nativecontacts
Define and track “native” contacts as determined by a simple distance cut-off. nativecontacts [<mask1> [<mask2>]] [writecontacts <outfile>] [resout <resfile>] … Read More
Tools and information for AMBER and CPPTRAJ examples
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
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
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