[gmx-users] Adding modified nucleotide to a forcefield
william Stebbeds
willstebbeds at hotmail.com
Fri Feb 4 07:25:11 CET 2011
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: jalemkul at vt.edu
> To: gmx-users at 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: jalemkul at vt.edu
> > > To: gmx-users at 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: jalemkul at vt.edu
> > > > > To: gmx-users at 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
> > > > >
> > > > > ========================================
> > > > > --
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> > > >
> > >
> > > --
> > > ========================================
> > >
> > > 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 at gromacs.org
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> >
>
> --
> ========================================
>
> 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 at 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
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