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.
http://oldwiki.gromacs.org/index.php/Coordinate_File#Sources
Mark
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