AMBER Archive (2007)

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

From: Hu, Shaowen \(JSC-SK\)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Fri Feb 23 2007 - 10:10:09 CST

Thank you so much. I found a way to prepare the starting structures.
Since I have some ideas of the expected binding modes, I have generated
some initial structures with the two parts almost contacting to each
other. What I try to do is following:
1. Add ions and waters,
2. Minimize the system,
3. Equilibrate the system with restrained solute at NVT condition (100
ps),
4. Minimize the whole system again,
5. Equilibrate the system without restraint at NPT condition (500 ps),
6. Product MD
Could you please let me know whether this procedure works? Or there are
some better ways?

Also I am newcomer in MD community. Could you refer some docking
programs? Thanks again.

Shaowen Hu
-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, February 22, 2007 8:02 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Is this system too large?

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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