remarks file toppar/dna-rna-allatom-hj-opls.top remarks all-hydrogen dna/rna topology using the OPLS force field !RNA TOPOLOGY FILE 'FRAMEWORK' FROM TOPALLHDG.DNA AND ATOM NAMES ! FROM DNA-RNA.PARAM !INCLUDES ALL NONEXCHANGEABLE HYDROGENS AND TERMS FOR BOND, ANGLE, AND !IMPROPERS. NONEXCHANGEABLE HYDROGEN CHARGES WERE ASSIGNED 0.035. !CARBON CHARGES WERE REDUCED 0.035 FOR EACH ATTACHED HYDROGEN. !CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE !CHANGED TO OPLSX CHARGES 6/2/07 -- HENRY JONKER ! DNA-RNA-ALLATOM.TOP set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result) set message=off echo=off end checkversion 1.3 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 ! PUR MASS N9P 14.00670! nitrogen in ring >N- MASS C2P 12.011! (prev CE) MASS N3P 14.00670! (prev NC) MASS C4P 12.01100! (prev CB) MASS C5P 12.01100! (prev CB) MASS C6P 12.01100! (prev CA) MASS N7P 14.00670! (prev NB) MASS C8P 12.011! (prev CE) ! 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 HR 1.00800! non-exchangeable Hydrogens MASS HN 1.00800! corresp. to H MASS H2 1.00800! hydrogen in -NH2 MASS H0 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=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.50 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9G CHARGE=-0.50 END ATOM C4 TYPE=C4G CHARGE=0.34 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3G CHARGE=-0.51 EXCLusion=( C6 ) END ATOM C2 TYPE=C2G CHARGE=0.46 EXCLusion=( C5 ) END GROUp ATOM N2 TYPE=N2G CHARGE=-0.80 END ATOM H21 TYPE=H2 CHARGE=0.40 END ATOM H22 TYPE=H2 CHARGE=0.40 END GROUp ATOM N1 TYPE=NNA CHARGE=-0.56 END ATOM H1 TYPE=HN CHARGE=0.38 END GROUp ATOM C6 TYPE=C6G CHARGE=0.52 END ATOM O6 TYPE=O6G CHARGE=-0.51 END GROUp ATOM C5 TYPE=C5G CHARGE=0.12 END ATOM N7 TYPE=N7G CHARGE=-0.49 END ATOM C8 TYPE=C8G CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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 O3' C3' C2' O2' DIHEdral O4' C1' N9 C4 DIHEdral C3' C2' O2' H2' } ! 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 !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' END {GUA} ! --------------------------------------------------------------------- RESIdue G ! same as GUA GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.50 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9G CHARGE=-0.50 END ATOM C4 TYPE=C4G CHARGE=0.34 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3G CHARGE=-0.51 EXCLusion=( C6 ) END ATOM C2 TYPE=C2G CHARGE=0.46 EXCLusion=( C5 ) END GROUp ATOM N2 TYPE=N2G CHARGE=-0.80 END ATOM H21 TYPE=H2 CHARGE=0.40 END ATOM H22 TYPE=H2 CHARGE=0.40 END GROUp ATOM N1 TYPE=NNA CHARGE=-0.56 END ATOM H1 TYPE=HN CHARGE=0.38 END GROUp ATOM C6 TYPE=C6G CHARGE=0.52 END ATOM O6 TYPE=O6G CHARGE=-0.51 END GROUp ATOM C5 TYPE=C5G CHARGE=0.12 END ATOM N7 TYPE=N7G CHARGE=-0.49 END ATOM C8 TYPE=C8G CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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 O3' C3' C2' O2' DIHEdral O4' C1' N9 C4 DIHEdral C3' C2' O2' H2' } ! 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 !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' END {G} ! --------------------------------------------------------------------- RESIdue DG ! deoxy form of GUA GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9G CHARGE=-0.50 END ATOM C4 TYPE=C4G CHARGE=0.34 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3G CHARGE=-0.51 EXCLusion=( C6 ) END ATOM C2 TYPE=C2G CHARGE=0.46 EXCLusion=( C5 ) END GROUp ATOM N2 TYPE=N2G CHARGE=-0.80 END ATOM H21 TYPE=H2 CHARGE=0.40 END ATOM H22 TYPE=H2 CHARGE=0.40 END GROUp ATOM N1 TYPE=NNA CHARGE=-0.56 END ATOM H1 TYPE=HN CHARGE=0.38 END GROUp ATOM C6 TYPE=C6G CHARGE=0.52 END ATOM O6 TYPE=O6G CHARGE=-0.51 END GROUp ATOM C5 TYPE=C5G CHARGE=0.12 END ATOM N7 TYPE=N7G CHARGE=-0.49 END ATOM C8 TYPE=C8G CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy ATOM H2' TYPE=HR CHARGE=0.10 END ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy GROUP ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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 C8 H8 BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' BOND C2' H2'' ! deoxy ! 