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

In my rush to get the GROMOS96NAMOTGROMACS 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 GROMOS96NAMOTGROMACS 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

sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1

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-NAMOT-GROMACS v1.

The script below is the precursor to the ffAMBER/NAMOT/GROMACS script posted previously. This script takes the output of a NAMOT or NAMOT2 DNA structure generation (.pdb) and does all of the atom label and atom label position conversions, correct 3′and 5′terminal H atom assignments, and makes changes throughout the .pdb file to provide something that should flow seamlessly into the GROMACS pdb2gmx .top generator for the GROMOS96 force field.

To reiterate a previous point: Did you need to post the entire script and not just provide the downloadable text file as a link? Of course, as I suspect no small number of people looking for how to convert a NAMOT pdb file into GROMOS96-speak will begin by searching based on GROMACS errors, which occur one missing residue label at a time. Hopefully, having the entire script readable by google and yahoo will cause it to pop up high in the search ranking.

The problem in the ffAMBER script with thymine (the lack of methyl hydrogens in the NAMOT and NAMOT2 pdb output) isn’t a problem for GROMOS96, as these hydrogen atoms (and all non-polar (C-H) hydrogen atoms) are subsumed into their associated carbons. That is, only DNA O-H, N-H, and pi-system C-H hydrogens are considered in the GROMOS96 force field.

How to use:

As a series of sed operations, you obviously need sed, which is available for all platforms and “pre-installed” with any self-respecting Linux/UNIX distro (which, of course, means OSX (the OS under which the script was generated).

To run this script, have the script and your NAMOT/NAMOT2-generated .pdb in the same directory and type:

./NAMOT_to_GROMOS96_in_GROMACS.script FILENAME.pdb NN

Where:

NAMOT_to_GROMOS96_in_GROMACS.script is the name of the script

FILENAME.pdb is the .pdb file (include the .pdb)

NN is the number of bases in each strand. This number is required in order to correctly change the atom types on the 3′ end of each strand.

This script is downloadable form the following link: NAMOT_to_GROMOS96_in_GROMACS.script

I also include a 35-base C-G double helix NAMOT .pdb file at C_G_NAMOT.pdb. To test the script on your machine, type the following in a Terminal window:

./NAMOT_to_GROMOS96_in_GROMACS.script C_G_NAMOT.pdb 35

As usual, if you have problems, comments, questions, concerns, etc. please either make an account and post a comment for this post or send me an email and I’ll keep the running tally.

