AMBER Archive (2008)

Subject: Re: AMBER: change in secondary structure during MD

From: Carlos Simmerling (
Date: Thu Feb 28 2008 - 06:15:58 CST

let us know more about it- in particular the solvent model
can have a big influence, as can the force field as Yong said.
It seems likely that you used GB since you would not normally expect
secondary structure changes in a protein in 5ns (unless there was
some problem with your initial structure that made things unstable).
on larger proteins sometimes works well, sometimes not, and there
are lots of choices that need to be made carefully such as which GB
model and which intrinsic Born radii to use.

On Wed, Feb 27, 2008 at 8:45 PM, Ibrahim Moustafa <> wrote:
> Dear amber users,
> I did a 5ns MD run on a protein using AMBER9. The analysis of the run
> showed that, overall, the structure averaged over the last 500 frames is
> pretty similar to the crystal structure after the run, apart from meaningful
> dynamics at some parts. However, while investigating the structure in Pymol,
> I noticed that there is a change in some secondary structure elements. More
> specific: a couple of B-strands changed to loops, two short parts of long
> loops turned to B-strands and finally, a short helix turned into a loop. I
> know I do need to investigate this further by calculating the secondary
> structure following DSSP. But, visually I can feel the changes mentioned
> above.
> I understand that, in principle, a change in secondary structure could
> happen during MD, as a non-folded structure can be folded during simulation.
> But, I want to be sure that what I see is not an artifact of the simulation.
> I remember I came across some comment about the sensitivity of AMBER to
> B-strands stability compared to helices. Of course, this comment could be
> true for the previous versions of the program (I'd love to hear the
> developers' comments on that) which might be not the case for the current
> version.
> I'd appreciate if people with more experience could give me their opinions,
> and point me to publications where secondary structure change is reported.
> Thanks in advance of your help and your valuable comments.
> Regards,
> Ibrahim
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