[gmx-users] Adding modified nucleotide to a forcefield
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 4 02:43:24 CET 2011
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
========================================
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