[gmx-users] Adding modified nucleotide to a forcefield

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 4 02:44:08 CET 2011


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: 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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