Tools and information for AMBER and CPPTRAJ examples
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
Updated: March 27, 2019
Retain only the specified number of solvent molecules closest to specified solute. closest <# to keep> <mask> [noimage] [first | oxygen] [center][closestout <filename>] [name <setname>] [outprefix <parmprefix>][parmout <file>] <# to keep> Number of solvent molecules to keep around… Read More
Updated: March 27, 2019
Report chirality around alpha carbons in amino acids (L, D). checkchirality [<name>] [<mask>] [out <filename>] [<name>] Data set name. [<mask>] Atoms to check. [out <filename>] File to write results to. DataSet Aspects: [L] Number of frames ’L’ for… Read More
Updated: March 27, 2019
Check for bad atomic overlaps or bond lengths. Can be used to skip corrupted frames. check [<mask>] [around <mask2>] [reportfile <report>] [noimage] [skipbadframes] [offset <offset>] [cut <cut>] [nobondcheck] [silent] [<mask>] Check structure of atoms in <mask> (all if not… Read More
Updated: June 12, 2020
Center specified coordinates to box center or onto reference structure. center [<mask>] [origin] [mass] [ reference | ref <name> | refindex <#> [<refmask>]] [<mask>] Center based on atoms in mask; default is all atoms. [origin] Center to origin… Read More
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