Coordinates (COORDS) Data Set Commands


Coordinate I/O tends to be the most time-consuming part of trajectory analysis. In addition, many types of analyses (for example two-dimensional RMSD and cluster analysis) require using coordinate frames multiple times. To simplify this, trajectory coordinates may be saved as a separate data set via the loadcrd command or createcrd action. Any action can then be performed on the COORDS data set with the crdaction command. The crdout command can be used to write coordinates to an output trajectory (similar to trajout).

Although COORDS data sets store everything internally with single-precision, they can still use a large amount of memory. Because of this there is a specialized type of COORDS data set called a TRAJ data set (trajectory), which functions exactly like a COORDS data set except all data is stored on disk. TRAJ data sets can be created with the loadtraj command. TRAJ data sets cannot be modified.

There are several analyses that can be performed using COORDS data sets, either as part of the normal analysis list or via the runanalysis command. Note that while these analyses can be run on specified COORDS data sets, if one is not specified a default COORDS data set will be created, made up of frames from trajin commands.

As an example of where this might be useful is in the calculation of atomic positional fluctuations. Previously this required two steps: one to generate an average structure, then a second to rms-fit to that average structure prior to calculating the fluctuations. This can now be done in one pass with the following input:

parm topology.parm7
# Generate average structure PDB, @CA only
crdaction average avg.pdb @CA
# Load average structure PDB as reference
parm avg.pdb
reference avg.pdb parm avg.pdb
# RMS-fit to average structure PDB
crdaction rms reference @CA
# Calculate atomic fluctuations for @CA only
crdaction atomicfluct out fluct.dat bfactor @CA

The following COORDS data set commands are available:

Command Description
catcrd Concatenate two or more COORDS sets.
combinecrd Combine two or more COORDS sets.
crdaction Run a single Action on a COORDS set.
crdout Write a COORDS set to a file.
crdtransform Transform a COORDS set to a file.
createcrd (Action) Create a COORDS set during a run.
emin Run simple energy minimization on a frame of a COORDS set.
extendedcomp Calculate extended comparison similarity values for each frame in COORDS set.
graft Graft part of one COORDS set onto another COORDS set.
loadcrd Create or append to a COORDS set from a file.
loadtraj Create special COORDS set where frames remain on disk.
permutedihedrals Rotate specified dihedral(s) in given COORDS set by specific interval or to random values.
prepareforleap Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber.
reference Load a single trajectory frame as a reference.
rotatedihedral Rotate specified dihedral to specified value orĀ  by given increment.
sequence Create a new molecule from a sequence of COORDS sets.
splitcoords Split molecules in a COORDS set into a trajectory.
zmatrix Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set.