Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan?

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Tue, 14 Apr 2020 11:47:13 -0300 (ARGSL-ST)

Hello,

let me suggest you a gaussian09 frozen scan or a semi-frozen scan. You
would freeze some atoms in the z-matrix not involved in the rotation of
interes.

Greeting,
Hector.



> Unless I missed, you haven't said what the molecule is. When I was doing
> similar things in ribonucleotides I had similar problems unless the 2',
> 3', and 5'-hydroxyls were restrained. However, the molecule was simple
> enough that I could see which other torsions had changed in 360o (=0o)
> structure. If I restrained that torsion to the original 0o value,
> optimized, removed restraint, and optimized I got the 360o structure to
> agree with the initial 0o structure.
> Best of luck
> Steve
>
> Steven M. Graham, Ph.D.
> Associate Professor and AAAS Fellow
> Department of Chemistry
> St. John€™s University
> Queens, NY 11439
>
> -----Original Message-----
> From: Gustavo Seabra [mailto:gustavo.seabra.gmail.com]
> Sent: Tuesday, April 14, 2020 10:28 AM
> To: 'AMBER Mailing List' <amber.ambermd.org>
> Subject: Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES
> Scan?
>
> * External Email *
>
> In a way, the referee is correct: One *should* expect the results at 0 and
> 360 degrees to be the same. But that is assuming nothing else changes, and
> after doing the scan (360) you arrive at exactly the same overall
> structure as in the beginning (0). What you are seeing there is, most
> likely, the effect of other degrees of freedom you are not controlling,
> and the molecule arrives at a different conformation at 360 than it had at
> 0.
>
> A couple of ideas for the top of my head now to solve this:
> - Do the transformation back and forth multiple times, until the results
> converge. Or,
> - At each point, you could run a small MD to generate alternative
> configurations of the other DoF, but at the same value for the angle you
> are controlling, then averaging the results, instead of relying on one
> single value for each point.
>
> All the best,
> --
> Gustavo Seabra
>
> -----Original Message-----
> From: Erdem Yeler <erdemyeler.gmail.com>
> Sent: Friday, April 10, 2020 7:02 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan?
>
> Hello,
> I parameterized a novel molecule and I sent it a as an article to journal
> and my article has been rejected.
> Here is my PES scan of x-y-z-t dihedral .
>
> [link for the picture: https://hizliresim.com/5CyhD0 ]
>
> [image: image.png]
>
> the referee says: "There is a strange transition at ~130° as well as a
> very large discontinuity at Φ = 0° and 360°. It is expected that
> Edihedral(0°) = Edihedral(360°); the green and yellow dotted lines in
> the plot below should be at the same level, but this does not seem to be
> the case"
>
> Actually I performed PES scan in gaussian09 and psi4 and I got the same
> results in different softwares so I thought this chart is not strange.
> Still I am not sure if referee is right or not. Before I send the article
> I saw some parameterization articles which didn't perform PES scan 0-360
> degree. Some of authors performed scan in the range of 0-60 degree or
> 0-120 exc.. degree and I didn't predict I will face a result like this.
> Should I perform single point energy for each angle instead of PES scan?
> or should I do another thing? What are your suggestions? How can I explain
> this?
> Thank you.
>
>
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--------------------------------------
 Dr. Hector A. Baldoni
 Profesor Titular (FQByF-UNSL)
 Investigador Adjunto (IMASL-CONICET)
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------


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Received on Tue Apr 14 2020 - 08:00:03 PDT
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