[gmx-users] special molecule

[Mark Abraham]

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