AMBER Archive (2005)

Subject: AMBER: question about placing a substrate in a protein pocket

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Mar 24 2005 - 22:33:26 CST

I have several analogs that I will need to place in a protein pocket
before running mechanics on them. Is there any way to do the "docking"
in xLeap? I didn't seem to see a way so I'm planning on using another
program (such as VMD) to do this. Do I have to do this for each
analog, or is there a way to tell xLeap to put the next analog where
the first one was? The analogs differ by a side chain. I've been told
that you could do this with the old "link" program. It would save a
lot of time.

Thanks for any help,

Kara Di Giorgio
University of the Pacific

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