[gmx-users] Missing H from residue

[Justin A. Lemkul]

Jack Shultz wrote:
> 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
> 

Forgive my typo, what I meant was OC1 and OC2.  You must always make sure the 
atoms in the structure file match those expected by the .rtp file.  You need OC1 
and OC2.

-Justin

> 
> -------------------------------------------------------
> 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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> 
> 
> 

-- 
========================================

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

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