VMD-L Mailing List

From: Mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Fri Apr 12 2013 - 10:48:44 CDT

Hello Sir,
               I have tried the above method, when the peptide is at point
A , I am finding the rotation transforamtion matrix using transoffset
command and applying it. I can see that peptide is not present between two
points but it is transformed to somewhere else. The detailed procedure with
command as follows

A(x1,y1,z1) B (x2,y2,z2)
set vec [vecsub $A $B] [ to find out the vector]
set sel [atomselect top all] [selecting the peptide]
set mat [transoffset $A] [ constructing translation/rotation matrix]
 $sel move $mat [ moving the peptide to point A]
 measure minmax $sel
set vec2 [vecsub $minmax] [ construction a vector for peptide]
set cosine [expr [vecdot $hd $ha] / ( [veclength $hd] * [veclength $ha])]
   [finding a cosangle between them]

 set acos [expr acos($cosine)*(180.0/$M_PI)]
set axis [transabout $A $acos] [ rotating the peptide about point A]
 $sel move $axis

In my view this should work , i dont know where i went wrong but unable to
transform peptide between two points. Please suggest me a way. I tried many
ways but could not find a way, sorry for asking basic doubt.

 Thanks for a reply in advance,
Mohan