##############################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
# This script takes the double helix output from NAMOT and NAMOT2 (a and b
# strands) and converts them into a format that the current GROMOS96 (53a6/5)
# force field in GROMACS can use in the generation of the GROMACS .top file.
#
################################################################################
#
# Generally, the following list of GROMACS runs should get you through an
# energy minimization without problem.  Note only 10 cations are added
# to your structure.  Change accordingly (or don't.  It doesn't matter for
# the test).
#
# Run these in order:
#
# pdb2gmx -nomerge -f DNA.pdb -o DNA_pdb2gmx.gro -p DNA_pdb2gmx.top
# editconf -f DNA_pdb2gmx.gro -o DNA_editconf.gro -d 1.0 -bt triclinic
# genbox -cp DNA_editconf.gro -cs -o DNA_genbox.gro -p DNA_pdb2gmx.top
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr
# genion -np 10 -norandom -pname Na -o DNA_genion.gro -s DNA_gromppem.tpr
#   -p DNA_pdb2gmx.top (this .top goes in the same line as the genion)
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr2
# mdrun -s DNA_grompp2em.tpr -o DNA_md_em.trr -c DNA_md_em.pdb -v
#
################################################################################
#
# In case you don't have one handy, here's the contents of an em.mpd file
# for use in the energy minimization test.
#
# Copy this content below, remove the "#", save as a text filed named
# -> em.mpd
#
# cpp                 =  /usr/bin/cpp
# define              =  -DFLEXIBLE
# integrator          =  steep
# nsteps              =  5000
# emtol               =  10.0
# emstep              =  0.01
# nstcgsteep          =  100
# coulombtype         = PME
# rvdw                = 1.0
# rlist               = 1.1
# rcoulomb            = 1.1
# pme_order           = 4
# ewald_rtol          = 1e-5
# vdwtype             = shift
# ns_type             = grid
# nstlist             = 10
#
################################################################################
#
# Here's the command line:
#
# ./NAMOT_to_ffAMBER_in_GROMACS.sed $1 $2
#
# $1 = file name (including the .pdb, as I often forget to not include it)
# $2 = number of the 3' base for conversion into Dn3 (n = A,T,G,C)
# the number in $2 will automatically do the 3' and 5' conversion (keep the
# terminal hydrogens on the PO4- groups)
#
################################################################################
################################################################################
#
# The magic happens below.
#
################################################################################
################################################################################
#
# First thing first, make a backup of the original pdb file in case you goof.
#
cp $1 $1_original
#
################################################################################
#
# This section converts all of the "*" with "z" so that you're not using the
# asterisk during the editing.  Replacing with the ffAMBER-requisite
# "single-quote" (') makes the sed script more complicated than it needs to be.
#
sed 's/*/z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# The section below deletes all of the non-polar CH2 and CH hydrogen atoms from
# the nucleic acids. In GROMACS, these are mass-subsumed into the carbon atom,
# so are ignored in the toplogy.
#
#
# deletes from ADE
#
sed '/H2Az ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from ADE
#
# deletes from CYT
#
sed '/H2Az CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from CYT
#
# deletes from GUA
#
sed '/H2Az GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from GUA
#
# deletes from THY
#
sed '/H2Az THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from THY
#
################################################################################
#
# This section changes the two nitrogen hydrogen labels to those expected by
# GROMACS.  Hn2/1, where n is the atom number in the formal labeling scheme.
#
#
# renames the NH2 hydrogen atoms for DADE
#
sed 's/HN6A/ H61/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN6B/ H62/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DADE
#
# renames the NH2 hydrogen atoms for DCYT
#
sed 's/HN4A/ H41/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN4B/ H42/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DCYT
#
# renames the NH2 hydrogen atoms for DGUA
#
sed 's/HN2A/ H21/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN2B/ H22/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DGUA
#
################################################################################
#
# This section renames the O3' and O5' oxygen atoms from the NAMOT output
# (O5T to O5* and O3T to O3*) to a PDB format so that the terminal H atoms
# can be added on with the T/F_NA topologies.
#
#
sed 's/O5T/O5z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
sed 's/O3T/O3z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section converts ADE, CYT, GUA, THY to DADE, DCYT, DGUA, DTHY in accord
# with the topology labels used by GROMACS for the nucleic acids.
#
#
sed 's/ADE /DADE/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/CYT /DCYT/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/GUA /DGUA/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/THY /DTHY/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section moves the column 23 chain labels to column 22 so that grompp
# can generate unique topology files for each unique chain.  As long as only
# lower-case letters are used for the chain labels (and this is the NAMOT
# default) the below moves everything and not any single-atom labels (which
# are generally all uppercase).
#
#
sed 's/ [a-z] /[a-z]  /' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section only replaces the FIRST nucleic acid for each chain with the F
# (5' end) labels for use with the F_NA topology.
#
# Yes, NAMOT starts its structures at the 5' end.
#
#
sed 's/DADEa   1/FADEa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa   1/FCYTa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa   1/FGUAa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa   1/FTHYa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
sed 's/DADEb   1/FADEb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb   1/FCYTb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb   1/FGUAb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb   1/FTHYb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
################################################################################
#
# This section changes the last base in the series to a "T" from the default
# "D" so that the topology corrects the 3' end.  Goes by units, tens, hun, thou
# and searches specifically for the pattern in question (taking care to follow
# the standard  format for base number.
#
################################################################################
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 1/a
#
sed 's/DADEa   '$2'/TADEa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa   '$2'/TCYTa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa   '$2'/TGUAa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa   '$2'/TTHYa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 2/b
#
sed 's/DADEb   '$2'/TADEb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb   '$2'/TCYTb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb   '$2'/TGUAb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb   '$2'/TTHYb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 1/a
#
sed 's/DADEa  '$2'/TADEa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa  '$2'/TCYTa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa  '$2'/TGUAa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa  '$2'/TTHYa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 2/b
#
sed 's/DADEb  '$2'/TADEb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb  '$2'/TCYTb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb  '$2'/TGUAb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb  '$2'/TTHYb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 1/a
#
sed 's/DADEa '$2'/TADEa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa '$2'/TCYTa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa '$2'/TGUAa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa '$2'/TTHYa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 2/b
#
sed 's/DADEb '$2'/TADEb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb '$2'/TCYTb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb '$2'/TGUAb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb '$2'/TTHYb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 1/a
#
sed 's/DADEa'$2'/TADEa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa'$2'/TCYTa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa'$2'/TGUAa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa'$2'/TTHYa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 2/b
#
sed 's/DADEb'$2'/TADEb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb'$2'/TCYTb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb'$2'/TGUAb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb'$2'/TTHYb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
################################################################################
#
# Home stretch.  Changes all of the "z" atoms in the pdb file to * for GROMACS.
#
sed 's/z/*/' $1 > $1_temp
rm $1
cp $1_temp $1
cp $1_temp $1_postscript
rm $1_temp
#
################################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
################################################################################

