diff --git a/OPLS_test.ff b/OPLS_test.ff new file mode 100644 index 0000000..31c0639 --- /dev/null +++ b/OPLS_test.ff @@ -0,0 +1,845 @@ +[ moleculetype ] +STY 3 +[ atoms ] + 1 ha 1 STY H15 65 0.13143744 1.008 + 2 c3 1 STY C0 9 -0.06796256 12.01 + 3 c3 1 STY C1 10 -0.02296256 12.01 + 4 ca 1 STY C2 11 -0.07186256 12.01 + 5 ca 1 STY C3 12 -0.12756256 12.01 + 6 ca 1 STY C4 13 -0.12856256 12.01 + 7 ca 1 STY C5 14 -0.13156156 12.01 + 8 ca 1 STY C6 15 -0.12856256 12.01 + 9 ca 1 STY C7 16 -0.12756256 12.01 +10 hc 1 STY H8 58 0.04763744 1.008 +11 hc 1 STY H9 59 0.04763744 1.008 +12 hc 1 STY H10 60 0.05713744 1.008 +13 ha 1 STY H11 61 0.13143744 1.008 +14 ha 1 STY H12 62 0.13043744 1.008 +15 ha 1 STY H13 63 0.13043744 1.008 +16 ha 1 STY H14 64 0.13043744 1.008 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H8 1 1.0962e-01 2.8891e+05 {} + C0 H9 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5147e-01 2.0410e+05 {} + C1 H10 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.3986e-01 2.9644e+05 {} + C2 C7 1 1.3986e-01 2.9644e+05 {} + C3 C4 1 1.3986e-01 2.9644e+05 {} + C3 H11 1 1.0860e-01 3.0183e+05 {} + C4 C5 1 1.3986e-01 2.9644e+05 {} + C4 H12 1 1.0860e-01 3.0183e+05 {} + C5 C6 1 1.3986e-01 2.9644e+05 {} + C5 H13 1 1.0860e-01 3.0183e+05 {} + C6 C7 1 1.3986e-01 2.9644e+05 {} + C6 H14 1 1.0860e-01 3.0183e+05 {} + C7 H15 1 1.0860e-01 3.0183e+05 {} +[ pairs ] + C0 C3 1 {} + C0 C7 1 {} + C1 C4 1 {} + C1 C6 1 {} + C1 H11 1 {} + C1 H15 1 {} + C2 C5 1 {} + C2 H8 1 {} + C2 H9 1 {} + C2 H12 1 {} + C2 H14 1 {} + C3 C6 1 {} + C3 H10 1 {} + C3 H13 1 {} + C3 H15 1 {} + C4 C7 1 {} + C4 H14 1 {} + C5 H11 1 {} + C5 H15 1 {} + C6 H12 1 {} + C7 H10 1 {} + C7 H11 1 {} + C7 H13 1 {} + H8 H10 1 {} + H9 H10 1 {} +H11 H12 1 {} +H12 H13 1 {} +H13 H14 1 {} +H14 H15 1 {} +[ angles ] + C0 C1 C2 1 1.1242e+02 5.0484e+02 {} + C0 C1 H10 1 1.0968e+02 3.6208e+02 {} + C1 C0 H8 1 1.0968e+02 3.6208e+02 {} + C1 C0 H9 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.2083e+02 5.0827e+02 {} + C1 C2 C7 1 1.2083e+02 5.0827e+02 {} + C2 C1 H10 1 1.1063e+02 3.6493e+02 {} + C2 C3 C4 1 1.2002e+02 5.3279e+02 {} + C2 C3 H11 1 1.1988e+02 3.7572e+02 {} + C2 C7 C6 1 1.2002e+02 5.3279e+02 {} + C2 C7 H15 1 1.1988e+02 3.7572e+02 {} + C3 C2 C7 1 1.2002e+02 5.3279e+02 {} + C3 C4 C5 1 1.2002e+02 5.3279e+02 {} + C3 C4 H12 1 1.1988e+02 3.7572e+02 {} + C4 C3 H11 1 1.1988e+02 3.7572e+02 {} + C4 C5 C6 1 1.2002e+02 5.3279e+02 {} + C4 C5 H13 1 1.1988e+02 3.7572e+02 {} + C5 C4 H12 1 1.1988e+02 3.7572e+02 {} + C5 C6 C7 1 1.2002e+02 5.3279e+02 {} + C5 C6 H14 1 1.1988e+02 3.7572e+02 {} + C6 C5 H13 1 1.1988e+02 3.7572e+02 {} + C6 C7 H15 1 1.1988e+02 3.7572e+02 {} + C7 C6 H14 1 1.1988e+02 3.7572e+02 {} + H8 C0 H9 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 180.00 1.00416 2 {} + C0 C1 C2 C7 9 180.00 1.00416 2 {} + C1 C2 C3 C4 9 180.00 15.16700 2 {} + C1 C2 C3 H11 9 180.00 15.16700 2 {} + C1 C2 C7 C6 9 180.00 15.16700 2 {} + C1 C2 C7 H15 9 180.00 15.16700 2 {} + C2 C1 C0 H8 9 0.00 0.65084 3 {} + C2 C1 C0 H9 9 0.00 0.65084 3 {} + C2 C3 C4 C5 9 180.00 15.16700 2 {} + C2 C3 C4 H12 9 180.00 15.16700 2 {} + C2 C7 C6 C5 9 180.00 15.16700 2 {} + C2 C7 C6 H14 9 180.00 15.16700 2 {} + C3 C2 C1 H10 9 0.00 0.00000 0 {} + C3 C2 C7 C6 9 180.00 15.16700 2 {} + C3 C2 C7 H15 9 180.00 15.16700 2 {} + C3 C4 C5 C6 9 180.00 15.16700 2 {} + C3 C4 C5 H13 9 180.00 15.16700 2 {} + C4 C3 C2 C7 9 180.00 15.16700 2 {} + C4 C5 C6 C7 9 180.00 15.16700 2 {} + C4 C5 C6 H14 9 180.00 15.16700 2 {} + C5 C4 C3 H11 9 180.00 15.16700 2 {} + C5 C6 C7 H15 9 180.00 15.16700 2 {} + C6 C5 C4 H12 9 180.00 15.16700 2 {} + C7 C2 C1 H10 9 0.00 0.00000 0 {} + C7 C2 C3 H11 9 180.00 15.16700 2 {} + C7 C6 C5 H13 9 180.00 15.16700 2 {} + H8 C0 C1 H10 9 0.00 0.50208 3 {} + H9 C0 C1 H10 9 0.00 0.50208 3 {} +H11 C3 C4 H12 9 180.00 15.16700 2 {} +H12 C4 C5 H13 9 180.00 15.16700 2 {} +H13 C5 C6 H14 9 180.00 15.16700 2 {} +H14 C6 C7 H15 9 180.00 15.16700 2 {} + C1 C3 C2 C7 4 180.00 4.60240 2 {} + C2 C4 C3 H11 4 180.00 4.60240 2 {} + C2 C6 C7 H15 4 180.00 4.60240 2 {} + C3 C5 C4 H12 4 180.00 4.60240 2 {} + C4 C6 C5 H13 4 180.00 4.60240 2 {} + C5 C7 C6 H14 4 180.00 4.60240 2 {} +[ edges ] +H15 C7 + C0 C1 + C0 H8 + C0 H9 + C1 C2 + C1 H10 + C2 C3 + C2 C7 + C3 C4 + C3 H11 + C4 C5 + C4 H12 + C5 C6 + C5 H13 + C6 C7 + C6 H14 +[ moleculetype ] +ETH 3 +[ atoms ] + 1 hc 1 ETH H4 74 0.03861682 1.008 + 2 hc 1 ETH H5 75 0.03861682 1.008 + 3 hc 1 ETH H6 76 0.03961682 1.008 + 4 hc 1 ETH H7 77 0.03961682 1.008 + 5 hc 1 ETH H8 78 0.04061682 1.008 + 6 hc 1 ETH H9 79 0.04061682 1.008 + 7 hc 1 ETH H10 80 0.03911682 1.008 + 8 hc 1 ETH H11 81 0.03911682 1.008 + 9 c3 1 ETH C0 21 -0.07848371 12.01 +10 c3 1 ETH C1 22 -0.07948355 12.01 +11 c3 1 ETH C2 23 -0.07948355 12.01 +12 c3 1 ETH C3 24 -0.07848371 12.01 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H4 1 1.0962e-01 2.8891e+05 {} + C0 H5 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5354e-01 1.9154e+05 {} + C1 H6 1 1.0962e-01 2.8891e+05 {} + C1 H7 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.5354e-01 1.9154e+05 {} + C2 H8 1 1.0962e-01 2.8891e+05 {} + C2 H9 1 1.0962e-01 2.8891e+05 {} + C3 H10 1 1.0962e-01 2.8891e+05 {} + C3 H11 1 1.0962e-01 2.8891e+05 {} +[ pairs ] + C0 C3 1 {} + C0 H8 1 {} + C0 H9 1 {} + C1 H10 1 {} + C1 H11 1 {} + C2 H4 1 {} + C2 H5 1 {} + C3 H6 1 {} + C3 H7 1 {} + H4 H6 1 {} + H4 H7 1 {} + H5 H6 1 {} + H5 H7 1 {} + H6 H8 1 {} + H6 H9 1 {} + H7 H8 1 {} + H7 H9 1 {} + H8 H10 1 {} + H8 H11 1 {} + H9 H10 1 {} + H9 H11 1 {} +[ angles ] + C0 C1 C2 1 1.1263e+02 5.0099e+02 {} + C0 C1 H6 1 1.0968e+02 3.6208e+02 {} + C0 C1 H7 1 1.0968e+02 3.6208e+02 {} + C1 C0 H4 1 1.0968e+02 3.6208e+02 {} + C1 C0 H5 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.1263e+02 5.0099e+02 {} + C1 C2 H8 1 1.0968e+02 3.6208e+02 {} + C1 C2 H9 1 1.0968e+02 3.6208e+02 {} + C2 C1 H6 1 1.0968e+02 3.6208e+02 {} + C2 C1 H7 1 1.0968e+02 3.6208e+02 {} + C2 C3 H10 1 1.0968e+02 3.6208e+02 {} + C2 C3 H11 1 1.0968e+02 3.6208e+02 {} + C3 C2 H8 1 1.0968e+02 3.6208e+02 {} + C3 C2 H9 1 1.0968e+02 3.6208e+02 {} + H4 C0 H5 1 1.0773e+02 2.9957e+02 {} + H6 C1 H7 1 1.0773e+02 2.9957e+02 {} + H8 C2 H9 1 1.0773e+02 2.9957e+02 {} +H10 C3 H11 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 0.00 2.17568 3 {} + C0 C1 C2 H8 9 0.00 0.54392 3 {} + C0 C1 C2 H9 9 0.00 0.54392 3 {} + C1 C2 C3 H10 9 0.00 0.54392 3 {} + C1 C2 C3 H11 9 0.00 0.54392 3 {} + C2 C1 C0 H4 9 0.00 0.54392 3 {} + C2 C1 C0 H5 9 0.00 0.54392 3 {} + C3 C2 C1 H6 9 0.00 0.54392 3 {} + C3 C2 C1 H7 9 0.00 0.54392 3 {} + H4 C0 C1 H6 9 0.00 0.50208 3 {} + H4 C0 C1 H7 9 0.00 0.50208 3 {} + H5 C0 C1 H6 9 0.00 0.50208 3 {} + H5 C0 C1 H7 9 0.00 0.50208 3 {} + H6 C1 C2 H8 9 0.00 0.50208 3 {} + H6 C1 C2 H9 9 0.00 0.50208 3 {} + H7 C1 C2 H8 9 0.00 0.50208 3 {} + H7 C1 C2 H9 9 0.00 0.50208 3 {} + H8 C2 C3 H10 9 0.00 0.50208 3 {} + H8 C2 C3 H11 9 0.00 0.50208 3 {} + H9 C2 C3 H10 9 0.00 0.50208 3 {} + H9 C2 C3 H11 9 0.00 0.50208 3 {} +[ edges ] + H4 C0 + H5 C0 + H6 C1 + H7 C1 + H8 C2 + H9 C2 +H10 C3 +H11 C3 + C0 C1 + C1 C2 + C2 C3 +[ moleculetype ] +BUT 3 +[ atoms ] + 1 hc 1 BUT H11 89 0.03253311 1.008 + 2 hc 1 BUT H4 82 0.04220011 1.008 + 3 hc 1 BUT H5 83 0.04220011 1.008 + 4 hc 1 BUT H6 84 0.05020011 1.008 + 5 hc 1 BUT H7 85 0.03870011 1.008 + 6 hc 1 BUT H8 86 0.03870011 1.008 + 7 hc 1 BUT H9 87 0.03253311 1.008 + 8 hc 1 BUT H10 88 0.03253311 1.008 + 9 c3 1 BUT C0 25 -0.07789996 12.01 +10 c3 1 BUT C1 26 -0.06319996 12.01 +11 c3 1 BUT C2 27 -0.07589996 12.01 +12 c3 1 BUT C3 28 -0.09259996 12.01 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H4 1 1.0962e-01 2.8891e+05 {} + C0 H5 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5354e-01 1.9154e+05 {} + C1 H6 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.5354e-01 1.9154e+05 {} + C2 H7 1 1.0962e-01 2.8891e+05 {} + C2 H8 1 1.0962e-01 2.8891e+05 {} + C3 H9 1 1.0962e-01 2.8891e+05 {} + C3 H10 1 1.0962e-01 2.8891e+05 {} + C3 H11 1 1.0962e-01 2.8891e+05 {} +[ pairs ] + C0 C3 1 {} + C0 H7 1 {} + C0 H8 1 {} + C1 H9 1 {} + C1 H10 1 {} + C1 H11 1 {} + C2 H4 1 {} + C2 H5 1 {} + C3 H6 1 {} + H4 H6 1 {} + H5 H6 1 {} + H6 H7 1 {} + H6 H8 1 {} + H7 H9 1 {} + H7 H10 1 {} + H7 H11 1 {} + H8 H9 1 {} + H8 H10 1 {} + H8 H11 1 {} +[ angles ] + C0 C1 C2 1 1.1263e+02 5.0099e+02 {} + C0 C1 H6 1 1.0968e+02 3.6208e+02 {} + C1 C0 H4 1 1.0968e+02 3.6208e+02 {} + C1 C0 H5 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.1263e+02 5.0099e+02 {} + C1 C2 H7 1 1.0968e+02 3.6208e+02 {} + C1 C2 H8 1 1.0968e+02 3.6208e+02 {} + C2 C1 H6 1 1.0968e+02 3.6208e+02 {} + C2 C3 H9 1 1.0968e+02 3.6208e+02 {} + C2 C3 H10 1 1.0968e+02 3.6208e+02 {} + C2 C3 H11 1 1.0968e+02 3.6208e+02 {} + C3 C2 H7 1 1.0968e+02 3.6208e+02 {} + C3 C2 H8 1 1.0968e+02 3.6208e+02 {} + H4 C0 H5 1 1.0773e+02 2.9957e+02 {} + H7 C2 H8 1 1.0773e+02 2.9957e+02 {} + H9 C3 H10 1 1.0773e+02 2.9957e+02 {} + H9 C3 H11 1 1.0773e+02 2.9957e+02 {} +H10 C3 H11 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 0.00 2.17568 3 {} + C0 C1 C2 H7 9 0.00 0.54392 3 {} + C0 C1 C2 H8 9 0.00 0.54392 3 {} + C1 C2 C3 H9 9 0.00 0.54392 3 {} + C1 C2 C3 H10 9 0.00 0.54392 3 {} + C1 C2 C3 H11 9 0.00 0.54392 3 {} + C2 C1 C0 H4 9 0.00 0.54392 3 {} + C2 C1 C0 H5 9 0.00 0.54392 3 {} + C3 C2 C1 H6 9 0.00 0.54392 3 {} + H4 C0 C1 H6 9 0.00 0.50208 3 {} + H5 C0 C1 H6 9 0.00 0.50208 3 {} + H6 C1 C2 H7 9 0.00 0.50208 3 {} + H6 C1 C2 H8 9 0.00 0.50208 3 {} + H7 C2 C3 H9 9 0.00 0.50208 3 {} + H7 C2 C3 H10 9 0.00 0.50208 3 {} + H7 C2 C3 H11 9 0.00 0.50208 3 {} + H8 C2 C3 H9 9 0.00 0.50208 3 {} + H8 C2 C3 H10 9 0.00 0.50208 3 {} + H8 C2 C3 H11 9 0.00 0.50208 3 {} +[ edges ] +H11 C3 + H4 C0 + H5 C0 + H6 C1 + H7 C2 + H8 C2 + H9 C3 +H10 C3 + C0 C1 + C1 C2 + C2 C3 +[ moleculetype ] +Hter 3 +[ atoms ] +1 hc 1 Hter H0 49 0.0357 1.008 +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++H8 {"resname": "STY"} ++C2 {"resname": "STY"} ++H9 {"resname": "STY"} ++C0 {"resname": "STY"} +H0 {"resname": "Hter"} ++H10 {"resname": "STY"} +[ bonds ] + +C0 H0 1 1.0962e-01 2.8891e+05 {"version": 0, "comment": "link"} +[ pairs ] + H0 +C2 1 {"version": 0, "comment": "link"} + H0 +H10 1 {"version": 1, "comment": "link"} +[ angles ] + +C1 +C0 H0 1 1.0968e+02 3.6208e+02 {"version": 0, "comment": "link"} + H0 +C0 +H9 1 1.0773e+02 2.9957e+02 {"version": 1, "comment": "link"} + H0 +C0 +H8 1 1.0773e+02 2.9957e+02 {"version": 2, "comment": "link"} +[ dihedrals ] + H0 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 0, "comment": "link"} + H0 +C0 +C1 +H10 9 0.00 0.50208 3 {"version": 1, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} +C7 {"resname": "STY"} +C1 {"resname": "STY"} ++H8 {"resname": "STY"} +H9 {"resname": "STY"} +H8 {"resname": "STY"} +C2 {"resname": "STY"} +H10 {"resname": "STY"} ++C2 {"resname": "STY"} ++H9 {"resname": "STY"} +C3 {"resname": "STY"} ++C0 {"resname": "STY"} +C0 {"resname": "STY"} ++H10 {"resname": "STY"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H8 1 {"version": 1, "comment": "link"} + C0 +H9 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H10 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H8 1 {"version": 6, "comment": "link"} + C2 +H9 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} + C7 +C0 1 {"version": 9, "comment": "link"} + +C1 H10 1 {"version": 10, "comment": "link"} + +C0 H8 1 {"version": 11, "comment": "link"} + +C0 H9 1 {"version": 12, "comment": "link"} + H10 +H8 1 {"version": 13, "comment": "link"} + H10 +H9 1 {"version": 14, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H8 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H9 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1242e+02 5.0484e+02 {"version": 4, "comment": "link"} + +C0 C1 H10 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H10 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 0.65084 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H8 9 0.00 0.65084 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H9 9 0.00 0.65084 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 180.00 1.00416 2 {"version": 8, "comment": "link"} + C7 C2 C1 +C0 9 180.00 1.00416 2 {"version": 9, "comment": "link"} + +C1 +C0 C1 H10 9 0.00 0.54392 3 {"version": 10, "comment": "link"} + +C0 C1 C0 H8 9 0.00 0.54392 3 {"version": 11, "comment": "link"} + +C0 C1 C0 H9 9 0.00 0.54392 3 {"version": 12, "comment": "link"} + H10 C1 +C0 +H8 9 0.00 0.50208 3 {"version": 13, "comment": "link"} + H10 C1 +C0 +H9 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "ETH"} ++H6 {"resname": "ETH"} +C1 {"resname": "STY"} +C7 {"resname": "STY"} +H9 {"resname": "STY"} +H8 {"resname": "STY"} +C2 {"resname": "STY"} +H10 {"resname": "STY"} ++H4 {"resname": "ETH"} ++H5 {"resname": "ETH"} ++C2 {"resname": "ETH"} +C3 {"resname": "STY"} ++C0 {"resname": "ETH"} +C0 {"resname": "STY"} ++H7 {"resname": "ETH"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H4 1 {"version": 1, "comment": "link"} + C0 +H5 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H6 1 {"version": 4, "comment": "link"} + C1 +H7 1 {"version": 5, "comment": "link"} + C2 +C1 1 {"version": 6, "comment": "link"} + C2 +H4 1 {"version": 7, "comment": "link"} + C2 +H5 1 {"version": 8, "comment": "link"} + C3 +C0 1 {"version": 9, "comment": "link"} + C7 +C0 1 {"version": 10, "comment": "link"} ++C0 H8 1 {"version": 11, "comment": "link"} ++C0 H9 1 {"version": 12, "comment": "link"} ++C1 H10 1 {"version": 13, "comment": "link"} +H10 +H4 1 {"version": 14, "comment": "link"} +H10 +H5 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1242e+02 5.0484e+02 {"version": 4, "comment": "link"} ++C0 C1 H10 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C1 +C0 +C1 +H7 9 0.00 0.54392 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 0.65084 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H4 9 0.00 0.65084 3 {"version": 7, "comment": "link"} + C2 C1 +C0 +H5 9 0.00 0.65084 3 {"version": 8, "comment": "link"} + C3 C2 C1 +C0 9 180.00 1.00416 2 {"version": 9, "comment": "link"} + C7 C2 C1 +C0 9 180.00 1.00416 2 {"version": 10, "comment": "link"} ++C0 C1 C0 H8 9 0.00 0.54392 3 {"version": 11, "comment": "link"} ++C0 C1 C0 H9 9 0.00 0.54392 3 {"version": 12, "comment": "link"} ++C1 +C0 C1 H10 9 0.00 0.54392 3 {"version": 13, "comment": "link"} +H10 C1 +C0 +H4 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +H10 C1 +C0 +H5 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "ETH"} ++H6 {"resname": "ETH"} +C1 {"resname": "ETH"} +H9 {"resname": "ETH"} +H8 {"resname": "ETH"} +C2 {"resname": "ETH"} +H10 {"resname": "ETH"} ++H4 {"resname": "ETH"} +H11 {"resname": "ETH"} ++H5 {"resname": "ETH"} ++C2 {"resname": "ETH"} +C3 {"resname": "ETH"} ++C0 {"resname": "ETH"} ++H7 {"resname": "ETH"} +[ bonds ] + C3 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C1 +C0 1 {"version": 0, "comment": "link"} + C2 +C1 1 {"version": 1, "comment": "link"} + C2 +H4 1 {"version": 2, "comment": "link"} + C2 +H5 1 {"version": 3, "comment": "link"} + C3 +C2 1 {"version": 4, "comment": "link"} + C3 +H6 1 {"version": 5, "comment": "link"} + C3 +H7 1 {"version": 6, "comment": "link"} ++C0 H8 1 {"version": 7, "comment": "link"} ++C0 H9 1 {"version": 8, "comment": "link"} ++C1 H10 1 {"version": 9, "comment": "link"} ++C1 H11 1 {"version": 10, "comment": "link"} +H10 +H4 1 {"version": 11, "comment": "link"} +H10 +H5 1 {"version": 12, "comment": "link"} +H11 +H4 1 {"version": 13, "comment": "link"} +H11 +H5 1 {"version": 14, "comment": "link"} +[ angles ] + C2 C3 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C3 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C3 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C3 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} ++C0 C3 H10 1 1.0968e+02 3.6208e+02 {"version": 4, "comment": "link"} ++C0 C3 H11 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C1 C2 C3 +C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C2 C3 +C0 +C1 9 0.00 2.17568 3 {"version": 1, "comment": "link"} + C2 C3 +C0 +H4 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C2 C3 +C0 +H5 9 0.00 0.54392 3 {"version": 3, "comment": "link"} + C3 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 4, "comment": "link"} + C3 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 5, "comment": "link"} + C3 +C0 +C1 +H7 9 0.00 0.54392 3 {"version": 6, "comment": "link"} ++C0 C3 C2 H8 9 0.00 0.54392 3 {"version": 7, "comment": "link"} ++C0 C3 C2 H9 9 0.00 0.54392 3 {"version": 8, "comment": "link"} ++C1 +C0 C3 H10 9 0.00 0.54392 3 {"version": 9, "comment": "link"} ++C1 +C0 C3 H11 9 0.00 0.54392 3 {"version": 10, "comment": "link"} +H10 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 11, "comment": "link"} +H10 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 12, "comment": "link"} +H11 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 13, "comment": "link"} +H11 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "BUT"} ++H6 {"resname": "BUT"} +C1 {"resname": "ETH"} +H9 {"resname": "ETH"} +H8 {"resname": "ETH"} +C2 {"resname": "ETH"} +H10 {"resname": "ETH"} ++H4 {"resname": "BUT"} +H11 {"resname": "ETH"} ++H5 {"resname": "BUT"} ++C2 {"resname": "BUT"} +C3 {"resname": "ETH"} ++C0 {"resname": "BUT"} +[ bonds ] + C3 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C1 +C0 1 {"version": 0, "comment": "link"} + C2 +C1 1 {"version": 1, "comment": "link"} + C2 +H4 1 {"version": 2, "comment": "link"} + C2 +H5 1 {"version": 3, "comment": "link"} + C3 +C2 1 {"version": 4, "comment": "link"} + C3 +H6 1 {"version": 5, "comment": "link"} ++C0 H8 1 {"version": 6, "comment": "link"} ++C0 H9 1 {"version": 7, "comment": "link"} ++C1 H10 1 {"version": 8, "comment": "link"} ++C1 H11 1 {"version": 9, "comment": "link"} +H10 +H4 1 {"version": 10, "comment": "link"} +H10 +H5 1 {"version": 11, "comment": "link"} +H11 +H4 1 {"version": 12, "comment": "link"} +H11 +H5 1 {"version": 13, "comment": "link"} +[ angles ] + C2 C3 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C3 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C3 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C3 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} ++C0 C3 H10 1 1.0968e+02 3.6208e+02 {"version": 4, "comment": "link"} ++C0 C3 H11 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C1 C2 C3 +C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C2 C3 +C0 +C1 9 0.00 2.17568 3 {"version": 1, "comment": "link"} + C2 C3 +C0 +H4 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C2 C3 +C0 +H5 9 0.00 0.54392 3 {"version": 3, "comment": "link"} + C3 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 4, "comment": "link"} + C3 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 5, "comment": "link"} ++C0 C3 C2 H8 9 0.00 0.54392 3 {"version": 6, "comment": "link"} ++C0 C3 C2 H9 9 0.00 0.54392 3 {"version": 7, "comment": "link"} ++C1 +C0 C3 H10 9 0.00 0.54392 3 {"version": 8, "comment": "link"} ++C1 +C0 C3 H11 9 0.00 0.54392 3 {"version": 9, "comment": "link"} +H10 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 10, "comment": "link"} +H10 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 11, "comment": "link"} +H11 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 12, "comment": "link"} +H11 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 13, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "BUT"} ++H6 {"resname": "BUT"} +C1 {"resname": "BUT"} +H5 {"resname": "BUT"} +H8 {"resname": "BUT"} +C2 {"resname": "BUT"} +H6 {"resname": "BUT"} ++H4 {"resname": "BUT"} ++H5 {"resname": "BUT"} ++C2 {"resname": "BUT"} +C3 {"resname": "BUT"} ++C0 {"resname": "BUT"} +C0 {"resname": "BUT"} +H7 {"resname": "BUT"} +H4 {"resname": "BUT"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H4 1 {"version": 1, "comment": "link"} + C0 +H5 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H6 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H4 1 {"version": 6, "comment": "link"} + C2 +H5 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} ++C0 H4 1 {"version": 9, "comment": "link"} ++C0 H5 1 {"version": 10, "comment": "link"} ++C0 H7 1 {"version": 11, "comment": "link"} ++C0 H8 1 {"version": 12, "comment": "link"} ++C1 H6 1 {"version": 13, "comment": "link"} + H6 +H4 1 {"version": 14, "comment": "link"} + H6 +H5 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 4, "comment": "link"} ++C0 C1 H6 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 0.00 2.17568 3 {"version": 8, "comment": "link"} ++C0 C1 C0 H4 9 0.00 0.54392 3 {"version": 9, "comment": "link"} ++C0 C1 C0 H5 9 0.00 0.54392 3 {"version": 10, "comment": "link"} ++C0 C1 C2 H7 9 0.00 0.54392 3 {"version": 11, "comment": "link"} ++C0 C1 C2 H8 9 0.00 0.54392 3 {"version": 12, "comment": "link"} ++C1 +C0 C1 H6 9 0.00 0.54392 3 {"version": 13, "comment": "link"} + H6 C1 +C0 +H4 9 0.00 0.50208 3 {"version": 14, "comment": "link"} + H6 C1 +C0 +H5 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} +C1 {"resname": "BUT"} ++H8 {"resname": "STY"} +H5 {"resname": "BUT"} +H8 {"resname": "BUT"} +C2 {"resname": "BUT"} +H6 {"resname": "BUT"} ++C2 {"resname": "STY"} ++H9 {"resname": "STY"} +C3 {"resname": "BUT"} ++C0 {"resname": "STY"} +C0 {"resname": "BUT"} +H7 {"resname": "BUT"} ++H10 {"resname": "STY"} +H4 {"resname": "BUT"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H8 1 {"version": 1, "comment": "link"} + C0 +H9 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H10 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H8 1 {"version": 6, "comment": "link"} + C2 +H9 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} + +C0 H4 1 {"version": 9, "comment": "link"} + +C0 H5 1 {"version": 10, "comment": "link"} + +C0 H7 1 {"version": 11, "comment": "link"} + +C0 H8 1 {"version": 12, "comment": "link"} + +C1 H6 1 {"version": 13, "comment": "link"} + H6 +H8 1 {"version": 14, "comment": "link"} + H6 +H9 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H8 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H9 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 4, "comment": "link"} + +C0 C1 H6 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H10 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 0.00 2.17568 3 {"version": 8, "comment": "link"} + +C0 C1 C0 H4 9 0.00 0.54392 3 {"version": 9, "comment": "link"} + +C0 C1 C0 H5 9 0.00 0.54392 3 {"version": 10, "comment": "link"} + +C0 C1 C2 H7 9 0.00 0.54392 3 {"version": 11, "comment": "link"} + +C0 C1 C2 H8 9 0.00 0.54392 3 {"version": 12, "comment": "link"} + +C1 +C0 C1 H6 9 0.00 0.54392 3 {"version": 13, "comment": "link"} + H6 C1 +C0 +H8 9 0.00 0.50208 3 {"version": 14, "comment": "link"} + H6 C1 +C0 +H9 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++H0 {"resname": "Hter"} +C7 {"resname": "STY"} +C1 {"resname": "STY"} +H9 {"resname": "STY"} +H8 {"resname": "STY"} +C2 {"resname": "STY"} +H10 {"resname": "STY"} +C3 {"resname": "STY"} +C0 {"resname": "STY"} +[ bonds ] + C1 +H0 1 1.0962e-01 2.8891e+05 {"version": 0, "comment": "link"} +[ pairs ] + C3 +H0 1 {"version": 0, "comment": "link"} + C7 +H0 1 {"version": 1, "comment": "link"} + H8 +H0 1 {"version": 2, "comment": "link"} + H9 +H0 1 {"version": 3, "comment": "link"} +[ angles ] + C0 C1 +H0 1 1.0968e+02 3.6208e+02 {"version": 0, "comment": "link"} + C2 C1 +H0 1 1.1063e+02 3.6493e+02 {"version": 1, "comment": "link"} ++H0 C1 H10 1 1.0773e+02 2.9957e+02 {"version": 2, "comment": "link"} +[ dihedrals ] + C3 C2 C1 +H0 9 0.00 0.00000 0 {"version": 0, "comment": "link"} + C7 C2 C1 +H0 9 0.00 0.00000 0 {"version": 1, "comment": "link"} + H8 C0 C1 +H0 9 0.00 0.50208 3 {"version": 2, "comment": "link"} + H9 C0 C1 +H0 9 0.00 0.50208 3 {"version": 3, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +C1 {"resname": "STY"} +++C0 {"resname": "ETH"} +[ pairs ] + C1 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +C3 {"resname": "ETH"} +++C0 {"resname": "BUT"} +[ pairs ] + C3 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +C1 {"resname": "BUT"} +++C0 {"resname": "STY"} +[ pairs ] + C1 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++H0 {"resname": "Hter"} +C1 {"resname": "STY"} +[ pairs ] + C1 ++H0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +H0 {"resname": "Hter"} +++C0 {"resname": "STY"} +[ pairs ] + H0 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +C1 {"resname": "STY"} +++C0 {"resname": "ETH"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +C3 {"resname": "ETH"} ++C0 {"resname": "BUT"} +++C0 {"resname": "BUT"} ++C1 {"resname": "BUT"} +[ dihedrals ] + C3 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "BUT"} ++C0 {"resname": "BUT"} +C1 {"resname": "BUT"} +++C0 {"resname": "STY"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +C1 {"resname": "BUT"} +++C0 {"resname": "STY"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +C1 {"resname": "STY"} +++H0 {"resname": "Hter"} +[ dihedrals ] + C1 +C0 +C1 ++H0 9 0.00 0.54392 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +H0 {"resname": "Hter"} +++C0 {"resname": "STY"} +[ dihedrals ] + H0 +C0 +C1 ++C0 9 0.00 0.54392 3 {"version": 0, "comment": "link"} +[ edges ] diff --git a/assets/coord.pdb b/assets/coord.pdb new file mode 100644 index 0000000..8da0ded --- /dev/null +++ b/assets/coord.pdb @@ -0,0 +1,237 @@ +TITLE smiles_molecule +REMARK THIS IS A SIMULATION BOX +CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 H0 Hter 1 45.730 44.240 58.780 1.00 0.00 +ATOM 2 H15 STY 2 45.720 46.620 55.960 1.00 0.00 +ATOM 3 C0 STY 2 45.780 45.080 58.070 1.00 0.00 +ATOM 4 C1 STY 2 45.350 46.400 58.750 1.00 0.00 +ATOM 5 C2 STY 2 45.460 47.650 57.870 1.00 0.00 +ATOM 6 C3 STY 2 45.390 48.920 58.470 1.00 0.00 +ATOM 7 C4 STY 2 45.480 50.090 57.710 1.00 0.00 +ATOM 8 C5 STY 2 45.660 50.010 56.320 1.00 0.00 +ATOM 9 C6 STY 2 45.750 48.750 55.700 1.00 0.00 +ATOM 10 C7 STY 2 45.650 47.580 56.470 1.00 0.00 +ATOM 11 H8 STY 2 46.810 45.150 57.710 1.00 0.00 +ATOM 12 H9 STY 2 45.140 44.830 57.220 1.00 0.00 +ATOM 13 H10 STY 2 46.090 46.530 59.550 1.00 0.00 +ATOM 14 H11 STY 2 45.250 49.010 59.550 1.00 0.00 +ATOM 15 H12 STY 2 45.410 51.070 58.190 1.00 0.00 +ATOM 16 H13 STY 2 45.740 50.920 55.720 1.00 0.00 +ATOM 17 H14 STY 2 45.900 48.690 54.630 1.00 0.00 +ATOM 18 H15 STY 3 42.700 45.860 55.920 1.00 0.00 +ATOM 19 C0 STY 3 43.990 46.280 59.520 1.00 0.00 +ATOM 20 C1 STY 3 42.650 46.180 58.720 1.00 0.00 +ATOM 21 C2 STY 3 42.570 44.900 57.870 1.00 0.00 +ATOM 22 C3 STY 3 42.460 43.660 58.530 1.00 0.00 +ATOM 23 C4 STY 3 42.390 42.460 57.800 1.00 0.00 +ATOM 24 C5 STY 3 42.420 42.490 56.390 1.00 0.00 +ATOM 25 C6 STY 3 42.530 43.720 55.730 1.00 0.00 +ATOM 26 C7 STY 3 42.600 44.920 56.460 1.00 0.00 +ATOM 27 H8 STY 3 44.050 45.400 60.170 1.00 0.00 +ATOM 28 H9 STY 3 43.920 47.120 60.220 1.00 0.00 +ATOM 29 H10 STY 3 41.870 46.060 59.490 1.00 0.00 +ATOM 30 H11 STY 3 42.430 43.620 59.610 1.00 0.00 +ATOM 31 H12 STY 3 42.300 41.510 58.320 1.00 0.00 +ATOM 32 H13 STY 3 42.360 41.570 55.830 1.00 0.00 +ATOM 33 H14 STY 3 42.550 43.750 54.640 1.00 0.00 +ATOM 34 H4 ETH 4 41.320 47.240 57.360 1.00 0.00 +ATOM 35 H5 ETH 4 42.980 47.780 57.240 1.00 0.00 +ATOM 36 H6 ETH 4 42.680 48.830 59.580 1.00 0.00 +ATOM 37 H7 ETH 4 40.980 48.390 59.480 1.00 0.00 +ATOM 38 H8 ETH 4 42.520 50.350 57.680 1.00 0.00 +ATOM 39 H9 ETH 4 40.900 49.770 57.280 1.00 0.00 +ATOM 40 H10 ETH 4 40.670 51.930 58.360 1.00 0.00 +ATOM 41 H11 ETH 4 40.000 50.690 59.390 1.00 0.00 +ATOM 42 C0 ETH 4 42.210 47.470 57.960 1.00 0.00 +ATOM 43 C1 ETH 4 41.860 48.660 58.880 1.00 0.00 +ATOM 44 C2 ETH 4 41.580 49.980 58.120 1.00 0.00 +ATOM 45 C3 ETH 4 40.950 51.080 59.000 1.00 0.00 +ATOM 46 H4 ETH 5 42.630 50.880 60.400 1.00 0.00 +ATOM 47 H5 ETH 5 42.370 52.490 59.800 1.00 0.00 +ATOM 48 H6 ETH 5 40.290 52.710 61.190 1.00 0.00 +ATOM 49 H7 ETH 5 41.750 52.480 62.140 1.00 0.00 +ATOM 50 H8 ETH 5 39.760 51.200 62.990 1.00 0.00 +ATOM 51 H9 ETH 5 39.740 50.240 61.520 1.00 0.00 +ATOM 52 H10 ETH 5 42.170 49.530 62.120 1.00 0.00 +ATOM 53 H11 ETH 5 41.900 50.280 63.680 1.00 0.00 +ATOM 54 C0 ETH 5 41.840 51.600 60.160 1.00 0.00 +ATOM 55 C1 ETH 5 41.070 51.970 61.450 1.00 0.00 +ATOM 56 C2 ETH 5 40.400 50.790 62.200 1.00 0.00 +ATOM 57 C3 ETH 5 41.390 49.790 62.840 1.00 0.00 +ATOM 58 H11 BUT 6 37.090 48.190 65.730 1.00 0.00 +ATOM 59 H4 BUT 6 41.600 47.820 63.670 1.00 0.00 +ATOM 60 H5 BUT 6 40.330 47.950 62.460 1.00 0.00 +ATOM 61 H6 BUT 6 39.920 49.490 65.000 1.00 0.00 +ATOM 62 H7 BUT 6 38.200 49.470 63.170 1.00 0.00 +ATOM 63 H8 BUT 6 37.960 47.760 63.410 1.00 0.00 +ATOM 64 H9 BUT 6 37.450 49.920 65.540 1.00 0.00 +ATOM 65 H10 BUT 6 36.210 49.150 64.530 1.00 0.00 +ATOM 66 C0 BUT 6 40.770 48.450 63.330 1.00 0.00 +ATOM 67 C1 BUT 6 39.700 48.550 64.470 1.00 0.00 +ATOM 68 C2 BUT 6 38.250 48.680 63.930 1.00 0.00 +ATOM 69 C3 BUT 6 37.190 49.010 65.000 1.00 0.00 +ATOM 70 H11 BUT 7 39.860 43.220 64.400 1.00 0.00 +ATOM 71 H4 BUT 7 40.910 47.370 65.840 1.00 0.00 +ATOM 72 H5 BUT 7 39.350 47.810 66.470 1.00 0.00 +ATOM 73 H6 BUT 7 38.230 46.090 65.110 1.00 0.00 +ATOM 74 H7 BUT 7 39.650 45.990 63.130 1.00 0.00 +ATOM 75 H8 BUT 7 41.030 45.410 64.060 1.00 0.00 +ATOM 76 H9 BUT 7 38.430 43.860 63.530 1.00 0.00 +ATOM 77 H10 BUT 7 39.970 43.630 62.680 1.00 0.00 +ATOM 78 C0 BUT 7 39.860 47.440 65.570 1.00 0.00 +ATOM 79 C1 BUT 7 39.310 46.000 65.280 1.00 0.00 +ATOM 80 C2 BUT 7 39.940 45.370 63.990 1.00 0.00 +ATOM 81 C3 BUT 7 39.520 43.930 63.640 1.00 0.00 +ATOM 82 H15 STY 8 38.210 45.570 69.170 1.00 0.00 +ATOM 83 C0 STY 8 39.520 45.090 66.530 1.00 0.00 +ATOM 84 C1 STY 8 38.370 44.070 66.800 1.00 0.00 +ATOM 85 C2 STY 8 37.140 44.680 67.500 1.00 0.00 +ATOM 86 C3 STY 8 35.860 44.480 66.940 1.00 0.00 +ATOM 87 C4 STY 8 34.720 45.000 67.570 1.00 0.00 +ATOM 88 C5 STY 8 34.830 45.710 68.770 1.00 0.00 +ATOM 89 C6 STY 8 36.100 45.910 69.340 1.00 0.00 +ATOM 90 C7 STY 8 37.250 45.400 68.700 1.00 0.00 +ATOM 91 H8 STY 8 40.470 44.550 66.420 1.00 0.00 +ATOM 92 H9 STY 8 39.650 45.720 67.420 1.00 0.00 +ATOM 93 H10 STY 8 38.020 43.730 65.820 1.00 0.00 +ATOM 94 H11 STY 8 35.750 43.930 66.010 1.00 0.00 +ATOM 95 H12 STY 8 33.740 44.830 67.130 1.00 0.00 +ATOM 96 H13 STY 8 33.950 46.100 69.260 1.00 0.00 +ATOM 97 H14 STY 8 36.200 46.460 70.270 1.00 0.00 +ATOM 98 H15 STY 9 38.650 43.990 71.190 1.00 0.00 +ATOM 99 C0 STY 9 38.840 42.760 67.490 1.00 0.00 +ATOM 100 C1 STY 9 39.590 42.910 68.840 1.00 0.00 +ATOM 101 C2 STY 9 38.890 42.200 70.000 1.00 0.00 +ATOM 102 C3 STY 9 38.670 40.810 69.940 1.00 0.00 +ATOM 103 C4 STY 9 38.040 40.140 71.010 1.00 0.00 +ATOM 104 C5 STY 9 37.620 40.870 72.140 1.00 0.00 +ATOM 105 C6 STY 9 37.850 42.250 72.200 1.00 0.00 +ATOM 106 C7 STY 9 38.480 42.920 71.130 1.00 0.00 +ATOM 107 H8 STY 9 37.970 42.110 67.620 1.00 0.00 +ATOM 108 H9 STY 9 39.500 42.230 66.790 1.00 0.00 +ATOM 109 H10 STY 9 40.600 42.480 68.730 1.00 0.00 +ATOM 110 H11 STY 9 38.990 40.240 69.070 1.00 0.00 +ATOM 111 H12 STY 9 37.860 39.070 70.950 1.00 0.00 +ATOM 112 H13 STY 9 37.130 40.360 72.960 1.00 0.00 +ATOM 113 H14 STY 9 37.530 42.820 73.070 1.00 0.00 +ATOM 114 H0 Hter 10 39.760 43.960 69.080 1.00 0.00 +TER +ENDMDL +CONECT 3 4 +CONECT 3 11 +CONECT 3 12 +CONECT 4 5 +CONECT 4 13 +CONECT 5 6 +CONECT 5 10 +CONECT 6 7 +CONECT 6 14 +CONECT 7 8 +CONECT 7 15 +CONECT 8 9 +CONECT 8 16 +CONECT 9 10 +CONECT 9 17 +CONECT 10 2 +CONECT 19 20 +CONECT 19 27 +CONECT 19 28 +CONECT 20 21 +CONECT 20 29 +CONECT 21 22 +CONECT 21 26 +CONECT 22 23 +CONECT 22 30 +CONECT 23 24 +CONECT 23 31 +CONECT 24 25 +CONECT 24 32 +CONECT 25 26 +CONECT 25 33 +CONECT 26 18 +CONECT 42 43 +CONECT 42 34 +CONECT 42 35 +CONECT 43 44 +CONECT 43 36 +CONECT 43 37 +CONECT 44 45 +CONECT 44 38 +CONECT 44 39 +CONECT 45 40 +CONECT 45 41 +CONECT 54 55 +CONECT 54 46 +CONECT 54 47 +CONECT 55 56 +CONECT 55 48 +CONECT 55 49 +CONECT 56 57 +CONECT 56 50 +CONECT 56 51 +CONECT 57 52 +CONECT 57 53 +CONECT 66 67 +CONECT 66 59 +CONECT 66 60 +CONECT 67 68 +CONECT 67 61 +CONECT 68 69 +CONECT 68 62 +CONECT 68 63 +CONECT 69 64 +CONECT 69 65 +CONECT 69 58 +CONECT 78 79 +CONECT 78 71 +CONECT 78 72 +CONECT 79 80 +CONECT 79 73 +CONECT 80 81 +CONECT 80 74 +CONECT 80 75 +CONECT 81 76 +CONECT 81 77 +CONECT 81 70 +CONECT 83 84 +CONECT 83 91 +CONECT 83 92 +CONECT 84 85 +CONECT 84 93 +CONECT 85 86 +CONECT 85 90 +CONECT 86 87 +CONECT 86 94 +CONECT 87 88 +CONECT 87 95 +CONECT 88 89 +CONECT 88 96 +CONECT 89 90 +CONECT 89 97 +CONECT 90 82 +CONECT 99 100 +CONECT 99 107 +CONECT 99 108 +CONECT 100 101 +CONECT 100 109 +CONECT 101 102 +CONECT 101 106 +CONECT 102 103 +CONECT 102 110 +CONECT 103 104 +CONECT 103 111 +CONECT 104 105 +CONECT 104 112 +CONECT 105 106 +CONECT 105 113 +CONECT 106 98 +CONECT 3 1 +CONECT 4 19 +CONECT 84 99 +CONECT 20 42 +CONECT 45 54 +CONECT 57 66 +CONECT 67 78 +CONECT 79 83 +CONECT 100 114 diff --git a/assets/md.mdp b/assets/md.mdp new file mode 100755 index 0000000..783ea5c --- /dev/null +++ b/assets/md.mdp @@ -0,0 +1,119 @@ +;------------------------------------------------------------------------------------------------------------------------------------------------- +; Author : F. Grunewald +; Last Edited : 07.01.2021 +; Force-Field : OPLS +; Solvent : TIP4P Water +; References : from virtualchemistry.org +; +;------------------------------------------------------------------------------------------------------------------------------------------------- + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe +include = +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) +define = + + +; RUN CONTROL PARAMETERS +; -------------------------------------------------------------------------------------------------------------------------------------------------- +integrator = md ; for equilibriation this is OK +tinit = 0 ; default +dt = 0.002 ; [1] +nsteps = 1000000 ; 8 ns of sampleing time +init-step = 0 ; default +simulation-part = 1 ; defualt +comm-mode = Linear ; default +nstcomm = 100 ; [1] +comm-grps = system ; [1] + +; OUTPUT CONTROL OPTIONS +; -------------------------------------------------------------------------------------------------------------------------------------------- +nstxout = 0 +nstvout = 0 +nstfout = 0 +nstlog = 0 +nstcalcenergy = 100 +nstenergy = 100 +nstxout-compressed = 1000 +compressed-x-precision = 1000 +compressed-x-grps = + + +; NEIGHBORSEARCHING PARAMETERS +; ------------------------------------------------------------------------------------------------------------------------------------------------- +cutoff-scheme = verlet ; should be faster at same accuracy +nstlist = 5 ; [1] +ns_type = grid ; default +pbc = xyz ; [1] +periodic-molecules = no +verlet-buffer-tolerance = 1e-6 ; non-default but should improve accuracy +rlist = 1.1 ; default + + +; OPTIONS FOR ELECTROSTATICS AND VDW +; ----------------------------------------------------------------------------------------------------------------------------------------------- +coulombtype = cutoff ; [1] +coulomb-modifier = Potential-shift-Verlet ; +rcoulomb-switch = 0 +rcoulomb = 3 +epsilon-r = 1 +epsilon-rf = 1 +vdw-type = cut-off +vdw-modifier = Potential-shift-Verlet +rvdw-switch = 0 +rvdw = 3 ; [1] +DispCorr = EnerPres +table-extension = 1 +energygrp-table = +fourierspacing = 0.1 +fourier-nx = 0 +fourier-ny = 0 +fourier-nz = 0 +pme_order = 4 +ewald_rtol = 1e-05 +ewald_rtol_lj = 1e-03 +lj-pme-comb-rule = geometric +ewald_geometry = 3d +epsilon_surface = 0 + + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; --------------------------------------------------------------------------------------------------------------------------------------------- +tcoupl = v_rescale ; We equilibriate so this is good enough +nsttcouple = 5 ; default +nh-chain-length = 10 ; N/A +print-nose-hoover-chain-variables = no ; N/A +tc-grps = system ; For small molecules OK +tau-t = 0.1 ; N/A overwritten by SD +ref-t = 298.15 ; standard condition +pcoupl = no +pcoupltype = isotropic ; We equilibriate so this is good enough +nstpcouple = 2 +tau-p = 1 +compressibility = 4.5e-5 +ref-p = 1 +refcoord-scaling = No + +; GENERATE VELOCITIES FOR STARTUP RUN +; --------------------------------------------------------------------------------------------------------------------------------------------- +gen-vel = yes ; for free energy stuff we don't want this +gen-temp = 298.15 ; N/A +gen-seed = -1 ; N/A + +; OPTIONS FOR BONDS +; --------------------------------------------------------------------------------------------------------------------------------------------- +constraints = None ; [1] water is done via shake +; Type of constraint algorithm +constraint-algorithm = Lincs ; default +continuation = no ; default +Shake-SOR = no ; default +shake-tol = 0.0001 ; default also same as in [1] +lincs-order = 4 ; default +lincs-iter = 1 ; default +lincs-warnangle = 90 ; default +morse = no ; default + +; Free energy variables +;---------------------------------------------------------------------------------------------------------------------------------------------- +free-energy = no ; only for equilibriation diff --git a/assets/smiles_molecule_GMX_OPLS.top b/assets/smiles_molecule_GMX_OPLS.top index 69ca63d..5cd6a4a 100644 --- a/assets/smiles_molecule_GMX_OPLS.top +++ b/assets/smiles_molecule_GMX_OPLS.top @@ -1,7 +1,7 @@ ; smiles_molecule_GMX_OPLS.top created by acpype (v: 2023.10.27) on Wed Nov 20 16:42:24 2024 ; Include forcefield parameters -#include forcefield.itp +#include "forcefield.itp" ; Include smiles_molecule_GMX.itp topology #include "smiles_molecule_GMX.itp" diff --git a/check.sh b/check.sh new file mode 100644 index 0000000..5728212 --- /dev/null +++ b/check.sh @@ -0,0 +1,2 @@ +#!/bin/bash +python compare.py -p polyply_output/polyply.top assets/smiles_molecule_GMX_OPLS.top -c assets/coord.pdb -f assets/md.mdp diff --git a/compare.py b/compare.py new file mode 100644 index 0000000..a7173cd --- /dev/null +++ b/compare.py @@ -0,0 +1,160 @@ +import sys +import os +import re +from pathlib import Path +import shutil +import numpy as np +import matplotlib.pyplot as plt +import networkx as nx +import gromacs +import vermouth +from vermouth.gmx.gro import write_gro +from vermouth.gmx.itp_read import read_itp +from vermouth.forcefield import ForceField +from vermouth.processors import MakeBonds +from polyply import gen_params +from polyply.src.graph_utils import find_one_ismags_match +from polyply.src.topology import Topology + +import gromacs.environment +gromacs.environment.flags['capture_output'] = True + +import argparse + +def _element_match(node1, node2): + """ + Checks if the element attribute of two nodes + is the same. + + Returns + -------- + bool + """ + return node1["element"] == node2["element"] + +def _is_not_digit(_str): + return not _str.isdigit() + +def align_coordinates(itp_file, ref_file, outname, polymer): + """ + Take an itp and a reference pdb file with coordinates + corresponding to the itp_file. Figure out which coordinates + belong to which atoms by using a subgraph isomorphism. + + Note the PDB file must have connect records. Order, atom names, + residue names are all ignored. + """ + # create empty system + ref_sys = vermouth.System() + # load PDB and add edges to ref molecule + vermouth.PDBInput(str(ref_file), modelidx=1).run_system(ref_sys) + MakeBonds(allow_name=False).run_system(ref_sys) + ref_mol = ref_sys.molecules[0] + # load the target molecule + top = Topology.from_gmx_topfile(itp_file, "polymer") + target_mol = top.molecules[0].molecule + #target_mol.make_edges_from_interaction_type(type_="bonds") + # assign elements to target_mol + for node in target_mol.nodes: + match = re.match(r"([a-z]+)([0-9]*)", target_mol.nodes[node]['atomname'], re.I) + element = match.groups()[0] + target_mol.nodes[node]['element'] = element + + match = find_one_ismags_match(ref_mol, target_mol, _element_match) + + for ref_node, target_node in match.items(): + target_mol.nodes[target_node]['position'] = ref_mol.nodes[ref_node]['position'] + ref_sys.molecules[0] = target_mol + # write out the matching coordinates + write_gro(ref_sys, f"./{outname}.gro", box=(10.0, 10.0, 10.0), defer_writing=False) + # convert to PDB file + gromacs.editconf(f=f"{outname}.gro", + o=f"{outname}.pdb",) + +def read_energies(filename): + with open(filename, "r") as _file: + lines = _file.readlines() + terms = [] + record = False + for line in lines: + tokens = line.strip().split() + if len(tokens) > 1 and tokens[1] == "s0": + record = True + if record and tokens[0] == "@": + terms.append(" ".join(tokens[3:])) + energies = map(float, tokens) + return dict(zip(terms, energies)) + +def read_smiles(filename): + """ + Read one or more smiles from a + file. + """ + smiles = [] + with open(filename) as _file: + for line in _file.readlines(): + smile = line.strip().split() + smiles += smile + return smiles + +def gmx_single_point(topfile, prefix, mdpfile): + """ + Compute GROMACS single point energy. + """ + gromacs.grompp(f=mdpfile, + c=f"{prefix}.pdb", + p=topfile, + o=f"{prefix}.tpr", + maxwarn=1) + gromacs.mdrun(s=f"{prefix}.tpr", + rerun=f"{prefix}.pdb", + deffnm=f"{prefix}") + gromacs.energy(f=f"{prefix}.edr", + input="1 \n 2 \n 3 \n 4 \n 5 \n 6 \n 7 \n 9", + o=f"{prefix}.xvg") + +def compute_molecule_energies(refpdb, topfiles, mdpfile, polymer): + """ + compute energies for the molecules in topfile given a single + set of refernce coordinates + """ + os.mkdir(f"comp_{polymer}") + os.chdir(f"comp_{polymer}") + print("align mol 1") + align_coordinates(topfiles[0], refpdb, "mol1", polymer) + print("align mol 2") + align_coordinates(topfiles[1], refpdb, "mol2", polymer) + # compute the energies + energies=[] + for topfile, tag in zip(topfiles, ["mol1", "mol2"]): + gmx_single_point(topfile, tag, mdpfile) + energies.append(read_energies(f"{tag}.xvg")) + return energies + +def __main__(): + + parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + ) + + parser.add_argument('-p', dest='topfiles', type=str, nargs=2, help='topology files; at most 2') + parser.add_argument('-c', dest='coordfile', type=str, help='coordinate file') + parser.add_argument('-f', dest='mdpfile', type=str, help='mdp file') + parser.add_argument('-mol', dest='molname', type=str, default='polymer', help='name of molecule') + + args = parser.parse_args() + + energies = compute_molecule_energies(Path(args.coordfile).resolve(), + [Path(top).resolve() for top in args.topfiles], + Path(args.mdpfile).resolve(), + args.molname) + + with open("energy_comp.dat", 'w') as _file: + e1 = energies[0] + e2 = energies[1] + for term in e1: + _file.write("{} {:3.8F} {:3.8F} {:3.8F}\n".format(term, e1[term], e2[term], e1[term]-e2[term])) + if np.abs(e1[term]-e2[term]) > 0.1: + print(args.molname, term, e1[term], e2[term], e1[term]-e2[term]) + +__main__() diff --git a/polyply_output/OPLS_test.ff b/polyply_output/OPLS_test.ff new file mode 100644 index 0000000..587421b --- /dev/null +++ b/polyply_output/OPLS_test.ff @@ -0,0 +1,845 @@ +[ moleculetype ] +STY 3 +[ atoms ] + 1 ha 1 STY H15 65 0.13143744 1.008 + 2 c3 1 STY C0 9 -0.06796256 12.01 + 3 c3 1 STY C1 10 -0.02296256 12.01 + 4 ca 1 STY C2 11 -0.07186256 12.01 + 5 ca 1 STY C3 12 -0.12756256 12.01 + 6 ca 1 STY C4 13 -0.12856256 12.01 + 7 ca 1 STY C5 14 -0.13156156 12.01 + 8 ca 1 STY C6 15 -0.12856256 12.01 + 9 ca 1 STY C7 16 -0.12756256 12.01 +10 hc 1 STY H8 58 0.04763744 1.008 +11 hc 1 STY H9 59 0.04763744 1.008 +12 hc 1 STY H10 60 0.05713744 1.008 +13 ha 1 STY H11 61 0.13143744 1.008 +14 ha 1 STY H12 62 0.13043744 1.008 +15 ha 1 STY H13 63 0.13043744 1.008 +16 ha 1 STY H14 64 0.13043744 1.008 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H8 1 1.0962e-01 2.8891e+05 {} + C0 H9 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5147e-01 2.0410e+05 {} + C1 H10 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.3986e-01 2.9644e+05 {} + C2 C7 1 1.3986e-01 2.9644e+05 {} + C3 C4 1 1.3986e-01 2.9644e+05 {} + C3 H11 1 1.0860e-01 3.0183e+05 {} + C4 C5 1 1.3986e-01 2.9644e+05 {} + C4 H12 1 1.0860e-01 3.0183e+05 {} + C5 C6 1 1.3986e-01 2.9644e+05 {} + C5 H13 1 1.0860e-01 3.0183e+05 {} + C6 C7 1 1.3986e-01 2.9644e+05 {} + C6 H14 1 1.0860e-01 3.0183e+05 {} + C7 H15 1 1.0860e-01 3.0183e+05 {} +[ pairs ] + C0 C3 1 {} + C0 C7 1 {} + C1 C4 1 {} + C1 C6 1 {} + C1 H11 1 {} + C1 H15 1 {} + C2 C5 1 {} + C2 H8 1 {} + C2 H9 1 {} + C2 H12 1 {} + C2 H14 1 {} + C3 C6 1 {} + C3 H10 1 {} + C3 H13 1 {} + C3 H15 1 {} + C4 C7 1 {} + C4 H14 1 {} + C5 H11 1 {} + C5 H15 1 {} + C6 H12 1 {} + C7 H10 1 {} + C7 H11 1 {} + C7 H13 1 {} + H8 H10 1 {} + H9 H10 1 {} +H11 H12 1 {} +H12 H13 1 {} +H13 H14 1 {} +H14 H15 1 {} +[ angles ] + C0 C1 C2 1 1.1242e+02 5.0484e+02 {} + C0 C1 H10 1 1.0968e+02 3.6208e+02 {} + C1 C0 H8 1 1.0968e+02 3.6208e+02 {} + C1 C0 H9 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.2083e+02 5.0827e+02 {} + C1 C2 C7 1 1.2083e+02 5.0827e+02 {} + C2 C1 H10 1 1.1063e+02 3.6493e+02 {} + C2 C3 C4 1 1.2002e+02 5.3279e+02 {} + C2 C3 H11 1 1.1988e+02 3.7572e+02 {} + C2 C7 C6 1 1.2002e+02 5.3279e+02 {} + C2 C7 H15 1 1.1988e+02 3.7572e+02 {} + C3 C2 C7 1 1.2002e+02 5.3279e+02 {} + C3 C4 C5 1 1.2002e+02 5.3279e+02 {} + C3 C4 H12 1 1.1988e+02 3.7572e+02 {} + C4 C3 H11 1 1.1988e+02 3.7572e+02 {} + C4 C5 C6 1 1.2002e+02 5.3279e+02 {} + C4 C5 H13 1 1.1988e+02 3.7572e+02 {} + C5 C4 H12 1 1.1988e+02 3.7572e+02 {} + C5 C6 C7 1 1.2002e+02 5.3279e+02 {} + C5 C6 H14 1 1.1988e+02 3.7572e+02 {} + C6 C5 H13 1 1.1988e+02 3.7572e+02 {} + C6 C7 H15 1 1.1988e+02 3.7572e+02 {} + C7 C6 H14 1 1.1988e+02 3.7572e+02 {} + H8 C0 H9 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 180.00 1.00416 2 {} + C0 C1 C2 C7 9 180.00 1.00416 2 {} + C1 C2 C3 C4 9 180.00 15.16700 2 {} + C1 C2 C3 H11 9 180.00 15.16700 2 {} + C1 C2 C7 C6 9 180.00 15.16700 2 {} + C1 C2 C7 H15 9 180.00 15.16700 2 {} + C2 C1 C0 H8 9 0.00 0.65084 3 {} + C2 C1 C0 H9 9 0.00 0.65084 3 {} + C2 C3 C4 C5 9 180.00 15.16700 2 {} + C2 C3 C4 H12 9 180.00 15.16700 2 {} + C2 C7 C6 C5 9 180.00 15.16700 2 {} + C2 C7 C6 H14 9 180.00 15.16700 2 {} + C3 C2 C1 H10 9 0.00 0.00000 0 {} + C3 C2 C7 C6 9 180.00 15.16700 2 {} + C3 C2 C7 H15 9 180.00 15.16700 2 {} + C3 C4 C5 C6 9 180.00 15.16700 2 {} + C3 C4 C5 H13 9 180.00 15.16700 2 {} + C4 C3 C2 C7 9 180.00 15.16700 2 {} + C4 C5 C6 C7 9 180.00 15.16700 2 {} + C4 C5 C6 H14 9 180.00 15.16700 2 {} + C5 C4 C3 H11 9 180.00 15.16700 2 {} + C5 C6 C7 H15 9 180.00 15.16700 2 {} + C6 C5 C4 H12 9 180.00 15.16700 2 {} + C7 C2 C1 H10 9 0.00 0.00000 0 {} + C7 C2 C3 H11 9 180.00 15.16700 2 {} + C7 C6 C5 H13 9 180.00 15.16700 2 {} + H8 C0 C1 H10 9 0.00 0.50208 3 {} + H9 C0 C1 H10 9 0.00 0.50208 3 {} +H11 C3 C4 H12 9 180.00 15.16700 2 {} +H12 C4 C5 H13 9 180.00 15.16700 2 {} +H13 C5 C6 H14 9 180.00 15.16700 2 {} +H14 C6 C7 H15 9 180.00 15.16700 2 {} + C1 C3 C2 C7 4 180.00 4.60240 2 {} + C2 C4 C3 H11 4 180.00 4.60240 2 {} + C2 C6 C7 H15 4 180.00 4.60240 2 {} + C3 C5 C4 H12 4 180.00 4.60240 2 {} + C4 C6 C5 H13 4 180.00 4.60240 2 {} + C5 C7 C6 H14 4 180.00 4.60240 2 {} +[ edges ] +H15 C7 + C0 C1 + C0 H8 + C0 H9 + C1 C2 + C1 H10 + C2 C3 + C2 C7 + C3 C4 + C3 H11 + C4 C5 + C4 H12 + C5 C6 + C5 H13 + C6 C7 + C6 H14 +[ moleculetype ] +ETH 3 +[ atoms ] + 1 hc 1 ETH H4 74 0.03861682 1.008 + 2 hc 1 ETH H5 75 0.03861682 1.008 + 3 hc 1 ETH H6 76 0.03961682 1.008 + 4 hc 1 ETH H7 77 0.03961682 1.008 + 5 hc 1 ETH H8 78 0.04061682 1.008 + 6 hc 1 ETH H9 79 0.04061682 1.008 + 7 hc 1 ETH H10 80 0.03911682 1.008 + 8 hc 1 ETH H11 81 0.03911682 1.008 + 9 c3 1 ETH C0 21 -0.07848371 12.01 +10 c3 1 ETH C1 22 -0.07948355 12.01 +11 c3 1 ETH C2 23 -0.07948355 12.01 +12 c3 1 ETH C3 24 -0.07848371 12.01 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H4 1 1.0962e-01 2.8891e+05 {} + C0 H5 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5354e-01 1.9154e+05 {} + C1 H6 1 1.0962e-01 2.8891e+05 {} + C1 H7 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.5354e-01 1.9154e+05 {} + C2 H8 1 1.0962e-01 2.8891e+05 {} + C2 H9 1 1.0962e-01 2.8891e+05 {} + C3 H10 1 1.0962e-01 2.8891e+05 {} + C3 H11 1 1.0962e-01 2.8891e+05 {} +[ pairs ] + C0 C3 1 {} + C0 H8 1 {} + C0 H9 1 {} + C1 H10 1 {} + C1 H11 1 {} + C2 H4 1 {} + C2 H5 1 {} + C3 H6 1 {} + C3 H7 1 {} + H4 H6 1 {} + H4 H7 1 {} + H5 H6 1 {} + H5 H7 1 {} + H6 H8 1 {} + H6 H9 1 {} + H7 H8 1 {} + H7 H9 1 {} + H8 H10 1 {} + H8 H11 1 {} + H9 H10 1 {} + H9 H11 1 {} +[ angles ] + C0 C1 C2 1 1.1263e+02 5.0099e+02 {} + C0 C1 H6 1 1.0968e+02 3.6208e+02 {} + C0 C1 H7 1 1.0968e+02 3.6208e+02 {} + C1 C0 H4 1 1.0968e+02 3.6208e+02 {} + C1 C0 H5 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.1263e+02 5.0099e+02 {} + C1 C2 H8 1 1.0968e+02 3.6208e+02 {} + C1 C2 H9 1 1.0968e+02 3.6208e+02 {} + C2 C1 H6 1 1.0968e+02 3.6208e+02 {} + C2 C1 H7 1 1.0968e+02 3.6208e+02 {} + C2 C3 H10 1 1.0968e+02 3.6208e+02 {} + C2 C3 H11 1 1.0968e+02 3.6208e+02 {} + C3 C2 H8 1 1.0968e+02 3.6208e+02 {} + C3 C2 H9 1 1.0968e+02 3.6208e+02 {} + H4 C0 H5 1 1.0773e+02 2.9957e+02 {} + H6 C1 H7 1 1.0773e+02 2.9957e+02 {} + H8 C2 H9 1 1.0773e+02 2.9957e+02 {} +H10 C3 H11 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 0.00 2.17568 3 {} + C0 C1 C2 H8 9 0.00 0.54392 3 {} + C0 C1 C2 H9 9 0.00 0.54392 3 {} + C1 C2 C3 H10 9 0.00 0.54392 3 {} + C1 C2 C3 H11 9 0.00 0.54392 3 {} + C2 C1 C0 H4 9 0.00 0.54392 3 {} + C2 C1 C0 H5 9 0.00 0.54392 3 {} + C3 C2 C1 H6 9 0.00 0.54392 3 {} + C3 C2 C1 H7 9 0.00 0.54392 3 {} + H4 C0 C1 H6 9 0.00 0.50208 3 {} + H4 C0 C1 H7 9 0.00 0.50208 3 {} + H5 C0 C1 H6 9 0.00 0.50208 3 {} + H5 C0 C1 H7 9 0.00 0.50208 3 {} + H6 C1 C2 H8 9 0.00 0.50208 3 {} + H6 C1 C2 H9 9 0.00 0.50208 3 {} + H7 C1 C2 H8 9 0.00 0.50208 3 {} + H7 C1 C2 H9 9 0.00 0.50208 3 {} + H8 C2 C3 H10 9 0.00 0.50208 3 {} + H8 C2 C3 H11 9 0.00 0.50208 3 {} + H9 C2 C3 H10 9 0.00 0.50208 3 {} + H9 C2 C3 H11 9 0.00 0.50208 3 {} +[ edges ] + H4 C0 + H5 C0 + H6 C1 + H7 C1 + H8 C2 + H9 C2 +H10 C3 +H11 C3 + C0 C1 + C1 C2 + C2 C3 +[ moleculetype ] +BUT 3 +[ atoms ] + 1 hc 1 BUT H11 89 0.03253311 1.008 + 2 hc 1 BUT H4 82 0.04220011 1.008 + 3 hc 1 BUT H5 83 0.04220011 1.008 + 4 hc 1 BUT H6 84 0.05020011 1.008 + 5 hc 1 BUT H7 85 0.03870011 1.008 + 6 hc 1 BUT H8 86 0.03870011 1.008 + 7 hc 1 BUT H9 87 0.03253311 1.008 + 8 hc 1 BUT H10 88 0.03253311 1.008 + 9 c3 1 BUT C0 25 -0.07789996 12.01 +10 c3 1 BUT C1 26 -0.06319996 12.01 +11 c3 1 BUT C2 27 -0.07589996 12.01 +12 c3 1 BUT C3 28 -0.09259996 12.01 +[ bonds ] + C0 C1 1 1.5354e-01 1.9154e+05 {} + C0 H4 1 1.0962e-01 2.8891e+05 {} + C0 H5 1 1.0962e-01 2.8891e+05 {} + C1 C2 1 1.5354e-01 1.9154e+05 {} + C1 H6 1 1.0962e-01 2.8891e+05 {} + C2 C3 1 1.5354e-01 1.9154e+05 {} + C2 H7 1 1.0962e-01 2.8891e+05 {} + C2 H8 1 1.0962e-01 2.8891e+05 {} + C3 H9 1 1.0962e-01 2.8891e+05 {} + C3 H10 1 1.0962e-01 2.8891e+05 {} + C3 H11 1 1.0962e-01 2.8891e+05 {} +[ pairs ] + C0 C3 1 {} + C0 H7 1 {} + C0 H8 1 {} + C1 H9 1 {} + C1 H10 1 {} + C1 H11 1 {} + C2 H4 1 {} + C2 H5 1 {} + C3 H6 1 {} + H4 H6 1 {} + H5 H6 1 {} + H6 H7 1 {} + H6 H8 1 {} + H7 H9 1 {} + H7 H10 1 {} + H7 H11 1 {} + H8 H9 1 {} + H8 H10 1 {} + H8 H11 1 {} +[ angles ] + C0 C1 C2 1 1.1263e+02 5.0099e+02 {} + C0 C1 H6 1 1.0968e+02 3.6208e+02 {} + C1 C0 H4 1 1.0968e+02 3.6208e+02 {} + C1 C0 H5 1 1.0968e+02 3.6208e+02 {} + C1 C2 C3 1 1.1263e+02 5.0099e+02 {} + C1 C2 H7 1 1.0968e+02 3.6208e+02 {} + C1 C2 H8 1 1.0968e+02 3.6208e+02 {} + C2 C1 H6 1 1.0968e+02 3.6208e+02 {} + C2 C3 H9 1 1.0968e+02 3.6208e+02 {} + C2 C3 H10 1 1.0968e+02 3.6208e+02 {} + C2 C3 H11 1 1.0968e+02 3.6208e+02 {} + C3 C2 H7 1 1.0968e+02 3.6208e+02 {} + C3 C2 H8 1 1.0968e+02 3.6208e+02 {} + H4 C0 H5 1 1.0773e+02 2.9957e+02 {} + H7 C2 H8 1 1.0773e+02 2.9957e+02 {} + H9 C3 H10 1 1.0773e+02 2.9957e+02 {} + H9 C3 H11 1 1.0773e+02 2.9957e+02 {} +H10 C3 H11 1 1.0773e+02 2.9957e+02 {} +[ dihedrals ] + C0 C1 C2 C3 9 0.00 2.17568 3 {} + C0 C1 C2 H7 9 0.00 0.54392 3 {} + C0 C1 C2 H8 9 0.00 0.54392 3 {} + C1 C2 C3 H9 9 0.00 0.54392 3 {} + C1 C2 C3 H10 9 0.00 0.54392 3 {} + C1 C2 C3 H11 9 0.00 0.54392 3 {} + C2 C1 C0 H4 9 0.00 0.54392 3 {} + C2 C1 C0 H5 9 0.00 0.54392 3 {} + C3 C2 C1 H6 9 0.00 0.54392 3 {} + H4 C0 C1 H6 9 0.00 0.50208 3 {} + H5 C0 C1 H6 9 0.00 0.50208 3 {} + H6 C1 C2 H7 9 0.00 0.50208 3 {} + H6 C1 C2 H8 9 0.00 0.50208 3 {} + H7 C2 C3 H9 9 0.00 0.50208 3 {} + H7 C2 C3 H10 9 0.00 0.50208 3 {} + H7 C2 C3 H11 9 0.00 0.50208 3 {} + H8 C2 C3 H9 9 0.00 0.50208 3 {} + H8 C2 C3 H10 9 0.00 0.50208 3 {} + H8 C2 C3 H11 9 0.00 0.50208 3 {} +[ edges ] +H11 C3 + H4 C0 + H5 C0 + H6 C1 + H7 C2 + H8 C2 + H9 C3 +H10 C3 + C0 C1 + C1 C2 + C2 C3 +[ moleculetype ] +Hter 3 +[ atoms ] +1 hc 1 Hter H0 49 0.0357 1.008 +[ edges ] +[ link ] +[ atoms ] +H0 {"resname": "Hter"} ++H8 {"resname": "STY"} ++H9 {"resname": "STY"} ++C0 {"resname": "STY"} ++H10 {"resname": "STY"} ++C1 {"resname": "STY"} ++C2 {"resname": "STY"} +[ bonds ] + +C0 H0 1 1.0962e-01 2.8891e+05 {"version": 0, "comment": "link"} +[ pairs ] + H0 +C2 1 {"version": 0, "comment": "link"} + H0 +H10 1 {"version": 1, "comment": "link"} +[ angles ] + +C1 +C0 H0 1 1.0968e+02 3.6208e+02 {"version": 0, "comment": "link"} + H0 +C0 +H9 1 1.0773e+02 2.9957e+02 {"version": 1, "comment": "link"} + H0 +C0 +H8 1 1.0773e+02 2.9957e+02 {"version": 2, "comment": "link"} +[ dihedrals ] + H0 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 0, "comment": "link"} + H0 +C0 +C1 +H10 9 0.00 0.50208 3 {"version": 1, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C2 {"resname": "STY"} +H8 {"resname": "STY"} ++H8 {"resname": "STY"} +C3 {"resname": "STY"} ++H9 {"resname": "STY"} ++C0 {"resname": "STY"} +C2 {"resname": "STY"} +C7 {"resname": "STY"} +H10 {"resname": "STY"} +H9 {"resname": "STY"} ++H10 {"resname": "STY"} ++C1 {"resname": "STY"} +C0 {"resname": "STY"} +C1 {"resname": "STY"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H8 1 {"version": 1, "comment": "link"} + C0 +H9 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H10 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H8 1 {"version": 6, "comment": "link"} + C2 +H9 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} + C7 +C0 1 {"version": 9, "comment": "link"} + +C1 H10 1 {"version": 10, "comment": "link"} + +C0 H8 1 {"version": 11, "comment": "link"} + +C0 H9 1 {"version": 12, "comment": "link"} + H10 +H8 1 {"version": 13, "comment": "link"} + H10 +H9 1 {"version": 14, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H8 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H9 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1242e+02 5.0484e+02 {"version": 4, "comment": "link"} + +C0 C1 H10 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H10 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 0.65084 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H8 9 0.00 0.65084 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H9 9 0.00 0.65084 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 180.00 1.00416 2 {"version": 8, "comment": "link"} + C7 C2 C1 +C0 9 180.00 1.00416 2 {"version": 9, "comment": "link"} + +C1 +C0 C1 H10 9 0.00 0.54392 3 {"version": 10, "comment": "link"} + +C0 C1 C0 H8 9 0.00 0.54392 3 {"version": 11, "comment": "link"} + +C0 C1 C0 H9 9 0.00 0.54392 3 {"version": 12, "comment": "link"} + H10 C1 +C0 +H8 9 0.00 0.50208 3 {"version": 13, "comment": "link"} + H10 C1 +C0 +H9 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C2 {"resname": "ETH"} +H8 {"resname": "STY"} ++H4 {"resname": "ETH"} +C3 {"resname": "STY"} ++H7 {"resname": "ETH"} ++C0 {"resname": "ETH"} ++H6 {"resname": "ETH"} +C2 {"resname": "STY"} +C7 {"resname": "STY"} +H10 {"resname": "STY"} +H9 {"resname": "STY"} ++C1 {"resname": "ETH"} ++H5 {"resname": "ETH"} +C0 {"resname": "STY"} +C1 {"resname": "STY"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H4 1 {"version": 1, "comment": "link"} + C0 +H5 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H6 1 {"version": 4, "comment": "link"} + C1 +H7 1 {"version": 5, "comment": "link"} + C2 +C1 1 {"version": 6, "comment": "link"} + C2 +H4 1 {"version": 7, "comment": "link"} + C2 +H5 1 {"version": 8, "comment": "link"} + C3 +C0 1 {"version": 9, "comment": "link"} + C7 +C0 1 {"version": 10, "comment": "link"} ++C0 H8 1 {"version": 11, "comment": "link"} ++C0 H9 1 {"version": 12, "comment": "link"} ++C1 H10 1 {"version": 13, "comment": "link"} +H10 +H4 1 {"version": 14, "comment": "link"} +H10 +H5 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1242e+02 5.0484e+02 {"version": 4, "comment": "link"} ++C0 C1 H10 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C1 +C0 +C1 +H7 9 0.00 0.54392 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 0.65084 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H4 9 0.00 0.65084 3 {"version": 7, "comment": "link"} + C2 C1 +C0 +H5 9 0.00 0.65084 3 {"version": 8, "comment": "link"} + C3 C2 C1 +C0 9 180.00 1.00416 2 {"version": 9, "comment": "link"} + C7 C2 C1 +C0 9 180.00 1.00416 2 {"version": 10, "comment": "link"} ++C0 C1 C0 H8 9 0.00 0.54392 3 {"version": 11, "comment": "link"} ++C0 C1 C0 H9 9 