; Include forcefield parameters #include "./charmm27_local.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Isoalloxazin 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 ISO rtp ISO q 0.0 1 NN3A 1 ISO N1 1 -0.6519 14.007 ; qtot -0.6519 2 CN1A 1 ISO C2 2 0.7481 12.011 ; qtot 0.0962 3 ON1 1 ISO O2 3 -0.7371 15.9994 ; qtot -0.6409 4 NN2U 1 ISO N3 4 -0.4064 14.007 ; qtot -1.047 5 HN2 1 ISO H3 5 0.358 1.008 ; qtot -0.6893 6 CN1B 1 ISO C4 6 0.4925 12.011 ; qtot -0.1968 7 ON1 1 ISO O4 7 -0.6824 15.9994 ; qtot -0.8792 8 CN5B 1 ISO C4A 8 0.0224 12.011 ; qtot -0.8568 9 NN3A 1 ISO N5 9 -0.2742 14.007 ; qtot -1.131 10 CPTB 1 ISO C5A 10 0.1797 12.011 ; qtot -0.9513 11 CA1 1 ISO C6 11 -0.2904 12.011 ; qtot -1.242 12 HP 1 ISO H6 12 0.3012 1.008 ; qtot -0.9405 13 CA2 1 ISO C7 13 0.1958 12.011 ; qtot -0.7447 14 CA3 1 ISO C8 14 0.07 12.011 ; qtot -0.6747 15 CA4 1 ISO C9 15 -0.0292 12.011 ; qtot -0.7039 16 HP 1 ISO H9 16 0.1949 1.008 ; qtot -0.509 17 CPTA 1 ISO C9A 17 -0.1901 12.011 ; qtot -0.6991 18 NN2G 1 ISO N10 18 0.273 14.007 ; qtot -0.4261 19 CN5A 1 ISO C0A 19 0.2618 12.011 ; qtot -0.1643 20 CT3 1 ISO C7M 20 -0.3701 12.011 ; qtot -0.5344 21 HAI 1 ISO H7A 21 0.1234 1.008 ; qtot -0.411 22 HAI 1 ISO H7B 22 0.1234 1.008 ; qtot -0.2876 23 HAI 1 ISO H7C 23 0.1234 1.008 ; qtot -0.1642 24 CT3 1 ISO C8M 24 -0.3645 12.011 ; qtot -0.5287 25 HAI 1 ISO H8A 25 0.1215 1.008 ; qtot -0.4072 26 HAI 1 ISO H8B 26 0.1215 1.008 ; qtot -0.2857 27 HAI 1 ISO H8C 27 0.1215 1.008 ; qtot -0.1642 28 CT3 1 ISO C0M 28 -0.3952 12.011 ; qtot -0.5594 29 HAI 1 ISO H0A 29 0.1317 1.008 ; qtot -0.4277 30 HAI 1 ISO H0B 30 0.1317 1.008 ; qtot -0.296 31 HAI 1 ISO H0C 31 0.1317 1.008 ; qtot -0.1643 32 HP 1 ISO H5 32 0.1643 1.008 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1.382 287.0 1 19 1 1.320 381.2 2 3 1 1.229 691.5 2 4 1 1.429 176.0 4 5 1 1.022 459.8 4 6 1 1.384 281.2 6 7 1 1.244 667.7 6 8 1 1.450 262.6 8 9 1 1.365 355.8 8 19 1 1.416 362.2 9 10 1 1.379 297.3 9 32 1 1.027 459.3 10 11 1 1.402 362.7 10 17 1 1.424 322.8 11 12 1 1.094 375.5 11 13 1 1.395 341.7 13 14 1 1.417 312.9 13 20 1 1.507 265.1 14 15 1 1.402 353.5 14 24 1 1.507 266.9 15 16 1 1.090 382.1 15 17 1 1.402 334.8 17 18 1 1.402 285.9 18 19 1 1.404 270.1 18 28 1 1.463 260.2 20 21 1 1.100 356.6 20 22 1 1.100 356.6 20 23 1 1.100 356.6 24 25 1 1.100 356.6 24 26 1 1.100 356.6 24 27 1 1.100 356.6 28 29 1 1.100 356.6 28 30 1 1.100 356.6 28 31 1 1.100 356.6 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 5 1 1 6 1 1 9 1 1 17 1 1 28 1 2 7 1 2 8 1 2 18 1 3 5 1 3 6 1 3 19 1 4 9 1 4 19 1 5 7 1 5 8 1 6 10 1 6 18 1 6 32 1 7 9 1 7 19 