NMR Restraints Grid

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

image mrblock_id pdb_id cing stage position program type
10787 1qby cing 1-original 2 XPLOR/CNS molecular system


 
AUTOGENERATE    ANGLES=true    END
{*==============================*}
 
{* DNA/RNA default atomic masses *}
MASS  H      1.00800
MASS  H2     1.00800
MASS  HT     1.00800
MASS  HO     1.00800
MASS  C     12.01100
MASS  CH    12.01100
MASS  C2    12.01100
MASS  CA    12.01100
MASS  CP    12.01100
MASS  CB    12.01100
MASS  CE    12.01100
MASS  CF    12.01100
MASS  C3    12.01100
MASS  CS    12.01100
MASS  N2    14.00670
MASS  NT    14.00670
MASS  NA    14.00670
MASS  NB    14.00670
MASS  NC    14.00670
MASS  NS    14.00670
MASS  NH2E  16.02270
MASS  NH3   14.02270
MASS  O     15.99940
MASS  O2    15.99940
MASS  OS    15.99940
MASS  OH    15.99940
MASS  SD    22.98980
MASS  P     30.97400
MASS  BR    79.90400
MASS  MG    24.30500
 
!========================================================================
 
! set H on C to .035 and take up slack on C (Kollman)
RESIdue G
 GROUP
  ATOM P    TYPE=P      CHARGE=1.20      END
  ATOM O1P  TYPE=O2     CHARge=-0.40     END
  ATOM O2P  TYPE=O2     CHARge=-0.40     END
  ATOM O5'  TYPE=OS     CHARge=-0.36     END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.07     END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035     END!"
  ATOM H5'' TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065     END!"
  ATOM H4'  TYPE=H      CHARge=0.035     END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30     END
  ATOM C1'  TYPE=CH     CHARge=0.165     END!"
  ATOM H1'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19     END
  ATOM C4   TYPE=CB     CHARge=0.19      EXCL=( N1 ) END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.50     EXCL=( C6 ) END
  ATOM C2   TYPE=CA     CHARge=0.50      EXCL=( C5 ) END
 GROUP
  ATOM N2   TYPE=N2     CHARge=-0.42     END!
  ATOM H21  TYPE=H2     CHARge=0.21      END!
  ATOM H22  TYPE=H2     CHARge=0.21      END!
 GROUP
  ATOM N1   TYPE=NA     CHARge=-0.26     END
  ATOM H1   TYPE=H      CHARge=0.26      END
 GROUP
  ATOM C6   TYPE=C      CHARge=0.30      END
  ATOM O6   TYPE=O      CHARge=-0.30     END
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02      END
  ATOM N7   TYPE=NB     CHARge=-0.25     END
  ATOM C8   TYPE=CE     CHARge=0.195     END
  ATOM H8   TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115     END!"
  ATOM H2'' TYPE=H      CHARge=0.035     END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40     END
  ATOM H2'  TYPE=HO     CHARge=0.25      END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035    END!"
  ATOM H3'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM O3'  TYPE=OS     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 O3'  +P *}
 BOND C2' O2'   BOND O2' H2'
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'    BOND C5' H5'
 BOND C5' H5''  BOND C8 H8
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P +O5' *}
 DIHE O4' C1' N9 C4     
 IMPRoper N3  C2 N2 H21
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 ! The ring-spanning impropers have been left out.
 ! And the chiral impropers are not needed with all hydrogens present
 {* IMPR C5' O4' C3' C4'    IMPR O3' C2' C4' C3'    IMPR N9  C2' O4' C1'  *}
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'


 IMPR C1' C4 C8 N9     ! THIS IS AN SP2 IMPROPER ABOUT N9
 IMPR N9 C4 C5 N7      IMPR C4 C5 N7 C8       IMPR C5 N7 C8 N9
 IMPR N7 C8 N9 C4      IMPR C8 N9 C4 C5       IMPR N2 N3 N1 C2
 IMPR H1 C2 C6 N1      IMPR O6 N1 C5 C6       IMPR C4 N3 C2 N1
 IMPR N3 C2 N1 C6      IMPR C2 N1 C6 C5       IMPR N1 C6 C5 C4
 IMPR C6 C5 C4 N3      IMPR C5 C4 N3 C2       IMPR H22 H21 C2 N2
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8 C4 C5 N1      IMPR C8 C5 C4 C2
 IMPR N3 C4 C5 N7      IMPR C6 C5 C4 N9
 {* IMPR  C2' C3' C1' O2'  *}
 IMPR H8 N7 N9 C8
 DONO H21  N2
 DONO H22  N2
 DONO H1   N1
 DONO H2'  O2'
 
 ACCE O6   C6
 ACCE N3   " "
 ACCE N7   " "   !added
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2'  " "
 ACCE O3'  " "
 ACCE O4'  " "
 ACCE O5'  " "
 
 
END {* GUA *}
!========================================================================
 
! set H on C to .035 and take up slack on C (Kollman)
RESIdue GSR
 GROUP
  ATOM P    TYPE=P      CHARGE=1.20      END
  ATOM O1P  TYPE=O2     CHARge=-0.40     END
  ATOM O2P  TYPE=O2     CHARge=-0.40     END
  ATOM O5'  TYPE=OS     CHARge=-0.36     END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.07     END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035     END!"
  ATOM H5'' TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065     END!"
  ATOM H4'  TYPE=H      CHARge=0.035     END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30     END
  ATOM C1'  TYPE=CH     CHARge=0.165     END!"
  ATOM H1'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19     END
  ATOM C4   TYPE=CB     CHARge=0.19      EXCL=( N1 ) END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.50     EXCL=( C6 ) END
  ATOM C2   TYPE=CA     CHARge=0.50      EXCL=( C5 ) END
 GROUP
  ATOM N2   TYPE=N2     CHARge=-0.42     END!
  ATOM H2  TYPE=H2     CHARge=0.21      END!
 GROUP 
  ATOM CA   TYPE=CT     CHARge=-0.10   END
  ATOM HA   TYPE=HA     CHARge=0.21    END
 GROUP 
  ATOM CB   TYPE=CT     CHARge=0.08    END
  ATOM HB'  TYPE=HA     CHARge=0.10    END
  ATOM HB'' TYPE=HA     CHARge=0.10    END
  ATOM OB   TYPE=OH     CHARge=-0.68   END
  ATOM HOB  TYPE=HO     CHARge=0.40    END
 GROUP 
  ATOM CJ   TYPE=CP     CHARge=0.03    EXCLUDE=(CP)  END
  ATOM CO   TYPE=CP     CHARge=-0.16   EXCLUDE=(CM') END
  ATOM HO   TYPE=HA     CHARge=0.14    END
  ATOM CO'  TYPE=CP     CHARge=-0.16   EXCLUDE=(CM)  END
  ATOM HO'  TYPE=HA     CHARge=0.14    END
  ATOM CM   TYPE=CP     CHARge=-0.15   EXCLUDE=(CO') END
  ATOM HM   TYPE=HA     CHARge=0.14    END
  ATOM CM'  TYPE=CP     CHARge=-0.15   EXCLUDE=(CO)  END
  ATOM HM'  TYPE=HA     CHARge=0.14    END
  ATOM CP   TYPE=CP     CHARge=-0.15   EXCLUDE=(CJ)  END
  ATOM HP   TYPE=HA     CHARge=0.14    END 
 GROUP
  ATOM N1   TYPE=NA     CHARge=-0.26     END
  ATOM H1   TYPE=H      CHARge=0.26      END
 GROUP
  ATOM C6   TYPE=C      CHARge=0.30      END
  ATOM O6   TYPE=O      CHARge=-0.30     END
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02      END
  ATOM N7   TYPE=NB     CHARge=-0.25     END
  ATOM C8   TYPE=CE     CHARge=0.195     END
  ATOM H8   TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115     END!"
  ATOM H2'' TYPE=H      CHARge=0.035     END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40     END
  ATOM H2'  TYPE=HO     CHARge=0.25      END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035    END!"
  ATOM H3'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM O3'  TYPE=OS     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 CA     BOND N2 H2     BOND CA HA      BOND CA CB 
 BOND CB  HB'   BOND CB HB''   BOND CB OB      BOND OB HOB
 BOND CA CJ     BOND CJ CO     BOND CO HO      
 BOND CO CM     BOND CM HM     BOND CM CP      BOND CP HP
 BOND CP CM'    BOND CM' HM'   BOND CM' CO'
 BOND CO' HO'   BOND CO' CJ
 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 O3'  +P *}
 BOND C2' O2'   BOND O2' H2'
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'    BOND C5' H5'
 BOND C5' H5''  BOND C8 H8
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P +O5' *}
 DIHE O4' C1' N9 C4     
 IMPRoper N3  C2 N2 H2
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 ! The ring-spanning impropers have been left out.
 ! And the chiral impropers are not needed with all hydrogens present
 {* IMPR C5' O4' C3' C4'    IMPR O3' C2' C4' C3'    IMPR N9  C2' O4' C1'  *}
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'


