Recently I was trying out the modes of Docking and Fold and Dock using symmetry, but I found that when I got the structures out, none of them were in the native form. The native structure is a dimer with 2 parallel monomers, but all of the structures had the 2 monomers in an antiparallel conformation. In order to understand where I went wrong I went back to the integration test to try it out, but I got antiparallel structures when creating this as well. I wanted to know if I was doing something wrong, had the wrong form of symmetry chosen, what it could be. Since this happened in Docking and Fold and Dock, I'm assuming it is the same problem so I thought I should look at the simplest one, the integration test for docking. Then when we find the problem i'll apply our solution to all of them.
The symmetry definition file I used is the simple cyclic dimer denovo file:
E = 2*VRT0001 + 1*(VRT0001:VRT0002)
start -1,0,0 0,1,0 0,0,0
rot Rz 2
connect_virtual JUMP1 VRT0001 VRT0002
set_dof BASEJUMP x(50) angle_x(0:360) angle_y(0:360) angle_z(0:360)
And these were the flags I used: