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

[Justin Lemkul]

On 10/5/19 10:53 AM, Quin K wrote:
> 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!

What is your objective in calculating RMSD?

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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