From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Nov 24 2014 - 10:54:04 CST

I think you could use the solvate plugin, with the amino acids as custom
solvent.
Also, perhaps you will find http://www.ime.unicamp.br/~martinez/packmol/
useful.

Best regards,
Ajasja