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

Quin K profiles.ke at gmail.com
Sat Oct 5 17:36:29 CEST 2019


OK thanks.
What should I pick for least square fit in following instances for example.
*RMSD of*
1. protein backbone+ligand
2. protein backbone
3. lingad only

On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/5/19 11:24 AM, Quin K wrote:
> > Thank you!
> > How important is the least square fit in these RMSD calculations?
>
> Very; it determines how to interpret the result.
>
> > Or should I just pick system for least square fit all time?
>
> You should never pick "System" for a fit.
>
> -Justin
>
> > 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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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