Thanks for suggestions!
Taking into account that in this model I need to refine loops only
(water-exposed regions) I didn't include membrane at all :-) I use 2
different aproaches for such refinement in both cases completely freezing
(applying strong restraints on) membrane-embedded buddle of the receptor
but not putting restraints on the loops: 1) implicit gb solvent + dihedral
boost 2)placing entirely receptor to the water box + dual bust. I guess in
this system modelling of the membrane would be expedable doesn't it? In
this regards I think that boost should be stronger because most part of it
could be damped by restraints applied to the buddle (because in amd we
apply boost on ENTIRELY system)
James
2014-07-23 19:28 GMT+04:00 Brian Radak <radak004.umn.edu>:
> I don't think any degree of boost will overcome suitably defined cartesian
> restraints, although something tells me mixing those two together could
> cause some instabilities in the integration (just a hunch though).
>
> If I recall, the boost estimates require the number of degrees of freedom
> as an input. You might consider calculating the boost by excluding the
> restrained atoms (*i.e.* treat them as constraints).
>
> Regards,
> Brian
>
>
> On Wed, Jul 23, 2014 at 10:54 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > Dan,
> >
> > so might it be assumed that *biggest* part of the boost will be damped by
> > the restraint forces applied on the bigger part of the protein? In this
> > case I guess to sample loops only (which are ~1/10 part of my whole
> system
> > for instance) I need to use boost 10 times higher doesn't it?
> >
> >
> > James
> >
> >
> > 2014-07-23 18:02 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >
> > > On Wed, Jul 23, 2014 at 3:08 AM, James Starlight <
> jmsstarlight.gmail.com
> > >
> > > wrote:
> > >
> > > > I wounder if the dihe boost of this value
> > > > have been applied to the whole protein (including its restrained
> parts)
> > > or
> > > > only to its unrestrained (in my case loops) parts?
> > >
> > >
> > > Currently the dihedral boost is always applied to all dihedrals. There
> is
> > > no way yet to apply aMD boost to only a subset of dihedrals.
> > >
> > > -Dan
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 201
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
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>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
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> Integrative Proteomics Room 308
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Received on Wed Jul 23 2014 - 12:30:02 PDT
