AMBER Archive (2007)

Subject: Re: AMBER: Is this system too large?

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 22 2007 - 20:01:52 CST

On Thu, Feb 22, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:

> Thanks a lot. I decided to switch to a smaller system, a subunit (51
> residues) of this protein interacting with a 14-mer DNA. However, I do
> not have an initial structure with both "molecules". Can I use Xleap to
> prepare some starting points, in which the two "molecules" locate
> themselves at specific position and distance?

In spite of its name, LEaP is not generally all that useful in preparing
starting structures if you don't have a good starting geometry. You might
want to consider homology modeling programs (maybe start with Swiss pdb?).
If you don't know where the protein and the DNA interact, a docking program
might be required. Preparing initial structures is an art, and general advice
is hard to give, since so much depends on each individual problem and how much
you know about it.

...good luck...dac

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