From: jing liang (
Date: Sat Feb 13 2016 - 11:15:34 CST


I need to introduce one atom in an existing molecule. I load the molecule
and then I load the "guess" coordinates of the extra atom. Then, I check out
the F (fixed) option in VMD for the molecule and only the extra atom is
able to move.
After that, I try to compute the distance between the
extra atom and some existing atoms to improve the guess coordinates.

However, it seems that the distances are not updated in VMD using
this procedure. Is there a way to do this manual docking procedure in VMD?