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.
The free component of the AMBER molecular dynamics package, 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 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.