Parameter/Reference Tagging

Parameter and reference files may be ’tagged’ (i.e. given a nickname).

These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’). This can be particularly useful when reading in many parameter or reference files. For example, when reading in multiple reference structures:

trajin Test1.crd
 reference 1LE1.NoWater.Xray.rst7 [xray]
 reference Test1.crd lastframe [last]
 reference Test2.crd 225 [open]
 rms Xray ref [xray] :2-12@CA out rmsd.dat
 rms Last ref [last] :2-12@CA out rmsd.dat
 rms Open ref [open] :2-12@CA out rmsd.dat

This defines three reference structures and gives them tags [xray], [last], and [open]. These reference structures can then be referred to by their tags instead of their filenames by any action that uses reference structures (in this case the RMSD action).

Similarly, this can be useful when reading in multiple parameter files:

 parm tz2.ff99sb.tip3p.truncoct.parm7 [tz2-water]
 parm tz2.ff99sb.mbondi2.parm7 [tz2-nowater]
 trajin parm [tz2-water]
 reference tz2.dry.rst7 parm [tz2-nowater] [tz2]
 rms ref [tz2] !(:WAT) out rmsd.dat

This defines two parm files and gives them tags [tz2-water] and [tz2-nowater], then reads in a trajectory associated with one, and a reference structure associated with the other. Note that in the ’reference’ command there are two tags; the first goes along with the ’parm’ keyword and specifies what parameter file the reference should use, the second is the tag given