!RNA_DNA_amber.top !This file is the parameter file that goes with RNA_DNA_amber.top. !It was developed from the topology file of Parkinson et al. (1). The principle !change is that all paths for all dihedral angles are explictly identified. Thus !torsional energies are computed as the sums of all of their components. In this !respect, thse files conform to AMBER usage (Cornell et al. (2)). !Created 9/97 by Jason P. Rife and Peter B. Moore. ! !1. Parkinson et al. (1996) Acta Cryst. D52, 57-64 !2. Cornell et al. (1995) JACS 117, 5197-5197 ! !Changed charges on O1P adn O2P per pbm's instructions from -0.3887 to !-0.6260. 12/31/97 ! ! This file must be used in conjunction with RNA_DNA_maber.par ! ! REMARK RNA_DNA_amber.top set echo=on end set message=on end AUTOGENERATE ANGLES=TRUE END {*==========================*} {* DNA/RNA default masses *} MASS P 30.97400! phosphorus MASS O1P 15.99940! O in phosphate MASS O2P 15.99940! O in phosphate MASS O5R 15.99940! ester -P-O-C- MASS C5R 12.011! corresp. to CH2E MASS C4R 12.011! corresp. to CH1E MASS C3R 12.011! corresp. to CH1E MASS C2R 12.011! corresp. to CH1E MASS C1R 12.011! corresp. to CH1E MASS O4R 15.99940! ester -P-O-C- MASS O3R 15.99940! ester -P-O-C- MASS O2R 15.99940! ester -P-O-C- MASS OH 15.99940! corresp. to OH1 !DEOXY SUGAR MASS C5D 14.02700! corresp. to CH2E MASS C4D 13.01900! corresp. to CH1E MASS C3D 13.01900! corresp. to CH1E MASS C2D 13.01900! corresp. to CH1E MASS C1D 13.01900! corresp. to CH1E MASS O4D 15.99940! ester -P-O-C- MASS O5D 15.99940! MASS O3D 15.99940! ! Insert Bases ! Generic MASS N2 14.00670! nitrogen in -NH2 MASS NNA 14.00670! corresp. to NH1 MASS ON 15.99940! corresp. to O MASS NC 14.00670! corresp. to NR MASS NS 14.00670! nitrogen in ring >N- ! Insert 4 Bases ! GUA MASS N9G 14.00670! nitrogen in ring >N- MASS C2G 12.011! (prev CE) MASS N3G 14.00670! (prev NC) MASS C4G 12.01100! (prev CB) MASS C5G 12.01100! (prev CB) MASS C6G 12.01100! (prev CN) MASS N7G 14.00670! (prev NB) MASS C8G 12.011! (prev CE) MASS O6G 15.99940! (prev CE) MASS N2G 14.00670! nitrogen in -NH2 ! ADE MASS N9A 14.00670! nitrogen in ring >N- MASS C2A 12.011! (prev CE) MASS N3A 14.00670! (prev NC) MASS C4A 12.01100! (prev CB) MASS C5A 12.01100! (prev CB) MASS C6A 12.01100! (prev CA) MASS N7A 14.00670! (prev NB) MASS C8A 12.011! (prev CE) MASS N6A 14.00670! nitrogen in -NH2 ! CYT MASS N1C 14.00670! nitrogen in ring >N- MASS C2C 12.01100! (prev CN) MASS C4C 12.01100! (prev CA) MASS C5C 12.011! (prev CF) MASS C6C 12.011! (prev CF) MASS N4C 14.00670! nitrogen in -NH2 ! THY MASS N1T 14.00670! nitrogen in ring >N- MASS N3T 14.00670! nitrogen in ring >N- MASS C2T 12.01100! (prev CN) MASS C4T 12.01100! (prev CN) MASS C5T 12.011! (prev CS) MASS C6T 12.011! (prev CF) MASS CC3E 12.01100! (prev CF) ! END MASS H 1.00800! non-exchangeable Hydrogens MASS HN 1.00800! corresp. to H MASS H2 1.00800! hydrogen in -NH2 MASS HO 1.00800! hydroxy hydrogen ! URI MASS N1U 14.00670! nitrogen in ring >N- MASS C2U 12.01100! (prev CN) MASS C4U 12.01100! (prev CA) MASS C5U 12.011! (prev CF) MASS C6U 12.011! (prev CF) MASS N3U 14.00670! RESIdue GUA GROUp ATOM P TYPE=P CHARGE=1.1662 END ATOM O1P TYPE=O1P CHARGE=-0.6260 END ATOM O2P TYPE=O2P CHARGE=-0.6260 END ATOM O5' TYPE=O5R CHARGE=-0.4989 END GROUp ATOM C5' TYPE=C5R CHARGE=0.0558 END ATOM H5' TYPE=H CHARGE=0.0679 END !JPR ATOM H5'' TYPE=H CHARGE=0.0679 END ATOM C4' TYPE=C4R CHARGE=0.1065 END ATOM H4' TYPE=H CHARGE=0.1174 END !JPR ATOM O4' TYPE=O4R CHARGE=-0.3548 END ATOM C1' TYPE=C1R CHARGE=0.0191 END !JPR ATOM H1' TYPE=H CHARGE=0.2006 END !JPR ! Insert Base GROUp ATOM N9 TYPE=N9G CHARGE=0.0492 END ATOM C4 TYPE=C4G CHARGE=0.122 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3G CHARGE=-0.6323 EXCLusion=( C6 ) END ATOM C2 TYPE=C2G CHARGE=0.7657 EXCLusion=( C5 ) END GROUp ATOM N2 TYPE=N2G CHARGE=-0.9672 END ATOM H21 TYPE=H2 CHARGE=0.4364 END ATOM H22 TYPE=H2 CHARGE=0.4364 END GROUp ATOM N1 TYPE=NNA CHARGE=-0.4787 END ATOM H1 TYPE=HN CHARGE=0.3424 END GROUp ATOM C6 TYPE=C6G CHARGE=0.4770 END ATOM O6 TYPE=O6G CHARGE=-0.5597 END GROUp ATOM C5 TYPE=C5G CHARGE=0.1744 END ATOM N7 TYPE=N7G CHARGE=-0.7509 END ATOM C8 TYPE=C8G CHARGE=0.1374 END ATOM H8 TYPE=H CHARGE=0.1640 END ! GROUP ATOM C2' TYPE=C2R CHARGE=0.0670 END ATOM H2' TYPE=H CHARGE=0.0972 END ATOM O2' TYPE=O2R CHARGE=-0.6139 END ATOM HO2' TYPE=HO CHARGE=0.4186 END GROUP ATOM C3' TYPE=C3R CHARGE=0.2022 END ATOM H3' TYPE=H CHARGE=0.0615 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.5246 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N9 BOND C1' C2' BOND N9 C4 BOND N9 C8 BOND C4 N3 BOND C4 C5 BOND N3 C2 BOND C2 N2 BOND C2 N1 BOND N2 H21 BOND N2 H22 BOND N1 H1 BOND N1 C6 BOND C6 O6 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND C8 H8 BOND O2' HO2' BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' !this is a test !X-N9-C8-X DIHE C1' N9 C8 N7 DIHE C1' N9 C8 H8 DIHE C4 N9 C8 N7 DIHE C4 N9 C8 H8 !X-C8-N7-X DIHE H8 C8 N7 C5 DIHE N9 C8 N7 C5 !X-N7-C5-X DIHE C8 N7 C5 C4 DIHE C8 N7 C5 C6 !X-C5-C4-X DIHE N7 C5 C4 N9 DIHE N7 C5 C4 N3 DIHE C6 C5 C4 N9 DIHE C6 C5 C4 N3 !X-C4-N3-X DIHE C5 C4 N3 C2 DIHE N9 C4 N3 C2 !X-N3-C2-X DIHE C4 N3 C2 N1 DIHE C4 N3 C2 N2 !X-C2-N2-X DIHE N3 C2 N2 H21 DIHE N3 C2 N2 H22 DIHE N1 C2 N2 H21 DIHE N1 C2 N2 H22 !X-C2-N1-X DIHE N3 C2 N1 H1 DIHE N3 C2 N1 C6 DIHE N2 C2 N1 H1 DIHE N2 C2 N1 C6 !X-N1-C6-X DIHE H1 N1 C6 O6 DIHE H1 N1 C6 C5 DIHE C2 N1 C6 O6 DIHE C2 N1 C6 C5 !X-C6-C5-X DIHE N1 C6 C5 C4 DIHE N1 C6 C5 N7 DIHE O6 C6 C5 C4 DIHE O6 C6 C5 N7 !X-C4-N9-X DIHE C5 C4 N9 C1' DIHE C5 C4 N9 C8 DIHE N3 C4 N9 C1' DIHE N3 C4 N9 C8 !GUA DIHE C8 N9 C1' H1' DIHE C8 N9 C1' C2' DIHE C8 N9 C1' O4' DIHE C4 N9 C1' H1' DIHE C4 N9 C1' C2' DIHE C4 N9 C1' O4' !RES !X-05R-C5R-X DIHE P O5' C5' H5' DIHE P O5' C5' H5'' DIHE P O5' C5' C4' !X-P-O5'-X DIHE O1P P O5' C5' DIHE O2P P O5' C5' !X-C5'-C4'-X DIHE O5' C5' C4' H4' DIHE H5' C5' C4' H4' DIHE H5'' C5' C4' H4' DIHE O5' C5' C4' O4' DIHE H5' C5' C4' O4' DIHE H5'' C5' C4' O4' DIHE O5' C5' C4' C3' DIHE H5' C5' C4' C3' DIHE H5'' C5' C4' C3' !Nu's !X-O4R-C1R-X DIHE C4' O4' C1' H1' DIHE C4' O4' C1' N9 DIHE C4' O4' C1' C2' !X-C1R-C2R-X DIHE O4' C1' C2' H2' DIHE H1' C1' C2' H2' DIHE N9 C1' C2' H2' DIHE O4' C1' C2' O2' DIHE H1' C1' C2' O2' DIHE N9 C1' C2' O2' DIHE O4' C1' C2' C3' DIHE H1' C1' C2' C3' DIHE N9 C1' C2' C3' !X-C2R-C3R-X DIHE C1' C2' C3' H3' DIHE H2' C2' C3' H3' DIHE O2' C2' C3' H3' DIHE C1' C2' C3' O3' DIHE H2' C2' C3' O3' DIHE O2' C2' C3' O3' DIHE C1' C2' C3' C4' DIHE H2' C2' C3' C4' DIHE O2' C2' C3' C4' !X-C3R-C2R-X DIHE C2' C3' C4' H4' DIHE O3' C3' C4' H4' DIHE H3' C3' C4' H4' DIHE C2' C3' C4' O4' DIHE O3' C3' C4' O4' DIHE H3' C3' C4' O4' DIHE C2' C3' C4' C5' DIHE