 IMPR C1' C4 C8 N9     ! THIS IS AN SP2 IMPROPER ABOUT N9
 IMPR N9 C4 C5 N7      IMPR C4 C5 N7 C8       IMPR C5 N7 C8 N9
 IMPR N7 C8 N9 C4      IMPR C8 N9 C4 C5       IMPR N2 N3 N1 C2
 IMPR H1 C2 C6 N1      IMPR O6 N1 C5 C6       IMPR C4 N3 C2 N1
 IMPR N3 C2 N1 C6      IMPR C2 N1 C6 C5       IMPR N1 C6 C5 C4
 IMPR C6 C5 C4 N3      IMPR C5 C4 N3 C2       IMPR CA H2 C2 N2
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8 C4 C5 N1      IMPR C8 C5 C4 C2
 IMPR N3 C4 C5 N7      IMPR C6 C5 C4 N9
 {* IMPR  C2' C3' C1' O2'  *}
 IMPR H8 N7 N9 C8
 ! To keep H's in phenyl planar
 IMPR HO'  CO'  CM'  CP
 IMPR HM'  CM'  CP   CM
 IMPR HP   CP   CM   CO
 IMPR HM   CM   CO   CJ
 IMPR HO   CO   CJ   CA 
 ! TO Keep carbons in phenyl planar
 IMPR CJ   CO   CM   CP
 IMPR CO   CM   CP   CM'
 IMPR CM   CP   CM'  CO'
 IMPR CP   CM'  CO'  CJ
 IMPR CM'  CO'  CJ   CO
 IMPR CO'  CJ   CO   CM
 IMPR CA   CJ   CO   CM

 IMPR HB'  HB'' CA   OB  ! STEREO AT CB
 IMPR HA   N2   CB   CJ  ! STEREO AT CA

 DIHE CO  CJ  CA  CB
 DONO H2  N2
 DONO H1   N1
 DONO H2'  O2'
 
 ACCE O6   C6
 ACCE N3   " "
 ACCE N7   " "   !added
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2'  " "
 ACCE O3'  " "
 ACCE O4'  " "
 ACCE O5'  " "
 
 
END {* GUA *}
  
!===========================================================================

RESIdue PDG
 GROUP
  ATOM P    TYPE=P      CHARGE=1.20      END
  ATOM O1P  TYPE=O2     CHARge=-0.40     END
  ATOM O2P  TYPE=O2     CHARge=-0.40     END
  ATOM O5'  TYPE=OS     CHARge=-0.36     END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.07     END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035     END!"
  ATOM H5'' TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065     END!"
  ATOM H4'  TYPE=H      CHARge=0.035     END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30     END
  ATOM C1'  TYPE=CH     CHARge=0.165     END!"
  ATOM H1'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.0084     END
  ATOM C4   TYPE=CB     CHARge=0.1642      EXCL=( N1 ) END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.3497     EXCL=( C6 ) END
  ATOM C2   TYPE=CA     CHARge=0.3939      EXCL=( C5 ) END
 GROUP
  ATOM N2   TYPE=NA     CHARge=-0.3609     END!
  ATOM H2   TYPE=H      CHARge=0.2091      END!
 GROUP
  ATOM C6A  TYPE=C2     CHARge=0.1686     END 
  ATOM H6A1 TYPE=H      CHARge=0.0209     END 
  ATOM H6A2 TYPE=H      CHARge=-0.0014    END 
  ATOM C7A  TYPE=C2     CHARge=-0.0507    END 
  ATOM H7A1 TYPE=H      CHARge=0.0299     END 
  ATOM H7A2 TYPE=H      CHARge=0.0285     END 
  ATOM C8A  TYPE=C2     CHARge=0.1668     END 
  ATOM H8A1 TYPE=H      CHARge=0.0376     END 
  ATOM H8A2 TYPE=H      CHARge=0.0164     END 
 GROUP
  ATOM N1   TYPE=NS     CHARge=-0.4106     END
 GROUP
  ATOM C6   TYPE=C      CHARge=0.4602      END
  ATOM O6   TYPE=O      CHARge=-0.3174     END
 GROUP
  ATOM C5   TYPE=CB     CHARge=-0.2304      END
  ATOM N7   TYPE=NB     CHARge=-0.1403     END
  ATOM C8   TYPE=CE     CHARge=0.0437     END
  ATOM H8   TYPE=H      CHARge=0.1300     END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115     END!"
  ATOM H2'' TYPE=H      CHARge=0.035     END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40     END
  ATOM H2'  TYPE=HO     CHARge=0.25      END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035    END!"
  ATOM H3'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM O3'  TYPE=OS     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 H2
 BOND N2 C6A    BOND C6A H6A1  BOND C6A H6A2   BOND C6A C7A    BOND C7A H7A1 
 BOND C7A H7A2  BOND C8A C7A   BOND C8A H8A1   BOND C8A H8A2   BOND N1 C8A   
 BOND N1 C6     BOND C6 O6     BOND C6 C5
 BOND C5 N7     BOND N7 C8     BOND C2' C3'    BOND C3' O3'  {* BOND O3'  +P *}
 BOND C2' O2'   BOND O2' H2'
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'    BOND C5' H5'
 BOND C5' H5''  BOND C8 H8     
      

 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P +O5' *}
 DIHE O4' C1' N9 C4     
 IMPRoper N3  C2 N2 H2
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 !
 !
 DIHE N2   C6A  C7A  C8A
 DIHE C6A  C7A  C8A  N1
 ! 
 ! The ring-spanning impropers have been left out.
 ! And the chiral impropers are not needed with all hydrogens present
 {* IMPR C5' O4' C3' C4'    IMPR O3' C2' C4' C3'    IMPR N9  C2' O4' C1'  *}
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'


 IMPR C1' C4 C8 N9     ! THIS IS AN SP2 IMPROPER ABOUT N9
 IMPR N9 C4 C5 N7      IMPR C4 C5 N7 C8       IMPR C5 N7 C8 N9
 IMPR N7 C8 N9 C4      IMPR C8 N9 C4 C5       IMPR N2 N3 N1 C2
 IMPR N1 C2 N2 C8A     IMPR O6 N1 C5 C6       IMPR C4 N3 C2 N1
 IMPR N3 C2 N1 C6      IMPR C2 N1 C6 C5       IMPR N1 C6 C5 C4
 IMPR C6 C5 C4 N3      IMPR C5 C4 N3 C2       IMPR N1 C2 N2 H2
 IMPR N1 C2 N2 N3      IMPR N2 C2 N1 C8A
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8 C4 C5 N1      IMPR C8 C5 C4 C2
 IMPR N3 C4 C5 N7      IMPR C6 C5 C4 N9
 {* IMPR  C2' C3' C1' O2'  *}
 IMPR H8 N7 N9 C8
 DONO H2   N2
 DONO H2'  O2'
 
 ACCE O6   C6
 ACCE N3   " "
 ACCE N7   " "   !added
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2'  " "
 ACCE O3'  " "
 ACCE O4'  " "
 ACCE O5'  " "
 
