[gmx-users] fatal error

[ahmet yıldırım]

Dear justin,

I looked at the pdb file. No NH2 reside contains carbon atom.

What should I do?

22 Ocak 2011 00:18 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as
>> far as I understand from mailing list. I am using 43a1 forcefield. I do not
>> understand what kind of changes should I do.
>>
>>
> You do not need to modify the .rtp file, you need to modify your coordinate
> file, as I said before.  The fatal error indicates that you have included a
> C atom in an NH2 residue, which is just a neutral amine and contains no
> carbon, as should be clear from the .rtp file.
>
> -Justin
>
>  *the aminoacids.rtp file:*
>>
>> [ ACE ]
>>  [ atoms ]
>>    CA   CH3   0.000     0
>>     C     C   0.380     1
>>     O     O  -0.380     1
>>  [ bonds ]
>>     C    CA   gb_26
>>     C     O   gb_4
>>     C    +N   gb_9
>>  [ angles ]
>>   CA     C     O    ga_30
>>   CA     C    +N    ga_18
>>    O     C    +N    ga_32
>>  [ impropers ]
>>    C    CA    +N     O    gi_1
>>
>> [ NH2 ]
>>  [ atoms ]
>>     N    NT   -0.83    0
>>     H1    H   0.415    0
>>     H2    H   0.415   0
>>  [ bonds ]
>>      N    H1  gb_2
>>      N    H2  gb_2       -C    N   gb_8
>>  [ angles ]
>>     -O -C N  ga_32
>>     -CA -C N ga_18
>>     -C N H1  ga_22
>>     -C N H2  ga_22
>>     H1 N H2  ga_23
>>  [ dihedrals ]
>>    -CA -C N H1 gd_4
>>  [ impropers ]
>>    -C -O N -CA gi_1
>>     N  H1 H2  -C gi_1
>>
>> [ ALA ]
>>  [ atoms ]
>>    N     N    -0.28000     0
>>    H     H     0.28000     0
>>   CA   CH1     0.00000     1
>>   CB   CH3     0.00000     1
>>    C     C       0.380     2
>>    O     O      -0.380     2
>>  [ bonds ]
>>    N     H    gb_2       N    CA    gb_20     CA     C    gb_26      C
>> O    gb_4       C    +N    gb_9      CA    CB    gb_26
>> 2011/1/21 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>>    ahmet yıldırım wrote:
>>
>>        Dear users,
>>
>>        Gromacs 4.5.3
>>        pdb2gmx -f xxx.pdb -water spc
>>        select Force Field:9
>>        *Fatal error:*
>>        atom C not found in buiding block 13NH2 while combining tdb and rtp
>>        For more information and tips for troubleshooting, please check
>>        the GROMACS
>>        website at http://www.gromacs.org/Documentation/Errors
>>
>>
>>        How can I fixed this error?
>>
>>
>>    You have a carbon atom in a residue that should only contain NH2.
>>     Refer to the .rtp file for what is expected, then make a suitable
>>    structure that conforms to those requirements.
>>
>>    This has been asked and answered hundreds of times, so please make
>>    use of the mailing list search.  You would have gotten your answer
>>    in minutes rather than hours.
>>
>>    -Justin
>>
>>
>>        Thanks in advance
>>
>>
>>        --         Ahmet YILDIRIM
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Ahmet YILDIRIM
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