[ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 9 2 1 3 1 0 ; ===================================================================== ; RNA ;----------------------------------------------------------------------- [ RA ] ; H61 H62; ; \ / ; N6 ; | ; C6 ; // \ ; N1 C5--N7\\ ; | || C8-H8 ; C2 C4--N9/ ; / \\ / \ ; H2 N3 \ ; \ ; \ ; \ ; O1P H5'1 H4' O4' \ ; | | \ / \ \ ; -P-O5'-C5'---C4' C1' ; | | \ / \ ; O2P H5'2 C3'--C2' H1' ; / \ / \ ; O3' H3' O2' H2'2 ; | | ; H2'1 ; [ atoms ] P P 1.50 0 O1P ON3 -0.78 1 O2P ON3 -0.78 2 O5' ON2 -0.57 3 C5' CN8B -0.08 4 H5'1 HN8 0.09 5 H5'2 HN8 0.09 6 C4' CN7 0.16 7 H4' HN7 0.09 8 O4' ON6B -0.50 9 C1' CN7B 0.16 10 H1' HN7 0.09 11 N9 NN2 -0.05 12 C5 CN5 0.28 13 N7 NN4 -0.71 14 C8 CN4 0.34 15 H8 HN3 0.12 16 N1 NN3A -0.74 17 C2 CN4 0.50 18 H2 HN3 0.13 19 N3 NN3A -0.75 20 C4 CN5 0.43 21 C6 CN2 0.46 22 N6 NN1 -0.77 23 H61 HN1 0.38 24 H62 HN1 0.38 25 C2' CN7B 0.14 26 H2'2 HN7 0.09 27 O2' ON5 -0.66 28 H2'1 HN5 0.43 29 C3' CN7 0.01 30 H3' HN7 0.09 31 O3' ON2 -0.57 32 [ bonds ] -O3' P P O1P P O2P P O5' O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6 H61 N6 H62 C6 C5 C5 N7 C2' C3' C2' O2' O2' H2'1 C3' O3' C1' H1' C2' H2'2 C3' H3' C4' H4' C5' H5'1 C5' H5'2 C8 H8 C2 H2 N1 C6 C2 N3 C4 C5 N7 C8 [ impropers ] N6 C6 H61 H62 C6 N1 C5 N6 ;-------------------------------------------------------------------------- [ RC ] ; ; H42 H41 ; \ / ; N4 ; | ; C4 ; / \\ ; H5-C5 N3 ; || | ; H6-C6 C2 ; \ / \\ ; N1 O2 ; \ ; \ ; \ ; O1P H5'1H4' O4' \ ; | | \ / \ \ ; -P-O5'-C5'---C4' C1' ; | | \ / \ ; O2P H5'2 C3'--C2' H1' ; / \ / \ ; O3' H3' O2' H2'2 ; | | ; H2'1 [ atoms ] P P 1.50 0 O1P ON3 -0.78 1 O2P ON3 -0.78 2 O5' ON2 -0.57 3 C5' CN8B -0.08 4 H5'1 HN8 0.09 5 H5'2 HN8 0.09 6 C4' CN7 0.16 7 H4' HN7 0.09 8 O4' ON6B -0.50 9 C1' CN7B 0.16 10 H1' HN7 0.09 11 N1 NN2 -0.13 12 C6 CN3 0.05 13 H6 HN3 0.17 14 C5 CN3 -0.13 15 H5 HN3 0.07 16 C2 CN1 0.52 17 O2 ON1C -0.49 18 N3 NN3 -0.66 19 C4 CN2 0.65 20 N4 NN1 -0.75 21 H41 HN1 0.37 22 H42 HN1 0.33 23 C2' CN7B 0.14 24 H2'2 HN7 0.09 25 O2' ON5 -0.66 26 H2'1 HN5 0.43 27 C3' CN7 0.01 28 H3' HN7 0.09 29 O3' ON2 -0.57 30 [ bonds ] -O3' P P O1P P O2P P O5' O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' C1' N1 C1' C2' N1 C2 N1 C6 C2 N3 C4 N4 N4 H41 N4 H42 C4 C5 C2' C3' C3' O3' C2' O2' O2' H2'1 C1' H1' C2' H2'2 C3' H3' C4' H4' C5' H5'1 C5' H5'2 