 
END {* PDG *}

!===========================================================================
RESIdue A
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END!"
  ATOM H5'  TYPE=H      CHARge=0.035   END!"
  ATOM H5'' TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19   END
  ATOM C4   TYPE=CB     CHARge=0.19    EXCL=( N1 )  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.26   EXCL=( C6 )  END
  ATOM C2   TYPE=CE     CHARge=0.225   EXCL=( C5 )  END !"
  ATOM H2   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N1   TYPE=NC     CHARge=-0.28   END
  ATOM C6   TYPE=CA     CHARge=0.28    END
 GROUP
  ATOM N6   TYPE=N2     CHARGE=-0.42   END!
  ATOM H61  TYPE=H2     CHARge=0.21    END!
  ATOM H62  TYPE=H2     CHARge=0.21    END!
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02    END
  ATOM N7   TYPE=NB     CHARge=-0.25   END
  ATOM C8   TYPE=CE     CHARge=0.195   END!"
  ATOM H8   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115   END!"
  ATOM H2'' TYPE=H      CHARge=0.035   END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40   END
  ATOM H2'  TYPE=HO     CHARge=0.25    END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035  END!"
  ATOM H3'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM O3'  TYPE=OS     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 O3'+P *}
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'  BOND C5' H5'
 BOND C5'  H5'' BOND C8 H8     BOND C2 H2
 
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P  +O5'  *}
 DIHE O4' C1' N9 C4     
 IMPRoper C5 C6 N6 H61
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 ! The ring-spanning impropers have been left out.
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N9   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C4   C8   N9
 IMPR N9   C4   C5   N7      IMPR C4   C5   N7   C8     IMPR C5   N7   C8   N9
 IMPR N7   C8   N9   C4      IMPR C8   N9   C4   C5     IMPR N6   N1   C5   C6
 IMPR H62  C6   H61  N6      IMPR C4   N3   C2   N1     IMPR N3   C2   N1   C6
 IMPR C2   N1   C6   C5      IMPR N1   C6   C5   C4     IMPR C6   C5   C4   N3
 IMPR C5   C4   N3   C2      IMPR H8   N7   N9   C8
 IMPR H2   N1   N3   C2
 !IMPR C2'  C3'  C1'  O2'
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8   C4   C5   N1      IMPR C8   C5   C4   C2
 IMPR N3   C4   C5   N7      IMPR C6   C5   C4   N9
 
 
 DONO H61  N6
 DONO H62  N6
 DONO H2'  O2'


 ACCE N3 " "
 ACCE N1 " "
 ACCE N7 " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* ADE *}
 
!=========================================================================
RESIdue ABP
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END!"
  ATOM H5'  TYPE=H      CHARge=0.035   END!"
  ATOM H5'' TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19   END
  ATOM C4   TYPE=CB     CHARge=0.19    EXCL=( N1 )  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.26   EXCL=( C6 )  END
  ATOM C2   TYPE=CE     CHARge=0.225   EXCL=( C5 )  END !"
  ATOM H2   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N1   TYPE=NC     CHARge=-0.28   END
  ATOM C6   TYPE=CA     CHARge=0.28    END
 GROUP
  ATOM N6   TYPE=N2     CHARGE=-0.42   END
  ATOM H6   TYPE=H2     CHARge=0.21    END
 GROUP
  ATOM C10  TYPE=CH     CHARge=0.1427  END
  ATOM H10  TYPE=H      CHARge=-0.004  END  
 GROUP
  ATOM C9   TYPE=CH     CHARge=0.1854  END
  ATOM H9   TYPE=H      CHARge=-0.0379 END
  ATOM O9   TYPE=OH     CHARge=-0.2722 END 
  ATOM HO9  TYPE=HO     CHARge=0.1558  END 
 GROUP
  ATOM C8A  TYPE=CH     CHARge=0.1824  END
  ATOM H8A  TYPE=H      CHARge=-0.0481 END
  ATOM O8A  TYPE=OH     CHARge=-0.2863 END 
  ATOM HO8A TYPE=HO     CHARge=0.1590  END 
 GROUP
  ATOM C7   TYPE=CH     CHARge=0.2036  END
  ATOM H7   TYPE=H      CHARge=-0.0082 END
  ATOM O7   TYPE=OH     CHARge=-0.2975 END 
  ATOM HO7  TYPE=HO     CHARge=0.1552  END
 GROUP
  ATOM C6A  TYPE=CP9    CHARge=0.0135  END
 GROUP 
  ATOM C6B  TYPE=CP8    CHARge=0.0051  END
  ATOM H6B  TYPE=HA     CHARge=-0.0271 END
  GROUP
  ATOM C5A  TYPE=CP7    CHARge=0.0239  END
 GROUP 
  ATOM C5B  TYPE=CP6    CHARge=0.0241  END
  ATOM H5B  TYPE=HA     CHARge=-0.0320 END
 GROUP 
  ATOM C4A  TYPE=CP5    CHARge=0.0510  END
  ATOM H4A  TYPE=HA     CHARge=-0.0295 END
 GROUP
  ATOM C3A  TYPE=CP4    CHARge=0.0300  END
 GROUP 
  ATOM C3   TYPE=CP3    CHARge=0.0076  END
  ATOM H3   TYPE=HA     CHARge=-0.0251 END
 GROUP 
  ATOM C2A  TYPE=CP2    CHARge=0.0253  END
  ATOM H2A  TYPE=HA     CHARge=-0.0270 END
 GROUP 
  ATOM C1   TYPE=CP1    CHARge=0.0095  END
  ATOM H1   TYPE=HA     CHARge=-0.0273 END
 GROUP
  ATOM C12A TYPE=CP14   CHARge=0.0295  END
  ATOM C12B TYPE=CP15   CHARge=0.0111  END
  ATOM C12C TYPE=CP16   CHARge=0.0008  END  
  ATOM C10A TYPE=CP10   CHARge=-.0153  END
  ATOM C10B TYPE=CP11   CHARge=0.0298  END
 GROUP 
  ATOM C11  TYPE=CP12   CHARge=0.0088  END
  ATOM H11  TYPE=HA     CHARge=-0.0288 END
 GROUP 
  ATOM C12  TYPE=CP13   CHARge=0.0219  END
  ATOM H12  TYPE=HA     CHARge=-0.0329 END
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02    END
  ATOM N7   TYPE=NB     CHARge=-0.25   END
  ATOM C8   TYPE=CE     CHARge=0.195   END!"
  ATOM H8   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115   END!"
  ATOM H2'' TYPE=H      CHARge=0.035   END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40   END
  ATOM H2'  TYPE=HO     CHARge=0.25    END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035  END!"
  ATOM H3'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM O3'  TYPE=OS     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  C10   BOND N6 H6     BOND C6 C5      BOND C5 N7    BOND N7 C8
 BOND C10 H10   BOND C10 C9    BOND C10 C10A
 BOND C9 H9     BOND C9 O9     BOND O9 HO9    BOND C9 C8A
 BOND C8A H8A   BOND C8A O8A   BOND O8A HO8A  BOND C8A C7
 BOND C7 H7     BOND C7 O7     BOND O7 HO7    BOND C7 C6A
 BOND C6A C10A  BOND C6A C6B
 BOND C6B H6B   BOND C6B C5A
 BOND C5A C12C  BOND C5A C5B
 BOND C5B H5B   BOND C5B C4A
 BOND C4A H4A   BOND C4A C3A
 BOND C3A C12B  BOND C3A C3
 BOND C3 H3     BOND C3 C2A
 BOND C2A H2A   BOND C2A C1
 BOND C1 H1     BOND C1 C12A
 BOND C12A C12  BOND C12A C12B
 BOND C12B C12C BOND C12C C10B
 BOND C10B C10A BOND C10B C11
 BOND C11 H11   BOND C11 C12   BOND C12 H12
 
