[gmx-users] pdb2gmx: Adding non standard residues and molecular moieties

[Mark Abraham]

Eddie Mende wrote:
> Greetings
> 
> I am trying to generate a topology file, and
> need to add the phosphate ion in my pdb
> 
> How to do this?

Check out http://wiki.gromacs.org/index.php/Parameterization and maybe 
http://wiki.gromacs.org/index.php/Exotic_Species

Generating a sensible topology is much harder than generating a starting 
structure.

Mark