Dear All <br>I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling.<br>But my ligand is located in a hole inside of protein.<br>If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole.<br>
Am I force to pull ligand along this line or I can pull along any line for generating configurations for umbrella sampling?<br>I think the important is to pull it out from the binding pocket and we need to pull it along a line <br>
which is connecting the center of pocket(no protein's COM)to ligand's COM.<br>What do you think.<br>Thanks in advance<br><br>