Anyone working on molecular modeling soon realizes that atomic structures sometimes contain errors. Some of these errors can generate quite dramatic effects when the structures are simulated using molecular dynamics techniques. For example, an incorrect cis peptide bond in an alpha helix that disrupts the hydrogen bonding network can lead to the unfolding of the helix. Furthermore, MD force fields do not contain terms that prevent changes in chirality, so simulations where large forces are applied may introduce chirality errors.
To address these issues, we have recently added two new plugins to the development version of VMD: cispeptide and chirality (written by Leonardo Trabuco and Eduard Schreiner). They can be used to identify, visualize, and fix certain structure errors. The plugins can also be used to prevent such errors from occurring in certain kinds of MD simulations, as exemplified in the MDFF tutorial. We just posted a new tutorial that explains how to use these new plugins.
The cispeptide plugin identifies all cis peptide bonds in a protein structure and displays them graphically. The user can change any of the cis peptide bonds to the more common trans configuration if needed. To achieve that while still providing a physically sound structure, an actual molecular dynamics simulation is performed from within VMD by making use of an updated version of the AutoIMD plugin, which interfaces with our molecular dynamics simulation software NAMD.
The chirality plugin works in a very similar way, identifying all unusual configuration in chiral centers of proteins and nucleic acids. The user can also easily display the identified errors and correct them from within VMD.
Please give these new plugins a try and let us know what you think. Enjoy!