Re: [AMBER] Why RMSD goes fast to 5 angstrom?

From: <steinbrt.rci.rutgers.edu>
Date: Wed, 18 Apr 2012 03:21:30 -0400 (EDT)

Hi,

what Jason says is correct, but I doubt it is the reason for your rmsd
increase.

>> analysis, I found that the C alpha RMSD is continiously increasing and
>> finally is is up to *5 …*. The averaged RMSD for the* 0-1ns*
>> simulation, *
>> 1-6ns* simulation, *6-11ns* simulation is *2.3** …, 2.86 …, 3.89
>> …,*respectively. Attached
>> is the RMSD figures.* It seems abnormal* and could you tell me where is
>> the
>> problem.

How do you know there is a problem? The first step would be to visualize
the structure and check what kind of dynamics are happening. Do you assume
the solvated structure to be stable and close to the X-ray coordinates? If
yes, why? Does the protein have very flexible termini (check residuewise
fluctuations)? Which structural parts behave different from what you
expected?

A total rmsd of 5A is a lot for typical proteins, but unless you find the
reason for it, which could be both a mistake in simulation setup or an
underlying structural reason, it is hard to say what you should do
different...

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Apr 18 2012 - 00:30:04 PDT
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