You don't need to fix the receptor center of mass at all. If you don't
want to bias the simulation, just let it diffuse freely as you say, then
all you need to do is apply a flat-bottom well (as bud dobson suggested)
that restricts the distance between say the center of the receptor and the
center of the ligand.
The restraint file would look something like this:
&rst
ialtd = 0
ir6 = 0
iresid = 0
igr1=1,2,3,4
igr2=5,6,7,8
iat = -1, -2
r1 = 0.0
r2 = 2.0
r3 = 12.0
r4 = 20.0
rk2 = 40.0
rk3 = 40.0
/
This makes it such that there is no force applied when the distance between
the center of atoms 1,2,3,4 and atoms 5,6,7,8 is between 2 and 12
angstroms, and then applies a force to restrict that distance becoming
greater.
You should read over section 6 of the AMBER11 manual.
~Aron
On Fri, Feb 17, 2012 at 11:43 PM, Danny Xu <quantum_mania.yahoo.com> wrote:
> I'd like to let the ligand diffuse freely into the receptor binding site,
> thus I need to fix receptor center of mass and constrain the ligand in a 3D
> box with the receptor enclosed so that it does not diffuse away.
>
> ------------------------------
> *From:* Aron Broom <broomsday.gmail.com>
>
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Cc:* Danny Xu <quantum_mania.yahoo.com>
> *Sent:* Friday, February 17, 2012 8:04 PM
>
> *Subject:* Re: [AMBER] restraints in igb simulation
>
> This feels like a communication problem, but maybe its just on my side.
> But as Jason said initially without some actual details about what you want
> to do, it's hard to recommend anything. For instance, why do you want to
> freeze the receptor in the first place?
>
> On Fri, Feb 17, 2012 at 7:03 PM, M. L. Dodson <mldodson.comcast.net>
> wrote:
>
> >
> > On Feb 17, 2012, at 5:44 PM, Danny Xu wrote:
> >
> > > Typo, how to constrain a ligand to move within a box in igb
> simulations.
> > >
> > >
> >
> > I think a box might be hard to achieve, but a sphere is easy. Search the
> > mailing list archives for "flat well restraint".
> >
> > Bud Dodson
> >
> > >
> > > ________________________________
> > > From: Danny Xu <quantum_mania.yahoo.com>
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Sent: Friday, February 17, 2012 4:39 PM
> > > Subject: Re: [AMBER] restraints in igb simulation
> > >
> > > I just wanted to constrain the receptor so that it does not move from
> > its initial position and also constrain a ligand so that it only moves
> with
> > a box. My question is simply how to achieve this in pmemd when igb is
> used?
> > Any thoughts are highly appreciated.
> > >
> > > -DX
> > >
> > >
> > >
> > > ________________________________
> > > From: Jason Swails <jason.swails.gmail.com>
> > > To: Danny Xu <quantum_mania.yahoo.com>; AMBER Mailing List <
> > amber.ambermd.org>
> > > Sent: Friday, February 17, 2012 5:52 AM
> > > Subject: Re: [AMBER] restraints in igb simulation
> > >
> > > It completely depends on what you're trying to do.
> > >
> > > Without that it's hard to give anything but the most generic
> (unhelpful)
> > advice.
> > >
> > > Think hard about the question you are trying to answer and what
> > simulation details would be required to probe that.
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > >
> > > On Feb 17, 2012, at 1:21 AM, Danny Xu <quantum_mania.yahoo.com> wrote:
> > >
> > >> Hello,
> > >>
> > >> In an igb simulation, what would be a good approach to:
> > >>
> > >> 1. restrain the protein to remove its rotation/translation, in another
> > word, fix its center of mass
> > >> 2. confine a ligand to move only inside a defined 3D box
> > >>
> > >> Thanks very much in advance!
> > >>
> > >> -DX
> > >> _______________________________________________
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> > >
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > M. L. Dodson
> > Business email: activesitedynamics-at-gmail-dot-com
> > Personal email: mldodson-at-comcast-dot-net
> > Gmail: mlesterdodson-at-gmail-dot-com
> > Phone: eight_three_two-five_63-386_one
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
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>
>
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Feb 17 2012 - 21:30:02 PST
