Tools and information for AMBER and CPPTRAJ examples
Updated: December 20, 2023
Print residue info for selected atoms. resinfo [parm <name> | parmindex <#> | <#>] <mask>[short [maxwidth <#res>]] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. <mask> Mask… 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
Updated: March 27, 2019
Print details for selected topology parminfo [parm <name> | parmindex <#> | <#>] [<mask>] Print a summary of information contained in the specified topology (first loaded topology by default) .
Updated: March 27, 2019
Modify box info for a loaded topology parmbox [parm <name> | parmindex <#> | <#>] [nobox] [truncoct] [x <xval>] [y <yval>] [z <zval>] [alpha <a>] [beta <b>] [gamma <g>] [parm <name> | parmindex <#> | <#>] Name/tag or… Read More
Updated: April 11, 2023
Load a topology file. parm [{[TAG] | name }] [{ nobondsearch | [bondsearch ] [searchtype {grid|pairlist}] }] [nomolsearch] [renumresidues] <filename> Parameter file to read in; format is auto-detected. [TAG] Optional tag (bounded in… Read More
Updated: March 27, 2019
Print molecule info for selected atoms. molinfo [parm <name> | parmindex <#> | <#>] [<mask>] Print molecule information for atoms in <mask> for selected topology (first loaded topology by default) with format: #Mol Natom #Res Name [SOLVENT] where… Read More
Updated: March 27, 2019
Print total mass for selected atoms. [<parmindex>] [parm <name> | parmindex <#> | <#>] <mask> Print the total mass of atoms in <mask> (in amu) for selected topology (first loaded topology by default).
Updated: March 27, 2019
Print dihedral info for selected atoms. dihedralinfo [parm <name> | parmindex <#> | <#>] [<mask>] [and] Print dihedral information of atoms in <mask> for selected topology (first loaded topology by default) with format: #Dihedral pk phase pn atoms… Read More
Updated: March 27, 2019
Compare two topologies and report differences. comparetop {parm <name> | parmindex <#>} {parm <name> | parmindex <#>} [out <file>] [atype] [lj] [bnd] [ang] [dih] [atoms] parm <name> | parmindex <#> Topologies to compare. out <file> Print results to… Read More
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