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

From: Ilyas Yildirim <>
Date: Fri, 10 Apr 2020 23:15:46 +0000

There is definitely a discontinuity at zero, but this is because of 130. Check out the structures around 130; one of the torsion probably went to a different value. You will need to restrain those torsions, which would change and put you in another basin (you dont want that) while doing to pes scan.


Sent from my iPad

> On Apr 10, 2020, at 7:03 PM, Erdem Yeler <> wrote:
> 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: ]
> [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 Fri Apr 10 2020 - 16:30:02 PDT
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