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?

Where's the problem? pdb2gmx makes a .top file for your non-special system, you #include the .itp file for your special part. There's nothing about atomic positions yet.... have a look at a .top file. Now grompp takes the .top and some file with atomic positions and makes a .tpr file. Same general procedure as normal.

Mark
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