Tools and information for AMBER and CPPTRAJ examples
Updated: February 28, 2024
Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber. prepareforleap crdset <coords set> [frame <#>] name <out coords set> [pdbout <pdbfile> [terbymol]] [leapunitname <unit>] [out <leap input file> [runleap… Read More
Category: CPPTRAJ, Data Sets and Data Files
Posted: April 5, 2022
Split molecules in a COORDS set into a trajectory. splitcoords <crd set> name <output set name> <crd set> COORDS set to split. name <output set name> Name of new set to create. Split trajectory specified by <crd set>… Read More
Category: CPPTRAJ, Data Sets and Data Files
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: April 5, 2022
Print improper info for selected atoms. improperinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3> <mask4>] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. [<mask1>]… Read More
Category: CPPTRAJ, Topology File Commands
Updated: February 29, 2024
Change specified parts of a topology. change [parm <name> | parmindex <#> | <#> | crdset <COORDS set> ] { resname from <mask> to <value> | chainid of <mask> to <value>… Read More
Category: CPPTRAJ, Topology File Commands
Posted: April 5, 2022
Perform hydrogen mass repartitioning. hmassrepartition [parm <name> | crdset <set> | parmindex <#> | <#>] [<mask>] [hmass <hydrogen new mass>] [dowater] parm <name> Modify topology selected by name. crdset<set> Modify topology of COORDS set. parmindex <#> | <#>… Read More
Category: CPPTRAJ, Topology File Commands
Updated: June 23, 2023
You want to create a hydrogen mass repartitioned topology using CPPTRAJ In order to speed up simulations, a trick that has been used for some time is to use a redistribution of the masses of the atoms. This… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General, Topology File Commands
Updated: November 3, 2021
Set the default random number generator used in CPPTRAJ random [setdefault {marsaglia|stdlib|mt|pcg32|xo128}] [createset count <#> [seed <#>] settype {int|float01|gauss [mean ] [sd ]}] setdefault If specified, change the default random number generator… Read More
Category: General Commands
Updated: December 8, 2022
Reorienting small molecules to fit the orientation of another molecule You want to screen a collection of small molecules into a receptor but need to re-orient them to match a starting structure. In this recipe we will use… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General, General Concepts, Topology File Commands, Tutorials
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
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