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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Received on Tue Apr 14 2020 - 08:00:02 PDT
