Custom index for protein segment and ligand

User discussions
1

GROMACS version: 2019.5
GROMACS modification: No

Greetings everyone,

I want to create the following two index files with:

  1. Backbone atoms of a selected segment of the protein molecule.

  2. Non-hydrogen atoms of a ligand molecule.

Please let me know how could I select these two groups for creating the index files. Thanks for reading.

2

Type help at the make_ndx prompt to see example syntax.

For a segment of protein residues, it is as simple as r X-Y where X and Y are the first and last residues. For the ligand without H, X & ! a H* where X is the group number of the ligand (which is a default group).

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