secstruct

Calculate secondary structure content using the DSSP algorithm

secstruct [<name>] [out <filename>] [<mask>] [sumout <filename>][assignout <filename>] [totalout <filename> [ptrajformat] [betadetail] [namen <N name>] [nameh <H name>] [nameca <CA name>][namec <C name>] [nameo <O name>]

[<name>] Output data set name.
[out <filename>] Output file name for secondary structure vs time.
[<mask>] Atom mask in which residues should be looked for.
[sumout <sumfilename>] Write average secondary structure values for each residue to <sumfilename>; if not specified <filename>.sum is used.
[assignout <filename>] Write overall secondary structure assignment (based on dominant secondary structure type for each residue) to file.
[ptrajformat] Write secondary structure as a string of characters for each frame, similar to ptraj output.
[betadetail] Record anti-parallel beta and parallel beta in place of extended and bridge secondary structure. If a residue could be both only anti-parallel is reported.
[namen <N name>] Backbone amide nitrogen atom name (default ’N’).
[nameh <H name>] Backbone amide hydrogen atom name (default ’H’).
[nameca <CA name>] Backbone alpha carbon atom name (default ’CA’).
[namec <C name>] Backbone carbonyl carbon atom name (default ’C’).
[nameo <O name>] Backbone carbonyl oxygen atom name (default ’O’).
[namesg <SG name>] Cysteine sulfur atom name, used to ignore disulfide connectivity (default ‘SG’).

Data Sets Created:
<name>[res] Residue secondary structure per frame; index corresponds to residue number. If ptrajformat specified these will be characters, otherwise integers (see table below).
<name>[avgss] Average of each type of secondary structure; index corresponds to secondary structure type (see table below; no index for “None”).
<name>[None] Total fraction of residues with no structure vs time.
<name>[Para] Total fraction of residues with parallel beta structure vs time.
<name>[Anti] Total fraction of residues with anti-parallel beta structure vs time.
<name>[3-10] Total fraction of 3-10 helical structure vs time.
<name>[Alpha] Total fraction of alpha helical structure vs time.
<name>[Pi] Total fraction of Pi helical structure vs time.
<name>[Turn] Total fraction of turn structure vs time.
<name>[Bend] Total fraction of bend structure vs time.

As of version 4.18.0, this command now produces output that better conforms with the original deinitions in Kabsch and Sander; namely that Extended beta (i.e. 2 or more consecutive beta bridges of the same type) and beta Bridge (i.e. an isolated beta bridge) are now reported instead of anti-parallel and parallel beta. To restore the original behavior the betadetail keyword must be specified

Note that when not using ptraj format, data sets are not generated until run is called.

Calculate secondary structural propensities for residues in <mask> (or all solute residues if no mask given) using the DSSP method of Kabsch and Sander, which assigns secondary structure types for residues based on backbone amide (N-H) and carbonyl (C=O) atom positions. By default CPPTRAJ assumes these atoms are named
“N”, “H”, “C”, and “O” respectively. If a different naming scheme is used (e.g. amide hydrogens are named “HN”) the backbone atom names can be customized with the nameX keywords (e.g. ’nameH HN’). Note that it is expected that some residues will not have all of these atoms (such as proline); in this case CPPTRAJ will print an informational message but the calculation will proceed normally.

Results will be written to filename specified by out with format:

<#Frame>     <ResX SS>     <ResX+1 SS>     ...     <ResN SS>

where <#Frame> is the frame number and <ResX SS> is an integer representing the calculated secondary structure type for residue X. If the keyword ptrajformat is specified, the output format will instead be:

<#Frame>     STRING

where STRING is a string of characters (one for each residue) where each character represents a different structural type (this format is similar to what ptraj outputs). The various secondary structure types and their corresponding integer/character are listed below:

Average structural propensities over all frames for each residue will be written to the file specified by sumout (or “<filename>.sum” if sumout is not specified). The total structural propensity over all residues for each secondary structure type will be written to the file specified by totalout. If assignout is specified, the overall secondary structure assignment for each residue will be printed in two line chunks of 50 residues, with the first line containing the residue number the line starts with and one character residue names, and the second line containing secondary structure assignment using DSSP-style characters, like so:

1 KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNTRn
      SSS   TH HHHTTSBBBB TTTBBBB SS     S

The output of secstruct command is amenable to visualization with gnuplot. To generate a 2D map-style plot of secondary structure vs time, with each residue on the Y axis simply give the output file a “.gnu” extension.

For example, to generate a 2D map of secondary structure vs time, with different colors representing different secondary structure types for residues 1-22:

secstruct :1-22 out dssp.gnu

The resulting file can be visualized with gnuplot: gnuplot dssp.gnu Similarly, the sumout file can be nicely visualized using xmgrace (use “.agr” extension).

secstruct :1-22 out dssp.gnu sumout dssp.agr

Values of dgbulk and dhbulk for different water models can be calculated from pure water simulations with the purewater keyword.