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Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1

In my rush to get the GROMOS96-NAMOT-GROMACS script posted, I forgot that an additional piece of information is required to make this script work smoothly (well, at all). While the nucleic acid residues between the 3′ and 5′ ends are accounted for by the G-N-G script (DADE, DCYT, DGUA, DTHY), the 3′ and 5′ ends are not and require having new topology data generated so that all of the atoms on either end are accounted for as NAMOT and NAMOT2 provide them in .pdb format. The .rtp topology additions provided below take care of this.

WHAT’S INCLUDED: Two types of nucleic acids are accounted for with these topologies.

1. FADE, FCYT, FGUA, FTHY – These are the 5′ ends of the DNA strands and INCLUDE a hydrogen atom on one of the 5′ phosphate oxygen atoms. NAMOT and NAMOT2 output does not include the 5′ phosphate by default (dephosphorylates the 5′ end before the structure even shows up on the screen). If you want the phosphate group on the 5′ end, there’s a little bit of file hacking involved. Specifically, you need to add n+1 bases to your structure then delete the first residue (the starting 5′ end) up to the sugar oxygen-phosphate junction. This then requires additional topology work that I may or may not get around to automating.

2. TADE, TCYT, TGUA, TTHY – These are the 3′ ends of the DNA strands and INCLUDE a hydrogen atom on the 3′ C-O oxygen atom. NAMOT and NAMOT2 includes this hydrogen in the output but the label needs to be changed (and atom type assigned).

NOTE: These residue topologies do not work for other GROMOS96 force fields (43a1, 43b1, 43a2, 45a3) or the OPLS-AA/L and Encad force fields available in GROMACS. All of these either do not have the same nucleic acid definitions to begin with or are simply missing required atom type assignments. These may, in fact, be trivial things to fix (the 45a3 being a specific case that is probably 5 steps from a workable script but that I’ve no need to use and so no need to implement).

HOW TO USE: The additional .rtp content below just gets pasted right into your current ffG53a6.rtp and/or ffG53a5.rtp files. Simply paste it at the bottom. There will be no conflicts with residue specifications if you did not modify these files to begin with. The GROMOS96-NAMOT-GROMACS script takes care of all of the residues between the 5′ and 3′ end (same naming convention is used as already exists for the d-nucleic acids (DADE, DCYT, DGUA, DTHY)). These residue topologies only correct and assign the 5′ and 3′ ends.

Simply copy the content below into the bottom of your ffG53a6.rtp and/or ffG53a5.rtp files or download and rename the whole files as provided below. The “;” are comment markers and associated lines are not read by pdb2gmx.

1. Download ffG53a6_NAMOT.rtp and/or ffG53a5_NAMOT.rtp

2. Rename (get rid of _NAMOT)

3. Place into your gromacs/share/top (or gromacs/share/gromacs/top) folder

;
; This section has been added to the ffG53a6 rtp file in order to have pdb2gmx correctly
; assign atom types and generate a correct topology file for NAMOT- and NAMOT2-generated
; DNA duplexes.
;
; Questions?  Problems?  Complaints?  Better Ideas?
; Damian Allis, damian@somewhereville.com, www.somewhereville.com
;