1 8 11 1 8 17 1 8 28 1 9 12 1 9 13 1 9 15 1 9 18 1 10 14 1 10 16 1 10 19 1 10 20 1 10 28 1 11 15 1 11 18 1 11 21 1 11 22 1 11 23 1 11 24 1 11 32 1 12 14 1 12 17 1 12 20 1 13 16 1 13 17 1 13 25 1 13 26 1 13 27 1 14 18 1 14 21 1 14 22 1 14 23 1 15 19 1 15 20 1 15 25 1 15 26 1 15 27 1 15 28 1 16 18 1 16 24 1 17 24 1 17 29 1 17 30 1 17 31 1 17 32 1 19 29 1 19 30 1 19 31 1 19 32 1 20 24 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 123.75 250.00 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 3 2 4 1 123.75 230.00 2 4 5 1 115.95 105.00 2 4 6 1 126.44 90.00 5 4 6 1 115.95 105.00 4 6 7 1 124.66 225.00 4 6 8 1 112.38 100.00 7 6 8 1 124.66 225.00 6 8 9 1 118.06 110.00 6 8 19 1 118.06 110.00 9 8 19 1 118.06 110.00 8 9 10 1 122.10 250.00 8 9 32 1 115.50 53.75 10 9 32 1 121.96 80.00 9 10 11 1 121.96 80.00 9 10 17 1 121.96 80.00 11 10 17 1 121.96 80.00 10 11 12 1 118.46 53.75 10 11 13 1 121.72 250.00 12 11 13 1 118.46 53.75 11 13 14 1 118.68 75.00 11 13 20 1 120.23 70.00 14 13 20 1 118.68 75.00 13 14 15 1 119.56 77.00 13 14 24 1 120.72 70.50 15 14 24 1 122.24 230.00 14 15 16 1 118.45 75.00 14 15 17 1 122.24 230.00 16 15 17 1 118.45 75.00 10 17 15 1 122.24 230.00 10 17 18 1 122.24 230.00 15 17 18 1 122.22 52.25 17 18 19 1 121.14 350.00 17 18 28 1 120.07 81.25 19 18 28 1 120.07 81.25 1 19 8 1 110.10 38.00 1 19 18 1 110.10 38.00 8 19 18 1 121.14 350.00 13 20 21 1 110.10 38.00 13 20 22 1 110.10 38.00 13 20 23 1 110.10 38.00 21 20 22 1 108.40 35.50 21 20 23 1 108.40 35.50 22 20 23 1 108.40 35.50 14 24 25 1 110.10 38.00 14 24 26 1 110.10 38.00 14 24 27 1 110.10 38.00 25 24 26 1 108.40 38.00 25 24 27 1 108.40 38.00 26 24 27 1 108.40 38.00 18 28 29 1 110.10 40.50 18 28 30 1 110.10 40.50 18 28 31 1 110.10 40.50 29 28 30 1 108.40 38.00 29 28 31 1 108.40 38.00 30 28 31 1 108.40 38.00 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 19 8 5 6 8 9 10 5 6 8 19 1 5 8 9 10 11 5 9 10 17 15 5 10 11 13 14 5 11 13 14 15 5 11 13 20 21 5 13 14 24 25 5 17 18 19 1 5 17 18 28 29 5 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 1 8 6 4 2 180 100 1 2 4 5 2 180 100 1 10 11 13 2 180 100 2 1 4 6 2 180 100 2 4 6 7 2 180 100 4 2 1 7 2 180 100 4 2 6 8 2 180 100 5 1 8 6 2 180 100 6 8 1 10 2 180 100 8 1 10 11 2 180 100 10 1 11 32 2 180 100 11 10 13 14 2 180 100 13 11 14 15 2 180 100 13 14 15 32 2 180 100 14 13 15 17 2 180 100 14 15 17 18 2 180 100 15 17 18 19 2 180 100 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "./charmm27_local.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm27_local.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Isoalloxazin 1 SOL 606