This repository contains a collection of scripts and resources for setting up and performing Molecular Dynamics Simulations of peptoids (oligomers of N-substituted glycine). Most of the tools were developed over the course of my dissertation research at New York University.
The broadest workflow supported by these tools is as follows:
- Look up peptoid residues from the Peptoid Data Bank (databank.peptoids.org) and save their associated SMILES string representation to individual files
- Generate capped monomer models of these residues and save them as .pdb files
- Generate Amber prepin files of these models for use with GAFF
- Generate Amber input files (topology and coordinate files) from some starting models containing peptoid residues.
The python script build_models.py depends on the rdkit package.
Scripts are also included for performing crystal structure analysis relevant to peptoid structures using the CSD python API from Cambridge Crystallographic Data Centre.