[ FADE ] ; 5' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
   HB     H     0.36000     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N9    NR    -0.20000     3
   C4     C     0.20000     3
   N3    NR    -0.54000     4
   C2     C     0.44000     4
   H2    HC     0.10000     4
   N1    NR    -0.54000     5
   C6     C     0.54000     5
   N6    NT    -0.83000     6
  H61     H     0.41500     6
  H62     H     0.41500     6
   C5     C     0.00000     7
   N7    NR    -0.54000     7
   C8     C     0.44000     7
   H8    HC     0.10000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
 [ bonds ]
   HB   O5*    gb_1   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N9    gb_22   
  C1*   C2*    gb_26   
   N9    C4    gb_10   
   N9    C8    gb_10   
   C4    N3    gb_12   
   C4    C5    gb_16   
   N3    C2    gb_7    
   C2    H2    gb_3    
   C2    N1    gb_7    
   N1    C6    gb_12   
   C6    N6    gb_9    
   C6    C5    gb_16   
   N6   H61    gb_2    
   N6   H62    gb_2    
   C5    N7    gb_10   
   N7    C8    gb_10   
   C8    H8    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    +P    gb_28   
 [ exclusions ]
;  ai    aj
  C1*    N3
  C1*    C5
  C1*    N7
  C1*    H8
   N9    C2
   N9    C6
   C4    H2
   C4    N1
   C4    N6
   C4    H8
   N3    C6
   N3    N7
   N3    C8
   C2    N6
   C2    C5
   H2    C6
   N1    N7
   C6    C8
   N6    N7
  H61    N7
  H62    N7
   C5    H8
 [ angles ]
;  ai    aj    ak   gromos type
   HB   O5*   C5*     ga_47   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N9     ga_9    
  O4*   C1*   C2*     ga_9    
   N9   C1*   C2*     ga_9    
  C1*    N9    C4     ga_37   
  C1*    N9    C8     ga_37   
   C4    N9    C8     ga_7    
   N9    C4    N3     ga_39   
   N9    C4    C5     ga_7    
   N3    C4    C5     ga_27   
   C4    N3    C2     ga_27   
   N3    C2    H2     ga_25   
   N3    C2    N1     ga_27   
   H2    C2    N1     ga_25   
   C2    N1    C6     ga_27   
   N1    C6    N6     ga_27   
   N1    C6    C5     ga_27   
   N6    C6    C5     ga_27   
   C6    N6   H61     ga_23   
   C6    N6   H62     ga_23   
  H61    N6   H62     ga_24   
   C4    C5    C6     ga_27   
   C4    C5    N7     ga_7    
   C6    C5    N7     ga_39   
   C5    N7    C8     ga_7    
   N9    C8    N7     ga_7    
   N9    C8    H8     ga_36   
   N7    C8    H8     ga_36   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    +P     ga_26   
 [ impropers ]
;  ai    aj    ak    al   gromos type
  C1*    C4    C8    N9     gi_1    
   N9    C4    C5    N7     gi_1    
   C4    N9    N3    C5     gi_1    
   C4    N9    C8    N7     gi_1    
   C4    N3    C2    N1     gi_1    
   C4    C5    N7    C8     gi_1    
   N3    C4    C5    C6     gi_1    
   N3    C2    N1    C6     gi_1    
   C2    N3    H2    N1     gi_1    
   C2    N1    C6    C5     gi_1    
   N1    C6    C5    C4     gi_1    
   N6    N1    C5    C6     gi_1    
   N6   H61   H62    C6     gi_1    
   C5    C4    N3    C2     gi_1    
   C5    C6    N7    C4     gi_1    
   C5    N7    C8    N9     gi_1    
   C8    N9    C4    C5     gi_1    
   C8    N9    N7    H8     gi_1    
  C2*   O4*    N9   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
   HB   O5*   C5*   C4*     gd_30   
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N9    C4     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   C5    C6    N6   H61     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    +P     gd_29   

[ FCYT ] ; 5' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
   HB     H     0.36000     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N1    NR    -0.20000     3
   C6     C     0.10000     3
   H6    HC     0.10000     3
   C2     C     0.45000     4
   O2     O    -0.45000     4
   N3    NR    -0.54000     5
   C4     C     0.54000     5
   N4    NT    -0.83000     6
  H41     H     0.41500     6
  H42     H     0.41500     6
   C5     C    -0.10000     7
   H5    HC     0.10000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
 [ bonds ]
   HB   O5*    gb_1   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N1    gb_23   
  C1*   C2*    gb_26   
   N1    C6    gb_17   
   N1    C2    gb_17   
   C6    H6    gb_3    
   C6    C5    gb_16   
   C2    O2    gb_5    
   C2    N3    gb_12   
   N3    C4    gb_12   
   C4    N4    gb_9    
   C4    C5    gb_16   
   N4   H41    gb_2    
   N4   H42    gb_2    
   C5    H5    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    +P    gb_28   
 [ exclusions ]
;  ai    aj
  C1*    H6
  C1*    O2
  C1*    N3
  C1*    C5
   N1    C4
   N1    H5
   C6    O2
   C6    N3
   C6    N4
   H6    C2
   H6    C4
   H6    H5
   C2    N4
   C2    C5
   O2    C4
   N3    H5
   N4    H5
 [ angles ]
;  ai    aj    ak   gromos type
   HB   O5*   C5*     ga_47   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N1     ga_9    
  O4*   C1*   C2*     ga_9    
   N1   C1*   C2*     ga_8    
  C1*    N1    C6     ga_27   
  C1*    N1    C2     ga_27   
   C6    N1    C2     ga_27   
   N1    C6    H6     ga_25   
   N1    C6    C5     ga_27   
   H6    C6    C5     ga_25   
   N1    C2    O2     ga_27   
   N1    C2    N3     ga_27   
   O2    C2    N3     ga_27   
   C2    N3    C4     ga_27   
   N3    C4    N4     ga_27   
   N3    C4    C5     ga_27   
   N4    C4    C5     ga_27   
   C4    N4   H41     ga_23   
   C4    N4   H42     ga_23   
  H41    N4   H42     ga_24   
   C6    C5    C4     ga_27   
   C6    C5    H5     ga_25   
   C4    C5    H5     ga_25   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    +P     ga_26   
 [ impropers ]
;  ai    aj    ak    al   gromos type
   N1    C6    C2   C1*     gi_1    
   N1    C6    C5    C4     gi_1    
   N1    C2    N3    C4     gi_1    
   C6    N1    C2    N3     gi_1    
   C6    N1    C5    H6     gi_1    
   C2    N1    C6    C5     gi_1    
   C2    N3    C4    C5     gi_1    
   O2    N1    N3    C2     gi_1    
   N3    C4    C5    C6     gi_1    
   N4    N3    C5    C4     gi_1    
   N4   H41   H42    C4     gi_1    
   C5    C6    C4    H5     gi_1    
  C2*   O4*    N1   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
   HB   O5*   C5*   C4*     gd_30   
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N1    C2     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   N3    C4    N4   H41     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    +P     gd_29   

