[gmx-users] Atom N not found....

Fri Apr 6 13:05:24 CEST 2012

On 6/04/2012 8:27 PM, rama david wrote:
> Hi Gromacs Friends and Justin ,
>
> Thank you for reply and suggestion.
>
> These is short part of my PDB .
>
> ATOM      1 1H   ACE     1       0.000   0.000   0.000
> ATOM      2  CH3 ACE     1       0.000   1.090   0.000
> ATOM      3 2H   ACE     1       1.028   1.453  -0.000
> ATOM      4 3H   ACE     1      -0.514   1.453  -0.890
> ATOM      5  C   ACE     1      -0.721   1.600   1.249
> ATOM      6  O   ACE     1      -0.839   2.806   1.453
> ATOM      7  N   PRO     2      -1.227   0.727   2.126
> ATOM      8  CA  PRO     2      -1.918   1.181   3.321
> ATOM      9  HA  PRO     2      -2.553   2.031   3.073
> ATOM     10  C   PRO     2      -0.928   1.587   4.404
> ATOM     11  O   PRO     2      -1.069   2.645   5.013
> ATOM     12  CB  PRO     2      -2.782   0.075   3.851
> ATOM     13 1HB  PRO     2      -2.469  -0.177   4.864
> ATOM     14 2HB  PRO     2      -3.822   0.401   3.862
> ATOM     15  CG  PRO     2      -2.645  -1.140   2.964
> ATOM     16 1HG  PRO     2      -2.232  -1.966   3.542
> ATOM     17 2HG  PRO     2      -3.606  -1.451   2.556
> ATOM     18  CD  PRO     2      -1.680  -0.755   1.882
> ATOM     19 1HD  PRO     2      -2.173  -0.830   0.913
> ATOM     20 2HD  PRO     2      -0.816  -1.419   1.895
> ATOM     21  N   GLY     3       0.076   0.740   4.644
> ATOM     22  H   GLY     3       0.135  -0.114   4.109
> ATOM     23  CA  GLY     3       1.083   1.012   5.650
>
> The gromacs96 53a6 .rtp file mention the following data...
>
>  bondedtypes ]
> ; bonds  angles  dihedrals  impropers
>     2       2          1          2
>
> [ ACE ]
>  [ atoms ]
>     CA   CH3   0.000     0
>      C     C   0.450     1
>      O     O  -0.450     1
>  [ bonds ]
>      C    CA   gb_27
>      C     O   gb_5
>      C    +N   gb_19
>  [ angles ]
>    CA     C     O    ga_30
>    CA     C    +N    ga_19
>     O     C    +N    ga_33
>  [ 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_9
>  [ angles ]
>      -O -C N  ga_33
>      -CA -C N ga_19
>      -C N H1  ga_23
>      -C N H2  ga_23
>      H1 N H2  ga_24
>  [ dihedrals ]
>     -CA -C N H1 gd_14
>  [ impropers ]
>     -C -O N -CA gi_1
>      N H1 H2 -C gi_1
>
> As per my pdb file N atom is the part of PROLINE , not the ACE...
> I got the topology by using the Amber 03 FF.
> But my priority  is to the GROMOS96 53a6 force field ...
>
> Could any suggest me the way to tackle these problem???

The default is to try to put termini on the protein chain. Your chain 
already has them, so you need to tell pdb2gmx not to try to add termini. 
See pdb2gmx -h.

Mark

>
> With Best Wishes,
> R.Davaid
>
> On Thu, Apr 5, 2012 at 4:13 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     rama david wrote:
>
>         Hi Gromacs friends,
>
>         When I given the command ...
>         pdb2gmx -f .. -o .. -p .. -ignh
>         I gate the following error..
>
>         ------------------------------------------------------
>         Program pdb2gmx, VERSION 4.5.4
>         Source code file:
>         /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070
>
>         Fatal error:
>         atom N not found in buiding block 1ACE while combining tdb and rtp
>         For more information and tips for troubleshooting, please
>         check the GROMACS
>         website at http://www.gromacs.org/Documentation/Errors
>
>         When I goes through the detail of the website at
>         http://www.gromacs.org/Documentation/Errors and document
>         I come to know that I have to modify the rtp file,
>
>
>     Nowhere in the explanation of the error does it suggest that you
>     should alter the .rtp file in this instance.  You have atoms in
>     your structure that are not in the .rtp entry.  Specifically, your
>     structure file has an N atom in ACE, but ACE only contains CA, C,
>     and O.  The N atom should be the first atom in the next residue,
>     not ACE.
>
>     -Justin
>
>     -- 
>     ========================================
>
>     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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