[gmx-users] Residue 'UNK' not found in residue topology database

[Mark Abraham]

Sagittarius wrote:
> Dear Gromacs users,
>  
> Could you please help me to find out what the problem is.

Curiously enough, pdb2gmx is telling you want the problem is.

> I use command
> pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p 
> outputName.top
> Fatal error:
> Residue 'UNK' not found in residue topology database

pdb2gmx can only generate topologies from structural monomers it know 
about - UNK isn't one of their names. Please read chapter 5 of the 
GROMACS manual and try again.

Mark