Re: [AMBER] Flexible protein!

From: Debarati DasGupta <>
Date: Fri, 13 Dec 2019 19:37:26 +0000

Hi Prof Case,
Thanks for your reply…
My system has 32082 atoms (protein+water) and my protein is composed of 151 amino acids.
I am trying to do local fits on the secondary structures and see if that helps.
I have never used “makeDIST_RST” but will read more about it.
I just don’t know how to quantify the flexibility of the protein, I will try to check how to do that.

Sent from Mail<> for Windows 10

From: David A Case<>
Sent: Friday, December 13, 2019 7:17 AM
To: AMBER Mailing List<>
Subject: Re: [AMBER] Flexible protein!

On Thu, Dec 12, 2019, Debarati DasGupta wrote:

>I m working on a Mediator complex activator (Med25) and just out of
>curiosity, I minimized and equilibrated the protein in TIP3P water-box
>and eventually tried to see the C-alpha RMSD deviation wrt the starting
>The RMSD fluctuation was in the range of 2 to 5 ANGSTROMS. This
>fluctuation is true of all the 10 conformers.

It would be helpful to know how big a system this is: NMR is attacking
ever-bigger proteins, and larger systems can show increasingly large
C-alpha deviations.

But more importantly, visualize some of the trajectories: are there
loops, and N-terminal or C-terminal residues that are floppy? These
regions can greatly affect an overall RMSD value. Consider just fitting
on regions of secondary structure, and see how much those flucutate.
But one trajectory visualization is worth many RMSD plots: does
everything look reasonable? how surprising is the trajcetory, given what
you know from the starting NMR ensemble?

You could also (with more effort) encode the experimental NMR
restraints; the makeDIST_RST can help you get started there. Then you
can see how greatly (if at all) your simulated structures violate the
input NMR restraints.

Finally, remember that the goal of a simulation is to learn something
new; it's not just to reproduce the existing ensemble.

...good luck...dac

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