O3' C3' C4' C5' DIHE H3' C3' C4' C5' !X-C4R-O4R-C1R DIHE H4' C4' O4' C1' DIHE C5' C4' O4' C1' DIHE C3' C4' O4' C1' ! These impropers are commented out so that they can be replaced ! with the AMBER set. They should be removed if AMBER works 11/4/97 ! ! IMPRoper N3 C2 N2 H21 IMPRoper C1' C4 C8 N9 ! IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 ! IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 ! IMPRoper C8 N9 C4 C5 IMPRoper N2 N3 N1 C2 ! IMPRoper H1 C2 C6 N1 IMPRoper O6 N1 C5 C6 ! IMPRoper C4 N3 C2 N1 IMPRoper N3 C2 N1 C6 ! IMPRoper C2 N1 C6 C5 IMPRoper N1 C6 C5 C4 ! IMPRoper C6 C5 C4 N3 IMPRoper C5 C4 N3 C2 ! IMPRoper H22 H21 C2 N2 ! IMPRoper H8 N7 N9 C8 !IMPRoper to keep the two purine rings parallel: ! IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 ! IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 ! AMBER Impropers IMPRoper C2 N1 N3 N2 IMPRoper C6 N1 C5 O6 IMPRoper C8 N9 N7 H8 IMPRoper N1 C2 C6 H1 IMPRoper N2 C2 H21 H22 IMPRoper N9 C4 C8 C1' !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N9 !C1' IMPRoper H2' C3' C1' O2' !C2' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' DONOr H21 N2 DONOr H22 N2 DONOr H1 N1 DONOr H2' O2' ACCEptor O6 C6 ACCEptor N3 " " ACCEptor O1P P ACCEptor O2P P ACCEptor O2' " " END {GUA} ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- RESIdue ADE GROUp ATOM P TYPE=P CHARGE=1.1662 END ATOM O1P TYPE=O1P CHARGE=-0.6260 END ATOM O2P TYPE=O2P CHARGE=-0.6260 END ATOM O5' TYPE=O5R CHARGE=-0.4989 END GROUp ATOM C5' TYPE=C5R CHARGE=0.0558 END ATOM H5' TYPE=H CHARGE=0.0679 END !JPR ATOM H5'' TYPE=H CHARGE=0.0679 END ATOM C4' TYPE=C4R CHARGE=0.1065 END ATOM H4' TYPE=H CHARGE=0.1174 END !JPR ATOM O4' TYPE=O4R CHARGE=-0.3548 END ATOM C1' TYPE=C1R CHARGE=0.0394 END ATOM H1' TYPE=H CHARGE=0.2007 END ! Insert Base GROUp ATOM N9 TYPE=N9A CHARGE=-0.0251 END ATOM C4 TYPE=C4A CHARGE=0.3053 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.6997 EXCLusion=( C6 ) END ATOM C2 TYPE=C2A CHARGE=0.5875 EXCLusion=( C5 ) END ATOM H2 TYPE=H CHARGE=0.0473 END GROUp ATOM N1 TYPE=NC CHARGE=-0.7615 END ATOM C6 TYPE=C6A CHARGE=0.7009 END GROUp ATOM N6 TYPE=N6A CHARGE=-0.9019 END ATOM H61 TYPE=H2 CHARGE=0.4115 END ATOM H62 TYPE=H2 CHARGE=0.4115 END GROUp ATOM C5 TYPE=C5A CHARGE=0.0515 END ATOM N7 TYPE=N7A CHARGE=-0.6073 END ATOM C8 TYPE=C8A CHARGE=0.2006 END ATOM H8 TYPE=H CHARGE=0.1553 END ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.0670 END ATOM H2' TYPE=H CHARGE=0.0972 END ATOM O2' TYPE=O2R CHARGE=-0.6139 END ATOM HO2' TYPE=HO CHARGE=0.4186 END GROUP ATOM C3' TYPE=C3R CHARGE=0.2022 END ATOM H3' TYPE=H CHARGE=0.0615 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.5246 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N9 BOND C1' C2' BOND N9 C4 BOND N9 C8 BOND C4 N3 BOND C4 C5 BOND N3 C2 BOND C2 N1 BOND N1 C6 BOND C6 N6 BOND N6 H61 BOND N6 H62 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C2' C3' BOND C2' O2' BOND C3' O3' BOND C8 H8 BOND C2 H2 BOND O2' HO2' BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' !this is a test !X-N9-C8-X DIHE C1' N9 C8 N7 DIHE C1' N9 C8 H8 DIHE C4 N9 C8 N7 DIHE C4 N9 C8 H8 !X-C8-N7-X DIHE H8 C8 N7 C5 DIHE N9 C8 N7 C5 !X-N7-C5-X DIHE C8 N7 C5 C4 DIHE C8 N7 C5 C6 !X-C5-C4-X DIHE N7 C5 C4 N9 DIHE N7 C5 C4 N3 DIHE C6 C5 C4 N9 DIHE C6 C5 C4 N3 !X-C4-N3-X DIHE C5 C4 N3 C2 DIHE N9 