Good morning,
I am running some Steered molecular dynamics in Amber 22 and want to set some restraints in the z-axis so as to imply certain distances from my ligand to its substrate. My goal is to derive the PMF and calculate the binding affinity.
However to do that I need to align the Z-axis to the TIM barrel domain of the protein.
I tried aligning using VMD, however I couldn't translate and rotate the biomolecule freely and the only alignment I could do was with the main axis of the protein, which is not the one I need.
Is there a way to move the protein freely in relation to the axis so I can align the axis manually?
Thanks in advance,
if align is your problem use cpptraj module.
parm xyz.parm
trajin xyz.nc
autoimage
autoimage anchor :1-10 mobile !:1-10 fixed :1-10 origin
trajout xyz_align.xtc
after doing this visualize the trajectory or file