---------- Forwarded message ---------- From: mohsen ramezanpour <[email protected]> Date: Sat, Dec 25, 2010 at 10:02 AM Subject: pulling To: Discussion list for GROMACS users <[email protected]>
Dear All I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling. But my ligand is located in a hole inside of protein. If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole. Am I force to pull ligand along this line or I can pull along any line for generating configurations for umbrella sampling? I think the important is to pull it out from the binding pocket and we need to pull it along a line which is connecting the center of pocket(no protein's COM)to ligand's COM. What do you think. Thanks in advance
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