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

rama david ramadavidgroup at gmail.com
Fri Apr 6 14:12:06 CEST 2012 

HI all ,
 sorry for above incomplete information ,
 I change CH3 of ACE residue of my pdb file to CA .

Thank you in advance

On Fri, Apr 6, 2012 at 5:34 PM, rama david <ramadavidgroup at gmail.com> wrote:

> Hi GROMACS Friends and Mark..
>
> Thank you for reply ...
> My command line is
> pdb2gmx -f ....pdb -o p.pdb -p p.top -ignh -ter
> I choose the G96 53a6 ff , along with spc water model.
>
> Select start terminus type for ACE-1
>  0: NH3+
>  1: NH2
>  2: None
> 2
> Start terminus ACE-1: None
>
> Select end terminus
>  0: COO-
>  1: COOH
>  2: None
> 0
> End terminus : COO-
>
> So I got the following out put...
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
> 655
>
> Fatal error:
> Atom CH3 in residue ACE 1 was not found in rtp entry ACE with 3 atoms
> while sorting atoms.
>
> .
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I have the limited experience for these problem..
> Can you tell me what to do in such conditions????
>
> I change the Atom CH3 in pdb to CA and  proceed with the above command
> line
> and option .
>    I got the following error
>
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line:
> 581
>
> Fatal error:
> Residue 'CE' not found in residue topology database
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>    I have the limited experience for these problem..
> Can you tell me what to do in such conditions????
>
>
> On Fri, Apr 6, 2012 at 4:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>>  On 6/04/2012 9:05 PM, Mark Abraham wrote:
>>
>> 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.
>>
>>
>> ... and if you'd also shown the last piece of your pdb2gmx output and
>> given us the whole command line you used, then you'd have gotten your
>> answer faster and wasted less of people's time guessing what the real
>> problem was.
>>
>> Mark
>>
>> --
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>
>
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