NMR Restraints Grid |
Result table
image | mrblock_id | pdb_id | cing | stage | position | program | type |
12447 | 1szy | cing | 1-original | 4 | XPLOR/CNS | molecular system |
!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 REMARK DNA-RNA-ALLATOM.TOP set echo=false 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=1.20 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 !JPR ATOM H5'' TYPE=H CHARGE=0.035 END !JPR GROUp ATOM C4' TYPE=C4R CHARGE=0.065 END ATOM H4' TYPE=H CHARGE=0.035 END !JPR ATOM O4' TYPE=O4R CHARGE=-0.30 END ATOM C1' TYPE=C1R CHARGE=0.165 END !JPR ATOM H1' TYPE=H CHARGE=0.035 END !JPR ! 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 ATOM C2 TYPE=C2G CHARGE=0.35 EXCLusion=( C5 ) END GROUp ATOM N2 TYPE=N2G CHARGE=-0.42 END ATOM H21 TYPE=H2 CHARGE=0.21 END ATOM H22 TYPE=H2 CHARGE=0.21 END GROUp ATOM N1 TYPE=NNA CHARGE=-0.26 END ATOM H1 TYPE=HN CHARGE=0.26 END GROUp ATOM C6 TYPE=C6G CHARGE=0.30 END ATOM O6 TYPE=O6G CHARGE=-0.30 END GROUp ATOM C5 TYPE=C5G CHARGE=0.02 END ATOM N7 TYPE=N7G CHARGE=-0.25 END ATOM C8 TYPE=C8G CHARGE=0.145 END ATOM H8 TYPE=H CHARGE=0.035 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' 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' 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=1.20 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=0.165 END ATOM H1' TYPE=H CHARGE=0.035 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 ATOM C2 TYPE=C2A CHARGE=0.225 EXCLusion=( C5 ) END ATOM H2 TYPE=H CHARGE=0.035 END GROUp ATOM N1 TYPE=NC CHARGE=-0.28 END ATOM C6 TYPE=C6A CHARGE=0.28 END GROUp ATOM N6 TYPE=N6A CHARGE=-0.42 END ATOM H61 TYPE=H2 CHARGE=0.21 END ATOM H62 TYPE=H2 CHARGE=0.21 END GROUp ATOM C5 TYPE=C5A CHARGE=0.02 END ATOM N7 TYPE=N7A CHARGE=-0.25 END ATOM C8 TYPE=C8A CHARGE=0.195 END ATOM H8 TYPE=H CHARGE=0.035 END ! 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' 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' 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=1.20 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=0.165 END ATOM H1' TYPE=H CHARGE=0.035 END ! Insert Base GROUp ATOM N1 TYPE=N1C CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6C CHARGE=0.155 EXCLUSION=( N3 ) END ATOM H6 TYPE=H CHARGE=0.035 END GROUp ATOM C2 TYPE=C2C CHARGE=0.30 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.30 END GROUp ATOM N3 TYPE=NC CHARGE=-0.28 END ATOM C4 TYPE=C4C CHARGE=0.28 END GROUp ATOM N4 TYPE=N4C CHARGE=-0.42 END ATOM H41 TYPE=H2 CHARGE=0.21 END ATOM H42 TYPE=H2 CHARGE=0.21 END GROUp ATOM C5 TYPE=C5C CHARGE=-0.035 END !CHRG ATOM H5 TYPE=H CHARGE=0.035 END 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 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' 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 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=1.20 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=0.165 END ATOM H1' TYPE=H CHARGE=0.035 END GROUp ATOM N1 TYPE=N1U CHARGE=-0.19 EXCLUSION=( C4 ) END ATOM C6 TYPE=C6U CHARGE=0.155 EXCLUSION=( N3 ) END ATOM H6 TYPE=H CHARGE=0.035 END GROUp ATOM C2 TYPE=C2U CHARGE=0.30 EXCLUSION=( C5 ) END ATOM O2 TYPE=ON CHARGE=-0.30 END GROUp ATOM N3 TYPE=N3U CHARGE=-0.28 END ATOM H3 TYPE=HN CHARGE=0.26 END GROUp ATOM C4 TYPE=C4U CHARGE=0.28 END ATOM O4 TYPE=ON CHARGE=-0.30 END GROUp ATOM C5 TYPE=C5U CHARGE=-0.035 END !JPR ATOM H5 TYPE=H CHARGE=0.035 END !JPR 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 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' 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 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=0.15 END MODIFY ATOM -O3' TYPE=OH CHARGE=-0.40 END ADD ATOM -H3T TYPE=HO CHARGE=0.25 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=0.25 END MODIFY ATOM +O5' TYPE=OH CHARGE=-0.40 END MODIFY ATOM +C5' TYPE=C5R CHARGE=0.15 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' ADD DIHEdral -O3' +P +O5' +C5' ADD DIHEdral -C4' -C3' -O3' +P ADD DIHEdral -C3' -O3' +P +O5' END {NUC} !------------------------------------------------------------------ set echo=true end
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