[gmx-users] pdb2gmx error

[Mark Abraham]

Hi,

Is it terminal? Are there specbonds in play? What's the GROMACS version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:

> Hi everyone,
>
> I'm getting the following warning when I try to run pdb2gmx on my protein
> structure:
>
> WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was
> mapped to an entry in the topology database, but the atom H used in an
> interaction of type dihedral in that entry is not found in the input file.
> Perhaps your atom and/or residue naming needs to be fixed.
>
> This warning is only present when I use the AMBER03 forcefield, all other
> forcefields seem to work fine. I have tried this with both a structure
> without hydrogens as well as a structure with hydrogens added, both with
> and without the -ignh flag. I tried looking at the amber03 database files
> as well as the amber99sb-ildn database files (amber99sb-ildn works just
> fine), but I could not find any reason why this particular residue would be
> problematic. pdb2gmx does not find any problems with the other proline
> residues in the protein (which look identical), so I am puzzled as to
> what's causing this.
>
> The proline residue is:
> ATOM   1384  N   PRO A 168     274.650  45.241  24.167  1.00180.63
>   N
> ATOM   1385  CA  PRO A 168     273.508  44.823  23.370  1.00180.63
>   C
> ATOM   1386  CD  PRO A 168     275.844  45.381  23.346  1.00180.63
>   C
> ATOM   1387  CB  PRO A 168     274.071  44.405  22.014  1.00180.63
>   C
> ATOM   1388  CG  PRO A 168     275.381  45.194  21.892  1.00180.63
>   C
> ATOM   1389  C   PRO A 168     272.551  43.776  23.888  1.00180.63
>   C
> ATOM   1390  O   PRO A 168     271.478  43.646  23.304  1.00180.63
>   O
>
> Does anyone know what's going on here?
>
> Thanks in advance!
> --
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