[gmx-users] Ligand moves out of box during EM steps

raja raja_28 at fastmail.us
Tue Mar 21 04:05:56 CET 2006

         During the course of steps to simulation of ligand and enzyme
         complex, I have been struck at the level of minimization, due
         to inability of keeping my ligand at active site. I am using
         position restraints for all heavy atoms of protein,counter ions
         and for all atoms of my ligand, but still at the end of the
         minimization, the ligand goes out of the active site and end up
         locating itself just outside of the water box. How to check the
         position restrined protocol of my ligand really taken for
         consideration in energy minimization? and how to prevent my
         ligand from moving it from its initial position.

With thanks !

  raja_28 at fastmail.us

http://www.fastmail.fm - Or how I learned to stop worrying and
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