 BOND C2' C3'   BOND C2' O2'   BOND O2' H2'    BOND C3' O3'  {* BOND O3'+P *}
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'  BOND C5' H5'
 BOND C5'  H5'' BOND C8 H8     BOND C2 H2
 
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P  +O5'  *}
 DIHE O4' C1' N9 C4     
 IMPRoper C5 C6 N6 H6
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
!Benzo(a)pyrene
 DIHE C10  C9   C8A  C7
 DIHE C9   C8A  C7   C6A
 DIHE C8A  C7   C6A  C10A
 !
 ! The ring-spanning impropers have been left out.
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N9   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C4   C8   N9
 IMPR N9   C4   C5   N7      IMPR C4   C5   N7   C8     IMPR C5   N7   C8   N9
 IMPR N7   C8   N9   C4      IMPR C8   N9   C4   C5     IMPR N6   N1   C5   C6
 IMPR C10  C6   H6   N6      IMPR C4   N3   C2   N1     IMPR N3   C2   N1   C6
 IMPR C2   N1   C6   C5      IMPR N1   C6   C5   C4     IMPR C6   C5   C4   N3
 IMPR C5   C4   N3   C2      IMPR H8   N7   N9   C8
 IMPR H2   N1   N3   C2
 !IMPR C2'  C3'  C1'  O2'
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8   C4   C5   N1      IMPR C8   C5   C4   C2
 IMPR N3   C4   C5   N7      IMPR C6   C5   C4   N9
 ! To Keep H's in pyrenyl ring planar
 IMPR H1   C1   C2A  C3
 IMPR H2A  C2A  C3   C3A
 IMPR H3   C3   C3A  C12B
 IMPR H4A  C4A  C5B  C5A
 IMPR H5B  C5B  C5A  C12C
 IMPR H6B  C6B  C6A  C10A
 IMPR H11  C11  C12  C12A
 IMPR H12  C12  C12A C12B
!
! To Keep carbons in pyrenyl ring planar
 IMPR C1   C2A  C3   C3A
 IMPR C2A  C3   C3A  C12B
 IMPR C3   C3A  C12B C12A
 IMPR C3A  C12B C12A C1
 IMPR C12B C12A C1   C2A
 IMPR C12A C1   C2A  C3
! 
 IMPR C12C C12B C3A  C4A
 IMPR C12B C3A  C4A  C5B
 IMPR C3A  C4A  C5B  C5A
 IMPR C4A  C5B  C5A  C12C
 IMPR C5B  C5A  C12C C12B
 IMPR C5A  C12C C12B C3A
!
 IMPR C11  C12  C12A C12B
 IMPR C12  C12A C12B C12C
 IMPR C12A C12B C12C C10B
 IMPR C12B C12C C10B C11
 IMPR C12C C10B C11  C12 
 IMPR C10B C11  C12  C12A
! 
 IMPR C10A C10B C12C C5A
 IMPR C10B C12C C5A  C6B
 IMPR C12C C5A  C6B  C6A
 IMPR C5A  C6B  C6A  C10A
 IMPR C6B  C6A  C10A C10B
 IMPR C6A  C10A C10B C12C 
 

! To Keep pyrene rings planner with respect to each other
 IMPR C10  C10A C10B C12C
 IMPR C7   C6A  C6B  C5A
 IMPR C12A C12B C3A  C4A
 IMPR C2A  C3   C3A  C4A 
 IMPR C1   C12A C12B C12C
 IMPR C12  C12A C12B C3A
 IMPR C12A C12B C12C C5A
 IMPR C11  C10B C12C C5A
 IMPR C11  C10B C10A C6A
 IMPR C12B C12C C5A  C6B
 IMPR C10B C12C C5A  C5B
 IMPR C3   C3A  C4A  C5B
 IMPR C10  C10A C10B C11
 IMPR C10  C10A C6A  C7
 
 IMPR H10  N6   C9   C10A ! STEREO AT C10

 DONO H61  N6
 DONO H62  N6
 DONO H2'  O2'
 DONO HO7  O7
 DONO HO8A O8A
 DONO HO9  O9
 
 ACCE N3 " "
 ACCE N1 " "
 ACCE N7 " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* ABP *}
!=========================================================================
RESIdue ABA
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END!"
  ATOM H5'  TYPE=H      CHARge=0.035   END!"
  ATOM H5'' TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.2100   END
  ATOM C4   TYPE=CB     CHARge=0.0783    EXCL=( N1 )  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.1841   EXCL=( C6 )  END
  ATOM C2   TYPE=CE     CHARge=0.1842    EXCL=( C5 )  END !"
  ATOM H2   TYPE=H      CHARge=0.1194    END!"
 GROUP
  ATOM N1   TYPE=NC     CHARge=-0.3563   END
  ATOM C6   TYPE=CA     CHARge=0.3065    END
 GROUP
  ATOM N6   TYPE=N2     CHARGE=-0.2910   END
  ATOM H6   TYPE=H2     CHARge=0.2071    END
!
 GROUP
  ATOM C4C  TYPE=CH     CHARge=0.2227    END
  ATOM H4C  TYPE=H      CHARge=0.0901    END  
 GROUP
  ATOM C9C  TYPE=CH     CHARge=0.0911    END
  ATOM H9C  TYPE=H      CHARge=0.0456    END
  ATOM O3   TYPE=OH     CHARge=-0.3361   END 
  ATOM H3   TYPE=HO     CHARge=0.1774    END 
 GROUP
  ATOM C8B  TYPE=CH     CHARge=0.0833    END
  ATOM H8B  TYPE=H      CHARge=0.0390    END
  ATOM O2   TYPE=OH     CHARge=-0.3179   END 
  ATOM HO2  TYPE=HO     CHARge=0.1884    END 
 GROUP
  ATOM C3B  TYPE=CH     CHARge=0.1440    END
  ATOM H3B  TYPE=H      CHARge=0.0532    END
  ATOM O1   TYPE=OH     CHARge=-0.3128   END 
  ATOM H1   TYPE=HO     CHARge=0.1866    END
 GROUP
  ATOM C3A  TYPE=CP23   CHARge=-0.0606   END
 GROUP 
  ATOM C2A  TYPE=CP22   CHARge=-0.0543   END
  ATOM H2A  TYPE=HA     CHARge=0.0760    END
  GROUP
  ATOM C4A  TYPE=CP24   CHARge=-0.0892   END
 GROUP 
  ATOM C1A  TYPE=CP21   CHARge=-0.0224   END
  ATOM H1A  TYPE=HA     CHARge=0.0673    END
 GROUP 
  ATOM C5A  TYPE=CP26   CHARge=-0.0376   END
  ATOM H5A  TYPE=HA     CHARge=0.0589    END
 GROUP
  ATOM C4B  TYPE=CP25   CHARge=-0.0322   END
 GROUP 
  ATOM C6A  TYPE=CP27   CHARge=-0.0497   END
  ATOM H6A  TYPE=HA     CHARge=0.0635    END
 GROUP 
  ATOM C7A  TYPE=CP28   CHARge=-0.0467   END
  ATOM H7A  TYPE=HA     CHARge=0.0643    END
 GROUP 
  ATOM C8A  TYPE=CP29   CHARge=-0.0540   END
  ATOM H8A  TYPE=HA     CHARge=0.0652    END
 GROUP
  ATOM C5B  TYPE=CP30   CHARge=-0.0235   END
  ATOM C9B  TYPE=CP31   CHARge=-0.0327   END
  ATOM C11  TYPE=CP32   CHARge=-0.0435   END  
 GROUP 
  ATOM C9A  TYPE=CP33   CHARge=-0.0444   END
  ATOM H9A  TYPE=HA     CHARge=0.0612    END
 GROUP 
  ATOM C10  TYPE=CP34   CHARge=-0.0124   END
  ATOM H10  TYPE=HA     CHARge=0.0624    END
!
!
 GROUP
  ATOM C5   TYPE=CB     CHARge=-0.1350   END
  ATOM N7   TYPE=NB     CHARge=-0.1903   END
  ATOM C8   TYPE=CE     CHARge=0.0714    END!"
  ATOM H8   TYPE=H      CHARge=0.1295    END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115     END!"
  ATOM H2'' TYPE=H      CHARge=0.035     END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40     END
  ATOM H2'  TYPE=HO     CHARge=0.25      END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035    END!"
  ATOM H3'  TYPE=H      CHARge=0.035     END!"
 GROUP
  ATOM O3'  TYPE=OS     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  C4C   BOND N6 H6     BOND C6 C5      BOND C5 N7    BOND N7 C8
 BOND C4C H4C   BOND C4C C9C   BOND C4C C4A
 BOND C9C H9C   BOND C9C O3    BOND O3 H3     BOND C9C C8B
 BOND C8B H8B   BOND C8B O2    BOND O2 HO2    BOND C8B C3B
 BOND C3B H3B   BOND C3B O1    BOND O1 H1     BOND C3B C3A
 BOND C3A C2A   BOND C3A C4A
 BOND C2A H2A   BOND C4A C4B
 BOND C4B C5A   BOND C5A C5B
 BOND C5A H5A   BOND C5B C6A   
 BOND C6A H6A   BOND C6A C7A
 BOND C7A H7A   BOND C7A C8A
 BOND C8A H8A   BOND C8A C9A
 BOND C9A H9A   BOND C9A C9B
 BOND C9B C5B   BOND C9B C10 
 BOND C10 C11   BOND C1A C11
 BOND C1A C2A   BOND C11 C4B
 BOND C1A H1A   BOND C10 H10
 
