[gmx-users] Missing H from residue

[Jack Shultz]

Thanks Justin! Got it now.

On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
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-- 
Jack

http://drugdiscoveryathome.com
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