Here are the topology file lines that I have added to my version of
ffG43a1.rtp
It should just work if you add these lines to this file. If anyone
has any comments then I would be happy to have them, this is the
first time I have done this.
Bryn
[ GTP ]
[ atoms ]
GN9 NR -0.20000 0
GC4 C 0.20000 0
GN3 NR -0.36000 1
GC2 C 0.36000 1
GN2 NT -0.83000 2
GH21 H 0.41500 2
GH22 H 0.41500 2
GN1 NR -0.28000 3
GH1 H 0.28000 3
GC6 C 0.38000 4
GO6 O -0.38000 4
GC5 C 0.00000 5
GN7 NR -0.36000 5
GC8 CR1 0.36000 5
GC2* CH1 0.15000 6
GO2* OA -0.54800 6
GH2* H 0.39800 6
GC3* CH1 0.15000 7 ; like ATP set to GC2*
GO3* OA -0.54800 7 ; like ATP set to GO2*
GH3* H 0.39800 7 ; like ATP set to GH2*
GC1* CH1 0.20000 8
GC4* CH1 0.16000 8
GO4* OA -0.36000 8
GC5* CH2 0.00000 9
GO5* OA -0.36000 10
GPA P 0.70500 10 ; from ATP
GO1PA OM -0.63500 10 ; from ATP
GO2PA OM -0.63500 10 ; from ATP
GO3PA OA -0.36000 11 ; from ATP
GPB P 0.70500 11 ; from ATP
GO1PB OM -0.63500 11 ; from ATP
GO2PB OM -0.63500 11 ; from ATP
GO3PB OA -0.36000 12 ; from ATP
GPG P 0.63000 12 ; from ATP
GO1PG OM -0.63500 12 ; from ATP
GO2PG OM -0.63500 12 ; from ATP
GO3PG OA -0.54800 12 ; from ATP
GH3PG H 0.39800 12 ; from ATP
[ bonds ]
GO5* GC5* gb_19
GC5* GC4* gb_25
GC4* GO4* gb_19
GC4* GC3* gb_25
GO4* GC1* gb_19
GC1* GN9 gb_21
GC1* GC2* gb_25
GN9 GC4 gb_9
GN9 GC8 gb_9
GC4 GN3 gb_11
GC4 GC5 gb_15
GN3 GC2 gb_11
GC2 GN2 gb_8
GC2 GN1 gb_16
GN2 GH21 gb_2
GN2 GH22 gb_2
GN1 GH1 gb_2
GN1 GC6 gb_16
GC6 GO6 gb_4
GC6 GC5 gb_15
GC5 GN7 gb_9
GN7 GC8 gb_9
GC2* GO2* gb_19
GO2* GH2* gb_1
GC2* GC3* gb_25
GC3* GO3* gb_19 ; like ATP set to GC2*
GO3* GH3* gb_1 ; like ATP set to GO2*
GO5* GPA gb_27 ; from ATP
GPA GO1PA gb_23 ; from ATP
GPA GO2PA gb_23 ; from ATP
GPA GO3PA gb_27 ; from ATP
GO3PA GPB gb_27 ; from ATP
GPB GO1PB gb_23 ; from ATP
GPB GO2PB gb_23 ; from ATP
GPB GO3PB gb_27 ; from ATP
GO3PB GPG gb_27 ; from ATP
GPG GO1PG gb_23 ; from ATP
GPG GO2PG gb_23 ; from ATP
GPG GO3PG gb_27 ; from ATP
GO3PG GH3PG gb_1 ; from ATP
[ exclusions ]
; ai aj
GC1* GN3
GC1* GC5
GC1* GN7
GN9 GC2
GN9 GC6
GC4 GN2
GC4 GN1
GC4 GO6
GN3 GH1
GN3 GC6
GN3 GN7
GN3 GC8
GC2 GO6
GC2 GC5
GN2 GH1
GN2 GC6
GN1 GN7
GH1 GO6
GH1 GC5
GC6 GC8
GO6 GN7
GO3PB GH3PG ; from ATP
GO1PG GH3PG ; from ATP
GO2PG GH3PG ; from ATP
[ angles ]
; ai aj ak gromos type
GO5* GC5* GC4* ga_8
GC5* GC4* GO4* ga_8
GC5* GC4* GC3* ga_7
GO4* GC4* GC3* ga_8
GC4* GO4* GC1* ga_9
GO4* GC1* GN9 ga_8
GO4* GC1* GC2* ga_8
GN9 GC1* GC2* ga_8
GC1* GN9 GC4 ga_36
GC1* GN9 GC8 ga_36
GC4 GN9 GC8 ga_6
GN9 GC4 GN3 ga_38
GN9 GC4 GC5 ga_6
GN3 GC4 GC5 ga_26
GC4 GN3 GC2 ga_26
GN3 GC2 GN2 ga_26
GN3 GC2 GN1 ga_26
GN2 GC2 GN1 ga_26
GC2 GN2 GH21 ga_22
GC2 GN2 GH22 ga_22
GH21 GN2 GH22 ga_23
GC2 GN1 GH1 ga_24
GC2 GN1 GC6 ga_26
GH1 GN1 GC6 ga_24
GN1 GC6 GO6 ga_26
GN1 GC6 GC5 ga_26
GO6 GC6 GC5 ga_26
GC4 GC5 GC6 ga_26
GC4 GC5 GN7 ga_6
GC6 GC5 GN7 ga_38
GC5 GN7 GC8 ga_6
GN9 GC8 GN7 ga_6
GC1* GC2* GC3* ga_7
