itp parser

[aspitaleri]

Hi folk,
I have been reading user guide and searching for it, but I couldn't find it. In few words, is it possible to modify a itp file in case we remove an atom (or more) from the itp file (and from the gro file respectively)? Removing an atom (or more) everything then should be renumbered accordingly. Hope I was clear.
Best

[orbeckst]

MDAnalysis has no real support for topology manipulation and that's on purpose because it's complicated and better left to specialized tools. Therefore, there's no support for changing an ITP file. Perhaps parmed (MDAnalysis has a parmed converter) or gromologist can do what you want?

You can use MDAnalysis to build different systems using Merge() (see also User Guide: constructing universes. In short, you select the parts you want as atomgroups and merge all the groups you want, leaving out what you want to delete.