C5 H5 C6 H6 C2 O2 C5 C6 N3 C4 [ impropers ] C2 N1 N3 O2 C4 N3 C5 N4 N4 C4 H41 H42 ; -------------------------------------------------------------------- [ RG ] ; O6 ; || ; C6 ; / \ ; H1-N1 C5--N7\\ ; | || C8-H8 ; C2 C4--N9/ ; / \\ / \ ; H21-N2 N3 \ ; | \ ; H22 \ ; \ ; O1P H5'1 H4' O4' \ ; | | \ / \ \ ; -P-O5'-C5'---C4' C1' ; | | \ / \ ; O2P H5'2 C3'--C2' H1' ; / \ / \ ; O3' H3' O2' H2'2 ; | | ; H2'1 [ atoms ] P P 1.50 0 O1P ON3 -0.78 1 O2P ON3 -0.78 2 O5' ON2 -0.57 3 C5' CN8B -0.08 4 H5'1 HN8 0.09 5 H5'2 HN8 0.09 6 C4' CN7 0.16 7 H4' HN7 0.09 8 O4' ON6B -0.50 9 C1' CN7B 0.16 10 H1' HN7 0.09 11 N9 NN2B -0.02 12 C4 CN5 0.26 13 N2 NN1 -0.68 14 H21 HN1 0.32 15 H22 HN1 0.35 16 N3 NN3G -0.74 17 C2 CN2 0.75 18 N1 NN2G -0.34 19 H1 HN2 0.26 20 C6 CN1 0.54 21 O6 ON1 -0.51 22 C5 CN5G 0.00 23 N7 NN4 -0.60 24 C8 CN4 0.25 25 H8 HN3 0.16 26 C2' CN7B 0.14 27 H2'2 HN7 0.09 28 O2' ON5 -0.66 29 H2'1 HN5 0.43 30 C3' CN7 0.01 31 H3' HN7 0.09 32 O3' ON2 -0.57 33 [ bonds ] -O3' P P O1P P O2P P O5' O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C2' C3' C3' O3' C2' O2' O2' H2'1 C1' H1' C2' H2'2 C3' H3' C4' H4' C5' H5'1 C5' H5'2 C8 H8 C2 N3 C4 C5 N7 C8 C6 O6 [ impropers ] C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 ;--------------------------------------------------------------------------- [ RU ] ; O4 ; || ; C4 H3 ; / \ / ; H5-C5 N3 ; || | ; H6-C6 C2 ; \ / \\ ; N1 O2 ; \ ; \ ; \ ; O1P H5'1H4' O4' \ ; | | \ / \ \ ; -P-O5'-C5'---C4' C1' ; | | \ / \ ; O2P H5'2 C3'--C2' H1' ; / \ / \ ; O3' H3' O2' H2'2 ; | | ; H2'1 ; [ atoms ] P P 1.50 0 O1P ON3 -0.78 1 O2P ON3 -0.78 2 O5' ON2 -0.57 3 C5' CN8B -0.08 4 H5'1 HN8 0.09 5 H5'2 HN8 0.09 6 C4' CN7 0.16 7 H4' HN7 0.09 8 O4' ON6B -0.50 9 C1' CN7B 0.16 10 H1' HN7 0.09 11 N1 NN2B -0.34 12 C6 CN3 0.20 13 H6 HN3 0.14 14 C2 CN1T 0.55 15 O2 ON1 -0.45 16 N3 NN2U -0.46 17 H3 HN2 0.36 18 C4 CN1 0.53 19 O4 ON1 -0.48 20 C5 CN3 -0.15 21 H5 HN3 0.10 22 C2' CN7B 0.14 23 H2'2 HN7 0.09 24 O2' ON5 -0.66 25 H2'1 HN5 0.43 26 C3' CN7 0.01 27 H3' HN7 0.09 28 O3' ON2 -0.57 29 [ bonds ] -O3' P P O1P P O2P P O5' O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' C1' N1 C1' C2' N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 C2' C3' C3' O3' C2' O2' O2' H2'1 C1' H1' C2' H2'2 C3' H3' C4' H4' C5' H5'1 C5' H5'2 C5 H5 C6 H6 C2 O2 C4 O4 C5 C6 [ impropers ] C2 N1 N3 O2 C4 N3 C5 O4