[ FGUA ] ; 5' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
   HB     H     0.36000     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N9    NR    -0.20000     3
   C4     C     0.20000     3
   N3    NR    -0.54000     4
   C2     C     0.54000     4
   N2    NT    -0.83000     5
  H21     H     0.41500     5
  H22     H     0.41500     5
   N1    NR    -0.31000     6
   H1     H     0.31000     6
   C6     C     0.45000     7
   O6     O    -0.45000     7
   C5     C     0.00000     8
   N7    NR    -0.54000     8
   C8     C     0.44000     8
   H8    HC     0.10000     8
  C2*  CH2R     0.00000     9
  C3*   CH1       0.000     9
  O3*    OA      -0.360    10
 [ bonds ]
   HB   O5*    gb_1   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N9    gb_22   
  C1*   C2*    gb_26   
   N9    C4    gb_10   
   N9    C8    gb_10   
   C4    N3    gb_12   
   C4    C5    gb_16   
   N3    C2    gb_12   
   C2    N2    gb_9    
   C2    N1    gb_17   
   N2   H21    gb_2    
   N2   H22    gb_2    
   N1    H1    gb_2    
   N1    C6    gb_17   
   C6    O6    gb_5    
   C6    C5    gb_16   
   C5    N7    gb_10   
   N7    C8    gb_10   
   C8    H8    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    +P    gb_28   
 [ exclusions ]
;  ai    aj
  C1*    N3
  C1*    C5
  C1*    N7
  C1*    H8
   N9    C2
   N9    C6
   C4    N2
   C4    N1
   C4    O6
   C4    H8
   N3    H1
   N3    C6
   N3    N7
   N3    C8
   C2    O6
   C2    C5
   N2    H1
   N2    C6
   N1    N7
   H1    O6
   H1    C5
   C6    C8
   O6    N7
   C5    H8
 [ angles ]
;  ai    aj    ak   gromos type
   HB   O5*   C5*     ga_47   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N9     ga_9    
  O4*   C1*   C2*     ga_9    
   N9   C1*   C2*     ga_9    
  C1*    N9    C4     ga_37   
  C1*    N9    C8     ga_37   
   C4    N9    C8     ga_7    
   N9    C4    N3     ga_39   
   N9    C4    C5     ga_7    
   N3    C4    C5     ga_27   
   C4    N3    C2     ga_27   
   N3    C2    N2     ga_27   
   N3    C2    N1     ga_27   
   N2    C2    N1     ga_27   
   C2    N2   H21     ga_23   
   C2    N2   H22     ga_23   
  H21    N2   H22     ga_24   
   C2    N1    H1     ga_25   
   C2    N1    C6     ga_27   
   H1    N1    C6     ga_25   
   N1    C6    O6     ga_27   
   N1    C6    C5     ga_27   
   O6    C6    C5     ga_27   
   C4    C5    C6     ga_27   
   C4    C5    N7     ga_7    
   C6    C5    N7     ga_39   
   C5    N7    C8     ga_7    
   N9    C8    N7     ga_7    
   N9    C8    H8     ga_36   
   N7    C8    H8     ga_36   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    +P     ga_26   
 [ impropers ]
;  ai    aj    ak    al   gromos type
  C1*    C4    C8    N9     gi_1    
   N9    C4    C5    N7     gi_1    
   C4    N9    N3    C5     gi_1    
   C4    N9    C8    N7     gi_1    
   C4    N3    C2    N1     gi_1    
   C4    C5    N7    C8     gi_1    
   N3    C4    C5    C6     gi_1    
   N3    C2    N1    C6     gi_1    
   C2    N1    C6    C5     gi_1    
   N2    N3    N1    C2     gi_1    
   N2   H21   H22    C2     gi_1    
   N1    C6    C5    C4     gi_1    
   H1    C2    C6    N1     gi_1    
   O6    N1    C5    C6     gi_1    
   C5    C4    N3    C2     gi_1    
   C5    C6    N7    C4     gi_1    
   C5    N7    C8    N9     gi_1    
   C8    N9    C4    C5     gi_1    
   C8    N9    N7    H8     gi_1    
  C2*   O4*    N9   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
   HB   O5*   C5*   C4*     gd_30   
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N9    C4     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   N3    C2    N2   H21     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    +P     gd_29   

