[gmx-users] Constraining positions according to B-factors

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 15 19:26:26 CET 2016


Hi Irem,

I think it would be better to actually build and simulate a crystal and use
the b-factors as a result of the model that allows you to do the comparison
with the diffraction data. Applying position restraints to reproduce the
b-factors will yield an unphysical system, from which I think little
meaningful can be deduced.

But yes, kJ/mol/nm^2

Cheers,

Tsjerk
On Jan 15, 2016 16:57, "Irem Altan" <irem.altan at duke.edu> wrote:

> Hi,
>
> Thank you for your answer, I will try that. I realize it’s unphysical, but
> I want to compare certain properties of the protein to diffraction data.
> Just to double check: the values in [position_restraints] are in units of
> kJ/(mol*nm^2), right?
>
> Best,
> Irem
>
> > On Jan 15, 2016, at 9:47 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> >
> > Hi Irem,
> >
> > Okay. First remove all bonded and nonbonded interactions, because these
> are
> > what gives rise to the thermal fluctuations in a real crystal. So you
> would
> > only need an [ atoms ] section and a section with [ position_restraints
> ].
> > You should be able to calculate a spring constants based on the
> > experimental b-factors. Then, if you perform the simulation and calculate
> > the b-factors, you should be able to reproduce what you put in.
> >
> > But seriously, why would you want that? There is no force in nature that
> > keeps atoms pinned to some xyz coordinate in space. What you see as
> thermal
> > motion is the result of the constraints due to the interactions there
> are.
> > Of course, that means in the context the molecule is in. If you want to
> > simulate b-factors in a crystal, you've gotta simulate a crystal. Using
> > physics, not using artificial means to try to reproduce what you put in.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> > On Fri, Jan 15, 2016 at 3:27 PM, Irem Altan <irem.altan at duke.edu> wrote:
> >
> >> Hi,
> >>
> >> Yes, assuming a harmonic potential, I want to be able to constrain atoms
> >> such that their mean square displacement during the simulation will be
> >> compatible with their B-factors.
> >>
> >> Best,
> >> Irem
> >>
> >>> On Jan 15, 2016, at 1:32 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >>>
> >>> Hey,
> >>>
> >>> Under the assumption that the B-factor is caused by some atom-specific
> >>> force that keeps it pinned to a certain position?
> >>>
> >>> Cheers,
> >>>
> >>> Tsjerk
> >>> On Jan 15, 2016 01:18, "Irem Altan" <irem.altan at duke.edu> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> I was wondering if it was possible to constrain protein atom positions
> >>>> according to their B-factors, so that their RMS displacement during
> the
> >>>> simulation will be compatible with their B-factors. If so, could you
> >> point
> >>>> me towards a helpful resource?
> >>>>
> >>>> Best,
> >>>> Irem
> >>>> --
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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