crdtransform
Transform a COORDS set in one of several ways. crdtransform <input crd set> [name <output crd set>] { rmsrefine [mask <mask>] [mass] [rmstol <tolerance>] | normcoords | trim [metric <metric>] [{ntrimmed <#>|cutoff… Read More
Tools and information for AMBER and CPPTRAJ examples
Posted: November 11, 2023
Transform a COORDS set in one of several ways. crdtransform <input crd set> [name <output crd set>] { rmsrefine [mask <mask>] [mass] [rmstol <tolerance>] | normcoords | trim [metric <metric>] [{ntrimmed <#>|cutoff… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: September 9, 2023
Parse timing data from CPPTRAJ output. parsetiming … [out ] [name ] [sortby {time|cores|filename}] [includebad] [showdetails] [type {trajproc|trajread|actframe}] [reverse] [groupout [grouptype {prefix|name|kind}]] <filename args> Files containing CPPTRAJ output to get timing data from. [out <file>] Write total sorted… Read More
Category: General Commands
Updated: July 13, 2023
Update/add parameters in/to a topology. parm <name> | parmindex <#> setname <parm set> parm <name> | parmindex <#> Topology to update. setname <parm set> Topology or parameter data set containing parameters to use. NOTE: This command is provided… Read More
Category: CPPTRAJ, Topology File Commands
Posted: July 1, 2023
Print Urey-Bradley info for selected atoms. printub [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2>] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. [<mask1>] Atoms to… Read More
Category: CPPTRAJ, Topology File Commands
Posted: July 1, 2023
Read cpin <file> cpin <file> Constant pH input (CPIN) file name. Note that when reading in constant pH data the data set aspect will be set to the residue name and the index will be set to the… Read More
Category: CPPTRAJ, Data File Options
Posted: May 30, 2023
Calculate average unit cell (box), primarily for unwrapping NPT trajectories. avgbox [name ] [out ] [name ] Average unit cell data set name. [out <file>] File to write average unit cell data to. DataSets created:… Read More
Category: Action Commands, CPPTRAJ
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
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