Re: [AMBER] restraints in simulations

From: Lara rajam <lara.4884.gmail.com>
Date: Tue, 26 Jan 2016 10:27:42 -0500

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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>
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Received on Tue Jan 26 2016 - 07:30:04 PST
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