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 IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N9 !C1' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' END {DG} ! --------------------------------------------------------------------- RESIdue ADE GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.50 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9A CHARGE=-0.50 END ATOM C4 TYPE=C4A CHARGE=0.38 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.55 EXCLusion=( C6 ) END ATOM C2 TYPE=C2A CHARGE=0.22 EXCLusion=( C5 ) END ATOM H2 TYPE=HR CHARGE=0.20 END GROUp ATOM N1 TYPE=NC CHARGE=-0.53 END ATOM C6 TYPE=C6A CHARGE=0.44 END GROUp ATOM N6 TYPE=N6A CHARGE=-0.81 END ATOM H61 TYPE=H2 CHARGE=0.355 END ATOM H62 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5A CHARGE=0.15 END ATOM N7 TYPE=N7A CHARGE=-0.49 END ATOM C8 TYPE=C8A CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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' N9 C4 DIHEdral C3' C2' O2' H2' } ! 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' END {ADE} ! --------------------------------------------------------------------- RESIdue A ! same as ADE GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.50 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9A CHARGE=-0.50 END ATOM C4 TYPE=C4A CHARGE=0.38 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.55 EXCLusion=( C6 ) END ATOM C2 TYPE=C2A CHARGE=0.22 EXCLusion=( C5 ) END ATOM H2 TYPE=HR CHARGE=0.20 END GROUp ATOM N1 TYPE=NC CHARGE=-0.53 END ATOM C6 TYPE=C6A CHARGE=0.44 END GROUp ATOM N6 TYPE=N6A CHARGE=-0.81 END ATOM H61 TYPE=H2 CHARGE=0.355 END ATOM H62 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5A CHARGE=0.15 END ATOM N7 TYPE=N7A CHARGE=-0.49 END ATOM C8 TYPE=C8A CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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' N9 C4 DIHEdral C3' C2' O2' H2' } ! 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' END {A} ! --------------------------------------------------------------------- RESIdue DA ! deoxy form at ADE GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9A CHARGE=-0.50 END ATOM C4 TYPE=C4A CHARGE=0.38 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.55 EXCLusion=( C6 ) END ATOM C2 TYPE=C2A CHARGE=0.22 EXCLusion=( C5 ) END ATOM H2 TYPE=HR CHARGE=0.20 END GROUp ATOM N1 TYPE=NC CHARGE=-0.53 END ATOM C6 TYPE=C6A CHARGE=0.44 END GROUp ATOM N6 TYPE=N6A CHARGE=-0.81 END ATOM H61 TYPE=H2 CHARGE=0.355 END ATOM H62 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5A CHARGE=0.15 END ATOM N7 TYPE=N7A CHARGE=-0.49 END ATOM C8 TYPE=C8A CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy ATOM H2' TYPE=HR CHARGE=0.10 END ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy GROUP ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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 C3' O3' BOND C8 H8 BOND C2 H2 BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' BOND C2' H2'' ! deoxy { 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 O4' C1' N9 C4 } ! 