Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA

From: menwer momo <>
Date: Fri, 18 Jul 2014 14:53:04 -0700

Thanks a lot.

On Saturday, July 19, 2014 12:48 AM, Jason Swails <> wrote:

On Fri, Jul 18, 2014 at 2:31 PM, menwer momo <> wrote:

> I checked RMS value (using align command in PyMOL) between the starting
> structure of this mutant and the structure after production runs it equals
> 1.6
> Whereas the RMS value for the wild type starting structure compared to
> that after production runs equals 1.8 , Is can I consider this as an
> evidence or the difference is too small?

​RMSD has poor resolution as far as structural studies go.  All it tells
you is about how far something has moved.  It tells you nothing about how
or where it has moved.

When asking these types of questions, imagine someone else was doing this
study and explaining these results to you.  Would you be convinced?  And be
critical -- you will do yourself no favors by being nicer to yourself than
potential reviewers will be.



Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 18 2014 - 15:00:03 PDT
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