 BOND C2' C3'   BOND C2' O2'   BOND O2' H2'    BOND C3' O3'  {* BOND O3'+P *}
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'  BOND C5' H5'
 BOND C5'  H5'' BOND C8 H8     BOND C2 H2
 
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P  +O5'  *}
 DIHE O4' C1' N9 C4     
 IMPR  C5 C6 N6 H6
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
!Benz[a]anthracene
! DIHE C4C  C9C   C8B   C3B
! DIHE C9C  C8B   C3B   C3A
  DIHE C5   C6    N6    H6
! DIHE C5   C6    N6    C4C
 
 ! The ring-spanning impropers have been left out.
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N9   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C4   C8   N9
 IMPR N9   C4   C5   N7      IMPR C4   C5   N7   C8     IMPR C5   N7   C8   N9
 IMPR N7   C8   N9   C4      IMPR C8   N9   C4   C5     IMPR N6   N1   C5   C6
 IMPR C4C  C6   H6   N6      IMPR C4   N3   C2   N1     IMPR N3   C2   N1   C6
 IMPR C2   N1   C6   C5      IMPR N1   C6   C5   C4     IMPR C6   C5   C4   N3
 IMPR C5   C4   N3   C2      IMPR H8   N7   N9   C8
 IMPR H2   N1   N3   C2
 !IMPR C2'  C3'  C1'  O2'
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8   C4   C5   N1      IMPR C8   C5   C4   C2
 IMPR N3   C4   C5   N7      IMPR C6   C5   C4   N9
 ! To Keep H's in pyrenyl ring planar
 IMPR H1A  C1A  C2A  C3A   
 IMPR H2A  C2A  C3A  C4A  
 IMPR H10  C10  C11  C4B 
 IMPR H5A  C5A  C5B  C9B 
 IMPR H6A  C6A  C7A  C8A 
 IMPR H7A  C7A  C8A  C9A  
 IMPR H8A  C8A  C9A  C9B  
 IMPR H9A  C9A  C9B  C5B
 
! To Keep carbons in pyrenyl ring planar
 IMPR C6A  C7A  C8A  C9A
 IMPR C7A  C8A  C9A  C9B
 IMPR C8A  C9A  C9B  C5B
 IMPR C9A  C9B  C5B  C6A
 IMPR C9B  C5B  C6A  C7A
 IMPR C5B  C6A  C7A  C8A

 IMPR C5A  C5B  C9B  C10
 IMPR C5B  C9B  C10  C11
 IMPR C9B  C10  C11  C4B
 IMPR C10  C11  C4B  C5A
 IMPR C11  C4B  C5A  C5B
 IMPR C4B  C5A  C5B  C9B

 IMPR C4A  C4B  C11  C1A 
 IMPR C4B  C11  C1A  C2A
 IMPR C11  C1A  C2A  C3A
 IMPR C1A  C2A  C3A  C4A
 IMPR C2A  C3A  C4A  C4B
 IMPR C3A  C4A  C4B  C11
 
! To Keep anthracene rings planner with respect to each other
 IMPR C4C  C4A  C4B  C11
 IMPR C3B  C3A  C2A  C1A
 IMPR C4C  C4A  C4B  C5A
 IMPR C4C  C4A  C3A  C3B
 IMPR C6A  C5B  C5A  C4B
 IMPR C9A  C9B  C10  C11
 IMPR C5A  C4B  C4A  C3A
 IMPR C10  C11  C1A  C2A
 IMPR C5A  C4B  C11  C1A
 IMPR C10  C11  C4B  C4A
 
 IMPR H4C  N6   C9C  C4A ! STEREO AT C4C 

 DONO H61  N6
 DONO H62  N6
 DONO H2'  O2'
 DONO H1   O1
 DONO HO2  O2
 DONO H3   O3
 
 ACCE N3 " "
 ACCE N1 " "
 ACCE N7 " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* ABA *}
!=========================================================================
!
 RESIdue AST
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END!"
  ATOM H5'  TYPE=H      CHARge=0.035   END!"
  ATOM H5'' TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19   END
  ATOM C4   TYPE=CB     CHARge=0.19    EXCL=( N1 )  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.26   EXCL=( C6 )  END
  ATOM C2   TYPE=CE     CHARge=0.225   EXCL=( C5 )  END !"
  ATOM H2   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N1   TYPE=NC     CHARge=-0.28   END
  ATOM C6   TYPE=CA     CHARge=0.28    END
 GROUP
  ATOM N6   TYPE=N2     CHARGE=-0.42   END!
  ATOM H6   TYPE=H2     CHARge=0.21    END!
 GROUP 
  ATOM CA   TYPE=CT     CHARge=-0.10   END
  ATOM HA   TYPE=HA     CHARge=0.21    END
 GROUP 
  ATOM CB   TYPE=CT     CHARge=0.08    END
  ATOM HB'  TYPE=HA     CHARge=0.10    END
  ATOM HB'' TYPE=HA     CHARge=0.10    END
  ATOM OB   TYPE=OH     CHARge=-0.68   END
  ATOM HOB  TYPE=HO     CHARge=0.40    END
 GROUP 
  ATOM CJ   TYPE=CP     CHARge=0.03    EXCLUDE=(CP)  END
  ATOM CO   TYPE=CP     CHARge=-0.16   EXCLUDE=(CM') END
  ATOM HO   TYPE=HA     CHARge=0.14    END
  ATOM CO'  TYPE=CP     CHARge=-0.16   EXCLUDE=(CM)  END
  ATOM HO'  TYPE=HA     CHARge=0.14    END
  ATOM CM   TYPE=CP     CHARge=-0.15   EXCLUDE=(CO') END
  ATOM HM   TYPE=HA     CHARge=0.14    END
  ATOM CM'  TYPE=CP     CHARge=-0.15   EXCLUDE=(CO)  END
  ATOM HM'  TYPE=HA     CHARge=0.14    END
  ATOM CP   TYPE=CP     CHARge=-0.15   EXCLUDE=(CJ)  END
  ATOM HP   TYPE=HA     CHARge=0.14    END
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02    END
  ATOM N7   TYPE=NB     CHARge=-0.25   END
  ATOM C8   TYPE=CE     CHARge=0.195   END!"
  ATOM H8   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115   END!"
  ATOM H2'' TYPE=H      CHARge=0.035   END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40   END
  ATOM H2'  TYPE=HO     CHARge=0.25    END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035  END!"
  ATOM H3'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM O3'  TYPE=OS     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 CA     BOND N6 H6     BOND CA HA      BOND CA CB 
 BOND CB  HB'   BOND CB HB''   BOND CB OB      BOND OB HOB
 BOND CA CJ     BOND CJ CO     BOND CO HO      
 BOND CO CM     BOND CM HM     BOND CM CP      BOND CP HP
 BOND CP CM'    BOND CM' HM'   BOND CM' CO'
 BOND CO' HO'   BOND CO' CJ
 BOND C6 C5     BOND C5 N7      BOND N7 C8
 BOND C2' C3'   BOND C2' O2'   BOND O2' H2'    BOND C3' O3'  {* BOND O3'+P *}
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'  BOND C5' H5'
 BOND C5'  H5'' BOND C8 H8     BOND C2 H2
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P  +O5'  *}
 DIHE O4' C1' N9 C4     
 IMPRoper C5 C6 N6 H6
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 ! The ring-spanning impropers have been left out.
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N9   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C4   C8   N9
 IMPR N9   C4   C5   N7      IMPR C4   C5   N7   C8     IMPR C5   N7   C8   N9
 IMPR N7   C8   N9   C4      IMPR C8   N9   C4   C5     IMPR N6   N1   C5   C6
 IMPR CA   C6   H6   N6      IMPR C4   N3   C2   N1     IMPR N3   C2   N1   C6
 IMPR C2   N1   C6   C5      IMPR N1   C6   C5   C4     IMPR C6   C5   C4   N3
 IMPR C5   C4   N3   C2      IMPR H8   N7   N9   C8
 IMPR H2   N1   N3   C2
 !IMPR C2'  C3'  C1'  O2'
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8   C4   C5   N1      IMPR C8   C5   C4   C2
 IMPR N3   C4   C5   N7      IMPR C6   C5   C4   N9
 ! To keep H's in phenyl planar
 IMPR HO'  CO'  CM'  CP
 IMPR HM'  CM'  CP   CM
 IMPR HP   CP   CM   CO
 IMPR HM   CM   CO   CJ
 IMPR HO   CO   CJ   CA 
 ! TO Keep carbons in phenyl planar
 IMPR CJ   CO   CM   CP
 IMPR CO   CM   CP   CM'
 IMPR CM   CP   CM'  CO'
 IMPR CP   CM'  CO'  CJ
 IMPR CM'  CO'  CJ   CO
 IMPR CO'  CJ   CO   CM
 IMPR CA   CJ   CO   CM

