[gmx-users] RMSD analysis of protein-ligand complex
Quin K
profiles.ke at gmail.com
Sat Oct 5 17:59:43 CEST 2019
Thank you.
I got following when I analysed Ligand RMSD protein backbone as east square
fit.
Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
Can you please comment why there's high fluctuation after like 23 ns?
What could this mean?
Thanks
Regards!
On Sat, Oct 5, 2019 at 9:08 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/5/19 11:36 AM, Quin K wrote:
> > 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
>
> I've already answered that. And again, it always depends on the question
> you are asking. You want the change in a structure relative to
> something. What is that something and how can you justify (to yourself
> and your reviewers!) that choice?
>
> -Justin
>
> > 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
> >>>>
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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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> >> posting!
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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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