C4 N3 C2 !X-N3-C2-X DIHE C4 N3 C2 N1 DIHE C4 N3 C2 H2 !X-C2-NC-X DIHE N3 C2 N1 C6 DIHE H2 C2 N1 C6 !X-NC-C6-X DIHE C2 N1 C6 N6 DIHE C2 N1 C6 C5 !X-C6-N6-X DIHE N1 C6 N6 H61 DIHE N1 C6 N6 H62 DIHE C5 C6 N6 H61 DIHE C5 C6 N6 H62 !X-C6-C5-X DIHE N1 C6 C5 C4 DIHE N1 C6 C5 N7 DIHE N6 C6 C5 C4 DIHE N6 C6 C5 N7 !X-C4-N9-X DIHE C5 C4 N9 C1' DIHE C5 C4 N9 C8 DIHE N3 C4 N9 C1' DIHE N3 C4 N9 C8 !ADE DIHE C8 N9 C1' H1' DIHE C8 N9 C1' C2' DIHE C8 N9 C1' O4' DIHE C4 N9 C1' H1' DIHE C4 N9 C1' C2' DIHE C4 N9 C1' O4' !RES !X-05R-C5R-X DIHE P O5' C5' H5' DIHE P O5' C5' H5'' DIHE P O5' C5' C4' !X-P-O5'-X DIHE O1P P O5' C5' DIHE O2P P O5' C5' !X-C5'-C4'-X DIHE O5' C5' C4' H4' DIHE H5' C5' C4' H4' DIHE H5'' C5' C4' H4' DIHE O5' C5' C4' O4' DIHE H5' C5' C4' O4' DIHE H5'' C5' C4' O4' DIHE O5' C5' C4' C3' DIHE H5' C5' C4' C3' DIHE H5'' C5' C4' C3' !Nu's !X-O4R-C1R-X DIHE C4' O4' C1' H1' DIHE C4' O4' C1' N9 DIHE C4' O4' C1' C2' !X-C1R-C2R-X DIHE O4' C1' C2' H2' DIHE H1' C1' C2' H2' DIHE N9 C1' C2' H2' DIHE O4' C1' C2' O2' DIHE H1' C1' C2' O2' DIHE N9 C1' C2' O2' DIHE O4' C1' C2' C3' DIHE H1' C1' C2' C3' DIHE N9 C1' C2' C3' !X-C2R-C3R-X DIHE C1' C2' C3' H3' DIHE H2' C2' C3' H3' DIHE O2' C2' C3' H3' DIHE C1' C2' C3' O3' DIHE H2' C2' C3' O3' DIHE O2' C2' C3' O3' DIHE C1' C2' C3' C4' DIHE H2' C2' C3' C4' DIHE O2' C2' C3' C4' !X-C3R-C2R-X DIHE C2' C3' C4' H4' DIHE O3' C3' C4' H4' DIHE H3' C3' C4' H4' DIHE C2' C3' C4' O4' DIHE O3' C3' C4' O4' DIHE H3' C3' C4' O4' DIHE C2' C3' C4' C5' DIHE O3' C3' C4' C5' DIHE H3' C3' C4' C5' !X-C4R-O4R-C1R DIHE H4' C4' O4' C1' DIHE C5' C4' O4' C1' DIHE C3' C4' O4' C1' ! AMBER IMPRoper C2 N3 N1 H2 IMPRoper C6 C5 N1 N6 IMPRoper C8 N9 N7 H8 IMPRoper N6 C6 H61 H62 IMPRoper N9 C4 C8 C1' ! !IMPRoper C5 C6 N6 H61 IMPRoper C1' C4 C8 N9 !IMPRoper N9 C4 C5 N7 IMPRoper C4 C5 N7 C8 !IMPRoper C5 N7 C8 N9 IMPRoper N7 C8 N9 C4 !IMPRoper C8 N9 C4 C5 IMPRoper N6 N1 C5 C6 !IMPRoper H62 C6 H61 N6 IMPRoper C4 N3 C2 N1 !IMPRoper N3 C2 N1 C6 IMPRoper C2 N1 C6 C5 !IMPRoper N1 C6 C5 C4 IMPRoper C6 C5 C4 N3 !IMPRoper C5 C4 N3 C2 !IMPRoper H2 N1 N3 C2 IMPRoper H8 N7 N9 C8 ! IMPRoper to keep the two purine rings parallel: !IMPRoper C8 C4 C5 N1 IMPRoper C8 C5 C4 C2 !IMPRoper N3 C4 C5 N7 IMPRoper C6 C5 C4 N9 !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N9 !C1' IMPRoper H2' C3' C1' O2' !C2' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' DONOr H61 N6 DONOr H62 N6 DONOr H2' O2' ACCEptor N3 " " ACCEptor N1 " " ACCEptor O1P P ACCEptor O2P P ACCEptor O2' " " END {ADE} ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- RESIdue CYT GROUp ATOM P TYPE=P CHARGE=1.1662 END ATOM O1P TYPE=O1P CHARGE=-0.6260 END ATOM O2P TYPE=O2P CHARGE=-0.6260 END ATOM O5' TYPE=O5R CHARGE=-0.4989 END GROUp ATOM C5' TYPE=C5R CHARGE=0.0558 END ATOM H5' TYPE=H CHARGE=0.0679 END !JPR ATOM H5'' TYPE=H CHARGE=0.0679 END ATOM C4' TYPE=C4R CHARGE=0.1065 END ATOM H4' TYPE=H CHARGE=0.1174 END !JPR ATOM O4' TYPE=O4R CHARGE=-0.3548 END ATOM C1' TYPE=C1R CHARGE=0.0066 END ATOM H1' TYPE=H CHARGE=0.2029 END ! Insert Base GROUp ATOM N1 TYPE=N1C CHARGE=-0.0484 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.0053 EXCLUSION=( N3 ) END ATOM H6 TYPE=H CHARGE=0.1958 END GROUp ATOM C2 TYPE=C2C CHARGE=0.7538 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.6252 END GROUp ATOM N3 TYPE=NC CHARGE=-0.7584 END ATOM C4 TYPE=C4C