 IMPR HB'  HB'' CA   OB  ! STEREO AT CB
 IMPR HA   N6   CB   CJ  ! STEREO AT CA

 DIHE CO  CJ  CA  CB
 
 DONO H61  N6
 DONO H62  N6
 DONO H2'  O2'
 DONO HOB  OB

 ACCE N3 " "
 ACCE N1 " "
 ACCE N7 " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* AST *}
 
!=========================================================================
 
RESIdue PUR
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END!"
  ATOM H5'  TYPE=H      CHARge=0.035   END!"
  ATOM H5'' TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N9   TYPE=NS     CHARge=-0.19   END
  ATOM C4   TYPE=CB     CHARge=0.19    EXCL=( N1 )  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.26   EXCL=( C6 )  END
  ATOM C2   TYPE=CE     CHARge=0.225   EXCL=( C5 )  END !"
  ATOM H2   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N1   TYPE=NC     CHARge=-0.28   END
  ATOM C6   TYPE=CE     CHARge=0.28    END
  ATOM H6   TYPE=H      CHARge= 0.035  END
 GROUP
  ATOM C5   TYPE=CB     CHARge=0.02    END
  ATOM N7   TYPE=NB     CHARge=-0.25   END
  ATOM C8   TYPE=CE     CHARge=0.195   END!"
  ATOM H8   TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115   END!"
  ATOM H2'' TYPE=H      CHARge=0.035   END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40   END
  ATOM H2'  TYPE=HO     CHARge=0.25    END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035  END!"
  ATOM H3'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM O3'  TYPE=OS     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 H6
 BOND C6 C5      BOND C5 N7    BOND N7 C8
 BOND C2' C3'   BOND C2' O2'   BOND O2' H2'    BOND C3' O3'  {* BOND O3'+P *}
 BOND C1' H1'   BOND C2' H2''  BOND C3' H3'    BOND C4' H4'  BOND C5' H5'
 BOND C5'  H5'' BOND C8 H8     BOND C2 H2
 
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'    DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'    DIHE C3' O3' +P  +O5'  *}
 DIHE O4' C1' N9 C4
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 ! The ring-spanning impropers have been left out.
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N9   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N9
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C4   C8   N9
 IMPR N9   C4   C5   N7      IMPR C4   C5   N7   C8     IMPR C5   N7   C8   N9
 IMPR N7   C8   N9   C4      IMPR C8   N9   C4   C5     IMPR H6   N1   C5   C6
 IMPR C4   N3   C2   N1     IMPR N3   C2   N1   C6
 IMPR C2   N1   C6   C5      IMPR N1   C6   C5   C4     
   {* removed: IMPR C6   C5   C4   N3, ATB *}
 IMPR C5   C4   N3   C2      IMPR H8   N7   N9   C8
 IMPR H2   N1   N3   C2
 !IMPR C2'  C3'  C1'  O2'
 ! Dihedrals to keep the two purine rings parallel:
 IMPR C8   C4   C5   N1      IMPR C8   C5   C4   C2
 IMPR N3   C4   C5   N7      IMPR C6   C5   C4   N9
 
  DONO H2'  O2'
 
 ACCE N3 " "
 ACCE N1 " "
 ACCE N7 " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* PUR *}
 
!=========================================================================
 
 
RESIdue C
 GROUP
  ATOM P    TYPE=P      CHARge=1.20     END
  ATOM O1P  TYPE=O2     CHARge=-0.40    END
  ATOM O2P  TYPE=O2     CHARge=-0.40    END
  ATOM O5'  TYPE=OS     CHARge=-0.36    END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070   END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035    END! "
  ATOM H5'' TYPE=H      CHARge=0.035    END! "
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065    END! "
  ATOM H4'  TYPE=H      CHARge=0.035    END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30    END
  ATOM C1'  TYPE=CH     CHARge=0.165    END!"
  ATOM H1'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM N1   TYPE=NS     CHARge=-0.19    EXCL=( C4 )  END
  ATOM C6   TYPE=CF     CHARge=0.155    EXCL=( N3 )  END !"
  ATOM H6   TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM C2   TYPE=C      CHARge=0.30     EXCL=( C5 )   END
  ATOM O2   TYPE=O      CHARge=-0.30    END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.28    END
  ATOM C4   TYPE=CA     CHARge=0.28     END
 GROUP
  ATOM N4   TYPE=N2     CHARge=-0.42    END!
  ATOM H41  TYPE=H2     CHARge=0.21     END!
  ATOM H42  TYPE=H2     CHARge=0.21     END!
 GROUP
  ATOM C5   TYPE=CF     CHARge=-0.035   END!"
  ATOM H5   TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115    END!"
  ATOM H2'' TYPE=H      CHARge=0.035    END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40    END
  ATOM H2'  TYPE=HO     CHARge=0.25     END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035   END!"
  ATOM H3'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM O3'  TYPE=OS     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 O3' +P *}
 BOND C2' O2'   BOND O2' H2'
 BOND C1' H1'   BOND C2' H2''   BOND C3' H3'    BOND C4' H4'   BOND C5' H5'
 BOND C5' H5''  BOND C5 H5      BOND C6 H6
 
  {* DIHE -O3' P O5' C5'     DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'      DIHE O5' C5' C4' O4'     DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P     DIHE C3' O3' +P +O5'     DIHE C3' O3' +P +O5' *}
 DIHE O4' C1' N1 C2      
 IMPRoper C5 C4 N4 H41
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N1   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N1
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C2   C6   N1
 IMPR O2   N1   N3   C2      IMPR N4   N3   C5   C4
 IMPR N1   C2   N3   C4      IMPR C2   N3   C4   C5     IMPR N3   C4   C5   C6
 IMPR C4   C5   C6   N1      IMPR C5   C6   N1   C2     IMPR C6   N1   C2   N3
 IMPR H42  C4   H41  N4      IMPR H6   N1   C5   C6
 IMPR H5   C4   C6   C5
 !IMPR C2'  C3'  C1'  O2'
 
