Dear GMXIONS,
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 !
B.Nataraj
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raja
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