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

[Justin A. Lemkul]

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

========================================