Tools and information for AMBER and CPPTRAJ examples
Updated: March 26, 2019
Calculate the RMSD of distance pairs within selected atoms. drmsd [<dataset name>] [<mask> [<refmask>]] [out <filename>] [ first | ref <refname> | refindex <#> | reftraj <trajname> [parm <trajparm> | parmindex <parm#>] ] [<dataset name>] Output data set… Read More
Updated: November 1, 2023
Calculate the distance between two points. distance [<name>] <mask1> [<mask2>] [point <x> <y> <z> ] [ reference | ref | refindex <#> ] [out <filename> ] [geom] [noimage] [type noe] Options for ’type noe’: [bound <lower> bound <upper>]… Read More
Updated: March 26, 2019
Bin dipoles of solvent molecules in 3D grid. Not well tested, may be obsolete. dipole <filename> {data <dsname> | <nx> <dx> <ny> <dy> <nz> <dz> [gridcenter <cx> <cy> <cz>]} [box|origin|center <mask>] [negative] [name <gridname>] <mask1> {origin | box}… Read More
Updated: September 22, 2023
Calculate the dihedral angle using four points. dihedral [<name>] <mask1> <mask2> <mask3> <mask4> [out <filename>] [mass] [type {alpha|beta|gamma|delta|epsilon|zeta|chi|c2p|h1p|phi|psi|omega|pchi}] [range360] [<name>] Output data… Read More
Updated: March 26, 2019
Calculate translational diffusion of molecules. Note that although the syntax for diffusion has changed as of version 16, the old syntax is still supported. diffusion [{out <filename> | separateout <suffix>}] [time <time per frame>] [noimage] [<mask>] [<set name>]… Read More
Updated: March 27, 2019
Calculate density along a coordinate. density [out <filename>] [name <set name>] [delta <resolution>] [x|y|z] [number|mass|charge|electron] [efile <filename>] <mask1> … <maskN> out Output file for histogram: relative distances vs. densities for each mask. delta Resolution, i.e. determines number of… Read More
Updated: March 26, 2019
Create a structure reservoir for use with reservoir REMD simulations. createreservoir <filename> ene <energy data set> [bin <cluster bin data set>] temp0 <temp0> iseed <iseed> [velocity] [parm <parmfile> | parmindex <#>] [title <title>] <filename> File name of the… Read More
Updated: March 26, 2019
Create a COORDS data set from input frames. createcrd [<name>] [ parm <name> | parmindex <#> ] This command creates a COORDS data set named <name> using trajectory frames that are associated with the specified topology. For example,… Read More
Updated: March 27, 2019
Older version of nativecontacts, retained for backwards compatibility. contacts [ first | reference | ref <ref> | refindex <#> ] [byresidue] [out <filename>] [time <interval>] [distance <cutoff>] [<mask>] NOTE: Users are encouraged to try the nativecontacts command, an… Read More
Updated: March 27, 2019
Assign frames into clusters based on binning of backbone dihedral angles in amino acids. clusterdihedral [phibins <N>] [psibins <M>] [out <outfile>] [dihedralfile <dfile> | <mask>] [framefile <framefile>] [clusterinfo <infofile>] [clustervtime <cvtfile>] [cut <CUT>] Cluster frames in a trajectory… Read More
Copyright © 2024 · All Rights Reserved · AMBER-hub
Theme: Structure Lite by Organic Themes