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

Fri Apr 6 12:27:07 CEST 2012

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???

With Best Wishes,
R.Davaid

On Thu, Apr 5, 2012 at 4:13 PM, Justin A. Lemkul <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<http://www.gromacs.org/Documentation/Errors>
>>
>> When I goes through the detail of the website at http://www.gromacs.org/*
>> *Documentation/Errors <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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