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

From: Vineet Pande <>
Date: Fri, 25 Mar 2005 09:41:18 +0000

>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.

Do you have Insight or Quanta ? I would recommend you to do modeling in one
of these programs, instead of automating the process. I don't think Leap is
a good tool to do that. Its a matter of minutes to superimpose all analogs
neatly onto a given template in these programs and write pdb files to be
read in through xleap... I am telling you to use a good modeling program
because, it is your initial docking stucture that is very crucial....since
while you superimpose the analogs one by one, you might find that some of
them make bumps into protein, or they, if given a slight torsion might
interact better with a group...and subjective things like that. Because
minimization would not change dramatically your starting models, subjective
efforts put in while docking are worth it!

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Received on Fri Mar 25 2005 - 09:53:00 PST
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