[gmx-users] pdb2gmx question

[Mark Abraham]

Amit Choubey wrote:
> hi everyone,
> I am trying to set up a very small simulation with DPPC lipid. I am using
> the GROMOS96 53a6 FF. Now i have my pdb file which looks like
> 
> ATOM      1  C33  DPPC    1      15.771  52.651   9.201  1.00  0.00
> ATOM      2  C34  DPPC    1      16.750  52.953  11.353  1.00  0.00
> ATOM      3  C35  DPPC    1      16.477  54.817   9.854  1.00  0.00
> ATOM      4  N    DPPC    1      16.796  53.384   9.947  1.00  0.00
> ATOM      5  C32  DPPC    1      18.082  53.008   9.318  1.00  0.00
> ATOM      6  C31  DPPC    1      19.292  53.957   9.530  1.00  0.00
> ATOM      7  O32  DPPC    1      19.653  54.093  10.906  1.00  0.00
> ATOM      8  P    DPPC    1      20.931  54.971  11.160  1.00  0.00
> ATOM      9  O33  DPPC    1      21.965  54.328  10.317  1.00  0.00
> ATOM     10  O34  DPPC    1      20.513  56.372  10.957  1.00  0.00
> ATOM     11  O31  DPPC    1      21.096  54.572  12.688  1.00  0.00
> ATOM     12  C3   DPPC    1      20.436  55.317  13.711  1.00  0.00
> ATOM     13  C2   DPPC    1      20.715  54.687  15.095  1.00  0.00
> ATOM     14  O21  DPPC    1      20.250  55.525  16.189  1.00  0.00
> ATOM     15  C21  DPPC    1      18.977  55.438  16.644  1.00  0.00
> ATOM     16  O22  DPPC    1      18.253  54.474  16.407  1.00  0.00
> ATOM     17  C22  DPPC    1      18.585  56.603  17.549  1.00  0.00
> ATOM     18  C23  DPPC    1      17.728  56.214  18.751  1.00  0.00
> ATOM     19  C24  DPPC    1      17.396  57.481  19.541  1.00  0.00
> ATOM     20  C25  DPPC    1      16.456  57.200  20.713  1.00  0.00
> ATOM     21  C26  DPPC    1      16.196  58.488  21.496  1.00  0.00
> ATOM     22  C27  DPPC    1      15.247  58.258  22.678  1.00  0.00
> ATOM     23  C28  DPPC    1      15.849  57.273  23.685  1.00  0.00
> ATOM     24  C29  DPPC    1      14.863  56.871  24.797  1.00  0.00
> ATOM     25  C210 DPPC    1      15.354  55.818  25.560  1.00  0.00
> ATOM     26  C211 DPPC    1      14.405  55.341  26.675  1.00  0.00
> 
> Now for atoms C210, C211 etc (with three no. after the element name) the
> pdb2gmx prints out following kind of warning
> 
> WARNING: atom C210 is missing in residue DPP 1 in the pdb file

Probably you've got the column-based formatting of the .pdb file wrong, 
since "DPPC" is being truncated to "DPP". Try shifting that entry one 
column left, keeping the rest in the same place.

Mark

> WARNING: atom C211 is missing in residue DPP 1 in the pdb file
> 
> I am sure that it has to do with the way i am writing the pdb file (ie
> format) . I am sure that the pdb2gmx is actually detecting the right kind of
> molecule (DPPC) . But i cannot figure out how exactly to write my pdb file.
> 
> Thank you in advance
> Amit
> 
> 
> 
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