Re: [AMBER] restraints in simulations

From: Lara rajam <lara.4884.gmail.com>
Date: Tue, 26 Jan 2016 13:08:56 -0500

Dear Amber !

I was going through the paper

Samsonov, S. A.; Gehrcke, J. P.; Pisabarro, M. T. ""Flexibility and
explicit solvent in molecular dynamics-based docking of
protein-glycosaminoglycan systems" ."
*Journal of Chemical Information and Modelling*, 54(2):582-592 *(2014)*

they have reported the approach for few small molecular docking, I was
trying to do the same .


On Tue, Jan 26, 2016 at 11:53 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Tue Jan 26 2016 - 10:30:03 PST
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