chemistry.csulb.edu/ffamber
namot.lanl.gov
www.gromacs.org
en.wikipedia.org/wiki/DNA
www.rcsb.org/pdb/home/home.do
en.wikipedia.org/wiki/GROMOS
en.wikipedia.org/wiki/Thymine
en.wikipedia.org/wiki/Sed
en.wikipedia.org/wiki/Linux
en.wikipedia.org/wiki/Unix
www.apple.com/macosx

sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1

In continuing efforts to streamline the simulation of atomistic DNA structures in GROMACS using the ffAMBER force field (the port of AMBER for GROMACS), the following script takes the .pdb output of NAMOT or NAMOT2 and does all of the atom label and atom label position conversions, correct 3′ and 5′ terminal H atom assignments, and random changes throughout the .pdb file to provide something that should flow seamlessly into GROMACS.

“Did you need to post the entire script and not just provide the downloadable text file as a link?” Of course, as I suspect no small number of people looking for how to convert a NAMOT pdb file into ffAMBER-speak will begin by searching based on GROMACS errors, which occur one missing residue label at a time. Hopefully, having the entire script readable by google and yahoo will cause it to pop up high in the search ranking.

Less searching, more simulating.

Now, there is one problem. NAMOT and NAMOT2 do not include the methyl group hydrogen atoms on the thymine residue, defaulting to a single C5M. In most of the GROMACS force fields, this is just fine, as the hydrogen atoms are subsumed into the methyl carbon (all non-polar C-H bonds are treated this way). For AMBER (ffAMBER, that is), all hydrogens are included. This fix is performed on the ffAMBER/GROMACS side in a modification to the .hdb and .rtp files that I will describe in an upcoming post.

How to use:

As a series of sed operations, you obviously need sed, which is available for all platforms and “pre-installed” with any self-respecting Linux/UNIX distro (which, of course, means OSX (the OS under which the script was generated).

To run this script, have the script and your NAMOT/NAMOT2-generated .pdb in the same directory and type:

./NAMOT_to_ffAMBER_in_GROMACS.script FILENAME.pdb NN

Where:

NAMOT_to_ffAMBER_in_GROMACS.script is the name of the script

FILENAME.pdb is the .pdb file (include the .pdb)

NN is the number of bases in each strand. This number is required in order to correctly change the atom types on the 3′ end of each strand.

This script is downloadable form the following link: NAMOT_to_ffAMBER_in_GROMACS.script

I also include a 35-base C-G double helix NAMOT .pdb file at C_G_NAMOT.pdb. To test the script on your machine, type the following in a Terminal window:

./NAMOT_to_ffAMBER_in_GROMACS.script C_G_NAMOT.pdb 35

As usual, if you have problems, comments, questions, concerns, etc. please either make an account and post a comment for this post or send me an email and I’ll keep the running tally.

C_Gpdb_QuteMolX_image_may2008

Also, this same scripting procedure works just fine for the GROMOS96 force fields (ffG53a5, ffG53a6, etc.) and I’ll be posting the one I use for those calculations in short order (they are, in fact, easier to work with for GROMACS, as they also neglect the methyl group hydrogen atoms on the Thymine. In fact, they neglect ALL of the non-polar C-H bonds, so you end up deleting atoms from the NAMOT/NAMOT2 .pdb files).

