On 4/02/2011 12:36 PM, 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).
Are you saying the coordinate file you gave to pdb2gmx has your modified
residue at one location, and the coordinate file it output has it at
some other location? (Because I doubt it). Please show us the sections
of those coordinate files including your modified residue and a few
atoms either side.
Also, what is your pdb2gmx command line and for what GROMACS version?
Mark
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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