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
>
> ========================================
> --
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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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