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Thanks for the reply,<br><br>ffamber99sb.rtp entry:<br>[ DGO ]<br> [ atoms ]<br> P amber99_46 1.16590 1<br> O1P amber99_45 -0.77610 2<br> O2P amber99_45 -0.77610 3<br> O5' amber99_44 -0.49540 4<br> C5' amber99_11 -0.00690 5<br> H5'1 amber99_19 0.07540 6<br> H5'2 amber99_19 0.07540 7<br> C4' amber99_11 0.16290 8<br> H4' amber99_19 0.11760 9<br> O4' amber99_44 -0.36910 10<br> C1' amber99_11 0.03580 11<br> H1' amber99_20 0.17460 12<br> N9 amber99_40 0.05770 13<br> C8 amber99_6 0.07360 14<br> O8 amber99_44 -0.36910 15<br> N7 amber99_36 -0.57250 16<br> C5 amber99_4 0.19910 17<br> C6 amber99_2 0.49180 18<br> O6 amber99_41 -0.56990 19<br> N1 amber99_35 -0.50530 20<br> H1 amber99_17 0.35200 21<br> C2 amber99_3 0.74320 22<br> N2 amber99_38 -0.92300 23<br> H21 amber99_17 0.42350 24<br> H22 amber99_17 0.42350 25<br> N3 amber99_37 -0.66360 26<br> C4 amber99_4 0.18140 27<br> C3' amber99_11 0.07130 28<br> H3' amber99_19 0.09850 29<br> C2' amber99_11 -0.08540 30<br> H2'1 amber99_18 0.07180 31<br> H2'2 amber99_18 0.07180 32<br> O3' amber99_44 -0.52320 33<br> [ bonds ]<br> P O1P<br> P O2P<br> P O5'<br> O5' C5'<br> C5' H5'1<br> C5' H5'2<br> C5' C4'<br> C4' H4'<br> C4' O4'<br> C4' C3'<br> O4' C1'<br> C1' H1'<br> C1' N9<br> C1' C2'<br> N9 C8<br> N9 C4<br> C8 O8<br> C8 N7<br> N7 C5<br> C5 C6<br> C5 C4<br> C6 O6<br> C6 N1<br> N1 H1<br> N1 C2<br> C2 N2<br> C2 N3<br> N2 H21<br> N2 H22<br> N3 C4<br> C3' H3'<br> C3' C2'<br> C3' O3'<br> C2' H2'1<br> C2' H2'2<br> -O3' P<br> [ dihedrals ]<br> O4' C1' N9 C4 proper_X_CT_N*_X <br> C1' N9 C8 O8 proper_X_CK_N*_X<br> C1' N9 C8 N7 proper_X_CK_N*_X<br> C1' N9 C4 C5 proper_X_CB_N*_X<br> C1' N9 C4 N3 proper_X_CB_N*_X<br> H1' C1' N9 C8 proper_X_CT_N*_X <br> H1' C1' N9 C4 proper_X_CT_N*_X <br> C8 N9 C4 C5 proper_X_CB_N*_X<br> C8 N9 C4 N3 proper_X_CB_N*_X<br> C5 C6 N1 H1 proper_X_C_NA_X<br> C5 C6 N1 C2 proper_X_C_NA_X<br> C6 N1 C2 N2 proper_X_CA_NA_X<br> C6 N1 C2 N3 proper_X_CA_NA_X<br> O6 C6 N1 H1 proper_X_C_NA_X<br> O6 C6 N1 C2 proper_X_C_NA_X<br> N1 C2 N3 C4 proper_X_CA_NC_X<br> H1 N1 C2 N2 proper_X_CA_NA_X<br> H1 N1 C2 N3 proper_X_CA_NA_X<br> N2 C2 N3 C4 proper_X_CA_NC_X<br> H8 C8 N7 C5 proper_X_CK_NB_X<br> N9 C8 N7 C5 proper_X_CK_NB_X<br> H8 C8 N9 C4 proper_X_CK_N*_X<br> N7 C8 N9 C4 proper_X_CK_N*_X<br> O4' C1' C2' H2'1 proper_H_CT_CT_O<br> O4' C1' C2' H2'2 proper_H_CT_CT_O<br> O3' C3' C2' H2'1 proper_H_CT_CT_O<br> O3' C3' C2' H2'2 proper_H_CT_CT_O<br> [ impropers ]<br> C4 C8 N9 C1' nucleic_imp_10<br> C5 N1 C6 O6<br> C6 C2 N1 H1 nucleic_imp_10<br> C2 H21 N2 H22<br> N9 N7 C8 O8<br> N2 N1 C2 N3 nucleic_imp_11<br><br>DGO was also added to residuetypes.dat. hdb file was also updated, as was dna.rtp within amber99sb.ff.<br><br>The problem is not a simple missing bond, as when the structure goes through pdb2gmx, the new nucleotide appears on the other side of the pbc, in a straight line (i.e. without form).<br><br>Thanks<br><br>Will<br><br>> Date: Thu, 3 Feb 2011 16:07:42 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield<br>> <br>> <br>> <br>> william Stebbeds wrote:<br>> > Hello,<br>> > <br>> > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the <br>> > amber99sb force field. This is a simple modification of the H8 hydrogen <br>> > on a guanine to an oxygen atom. I have followed the instructions on the <br>> > gromacs site on adding residues.<br>> > <br>> > However the new nucleotide will not work, it will not attach to the <br>> > adjacent nucleotides in the sequence.<br>> > <br>> <br>> So a bond is missing?<br>> <br>> > Any help would be very much appreciated, if any more information is <br>> > required please let me know.<br>> > <br>> <br>> A lot more information is needed, at the very least, your .rtp entry.<br>> <br>> -Justin<br>> <br>> > Best Regards<br>> > <br>> > William Stebbeds<br>> > Cranfield University<br>> > UK<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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