0.00 0.54392 3 {"version": 12, "comment": "link"} ++C1 +C0 C1 H10 9 0.00 0.54392 3 {"version": 13, "comment": "link"} +H10 C1 +C0 +H4 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +H10 C1 +C0 +H5 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +H8 {"resname": "ETH"} ++H4 {"resname": "ETH"} +C3 {"resname": "ETH"} ++H7 {"resname": "ETH"} ++C0 {"resname": "ETH"} ++H6 {"resname": "ETH"} +H11 {"resname": "ETH"} +C2 {"resname": "ETH"} +H10 {"resname": "ETH"} +H9 {"resname": "ETH"} ++C1 {"resname": "ETH"} ++H5 {"resname": "ETH"} ++C2 {"resname": "ETH"} +C1 {"resname": "ETH"} +[ bonds ] + C3 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C1 +C0 1 {"version": 0, "comment": "link"} + C2 +C1 1 {"version": 1, "comment": "link"} + C2 +H4 1 {"version": 2, "comment": "link"} + C2 +H5 1 {"version": 3, "comment": "link"} + C3 +C2 1 {"version": 4, "comment": "link"} + C3 +H6 1 {"version": 5, "comment": "link"} + C3 +H7 1 {"version": 6, "comment": "link"} ++C0 H8 1 {"version": 7, "comment": "link"} ++C0 H9 1 {"version": 8, "comment": "link"} ++C1 H10 1 {"version": 9, "comment": "link"} ++C1 H11 1 {"version": 10, "comment": "link"} +H10 +H4 1 {"version": 11, "comment": "link"} +H10 +H5 1 {"version": 12, "comment": "link"} +H11 +H4 1 {"version": 13, "comment": "link"} +H11 +H5 1 {"version": 14, "comment": "link"} +[ angles ] + C2 C3 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C3 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C3 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C3 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} ++C0 C3 H10 1 1.0968e+02 3.6208e+02 {"version": 4, "comment": "link"} ++C0 C3 H11 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C1 C2 C3 +C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C2 C3 +C0 +C1 9 0.00 2.17568 3 {"version": 1, "comment": "link"} + C2 C3 +C0 +H4 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C2 C3 +C0 +H5 9 0.00 0.54392 3 {"version": 3, "comment": "link"} + C3 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 4, "comment": "link"} + C3 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 5, "comment": "link"} + C3 +C0 +C1 +H7 9 0.00 0.54392 3 {"version": 6, "comment": "link"} ++C0 C3 C2 H8 9 0.00 0.54392 3 {"version": 7, "comment": "link"} ++C0 C3 C2 H9 9 0.00 0.54392 3 {"version": 8, "comment": "link"} ++C1 +C0 C3 H10 9 0.00 0.54392 3 {"version": 9, "comment": "link"} ++C1 +C0 C3 H11 9 0.00 0.54392 3 {"version": 10, "comment": "link"} +H10 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 11, "comment": "link"} +H10 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 12, "comment": "link"} +H11 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 13, "comment": "link"} +H11 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 14, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +H8 {"resname": "ETH"} ++H4 {"resname": "BUT"} +C3 {"resname": "ETH"} ++C0 {"resname": "BUT"} ++H6 {"resname": "BUT"} +H11 {"resname": "ETH"} +C2 {"resname": "ETH"} +H10 {"resname": "ETH"} +H9 {"resname": "ETH"} ++C1 {"resname": "BUT"} ++H5 {"resname": "BUT"} ++C2 {"resname": "BUT"} +C1 {"resname": "ETH"} +[ bonds ] + C3 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C1 +C0 1 {"version": 0, "comment": "link"} + C2 +C1 1 {"version": 1, "comment": "link"} + C2 +H4 1 {"version": 2, "comment": "link"} + C2 +H5 1 {"version": 3, "comment": "link"} + C3 +C2 1 {"version": 4, "comment": "link"} + C3 +H6 1 {"version": 5, "comment": "link"} ++C0 H8 1 {"version": 6, "comment": "link"} ++C0 H9 1 {"version": 7, "comment": "link"} ++C1 H10 1 {"version": 8, "comment": "link"} ++C1 H11 1 {"version": 9, "comment": "link"} +H10 +H4 1 {"version": 10, "comment": "link"} +H10 +H5 1 {"version": 11, "comment": "link"} +H11 +H4 1 {"version": 12, "comment": "link"} +H11 +H5 1 {"version": 13, "comment": "link"} +[ angles ] + C2 C3 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C3 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C3 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C3 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} ++C0 C3 H10 1 1.0968e+02 3.6208e+02 {"version": 4, "comment": "link"} ++C0 C3 H11 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C1 C2 C3 +C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C2 C3 +C0 +C1 9 0.00 2.17568 3 {"version": 1, "comment": "link"} + C2 C3 +C0 +H4 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C2 C3 +C0 +H5 9 0.00 0.54392 3 {"version": 3, "comment": "link"} + C3 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 4, "comment": "link"} + C3 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 5, "comment": "link"} ++C0 C3 C2 H8 9 0.00 0.54392 3 {"version": 6, "comment": "link"} ++C0 C3 C2 H9 9 0.00 0.54392 3 {"version": 7, "comment": "link"} ++C1 +C0 C3 H10 9 0.00 0.54392 3 {"version": 8, "comment": "link"} ++C1 +C0 C3 H11 9 0.00 0.54392 3 {"version": 9, "comment": "link"} +H10 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 10, "comment": "link"} +H10 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 11, "comment": "link"} +H11 C3 +C0 +H4 9 0.00 0.50208 3 {"version": 12, "comment": "link"} +H11 C3 +C0 +H5 9 0.00 0.50208 3 {"version": 13, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C2 {"resname": "BUT"} +H5 {"resname": "BUT"} +H8 {"resname": "BUT"} +H7 {"resname": "BUT"} ++H4 {"resname": "BUT"} +C3 {"resname": "BUT"} ++C0 {"resname": "BUT"} ++H6 {"resname": "BUT"} +H6 {"resname": "BUT"} +C2 {"resname": "BUT"} ++C1 {"resname": "BUT"} +H4 {"resname": "BUT"} ++H5 {"resname": "BUT"} +C0 {"resname": "BUT"} +C1 {"resname": "BUT"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H4 1 {"version": 1, "comment": "link"} + C0 +H5 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H6 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H4 1 {"version": 6, "comment": "link"} + C2 +H5 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} ++C0 H4 1 {"version": 9, "comment": "link"} ++C0 H5 1 {"version": 10, "comment": "link"} ++C0 H7 1 {"version": 11, "comment": "link"} ++C0 H8 1 {"version": 12, "comment": "link"} ++C1 H6 1 {"version": 13, "comment": "link"} + H6 +H4 1 {"version": 14, "comment": "link"} + H6 +H5 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H4 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H5 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 4, "comment": "link"} ++C0 C1 H6 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 2.17568 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H6 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H4 9 0.00 0.54392 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H5 9 0.00 0.54392 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 0.00 2.17568 3 {"version": 8, "comment": "link"} ++C0 C1 C0 H4 9 0.00 0.54392 3 {"version": 9, "comment": "link"} ++C0 C1 C0 H5 9 0.00 0.54392 3 {"version": 10, "comment": "link"} ++C0 C1 C2 H7 9 0.00 0.54392 3 {"version": 11, "comment": "link"} ++C0 C1 C2 H8 9 0.00 0.54392 3 {"version": 12, "comment": "link"} ++C1 +C0 C1 H6 9 0.00 0.54392 3 {"version": 13, "comment": "link"} + H6 C1 +C0 +H4 9 0.00 0.50208 3 {"version": 14, "comment": "link"} + H6 C1 +C0 +H5 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C2 {"resname": "STY"} +H5 {"resname": "BUT"} +H8 {"resname": "BUT"} +H7 {"resname": "BUT"} ++H8 {"resname": "STY"} +C3 {"resname": "BUT"} ++H9 {"resname": "STY"} ++C0 {"resname": "STY"} +H6 {"resname": "BUT"} +C2 {"resname": "BUT"} ++H10 {"resname": "STY"} ++C1 {"resname": "STY"} +H4 {"resname": "BUT"} +C0 {"resname": "BUT"} +C1 {"resname": "BUT"} +[ bonds ] + C1 +C0 1 1.5354e-01 1.9154e+05 {"version": 0, "comment": "link"} +[ pairs ] + C0 +C1 1 {"version": 0, "comment": "link"} + C0 +H8 1 {"version": 1, "comment": "link"} + C0 +H9 1 {"version": 2, "comment": "link"} + C1 +C2 1 {"version": 3, "comment": "link"} + C1 +H10 1 {"version": 4, "comment": "link"} + C2 +C1 1 {"version": 5, "comment": "link"} + C2 +H8 1 {"version": 6, "comment": "link"} + C2 +H9 1 {"version": 7, "comment": "link"} + C3 +C0 1 {"version": 8, "comment": "link"} + +C0 H4 1 {"version": 9, "comment": "link"} + +C0 H5 1 {"version": 10, "comment": "link"} + +C0 H7 1 {"version": 11, "comment": "link"} + +C0 H8 1 {"version": 12, "comment": "link"} + +C1 H6 1 {"version": 13, "comment": "link"} + H6 +H8 1 {"version": 14, "comment": "link"} + H6 +H9 1 {"version": 15, "comment": "link"} +[ angles ] + C0 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 0, "comment": "link"} + C1 +C0 +C1 1 1.1263e+02 5.0099e+02 {"version": 1, "comment": "link"} + C1 +C0 +H8 1 1.0968e+02 3.6208e+02 {"version": 2, "comment": "link"} + C1 +C0 +H9 1 1.0968e+02 3.6208e+02 {"version": 3, "comment": "link"} + C2 C1 +C0 1 1.1263e+02 5.0099e+02 {"version": 4, "comment": "link"} + +C0 C1 H6 1 1.0968e+02 3.6208e+02 {"version": 5, "comment": "link"} +[ dihedrals ] + C0 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 0, "comment": "link"} + C0 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 1, "comment": "link"} + C0 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 2, "comment": "link"} + C1 +C0 +C1 +C2 9 0.00 0.65084 3 {"version": 3, "comment": "link"} + C1 +C0 +C1 +H10 9 0.00 0.54392 3 {"version": 4, "comment": "link"} + C2 C1 +C0 +C1 9 0.00 2.17568 3 {"version": 5, "comment": "link"} + C2 C1 +C0 +H8 9 0.00 0.54392 3 {"version": 6, "comment": "link"} + C2 C1 +C0 +H9 9 0.00 0.54392 3 {"version": 7, "comment": "link"} + C3 C2 C1 +C0 9 