<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">mohsen ramezanpour</b> <span dir="ltr"><<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>></span><br>
Date: Sat, Dec 25, 2010 at 10:02 AM<br>Subject: pulling<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><br><br>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>
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