[gmx-users] best software to design molecules?

[Xavier Periole]

To create a protein from scratch I am not sure. I just
took a look and di not find anything straighforward. But
you can load a protein and delete residues and create
others or mutate. So yes you can build up a protein. 

For non biochem molecules, I am affraid it is not possible.
I think only proteins and DNA are defined. But check the 
web site, who knows ?? 
http://us.expasy.org/spdbv/

Xavier