Re: [AMBER] RMSF plot error

From: David A Case <>
Date: Sun, 20 Sep 2020 08:53:24 -0400

On Sun, Sep 20, 2020, Fatemeh Arabi wrote:
> Dear AMBER developers,I have performed 25ns MD simulation on 3
> protein-protein complex systems using AmberTools20 based on MM/PBSA
> tutorial on website. Trajectories analyses were done by
> AmberTools15. RMSF plot of my simulated complex in all three cases shows
> unusual fluctuations and it's plot looks wrong. I'm unable to understand
> the reason. RMSD and RMSF plot are attached below.Kindly help me.Best
> regards,Fatemeh

You should visualize the trajectories to see what is going on. The RMSD
(from the starting structure?) rises to above 5 , which is pretty
large, so the average structure (from which the fluctuations are
computed) may not make a lot of sense.

There are, of course, lots of other reasons you might be getting these
results: you could have included some solvent molecules in the mask you
are using by mistake, etc. Read the output from cpptraj carefully, to
see if there is anything odd reported there.

Finally, there may be nothing wrong with the plots at all. If the
overall structure moved by 5 , then an individual residue might well
have very large fluctuations. You'll see that right way when you look
at an animation.

...good luck...dac

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Received on Sun Sep 20 2020 - 06:00:06 PDT
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