Re: The vector direction in SMD

From: JC Gumbart (
Date: Fri Nov 04 2005 - 15:16:30 CST

You will need to find a point in this cavern. You can use 0 - Query
and then click on an atom near the center of this to find its
coordinates. Then you can define a vector between the two points.

To visualize it, you can use the tcl command "draw line {point 1}
{point 2} width 10".

On Nov 4, 2005, at 3:01 PM, Grace Shen wrote:

> Dear All:
> I am trying to run SMD for my ligand-protein complex. The purpose of
> the simulation is to drag the ligand out of the complex.
> I can see the direction I want to pull the ligand visually. But I do
> not know how to use the VMD to get the exact pulling vector direction.
> The start point of the vector is fixed as the center of mass of the
> ligand. The end point is the carven in the receptor.
> Thanks for help,
> Grace
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