[gmx-users] Adding modified nucleotide to a forcefield

william Stebbeds willstebbeds at hotmail.com
Fri Feb 4 02:36:44 CET 2011 

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).

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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