[gmx-users] a pdb2gmx problem for NON aminoacids

[Marc Lensink]

Markus O Kaukonen wrote:
> 
> I generated by hand a rather poor starting guess for CH3CH2OH
> in xyz format:
> ---------------
> 9
> ch3ch2oh to be done
> C       0.      0.      0.
> H       0.      0.      -1.0
> H       -.7.    -.7     0.0
> H       .7      .7      0.0
> C       0.      0.      1.5
> H       0.      1.      1.5
> H       0.      -1.     1.5
> O       0.      0.      3.0
> H       0.      0.      4.0
> --------------------------
> 
> then translated it to pdb format:
> ----------
> ATOM      1  C   UNK     1       0.000   0.000   0.000  1.00  0.00
> ATOM      2  H   UNK     1       0.000   0.000  -1.000  1.00  0.00
> ATOM      3  H   UNK     1      -0.700  -0.700   0.000  1.00  0.00
> ATOM      4  H   UNK     1       0.700   0.700   0.000  1.00  0.00
> ATOM      5  C   UNK     1       0.000   0.000   1.500  1.00  0.00
> ATOM      6  H   UNK     1       0.000   1.000   1.500  1.00  0.00
> ATOM      7  H   UNK     1       0.000  -1.000   1.500  1.00  0.00
> ATOM      8  O   UNK     1       0.000   0.000   3.000  1.00  0.00
> ATOM      9  H   UNK     1       0.000   0.000   4.000  1.00  0.00
> -------------------
> 
> then tried to change it to gromacs format end get the topology file:
> pdb2gmx -f c-c-o.pdb
> but got
> Fatal error: Residue 'UNK' not found in residue topology database
> after giving 0 for force field.

You only specified coordinates, and no topology for your molecule. You
should add an entry in the residue topology database (something.rtp).

Marc