[gmx-users] fatal error

[Justin A. Lemkul]

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

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