Re: [AMBER] Dimer Rotations

From: Kenneth Huang <>
Date: Fri, 12 Jun 2015 18:18:33 -0400


Do you mean rotations of the dimers relative to an axis or each other after
re-imaging? I don't think there's a general answer in terms of biological
function- it's something that you probably have to make sense of in context
of the protein itself. I believe hemoglobin is a good example, where the
subunits undergo a slight rotation relative to a principal axis when moving
between T and R states.

I've dealt with tetramers that have the dimer subunits undergoing a slight
rotational shift over the course of the trajectory, but in my case, it's
also behaviour that can be correlated to the protein's transition between
an active and inactive state. My best suggestion would probably be to take
a look at the literature to see if there's anyone else who's done work on
the matter, or looking at the available structures.



On Fri, Jun 12, 2015 at 5:56 PM, Brittany Boykin <> wrote:

> Hello users,
> I am working on a dimer system with a co-factor in the active site and I
> am experiencing several rotations after using AMBER as well as Advanced
> Molecular Dynamics (aMD) when analyzing the movie. Has anyone dealt with
> dimers, and if so, experienced several rotations after simulations? What
> are the rotations saying?
> Thank you in advance!
> Brittany Boykin
> Graduate Student
> Auburn University
> Department of Chemistry and Biochemistry
> e:
> c: (404)545.1036
> _______________________________________________
> AMBER mailing list

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Received on Fri Jun 12 2015 - 15:30:03 PDT
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