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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