Can also be used to get min/max distances between groups of atoms. Cannot do partial surface areas.Ĭalculate multiple dihedral angles of specified/given types.Ĭalculate multiple vectors between specified atoms.Ĭalculate native contacts within a region or between two regions using a given reference. Good for distance-based masks.Ĭalculate a matrix of the specified type from input coordinates.Ĭalculate minimum non-self imaged distance between atoms in specified masks.Ĭalculate Connolly surface area of specified atoms. Print the results of selection by specified atom mask. Modify structure by applying dihedral values to specified residues. Split/average frames from LES trajectories.Ĭalculate linear interaction energy between user-specified ligand and surroundings.Ĭalculate order parameters for lipids in planar membranes.Ĭalculate lipid order parameters SCD(||) for lipid chains. The autoimage command typically provides better results.Ĭalculate J-coupling values from specified dihedral angles. Perform grid inhomogenous solvation theory.Ĭalculate hydrogen bonds using geometric criteria. Not well tested, may be obsolete.Ĭalculate the distance between two points.Ĭalculate the RMSD of distance pairs within selected atoms.Ĭalculate secondary structure content using the DSSP algorithmĬalculate simple bond, angle, dihedral, and non-bonded energy terms (no PME).Ĭalculate energies using via SANDER requires compilation with the SANDER API.įilter frames for subsequent Actions using data sets and user defined criteria.įix atom ordering so that all atoms in molecules are sequential.įix bonds which have been split across periodic boundaries by imaging. Older version of nativecontacts, retained for backwards compatibility.Ĭreate a COORDS data set from input frames.Ĭreate a structure reservoir for use with reservoir REMD simulations.Ĭalculate translational diffusion of molecules.Ĭalculate the dihedral angle using four points.Ĭalculate the RMSD of dihedrals to dihedrals in a reference structure.īin dipoles of solvent molecules in 3D grid. Retain only the specified number of solvent molecules closest to specified solute.Īssign frames into clusters based on binning of backbone dihedral angles in amino acids. Report chirality around alpha carbons in amino acids (L, D). Set or overwrite box information for frames.Ĭenter specified coordinates to box center or onto reference structure.Ĭheck for bad atomic overlaps or bond lengths. Can be used to skip corrupted frames. Use vector center (optionally with keyword magnitude) instead.Ĭalculate the min/max coordinates for specified atoms. CommandĬalculate the angle between three points.Ĭalculate area per molecule for molecules in a specified plane.Ĭalculate average correlation between motions of specified atoms.Ĭalculate root mean square fluctuation of specified atoms/residues.Īttempt to create a map between atoms in molecules with different atom ordering.Ĭalculate average unit cell (box), primarily for unwrapping NPT trajectories. If an Action may modify coordinate/topology information for subsequent Actions it is denoted with an X in the Mod column. the number of atoms and the ordering of selected atoms must be the same. rms, drmsd, symmrmsd, etc.) there must be a 1 to 1 correspondence between the atoms in each mask, i.e. Note that for commands which can use a reference mask as well as a target mask (e.g. The first rms command will be valid, but the second rms command will not since all residues named WAT are removed from the state by the strip command. For example, given a solvated system with water residues named WAT and the following Action commands: rmsd R1 first :WAT out water-rmsd.dat When a frame is modified by an Action, it is modified for every Action that follows them during trajectory processing. However, Actions can be executed immediately on COORDS data sets via the crdaction command. Unlike some other command types, when an Action command is issued it is by default added to the Action queue and is not executed until trajectory processing is started (e.g. Some Action commands in CPPTRAJ have extra functionality compared to ptraj (such as the per-residue RMSD function of the rmsd Action, or the ability to write out stripped topologies for visualization in the strip Action), while other Actions produce slightly different output (like the hbond/ secstruct Actions). Most Actions in CPPTRAJ function exactly the way they do in ptraj and are backwards-compatible. Commands to perform analysis on frames and topology.Īctions in CPPTRAJ operate on frames read in by the trajin or ensemble commands one at a time and extract derived data, modify the coordinates/topology in some way, or both.
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