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

[Quin K]

To see if complex is stable and to see how it fluctuate in the binding
site.

On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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