Tools and information for AMBER and CPPTRAJ examples
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: December 1, 2022
Change specified parts of a topology. change [parm <name> | parmindex <#> | <#> | crdset <COORDS set> ] { resname from <mask> to <value> | chainid of <mask> to <value> | oresnums of <mask> min <range min>… 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: April 10, 2022
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: 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: March 27, 2019
Change which molecules are considered solvent solvent [parm <name> | parmindex <#> | <#>] { <mask> | none } Set solvent for selected topology (first loaded topology by default) based on <mask>, or set nothing as solvent if… Read More
Updated: March 27, 2019
Scale selected dihedral force constants. scaledihedralk [parm <name> | parmindex <#>] <scale factor> [<mask> [useall]] Scale dihedral force constants for dihderals selected by <mask> for specified topology. If useall is specified all atoms in <mask> must be present… Read More
Updated: March 27, 2019
Print residue info for selected atoms. resinfo [parm <name> | parmindex <#> | <#>] [<mask>] [short] Print residue information for atoms in <mask> for selected topology (first loaded topology by default) with format: #Res Name First Last Natom … Read More
Updated: March 27, 2019
Write selected topology to file. parmwrite out <filename> [{parm <name> | parmindex <#> | <#> | crdset <setname>}] [<fmt>] [nochamber] <filename> File to write to. [parm <name> | parmindex <#> | <#>] Topology to write out. [crdset <setname>]… Read More
Updated: March 27, 2019
Remove selected atoms from topology. parmstrip <mask> [parm <name> | parmindex <#> | <#>] Strip atoms in <mask> from specified topology (by default the first topology loaded). Note that unlike the strip Action, this permanently modifies the topology… Read More
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