AMBER Archive (2004)

Subject: RE: AMBER: RMSD result from GB model

From: Ross Walker (
Date: Wed Aug 04 2004 - 13:06:50 CDT

Dear Yongshi,

> I want to make sure if RMSD of 9.7 (fit) in a 2 ns GB
> MD is necessarily a problem. The protein consists of 3
> domains, 1278 residues. The ID is 3BTA. In the input
> file, I assigned igb=5.

This depends on several factors. The most important being whether your
initial structure actually represented an "equilibrium" structure. Have you
visualised the trajectory? Is there anything obviously wrong with it.
Measuring an RMSD is a good way to judge if your simulation is working but
this relies on the assumption that the initial (x-ray?) structure represents
the solution structure. If you protein starts to unfold then the RMSD will
increase. But maybe only part of it is unfolding or going through a specific
conformational change. This might be expected in which case the high RMSD
would also be expected. Have you tried plotting the RMSD for each residue -
can you isolate the large deviation to one section of the protein. Also, if
you plot RMSD vs time what does it look like? Does it shoot up to 9.7 and
then remain there? This would suggest a specific conformational change. Or
does the rmsd increase steadily over the duration? Suggesting the system is
slowly unfolding...

Your best option is to visually look at the trajectory and see if there is
anything obviously wrong. If not then see if you can track down the
structural origin of the high RMSD.

I hope this helps
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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