Re: [AMBER] restraints in simulations

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 26 Jan 2016 11:53:48 -0500

I think that could be very difficult and I would not expect it to work
well. when you restrain the ligand at a far distance, it can move in the
sphere surrounding the binding pocket, nothing keeps it in line with the
pocket, eventually it can run into the protein surface at a site other than
the pocket and get stuck there. in other words, distance is not a
sufficient progress variable to describe binding as it says nothing about
the angular coordinates that direct it toward the part of the protein with
the binding site. using it for unbinding can be better since it is more
constrained by sterics to exit the pocket as distance increases.


On Tue, Jan 26, 2016 at 10:27 AM, Lara rajam <lara.4884.gmail.com> wrote:

> Dear Amber !
>
> Thank you for the reply. I am not interested in steered dynamics , rather I
> want to do a kind of targeted dynamics ,
> So that I can bring the ligand to the receptor binding site from a far
> distance. I have gone through the literatures ,
> but I have problem in handling forces to make the decrease in distance as
> linear component of time,
> any insight will help for my better understanding
>
> thank you
>
> On Tue, Jan 26, 2016 at 7:50 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Mon, Jan 25, 2016 at 1:23 PM, Lara rajam <lara.4884.gmail.com> wrote:
> >
> > > Dear Amber
> > >
> > > I would like to bring the ligand from far distance from the receptor to
> > the
> > > surface of the receptor. The atoms that I have selected on the ligand
> and
> > > on the receptors are now 22.5 angstrom apart. I need to pull the ligand
> > to
> > > near the surface of the receptor, which is 16.2 angstrom from the
> > receptor
> > > fixed atom. I have used the following parameters to run the
> simulation.
> > I
> > > have enclosed restrain file too. In restrain for these kind of
> simulation
> > > the ifvari=1 should be applied. When I see the distance change between
> > the
> > > two points it is not linear it jumps randomly. How I can control the
> > > variables to make the force so that the distance decrease with respect
> to
> > > time is linear.
> > >
> >
> > ‚ÄčIt sounds like you are trying to do "steered" molecular dynamics. You
> can
> > find an example of a steered MD simulation in $AMBERHOME/test/jar. I
> would
> > also recommend reviewing some literature to see how this type of study
> has
> > been performed in the past (in my experience, two species are usually
> > pulled *apart* rather than *together* due to the decrease in entropy
> > associated with binding events.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Jan 26 2016 - 09:00:07 PST
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