[gmx-users] PDB and GRO files

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jul 25 01:30:40 CEST 2009

Jim Kress wrote:
> Try Openbabel.  
> http://openbabel.org/wiki/Main_Page
> It intercoverts most file types so, you could build your molecule with any
> of the 3D model builders that serve as front ends to Quantum Chemistry
> programs.  Export it as an XYZ file and then use Openbabel to convert it to
> a pdb format.  Some will even export pdb formatted files.
> For that matter, you could use ArgusLab to build your protein and/ or import
> it from a known pdb file database.  If you choose to build your protein, it
> will export it in a pdb format.  If you download one from a database,
> obviously you can save it in a pdb format.
> ArgusLab is also specifically designed to make building proteins simpler
> (not simple - just simpler) with a built-in library of amino acids in
> fragment forms that can be connected to create the protein of your choice
> along with side chain fragments, solvation species, etc.
> http://www.arguslab.com/
> Highly recommended.

Wikified, thanks. 


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