[gmx-users] First question.

[Ivan R. Judson]

Hi,

I'm just getting started with gromacs. Here's what I'm trying to do: I have a molecule in mdl .mol format and I want to use it in
the gmxdemo instead of the cpeptide.pdb. Clearly, I have to convert it to PDB before I can do that. I used babel to convert, it
succeeds but it labels all the residues UNK. This isn't really a problem, since I don't care about those for this process anyhow,
however, pdb2gmx dies fatally when it sees UNK.

Is there a way to make pdb2gmx ignore the UNK's or convert directly from .mol to .gro?

Thanks for your suggestions.

--Ivan