The Theoretical and Computational Biophysics Group (TCBG) is pleased to announce the release of the "Structure Check" tutorial. The purpose of this tutorial is to demonstrate how to use the VMD plugins cispeptide and chirality together with AutoIMD to ensure proper structure of peptide bonds and correct stereochemistry of proteins and nucleic acids. The described plugins are designed to work with proteins and nucleic acids and understand atom names as used by the force fields CHARMM and AMBER as well as the standard PDB naming convention for non-hydrogen atoms. The plugins can also be used to prevent these errors from occuring in simulations with NAMD.

The tutorial consists of a text in pdf format, and files required for the tutorial, available below. The TCBG software programs VMD and NAMD are also required for the tutorial.

Structure Check (pdf, 628k) (required tutorial files [.tar.gz, 762k], [.zip, 753k], individual files)

See the tutorials page for more tutorials using VMD and NAMD, and our case studies studies page for more in-depth explorations of scientific topics using our software.