AMBER Archive (2005)

Subject: Re: AMBER: Sander.LES questions

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Tue Dec 20 2005 - 09:07:12 CST

have you read the article on GB with LES?
I think that 310K is too high for 5 copies.
also, are you sure that you defined multiple
regions and used GB with LES? The code should NOT
let you do that, only a single region is allowed with GB.

Bing Liu wrote:

> Dear Amber,
>
> I try to simulate a protein using Amber 8. This protein has a helix
> contains 16 residues. That helix orients a quite different position
> compared with WT because of a single point mutation. I simulated the
> WT and mutant using both GB and TIP3P model of sander at 310K, but the
> helix of mutant didn¡¯t make any dramatic move just like that of WT.
> Then, I try to simulate that phenomenon using sander.LES, but
> unfortunately, both WT and mutant moved significantly. That wasn¡¯t I
> wanted. The fact is only the helix of mutant make a large movement.
> How can I modify the parameters to simulate the fact? I define a
> region every 3 residues of that helix, 5 copies for each region, using
> GB model at 310K by sander.LES.
> Your help will be much appreciated! Thanks a lot!
>
> Bing Liu
> McGill University
>
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