 0.1229 476976.000 + 6 4 1 0.1327 179075.200 + 7 6 1 0.1410 267776.000 + 8 1 1 0.1090 284512.000 + 9 1 1 0.1090 284512.000 + 10 3 1 0.1090 284512.000 + 11 3 1 0.1090 284512.000 + 12 3 1 0.1090 284512.000 + 13 7 1 0.1090 284512.000 + 14 7 1 0.1090 284512.000 + 15 7 1 0.1090 284512.000 +[ angles ] + 1 2 3 1 112.700 488.273 + 1 2 4 1 111.100 527.184 + 2 4 5 1 120.400 669.440 + 2 4 6 1 111.400 677.808 + 4 6 7 1 116.900 694.544 + 2 3 10 1 110.700 313.800 + 2 3 11 1 110.700 313.800 + 2 3 12 1 110.700 313.800 + 6 7 13 1 109.500 292.880 + 6 7 14 1 109.500 292.880 + 6 7 15 1 109.500 292.880 + 13 7 14 1 107.800 276.144 + 5 4 6 1 123.400 694.544 + 3 2 4 1 111.100 527.184 + 10 3 11 1 107.800 276.144 + 10 3 12 1 107.800 276.144 + 2 1 8 1 110.700 313.800 + 13 7 15 1 107.800 276.144 + 11 3 12 1 107.800 276.144 + 2 1 9 1 110.700 313.800 + 14 7 15 1 107.800 276.144 + 8 1 9 1 107.800 276.144 +[ dihedrals ] + 6 4 2 5 4 180.000 43.932 2 +[ dihedrals ] + 7 6 4 2 3 31.206 -9.768 -21.439 -0.000 -0.000 0.000 + 7 6 4 5 3 21.439 0.000 -21.439 -0.000 -0.000 0.000 + 10 3 2 4 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 8 1 2 4 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 12 3 2 4 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 9 1 2 4 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 11 3 2 4 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 11 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 12 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 8 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 9 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 10 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 13 7 6 4 3 0.414 1.243 0.000 -1.657 -0.000 0.000 + 14 7 6 4 3 0.414 1.243 0.000 -1.657 -0.000 0.000 + 15 7 6 4 3 0.414 1.243 0.000 -1.657 -0.000 0.000 + 5 4 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 5 4 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 6 4 2 1 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 + 6 4 2 3 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 +[ pairs ] + 1 5 1 + 1 6 1 + 3 5 1 + 3 6 1 + 2 7 1 + 5 7 1 + 3 8 1 + 1 10 1 + 4 8 1 + 3 9 1 + 1 11 1 + 4 9 1 + 1 12 1 + 4 10 1 + 4 11 1 + 4 12 1 + 4 13 1 + 4 14 1 + 4 15 1 +[ citation ] +OPLSLigParGen1 +OPLSLigParGen2 +polyply +[ moleculetype ] +CH3a 3 +[ atoms ] + 1 opls_135 1 CH3a C1 1 -0.2565 12.0110 + 2 opls_140 1 CH3a H2 2 0.0855 1.0080 + 3 opls_140 1 CH3a H3 3 0.0855 1.0080 + 4 opls_140 1 CH3a H4 4 0.0855 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 ] + 2 1 3 1 107.800 276.144 + 3 1 4 1 107.800 276.144 + 2 1 4 1 107.800 276.144 +[ dihedrals ] +[ dihedrals ] +[ pairs ] +[ moleculetype ] +CH3b 3 +[ atoms ] + 1 opls_135 1 CH3b C1 1 -0.2553 12.0110 + 2 opls_140 1 CH3b H2 2 0.0851 1.0080 + 3 opls_140 1 CH3b H3 3 0.0851 1.0080 + 4 opls_140 1 CH3b H4 4 0.0851 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 ] + 2 1 3 1 107.800 276.144 + 3 1 4 1 107.800 276.144 + 2 1 4 1 107.800 276.144 +[ dihedrals ] +[ dihedrals ] +[ pairs ] +[link] +resname "PMMA" +[ 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"} + C02 +C01 +H01 1 110.700 313.800 {"comment":"intermonomer"} + C02 +C01 +H02 1 110.700 313.800 {"comment":"intermonomer"} + C03 C02 +C01 1 112.700 488.273 {"comment":"intermonomer"} + C04 C02 +C01 1 111.100 527.184 {"comment":"intermonomer"} +[ dihedrals ] +[ dihedrals ] + +C04 +C02 +C01 C02 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C04 O05 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"intermonomer"} + +C01 C02 C04 O06 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C04 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C03 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C02 +C01 C02 C01 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} + +C03 +C02 +C01 C02 3 2.301 -1.464 0.837 -1.674 -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"} + H02 C01 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"} + +H01 +C01 C02 C03 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"} + +H02 +C01 C02 C01 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 +C01 3 0.628 1.883 0.000 -2.510 -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"} + H05 C03 C02 +C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"intermonomer"} +[ pairs ] + C01 +C02 1 {"comment":"intermonomer"} + C03 +C02 1 {"comment":"intermonomer"} + C02 +C03 1 {"comment":"intermonomer"} + O05 +C01 1 {"comment":"intermonomer"} + C04 +C02 1 {"comment":"intermonomer"} + C02 +C04 1 {"comment":"intermonomer"} + O06 +C01 1 {"comment":"intermonomer"} + +C01 H01 1 {"comment":"intermonomer"} + +C01 H02 1 {"comment":"intermonomer"} + C01 +H01 1 {"comment":"intermonomer"} + +C01 H03 1 {"comment":"intermonomer"} + C01 +H02 1 {"comment":"intermonomer"} + +C01 H04 1 {"comment":"intermonomer"} + C03 +H01 1 {"comment":"intermonomer"} + +C01 H05 1 {"comment":"intermonomer"} + C04 +H01 1 {"comment":"intermonomer"} + C03 +H02 1 {"comment":"intermonomer"} + C04 +H02 1 {"comment":"intermonomer"} +[link] +; for bonded terms spanning three residues +resname "PMMA" +[dihedrals] +++C01 +C02 +C01 C02 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"intermonomer"} +[pairs] + C02 ++C01 1 {"comment":"intermonomer"} +[link] +resname "CH3a|PMMA" +[ atoms ] +[ bonds ] + +C01 C1 1 0.1529 224262.400 {"comment":"alpha-C-link"} +[ angles ] + C1 +C01 +C02 1 112.700 488.273 {"comment":"alpha-C-link"} + +C01 C1 H2 1 110.700 313.800 {"comment":"alpha-C-link"} + +C01 C1 H3 1 110.700 313.800 {"comment":"alpha-C-link"} + +C01 C1 H4 1 110.700 313.800 {"comment":"alpha-C-link"} + C1 +C01 +H01 1 110.700 313.800 {"comment":"alpha-C-link"} + C1 +C01 +H02 1 110.700 313.800 {"comment":"alpha-C-link"} +[ dihedrals ] +[ dihedrals ] + +C04 +C02 +C01 C1 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"alpha-C-link"} + +C03 +C02 +C01 C1 3 2.301 -1.464 0.837 -1.674 -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"} + 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"} + +H01 +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 H4 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"} + +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"} +[ pairs ] + C1 +C03 1 {"comment":"alpha-C-link"} + C1 +C04 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"} + H2 +H01 1 {"comment":"alpha-C-link"} + H3 +H01 1 {"comment":"alpha-C-link"} + H2 +H02 1 {"comment":"alpha-C-link"} + H4 +H01 1 {"comment":"alpha-C-link"} + H3 +H02 1 {"comment":"alpha-C-link"} + H4 +H02 1 {"comment":"alpha-C-link"} +[link] +; for bonded terms spanning three residues +resname "CH3a|PMMA" +[dihedrals] +++C01 +C02 +C01 C1 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link"} +[pairs] + C1 ++C01 1 {"comment":"alpha-C-link"} +[link] +resname "PMMA|CH3b" +[ atoms ] +[ bonds ] + C1 -C02 1 0.1529 224262.400 {"comment":"beta-C-link"} +[ angles ] + -C01 -C02 C1 1 112.700 488.273 {"comment":"beta-C-link"} + -C02 C1 H2 1 110.700 313.800 {"comment":"beta-C-link"} + -C02 C1 H3 1 110.700 313.800 {"comment":"beta-C-link"} + -C02 C1 H4 1 110.700 313.800 {"comment":"beta-C-link"} + -C03 -C02 C1 1 112.700 488.273 {"comment":"beta-C-link"} + -C04 -C02 C1 1 111.100 527.184 {"comment":"beta-C-link"} +[ dihedrals ] +[ dihedrals ] + 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"} + 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"} + -H02 -C01 -C02 C1 3 0.628 1.883 0.000 -2.510 -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"} + H4 C1 -C02 -C01 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"} + H2 C1 -C02 -C03 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"} + -H05 -C03 -C02 C1 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"} + -H04 -C03 -C02 C1 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 -C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link"} +[ pairs ] + -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"} + -C01 H2 1 {"comment":"beta-C-link"} + C1 -H03 1 {"comment":"beta-C-link"} + -C01 H3 1 {"comment":"beta-C-link"} + C1 -H04 1 {"comment":"beta-C-link"} + -C03 H2 1 {"comment":"beta-C-link"} + -C01 H4 1 {"comment":"beta-C-link"} + C1 -H05 1 {"comment":"beta-C-link"} + -C04 H2 1 {"comment":"beta-C-link"} + -C03 H3 1 {"comment":"beta-C-link"} + -C04 H3 1 {"comment":"beta-C-link"} + -C03 H4 1 {"comment":"beta-C-link"} + -C04 H4 1 {"comment":"beta-C-link"} +[link] +; for bonded terms spanning three residues +resname "PMMA|CH3b" +[dihedrals] + C1 -C02 -C01 --C02 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link"} +[pairs] +--C02 C1 1 {"comment":"beta-C-link"}