I think you can use editconf to convert your original pdb to a gro file.
On Mon, 2006-06-12 at 13:48 +0000, Tamas Horvath wrote:
> As I understand, if there are "special" molecules in a pdb file,
> pdb2gmx cannot convert it. However, PRODRG can create an *.itp file
> for that molecule, so that I can include it in the generated topology
> file. But how can I place the molecule in it's original position? Or
> even better, how can I convert the original ("full") .pdb file for
> gromacs?
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