GC1* GC2* GO2* ga_8
GO2* GC2* GC3* ga_8
GC2* GO2* GH2* ga_11
GC3* GO3* GH3* ga_11 ; like ATP set to GC2*
GC4* GC3* GC2* ga_7
GC4* GC3* GO3* ga_8
GC2* GC3* GO3* ga_8
GC5* GO5* GPA ga_25 ; from ATP
GO5* GPA GO1PA ga_13 ; from ATP
GO5* GPA GO2PA ga_13 ; from ATP
GO5* GPA GO3PA ga_4 ; from ATP
GO1PA GPA GO2PA ga_28 ; from ATP
GO1PA GPA GO3PA ga_13 ; from ATP
GO2PA GPA GO3PA ga_13 ; from ATP
GPA GO3PA GPB ga_25 ; from ATP
GO3PA GPB GO1PB ga_13 ; from ATP
GO3PA GPB GO2PB ga_13 ; from ATP
GO3PA GPB GO3PB ga_4 ; from ATP
GO1PB GPB GO2PB ga_28 ; from ATP
GO1PB GPB GO3PB ga_13 ; from ATP
GO2PB GPB GO3PB ga_13 ; from ATP
GPB GO3PB GPG ga_25 ; from ATP
GO3PB GPG GO1PG ga_13 ; from ATP
GO3PB GPG GO2PG ga_13 ; from ATP
GO3PB GPG GO3PG ga_4 ; from ATP
GO1PG GPG GO2PG ga_28 ; from ATP
GO1PG GPG GO3PG ga_13 ; from ATP
GO2PG GPG GO3PG ga_13 ; from ATP
GPG GO3PG GH3PG ga_11 ; from ATP
[ impropers ]
; ai aj ak al gromos type
GC4* GO4* GC5* GC3* gi_2
GC3* GC2* GO3* GC4* gi_2
GC1* GN9 GO4* GC2* gi_2
GN9 GC8 GC4 GC1* gi_1
GC4 GN9 GC8 GN7 gi_1
GC8 GN9 GC4 GC5 gi_1
GN9 GC8 GN7 GC5 gi_1
GN9 GC4 GC5 GN7 gi_1
GC8 GN7 GC5 GC4 gi_1
GC4 GN9 GN3 GC5 gi_1
GC5 GC6 GN7 GC4 gi_1
GN3 GC4 GC5 GC6 gi_1
GC4 GC5 GC6 GN1 gi_1
GC5 GC4 GN3 GC2 gi_1
GC5 GC6 GN1 GC2 gi_1
GC4 GN3 GC2 GN1 gi_1
GN3 GC2 GN1 GC6 gi_1
GC2 GN1 GN3 GN2 gi_1
GN2 GH21 GH22 GC2 gi_1
GN1 GC6 GC2 GH1 gi_1
GC6 GC5 GN1 GO6 gi_1
GC2* GO2* GC3* GC1* gi_2
[ dihedrals ]
; ai aj ak al gromos type
GO5* GC5* GC4* GC3* gd_17
GO5* GC5* GC4* GC3* gd_7
GO5* GC5* GC4* GO4* gd_8
GC5* GC4* GC3* GC2* gd_17
GC5* GC4* GC3* GO3* gd_7
GO4* GC4* GC3* GC2* gd_7
GO4* GC4* GC3* GO3* gd_8
GC4* GC3* GC2* GC1* gd_17
GO3* GC3* GC2* GC1* gd_7
GC4* GC3* GC2* GO2* gd_7
GO3* GC3* GC2* GO2* gd_8
GC3* GC2* GC1* GO4* gd_17
GC3* GC2* GC1* GO4* gd_7
GO2* GC2* GC1* GN9 gd_7
GO2* GC2* GC1* GO4* gd_8
GC1* GC2* GO2* GH2* gd_12
GC4* GC3* G03* GH3* gd_12 ; like ATP set to GC2*
GC2* GC3* GO3* GH3* gd_12 ; like GLCB
GC3* GC4* GO4* GC1* gd_14
GC4* GO4* GC1* GC2* gd_14
GO4* GC1* GN9 GC4 gd_6
GN3 GC2 GN2 GH21 gd_4
GC4* GC5* GO5* GPA gd_14 ; from ATP
GC5* GO5* GPA GO3PA gd_11 ; from ATP
GC5* GO5* GPA GO3PA gd_9 ; from ATP
GO5* GPA GO3PA GPB gd_11 ; from ATP
GO5* GPA GO3PA GPB gd_9 ; from ATP
GPA GO3PA GPB GO3PB gd_11 ; from ATP
GPA GO3PA GPB GO3PB gd_9 ; from ATP
GO3PA GPB GO3PB GPG gd_11 ; from ATP
GO3PA GPB GO3PB GPG gd_9 ; from ATP
GPB GO3PB GPG GO3PG gd_11 ; from ATP
GPB GO3PB GPG GO3PG gd_9 ; from ATP
GO3PB GPG GO3PG GH3PG gd_11 ; from ATP
GO3PB GPG GO3PG GH3PG gd_9 ; from ATP
==========================================================
R. Bryn Fenwick Department of Biochemistry,
[EMAIL PROTECTED] University of Cambridge,
[EMAIL PROTECTED] 80 Tennis Court Road,
Tel: +44 1223 766018 Old Addenbrookes Site,
Fax: +44 1223 766002 Cambridge, CB2 1GA, UK.
==========================================================
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