[gmx-users] Missing H from residue

[Jack Shultz]

On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Jack Shultz wrote:
>
> <snip>
>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.0.5
>> Source code file: pdb2gmx.c, line: 429
>>
>> Fatal error:
>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms
>>             while sorting atoms
>> -------------------------------------------------------
>>
>> But we got an O here
>> ATOM   3822  O   CARG  153      -4.455 -21.080   2.791  1.00  0.00
>>   O
>>
>
> The error is not telling you that the O atom is missing from the .pdb file;
> it is telling you that it is present in the .pdb, but not in the .rtp entry.
>  Look at the .rtp entry for CARG

[ CARG ]
 [ atoms ]
     N    amber99_34  -0.34810     1
     H    amber99_17   0.27640     2
    CA    amber99_11  -0.30680     3
    HA    amber99_19   0.14470     4
    CB    amber99_11  -0.03740     5
   HB1    amber99_18   0.03710     6
   HB2    amber99_18   0.03710     7
    CG    amber99_11   0.07440     8
   HG1    amber99_18   0.01850     9
   HG2    amber99_18   0.01850    10
    CD    amber99_11   0.11140    11
   HD1    amber99_19   0.04680    12
   HD2    amber99_19   0.04680    13
    NE    amber99_38  -0.55640    14
    HE    amber99_17   0.34790    15
    CZ    amber99_3    0.83680    16
   NH1    amber99_38  -0.87370    17
  HH11    amber99_17   0.44930    18
  HH12    amber99_17   0.44930    19
   NH2    amber99_38  -0.87370    20
  HH21    amber99_17   0.44930    21
  HH22    amber99_17   0.44930    22
     C    amber99_2    0.85570    23
   OC1    amber99_45  -0.82660    24
   OC2    amber99_45  -0.82660    25

- you should have an O1 and O2 atom for the

I made the following modification
ATOM   1900  O1  CARG  153     -17.391 -20.267  11.508  1.00  0.00           O
ATOM   1909  O2  CARG  153     -18.666 -19.390  13.107  1.00  0.00           O


-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom O in residue CARG 122 not found in rtp entry with 25 atoms
             while sorting atoms
-------------------------------------------------------


> C-terminal carboxylate.
>
> -Justin
>
> --
> ========================================
>
> 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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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org