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

[Mark Abraham]

kong.winter wrote:
> Hi all,
> when I use the following command:"pdb2gmx -f 1G1T.pdb -p gr.top -o gr.gro"
> There's a fatal error:
> Residue 'SIA' not found in residue topology database
>  
> I checked the PDB file, the following details:
> HET           SIA  C 601      20
> HETNAM     SIA O-SIALIC ACID
> FORMUL     2  SIA    C11 H19 N1 O9
> ..........
>  
>  
> Who knows how to solve it?
> Any tip is appreciated, thank you very much.

This means what it says: the force field you're using doesn't have an
entry for residue SIA, which is apparently sialic acid. If you want to
simulate with this molecule in the system, you'll need to develop a
topology for it (and maybe parameters - this is not encouraged for
newcomers), and put that into the .rtp file (read chapter five).
Otherwise, delete it from your .pdb file.

Mark