Re: [AMBER] How to defined a steered direction in SMD?

From: Jason Swails <>
Date: Sun, 11 Jan 2015 10:05:16 -0500

On Sun, Jan 11, 2015 at 7:50 AM, Emilio Lence <> wrote:

> Hi.
> Have you think to use the centre of mass of the protein instead? (or all
> the CA of the protein if it's easy) That way the ligand will be getting
> separated from the protein, instead of moving over the surface.
> Other alternative is going farther away with the distance, instead of
> stopping at 20 move it to 40 or 50 and see if it moves away from the
> surface.

‚ÄčThis isn't going to work. Don't forget the center of mass of the protein
is a single point, and the set of all points that is a set distance away
from a *specific* point is a circle, so this would not prevent the ligand
from tracking along the surface of the protein.

One possibility is to add a dummy particle that is tethered to the active
site by a couple bonds to maintain its orientation *away* from the protein
and set up a LCOD that is a difference between the distance to the active
site and the distance to the dummy particle.

However, I am curious to know why the ligand tracing along the surface is
bad? In my opinion, the more restrictions you build into your simulation,
the less you can learn from them.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jan 11 2015 - 07:30:02 PST
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