[ FTHY ] ; 5' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
   HB     H     0.36000     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N1    NR    -0.20000     3
   C6     C     0.10000     3
   H6    HC     0.10000     3
   C2     C     0.45000     4
   O2     O    -0.45000     4
   N3    NR    -0.31000     5
   H3     H     0.31000     5
   C4     C     0.45000     6
   O4     O    -0.45000     6
   C5     C     0.00000     7
  C5M   CH3     0.00000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
 [ bonds ]
   HB   O5*    gb_1   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N1    gb_23   
  C1*   C2*    gb_26   
   N1    C6    gb_17   
   N1    C2    gb_17   
   C6    H6    gb_3    
   C6    C5    gb_16   
   C2    O2    gb_5    
   C2    N3    gb_17   
   N3    H3    gb_2    
   N3    C4    gb_17   
   C4    O4    gb_5    
   C4    C5    gb_16   
   C5   C5M    gb_27   
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    +P    gb_28   
 [ exclusions ]
;  ai    aj
  C1*    H6
  C1*    O2
  C1*    N3
  C1*    C5
   N1    H3
   N1    C4
   N1   C5M
   C6    O2
   C6    N3
   C6    O4
   H6    C2
   H6    C4
   H6   C5M
   C2    O4
   C2    C5
   O2    H3
   O2    C4
   N3   C5M
   H3    O4
   H3    C5
   O4   C5M
 [ angles ]
;  ai    aj    ak   gromos type
   HB   O5*   C5*     ga_47   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N1     ga_9    
  O4*   C1*   C2*     ga_9    
   N1   C1*   C2*     ga_8    
  C1*    N1    C6     ga_27   
  C1*    N1    C2     ga_27   
   C6    N1    C2     ga_27   
   N1    C6    H6     ga_25   
   N1    C6    C5     ga_27   
   H6    C6    C5     ga_25   
   N1    C2    O2     ga_27   
   N1    C2    N3     ga_27   
   O2    C2    N3     ga_27   
   C2    N3    H3     ga_25   
   C2    N3    C4     ga_27   
   H3    N3    C4     ga_25   
   N3    C4    O4     ga_27   
   N3    C4    C5     ga_27   
   O4    C4    C5     ga_27   
   C6    C5    C4     ga_27   
   C6    C5   C5M     ga_27   
   C4    C5   C5M     ga_27   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    +P     ga_26   
 [ impropers ]
;  ai    aj    ak    al   gromos type
   N1    C6    C2   C1*     gi_1    
   N1    C6    C5    C4     gi_1    
   N1    C2    N3    C4     gi_1    
   C6    N1    C2    N3     gi_1    
   C6    N1    C5    H6     gi_1    
   C2    N1    C6    C5     gi_1    
   C2    N3    C4    C5     gi_1    
   O2    N1    N3    C2     gi_1    
   N3    C4    C5    C6     gi_1    
   H3    C2    C4    N3     gi_1    
   O4    N3    C5    C4     gi_1    
   C5    C6    C4   C5M     gi_1    
  C2*   O4*    N1   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
   HB   O5*   C5*   C4*     gd_30   
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N1    C2     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    +P     gd_29   

