[gmx-users] fatal error

[ahmet yıldırım]

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.

*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>

>
>
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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-- 
Ahmet YILDIRIM
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