Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 ( System) has 50085 elements Group 1 ( Protein) has 4590 elements Group 2 ( Protein-H) has 2307 elements Group 3 ( C-alpha) has 282 elements Group 4 ( Backbone) has 846 elements Group 5 ( MainChain) has 1127 elements Group 6 ( MainChain+Cb) has 1396 elements Group 7 ( MainChain+H) has 1399 elements Group 8 ( SideChain) has 3191 elements Group 9 ( SideChain-H) has 1180 elements Group 10 ( Prot-Masses) has 4590 elements Group 11 ( non-Protein) has 45495 elements Group 12 ( Other) has 31 elements Group 13 ( MPPA) has 31 elements Group 14 ( NA) has 2 elements Group 15 ( Water) has 45462 elements Group 16 ( SOL) has 45462 elements Group 17 ( non-Water) has 4623 elements Group 18 ( Ion) has 2 elements Group 19 ( MPPA) has 31 elements Group 20 ( NA) has 2 elements Group 21 ( Water_and_ions) has 45464 elements Group 22 ( Protein_MPPA) has 4621 elements
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