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

[Mark Abraham]

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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