Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 43, Issue 13, Pages 930-935Publisher
WILEY
DOI: 10.1002/jcc.26847
Keywords
Amber; carbohydrates; CPPTRAJ; molecular dynamics; system preparation
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Funding
- National Heart, Lung and Blood Institute (NHLBI) of the National Institutes of Health [NHLBI Z01 HL001051-23]
- NIST Biomanufacturing Program
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This tool can automatically identify various properties of carbohydrates and generate the necessary commands and files, simplifying the complexity of setting up molecular dynamics simulations from experimentally determined structures.
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 anomer types 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 anomer type, configuration, 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.
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