For the oscillatory pieces of protein/DNA, yes.
For the random walk pieces of protein/DNA, yes.
However, protein/DNA have many pieces which are neither. If I put
methanol into solution, we would all agree the methyls will rotate
wildly. "The" position of the hydrogens is non-existent, since it is
oscillatory." But we would all agree that the hydrogen bond between
H-----O-H is not oscillatory; it will persist for a meaningful period of
time. Proteins/DNA are filled with pieces which are "stuck" somewhere,
due to hydrogen bonds or whatever, and their average position is more
interesting.
This is a lot like discussing radial distribution functions, or why
certain crystal structures have poorly resolved elements, if a common
reference is useful. Poorly resolved elements in crystal structures
sometimes reflect that a piece just moves around wildly, such that you
are not diffracting a regularly ordered piece (it's a random walk in
this case)
On 10/25/21 3:48 PM, James Kress wrote:
> Adrian: Thanks.
>
> Robert: Then isn't the determination of an "average" structure just a waste of time producing a useless result?
>
> Jim
>
> James Kress Ph.D., President
> The KressWorks® Institute
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
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>
> -----Original Message-----
> From: Robert Molt <rwmolt07.gmail.com>
> Sent: Monday, October 25, 2021 3:31 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16
>
> The average structure is like taking the average value of sine(x) between arbitrary bounds (say 0 to 1 vs. 0 to 1.1). Does the average mean anything? Not really, it's just oscillating. The average exists, but it is worthless. Methyl rotors, among other things chemistry units, are periodic functions. The same could be said for freely translating pieces (think of the tail end of a protein, which just wiggles wildly, and the average position is a random walk).
>
> On 10/25/21 2:53 PM, James Kress wrote:
>> Why do you minimize the average structure? Won't that minimization
>> just result in another, non-average structure?
>>
>> Jim
>>
>> James Kress Ph.D., President
>> The KressWorksR Institute
>> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
>> "ENGINEERING THE CURE" C
>> (248) 573-5499
>>
>> Learn More and Donate At:
>> Website: http://www.kressworks.org
>>
>> Confidentiality Notice | This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential or proprietary information. Any unauthorized
>> review, use, disclosure or distribution is prohibited. If you are not
>> the intended recipient, immediately contact the sender by reply e-mail
>> and destroy all copies of the original message.
>>
>> -----Original Message-----
>> From: Adrian Roitberg <roitberg.ufl.edu>
>> Sent: Monday, October 25, 2021 10:52 AM
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Does minimization require for average pdb
>> structure extract from 2drms plot using CPPTRAJ AMBER 16
>>
>> Hi Priya
>>
>> That script is not for a 2drms, it is just a simple 1D rmsd versus the
>> initial frame, and then the does average.
>>
>> Once you get the average, yes, you need to minimize it. The process of
>> averaging can create some weird structures.
>>
>> I would recommend a different path: Compute the average and THEN
>> recalculate the RMSD of the trajectory against the average pdb. Look
>> for what frame is closest to the average (lowest rmsd value), extract
>> it, and minimize THAT frame.
>>
>> Adrian
>>
>>
>> On 10/24/21 10:23 PM, priya murugan wrote:
>>> [External Email]
>>>
>>> Hi researcher,
>>>
>>> I'm really looking for your guidance and help in order for me to
>>> pursue my next step in computational work. I'm new to computational
>>> work and keen to learn more. Currently, I'm using AMBER 16 to do
>>> Molecular Dynamic (MD) simulation and trajectory analysis. The
>>> protein I'm
>> working with is 5IBE.
>>> I used CPPTRAJ to extract RMSD'd PDB's from trajectories. I extract
>>> specific frames of the trajectory in a 2drms plot, to generate the
>>> average structure in PDB format. This is the script I used to
>>> generate the average PDB structure from a 2drms plot.
>>>
>>> cpptraj.in file
>>> trajin 5IBE_heme_md_pc.binpos 2100 2500 rms first mass @C,CA,N
>>> average 5IBE_heme_md_pc_2100-2500.pdb pdb
>>>
>>> 2100-2500 is the frame value from the 2drms plot.
>>>
>>> My question is do I need to minimize the average PDB structure that I
>>> got from CPPTRAJ analysis before continuing with molecular docking?
>>> Is that ok If I continue using this average PDB structure for the
>>> docking process without minimization? Please let me know, I need some
>> clarification.
>>> I would be grateful for every suggestion that will be given to me.
>>>
>>> Thanks & Regards
>>>
>>> *PRIYA MURUGAN *
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org
>>> _
>>> mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbd
>>> v
>>> o14I2ndQf4w&m=25jBCvJrkndhFtaLxZ0Uokk3VCTvdbWtce26Et97R6I&s=EnQfsYTOd
>>> E
>>> NF2HPhvz_4Qbf38Tu9JjE86wFvqUcwVEo&e=
>> --
>> Dr. Adrian E. Roitberg
>> V.T. and Louise Jackson Professor in Chemistry Department of Chemistry
>> University of Florida roitberg.ufl.edu
>> 352-392-6972
>>
>>
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> --
> Dr. Robert Molt Jr.
>
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Received on Mon Oct 25 2021 - 13:00:03 PDT
