Tools and information for AMBER and CPPTRAJ examples
Updated: September 30, 2025
Calculate the RMSD of dihedrals to dihedrals in a reference structure. Not to be confused with multidihedral dihedralrms [<name>] <dihedral types> [out <file>] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm… Read More
Category: Action Commands, CPPTRAJ
Updated: November 11, 2023
Keep specified atoms in system. keep [ bridgedata <bridge data set> [nbridge <#>] [nobridgewarn] [bridgeresname <res name>] bridgeresonly <resrange>] ] [keepmask <atoms to keep>] [charge <new charge>] … Read More
Category: Action Commands, CPPTRAJ
Updated: September 23, 2023
Align structure to a reference. align <mask> [<refmask>] [move <mask>] [mass] [ first | reference | ref <name> | refindex… Read More
Category: Action Commands, CPPTRAJ
Updated: September 17, 2025
Calculate radial distribution function. radial [out <outfilename>] <spacing> <maximum> <solvent mask1> [<solute mask2>] [noimage] [mass] [density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf <file>] [{{center1|center2|nointramol|toxyz <x>,<y>,<z>} | … Read More
Updated: March 25, 2019
Calculate the number of waters in the first and second solvation shells based on distance critera. watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper cut>] [noimage] [<solventmask>] <solutemask> Atom mask corresponding to solute of interest (required). [out… Read More
Updated: March 25, 2019
Calculate unit cell volume. volume [<name>] [out <filename>] <name> Data set name. out <filename> Output file name.
Updated: March 25, 2019
Create volumetric map for specified coordinates; similar to grid but takes into account atomic radii. Similar to VMD volmap. volmap filename dx dy dz <mask> [radscale <factor>] { data <existing set> | name <setname> { size <x,y,z> [center… Read More
Updated: March 25, 2019
Calculate velocity autocorrelation function. velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout <file>] [maxlag <frames>] [tstep <timestep>] [direct] [norm] [<set name>] Data set name. [<mask>] Atoms(s) to calculate velocity autocorrelation (VAC) function for. [usevelocity] Use velocity information in… Read More
Updated: November 20, 2024
Calculate various types of vector quantities. vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>] [magnitude] [geom] [ired] [gridset <grid>] [debye] <Type> = { mask | minimage | dipole | center | corrplane | box | boxcenter | ucellx… Read More
Updated: May 12, 2023
Reverse of image; unwrap selected atoms so they have continuous trajectories. unwrap [center] [{bymol | byres | byatom}] [ reference | ref <name> | refindex <#> ] [<mask>] [center]… Read More
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