[gmx-users] Fwd: pulling

[mohsen ramezanpour]

---------- Forwarded message ----------
From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
Date: Sat, Dec 25, 2010 at 10:02 AM
Subject: pulling
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


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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