remarks file toppar/dna-rna.top remarks dna/rna topology for crystallographic structure determination ! removed references to CA, CF, CS, MG, NH3, OS (ATB 12/30/94) ! removed TIP3 water model (ATB 12/30/94) ! mapped NA->NNA, CH3E->CC3E (ATB 12/30/94) ! !Please cite the following reference when using these parameters: !G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, ! New Parameters for the Refinement of Nucleic Acid Containing Structures, ! Acta Cryst. D, 52, 57-64 (1996). ! ! Oct. 8, 1996 - Modified by Alexey Bochkarev (McMaster University) ! to process properly 5PHO (5'-terminus with phosphate) patch. ! Geometry and charges of -O5'-PO3 group were taken from ! Saenger W. 1984. Principles of Nucleic Acid Structure ! All modifications are placed between: !***AB*** !....included fragment !***AB end*** ! New atomic types were introduced to describe ! -O5'-PO3 group: O5H (O5') O1PH (O1P) O2PH (O2P) ! in addition to existing OH (O5T) set echo=false end checkversion 1.2 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- !***AB*** MASS O5H 15.99940! ester -C-O-PO3 MASS O1PH 15.99940! O in 5'-terminus phosphate MASS O2PH 15.99940! O in 5'-terminus phosphate (One more O is OH) !***AB end*** MASS C5R 14.02700! corresp. to CH2E MASS C4R 13.01900! corresp. to CH1E MASS C3R 13.01900! corresp. to CH1E MASS C2R 13.01900! corresp. to CH1E MASS C1R 13.01900! 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- ! 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 13.01900! (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 13.01900! (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 13.01900! (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 13.01900! (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 13.01900! (prev CF) MASS C6C 13.01900! (prev CF) MASS N4C 14.00670! nitrogen in -NH2 ! THY MASS N1T 14.00670! nitrogen in ring >N- MASS C2T 12.01100! (prev CN) MASS C4T 12.01100! (prev CN) MASS C5T 13.01900! (prev CS) MASS C6T 13.01900! (prev CF) MASS CC3E 15.03500! (prev CF) ! END MASS HN 1.00800! corresp. to H MASS H2 1.00800! hydrogen in -NH2 MASS HHO 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 13.01900! (prev CF) MASS C6U 13.01900! (prev CF) MASS N3U 14.00670! nitrogen in -NH2 MASS I5U 126.9045! iodine in modified uracil ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- ! Modifications to the param11.dna were made to include ! C5'-C4'-C3'-O3' (delta), C4'-O4'-C1'-N9/N1 and remove O5'-C5'-C4'-O4' RESIdue GUA 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ! Insert Base GROUp ATOM N9 TYPE=N9G CHARGE=-0.19 END ATOM C4 TYPE=C4G CHARGE=0.19 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3G CHARGE=-0.35 EXCLusion=( C6 ) END !H ATOM C2 TYPE=C2G CHARGE=0.35 EXCLusion=( C5 ) END !H GROUp ATOM N2 TYPE=N2G CHARGE=-0.42 END !H ATOM H21 TYPE=H2 CHARGE=0.21 END !H ATOM H22 TYPE=H2 CHARGE=0.21 END !H GROUp ATOM N1 TYPE=NNA CHARGE=-0.26 END !H ATOM H1 TYPE=HN CHARGE=0.26 END !H GROUp ATOM C6 TYPE=C6G CHARGE=0.30 END !H ATOM O6 TYPE=O6G CHARGE=-0.30 END !H GROUp ATOM C5 TYPE=C5G CHARGE=0.02 END ATOM N7 TYPE=N7G CHARGE=-0.25 END ATOM C8 TYPE=C8G CHARGE=0.23 END ! GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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' 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 O2' H2' 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 N3 C2 N2 H21 DIHEdral C3' C2' O2' H2' ! Dihedrals to keep the two purine rings parallel: DIHEdral C8 C4 C5 N1 DIHEdral C8 C5 C4 C2 DIHEdral N3 C4 C5 N7 DIHEdral C6 C5 C4 N9 ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N9 ! The ring-spanning impropers have been left out. IMPRoper C5' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N9 C2' O4' C1' 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 C2' C3' C1' O2' END {GUA} ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- RESIdue ADE 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ! Insert Base GROUp ATOM N9 TYPE=N9A CHARGE=-0.19 END ATOM C4 TYPE=C4A CHARGE=0.19 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.26 