[Lambin]

I'm doing undergraduate research with my professor at my university on computational chemistry and my task is to run energy minimization calculations with molecular mechanics for the protein, fibronectin. I'm using TINKER for energy calculations, however, it requires a third-party molecular editor that can generate coordinate files (i.e. .xyz, .pdb, etc.) in the appropriate file format. Is there someone with experience with computational chemistry? I'm interested in building coordinates for this particular peptide sequence,

YAVTGRGDSPASSKPISINYRTEIG KPSQMC

The problem is that I can't find a decent molecular editor, if there is one that I could just input the peptide sequence without having to manually construct it that would be very helpful.

[tamim83]

Try Avogadro: http://avogadro.openmolecules.net/wiki/Main_Page

It has a peptide builder, all you do is select the amino acids you want and a few other parameters, and it generates it for you.  Then you can save it as an .xyz or another file format.  It is also free. 

Good Luck 

[Lambin]

Thank you for your suggestion, Tamim. I like Avogadro and I was able to do the construction I intended.