[ TADE ] ; 3' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
    P     P     0.99000     0
  O1P    OM    -0.63500     0
  O2P    OM    -0.63500     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N9    NR    -0.20000     3
   C4     C     0.20000     3
   N3    NR    -0.54000     4
   C2     C     0.44000     4
   H2    HC     0.10000     4
   N1    NR    -0.54000     5
   C6     C     0.54000     5
   N6    NT    -0.83000     6
  H61     H     0.41500     6
  H62     H     0.41500     6
   C5     C     0.00000     7
   N7    NR    -0.54000     7
   C8     C     0.44000     7
   H8    HC     0.10000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
   HE     H     0.36000     9
 [ bonds ]
    P   O1P    gb_24   
    P   O2P    gb_24   
    P   O5*    gb_28   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N9    gb_22   
  C1*   C2*    gb_26   
   N9    C4    gb_10   
   N9    C8    gb_10   
   C4    N3    gb_12   
   C4    C5    gb_16   
   N3    C2    gb_7    
   C2    H2    gb_3    
   C2    N1    gb_7    
   N1    C6    gb_12   
   C6    N6    gb_9    
   C6    C5    gb_16   
   N6   H61    gb_2    
   N6   H62    gb_2    
   C5    N7    gb_10   
   N7    C8    gb_10   
   C8    H8    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    HE    gb_1   
 [ exclusions ]
;  ai    aj
  C1*    N3
  C1*    C5
  C1*    N7
  C1*    H8
   N9    C2
   N9    C6
   C4    H2
   C4    N1
   C4    N6
   C4    H8
   N3    C6
   N3    N7
   N3    C8
   C2    N6
   C2    C5
   H2    C6
   N1    N7
   C6    C8
   N6    N7
  H61    N7
  H62    N7
   C5    H8
 [ angles ]
;  ai    aj    ak   gromos type
 -O3*     P   O1P     ga_14   
 -O3*     P   O2P     ga_14   
 -O3*     P   O5*     ga_5    
  O1P     P   O2P     ga_29   
  O1P     P   O5*     ga_14   
  O2P     P   O5*     ga_14   
    P   O5*   C5*     ga_26   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N9     ga_9    
  O4*   C1*   C2*     ga_9    
   N9   C1*   C2*     ga_9    
  C1*    N9    C4     ga_37   
  C1*    N9    C8     ga_37   
   C4    N9    C8     ga_7    
   N9    C4    N3     ga_39   
   N9    C4    C5     ga_7    
   N3    C4    C5     ga_27   
   C4    N3    C2     ga_27   
   N3    C2    H2     ga_25   
   N3    C2    N1     ga_27   
   H2    C2    N1     ga_25   
   C2    N1    C6     ga_27   
   N1    C6    N6     ga_27   
   N1    C6    C5     ga_27   
   N6    C6    C5     ga_27   
   C6    N6   H61     ga_23   
   C6    N6   H62     ga_23   
  H61    N6   H62     ga_24   
   C4    C5    C6     ga_27   
   C4    C5    N7     ga_7    
   C6    C5    N7     ga_39   
   C5    N7    C8     ga_7    
   N9    C8    N7     ga_7    
   N9    C8    H8     ga_36   
   N7    C8    H8     ga_36   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    HE     ga_47   
 [ impropers ]
;  ai    aj    ak    al   gromos type
  C1*    C4    C8    N9     gi_1    
   N9    C4    C5    N7     gi_1    
   C4    N9    N3    C5     gi_1    
   C4    N9    C8    N7     gi_1    
   C4    N3    C2    N1     gi_1    
   C4    C5    N7    C8     gi_1    
   N3    C4    C5    C6     gi_1    
   N3    C2    N1    C6     gi_1    
   C2    N3    H2    N1     gi_1    
   C2    N1    C6    C5     gi_1    
   N1    C6    C5    C4     gi_1    
   N6    N1    C5    C6     gi_1    
   N6   H61   H62    C6     gi_1    
   C5    C4    N3    C2     gi_1    
   C5    C6    N7    C4     gi_1    
   C5    N7    C8    N9     gi_1    
   C8    N9    C4    C5     gi_1    
   C8    N9    N7    H8     gi_1    
  C2*   O4*    N9   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
 -C3*  -O3*     P   O5*     gd_20   
 -C3*  -O3*     P   O5*     gd_27   
 -O3*     P   O5*   C5*     gd_20   
 -O3*     P   O5*   C5*     gd_27   
    P   O5*   C5*   C4*     gd_7    
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N9    C4     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   C5    C6    N6   H61     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    HE     gd_30   

