Category: CPPTRAJ

change

Updated: May 20, 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

hmassrepartition

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

Creating a hydrogen mass repartitioned topology

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

random

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

Reorienting small molecules

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

graft

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

set

Updated: May 26, 2024

Set or update a script variable. set { <variable> <OP> <value> | <variable> <OP> {atoms|residues|molecules} inmask <mask> [parm <name> | parmindex <#> | <#>] <variable> <OP> trajinframes } Available <OP> : ’=’, ’+=’… Read More

Category: Variables and Control Structures

for

Updated: July 28, 2024

Create a ’for’ loop. for { {atoms|residues|molecules|molfirstres|mollastres} <var> inmask <mask> [parm <name> | parmindex <#> | <#>] | <var> in <list> | <var> oversets <list> | <var> datasetblocks… Read More

Category: Variables and Control Structures

show

Posted: August 10, 2020

Show all current script variables and their values. show [<var1> …] If no variable names specified, show all current script variables and their values. Otherwise, show the values of the specified script variables.

Category: Variables and Control Structures

Create an ensemble of PDBs from a trajectory

Updated: July 31, 2020

You want to create an ensemble of PDBs from a NetCDF trajectory file. Sometimes is useful or required to extract multiple PDB files from a trajectory. In this recipe we will use the trajout command to build a… Read More

Category: CPPTRAJ, CPPTRAJ recipes, General