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

[Quin K]

Thank you!
How important is the least square fit in these RMSD calculations?
Or should I just pick system for least square fit all time?

On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/5/19 11:11 AM, Quin K wrote:
> > To see if complex is stable and to see how it fluctuate in the binding
> > site.
>
> Stability of the complex can mean multiple things. If you want to show
> that the protein structure is stable in the presence of the ligand, you
> would compute the RMSD of the protein (probably backbone) and compare
> the result against that of an apo simulation. If you want to show that
> the complex is stable in terms of the association of the protein and
> ligand, that's not something you do via RMSD; you compute distances,
> angles, etc. related to the interactions of the protein that hold the
> ligand in the active site.
>
> You need to define what "it" is in the context of fluctuations.
> Fluctuation of the ligand in the binding can be computed by calculating
> RMSD of the ligand after a fit to the protein (to get relative motion).
> You can also do RMSF (e.g. of binding site residues, again to be
> compared against apo data for context/control).
>
> -Justin
>
> > 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
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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