PrepareForLeap: An automated tool for fast PDB-to-parameter generation

Published

March 23, 2022

Author(s)

Daniel R. Roe, Christina Bergonzo

Abstract

Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several forms which can be linked in a variety of ways. Here we present a stand-alone tool implemented in the widely-used software CPPTRAJ that can be used to automate building structures and generating a "ready to run" parameter and coordinate file pair. This tool automatically identifies carbohydrate form, chirality, linkage, and functional groups, and performs topology modifications (e.g. renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.

Citation

Journal of Computational Chemistry

Pub Type

Journals

Download Paper

https://doi.org/10.1002/jcc.26847

Local Download

Keywords

Molecular dynamics, System preparation, Amber, CPPTRAJ, Carbohydrates

Citation

Roe, D. and Bergonzo, C. (2022), PrepareForLeap: An automated tool for fast PDB-to-parameter generation, Journal of Computational Chemistry, [online], https://doi.org/10.1002/jcc.26847, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=934240 (Accessed October 8, 2025)