[gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

[Gunnar Widtfeldt Reginsson]

Hi. Can someone please help me.
I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I
start by making a topology file form the pdb file. When I run pdb2gmx and
the amber99 force field I get this fatal error:'Atom 02 in residue DT 3 not
found in rtp entry with 32 atoms while sorting atoms'

Here is the portion of the pdb file containing the atom in question:
ATOM     37  C4   DA A   2       2.705  -1.868   3.118  1.00  0.00

ATOM     38  C3'  DA A   2       6.858  -4.420   2.715  1.00  0.00

ATOM     39  C2'  DA A   2       5.664  -4.141   3.627  1.00  0.00

ATOM     40  O3'  DA A   2       7.933  -3.562   3.073  1.00  0.00

ATOM     41  P     DT A   3       8.308  -3.390   4.619  1.00  0.00

ATOM     42  O1P DT A   3       9.773  -3.228   4.760  1.00  0.00
ATOM     43  O2P DT A   3       7.705  -4.493   5.401  1.00  0.00
ATOM     44  O5'   DT A   3       7.575  -2.013   4.972  1.00  0.00

ATOM     45  C5'   DT A   3       7.588  -0.948   4.004  1.00  0.00

Where atom 02 must be O1P in DT 3

Here is the portion of the amber99 .rtf file for the DT nucleotide:
[ DT ]
 [ 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    0.06800    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

I can't see why atom 02 shouldn't be found.

I am running GROMACS 4.0.5 on Mac OS 10.5

Thanks,
Gunnar W.
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