EXCLusion=( C6 ) END !H ATOM C2 TYPE=C2A CHARGE=0.26 EXCLusion=( C5 ) END !H GROUp ATOM N1 TYPE=NC CHARGE=-0.28 END !H ATOM C6 TYPE=C6A CHARGE=0.28 END !H GROUp ATOM N6 TYPE=N6A CHARGE=-0.42 END !H ATOM H61 TYPE=H2 CHARGE=0.21 END !H ATOM H62 TYPE=H2 CHARGE=0.21 END !H GROUp ATOM C5 TYPE=C5A CHARGE=0.02 END ATOM N7 TYPE=N7A CHARGE=-0.25 END ATOM C8 TYPE=C8A CHARGE=0.23 END ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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' 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 O2' H2' BOND C3' O3' 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 C5 C6 N6 H61 DIHEdral C3' C2' O2' H2' ! Dihedrals to keep the two purine rings parallel: DIHEdral C8 C4 C5 N1 DIHEdral C8 C5 C4 C2 DIHEdral N3 C4 C5 N7 DIHEdral C6 C5 C4 N9 ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N9 ! The ring-spanning impropers have been left out. IMPRoper C5' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N9 C2' O4' C1' 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 C2' C3' C1' O2' END {ADE} ! --------------------------------------------------------------------- ! --------------------------------------------------------------------- RESIdue CYT 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ! Insert Base GROUp ATOM N1 TYPE=N1C CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.19 EXCLUSION=( N3 ) END GROUp ATOM C2 TYPE=C2C CHARGE=0.30 EXCLUSION=( C5 ) END !H ATOM O2 TYPE=ON CHARGE=-0.30 END !H GROUp ATOM N3 TYPE=NC CHARGE=-0.28 END !H ATOM C4 TYPE=C4C CHARGE=0.28 END !H GROUp ATOM N4 TYPE=N4C CHARGE=-0.42 END !H ATOM H41 TYPE=H2 CHARGE=0.21 END !H ATOM H42 TYPE=H2 CHARGE=0.21 END !H GROUp ATOM C5 TYPE=C5C CHARGE=0.00 END GROUp ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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 C4 BOND C4 N4 BOND N4 H41 BOND N4 H42 BOND C4 C5 BOND C5 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND O2' H2' DIHEdral C3' C2' O2' H2' 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' !modified ! DIHEdral O4' C1' C2' O2' ! **** DIHEdral O2' C2' C3' O3' !added, ATB, 6-9-84 DIHEdral C1' C2' C3' C4' DIHEdral O4' C4' C3' O3' ! DIHEdral O4' C4' C3' O3' ! **** DIHEdral C5' C4' C3' C2' DIHEdral O4' C1' N1 C2 DIHEdral C5 C4 N4 H41 ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N1 IMPRoper C5' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N1 C2' O4' C1' 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 C2' C3' C1' O2' 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ! Insert Base GROUp ATOM N1 TYPE=N1T CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6T CHARGE=0.19 EXCLUSION=( N3 ) END GROUp ATOM C2 TYPE=C2T CHARGE=0.35 EXCLUSION=( C5 ) END !H ATOM O2 TYPE=ON CHARGE=-0.35 END !H GROUp ATOM N3 TYPE=NNA CHARGE=-0.26 END !H ATOM H3 TYPE=HN CHARGE=0.26 END !H GROUp ATOM C4 TYPE=C4T CHARGE=0.30 END !H ATOM O4 TYPE=ON CHARGE=-0.30 END !H GROUp ATOM C5 TYPE=C5T CHARGE=0.00 END ATOM C5A TYPE=CC3E CHARGE=0.00 END GROUp ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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 C5A BOND C5 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND O2' H2' DIHEdral C3' C2' O2' H2' DIHEdral O3' C3' C2' O2' 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' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N1 C2' O4' C1' IMPRoper C1' C2 C6 N1 IMPRoper O2 N1 N3 C2 IMPRoper H3 C2 C4 N3 IMPRoper O4 N3 C5 C4 IMPRoper C5A C4 C6 C5 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 C2' C3' C1' O2' END {THY} !