CHARGE=0.8185 END GROUp ATOM N4 TYPE=N4C CHARGE=-0.9530 END ATOM H41 TYPE=H2 CHARGE=0.4234 END ATOM H42 TYPE=H2 CHARGE=0.4234 END GROUp ATOM C5 TYPE=C5C CHARGE=-0.5215 END !CHRG ATOM H5 TYPE=H CHARGE=0.1928 END GROUp ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.0670 END ATOM H2' TYPE=H CHARGE=0.0972 END ATOM O2' TYPE=O2R CHARGE=-0.6139 END ATOM HO2' TYPE=HO CHARGE=0.4186 END GROUP ATOM C3' TYPE=C3R CHARGE=0.2022 END ATOM H3' TYPE=H CHARGE=0.0615 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.5246 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 N3 BOND N3 C4 BOND C4 N4 BOND N4 H41 BOND N4 H42 BOND C2 O2 BOND C4 C5 BOND C5 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND C6 H6 BOND C5 H5 BOND O2' HO2' BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' !X-N1-C6-X DIHE C1' N1 C6 C5 DIHE C1' N1 C6 H6 DIHE C2 N1 C6 C5 DIHE C2 N1 C6 H6 !X-C6-C5-X DIHE H6 C6 C5 H5 DIHE H6 C6 C5 C4 DIHE N1 C6 C5 H5 DIHE N1 C6 C5 C4 !X-C5-C4-X DIHE H5 C5 C4 N4 DIHE H5 C5 C4 N3 DIHE C6 C5 C4 N4 DIHE C6 C5 C4 N3 !X-C4-N4-X DIHE C5 C4 N4 H41 DIHE C5 C4 N4 H42 DIHE N3 C4 N4 H41 DIHE N3 C4 N4 H42 !X-C4-N3-X DIHE C5 C4 N3 C2 DIHE N4 C4 N3 C2 !X-N3-C2-X DIHE C4 N3 C2 O2 DIHE C4 N3 C2 N1 !X-C2-N1-X DIHE N3 C2 N1 C6 DIHE N3 C2 N1 C1' DIHE O2 C2 N1 C6 DIHE O2 C2 N1 C1' !CYT DIHE C6 N1 C1' H1' DIHE C6 N1 C1' C2' DIHE C6 N1 C1' O4' DIHE C2 N1 C1' H1' DIHE C2 N1 C1' C2' DIHE C2 N1 C1' O4' !RES !X-05R-C5R-X DIHE P O5' C5' H5' DIHE P O5' C5' H5'' DIHE P O5' C5' C4' !X-P-O5'-X DIHE O1P P O5' C5' DIHE O2P P O5' C5' !X-C5'-C4'-X DIHE O5' C5' C4' H4' DIHE H5' C5' C4' H4' DIHE H5'' C5' C4' H4' DIHE O5' C5' C4' O4' DIHE H5' C5' C4' O4' DIHE H5'' C5' C4' O4' DIHE O5' C5' C4' C3' DIHE H5' C5' C4' C3' DIHE H5'' C5' C4' C3' !Nu's !X-O4R-C1R-X DIHE C4' O4' C1' H1' DIHE C4' O4' C1' N1 DIHE C4' O4' C1' C2' !X-C1R-C2R-X DIHE O4' C1' C2' H2' DIHE H1' C1' C2' H2' DIHE N1 C1' C2' H2' DIHE O4' C1' C2' O2' DIHE H1' C1' C2' O2' DIHE N1 C1' C2' O2' DIHE O4' C1' C2' C3' DIHE H1' C1' C2' C3' DIHE N1 C1' C2' C3' !X-C2R-C3R-X DIHE C1' C2' C3' H3' DIHE H2' C2' C3' H3' DIHE O2' C2' C3' H3' DIHE C1' C2' C3' O3' DIHE H2' C2' C3' O3' DIHE O2' C2' C3' O3' DIHE C1' C2' C3' C4' DIHE H2' C2' C3' C4' DIHE O2' C2' C3' C4' !X-C3R-C2R-X DIHE C2' C3' C4' H4' DIHE O3' C3' C4' H4' DIHE H3' C3' C4' H4' DIHE C2' C3' C4' O4' DIHE O3' C3' C4' O4' DIHE H3' C3' C4' O4' DIHE C2' C3' C4' C5' DIHE O3' C3' C4' C5' DIHE H3' C3' C4' C5' !X-C4R-O4R-C1R DIHE H4' C4' O4' C1' DIHE C5' C4' O4' C1' DIHE C3' C4' O4' C1' ! AMBER IMPRoper C2 N1 N3 O2 IMPRoper C4 N4 C5 N3 IMPRoper C5 C4 C5 H5 IMPRoper C6 N1 C5 H6 IMPRoper N1 C2 C6 C1' IMPRoper N4 C4 H41 H42 ! IMPRoper C5 C4 N4 H41 IMPRoper C1' C2 C6 N1 ! IMPRoper O2 N1 N3 C2 IMPRoper N4 N3 C5 C4 ! IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 ! IMPRoper N3 C4 C5 C6 IMPRoper C4 C5 C6 N1 ! IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 ! IMPRoper H42 C4 H41 N4 ! IMPRoper H5 C4 C6 C5 IMPRoper H6 N1 C5 C6 !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N1 !C1' IMPRoper H2' C3' C1' O2' !C2' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' DONOr H42 N4 DONOr H2' O2' DONOr H41 N4 ACCEptor O2 C2 ACCEptor N3 " " ACCEptor O1P P ACCEptor O2P P ACCEptor O2' " " ! added, ATB, 8-9-84 END {CYT} !