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, > [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. > ========================================================== > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