 DONO H42  N4
 DONO H2'  O2'
 DONO H41  N4
 
 ACCE O2   C2
 ACCE N3  " "
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* CYT *}
 
!========================================================================
 
 
RESIdue C+
 GROUP
  ATOM P    TYPE=P      CHARge=1.20     END
  ATOM O1P  TYPE=O2     CHARge=-0.40    END
  ATOM O2P  TYPE=O2     CHARge=-0.40    END
  ATOM O5'  TYPE=OS     CHARge=-0.36    END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070   END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035    END! "
  ATOM H5'' TYPE=H      CHARge=0.035    END! "
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065    END! "
  ATOM H4'  TYPE=H      CHARge=0.035    END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30    END
  ATOM C1'  TYPE=CH     CHARge=0.165    END!"
  ATOM H1'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM N1   TYPE=NS     CHARge=-0.057   EXCL=( C4 )  END
  ATOM C6   TYPE=CF     CHARge=0.286    EXCL=( N3 )  END !"
  ATOM H6   TYPE=H      CHARge=0.1364   END!"
 GROUP
  ATOM C2   TYPE=C      CHARge=0.4729   EXCL=( C5 )   END
  ATOM O2   TYPE=O      CHARge=-0.2359  END
 GROUP
  ATOM N3   TYPE=NC     CHARge=-0.3401  END
  ATOM H3   TYPE=H      CHARge=0.2509   END
  ATOM C4   TYPE=CA     CHARge=0.4445   END
 GROUP
  ATOM N4   TYPE=N2     CHARge=-0.2805  END!
  ATOM H41  TYPE=H2     CHARge=0.2467   END!
  ATOM H42  TYPE=H2     CHARge=0.2378   END!
 GROUP
  ATOM C5   TYPE=CF     CHARge=-0.2929  END!"
  ATOM H5   TYPE=H      CHARge=0.1312   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115    END!"
  ATOM H2'' TYPE=H      CHARge=0.035    END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40    END
  ATOM H2'  TYPE=HO     CHARge=0.25     END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035   END!"
  ATOM H3'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM O3'  TYPE=OS     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 N4     BOND N4 H41    BOND N4 H42
 BOND C4 C5     BOND C5 C6      BOND C2' C3'    BOND C3' O3'   {* BOND O3' +P *}
 BOND C2' O2'   BOND O2' H2'
 BOND C1' H1'   BOND C2' H2''   BOND C3' H3'    BOND C4' H4'   BOND C5' H5'
 BOND C5' H5''  BOND C5 H5      BOND C6 H6
 
  {* DIHE -O3' P O5' C5'     DIHE -O3' P O5' C5'  *}
 DIHE P O5' C5' C4'      DIHE O5' C5' C4' O4'     DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P     DIHE C3' O3' +P +O5'     DIHE C3' O3' +P +O5' *}
 DIHE O4' C1' N1 C2      
 IMPRoper C5 C4 N4 H41
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N1   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N1
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C2   C6   N1
 IMPR O2   N1   N3   C2      IMPR N4   N3   C5   C4
 IMPR N1   C2   N3   C4      IMPR C2   N3   C4   C5     IMPR N3   C4   C5   C6
 IMPR C4   C5   C6   N1      IMPR C5   C6   N1   C2     IMPR C6   N1   C2   N3
 IMPR H42  C4   H41  N4      IMPR H6   N1   C5   C6
 IMPR H5   C4   C6   C5
 !IMPR C2'  C3'  C1'  O2'
 
 DONO H42  N4
 DONO H2'  O2'
 DONO H41  N4
 DONO H3   N3
 
 ACCE O2   C2
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* C+ *}
 
!========================================================================
 
RESIdue T
 GROUP
  ATOM P    TYPE=P      CHARge=1.20    END
  ATOM O1P  TYPE=O2     CHARge=-0.40   END
  ATOM O2P  TYPE=O2     CHARge=-0.40   END
  ATOM O5'  TYPE=OS     CHARge=-0.36   END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070  END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035   END! "
  ATOM H5'' TYPE=H      CHARge=0.035   END! "
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065   END! "
  ATOM H4'  TYPE=H      CHARge=0.035   END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30   END
  ATOM C1'  TYPE=CH     CHARge=0.165   END!"
  ATOM H1'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM N1   TYPE=NS     CHARge=-0.19   EXCL=( C4 )  END
  ATOM C6   TYPE=CF     CHARge=0.155   EXCL=( N3 )  END
  ATOM H6   TYPE=H      CHARge=0.035   END
 GROUP
  ATOM C2   TYPE=C      CHARge=0.35    EXCL=( C5 )  END
  ATOM O2   TYPE=O      CHARge=-0.35   END
 GROUP
  ATOM N3   TYPE=NA     CHARge=-0.26   END
  ATOM H3   TYPE=H      CHARge=0.26    END
 GROUP
  ATOM C4   TYPE=C      CHARge=0.30    END
  ATOM O4   TYPE=O      CHARge=-0.30   END
 GROUP
  ATOM C5   TYPE=CS     CHARge=-0.035  END!  THESE CHARGES ?
  ATOM C5A  TYPE=C3     CHARge=-0.070  END!"
  ATOM H51  TYPE=H      CHARge=0.035   END!"
  ATOM H52  TYPE=H      CHARge=0.035   END!"
  ATOM H53  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115   END!"
  ATOM H2'' TYPE=H      CHARge=0.035   END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40   END
  ATOM H2'  TYPE=HO     CHARge=0.25    END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035  END!"
  ATOM H3'  TYPE=H      CHARge=0.035   END!"
 GROUP
  ATOM O3'  TYPE=OS     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 O3' +P *}
 BOND C2' O2'    BOND O2' H2'
 BOND C1' H1'    BOND C2' H2''   BOND C3' H3'     BOND C4' H4'    BOND C5' H5'
 BOND C5' H5''   BOND C6 H6      BOND C5A H51     BOND C5A H52    BOND C5A H53
 
 DIHE C6   C5   C5A  H51
 DIHE C6   C5   C5A  H52
 DIHE C6   C5   C5A  H53
 {* DIHE -O3' P O5' C5'      DIHE -O3' P O5' C5' *}
 DIHE P O5' C5' C4'       DIHE O5' C5' C4' O4'      DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P      DIHE C3' O3' +P +O5'      DIHE C3' O3' +P +O5' *}
 DIHE O4'  C1'  N1   C2
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N1   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N1
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C2   C6   N1
 IMPR O2   N1   N3   C2      IMPR H3   C2   C4   N3
 IMPR O4   N3   C5   C4      IMPR C5A  C4   C6   C5     IMPR N1   C2   N3   C4
 IMPR C2   N3   C4   C5      IMPR N3   C4   C5   C6     IMPR C4   C5   C6   N1
 IMPR C5   C6   N1   C2      IMPR C6   N1   C2   N3
 IMPR H6   N1   C5   C6
 !IMPR C2'  C3'  C1'  O2'
 
 DONO H3   N3
 DONO H2'  O2'
 
 ACCE O2   C2
 ACCE O4   C4
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* THY *}
 
