Scripts to help with setting up molecular dynamics simulations.
gzmat_to_polymod.py (docs)
Convert a Gaussian gzmat file (infile) for a monomer with nbackbone backbone atoms to a Z-matrix file for use with NanoHUB Polymer Modeler. Gaussian gzmat files can be created from other types of structure files using Open Babel. See this post.
CHARMM-GUI_PLA_to_PLGA (docs)
Convert polylactic acid built with CHARMM-GUI Polymer Builder to poly(lactic-co-gylcolic acid) 50:50. Could easily be extended to arbitrary ratios of monomer types. Also see this post.
LigninBuilder_GROMACS (docs)
Build chosen library(ies) that come with LigninBuilder, sort structures by number of monomers, create GROMACS .top files for structures with desired sizes, energy minimize structures with GROMACS. Also see this post.