> On Mar 26, 2016, at 3:45 PM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
>
> 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?
But they do their best to fix the atoms I space so what you described doesn't happen! The mobile parts don't resolve well, again, precisely for this reason.
> 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?
Any of them. They are all part of the equilibrium distribution. The average structure is not.
HTH,
Jason
>
> 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 - 13:30:03 PDT
