extendedcomp
Calculate extended comparison similarity values for each frame in COORDS set. extendedcomp <input crd set> [name <output data set>] [metric <metric>] [out <file>]… Read More
Tools and information for AMBER and CPPTRAJ examples
Updated: November 11, 2023
Calculate extended comparison similarity values for each frame in COORDS set. extendedcomp <input crd set> [name <output data set>] [metric <metric>] [out <file>]… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 11, 2023
Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set. zmatrix <COORDS set name> [name <output set name>] { zset <input zmatrix set> [parm <top>|parmindex <#>] | … Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 18, 2023
Create a new molecule from a sequence of COORDS sets. sequence name <output set name> <unit0> <unit1> … [{libset <libsetname>} …] name <output set name> Name of final molecule. <unit0> <unit1> Name of COORDS set (with connection info)…. Read More
Category: Coordinates Data Set commands, CPPTRAJ
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: 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
Posted: April 5, 2022
Concatenate two or more COORDS sets. catcrd <crd1> <crd2> … name <name> <crdX> COORDS data sets to concatenate, specify 2 or more. name <name> New COORDS set name. Concatenate two or more COORDS data sets into a single… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 11, 2023
Graft part of one COORDS set onto another COORDS set graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharge>]] … Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: August 31, 2023
Combine two or more COORDS sets combinecrd <crd1> <crd2> … [parmname <topname>] [crdname <crdname>] <crdX> COORDS data set to combine, specify 2 or more. [parmname <topname>] Name of combined Topology. [crdname <crdname>] Name of combined COORDS data set…. Read More
Updated: February 26, 2020
Run a single Action on a COORDS set. crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offset>] Perform action <actioncmd> on COORDS data set <crd set>. A subset of frames in the COORDS data set can be specified with… Read More
Updated: April 5, 2022
Write a COORDS set to a file crdout <crd set> <filename> [<trajout args>] [crdframes <start>,<stop>,<offset>] Write COORDS data set <crd set> to trajectory named <filename>. A subset of frames in the COORDS data set can be specified with… Read More
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