[gmx-users] a pdb2gmx problem for NON aminoacids

[Markus O Kaukonen]

Hi,
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.

Must all the atoms in the system really belong to some aminoacid?

I also tried residue id 'SOL' but got error:
Fatal error: Atom C in residue HOH 1 not found in database
             while sorting atoms

What is the simple workaround?
I just want to optimise the structure of this molecule.

Cheers, Markus
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