Default Index Groups

For convenience, various analysis and post-processing tools generate certain default index groups, such that the user need not create them.  These groups include the following:

• System: all the atoms in the system
• Protein: all atoms in residues listed as "Protein" in residuetypes.dat
• Protein-H: all protein atoms except hydrogen
• C-alpha: alpha carbons in the protein backbone
• Backbone: all protein backbone atoms (C-alpha, N, C)
• MainChain: backbone atoms, plus the carbonyl oxygens
• MainChain+Cb: main chain atoms, plus beta carbons (from side chains)
• MainChain+H: main chain atoms, plus hydrogen atoms
• SideChain: all non-main chain atoms
• SideChain-H: all side chain atoms except hydrogen atoms
• Prot-Masses: all protein atoms with mass (used when virtual sites are present, thus leaving some "Protein" atoms without mass)
• Non-Protein: anything that is not protein
• DNA: all atoms in residues listed as "DNA" in residuetypes.dat
• RNA: all atoms in residues listed as "RNA" in residuetypes.dat
• Water: any water molecule name (SOL, HOH, WAT, etc.) listed as such in residuetypes.dat
• non-Water: anything not considered water
• Ions: any ion listed in residuetypes.dat
• Water_and_Ions: a combination of the Water and Ions groups
• Other

In addition, groups for all other molecule types (other molecules you may have present in the system - lipids, ligands, co-solvents, etc.) will be generated.  For custom index group generation, see the make_ndx page, or type "help" at the make_ndx prompt.