From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
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
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/index.html
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.
Marcos
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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