------------------------------------------------------------------ ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- RESIdue THY GROUp ATOM P TYPE=P CHARGE=1.20 END ATOM O1P TYPE=O1P CHARGE=-0.40 END ATOM O2P TYPE=O2P CHARGE=-0.40 END ATOM O5' TYPE=O5R CHARGE=-0.36 END GROUp ATOM C5' TYPE=C5R CHARGE=-0.070 END ATOM H5' TYPE=H CHARGE=0.035 END ATOM H5'' TYPE=H CHARGE=0.035 END GROUp ATOM C4' TYPE=C4R CHARGE=0.065 END ATOM H4' TYPE=H CHARGE=0.035 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ATOM H1' TYPE=H CHARGE=0.165 END ! Insert Base GROUp ATOM N1 TYPE=N1T CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6T CHARGE=0.155 EXCLUSION=( N3 ) END ATOM H6 TYPE=H CHARGE=0.035 END GROUp ATOM C2 TYPE=C2T CHARGE=0.35 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.35 END GROUp ATOM N3 TYPE=N3T CHARGE=-0.26 END ATOM H3 TYPE=HN CHARGE=0.26 END GROUp ATOM C4 TYPE=C4T CHARGE=0.30 END ATOM O4 TYPE=ON CHARGE=-0.30 END GROUp ATOM C5 TYPE=C5T CHARGE=-0.035 END ATOM C7 TYPE=CC3E CHARGE=-0.070 END ! name per IUPAC-IUB recomm. ATOM H71 TYPE=H CHARGE=0.035 END ! name per IUPAC-IUB recomm. ATOM H72 TYPE=H CHARGE=0.035 END ! name per IUPAC-IUB recomm. ATOM H73 TYPE=H CHARGE=0.035 END ! name per IUPAC-IUB recomm. GROUp ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.115 END ATOM H2' TYPE=H CHARGE=0.035 END ATOM O2' TYPE=O2R CHARGE=-0.40 END ATOM HO2' TYPE=HO CHARGE=0.25 END GROUP ATOM C3' TYPE=C3R CHARGE=-0.035 END ATOM H3' TYPE=H CHARGE=0.035 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 O2 BOND C2 N3 BOND N3 H3 BOND N3 C4 BOND C4 O4 BOND C4 C5 BOND C5 C7 BOND C5 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND O2' H2' BOND O2' HO2' BOND C5' H5' BOND C5' H5'' BOND C3' H3' BOND C2' H2' BOND C1' H1' BOND C4' H4' BOND C7 H71 BOND C7 H72 BOND C7 H73 BOND C6 H6 DIHEdral P O5' C5' C4' DIHEdral O5' C5' C4' O4' DIHEdral O5' C5' C4' C3' DIHEdral C3' C4' O4' C1' DIHEdral C4' O4' C1' C2' DIHEdral O4' C1' C2' C3' DIHEdral C1' C2' C3' C4' DIHEdral O4' C4' C3' O3' DIHEdral C5' C4' C3' C2' DIHEdral O2' C2' C3' O3' DIHEdral O4' C1' N1 C2 DIHEdral C3' C2' O2' H2' ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 ! AMBER IMPRoper C2 N1 N3 O2 IMPRoper C4 N3 C5 O4 IMPRoper C5 C6 C4 C7 IMPRoper C6 N1 C5 H6 IMPRoper N1 C2 C6 C1' IMPRoper N3 C2 C4 H3 ! IMPRoper O4 N3 C5 C4 IMPRoper C1' C2 C6 N1 ! IMPRoper O2 N1 N3 C2 IMPRoper C4 C5 C6 N1 ! IMPRoper N1 C2 N3 C4 IMPRoper C2 N3 C4 C5 ! IMPRoper N3 C4 C5 C6 ! IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 N3 ! IMPRoper H3 C2 C4 N3 ! IMPRoper C7 C4 C6 C5 IMPRoper H6 N1 C5 C6 !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N1 ! C1' IMPRoper H2' C3' C1' O2' !C2' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' DONOr H3 N3 DONOr HO2' O2' ACCEptor O2 C2 ACCEptor O4 C4 ACCEptor O1P P ACCEptor O2P P ACCEptor O2' " " ! added, ATB, 8-9-84 END {THY} !------------------------------------------------------------------ RESIdue URI GROUp ATOM P TYPE=P CHARGE=1.1662 END ATOM O1P TYPE=O1P CHARGE=-0.6260 END ATOM O2P TYPE=O2P CHARGE=-0.6260 END ATOM O5' TYPE=O5R CHARGE=-0.4989 END GROUp ATOM C5' TYPE=C5R CHARGE=0.0558 END ATOM H5' TYPE=H CHARGE=0.0679 END !JPR ATOM H5'' TYPE=H CHARGE=0.0679 END ATOM C4' TYPE=C4R CHARGE=0.1065 END ATOM H4' TYPE=H CHARGE=0.1174 END !JPR ATOM O4' TYPE=O4R CHARGE=-0.3548 END ATOM C1' TYPE=C1R CHARGE=0.0674 END ATOM H1' TYPE=H CHARGE=0.1824 END GROUp ATOM N1 TYPE=N1U CHARGE=0.0418 