Refinement Parameters
! 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)
! 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 (1996) v. 52 57-64
remark top_ndbx.dna
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 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 !Mod HO to HHO 05/15/96
! 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
! ---------------------------------------------------------------------
! ---------------------------------------------------------------------
! 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 !!Mod HO to HHO 05/15/96
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'
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' " " ! added, ATB, 6-9-84
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 !!Mod HO to HHO 05/15/96
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'
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=0.00 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 !!Mod HO to HHO 05/15/96
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' C3' !DIHEdral O5' C5' C4' O4'
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'
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=0.00 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 !!Mod HO to HHO 05/15/96
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'
DONOr H3 N3 DONOr H2' O2'
ACCEptor O2 C2 ACCEptor O4 C4
ACCEptor O1P P ACCEptor O2P P
ACCEptor O2' " " ! added, ATB, 8-9-84
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 !!Mod HO to HHO 05/15/96
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'
DONOr H61 N6 DONOr H62 N6 DONOr H2' O2'
ACCEptor N3 " " ACCEptor N1 " "
ACCEptor O1P P ACCEptor O2P P
ACCEptor 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 !!Mod HO to HHO 05/15/96
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'
DONOr H3 N3 DONOr H2' O2'
ACCEptor O2 C2 ACCEptor O4 C4
ACCEptor O1P P ACCEptor O2P P
ACCEptor O2' " " ! added, ATB, 8-9-84
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
ADD ATOM +H5T TYPE=HHO CHARGE=0.15 END !!Mod HO to HHO 05/15/96
ADD ATOM +O5T TYPE=OH CHARGE=-0.15 END
!PERHAPS ONE SHOULD CHANGE THE P CHARGE AS WELL????
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 !H
MODIFY ATOM -O3' TYPE=OH CHARGE=-0.40 END !H
ADD ATOM -H3T TYPE=HHO CHARGE=0.25 END !!Mod HO to HHO 05/15/96
!
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=HHO CHARGE=0.25 END !!Mod HO to HHO 05/15/96
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'
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
©1995-2004 The Nucleic Acid Database Project
Rutgers, The State University of New Jersey
