emin
Run simple energy minimization on a frame of a COORDS set. emin crdset <name> [trajoutname <name>] [rmstol <tol>] [nsteps <#>] [<mask>] [frame <#>] [dx0 <step0>] [out… Read More
Updated: June 30, 2023
Run simple energy minimization on a frame of a COORDS set. emin crdset <name> [trajoutname <name>] [rmstol <tol>] [nsteps <#>] [<mask>] [frame <#>] [dx0 <step0>] [out… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 1, 2022
You want to calculate the ion density around a biomolecule (protein or nucleic acid) For this recipe, we can use the Radial Distribution Function available in CPPTRAJ to calculate how the density of ions varies as a function… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General
Updated: April 10, 2022
Calculate lipid order parameters SCD(|<P2>|) for lipid chains. Automatically identifies lipids. lipidscd [<name>] [<mask>] [{x|y|z}] [out <file>] [p2] <name> Output data set name. <mask> Atom mask specifying where to search for lipids. x|y|z Axis to calculate order parameters… Read More
Category: Action Commands, CPPTRAJ
Updated: November 28, 2023
Re-map atoms according to a given data set. remap data <setname> [outprefix <prefix>] [nobox] [parmout <filename>] … Read More
Category: Action Commands, CPPTRAJ
Updated: April 10, 2022
Add/remove/modify time information in frames. time {time0 <initial time> dt <step> [update] | remove} time0 <initial time> Time of the first frame (ps). dt <step> Time step between frames (ps). [update] If specified, modify any existing time info…. Read More
Category: Action Commands, CPPTRAJ
Updated: April 10, 2022
Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume. xtalsymm <mask> group <space group> [collect [centroid]] [ first | reference | ref <name> | refindex <#> ] [na <na>] [nb <nb>] [nc <nc>] <mask>… Read More
Category: Action Commands, CPPTRAJ
Posted: April 10, 2022
Fix bonds which have been split across periodic boundaries by imaging. fiximagedbonds [<mask>] <mask> Mask expression of atoms to check. Fix bonds that have been split across periodic boundary conditions by imaging. It may be desirable to reimage… Read More
Category: Action Commands, CPPTRAJ
Updated: April 10, 2022
Calculate the RMSD of dihedrals to dihedrals in a reference structure. dihedralrms [<name>] <dihedral types> [out <file>] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <name> | parmindex <#>] ]… Read More
Category: Action Commands, CPPTRAJ
Updated: November 11, 2023
Keep specified atoms in system. keep [ bridgedata <bridge data set> [nbridge <#>] [nobridgewarn] [bridgeresname <res name>] bridgeresonly <resrange>] ] [keepmask <atoms to keep>] [charge <new charge>] … Read More
Category: Action Commands, CPPTRAJ
Updated: September 23, 2023
Align structure to a reference. align <mask> [<refmask>] [move <mask>] [mass] [ first | reference | ref <name> | refindex… Read More
Category: Action Commands, CPPTRAJ
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