Module: secondarystructure
| Description | Usage |
|---|---|
| variables for detecting the degree of secondary structure in a protein | |
| Authors: Gareth Tribello |   |
Details
The variables within this module can be used to detect the presence of secondary structure elements such as alpha helices or parallel and antiparallel beta sheets in a protein.
Notice that the ALPHARMSD, ANTIBETARMSD and PARABETARMSD are implemented as shortcuts. In other words, the only non shortcut action in this module is the SECONDARY_STRUCTURE_RMSD that calculates the RMSD distance between each segement of residue and the idealised version of secondary structure element. This structure makes it easy to add additional CVs that work similarly to the ALPHARMSD, ANTIBETARMSD and PARABETARMSD either directly in the input file or by adding a new shortcut action.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| ALPHARMSD | Probe the alpha helical content of a protein structure. | COLVAR |
| ANTIBETARMSD | Probe the antiparallel beta sheet content of your protein structure. | COLVAR |
| PARABETARMSD | Probe the parallel beta sheet content of your protein structure. | COLVAR |
| SECONDARY_STRUCTURE_DRMSD | Calclulate the DRMSD between segments of a protein and a reference structure of interest | MCOLVAR |
| SECONDARY_STRUCTURE_RMSD | Calclulate the RMSD between segments of a protein and a reference structure of interest | MCOLVAR |
References
More information about this module is available in the following articles: