Dear Jason,
Thank you for your response.
You wrote: "It is generally a mistake to think that an average structure will be
physically realistic."
What is a crystal structure of protein molecule identified by x-ray?
Isn't it an average structure over all protein molecules in real physical system?
Following your statement what single frame on the MD trajectory should be used
as a resulting computational structure simulating a protein structure in a real physical system?
Regards,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Saturday, March 26, 2016 10:18 PM
To: AMBER Mailing List
Subject: Re: [AMBER] membrane protein problem
On Sat, Mar 26, 2016 at 2:35 PM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:
> Dear AMBER experts.
>
>
> Applying AMBE14 and AmberTools15, I have simulated a protein in membrane
> by MD in periodic cell.
>
> The next step is calculation of the average structure from
> the fragment of the production trajectory that satisfies a desired protein
> backbone RMSD condition.
>
> Finally, to obtain a representative protein structure the latter step must
> be minimization.
>
>
> The adequate minimization of a membarne protein can be conducted in
> membrane environment only. That is why I have accounted in the averaging
> procedure
>
> the whole soup in the periodic cell: protein, membrane, water, and counter
> ions.
>
> In this purpose I have applied the following cpptraj script:
>
>
> parm ../*.prmtop
>
> trajin prod4.mdcrd 3000 10000
>
> center :1-9308 mass origin
>
> autoimage origin
>
> rms first .C,CA,N
>
> average average_prod4_3000-10000.pdb PDB
>
> run
>
> quit
>
>
>
> The problem I faced is that despite the final pdb file contains also
> solvent water molecules and counter ions their coordinates are corrupted.
>
> Water molecules and counter ions are collapsed
>
> in a very small condensed area in the center of periodic cell
> like in a black hole.
>
This is exactly what I would expect to happen in a converged simulation.
Picture a droplet of water that is suspended in zero-G (free-fall) for a
long time. Each molecule is constantly moving, and the ready exchange of
water (due to typical diffusion) means that each water molecule spends
equal time at every "location" within the droplet as long as it has enough
time to diffuse everywhere. If its probability density in the droplet is
uniform, its *average* position is the center of the droplet. And this
holds true for *every* water molecule.
It is generally a mistake to think that an average structure will be
physically realistic.
HTH,
Jason
--
Jason M. Swails
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Received on Sat Mar 26 2016 - 13:00:03 PDT
