[gmx-users] RMSD analysis of protein-ligand complex

[Quin K]

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

Thanks & regards!