NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

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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