0.00 2.17568 3 {"version": 8, "comment": "link"} + +C0 C1 C0 H4 9 0.00 0.54392 3 {"version": 9, "comment": "link"} + +C0 C1 C0 H5 9 0.00 0.54392 3 {"version": 10, "comment": "link"} + +C0 C1 C2 H7 9 0.00 0.54392 3 {"version": 11, "comment": "link"} + +C0 C1 C2 H8 9 0.00 0.54392 3 {"version": 12, "comment": "link"} + +C1 +C0 C1 H6 9 0.00 0.54392 3 {"version": 13, "comment": "link"} + H6 C1 +C0 +H8 9 0.00 0.50208 3 {"version": 14, "comment": "link"} + H6 C1 +C0 +H9 9 0.00 0.50208 3 {"version": 15, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +H8 {"resname": "STY"} ++H0 {"resname": "Hter"} +C3 {"resname": "STY"} +C2 {"resname": "STY"} +H10 {"resname": "STY"} +H9 {"resname": "STY"} +C0 {"resname": "STY"} +C7 {"resname": "STY"} +C1 {"resname": "STY"} +[ bonds ] + C1 +H0 1 1.0962e-01 2.8891e+05 {"version": 0, "comment": "link"} +[ pairs ] + C3 +H0 1 {"version": 0, "comment": "link"} + C7 +H0 1 {"version": 1, "comment": "link"} + H8 +H0 1 {"version": 2, "comment": "link"} + H9 +H0 1 {"version": 3, "comment": "link"} +[ angles ] + C0 C1 +H0 1 1.0968e+02 3.6208e+02 {"version": 0, "comment": "link"} + C2 C1 +H0 1 1.1063e+02 3.6493e+02 {"version": 1, "comment": "link"} ++H0 C1 H10 1 1.0773e+02 2.9957e+02 {"version": 2, "comment": "link"} +[ dihedrals ] + C3 C2 C1 +H0 9 0.00 0.00000 0 {"version": 0, "comment": "link"} + C7 C2 C1 +H0 9 0.00 0.00000 0 {"version": 1, "comment": "link"} + H8 C0 C1 +H0 9 0.00 0.50208 3 {"version": 2, "comment": "link"} + H9 C0 C1 +H0 9 0.00 0.50208 3 {"version": 3, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "ETH"} +C1 {"resname": "STY"} +[ pairs ] + C1 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "BUT"} +C3 {"resname": "ETH"} +[ pairs ] + C3 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "STY"} +C1 {"resname": "BUT"} +[ pairs ] + C1 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++H0 {"resname": "Hter"} +C1 {"resname": "STY"} +[ pairs ] + C1 ++H0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "STY"} +H0 {"resname": "Hter"} +[ pairs ] + H0 ++C0 1 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "ETH"} ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +C1 {"resname": "STY"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "BUT"} +C3 {"resname": "ETH"} ++C0 {"resname": "BUT"} +++C0 {"resname": "BUT"} +[ dihedrals ] + C3 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "STY"} ++C1 {"resname": "BUT"} ++C0 {"resname": "BUT"} +C1 {"resname": "BUT"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] +++C0 {"resname": "STY"} ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +C1 {"resname": "BUT"} +[ dihedrals ] + C1 +C0 +C1 ++C0 9 0.00 2.17568 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} ++C0 {"resname": "STY"} +++H0 {"resname": "Hter"} +C1 {"resname": "STY"} +[ dihedrals ] + C1 +C0 +C1 ++H0 9 0.00 0.54392 3 {"version": 0, "comment": "link"} +[ edges ] +[ link ] +[ atoms ] ++C1 {"resname": "STY"} +H0 {"resname": "Hter"} ++C0 {"resname": "STY"} +++C0 {"resname": "STY"} +[ dihedrals ] + H0 +C0 +C1 ++C0 9 0.00 0.54392 3 {"version": 0, "comment": "link"} +[ edges ] diff --git a/polyply_output/polymer.itp b/polyply_output/polymer.itp new file mode 100644 index 0000000..0b3c436 --- /dev/null +++ b/polyply_output/polymer.itp @@ -0,0 +1,1132 @@ +; repro.py + +; Please cite the following papers: + +[ moleculetype ] +polymer 3 + +[ atoms ] + 1 hc 1 Hter H0 49 0.0357 1.008 + 2 ha 2 STY H15 114 0.13143744 1.008 + 3 c3 2 STY C0 58 -0.06796256 12.01 + 4 c3 2 STY C1 59 -0.02296256 12.01 + 5 ca 2 STY C2 60 -0.07186256 12.01 + 6 ca 2 STY C3 61 -0.12756256 12.01 + 7 ca 2 STY C4 62 -0.12856256 12.01 + 8 ca 2 STY C5 63 -0.13156156 12.01 + 9 ca 2 STY C6 64 -0.12856256 12.01 + 10 ca 2 STY C7 65 -0.12756256 12.01 + 11 hc 2 STY H8 107 0.04763744 1.008 + 12 hc 2 STY H9 108 0.04763744 1.008 + 13 hc 2 STY H10 109 0.05713744 1.008 + 14 ha 2 STY H11 110 0.13143744 1.008 + 15 ha 2 STY H12 111 0.13043744 1.008 + 16 ha 2 STY H13 112 0.13043744 1.008 + 17 ha 2 STY H14 113 0.13043744 1.008 + 18 ha 3 STY H15 178 0.13143744 1.008 + 19 c3 3 STY C0 122 -0.06796256 12.01 + 20 c3 3 STY C1 123 -0.02296256 12.01 + 21 ca 3 STY C2 124 -0.07186256 12.01 + 22 ca 3 STY C3 125 -0.12756256 12.01 + 23 ca 3 STY C4 126 -0.12856256 12.01 + 24 ca 3 STY C5 127 -0.13156156 12.01 + 25 ca 3 STY C6 128 -0.12856256 12.01 + 26 ca 3 STY C7 129 -0.12756256 12.01 + 27 hc 3 STY H8 171 0.04763744 1.008 + 28 hc 3 STY H9 172 0.04763744 1.008 + 29 hc 3 STY H10 173 0.05713744 1.008 + 30 ha 3 STY H11 174 0.13143744 1.008 + 31 ha 3 STY H12 175 0.13043744 1.008 + 32 ha 3 STY H13 176 0.13043744 1.008 + 33 ha 3 STY H14 177 0.13043744 1.008 + 34 hc 4 ETH H4 251 0.03861682 1.008 + 35 hc 4 ETH H5 252 0.03861682 1.008 + 36 hc 4 ETH H6 253 0.03961682 1.008 + 37 hc 4 ETH H7 254 0.03961682 1.008 + 38 hc 4 ETH H8 255 0.04061682 1.008 + 39 hc 4 ETH H9 256 0.04061682 1.008 + 40 hc 4 ETH H10 257 0.03911682 1.008 + 41 hc 4 ETH H11 258 0.03911682 1.008 + 42 c3 4 ETH C0 198 -0.07848371 12.01 + 43 c3 4 ETH C1 199 -0.07948355 12.01 + 44 c3 4 ETH C2 200 -0.07948355 12.01 + 45 c3 4 ETH C3 201 -0.07848371 12.01 + 46 hc 5 ETH H4 275 0.03861682 1.008 + 47 hc 5 ETH H5 276 0.03861682 1.008 + 48 hc 5 ETH H6 277 0.03961682 1.008 + 49 hc 5 ETH H7 278 0.03961682 1.008 + 50 hc 5 ETH H8 279 0.04061682 1.008 + 51 hc 5 ETH H9 280 0.04061682 1.008 + 52 hc 5 ETH H10 281 0.03911682 1.008 + 53 hc 5 ETH H11 282 0.03911682 1.008 + 54 c3 5 ETH C0 222 -0.07848371 12.01 + 55 c3 5 ETH C1 223 -0.07948355 12.01 + 56 c3 5 ETH C2 224 -0.07948355 12.01 + 57 c3 5 ETH C3 225 -0.07848371 12.01 + 58 hc 6 BUT H11 314 0.03253311 1.008 + 59 hc 6 BUT H4 307 0.04220011 1.008 + 60 hc 6 BUT H5 308 0.04220011 1.008 + 61 hc 6 BUT H6 309 0.05020011 1.008 + 62 hc 6 BUT H7 310 0.03870011 1.008 + 63 hc 6 BUT H8 311 0.03870011 1.008 + 64 hc 6 BUT H9 312 0.03253311 1.008 + 65 hc 6 BUT H10 313 0.03253311 1.008 + 66 c3 6 BUT C0 250 -0.07789996 12.01 + 67 c3 6 BUT C1 251 -0.06319996 12.01 + 68 c3 6 BUT C2 252 -0.07589996 12.01 + 69 c3 6 BUT C3 253 -0.09259996 12.01 + 70 hc 7 BUT H11 342 0.03253311 1.008 + 71 hc 7 BUT H4 335 0.04220011 1.008 + 72 hc 7 BUT H5 336 0.04220011 1.008 + 73 hc 7 BUT H6 337 0.05020011 1.008 + 74 hc 7 BUT H7 338 0.03870011 1.008 + 75 hc 7 BUT H8 339 0.03870011 1.008 + 76 hc 7 BUT H9 340 0.03253311 1.008 + 77 hc 7 BUT H10 341 0.03253311 1.008 + 78 c3 7 BUT C0 278 -0.07789996 12.01 + 79 c3 7 BUT C1 279 -0.06319996 12.01 + 80 c3 7 BUT C2 280 -0.07589996 12.01 + 81 c3 7 BUT C3 281 -0.09259996 12.01 + 82 ha 8 STY H15 346 0.13143744 1.008 + 83 c3 8 STY C0 290 -0.06796256 12.01 + 84 c3 8 STY C1 291 -0.02296256 12.01 + 85 ca 8 STY C2 292 -0.07186256 12.01 + 86 ca 8 STY C3 293 -0.12756256 12.01 + 87 ca 8 STY C4 294 -0.12856256 12.01 + 88 ca 8 STY C5 295 -0.13156156 12.01 + 89 ca 8 STY C6 296 -0.12856256 12.01 + 90 ca 8 STY C7 297 -0.12756256 12.01 + 91 hc 8 STY H8 339 0.04763744 1.008 + 92 hc 8 STY H9 340 0.04763744 1.008 + 93 hc 8 STY H10 341 0.05713744 1.008 + 94 ha 8 STY H11 342 0.13143744 1.008 + 95 ha 8 STY H12 343 0.13043744 1.008 + 96 ha 8 STY 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link + 83 79 80 74 9 0.00 0.54392 3 ; link + 83 79 80 75 9 0.00 0.54392 3 ; link + 84 83 79 73 9 0.00 0.54392 3 ; link + 73 79 83 91 9 0.00 0.50208 3 ; link + 73 79 83 92 9 0.00 0.50208 3 ; link +102 101 100 114 9 0.00 0.00000 0 ; link +106 101 100 114 9 0.00 0.00000 0 ; link +107 99 100 114 9 0.00 0.50208 3 ; link +108 99 100 114 9 0.00 0.50208 3 ; link + 4 19 20 42 9 0.00 2.17568 3 ; link + 57 66 67 78 9 0.00 2.17568 3 ; link + 67 78 79 83 9 0.00 2.17568 3 ; link + 79 83 84 99 9 0.00 2.17568 3 ; link + 84 99 100 114 9 0.00 0.54392 3 ; link + 1 3 4 19 9 0.00 0.54392 3 ; link + diff --git a/polyply_output/polyply.top b/polyply_output/polyply.top new file mode 100644 index 0000000..b1b7bf6 --- /dev/null +++ b/polyply_output/polyply.top @@ -0,0 +1,18 @@ +; Include forcefield parameters +#include "../assets/forcefield.itp" + +[ atomtypes ] +;name bond_type mass charge ptype sigma epsilon Amb + c3 c3 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078 + ca ca 0.00000 0.00000 A 3.31521e-01 4.13379e-01 ; 1.86 0.0988 + hc hc 0.00000 0.00000 A 2.60018e-01 8.70272e-02 ; 1.46 0.0208 + ha ha 0.00000 0.00000 A 2.62548e-01 6.73624e-02 ; 1.47 0.0161 +; Include smiles_molecule_GMX.itp topology +#include "polymer.itp" + +[ system ] + smiles_molecule + +[ molecules ] +; Compound nmols + polymer 1 diff --git a/repro.py b/repro.py index df2a188..63fa460 100644 --- a/repro.py +++ b/repro.py @@ -3,18 +3,23 @@ https://github.com/marrink-lab/polyply_1.0/pull/383#discussion_r1835118580 """ - from pathlib import Path from polyply.src.gen_ff import gen_ff - +from polyply import gen_params def main(): + # generate the ff file gen_ff(itppath=Path("assets/smiles_molecule_GMX_OPLS.top"), - smile_str="{[#styrene]|2[#ethylene]|2[#butylene]|2[#styrene]|2}.{#styrene=[<]CC[>]c1ccccc1,#ethylene=[<]CCCC[>],#butylene=[<]CC[>](CC)}", - outpath=".") - + smile_str="{[#Hter][#STY]|2[#ETH]|2[#BUT]|2[#STY]|2[#Hter]}.{#Hter=[>][<][H],#STY=[<]CC[>]c1ccccc1,#ETH=[<]CCCC[>],#BUT=[<]CC[>](CC)}", + outpath="./polyply_output/OPLS_test.ff", + res_charges=[("STY", 0), ("ETH", 0), ("BUT", 0), ("Hter", 0)]) + + # generate the itp file of the same seq + gen_params(inpath=[Path('./polyply_output/OPLS_test.ff')], + seq=["{[#Hter][#STY]|2[#ETH]|2[#BUT]|2[#STY]|2[#Hter]}"], + outpath=Path("./polyply_output/polymer.itp")) if __name__ == "__main__": main()