!============================================================================
 
RESIdue URI
 GROUP
  ATOM P    TYPE=P      CHARge=1.20     END
  ATOM O1P  TYPE=O2     CHARge=-0.40    END
  ATOM O2P  TYPE=O2     CHARge=-0.40    END
  ATOM O5'  TYPE=OS     CHARge=-0.36    END
 GROUP
  ATOM C5'  TYPE=C2     CHARge=-0.070   END! rationalized
  ATOM H5'  TYPE=H      CHARge=0.035    END! "
  ATOM H5'' TYPE=H      CHARge=0.035    END! "
 GROUP
  ATOM C4'  TYPE=CH     CHARge=0.065    END! "
  ATOM H4'  TYPE=H      CHARge=0.035    END!"
  ATOM O4'  TYPE=OS     CHARge=-0.30    END
  ATOM C1'  TYPE=CH     CHARge=0.165    END!"
  ATOM H1'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM N1   TYPE=NS     CHARge=-0.19    EXCL=( C4 )  END
  ATOM C6   TYPE=CF     CHARge=0.155    EXCL=( N3 )  END
  ATOM H6   TYPE=H      CHARge=0.035    END
 GROUP
  ATOM C2   TYPE=C      CHARge=0.35     EXCL=( C5 )  END
  ATOM O2   TYPE=O      CHARge=-0.35    END
 GROUP
  ATOM N3   TYPE=NA     CHARge=-0.26    END
  ATOM H3   TYPE=H      CHARge=0.26     END
 GROUP
  ATOM C4   TYPE=C      CHARge=0.30     END
  ATOM O4   TYPE=O      CHARge=-0.30    END
 GROUP
  ATOM C5   TYPE=CF     CHARge=-0.035   END
  ATOM H5   TYPE=H      CHARge=0.035    END
 GROUP
  ATOM C2'  TYPE=CH     CHARge=0.115    END!"
  ATOM H2'' TYPE=H      CHARge=0.035    END!"
  ATOM O2'  TYPE=OH     CHARge=-0.40    END
  ATOM H2'  TYPE=HO     CHARge=0.25     END
 GROUP
  ATOM C3'  TYPE=CH     CHARge=-0.035   END!"
  ATOM H3'  TYPE=H      CHARge=0.035    END!"
 GROUP
  ATOM O3'  TYPE=OS     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 O3' +P *}
 BOND C2' O2'    BOND O2' H2'
 BOND C1' H1'    BOND C2' H2''   BOND C3' H3'    BOND C4' H4'     BOND C5'  H5'
 BOND C5' H5''   BOND C5 H5      BOND C6 H6
 
 {* DIHE -O3' P O5' C5'    DIHE -O3' P O5' C5' *}
 DIHE P O5' C5' C4'     DIHE O5' C5' C4' O4'      DIHE O5' C5' C4' C3'
 {* DIHE C4' C3' O3' +P    DIHE C3' O3' +P +O5'      DIHE C3' O3' +P +O5'  *}
 DIHE O4'  C1'  N1   C2
 ! N O T E:  SUGAR RING TERMS SET UP AS W. OLSON DOES IT
 DIHE O4'  C1'  C2'  C3' ! O-C-C-C, twofold term
 DIHE O4'  C1'  C2'  C3'
 DIHE C1'  C2'  C3'  C4'
 DIHE C2'  C3'  C4'  O4' ! O-C-C-C, twofold term
 DIHE C2'  C3'  C4'  O4'
 DIHE C3'  C4'  O4'  C1'
 DIHE C4'  O4'  C1'  C2'
 ! AND THE SPECIAL GAUCHE TERMS
 DIHE C5'  C4'  C3'  O3'
 DIHE O4'  C4'  C3'  O3'
 DIHE O4'  C1'  C2'  O2'
 DIHE C1'  C2'  C3'  O3'
 DIHE C4'  C3'  C2'  O2'
 DIHE O3'  C3'  C2'  O2'
 DIHE C3'  C2'  O2'  H2'
 ! SO THE ALLHYDROGEN TERMS
 DIHE O4'  C4'  C3'  H3'
 DIHE O4'  C1'  C2'  H2''
 DIHE C4'  O4'  C1'  H1'
 DIHE C1'  O4'  C4'  H4'
 DIHE C3'  C4'  C5'  H5'
 DIHE C3'  C4'  C5'  H5''
 
 !IMPR C5'  O4'  C3'  C4'    IMPR O3'  C2'  C4'  C3'    IMPR N1   C2'  O4'  C1'
 {* chiral impropers included for DG and SA *}
 improper H1'  C2'  O4'  N1
 improper H2'' C3'  C1'  O2'
 improper H3'  C4'  C2'  O3'
 improper H4'  C5'  C3'  O4'
 IMPR C1'  C2   C6   N1     IMPR O2   N1   N3   C2     IMPR H3   C2   C4   N3
 IMPR O4   N3   C5   C4     IMPR N1   C2   N3   C4
 IMPR C2   N3   C4   C5     IMPR N3   C4   C5   C6     IMPR C4   C5   C6   N1
 IMPR C5   C6   N1   C2     IMPR C6   N1   C2   N3
 IMPR H6   N1   C5   C6     IMPR H5   C4   C6   C5
 !IMPR C2'  C3'  C1'  O2'
 
 DONO H3   N3
 DONO H2'  O2'
 
 ACCE O2   C2
 ACCE O4   C4
 ACCE O1P  P
 ACCE O2P  P
 ACCE O2' " "
 ACCE O3' " "
 ACCE O4' " "
 ACCE O5' " "
 
 
END {* URI *}
 
!============================================================================
 
 
!------------------------------------------------------------------
 
 
PRESidue DEOX    ! Patch to make DEOXYribose of the ribose
  DELETE ATOM O2'   END
 GROUP
  MODIFY ATOM C2'  TYPE=C2   CHARGE=-0.07    END
  MODIFY ATOM H2'  TYPE=H    CHARGE=0.035   END
  MODIFY 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 DIHEDRAL O4' C1' C2' H2'
END {DEOX}
 
!---------------------------------------------------------------------
 
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   !H
  MODIFY ATOM +O5'  TYPE=OH  CHARGE=-0.40  END   !H
  MODIFY ATOM +C5'  TYPE=C2  CHARGE=0.08   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 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
        !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=CH    CHARGE=0.115   END
  MODIFY ATOM -H3'    TYPE=H     CHARGE=0.035   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 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' !\ double
 ADD DIHEdral -O3' +P  +O5'  +C5' !/ dihedral
 ADD DIHEdral -C4' -C3' -O3'  +P
 ADD DIHEdral -C3' -O3' +P   +O5' !\ double
 ADD DIHEdral -C3' -O3' +P   +O5' !/ dihedral
END {NUC}
 
!------------------------------------------------------------------
 
 
PRESidue FC          ! patch for fully charged phosphate group
 GROUP
  MODIFY ATOM  O3'   CHARGE=-0.46     END
  MODIFY ATOM  P     CHARGE=1.36      END
  MODIFY ATOM  O1P   CHARGE=-0.72     END
  MODIFY ATOM  O2P   CHARGE=-0.72     END
  MODIFY ATOM  O5'   CHARGE=-0.46     END
END {FC}
 
!------------------------------------------------------------------
 
 
RESIdue NA          ! Fully charged Na
 GROUP
  ATOM NA  TYPE=SD    CHARGE=1.00   END
END {NA}
 
!------------------------------------------------------------------
 
 
RESIdue MG
 GROUp
  ATOM MG  TYPE=MG    CHARGE=2.0    END
END {MG}
 
!------------------------------------------------------------------
!------------------------------------------------------------------



PRESidue RMHB  ! removes hbond donor in the backbone
  DELETE DONOR H2' O2' 
END

PRESidue UNPR  ! removes hydrogen bond acceptors and donors in
               ! unpaired base
  DELETE DONOR H21 N2   
  DELETE DONOR H21  N2  
  DELETE DONOR H22  N2  
  DELETE DONOR H1   N1  
  DELETE DONO H61  N6   
  DELETE DONO H62  N6   
  DELETE DONO H42  N4   
  DELETE DONO H41  N4   
  DELETE DONO H3   N3   

  DELETE ACCEPTOR O6   C6          
  DELETE ACCEPTOR N3   " "   
  DELETE ACCEPTOR N7   " "   
  DELETE ACCEPTOR N1 " "     
  DELETE ACCEPTOR O2   C2    
  DELETE ACCEPTOR O4   C4    


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