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6U CHARGE=-0.1226 EXCLUSION=( N3 ) END ATOM H6 TYPE=H CHARGE=0.2188 END GROUp ATOM C2 TYPE=C2U CHARGE=0.4687 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.5477 END GROUp ATOM N3 TYPE=N3U CHARGE=-0.3549 END ATOM H3 TYPE=HN CHARGE=0.3154 END GROUp ATOM C4 TYPE=C4U CHARGE=0.5952 END ATOM O4 TYPE=ON CHARGE=-0.5761 END GROUp ATOM C5 TYPE=C5U CHARGE=-0.3635 END !JPR ATOM H5 TYPE=H CHARGE=0.1811 END !JPR GROUP ATOM C2' TYPE=C2R CHARGE=0.0670 END ATOM H2' TYPE=H CHARGE=0.0972 END ATOM O2' TYPE=O2R CHARGE=-0.6139 END ATOM HO2' TYPE=HO CHARGE=0.4186 END GROUP ATOM C3' TYPE=C3R CHARGE=0.2022 END ATOM H3' TYPE=H CHARGE=0.0615 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.5246 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 O2 BOND C2 N3 BOND N3 H3 BOND N3 C4 BOND C4 O4 BOND C4 C5 BOND C5 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND C5 H5 BOND C6 H6 BOND O2' HO2' BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' !X-N1-C6-X DIHE C1' N1 C6 C5 DIHE C1' N1 C6 H6 DIHE C2 N1 C6 C5 DIHE C2 N1 C6 H6 !X-C6-C5-X DIHE H6 C6 C5 H5 DIHE H6 C6 C5 C4 DIHE N1 C6 C5 H5 DIHE N1 C6 C5 C4 !X-C5-C4-X DIHE H5 C5 C4 O4 DIHE H5 C5 C4 N3 DIHE C6 C5 C4 O4 DIHE C6 C5 C4 N3 !X-C4-N3-X DIHE C5 C4 N3 C2 DIHE O4 C4 N3 C2 DIHE C5 C4 N3 H3 DIHE O4 C4 N3 H3 !X-N3-C2-X DIHE C4 N3 C2 O2 DIHE C4 N3 C2 N1 DIHE H3 N3 C2 O2 DIHE H3 N3 C2 N1 !X-C2-N1-X DIHE N3 C2 N1 C6 DIHE N3 C2 N1 C1' DIHE O2 C2 N1 C6 DIHE O2 C2 N1 C1' !URI DIHE C6 N1 C1' H1' DIHE C6 N1 C1' C2' DIHE C6 N1 C1' O4' DIHE C2 N1 C1' H1' DIHE C2 N1 C1' C2' DIHE C2 N1 C1' O4' !RES !X-05R-C5R-X DIHE P O5' C5' H5' DIHE P O5' C5' H5'' DIHE P O5' C5' C4' !X-P-O5'-X DIHE O1P P O5' C5' DIHE O2P P O5' C5' !X-C5'-C4'-X DIHE O5' C5' C4' H4' DIHE H5' C5' C4' H4' DIHE H5'' C5' C4' H4' DIHE O5' C5' C4' O4' DIHE H5' C5' C4' O4' DIHE H5'' C5' C4' O4' DIHE O5' C5' C4' C3' DIHE H5' C5' C4' C3' DIHE H5'' C5' C4' C3' !Nu's !X-O4R-C1R-X DIHE C4' O4' C1' H1' DIHE C4' O4' C1' N1 DIHE C4' O4' C1' C2' !X-C1R-C2R-X DIHE O4' C1' C2' H2' DIHE H1' C1' C2' H2' DIHE N1 C1' C2' H2' DIHE O4' C1' C2' O2' DIHE H1' C1' C2' O2' DIHE N1 C1' C2' O2' DIHE O4' C1' C2' C3' DIHE H1' C1' C2' C3' DIHE N1 C1' C2' C3' !X-C2R-C3R-X DIHE C1' C2' C3' H3' DIHE H2' C2' C3' H3' DIHE O2' C2' C3' H3' DIHE C1' C2' C3' O3' DIHE H2' C2' C3' O3' DIHE O2' C2' C3' O3' DIHE C1' C2' C3' C4' DIHE H2' C2' C3' C4' DIHE O2' C2' C3' C4' !X-C3R-C2R-X DIHE C2' C3' C4' H4' DIHE O3' C3' C4' H4' DIHE H3' C3' C4' H4' DIHE C2' C3' C4' O4' DIHE O3' C3' C4' O4' DIHE H3' C3' C4' O4' DIHE C2' C3' C4' C5' DIHE O3' C3' C4' C5' DIHE H3' C3' C4' C5' !X-C4R-O4R-C1R DIHE H4' C4' O4' C1' DIHE C5' C4' O4' C1' DIHE C3' C4' O4' C1' ! AMBER IMPRoper C2 N1 N3 O2 IMPRoper C4 N3 C5 O4 IMPRoper C5 C6 C4 H5 IMPRoper C6 N1 C5 H6 IMPRoper N1 C2 C6 C1' IMPRoper N3 C2 C4 H3 ! IMPRoper C1' C2 C6 N1 ! IMPRoper O2 N1 N3 C2 IMPRoper H3 C2 C4 N3 ! IMPRoper O4 N3 C5 C4 IMPRoper N1 C2 N3 C4 ! IMPRoper C2 N3 C4 C5 IMPRoper N3 C4 C5 C6 ! IMPRoper C4 C5 C6 N1 IMPRoper C5 C6 N1 C2 ! IMPRoper C6 N1 C2 N3 ! IMPRoper H5 C4 C6 C5 IMPRoper H6 N1 C5 C6 !GENERAL RIBOSE IMPROPERS IMPRoper H1' C2' O4' N1 !C1' IMPRoper H2' C3' C1' O2' !C2' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' DONOr H3 N3 DONOr H2' O2' ACCEptor O2 C2 ACCEptor O4 C4 ACCEptor O1P P ACCEptor O2P P ACCEptor O2' " " END {URI} !