Success! Following your advice, and with a few tweaks everything is running smoothly, thank you so much for your help. all the best Will
> Date: Thu, 3 Feb 2011 22:44:48 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > william Stebbeds wrote: > > Thanks again, > > > > You were right, it was a misaligned pdb file :). > > > > However I now get an error when I use grompp: > > > > ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]: > > No default Bond types > > > > > > ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]: > > No default Angle types > > > > > > ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]: > > No default Angle types > > > > > > ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]: > > No default Improper Dih. types > > > > My assumption is that I have not set the angles and dihedrals properly > > but have rechecked the rtp entry and all seems to be correct. > > > > The errors indicate that you've specified bonded parameters that do not exist > in > the force field. Look into the referenced .itp file at those lines, map back > the atoms in question, and identify which terms they correspond to. If you > don't find matching entries in ffbonded.itp, then either you have to derive > them > yourself or find suitable parameters for them. > > -Justin > > > Once Again thank you for helping out a gromacs newbie. > > > > > > > > > Date: Thu, 3 Feb 2011 20:43:24 -0500 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > > > > > > > > > william Stebbeds wrote: > > > > Thanks for the reply, > > > > > > > > ffamber99sb.rtp entry: > > > > [ DGO ] > > > > [ atoms ] > > > > P amber99_46 1.16590 1 > > > > O1P amber99_45 -0.77610 2 > > > > O2P amber99_45 -0.77610 3 > > > > O5' amber99_44 -0.49540 4 > > > > C5' amber99_11 -0.00690 5 > > > > H5'1 amber99_19 0.07540 6 > > > > H5'2 amber99_19 0.07540 7 > > > > C4' amber99_11 0.16290 8 > > > > H4' amber99_19 0.11760 9 > > > > O4' amber99_44 -0.36910 10 > > > > C1' amber99_11 0.03580 11 > > > > H1' amber99_20 0.17460 12 > > > > N9 amber99_40 0.05770 13 > > > > C8 amber99_6 0.07360 14 > > > > O8 amber99_44 -0.36910 15 > > > > N7 amber99_36 -0.57250 16 > > > > C5 amber99_4 0.19910 17 > > > > C6 amber99_2 0.49180 18 > > > > O6 amber99_41 -0.56990 19 > > > > N1 amber99_35 -0.50530 20 > > > > H1 amber99_17 0.35200 21 > > > > C2 amber99_3 0.74320 22 > > > > N2 amber99_38 -0.92300 23 > > > > H21 amber99_17 0.42350 24 > > > > H22 amber99_17 0.42350 25 > > > > N3 amber99_37 -0.66360 26 > > > > C4 amber99_4 0.18140 27 > > > > C3' amber99_11 0.07130 28 > > > > H3' amber99_19 0.09850 29 > > > > C2' amber99_11 -0.08540 30 > > > > H2'1 amber99_18 0.07180 31 > > > > H2'2 amber99_18 0.07180 32 > > > > O3' amber99_44 -0.52320 33 > > > > [ bonds ] > > > > P O1P > > > > P O2P > > > > P O5' > > > > O5' C5' > > > > C5' H5'1 > > > > C5' H5'2 > > > > C5' C4' > > > > C4' H4' > > > > C4' O4' > > > > C4' C3' > > > > O4' C1' > > > > C1' H1' > > > > C1' N9 > > > > C1' C2' > > > > N9 C8 > > > > N9 C4 > > > > C8 O8 > > > > C8 N7 > > > > N7 C5 > > > > C5 C6 > > > > C5 C4 > > > > C6 O6 > > > > C6 N1 > > > > N1 H1 > > > > N1 C2 > > > > C2 N2 > > > > C2 N3 > > > > N2 H21 > > > > N2 H22 > > > > N3 C4 > > > > C3' H3' > > > > C3' C2' > > > > C3' O3' > > > > C2' H2'1 > > > > C2' H2'2 > > > > -O3' P > > > > [ dihedrals ] > > > > O4' C1' N9 C4 proper_X_CT_N*_X > > > > C1' N9 C8 O8 proper_X_CK_N*_X > > > > C1' N9 C8 N7 proper_X_CK_N*_X > > > > C1' N9 C4 C5 proper_X_CB_N*_X > > > > C1' N9 C4 N3 proper_X_CB_N*_X > > > > H1' C1' N9 C8 proper_X_CT_N*_X > > > > H1' C1' N9 C4 proper_X_CT_N*_X > > > > C8 N9 C4 C5 proper_X_CB_N*_X > > > > C8 N9 C4 N3 proper_X_CB_N*_X > > > > C5 C6 N1 H1 