Re: protein collapsing problem!

From: Joshua Adelman (
Date: Thu Jun 25 2009 - 01:10:52 CDT

Dear Yandong,

Without knowing any specific details about your protein or the system
setup, it's hard to diagnose what might be going wrong though. If you
supply the list with more details, perhaps we could be of better

With that in mind, one thing that might be something to look at is the
force-field you're using. I know that I've run into problems using the
straight Charmm22 force-field for a large protein once I got out to
the 20-40ns range, although my protein did not fall apart to the
extent that yours seems to be. Using the Charmm22 with the CMAP
corrections seemed to result in more stable simulations for my system
at least. I've also had decent success with the Amber ff99SB force-
field as well.


On Jun 24, 2009, at 10:08 PM, ydhuang2727 wrote:

> Hi,
> I'm running a somewhat big monomer protein with about 448 residues
> and about 7000 atoms, the total number after adding periodic water
> box is 80383. It gets 11 beta-sheet and 13 alpha-helices.At the
> beginning 5 ns, everything goes well. While after 5 ns, its total
> secondary structure number, let's ignore what happens to tertiary
> structure firstly, start decreases, especially those alpha-helices
> who contact with water moleculars. Till 15ns, there are only 6 alpha-
> helices left and 10 beta-sheets. As to the tertiary structure, the
> whole struture seems to unstable after 15ns.
> The protein's intrinsic allosteric trait require a long-time running.
> Whit such a problem, i'm not be able to go on with my simulation.
> What should i do ?
> Can anybody help me out?
> Thanks so much for your kind consideration and look forward to your
> reply!
> Good day!
> Yandong,
> 200万种商品,最低价格,疯狂诱惑你

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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