[ TCYT ] ; 3' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
    P     P     0.99000     0
  O1P    OM    -0.63500     0
  O2P    OM    -0.63500     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N1    NR    -0.20000     3
   C6     C     0.10000     3
   H6    HC     0.10000     3
   C2     C     0.45000     4
   O2     O    -0.45000     4
   N3    NR    -0.54000     5
   C4     C     0.54000     5
   N4    NT    -0.83000     6
  H41     H     0.41500     6
  H42     H     0.41500     6
   C5     C    -0.10000     7
   H5    HC     0.10000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
   HE     H     0.36000     9
 [ bonds ]
    P   O1P    gb_24   
    P   O2P    gb_24   
    P   O5*    gb_28   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N1    gb_23   
  C1*   C2*    gb_26   
   N1    C6    gb_17   
   N1    C2    gb_17   
   C6    H6    gb_3    
   C6    C5    gb_16   
   C2    O2    gb_5    
   C2    N3    gb_12   
   N3    C4    gb_12   
   C4    N4    gb_9    
   C4    C5    gb_16   
   N4   H41    gb_2    
   N4   H42    gb_2    
   C5    H5    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    HE    gb_1   
 [ exclusions ]
;  ai    aj
  C1*    H6
  C1*    O2
  C1*    N3
  C1*    C5
   N1    C4
   N1    H5
   C6    O2
   C6    N3
   C6    N4
   H6    C2
   H6    C4
   H6    H5
   C2    N4
   C2    C5
   O2    C4
   N3    H5
   N4    H5
 [ angles ]
;  ai    aj    ak   gromos type
 -O3*     P   O1P     ga_14   
 -O3*     P   O2P     ga_14   
 -O3*     P   O5*     ga_5    
  O1P     P   O2P     ga_29   
  O1P     P   O5*     ga_14   
  O2P     P   O5*     ga_14   
    P   O5*   C5*     ga_26   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N1     ga_9    
  O4*   C1*   C2*     ga_9    
   N1   C1*   C2*     ga_8    
  C1*    N1    C6     ga_27   
  C1*    N1    C2     ga_27   
   C6    N1    C2     ga_27   
   N1    C6    H6     ga_25   
   N1    C6    C5     ga_27   
   H6    C6    C5     ga_25   
   N1    C2    O2     ga_27   
   N1    C2    N3     ga_27   
   O2    C2    N3     ga_27   
   C2    N3    C4     ga_27   
   N3    C4    N4     ga_27   
   N3    C4    C5     ga_27   
   N4    C4    C5     ga_27   
   C4    N4   H41     ga_23   
   C4    N4   H42     ga_23   
  H41    N4   H42     ga_24   
   C6    C5    C4     ga_27   
   C6    C5    H5     ga_25   
   C4    C5    H5     ga_25   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    HE     ga_47   
 [ impropers ]
;  ai    aj    ak    al   gromos type
   N1    C6    C2   C1*     gi_1    
   N1    C6    C5    C4     gi_1    
   N1    C2    N3    C4     gi_1    
   C6    N1    C2    N3     gi_1    
   C6    N1    C5    H6     gi_1    
   C2    N1    C6    C5     gi_1    
   C2    N3    C4    C5     gi_1    
   O2    N1    N3    C2     gi_1    
   N3    C4    C5    C6     gi_1    
   N4    N3    C5    C4     gi_1    
   N4   H41   H42    C4     gi_1    
   C5    C6    C4    H5     gi_1    
  C2*   O4*    N1   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
 -C3*  -O3*     P   O5*     gd_20   
 -C3*  -O3*     P   O5*     gd_27   
 -O3*     P   O5*   C5*     gd_20   
 -O3*     P   O5*   C5*     gd_27   
    P   O5*   C5*   C4*     gd_7    
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N1    C2     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   N3    C4    N4   H41     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    HE     gd_30   

[ TGUA ] ; 3' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
    P     P     0.99000     0
  O1P    OM    -0.63500     0
  O2P    OM    -0.63500     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N9    NR    -0.20000     3
   C4     C     0.20000     3
   N3    NR    -0.54000     4
   C2     C     0.54000     4
   N2    NT    -0.83000     5
  H21     H     0.41500     5
  H22     H     0.41500     5