------------------------------------------------------------------ RESIdue CMP 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END ! Insert Base GROUp ATOM N9 TYPE=N9A CHARGE=-0.19 END ATOM C4 TYPE=C4A CHARGE=0.19 EXCLusion=( N1 ) END GROUp ATOM N3 TYPE=N3A CHARGE=-0.26 EXCLusion=( C6 ) END !H ATOM C2 TYPE=C2A CHARGE=0.26 EXCLusion=( C5 ) END !H GROUp ATOM N1 TYPE=NC CHARGE=-0.28 END !H ATOM C6 TYPE=C6A CHARGE=0.28 END !H GROUp ATOM N6 TYPE=N6A CHARGE=-0.42 END !H ATOM H61 TYPE=H2 CHARGE=0.21 END !H ATOM H62 TYPE=H2 CHARGE=0.21 END !H GROUp ATOM C5 TYPE=C5A CHARGE=0.02 END ATOM N7 TYPE=N7A CHARGE=-0.25 END ATOM C8 TYPE=C8A CHARGE=0.23 END ! END GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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' 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 O2' H2' BOND C3' O3' BOND P O3' 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 C5 C6 N6 H61 DIHEdral C3' C2' O2' H2' ! Dihedrals to keep the two purine rings parallel: DIHEdral C8 C4 C5 N1 DIHEdral C8 C5 C4 C2 DIHEdral N3 C4 C5 N7 DIHEdral C6 C5 C4 N9 DIHEdral P O3' C3' C2' DIHEdral P O3' C3' C4' ! New dihedrals DIHEdral C5' C4' C3' O3' DIHEdral C4' O4' C1' N9 ! The ring-spanning impropers have been left out. IMPRoper C5' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N9 C2' O4' C1' 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 C2' C3' C1' O2' END {CMP} !------------------------------------------------------------------ RESIdue URI 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=0.00 END GROUp ATOM C4' TYPE=C4R CHARGE=0.10 END ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.20 END GROUp ATOM N1 TYPE=N1U CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6U CHARGE=0.19 EXCLUSION=( N3 ) END GROUp ATOM C2 TYPE=C2U CHARGE=0.30 EXCLUSION=( C5 ) END !H ATOM O2 TYPE=ON CHARGE=-0.30 END !H GROUp ATOM N3 TYPE=N3U CHARGE=-0.28 END !H ATOM H3 TYPE=HN CHARGE=0.26 END !H GROUp ATOM C4 TYPE=C4U CHARGE=0.28 END !H ATOM O4 TYPE=ON CHARGE=-0.30 END !H GROUp ATOM C5 TYPE=C5U CHARGE=0.00 END GROUP ATOM C2' TYPE=C2R CHARGE=0.15 END ATOM O2' TYPE=O2R CHARGE=-0.40 END !H ATOM H2' TYPE=HHO CHARGE=0.25 END !H GROUP ATOM C3' TYPE=C3R CHARGE=0.00 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 C6 BOND C2' C3' BOND C3' O3' BOND C2' O2' BOND O2' H2' DIHEdral C3' C2' O2' H2' DIHEdral O3' C3' C2' O2' 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' O4' C3' C4' IMPRoper O3' C2' C4' C3' IMPRoper N1 C2' O4' C1' 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 C2' C3' C1' O2' END {URI} !------------------------------------------------------------------ !------------------------------------------------------------------ PRESidue DEOX ! Patch to make DEOXYribose of the ribose DELETE ATOM O2' END DELETE ATOM H2' END GROUP MODIFY ATOM C2' TYPE=C2D CHARGE=0.00 END MODIFY ATOM C5' TYPE=C5D CHARGE=0.00 END MODIFY ATOM C4' TYPE=C4D CHARGE=0.10 END MODIFY ATOM O4' TYPE=O4D CHARGE=-0.30 END MODIFY ATOM C1' TYPE=C1D CHARGE=0.20 END MODIFY ATOM C3' TYPE=C3D CHARGE=0.00 END 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 !***AB*** ! ADD ATOM +H5T TYPE=HHO CHARGE=0.15 END ! ADD ATOM +O5T TYPE=OH CHARGE=-0.15 END ! !PERHAPS ONE SHOULD CHANGE THE P CHARGE AS WELL???? ! ! I do not think it is necessary. At least for X-ray. ! We discharge all atoms any way. But ... A.B. ! ADD ATOM +O5T TYPE=OH CHARGE=-0.84 END ADD ATOM +H5T TYPE=HHO CHARGE= 0.15 END MODIFY ATOM +P TYPE=P CHARGE= 0.75 END MODIFY ATOM +O1P TYPE=O1PH CHARGE=-0.84 END MODIFY ATOM +O2P TYPE=O2PH CHARGE=-0.84 END MODIFY ATOM +O5' TYPE=O5H CHARGE=-0.47 END !***AB 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 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 RNA residue MODIFY ATOM -C3' TYPE=C3R CHARGE=0.15 END !H MODIFY ATOM -O3' TYPE=OH CHARGE=-0.40 END !H ADD ATOM -H3T TYPE=HHO CHARGE=0.25 END !H ! 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 residue ADD ATOM +H5T TYPE=HHO CHARGE=0.25 END !H MODIFY ATOM +O5' TYPE=OH CHARGE=-0.40 END !H MODIFY ATOM +C5' TYPE=C5R CHARGE=0.15 END !H 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' 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' ADD DIHEdral -O3' +P +O5' +C5' ADD DIHEdral -C4' -C3' -O3' +P ADD DIHEdral -C3' -O3' +P +O5' END {NUC} !------------------------------------------------------------------ PRESidue U5I ! Patch to add I to C5 of uracil GROUp MODIFY ATOM C5 END ADD ATOM I5 TYPE=I5U CHARge=0.0 END ADD BOND C5 I5 ADD ANGLe I5 C5 C4 ADD ANGLe I5 C5 C6 ADD IMPRoper I5 O4 C6 C5 END {U5I} !------------------------------------------------------------------ set echo=true end