Tools and information for AMBER and CPPTRAJ examples
Updated: March 26, 2019
Perform grid inhomogenous solvation theory. gist [doorder] [doeij] [skipE] [refdens <rdval>] [temp <tval>] [noimage] [gridcntr <xval> <yval> <zval>] [griddim <xval> <yval> <zval>] [gridspacn <spaceval>] [prefix <filename prefix>] [ext <grid extension>] [out <output>] [info <info>] [doorder] Calculate the water… Read More
Updated: April 12, 2023
Fix atom ordering so that all atoms in molecules are sequential. fixatomorder [outprefix <prefix>] [nobox] [parmout <filename>] [parmopts <comma-separated-list>] … Read More
Updated: April 12, 2023
Filter frames for subsequent Actions using data sets and user defined criteria. filter {<dataset arg> min <min> max <max> …} [out <file> [name <setname>]] {[multi] | [filterset <set> [newset <newname>]] [countout <countfile>]}… Read More
Updated: April 6, 2023
Calculate energies using via SANDER; requires compilation with the SANDER API. esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles] [<namelist vars> …] [<name>] Data set name. [out <filename>] File to write results to. [saveforces] If specified, save forces… Read More
Updated: August 3, 2023
Calculate simple bond, angle, dihedral, and non-bonded energy terms (no PME). energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]] [bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]} [{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}] [ etype { simple |… Read More
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
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