################################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
# This script takes the double helix output from NAMOT and NAMOT2 (a and b
# strands) and converts them into a format that the current ffAMBER
# implementation for GROMACS can use in the generation of the GROMACS .top file.
#
################################################################################
#
# Generally, the following list of GROMACS runs should get you through an
# energy minimization without problem.  Note only 10 cations are added
# to your structure.  Change accordingly (or don't.  It doesn't matter for
# the test).
#
# Run these in order:
#
# pdb2gmx -nomerge -f DNA.pdb -o DNA_pdb2gmx.gro -p DNA_pdb2gmx.top
# editconf -f DNA_pdb2gmx.gro -o DNA_editconf.gro -d 1.0 -bt triclinic
# genbox -cp DNA_editconf.gro -cs -o DNA_genbox.gro -p DNA_pdb2gmx.top
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr
# genion -np 10 -norandom -pname Na -o DNA_genion.gro -s DNA_gromppem.tpr
#   -p DNA_pdb2gmx.top (this .top goes in the same line as the genion)
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr2
# mdrun -s DNA_grompp2em.tpr -o DNA_md_em.trr -c DNA_md_em.pdb -v
#
################################################################################
#
# In case you don't have one handy, here's the contents of an em.mpd file
# for use in the energy minimization test.
#
# Copy this content below, remove the "#", save as a text filed named
# -> em.mpd
#
# cpp                 =  /usr/bin/cpp
# define              =  -DFLEXIBLE
# integrator          =  steep
# nsteps              =  5000
# emtol               =  10.0
# emstep              =  0.01
# nstcgsteep          =  100
# coulombtype         = PME
# rvdw                = 1.0
# rlist               = 1.1
# rcoulomb            = 1.1
# pme_order           = 4
# ewald_rtol          = 1e-5
# vdwtype             = shift
# ns_type             = grid
# nstlist             = 10
#
################################################################################
#
# Here's the command line:
#
# ./NAMOT_to_ffAMBER_in_GROMACS.sed $1 $2
#
# $1 = file name (including the .pdb, as I often forget to not include it)
# $2 = number of the 3' base for conversion into Dn3 (n = A,T,G,C)
# the number in $2 will automatically do the 3' and 5' conversion (keep the
# terminal hydrogens on the PO4- groups)
#
################################################################################
################################################################################
#
# The magic happens below.
#
################################################################################
################################################################################
#
# First thing first, make a backup of the original pdb file in case you goof.
#
cp $1 $1_original
#
################################################################################
#
# This section converts all of the "*" with "z" so that you're not using the
# asterisk during the editing.  Replacing with the ffAMBER-requisite
# "single-quote" (') makes the sed script more complicated than it needs to be.
#
sed 's/*/z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section changes the nitrogen hydrogen (NH2) labels to those expected by
# ffMABER.  Hn2/1, where n is the atom number in the formal labeling scheme.
#
# THYIME is its own problem, as the methyl carbon needs modification.
# This is addressed by a separate ffAMBER modification.  Check
# http://www.somewhereville.com/?cat=74 (my AMBER category) for details.
#
#
# HN2A/B occurs in GUANINE.
#
sed 's/HN2A/ H21/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN2B/ H22/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
# HN4A/B occurs in CYTOSINE.
#
sed 's/HN4A/ H41/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN4B/ H42/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
# HN6A/B occurs in ADENINE.
#
sed 's/HN6A/ H61/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN6B/ H62/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section converts ADE, CYT, GUA, THY in the NAMOT output to DA, DC, DG, DT
# in accord with the topology labels used by ffAMBER in GROMACS for the nucleic
# acids.
#
#
sed 's/ADE / DA /' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/CYT / DC /' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/GUA / DG /' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/THY / DT /' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This is the bulk of the conversion, moving atoms around and formatting.
# Mostly, just moving atom labels over one column to the left.  This doesn't
# necessarily have to be done, but conforms to pdb format better and some
# program may need the atom labels in the columns as defined below.
#
# This section changes all of the hydrogen atom labels.
#
sed 's/1H5z/H5z1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/2H5z/H5z2/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/H2Az/H2z1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/H2Bz/H2z2/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# These are global changes in column position and fix all nucleic acids.
#
sed 's/  P  D/P    D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ N9  D/N9   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ N7  D/N7   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ N6  D/N6   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ N3  D/N3   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ N1  D/N1   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ C8  D/C8   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ C6  D/C6   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ C5  D/C5   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ C4  D/C4   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ C2  D/C2   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ H8  D/H8   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ H2  D/H2   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ H3  D/H3   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ H6  D/H6   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ O3  D/O3   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ O4  D/O4   D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ O2  D/O    D/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/C5M  D/C7   D/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section converts the 5' end of both chains into ffAMBER format.  Always
# begins with "1".  If you deleted some of the double strand at the 5' end and
# the first base number is NOT 1, this script will still run but give you
# a final structure that will require additional modification before running
# the pdb2gmx topology generator.
#
################################################################################
#
# chain a ADENINE adjustment
#
sed 's/  DA a   1/ DA5 a   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DA5/H5T DA5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DA5/O5z DA5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DA/H3T DA3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DA/O3z DA3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# chain b ADENINE adjustment
#
sed 's/  DA b   1/ DA5 b   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DA5/H5T DA5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DA5/O5z DA5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DA/H3T DA3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DA/O3z DA3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# chain a THYMINE adjustment
#
sed 's/  DT a   1/ DT5 a   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DT5/H5T DT5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DT5/O5z DT5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DT/H3T DT3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DT/O3z DT3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/  DG a   1/ DG5 a   1/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# chain b THYMINE adjustment
#
sed 's/  DT b   1/ DT5 b   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DT5/H5T DT5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DT5/O5z DT5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DT/H3T DT3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DT/O3z DT3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# chain a GUANINE adjustment
#
sed 's/ HB DG5/H5T DG5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DG5/O5z DG5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DG/H3T DG3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DG/O3z DG3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# chain b GUANINE adjustment
#
sed 's/  DG b   1/ DG5 b   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DG5/H5T DG5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DG5/O5z DG5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE DG3/H3T DG3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T DG3/O3z DG3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# chain a CYTOSINE adjustment
#
sed 's/  DC a   1/ DC5 a   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DC5/H5T DC5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DC5/O5z DC5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE  DC/H3T DC3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T  DC/O3z DC3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# chain b CYTOSINE adjustment
#
sed 's/  DC b   1/ DC5 b   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HB DC5/H5T DC5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O5T DC5/O5z DC5/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ HE DC3/H3T DC3/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/O3T DC3/O3z DC3/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section changes the last base in each chain (a and b) from the default
# "Dn" to "Dn3" so that the topology generation gets the 3' end correct.
# Goes by units, tens, hun, thou and searches specifically for the pattern
# in question (taking care to follow the standard  format for base number.
#
# NOTE: We do the junction, crossover, etc. generation outside of NAMOT.
# Therefore, each file output by NAMOT only has chain "a" and chain "b".
#
################################################################################
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 1/a
#
sed 's/ DA a   '$2'/DA3 a   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC a   '$2'/DC3 a   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG a   '$2'/DG3 a   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT a   '$2'/DT3 a   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 2/b
#
sed 's/ DA b   '$2'/DA3 b  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC b   '$2'/DC3 b   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG b   '$2'/DG3 b   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT b   '$2'/DT3 b   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 1/a
#
sed 's/ DA a  '$2'/DA3 a  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC a  '$2'/DC3 a  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG a  '$2'/DG3 a  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT a  '$2'/DT3 a  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 2/b
#
sed 's/ DA b  '$2'/DA3 b  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC b  '$2'/DC3 b  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG b  '$2'/DG3 b  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT b  '$2'/DT3 b  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 1/a
#
sed 's/ DA a '$2'/DA3 a '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC a '$2'/DC3 a '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG a '$2'/DG3 a '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT a '$2'/DT3 a '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 2/b
#
sed 's/ DA b '$2'/DA3 b '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC b '$2'/DC3 b '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG b '$2'/DG3 b '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT b '$2'/DT3 b '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 1/a
#
sed 's/ DA a'$2'/DA3 a'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC a'$2'/DC3 a'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG a'$2'/DG3 a'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT a'$2'/DT3 a'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 2/b
#
sed 's/ DA b'$2'/DA3 b'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DC b'$2'/DC3 b'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DG b'$2'/DG3 b'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/ DT b'$2'/DT3 b'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# Home stretch.  Changes all of the "z" atoms in the pdb file to ' (single-
# quotes) for ffMABER.
#
sed s/\z/\'/g $1 > $1_temp
rm $1
mv $1_temp $1_proper_pdb
#
#
################################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
################################################################################

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