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 IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N9 !C1' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' END {DA} ! --------------------------------------------------------------------- RESIdue PUR GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.50 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N9 TYPE=N9P CHARGE=-0.50 END ATOM C4 TYPE=C4P CHARGE=0.36 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3P CHARGE=-0.55 EXCLusion=( C6 ) END ATOM C2 TYPE=C2P CHARGE=0.22 EXCLusion=( C5 ) END ATOM H2 TYPE=HR CHARGE=0.20 END GROUp ATOM N1 TYPE=NC CHARGE=-0.53 END ATOM C6 TYPE=C6P CHARGE=0.28 END ATOM H6 TYPE=HR CHARge= 0.20 END GROUp ATOM C5 TYPE=C5P CHARGE=0.13 END ATOM N7 TYPE=N7P CHARGE=-0.49 END ATOM C8 TYPE=C8P CHARGE=0.20 END ATOM H8 TYPE=HR CHARGE=0.20 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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 H6 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' { 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' N9 C4 DIHEdral C3' C2' O2' H2' } ! IMPRoper H6 N1 C5 C6 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 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 C2' C3' C1' O2' 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' END {PUR} ! --------------------------------------------------------------------- RESIdue CYT GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.53 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1C CHARGE=-0.56 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.10 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2C CHARGE=0.55 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.48 END GROUp ATOM N3 TYPE=NC CHARGE=-0.54 END ATOM C4 TYPE=C4C CHARGE=0.46 END GROUp ATOM N4 TYPE=N4C CHARGE=-0.79 END ATOM H41 TYPE=H2 CHARGE=0.355 END ATOM H42 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5C CHARGE=-0.06 END ATOM H5 TYPE=HR CHARGE=0.10 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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 } 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' END {CYT} ! --------------------------------------------------------------------- RESIdue C ! same as CYT GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.53 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1C CHARGE=-0.56 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.10 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2C CHARGE=0.55 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.48 END GROUp ATOM N3 TYPE=NC CHARGE=-0.54 END ATOM C4 TYPE=C4C CHARGE=0.46 END GROUp ATOM N4 TYPE=N4C CHARGE=-0.79 END ATOM H41 TYPE=H2 CHARGE=0.355 END ATOM H42 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5C CHARGE=-0.06 END ATOM H5 TYPE=HR CHARGE=0.10 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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 } 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' END {C} ! --------------------------------------------------------------------- RESIdue DC ! deoxy form of CYT GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1C CHARGE=-0.56 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.10 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2C CHARGE=0.55 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.48 END GROUp ATOM N3 TYPE=NC CHARGE=-0.54 END ATOM C4 TYPE=C4C CHARGE=0.46 END GROUp ATOM N4 TYPE=N4C CHARGE=-0.79 END ATOM H41 TYPE=H2 CHARGE=0.355 END ATOM H42 TYPE=H2 CHARGE=0.385 END GROUp ATOM C5 TYPE=C5C CHARGE=-0.06 END ATOM H5 TYPE=HR CHARGE=0.10 END GROUp ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy ATOM H2' TYPE=HR CHARGE=0.10 END ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy GROUP ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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 C6 H6 BOND C5 H5 BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND C2' H2' BOND C1' H1' BOND C2' H2'' ! deoxy { 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 O4' C1' N1 C2 ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 } 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 IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N1 !C1' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' END {DC} !