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Nucleic Acid Standards

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

					

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