What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.




You have several options to generate smaller peptides using the peptide builders in 


* [Avogadro](http://avogadro.cc/wiki/Tutorials:Insert_a_Peptide) or
* [PyMol](http://www.pymolwiki.org/index.php/Peptide_Sequence)


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The free component of the [AMBER molecular dynamics package](http://ambermd.org/), AmberTools, contains a very nice interface (`tleap`) for automatically generating coordinates of peptides and proteins from a sequence of three-letter amino acid codes. There's a [tutorial](http://ambermd.org/tutorials/basic/tutorial0/) on how to build and simulate a peptide using AMBER, but you don't have to run the dynamics. You can use the peptide building functionality on its own. It exports a pretty standard PDB file once you're done.


You could write a Python script that generates the `tleap` input, or if the peptide is short enough, write a `tleap` script with the three-letter amino acid codes by hand.


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