------------------------------------------------------------------ RESIdue THY GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.56 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1T CHARGE=-0.60 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6T CHARGE=0.08 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2T CHARGE=0.50 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.40 END GROUp ATOM N3 TYPE=N3T CHARGE=-0.51 END ATOM H3 TYPE=HN CHARGE=0.36 END GROUp ATOM C4 TYPE=C4T CHARGE=0.45 END ATOM O4 TYPE=ON CHARGE=-0.42 END GROUp ATOM C5 TYPE=C5T CHARGE=-0.07 END ATOM C7 TYPE=CC3E CHARGE=-0.14 END ! name per IUPAC-IUB recomm. ATOM H71 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. ATOM H72 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. ATOM H73 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' 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 } 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' END {THY} !------------------------------------------------------------------ RESIdue DT ! deoxy form of THY GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5D CHARGE=0.00 END ! deoxy ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4D CHARGE=0.15 END ! deoxy ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4D CHARGE=-0.50 END ! deoxy ATOM C1' TYPE=C1D CHARGE=0.53 END ! deoxy ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1T CHARGE=-0.60 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6T CHARGE=0.08 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2T CHARGE=0.50 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.40 END GROUp ATOM N3 TYPE=N3T CHARGE=-0.51 END ATOM H3 TYPE=HN CHARGE=0.36 END GROUp ATOM C4 TYPE=C4T CHARGE=0.45 END ATOM O4 TYPE=ON CHARGE=-0.42 END GROUp ATOM C5 TYPE=C5T CHARGE=-0.07 END ATOM C7 TYPE=CC3E CHARGE=-0.14 END ! name per IUPAC-IUB recomm. ATOM H71 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. ATOM H72 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. ATOM H73 TYPE=HR CHARGE=0.08 END ! name per IUPAC-IUB recomm. GROUP ATOM C2' TYPE=C2D CHARGE=-0.20 END ! deoxy ATOM H2' TYPE=HR CHARGE=0.10 END ATOM H2'' TYPE=HR CHARGE=0.1 END ! deoxy GROUP ATOM C3' TYPE=C3D CHARGE=-0.10 END ! deoxy ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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 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 BOND C2' H2'' ! deoxy { 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 O4' C1' N1 C2 ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 } 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 IMPRoper H2' C3' H2'' C1'! C2' chirality term ! deoxy !RIBOSE IMPROPERS IMPRoper H1' C2' O4' N1 ! C1' IMPRoper H3' C4' C2' O3' !C3' IMPRoper H4' C5' C3' O4' !C4' IMPRoper H5' O5' H5'' C4' !C5' END {DT} !------------------------------------------------------------------ RESIdue URI GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.56 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1U CHARGE=-0.60 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6U CHARGE=0.08 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2U CHARGE=0.50 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.40 END GROUp ATOM N3 TYPE=N3U CHARGE=-0.51 END ATOM H3 TYPE=HN CHARGE=0.36 END GROUp ATOM C4 TYPE=C4U CHARGE=0.45 END ATOM O4 TYPE=ON CHARGE=-0.42 END GROUp ATOM C5 TYPE=C5U CHARGE=-0.07 END ATOM H5 TYPE=HR CHARGE=0.10 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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' DIHEdral P O3' C3' C2' DIHEdral P O3' C3' C4' ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 } 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' END {URI} !