Re: The vector direction in SMD

From: Marcos Sotomayor (
Date: Fri Nov 04 2005 - 15:29:52 CST

you could also use atomselections and tcl commands to get the appropriate
vector as in the third part of the NAMD tutorial

For instance, you can type in the Tk Console (Extensions menu of VMD)

set lig [atomselect top "chain X"]
set cav [atomselect top "resid Y"]
set ligcm [measure center $lig]
set cavpos [lindex [$cav get {x y z}] 0]
vecnorm [vecsub $cavpos $ligcm]

Where X is the chain label of the ligand and Y is some residue close to
the other point.


On Fri, 4 Nov 2005, JC Gumbart wrote:

> 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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