proper_X_C_NA_X > > > > C5 C6 N1 C2 proper_X_C_NA_X > > > > C6 N1 C2 N2 proper_X_CA_NA_X > > > > C6 N1 C2 N3 proper_X_CA_NA_X > > > > O6 C6 N1 H1 proper_X_C_NA_X > > > > O6 C6 N1 C2 proper_X_C_NA_X > > > > N1 C2 N3 C4 proper_X_CA_NC_X > > > > H1 N1 C2 N2 proper_X_CA_NA_X > > > > H1 N1 C2 N3 proper_X_CA_NA_X > > > > N2 C2 N3 C4 proper_X_CA_NC_X > > > > H8 C8 N7 C5 proper_X_CK_NB_X > > > > N9 C8 N7 C5 proper_X_CK_NB_X > > > > H8 C8 N9 C4 proper_X_CK_N*_X > > > > N7 C8 N9 C4 proper_X_CK_N*_X > > > > O4' C1' C2' H2'1 proper_H_CT_CT_O > > > > O4' C1' C2' H2'2 proper_H_CT_CT_O > > > > O3' C3' C2' H2'1 proper_H_CT_CT_O > > > > O3' C3' C2' H2'2 proper_H_CT_CT_O > > > > [ impropers ] > > > > C4 C8 N9 C1' nucleic_imp_10 > > > > C5 N1 C6 O6 > > > > C6 C2 N1 H1 nucleic_imp_10 > > > > C2 H21 N2 H22 > > > > N9 N7 C8 O8 > > > > N2 N1 C2 N3 nucleic_imp_11 > > > > > > > > DGO was also added to residuetypes.dat. hdb file was also updated, as > > > > was dna.rtp within amber99sb.ff. > > > > > > > > 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). > > > > > > > > > > As in, the atoms of DGO are visually a straight line? That would be a > > > consequence of an incorrectly-formatted input file. If you're using a > > .pdb > > > file, it's fixed-format, so any incorrect spacing will screw up the > > coordinates. > > > > > > To clarify, are you missing a bond, as your first message would > > imply? I can > > > see how you might be missing bonds; your residue definition doesn't > > specify a > > > bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3' > > ending > > > nucleotide, this wouldn't apply. If it's an internal residue, you may > > also be > > > missing necessary dihedral definitions as well. > > > > > > -Justin > > > > > > > Thanks > > > > > > > > Will > > > > > > > > > Date: Thu, 3 Feb 2011 16:07:42 -0500 > > > > > From: jalem...@vt.edu > > > > > To: gmx-users@gromacs.org > > > > > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield > > > > > > > > > > > > > > > > > > > > william Stebbeds wrote: > > > > > > Hello, > > > > > > > > > > > > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the > > > > > > amber99sb force field. This is a simple modification of the H8 > > > > hydrogen > > > > > > on a guanine to an oxygen atom. I have followed the > > instructions on > > > > the > > > > > > gromacs site on adding residues. > > > > > > > > > > > > However the new nucleotide will not work, it will not attach to the > > > > > > adjacent nucleotides in the sequence. > > > > > > > > > > > > > > > > So a bond is missing? > > > > > > > > > > > Any help would be very much appreciated, if any more information is > > > > > > required please let me know. > > > > > > > > > > > > > > > > A lot more information is needed, at the very least, your .rtp entry. > > > > > > > > > > -Justin > > > > > > > > > > > Best Regards > > > > > > > > > > > > William Stebbeds > > > > > > Cranfield University > > > > > > UK > > > > > > > > > > > > > > > > -- > > > > > ======================================== > > > > > > > > > > Justin A. Lemkul > > > > > Ph.D. Candidate > > > > > ICTAS Doctoral Scholar > > > > > MILES-IGERT Trainee > > > > > Department of Biochemistry > > > > > Virginia Tech > > > > > Blacksburg, VA > > > > > jalemkul[at]vt.edu | (540) 231-9080 > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > > > ======================================== > > > > > -- > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > > Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > -- > > > ======================================== > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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