lie
Calculate linear interaction energy between user-specified ligand and surroundings. lie [<name>] <Ligand mask> [<Surroundings mask>] [out <filename>] [nopbc] [noelec] [novdw] … Read More
Tools and information for AMBER and CPPTRAJ examples
Updated: December 18, 2023
Calculate linear interaction energy between user-specified ligand and surroundings. lie [<name>] <Ligand mask> [<Surroundings mask>] [out <filename>] [nopbc] [noelec] [novdw] … Read More
Updated: March 26, 2019
Split/average frames from LES trajectories. lessplit [out <filename prefix>] [average <avg filename>] <trajout args> [out <filename prefix>] Write split LES trajectories to <filename prefix>.X, where X is an integer. [average <avg filename>] Write trajectory of averaged LES regions… Read More
Updated: March 26, 2019
Calculate J-coupling values from specified dihedral angles. jcoupling <mask> [outfile <filename>] [kfile <param file>] [out <filename>] [name <dsname>] <mask> Atom mask in which to search for dihedrals within. [outfile <filename>] File to write j-coupling values to with fixed… Read More
Updated: March 26, 2019
Re-image coordinates. image [origin] [center] [triclinic | familiar [com <commask>]] [<mask>] [ bymol | byres | byatom ] [xoffset <x>] [yoffset <y>] [zoffset <z>] [origin] Image to coordinate origin (0.0, 0.0, 0.0); default is to image to box… Read More
Updated: April 12, 2023
Bin selected atoms on a 3D grid. grid [ out <filename>] { data <dsname> | boxref <ref name/tag> <nx> <ny> <nz> | <nx> <dx> <ny> <dy> <nz> <dz> … Read More
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
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