[gmx-users] problem in simulation of dna-protein complex

[nitu sharma]

Dear all

                        I am doing simulation of DNA -protein complex  using
amber port with gromacs-4.0.3  . for this I have to make changes in my .pdb
file a/c to entry in .rtp file of amber force field.

I have all possible changes  but when I run the pdb2gmx command the error
came like this-

Fatal error:
Atom O2 in residue DT 1 not found in rtp entry with 32 atoms
             while sorting atoms

and entry of atom in .rtp file like this-
 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    0.06800    11
   H1'    amber99_20    0.18040    12
    N1    amber99_40   -0.02390    13
    C6    amber99_7    -0.22090    14
    H6    amber99_23    0.26070    15
    C5    amber99_7     0.00250    16
    C7    amber99_11   -0.22690    17
   H71    amber99_18    0.07700    18
   H72    amber99_18    0.07700    19
   H73    amber99_18    0.07700    20
    C4    amber99_2     0.51940    21
    O4    amber99_41   -0.55630    22
    N3    amber99_35   -0.43400    23
    H3    amber99_17    0.34200    24
    C2    amber99_2     0.56770    25
     O    amber99_41   -0.58810    26
   C3'    amber99_11    0.07130    27
   H3'    amber99_19    0.09850    28
   C2'    amber99_11   -0.08540    29
  H2'1    amber99_18    0.07180    30
  H2'2    amber99_18    0.07180    31
   O3'    amber99_44   -0.52320    32

So, can anyone suggest me at the place 02 what name I can change in my .pdb
file.

Thanking you
Nitu sharma
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