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

[Gunnar Widtfeldt Reginsson]

Problem is solved. The atom needed to be called O not O2.
Thanks,

On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Gunnar Widtfeldt Reginsson wrote:
>
>> 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
>>
>>
> I don't know how you reach the conclusion that pdb2gmx is confusing atom 02
> (which by the way is a "zero"-2 in the error message, not an "oh", if you
> have copied and pasted directly) with atom O1P.
>
> It could be a problem of formatting (incorrect spacing), or somewhere else
> in the residue you have an atom labeled 02 (with a zero).
>
> -Justin
>
>  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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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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