Tools and information for AMBER and CPPTRAJ examples
Updated: March 26, 2019
Project coordinates along given eigenvectors. projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>] [<mask>] [dihedrals <dataset arg>] [start <start>] [stop <stop>] [offset <offset>] [<name>] Output data set name. evecs <dataset name> Data set containing eigenvectors… Read More
Updated: March 26, 2019
Calculate and optionally align system along principal axes. principal [<mask>] [dorotation] [out <filename>] [name <dsname>] [<mask>] Mask of atoms used to determine principal axes (default all). [dorotation] Align coordinates along principal axes. [out <filename>] Write resulting eigenvalues/eigenvectors to… Read More
Updated: March 26, 2019
Calculate pair-wise non-bonded energies. pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>] [ reference | ref <name> | refindex <#> ] [cutout <cut mol2 prefix>] [vmapout <vdw map>] [emapout <elec map>] [avgout <avg file>] [eout <eout file>]… Read More
Updated: March 26, 2019
Calculate pair distribution function. pairdist out <filename> mask <mask> [delta <resolution>] Calculate pair distribution function. In the following, defaults are given in parentheses. The out keyword specifies output file for histogram: distance, P(r), s(P(r)). The mask option specifies… Read More
Updated: December 17, 2019
Write frames to a trajectory file within a list of Actions. outtraj <filename> [ trajout args ][maxmin <dataset> min <min> max <max>] <filename> Output trajectory file name. [trajout args] Output trajectory arguments (see the trajout command). [maxmin <dataset>… Read More
Updated: February 24, 2024
Define and track “native” contacts as determined by a simple distance cut-off. nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>] … Read More
Updated: September 20, 2023
Perform nucleic acid structure analysis. nastruct [<dataset name>] [resrange <range>] [sscalc] [naout <suffix>] [noheader] [resmap <ResName>:{A,C,G,T,U} …] [calcnohb] [noframespaces] [baseref <file>] … [bpmode {3dna | babcock}]… Read More
Updated: March 26, 2019
Calculate multiple vectors between specified atoms. multivector [<name>] [resrange <range>] name1 <name1> name2 <name2> [out <filename>] [ired] [<name>] Data set name. [resrange <range>] Range of residues to look for vectors in. name1 <name1> Name of first atom in… Read More
Updated: November 19, 2023
Calculate multiple dihedral angles of specified/given types. multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>] [range360] … Read More
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
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