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Success! Following your advice, and with a few tweaks everything is running smoothly, thank you so much for your help.<div><br></div><div>all the best</div><div><br></div><div>Will <br><br><br><br><br>> Date: Thu, 3 Feb 2011 22:44:48 -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>> > Thanks again,<br>> > <br>> > You were right, it was a misaligned pdb file :).<br>> > <br>> > However I now get an error when I use grompp:<br>> > <br>> > ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]:<br>> > No default Bond types<br>> > <br>> > <br>> > ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]:<br>> > No default Angle types<br>> > <br>> > <br>> > ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]:<br>> > No default Angle types<br>> > <br>> > <br>> > ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]:<br>> > No default Improper Dih. types<br>> > <br>> > My assumption is that I have not set the angles and dihedrals properly <br>> > but have rechecked the rtp entry and all seems to be correct.<br>> > <br>> <br>> The errors indicate that you've specified bonded parameters that do not exist in <br>> the force field. Look into the referenced .itp file at those lines, map back <br>> the atoms in question, and identify which terms they correspond to. If you <br>> don't find matching entries in ffbonded.itp, then either you have to derive them <br>> yourself or find suitable parameters for them.<br>> <br>> -Justin<br>> <br>> > Once Again thank you for helping out a gromacs newbie.<br>> > <br>> > <br>> > <br>> > > Date: Thu, 3 Feb 2011 20:43:24 -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>> > > > 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<br>> > > > was dna.rtp within amber99sb.ff.<br>> > > ><br>> > > > The problem is not a simple missing bond, as when the structure goes<br>> > > > through pdb2gmx, the new nucleotide appears on the other side of the<br>> > > > pbc, in a straight line (i.e. without form).<br>> > > ><br>> > ><br>> > > As in, the atoms of DGO are visually a straight line? That would be a<br>> > > consequence of an incorrectly-formatted input file. If you're using a <br>> > .pdb<br>> > > file, it's fixed-format, so any incorrect spacing will screw up the <br>> > coordinates.<br>> > ><br>> > > To clarify, are you missing a bond, as your first message would <br>> > imply? I can<br>> > > see how you might be missing bonds; your residue definition doesn't <br>> > specify a<br>> > > bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3' <br>> > ending<br>> > > nucleotide, this wouldn't apply. If it's an internal residue, you may <br>> > also be<br>> > > missing necessary dihedral definitions as well.<br>> > ><br>> > > -Justin<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<br>> > > > hydrogen<br>> > > > > > on a guanine to an oxygen atom. I have followed the <br>> > instructions on<br>> > > > 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<br>> > > > 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>> > > ><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 <br>> > 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>> > <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></div> </body>
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