changuing dihedral angle slowly (complete message)

From: Leonardo Sepulveda Durán (
Date: Fri Jun 24 2005 - 17:47:02 CDT

I Am trying to change the conformation of one of my protein helices.
It have a kink in the middle due to a proline residue. I would like to
make the helix being rotated along that proline residue to make it
linear. I thought a posible way to do that is using a rotating
constraint along a C-N bond as below

                  / :
                / :
              / :
CA--------C :

           P1 P2

in this case the rotconsaxis wouldbe the CA-C vector, but I am
confused about the rotConspivot. It can be the C (P1) atom or it has
to be the proyection of C-N along CA-C (P2) ???.

Or Maybe there is a less tricky way to rotate a dihedral angle slowly.
It seems that using a rotating constraint with a defined pivot and
axis would be problematic, because if my protein moves the position of
the pivot and axis must change to avoid rare forces.

Any comment would be very usefull


Universidad de Chile

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