mdload

Load protein and spin label data from molecular dynamics simulation trajectory output files.

Syntax

MD = mdload(TrajFile,TopFile,Info);
MD = mdload(TrajFile,TopFile,Info,Opt);

Description

This function loads spin label frame data with and without protein global rotational diffusion, rotation matrices representing the protein's orientation, and spin label side chain dihedral angles data from molecular dynamics (MD) simulation trajectory output files.

Input: Trajectory file information

TrajFile is the trajectory filename or set of filenames to be loaded. If TrajFile is just a file name without a directory (e.g. 'TrajFile1.DCD'), mdload looks for it in Matlab's current directory. TrajFile can also include the full path to the file (e.g. C:\mydata\sample5\TrajFile1.DCD'). For multiple trajectory files, TrajFile can be set to a cell array containing character arrays as entries (e.g. {'TrajFile1.DCD','TrajFile2.DCD'}).

TopFile is the name of the topology input file. Please specify the full path.

Formats are identified by the extension of the file name specified in TrajFile and TopFile. The following MD simulation programs, their default output trajectory file extensions, and their input topology file extensions are supported:

MD program	Trajectory file extension	Topology file extension
NAMD	`DCD`	`PSF`
CHARMM	`DCD`	`PSF`

Input: Topology information

Info is a structure containing information regarding the structure and organization of the MD trajectory data.

SegName

Name of the segment in TopFile assigned to the spin-labeled protein.

ResName

Name of the residue in TopFile assigned to the spin-label, e.g. 'CYR1' is the default name given to R1 by CHARMM-GUI.

LabelName

Name of the spin label in TopFile, either 'R1' (default) or 'TOAC'.

AtomNames

A structure containing the names of the spin label's individual atoms used by TopFile.

For R1, the atom names should be given as the following fields: ONname, NNname, C1name, C2name, C1Rname, C2Rname, C1Lname, S1Lname, SGname, CBname, CAname, Nname.
For TOAC, the required atom names are ONname, NNname, CGSname, CGRname, CBSname, CBRname, CAname, Nname.

Input: Output options

Opt is a structure containing options regarding the output of mdload. The field Verbosity controls whether or not mdload will display messages to the console regarding its progress. Since MD simulation trajectory output files can be quite large (several gigabytes), loading and processing their data can be time-consuming, and Verbosity is set to 1 by default.

Output: Processed MD data

MD is a structure containing all output from mdload, including all raw and processed data that can be used by cardamom to simulate an EPR spectrum.

nSteps

Number of snapshots in the MD simulation output.

dt

Time step between snapshots, in seconds.

RProtDiff

An array of size 3x3xnTrajxnSteps containing the rotation matrices representing the global rotational diffusion of the protein.

FrameTraj

An array of size 3x3xnTrajxnSteps containing the cartesian coordinates of the spin label tensor frame's x-, y-, and z-coordinate frame axis vectors with respect to the MD simulation box frame, in Å.

FrameTrajwrtProt

Same as FrameTraj, but without global rotational diffusion of the host protein, in Å.

Examples

To load and process a DCD trajectory file myTraj.DCD generated by NAMD, with a PSF topology input file myTop.PSF, use

TrajFile = 'myTop.DCD';
TopFile = 'myTop.PSF';
Info.ResName = 'CYR1';
Info.SegName = 'PROA';
MD = mdload(TrajFile,TopFile,Info);