   N1    NR    -0.31000     6
   H1     H     0.31000     6
   C6     C     0.45000     7
   O6     O    -0.45000     7
   C5     C     0.00000     8
   N7    NR    -0.54000     8
   C8     C     0.44000     8
   H8    HC     0.10000     8
  C2*  CH2R     0.00000     9
  C3*   CH1       0.000     9
  O3*    OA      -0.360    10
   HE     H     0.36000     9
 [ bonds ]
    P   O1P    gb_24   
    P   O2P    gb_24   
    P   O5*    gb_28   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N9    gb_22   
  C1*   C2*    gb_26   
   N9    C4    gb_10   
   N9    C8    gb_10   
   C4    N3    gb_12   
   C4    C5    gb_16   
   N3    C2    gb_12   
   C2    N2    gb_9    
   C2    N1    gb_17   
   N2   H21    gb_2    
   N2   H22    gb_2    
   N1    H1    gb_2    
   N1    C6    gb_17   
   C6    O6    gb_5    
   C6    C5    gb_16   
   C5    N7    gb_10   
   N7    C8    gb_10   
   C8    H8    gb_3    
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    HE    gb_1   
 [ exclusions ]
;  ai    aj
  C1*    N3
  C1*    C5
  C1*    N7
  C1*    H8
   N9    C2
   N9    C6
   C4    N2
   C4    N1
   C4    O6
   C4    H8
   N3    H1
   N3    C6
   N3    N7
   N3    C8
   C2    O6
   C2    C5
   N2    H1
   N2    C6
   N1    N7
   H1    O6
   H1    C5
   C6    C8
   O6    N7
   C5    H8
 [ angles ]
;  ai    aj    ak   gromos type
 -O3*     P   O1P     ga_14   
 -O3*     P   O2P     ga_14   
 -O3*     P   O5*     ga_5    
  O1P     P   O2P     ga_29   
  O1P     P   O5*     ga_14   
  O2P     P   O5*     ga_14   
    P   O5*   C5*     ga_26   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N9     ga_9    
  O4*   C1*   C2*     ga_9    
   N9   C1*   C2*     ga_9    
  C1*    N9    C4     ga_37   
  C1*    N9    C8     ga_37   
   C4    N9    C8     ga_7    
   N9    C4    N3     ga_39   
   N9    C4    C5     ga_7    
   N3    C4    C5     ga_27   
   C4    N3    C2     ga_27   
   N3    C2    N2     ga_27   
   N3    C2    N1     ga_27   
   N2    C2    N1     ga_27   
   C2    N2   H21     ga_23   
   C2    N2   H22     ga_23   
  H21    N2   H22     ga_24   
   C2    N1    H1     ga_25   
   C2    N1    C6     ga_27   
   H1    N1    C6     ga_25   
   N1    C6    O6     ga_27   
   N1    C6    C5     ga_27   
   O6    C6    C5     ga_27   
   C4    C5    C6     ga_27   
   C4    C5    N7     ga_7    
   C6    C5    N7     ga_39   
   C5    N7    C8     ga_7    
   N9    C8    N7     ga_7    
   N9    C8    H8     ga_36   
   N7    C8    H8     ga_36   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    HE     ga_47   
 [ impropers ]
;  ai    aj    ak    al   gromos type
  C1*    C4    C8    N9     gi_1    
   N9    C4    C5    N7     gi_1    
   C4    N9    N3    C5     gi_1    
   C4    N9    C8    N7     gi_1    
   C4    N3    C2    N1     gi_1    
   C4    C5    N7    C8     gi_1    
   N3    C4    C5    C6     gi_1    
   N3    C2    N1    C6     gi_1    
   C2    N1    C6    C5     gi_1    
   N2    N3    N1    C2     gi_1    
   N2   H21   H22    C2     gi_1    
   N1    C6    C5    C4     gi_1    
   H1    C2    C6    N1     gi_1    
   O6    N1    C5    C6     gi_1    
   C5    C4    N3    C2     gi_1    
   C5    C6    N7    C4     gi_1    
   C5    N7    C8    N9     gi_1    
   C8    N9    C4    C5     gi_1    
   C8    N9    N7    H8     gi_1    
  C2*   O4*    N9   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
 -C3*  -O3*     P   O5*     gd_20   
 -C3*  -O3*     P   O5*     gd_27   
 -O3*     P   O5*   C5*     gd_20   
 -O3*     P   O5*   C5*     gd_27   
    P   O5*   C5*   C4*     gd_7    
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N9    C4     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
   N3    C2    N2   H21     gd_14   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    HE     gd_30   

[ TTHY ] ; 3' END OF THE DNA FROM THE NAMOT FILE
 [ atoms ]
    P     P     0.99000     0
  O1P    OM    -0.63500     0
  O2P    OM    -0.63500     0
  O5*    OA    -0.36000     0
  C5*   CH2     0.00000     1
  C4*   CH1     0.16000     2
  O4*    OA    -0.36000     2
  C1*   CH1     0.20000     2
   N1    NR    -0.20000     3
   C6     C     0.10000     3
   H6    HC     0.10000     3
   C2     C     0.45000     4
   O2     O    -0.45000     4
   N3    NR    -0.31000     5
   H3     H     0.31000     5
   C4     C     0.45000     6
   O4     O    -0.45000     6
   C5     C     0.00000     7
  C5M   CH3     0.00000     7
  C2*  CH2R     0.00000     8
  C3*   CH1       0.000     8
  O3*    OA      -0.360     9
   HE     H     0.36000     9
 [ bonds ]
    P   O1P    gb_24   
    P   O2P    gb_24   
    P   O5*    gb_28   
  O5*   C5*    gb_20   
  C5*   C4*    gb_26   
  C4*   O4*    gb_20   
  C4*   C3*    gb_26   
  O4*   C1*    gb_20   
  C1*    N1    gb_23   
  C1*   C2*    gb_26   
   N1    C6    gb_17   
   N1    C2    gb_17   
   C6    H6    gb_3    
   C6    C5    gb_16   
   C2    O2    gb_5    
   C2    N3    gb_17   
   N3    H3    gb_2    
   N3    C4    gb_17   
   C4    O4    gb_5    
   C4    C5    gb_16   
   C5   C5M    gb_27   
  C2*   C3*    gb_26   
  C3*   O3*    gb_20   
  O3*    HE    gb_1   
 [ exclusions ]
;  ai    aj
  C1*    H6
  C1*    O2
  C1*    N3
  C1*    C5
   N1    H3
   N1    C4
   N1   C5M
   C6    O2
   C6    N3
   C6    O4
   H6    C2
   H6    C4
   H6   C5M
   C2    O4
   C2    C5
   O2    H3
   O2    C4
   N3   C5M
   H3    O4
   H3    C5
   O4   C5M
 [ angles ]
;  ai    aj    ak   gromos type
 -O3*     P   O1P     ga_14   
 -O3*     P   O2P     ga_14   
 -O3*     P   O5*     ga_5    
  O1P     P   O2P     ga_29   
  O1P     P   O5*     ga_14   
  O2P     P   O5*     ga_14   
    P   O5*   C5*     ga_26   
  O5*   C5*   C4*     ga_9    
  C5*   C4*   O4*     ga_9    
  C5*   C4*   C3*     ga_8    
  O4*   C4*   C3*     ga_9    
  C4*   O4*   C1*     ga_10   
  O4*   C1*    N1     ga_9    
  O4*   C1*   C2*     ga_9    
   N1   C1*   C2*     ga_8    
  C1*    N1    C6     ga_27   
  C1*    N1    C2     ga_27   
   C6    N1    C2     ga_27   
   N1    C6    H6     ga_25   
   N1    C6    C5     ga_27   
   H6    C6    C5     ga_25   
   N1    C2    O2     ga_27   
   N1    C2    N3     ga_27   
   O2    C2    N3     ga_27   
   C2    N3    H3     ga_25   
   C2    N3    C4     ga_27   
   H3    N3    C4     ga_25   
   N3    C4    O4     ga_27   
   N3    C4    C5     ga_27   
   O4    C4    C5     ga_27   
   C6    C5    C4     ga_27   
   C6    C5   C5M     ga_27   
   C4    C5   C5M     ga_27   
  C1*   C2*   C3*     ga_8    
  C4*   C3*   C2*     ga_8    
  C4*   C3*   O3*     ga_9    
  C2*   C3*   O3*     ga_9    
  C3*   O3*    HE     ga_47   
 [ impropers ]
;  ai    aj    ak    al   gromos type
   N1    C6    C2   C1*     gi_1    
   N1    C6    C5    C4     gi_1    
   N1    C2    N3    C4     gi_1    
   C6    N1    C2    N3     gi_1    
   C6    N1    C5    H6     gi_1    
   C2    N1    C6    C5     gi_1    
   C2    N3    C4    C5     gi_1    
   O2    N1    N3    C2     gi_1    
   N3    C4    C5    C6     gi_1    
   H3    C2    C4    N3     gi_1    
   O4    N3    C5    C4     gi_1    
   C5    C6    C4   C5M     gi_1    
  C2*   O4*    N1   C1*     gi_2    
  C3*   C5*   O4*   C4*     gi_2    
  C3*   C2*   O3*   C4*     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
 -C3*  -O3*     P   O5*     gd_20   
 -C3*  -O3*     P   O5*     gd_27   
 -O3*     P   O5*   C5*     gd_20   
 -O3*     P   O5*   C5*     gd_27   
    P   O5*   C5*   C4*     gd_7    
  O5*   C5*   C4*   O4*     gd_8    
  O5*   C5*   C4*   O4*     gd_25   
  O5*   C5*   C4*   C3*     gd_17   
  O5*   C5*   C4*   C3*     gd_34   
  C3*   C4*   O4*   C1*     gd_29   
  C5*   C4*   C3*   C2*     gd_34   
  C5*   C4*   C3*   O3*     gd_17   
  O4*   C4*   C3*   C2*     gd_17   
  O4*   C4*   C3*   O3*     gd_18   
  C4*   O4*   C1*   C2*     gd_29   
  O4*   C1*    N1    C2     gd_16   
  O4*   C1*   C2*   C3*     gd_17   
  O4*   C1*   C2*   C3*     gd_34   
  C1*   C2*   C3*   C4*     gd_34   
  C1*   C2*   C3*   O3*     gd_17   
  C4*   C3*   O3*    HE     gd_30   

My thanks go to Dr. Syma Khalid at the University of Southampton School of Chemistry for trying the original NAMOT-GROMOS96-GROMACS script and pointing out the lack of .rtp information.

en.wikipedia.org/wiki/GROMOS
namot.lanl.gov
www.gromacs.org
www.somewhereville.com/?p=117
en.wikipedia.org/wiki/DNA
www.gromacs.org/documentation/reference/online/rtp.html
www.gromacs.org/documentation/reference/online/pdb2gmx.html
www.soton.ac.uk/chemistry/research/khalid/khalid.html
www.soton.ac.uk
www.soton.ac.uk/chemistry

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2 Responses to “Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1”

  1. www.somewhereville.com » Blog Archive » sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1
    August 7th, 2008 22:45
    1

    [...] NOTE: This script works with additions to the ffG53a5/6.rtp (residue topology) files. This information is available at Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-…. [...]

  2. www.somewhereville.com » Blog Archive » NAMOT Pre-Release 2.2.0-pre4 In OSX 10.8 (Maybe Older Versions)
    January 13th, 2013 20:41
    2

    [...] for more assistance with producing DNA files for GROMACS, consider the Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-…, sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS [...]

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