Tools and information for AMBER and CPPTRAJ examples
Updated: March 26, 2019
Calculate Connolly surface area of specified atoms. molsurf [<name>] [<mask>] [out filename] [probe <probe_rad>] [radii {gb | parse | vdw}] [offset <rad_offset>] [<name>] Name of surface area data set. [<mask>] Atoms to calculate surface area of. [out <filename>]… Read More
Updated: March 26, 2019
Calculate minimum non-self imaged distance between atoms in specified masks. minimage [<name>] <mask1> <mask2> [out <filename>] [geom] [maskcenter] <name> Data set name. <mask1> First atom mask. <mask2> Second atom mask. out <filename> File to write to. geom (maskcenter… Read More
Updated: March 26, 2019
Calculate a matrix of the specified type from input coordinates. matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>] [name <name>] [ byatom | byres [mass] | bymask [mass] ] [ ired [order <#>] ] [ {distcovar |… Read More
Updated: November 11, 2023
Print the results of selection by specified atom mask. Good for distance-based masks mask <mask> [maskout <filename>] [out <filename>] [nselectedout <filename>] [name <setname>] [ {maskpdb <filename> | maskmol2… Read More
Updated: March 26, 2019
Modify structure by applying dihedral values to specified residues. makestructure <List of Args> Apply dihedrals to specified residues using arguments found in <List of Args>, where an argument is 1 or more of the following arg types: <sstype… Read More
Updated: March 26, 2019
Calculate order parameters for lipids in planar membranes. order out <filename> [x|y|z] [scd] [unsat <mask>][taildist <filename> [delta <resolution>] tailstart <mask> tailend <mask>] <mask0> … <maskN> out Output file for order parameters: Sx, Sy, Sz (each succeeded by the… Read More
Updated: December 18, 2023
Calculate linear interaction energy between user-specified ligand and surroundings. lie [<name>] <Ligand mask> [<Surroundings mask>] [out <filename>] [nopbc] [noelec] [novdw] … Read More
Updated: March 26, 2019
Split/average frames from LES trajectories. lessplit [out <filename prefix>] [average <avg filename>] <trajout args> [out <filename prefix>] Write split LES trajectories to <filename prefix>.X, where X is an integer. [average <avg filename>] Write trajectory of averaged LES regions… Read More
Updated: March 26, 2019
Calculate J-coupling values from specified dihedral angles. jcoupling <mask> [outfile <filename>] [kfile <param file>] [out <filename>] [name <dsname>] <mask> Atom mask in which to search for dihedrals within. [outfile <filename>] File to write j-coupling values to with fixed… Read More
Updated: March 26, 2019
Re-image coordinates. image [origin] [center] [triclinic | familiar [com <commask>]] [<mask>] [ bymol | byres | byatom ] [xoffset <x>] [yoffset <y>] [zoffset <z>] [origin] Image to coordinate origin (0.0, 0.0, 0.0); default is to image to box… Read More
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