[gmx-users] GTP topology
Christian Burisch
burisch at bph.rub.de
Mon Dec 3 17:08:45 CET 2007
Hi Robert,
without looking any further into the data (no impropers on the
phosphates seem to be OK though): Are you sure you need a protonated
phosphate?
Regards
Christian
Robert Fenwick schrieb:
>
> 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,
> rbf22 at cam.ac.uk University of Cambridge,
> bryn.fenwick at cantab.net 80 Tennis Court Road,
> Tel: +44 1223 766018 Old Addenbrookes Site,
> Fax: +44 1223 766002 Cambridge, CB2 1GA, UK.
> ==========================================================
>
>
>
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--
Dr. Christian Burisch
Protein Mechanics and Evolution Group
CAS-MPG Partner Institute for Computational Biology
Shanghai Institutes for Biological Sciences
320 Yue Yang Road, 200031 Shanghai, P. R. China
Tel: +86 21 54920478 Fax: +86 21 54920451
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