------------------------------------------------------------------ !------------------------------------------------------------------ !note: O3' and O5' will remain O3R and O5R for DNA molecules !this is consistent with values in parameter files PRESidue DEOX ! Patch to make DEOXYribose of the ribose DELETE ATOM O2' END DELETE ATOM HO2' END GROUP MODIFY ATOM C2' TYPE=C2D CHARGE=-0.07 END MODIFY ATOM C5' TYPE=C5D CHARGE=-0.07 END MODIFY ATOM C4' TYPE=C4D CHARGE=0.065 END MODIFY ATOM O4' TYPE=O4D CHARGE=-0.30 END MODIFY ATOM C1' TYPE=C1D CHARGE=0.165 END MODIFY ATOM C3' TYPE=C3D CHARGE=-0.035 END ADD ATOM H2'' TYPE=H CHARGE=0.035 END ADD BOND C2' H2'' ADD ANGLE C1' C2' H2' ADD ANGLE C3' C2' H2'' ADD ANGLE H2' C2' H2'' ADD IMPRoper H2' C3' H2'' C1'! C2' chirality term END {DEOX} !------------------------------------------------------------------ !------------------------------------------------------------------ PRESidue 5PHO ! 5-terminus (with phosphate) ! ! should be used as "FIRST 5PHO TAIL + * END" GROUp ! i.e. to be patched to the first RNA residue ADD ATOM +H5T TYPE=HO CHARGE=0.15 END ADD ATOM +O5T TYPE=OH CHARGE=-0.15 END ADD BOND +H5T +O5T ADD BOND +O5T +P ADD ANGLe +H5T +O5T +P ADD ANGLe +O5' +P +O5T ADD ANGLe +O5T +P +O1P ADD ANGLe +O5T +P +O2P !NEW ADD DIHE +O1P +P +O5' +C5' ADD DIHE +O2P +P +O5' +C5' ADD DIHEdral +O5' +P +O5T +H5T ADD DIHEdral +C5' +O5' +P +O5T ADD DONOr +H5T +O5T END {5PHO} !------------------------------------------------------------------ PRESidue 3TER ! 3-terminus (without phosphate) ! should be used as "LAST 3TER HEAD - * END" GROUp ! i.e. to be patched to the last RNA residue MODIFY ATOM -C3' TYPE=C3R CHARGE=0.2022 END MODIFY ATOM -O3' TYPE=OH CHARGE=-0.6541 END ADD ATOM -H3T TYPE=HO CHARGE=0.4376 END ! ADD BOND -O3' -H3T ADD ANGLe -C3' -O3' -H3T ADD DIHEdral -C4' -C3' -O3' -H3T ADD DONOr -H3T -O3' END {3TER} !------------------------------------------------------------------ PRESidue 5TER ! 5-terminus (without phosphate) ! ! should be used as "FIRST 5TER TAIL + * END" GROUp ! i.e. to be patched to the first RNA residue ADD ATOM +H5T TYPE=HO CHARGE=0.4295 END MODIFY ATOM +O5' TYPE=OH CHARGE=-0.6223 END MODIFY ATOM +C5' TYPE=C5R CHARGE=0.0558 END DELETE ATOM +P END DELETE ATOM +O1P END DELETE ATOM +O2P END ! ADD BOND +H5T +O5' ADD ANGLe +H5T +O5' +C5' ADD DIHEdral +H5T +O5' +C5' +C4' ADD DONOr +H5T +O5' END {5TER} ! --------------------------------------------------------------------- !------------------------------------------------------------------ PRESidue NUC ! patch for nucleic acid backbone ! should be used as "LINK NUC HEAD - * TAIL + * END" ! i.e. it links the previous RNA residue (-) with ! the current one (+) GROUp MODIFY ATOM -O3' END ! MODIFY ATOM +P END ! MODIFY ATOM +O1P END ! this should correctly define the electrostatic MODIFY ATOM +O2P END ! group boundary MODIFY ATOM +O5' END ! ADD BOND -O3' +P ADD ANGLE -C3' -O3' +P ADD ANGLE -O3' +P +O1P ADD ANGLE -O3' +P +O2P ADD ANGLE -O3' +P +O5' !NEW: !NUC ADD DIHE -O3' +P +O5' +C5' !X-C3R-O3R-X ADD DIHE -C4' -C3' -O3' +P ADD DIHE -H3' -C3' -O3' +P ADD DIHE -C2' -C3' -O3' +P !X-O3R-P-X ADD DIHE -C3' -O3' +P +O1P ADD DIHE -C3' -O3' +P +O2P ADD DIHE -C3' -O3' +P +O5' ADD IMPROper +O1P -O3' +O2P +O5' END {NUC} !------------------------------------------------------------------ set echo=true end