[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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