------------------------------------------------------------------ RESIdue U ! same as URI GROUp ATOM P TYPE=P CHARGE=0.78 END ATOM OP1 TYPE=O1P CHARGE=-0.66 END ATOM OP2 TYPE=O2P CHARGE=-0.66 END ATOM O5' TYPE=O5R CHARGE=-0.43 END GROUp ATOM C5' TYPE=C5R CHARGE=0.00 END ATOM H5' TYPE=HR CHARGE=0.10 END ATOM H5'' TYPE=HR CHARGE=0.10 END GROUp ATOM C4' TYPE=C4R CHARGE=0.15 END ATOM H4' TYPE=HR CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.50 END ATOM C1' TYPE=C1R CHARGE=0.56 END ATOM H1' TYPE=HR CHARGE=0.10 END GROUp ATOM N1 TYPE=N1U CHARGE=-0.60 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6U CHARGE=0.08 EXCLUSION=( N3 ) END ATOM H6 TYPE=HR CHARGE=0.10 END GROUp ATOM C2 TYPE=C2U CHARGE=0.50 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.40 END GROUp ATOM N3 TYPE=N3U CHARGE=-0.51 END ATOM H3 TYPE=HN CHARGE=0.36 END GROUp ATOM C4 TYPE=C4U CHARGE=0.45 END ATOM O4 TYPE=ON CHARGE=-0.42 END GROUp ATOM C5 TYPE=C5U CHARGE=-0.07 END ATOM H5 TYPE=HR CHARGE=0.10 END GROUP ATOM C2' TYPE=C2R CHARGE=0.165 END ATOM H2' TYPE=HR CHARGE=0.10 END ATOM O2' TYPE=O2R CHARGE=-0.70 END ATOM HO2' type=H0 CHARGE=0.435 END GROUP ATOM C3' TYPE=C3R CHARGE=0.10 END ATOM H3' TYPE=HR CHARGE=0.10 END GROUP ATOM O3' TYPE=O3R CHARGE=-0.43 END BOND P OP1 BOND P OP2 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' { 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' DIHEdral P O3' C3' C2' DIHEdral P O3' C3' C4' ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 } 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' END {U} !------------------------------------------------------------------ !------------------------------------------------------------------ !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=-0.20 END MODIFY ATOM C5' TYPE=C5D CHARGE=0.00 END MODIFY ATOM C4' TYPE=C4D CHARGE=0.15 END MODIFY ATOM O4' TYPE=O4D CHARGE=-0.50 END MODIFY ATOM C1' TYPE=C1D CHARGE=0.53 END MODIFY ATOM C3' TYPE=C3D CHARGE=-0.10 END ADD ATOM H2'' TYPE=HR CHARGE=0.10 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/DNA residue ADD ATOM +H5T type=H0 CHARGE=0.50 END ADD ATOM +O5T TYPE=OH CHARGE=-0.70 END ADD BOND +H5T +O5T ADD BOND +O5T +P ADD ANGLe +H5T +O5T +P ADD ANGLe +O5' +P +O5T ADD ANGLe +O5T +P +OP1 ADD ANGLe +O5T +P +OP2 ! ADD DIHEdral +O5' +P +O5T +H5T ! ADD DIHEdral +C5' +O5' +P +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 RMA/DNA residue MODIFY ATOM -C3' TYPE=C3R CHARGE=0.10 END MODIFY ATOM -O3' TYPE=OH CHARGE=-0.70 END ADD ATOM -H3T type=H0 CHARGE=0.50 END ! ADD BOND -O3' -H3T ADD ANGLe -C3' -O3' -H3T ! ADD DIHEdral -C4' -C3' -O3' -H3T 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/DNA residue ADD ATOM +H5T type=H0 CHARGE=0.50 END MODIFY ATOM +O5' TYPE=OH CHARGE=-0.70 END MODIFY ATOM +C5' TYPE=C5R CHARGE=0.00 END DELETE ATOM +P END DELETE ATOM +OP1 END DELETE ATOM +OP2 END ! ADD BOND +H5T +O5' ADD ANGLe +H5T +O5' +C5' ! ADD DIHEdral +H5T +O5' +C5' +C4' 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/DNA residue (-) with ! the current one (+) GROUp MODIFY ATOM -O3' END ! MODIFY ATOM +P END ! MODIFY ATOM +OP1 END ! this should correctly define the electrostatic MODIFY ATOM +OP2 END ! group boundary MODIFY ATOM +O5' END ! ADD BOND -O3' +P ADD ANGLE -C3' -O3' +P ADD ANGLE -O3' +P +OP1 ADD ANGLE -O3' +P +OP2 ADD ANGLE -O3' +P +O5' !ADD DIHEdral -O3' +P +O5' +C5' ! ADD DIHEdral -C4' -C3' -O3' +P ! ADD DIHEdral -C3' -O3' +P +O5' END {NUC} !------------------------------------------------------------------ PRESidue DNUC ! reverses the NUC patch, i.e, breask the bond between ! two residues ! should be used as "LINK DNUC HEAD - * TAIL + * END" ! i.e. it links the previous residue (-) with ! the current one (+) DELETE BOND -O3' +P DELETE ANGLE -C3' -O3' +P DELETE ANGLE -O3' +P +OP1 DELETE ANGLE -O3' +P +OP2 DELETE ANGLE -O3' +P +O5' ! DELETE DIHEdral -O3' +P +O5' +C5' ! DELETE DIHEdral -C4' -C3' -O3' +P ! DELETE DIHEdral -C3' -O3' +P +O5' END {DNUC} !------------------------------------------------------------------ set message=$old_message echo=$old_echo end